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Lin S, Wu F, Zhang Y, Chen H, Guo H, Chen Y, Liu J. Surface-modified bacteria: synthesis, functionalization and biomedical applications. Chem Soc Rev 2023; 52:6617-6643. [PMID: 37724854 DOI: 10.1039/d3cs00369h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/21/2023]
Abstract
The past decade has witnessed a great leap forward in bacteria-based living agents, including imageable probes, diagnostic reagents, and therapeutics, by virtue of their unique characteristics, such as genetic manipulation, rapid proliferation, colonization capability, and disease site targeting specificity. However, successful translation of bacterial bioagents to clinical applications remains challenging, due largely to their inherent susceptibility to environmental insults, unavoidable toxic side effects, and limited accumulation at the sites of interest. Cell surface components, which play critical roles in shaping bacterial behaviors, provide an opportunity to chemically modify bacteria and introduce different exogenous functions that are naturally unachievable. With the help of surface modification, a wide range of functionalized bacteria have been prepared over the past years and exhibit great potential in various biomedical applications. In this article, we mainly review the synthesis, functionalization, and biomedical applications of surface-modified bacteria. We first introduce the approaches of chemical modification based on the bacterial surface structure and then highlight several advanced functions achieved by modifying specific components on the surface. We also summarize the advantages as well as limitations of surface chemically modified bacteria in the applications of bioimaging, diagnosis, and therapy and further discuss the current challenges and possible solutions in the future. This work will inspire innovative design thinking for the development of chemical strategies for preparing next-generation biomedical bacterial agents.
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Affiliation(s)
- Sisi Lin
- Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Institute of Molecular Medicine, State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China.
| | - Feng Wu
- Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Institute of Molecular Medicine, State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China.
| | - Yifan Zhang
- Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Institute of Molecular Medicine, State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China.
| | - Huan Chen
- Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Institute of Molecular Medicine, State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China.
| | - Haiyan Guo
- Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Institute of Molecular Medicine, State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China.
| | - Yanmei Chen
- Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Institute of Molecular Medicine, State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China.
| | - Jinyao Liu
- Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Institute of Molecular Medicine, State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China.
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Yuan J, Zhao K, Tan X, Xue R, Zeng Y, Ratti C, Trivedi P. Perspective on the development of synthetic microbial community (SynCom) biosensors. Trends Biotechnol 2023; 41:1227-1236. [PMID: 37183053 DOI: 10.1016/j.tibtech.2023.04.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 04/10/2023] [Accepted: 04/20/2023] [Indexed: 05/16/2023]
Abstract
Synthetic microbial community (SynCom) biosensors are a promising technology for detecting and responding to environmental cues and target molecules. SynCom biosensors use engineered microorganisms to create a more complex and diverse sensing system, enabling them to respond to stimuli with enhanced sensitivity and accuracy. Here, we give a definition of SynCom biosensors, outline their construction workflow, and discuss current biosensing technology. We also highlight the challenges and future for developing and optimizing SynCom biosensors and the potential applications in agriculture and food management, biotherapeutic development, home sensing, urban and environmental monitoring, and the One Health foundation. We believe SynCom biosensors could be used in a real-time and remote-controlled manner to sense the chaos of constantly dynamic environments.
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Affiliation(s)
- Jing Yuan
- Microbiome Network and Department of Agricultural Biology, Colorado State University, Fort Collins, CO 80524, USA; Senseable City Lab, Department of Urban Studies and Planning, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Kankan Zhao
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xiangfeng Tan
- Institute of Digital Agriculture, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, 310021, China
| | - Ran Xue
- Hangzhou Innovation Center, Zhejiang University, Hangzhou 311200, China
| | - Yuan Zeng
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, USA; Southern Piedmont Agricultural Research and Extension Center, Virginia Tech, Blackstone, VA 23824, USA
| | - Carlo Ratti
- Senseable City Lab, Department of Urban Studies and Planning, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Pankaj Trivedi
- Microbiome Network and Department of Agricultural Biology, Colorado State University, Fort Collins, CO 80524, USA
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Fogelson KA, Dorrestein PC, Zarrinpar A, Knight R. The Gut Microbial Bile Acid Modulation and Its Relevance to Digestive Health and Diseases. Gastroenterology 2023; 164:1069-1085. [PMID: 36841488 PMCID: PMC10205675 DOI: 10.1053/j.gastro.2023.02.022] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/31/2023] [Accepted: 02/09/2023] [Indexed: 02/27/2023]
Abstract
The human gut microbiome has been linked to numerous digestive disorders, but its metabolic products have been much less well characterized, in part due to the expense of untargeted metabolomics and lack of ability to process the data. In this review, we focused on the rapidly expanding information about the bile acid repertoire produced by the gut microbiome, including the impacts of bile acids on a wide range of host physiological processes and diseases, and discussed the role of short-chain fatty acids and other important gut microbiome-derived metabolites. Of particular note is the action of gut microbiome-derived metabolites throughout the body, which impact processes ranging from obesity to aging to disorders traditionally thought of as diseases of the nervous system, but that are now recognized as being strongly influenced by the gut microbiome and the metabolites it produces. We also highlighted the emerging role for modifying the gut microbiome to improve health or to treat disease, including the "engineered native bacteria'' approach that takes bacterial strains from a patient, modifies them to alter metabolism, and reintroduces them. Taken together, study of the metabolites derived from the gut microbiome provided insights into a wide range of physiological and pathophysiological processes, and has substantial potential for new approaches to diagnostics and therapeutics of disease of, or involving, the gastrointestinal tract.
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Affiliation(s)
- Kelly A Fogelson
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, California
| | - Pieter C Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California; Department of Pediatrics, University of California San Diego, San Diego, California; Center for Microbiome Innovation, University of California San Diego, San Diego, California.
| | - Amir Zarrinpar
- Center for Microbiome Innovation, University of California San Diego, San Diego, California; Division of Gastroenterology, Jennifer Moreno Department of Veterans Affairs Medical Center, San Diego, California; Division of Gastroenterology, University of California San Diego, San Diego, California; Institute of Diabetes and Metabolic Health, University of California San Diego, San Diego, California.
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, San Diego, California; Center for Microbiome Innovation, University of California San Diego, San Diego, California; Department of Bioengineering, University of California San Diego, San Diego, California; Department of Computer Science and Engineering, University of California San Diego, San Diego, California.
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Zhang P, Zhu Y, Li Z, Zhang W, Guang C, Mu W. Designing a Highly Efficient Biosynthetic Route for Lacto- N-Neotetraose Production in Escherichia coli. J Agric Food Chem 2022; 70:9961-9968. [PMID: 35938974 DOI: 10.1021/acs.jafc.2c04416] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Recently, the biosynthesis of human milk oligosaccharides (HMOs) has been attracting increasing attention. Lacto-N-neotetraose (LNnT) is one of the most important neutral-core HMOs with promising health effects for infants. It has received Generally Recognized as Safe (GRAS) status and is the second HMO commercially added in infant formula after 2'-fucosyllactose. In previous studies, a series of engineered Escherichia coli strains have been constructed and optimized to produce high titers of precursor lacto-N-triose II. On the basis of these strains, LNnT-producing strains were constructed by overexpressing the β1,4-galactosyltransferase-encoding gene from Aggregatibacter actinomycetemcomitans NUM4039 (Aa-β1,4-GalT). Interestingly, an appreciable LNnT titer was obtained by weakening the metabolic flux of the UDP-GlcNAc pathway and simply overexpressing the essential genes lgtA, galE, and Aa-β1,4-GalT in lacZ-, wecB-, and nagB-deleted E. coli. Subsequently, LNnT synthesis was optimized through balancing the expression of these three biosynthetic enzymes. The optimized strain produced LNnT with an extracellular titer of 12.1 g/L in fed-batch cultivation, with the productivity and specific yield of 0.25 g/L·h and 0.27 g/g dry cell weight, respectively.
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Affiliation(s)
- Pan Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Yingying Zhu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Zeyu Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Wenli Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Cuie Guang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Wanmeng Mu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
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Diebold O, Gonzalez V, Venditti L, Sharp C, Blake RA, Tan WS, Stevens J, Caddy S, Digard P, Borodavka A, Gaunt E. Using Species a Rotavirus Reverse Genetics to Engineer Chimeric Viruses Expressing SARS-CoV-2 Spike Epitopes. J Virol 2022; 96:e0048822. [PMID: 35758692 PMCID: PMC9327695 DOI: 10.1128/jvi.00488-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 05/31/2022] [Indexed: 02/02/2023] Open
Abstract
Species A rotavirus (RVA) vaccines based on live attenuated viruses are used worldwide in humans. The recent establishment of a reverse genetics system for rotoviruses (RVs) has opened the possibility of engineering chimeric viruses expressing heterologous peptides from other viral or microbial species in order to develop polyvalent vaccines. We tested the feasibility of this concept by two approaches. First, we inserted short SARS-CoV-2 spike peptides into the hypervariable region of the simian RV SA11 strain viral protein (VP) 4. Second, we fused the receptor binding domain (RBD) of the SARS-CoV-2 spike protein, or the shorter receptor binding motif (RBM) nested within the RBD, to the C terminus of nonstructural protein (NSP) 3 of the bovine RV RF strain, with or without an intervening Thosea asigna virus 2A (T2A) peptide. Mutating the hypervariable region of SA11 VP4 impeded viral replication, and for these mutants, no cross-reactivity with spike antibodies was detected. To rescue NSP3 mutants, we established a plasmid-based reverse genetics system for the bovine RV RF strain. Except for the RBD mutant that demonstrated a rescue defect, all NSP3 mutants delivered endpoint infectivity titers and exhibited replication kinetics comparable to that of the wild-type virus. In ELISAs, cell lysates of an NSP3 mutant expressing the RBD peptide showed cross-reactivity with a SARS-CoV-2 RBD antibody. 3D bovine gut enteroids were susceptible to infection by all NSP3 mutants, but cross-reactivity with SARS-CoV-2 RBD antibody was only detected for the RBM mutant. The tolerance of large SARS-CoV-2 peptide insertions at the C terminus of NSP3 in the presence of T2A element highlights the potential of this approach for the development of vaccine vectors targeting multiple enteric pathogens simultaneously. IMPORTANCE We explored the use of rotaviruses (RVs) to express heterologous peptides, using SARS-CoV-2 as an example. Small SARS-CoV-2 peptide insertions (<34 amino acids) into the hypervariable region of the viral protein 4 (VP4) of RV SA11 strain resulted in reduced viral titer and replication, demonstrating a limited tolerance for peptide insertions at this site. To test the RV RF strain for its tolerance for peptide insertions, we constructed a reverse genetics system. NSP3 was C-terminally tagged with SARS-CoV-2 spike peptides of up to 193 amino acids in length. With a T2A-separated 193 amino acid tag on NSP3, there was no significant effect on the viral rescue efficiency, endpoint titer, and replication kinetics. Tagged NSP3 elicited cross-reactivity with SARS-CoV-2 spike antibodies in ELISA. We highlight the potential for development of RV vaccine vectors targeting multiple enteric pathogens simultaneously.
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Affiliation(s)
- Ola Diebold
- Infection and Immunity Division, Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom
| | - Victoria Gonzalez
- Infection and Immunity Division, Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom
| | - Luca Venditti
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Colin Sharp
- Infection and Immunity Division, Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom
| | - Rosemary A. Blake
- Infection and Immunity Division, Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom
| | - Wenfang S. Tan
- Infection and Immunity Division, Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom
| | - Joanne Stevens
- Infection and Immunity Division, Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom
| | - Sarah Caddy
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Paul Digard
- Infection and Immunity Division, Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom
| | - Alexander Borodavka
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Eleanor Gaunt
- Infection and Immunity Division, Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom
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Ingle S, Chhabra S, Chen J, Lazarus MB, Luo X, Bechhofer DH. Discovery and initial characterization of YloC, a novel endoribonuclease in Bacillus subtilis. RNA 2022; 28:227-238. [PMID: 34815358 PMCID: PMC8906540 DOI: 10.1261/rna.078962.121] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 11/02/2021] [Indexed: 06/13/2023]
Abstract
The Bacillus subtilis genome is predicted to encode numerous ribonucleases, including four 3' exoribonucleases that have been characterized to some extent. A strain containing gene knockouts of all four known 3' exoribonucleases is viable, suggesting that one or more additional RNases remain to be discovered. A protein extract from the quadruple RNase mutant strain was fractionated and RNase activity was followed, resulting in the identification of an enzyme activity catalyzed by the YloC protein. YloC is an endoribonuclease and is a member of the highly conserved "YicC family" of proteins that is widespread in bacteria. YloC is a metal-dependent enzyme that catalyzes the cleavage of single-stranded RNA, preferentially at U residues, and exists in an oligomeric form, most likely a hexamer. As such, YloC shares some characteristics with the SARS-CoV Nsp15 endoribonuclease. While the in vivo function of YloC in B. subtilis is yet to be determined, YloC was found to act similarly to YicC in an Escherichia coli in vivo assay that assesses decay of the small RNA, RyhB. Thus, YloC may play a role in small RNA regulation.
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Affiliation(s)
- Shakti Ingle
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Shivani Chhabra
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Jiandong Chen
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Michael B Lazarus
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Xing Luo
- Laboratory of Molecular Biology, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - David H Bechhofer
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
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Yu Y, Shi K, Li X, Luo X, Wang M, Li L, Wang G, Li M. Reducing cadmium in rice using metallothionein surface-engineered bacteria WH16-1-MT. Environ Res 2022; 203:111801. [PMID: 34339701 DOI: 10.1016/j.envres.2021.111801] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 07/23/2021] [Accepted: 07/27/2021] [Indexed: 06/13/2023]
Abstract
Cadmium (Cd) accumulation in rice grains poses a health risk for humans. In this study, a bacterium, Alishewanella sp. WH16-1-MT, was engineered to express metallothionein on the cell surface. Compared with the parental WH16-1 strain, Cd2+ adsorption efficiency of WH16-1-MT in medium was increased from 1.2 to 2.6 mg/kg dry weight. The WH16-1-MT strain was then incubated with rice in moderately Cd-contaminated paddy soil. Compared with WH16-1, inoculation with WH16-1-MT increased plant height, panicle length and thousand-kernel weight, and decreased the levels of ascorbic acid and glutathione and the activity of peroxidase. Compared with WH16-1, WH16-1-MT inoculation significantly reduced the concentrations of Cd in brown rice, husks, roots and shoots by 44.0 %, 45.5 %, 36.1 % and 47.2 %, respectively. Moreover, inoculation with WH16-1-MT reduced the bioavailability of Cd in soil, with the total Cd proportion in oxidizable and residual states increased from 29 % to 32 %. Microbiome analysis demonstrated that the addition of WH16-1-MT did not significantly alter the original bacterial abundance and community structure in soil. These results indicate that WH16-1-MT can be used as a novel microbial treatment approach to reduce Cd in rice grown in moderately Cd-contaminated paddy soil.
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Affiliation(s)
- Ying Yu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, PR China
| | - Kaixiang Shi
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, PR China
| | - Xuexue Li
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, PR China
| | - Xiong Luo
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, PR China
| | - Mengjie Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, PR China
| | - Lin Li
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, PR China
| | - Gejiao Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, PR China
| | - Mingshun Li
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, PR China.
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Lin Z, Xu K, Cai G, Liu Y, Li Y, Zhang Z, Nielsen J, Shi S, Liu Z. Characterization of cross-species transcription and splicing from Penicillium to Saccharomyces cerevisiae. J Ind Microbiol Biotechnol 2021; 48:kuab054. [PMID: 34387324 PMCID: PMC8788760 DOI: 10.1093/jimb/kuab054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 08/04/2021] [Indexed: 11/14/2022]
Abstract
Heterologous expression of eukaryotic gene clusters in yeast has been widely used for producing high-value chemicals and bioactive secondary metabolites. However, eukaryotic transcription cis-elements are still undercharacterized, and the cross-species expression mechanism remains poorly understood. Here we used the whole expression unit (including original promoter, terminator, and open reading frame with introns) of orotidine 5'-monophosphate decarboxylases from 14 Penicillium species as a showcase, and analyzed their cross-species expression in Saccharomyces cerevisiae. We found that pyrG promoters from the Penicillium species could drive URA3 expression in yeast, and that inefficient cross-species splicing of Penicillium introns might result in weak cross-species expression. Thus, this study demonstrates cross-species expression from Penicillium to yeast, and sheds light on the opportunities and challenges of cross-species expression of fungi expression units and gene clusters in yeast without refactoring for novel natural product discovery.
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Affiliation(s)
- Zhenquan Lin
- College of Life Science and Technology, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, 100029 Beijing, China
| | - Kang Xu
- College of Life Science and Technology, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, 100029 Beijing, China
| | - Guang Cai
- College of Life Science and Technology, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, 100029 Beijing, China
| | - Yangqingxue Liu
- College of Life Science and Technology, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, 100029 Beijing, China
| | - Yi Li
- College of Life Science and Technology, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, 100029 Beijing, China
| | - Zhihao Zhang
- College of Life Science and Technology, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, 100029 Beijing, China
| | - Jens Nielsen
- College of Life Science and Technology, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, 100029 Beijing, China
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
- BioInnovation Institute, Ole Maaløes Vej 3, DK 2200 Copenhagen N, Denmark
| | - Shuobo Shi
- College of Life Science and Technology, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, 100029 Beijing, China
| | - Zihe Liu
- College of Life Science and Technology, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, 100029 Beijing, China
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Haluska C, Jin F, Wang Y. Protein phosphatase 2A (PP2A) promotes anaphase entry after DNA replication stress in budding yeast. Mol Biol Cell 2021; 32:ar36. [PMID: 34668760 PMCID: PMC8694091 DOI: 10.1091/mbc.e21-04-0222] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 10/01/2021] [Accepted: 10/05/2021] [Indexed: 12/31/2022] Open
Abstract
DNA replication stress activates the S-phase checkpoint that arrests the cell cycle, but it is poorly understood how cells recover from this arrest. Cyclin-dependent kinase (CDK) and protein phosphatase 2A (PP2A) are key cell cycle regulators, and Cdc55 is a regulatory subunit of PP2A in budding yeast. We found that yeast cells lacking functional PP2ACdc55 showed slow growth in the presence of hydroxyurea (HU), a DNA synthesis inhibitor, without obvious viability loss. Moreover, PP2A mutants exhibited delayed anaphase entry and sustained levels of anaphase inhibitor Pds1 after HU treatment. A DNA damage checkpoint Chk1 phosphorylates and stabilizes Pds1. We show that chk1Δ and mutation of the Chk1 phosphorylation sites in Pds1 largely restored efficient anaphase entry in PP2A mutants after HU treatment. In addition, deletion of SWE1, which encodes the inhibitory kinase for CDK or mutation of the Swe1 phosphorylation site in CDK (cdc28F19), also suppressed the anaphase entry delay in PP2A mutants after HU treatment. Our genetic data suggest that Swe1/CDK acts upstream of Pds1. Surprisingly, cdc55Δ showed significant suppression to the viability loss of S-phase checkpoint mutants during DNA synthesis block. Together, our results uncover a PP2A-Swe1-CDK-Chk1-Pds1 axis that promotes recovery from DNA replication stress.
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Affiliation(s)
- Cory Haluska
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, FL 32306-4300
| | - Fengzhi Jin
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, FL 32306-4300
| | - Yanchang Wang
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, FL 32306-4300
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10
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Song W, Zheng K, Xu X, Gao C, Guo L, Liu J, Chen X, Liu L, Hu G, Wu J. Enzymatic Production of Ascorbic Acid-2-Phosphate by Engineered Pseudomonas aeruginosa Acid Phosphatase. J Agric Food Chem 2021; 69:14215-14221. [PMID: 34786944 DOI: 10.1021/acs.jafc.1c04685] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
l-Ascorbic acid-2-phosphate (AsA-2P) is stable in aqueous solution and at high temperatures and is widely used in foods, pharmaceuticals, cosmetics, and fodders; however, practical application of enzymatic synthesis methods to promote industrial-scale production of AsA-2P remains a major challenge. In this study, we enhanced the phosphorylation efficiency of Pseudomonas aeruginosa acid phosphatase (APase; EC 3.1.3.2) for AsA-2P production via protein engineering. Among the mutants obtained, we selected the most efficient mutant (Var5; G125E/D135T/S136N), which exhibited an increased kcat of 18.6 s-1 and a Km for AsA of 223.9 mM. In addition, Var5 exhibited a maximum enzyme activity of 2080.4 U/L after 10 h of fermentation, which was 80% higher than the wild-type enzyme. Furthermore, under optimal conditions, Var5 showed a maximal conversion of 48.6% and achieved a final AsA-2P titer of 61.5 g/L at 8 h, which is considerably higher than that reported for other similar biocatalytic approaches. These findings demonstrate the potential of this method for the large-scale production of AsA-2P.
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Affiliation(s)
- Wei Song
- School of Pharmaceutical Science, Jiangnan University, Wuxi 214122, China
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Kai Zheng
- School of Pharmaceutical Science, Jiangnan University, Wuxi 214122, China
| | - Xin Xu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Cong Gao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Liang Guo
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Jia Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Guipeng Hu
- School of Pharmaceutical Science, Jiangnan University, Wuxi 214122, China
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Jing Wu
- School of Pharmaceutical Science, Jiangnan University, Wuxi 214122, China
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11
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Jutras PV, Soldan R, Dodds I, Schuster M, Preston GM, van der Hoorn RAL. AgroLux: bioluminescent Agrobacterium to improve molecular pharming and study plant immunity. Plant J 2021; 108:600-612. [PMID: 34369027 DOI: 10.1111/tpj.15454] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 07/19/2021] [Accepted: 08/02/2021] [Indexed: 06/13/2023]
Abstract
Agroinfiltration in Nicotiana benthamiana is widely used to transiently express heterologous proteins in plants. However, the state of Agrobacterium itself is not well studied in agroinfiltrated tissues, despite frequent studies of immunity genes conducted through agroinfiltration. Here, we generated a bioluminescent strain of Agrobacterium tumefaciens GV3101 to monitor the luminescence of Agrobacterium during agroinfiltration. By integrating a single copy of the lux operon into the genome, we generated a stable 'AgroLux' strain, which is bioluminescent without affecting Agrobacterium growth in vitro and in planta. To illustrate its versatility, we used AgroLux to demonstrate that high light intensity post infiltration suppresses both Agrobacterium luminescence and protein expression. We also discovered that AgroLux can detect Avr/Cf-induced immune responses before tissue collapse, establishing a robust and rapid quantitative assay for the hypersensitive response (HR). Thus, AgroLux provides a non-destructive, versatile and easy-to-use imaging tool to monitor both Agrobacterium and plant responses.
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Affiliation(s)
- Philippe V Jutras
- Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, South Park Road, Oxford, OX1 3RB, UK
| | - Riccardo Soldan
- Department of Plant Sciences, University of Oxford, South Park Road, Oxford, OX1 3RB, UK
| | - Isobel Dodds
- Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, South Park Road, Oxford, OX1 3RB, UK
| | - Mariana Schuster
- Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, South Park Road, Oxford, OX1 3RB, UK
| | - Gail M Preston
- Department of Plant Sciences, University of Oxford, South Park Road, Oxford, OX1 3RB, UK
| | - Renier A L van der Hoorn
- Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, South Park Road, Oxford, OX1 3RB, UK
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12
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Olzhausen J, Grigat M, Seifert L, Ulbricht T, Schüller HJ. Increased biosynthesis of acetyl-CoA in the yeast Saccharomyces cerevisiae by overexpression of a deregulated pantothenate kinase gene and engineering of the coenzyme A biosynthetic pathway. Appl Microbiol Biotechnol 2021; 105:7321-7337. [PMID: 34491400 PMCID: PMC8494682 DOI: 10.1007/s00253-021-11523-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 07/20/2021] [Accepted: 08/06/2021] [Indexed: 12/04/2022]
Abstract
Coenzyme A (CoA) and its derivatives such as acetyl-CoA are essential metabolites for several biosynthetic reactions. In the yeast S. cerevisiae, five enzymes (encoded by essential genes CAB1-CAB5; coenzyme A biosynthesis) are required to perform CoA biosynthesis from pantothenate, cysteine, and ATP. Similar to enzymes from other eukaryotes, yeast pantothenate kinase (PanK, encoded by CAB1) turned out to be inhibited by acetyl-CoA. By genetic selection of intragenic suppressors of a temperature-sensitive cab1 mutant combined with rationale mutagenesis of the presumed acetyl-CoA binding site within PanK, we were able to identify the variant CAB1 W331R, encoding a hyperactive PanK completely insensitive to inhibition by acetyl-CoA. Using a versatile gene integration cassette containing the TPI1 promoter, we constructed strains overexpressing CAB1 W331R in combination with additional genes of CoA biosynthesis (CAB2, CAB3, HAL3, CAB4, and CAB5). In these strains, the level of CoA nucleotides was 15-fold increased, compared to a reference strain without additional CAB genes. Overexpression of wild-type CAB1 instead of CAB1 W331R turned out as substantially less effective (fourfold increase of CoA nucleotides). Supplementation of overproducing strains with additional pantothenate could further elevate the level of CoA (2.3-fold). Minor increases were observed after overexpression of FEN2 (encoding a pantothenate permease) and deletion of PCD1 (CoA-specific phosphatase). We conclude that the strategy described in this work may improve the efficiency of biotechnological applications depending on acetyl-CoA. Key points • A gene encoding a hyperactive yeast pantothenate kinase (PanK) was constructed. • Overexpression of CoA biosynthetic genes elevated CoA nucleotides 15-fold. • Supplementation with pantothenate further increased the level of CoA nucleotides.
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Affiliation(s)
- Judith Olzhausen
- Center for Functional Genomics of Microbes, Abteilung Molekulare Genetik und Infektionsbiologie, Universität Greifswald, Felix-Hausdorff-Strasse 8, 17487, Greifswald, Germany
- Cendres+Métaux SA, CH-2501, Biel/Bienne, Switzerland
| | - Mathias Grigat
- Center for Functional Genomics of Microbes, Abteilung Molekulare Genetik und Infektionsbiologie, Universität Greifswald, Felix-Hausdorff-Strasse 8, 17487, Greifswald, Germany
| | - Larissa Seifert
- Center for Functional Genomics of Microbes, Abteilung Molekulare Genetik und Infektionsbiologie, Universität Greifswald, Felix-Hausdorff-Strasse 8, 17487, Greifswald, Germany
- Universitätsklinikum Hamburg-Eppendorf, Medizinische Klinik, Nephrologie, Hamburg, Germany
| | - Tom Ulbricht
- Center for Functional Genomics of Microbes, Abteilung Molekulare Genetik und Infektionsbiologie, Universität Greifswald, Felix-Hausdorff-Strasse 8, 17487, Greifswald, Germany
| | - Hans-Joachim Schüller
- Center for Functional Genomics of Microbes, Abteilung Molekulare Genetik und Infektionsbiologie, Universität Greifswald, Felix-Hausdorff-Strasse 8, 17487, Greifswald, Germany.
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13
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Pisu D, Huang L, Narang V, Theriault M, Lê-Bury G, Lee B, Lakudzala AE, Mzinza DT, Mhango DV, Mitini-Nkhoma SC, Jambo KC, Singhal A, Mwandumba HC, Russell DG. Single cell analysis of M. tuberculosis phenotype and macrophage lineages in the infected lung. J Exp Med 2021; 218:e20210615. [PMID: 34292313 PMCID: PMC8302446 DOI: 10.1084/jem.20210615] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 05/19/2021] [Accepted: 06/24/2021] [Indexed: 12/11/2022] Open
Abstract
In this study, we detail a novel approach that combines bacterial fitness fluorescent reporter strains with scRNA-seq to simultaneously acquire the host transcriptome, surface marker expression, and bacterial phenotype for each infected cell. This approach facilitates the dissection of the functional heterogeneity of M. tuberculosis-infected alveolar (AMs) and interstitial macrophages (IMs) in vivo. We identify clusters of pro-inflammatory AMs associated with stressed bacteria, in addition to three different populations of IMs with heterogeneous bacterial phenotypes. Finally, we show that the main macrophage populations in the lung are epigenetically constrained in their response to infection, while inter-species comparison reveals that most AMs subsets are conserved between mice and humans. This conceptual approach is readily transferable to other infectious disease agents with the potential for an increased understanding of the roles that different host cell populations play during the course of an infection.
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MESH Headings
- Animals
- Antitubercular Agents/pharmacology
- Bronchoalveolar Lavage Fluid/microbiology
- CD11 Antigens/immunology
- CD11 Antigens/metabolism
- Epigenesis, Genetic
- Gene Expression Regulation, Bacterial
- Heme/metabolism
- Host-Pathogen Interactions
- Humans
- Lung/microbiology
- Lung/pathology
- Macrophages, Alveolar/immunology
- Macrophages, Alveolar/microbiology
- Macrophages, Alveolar/pathology
- Mice, Inbred C57BL
- Microorganisms, Genetically-Modified
- Mycobacterium tuberculosis/drug effects
- Mycobacterium tuberculosis/genetics
- Mycobacterium tuberculosis/immunology
- Mycobacterium tuberculosis/pathogenicity
- Sequence Analysis, RNA
- Single-Cell Analysis
- Tuberculosis, Pulmonary/genetics
- Tuberculosis, Pulmonary/microbiology
- Tuberculosis, Pulmonary/pathology
- Mice
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Affiliation(s)
- Davide Pisu
- Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY
| | - Lu Huang
- Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY
- Microbiology and Immunology, University of Arkansas for Medical Sciences, Little Rock, AR
| | - Vipin Narang
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore
| | - Monique Theriault
- Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY
| | - Gabrielle Lê-Bury
- Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY
| | - Bernett Lee
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore
| | - Agnes E. Lakudzala
- Malawi Liverpool Wellcome Trust Clinical Research Program, University of Malawi College of Medicine, Blantyre, Malawi
| | - David T. Mzinza
- Malawi Liverpool Wellcome Trust Clinical Research Program, University of Malawi College of Medicine, Blantyre, Malawi
| | - David V. Mhango
- Malawi Liverpool Wellcome Trust Clinical Research Program, University of Malawi College of Medicine, Blantyre, Malawi
| | - Steven C. Mitini-Nkhoma
- Malawi Liverpool Wellcome Trust Clinical Research Program, University of Malawi College of Medicine, Blantyre, Malawi
| | - Kondwani C. Jambo
- Malawi Liverpool Wellcome Trust Clinical Research Program, University of Malawi College of Medicine, Blantyre, Malawi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Amit Singhal
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore
- A*STAR Infectious Diseases Laboratories, Agency for Science, Technology and Research, Singapore
| | - Henry C. Mwandumba
- Malawi Liverpool Wellcome Trust Clinical Research Program, University of Malawi College of Medicine, Blantyre, Malawi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - David G. Russell
- Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY
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14
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Ju H, Li D, Li D, Yang X, Liu Y. Overexpression of ZmDHN11 could enhance transgenic yeast and tobacco tolerance to osmotic stress. Plant Cell Rep 2021; 40:1723-1733. [PMID: 34142216 DOI: 10.1007/s00299-021-02734-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 06/10/2021] [Indexed: 05/14/2023]
Abstract
KEY MESSAGE Maize group II LEA protein ZmDHN11 could protect protein activity and confer resistance to osmotic stress on transgenic yeast and tobacco. Late embryogenesis abundant (LEA) proteins are widely assumed to play crucial roles in environmental stress tolerance, but their function has remained obscure. Dehydrins are group II LEA proteins, which are highly hydrophilic plant stress proteins. In the present study, a novel group II LEA protein, ZmDHN11, was cloned and identified from maize. The expression of ZmDHN11 was induced by high osmotic stress, low temperature, salinity, and ABA (abscisic acid). The ZmDHN11 protein specifically accumulated in the nuclei and cytosol. Further study indicated that ZmDHN11 is phosphorylated by the casein kinase CKII. ZmDHN11 protected the activity of LDH under water-deficit stress. The overexpression of ZmDHN11 endows transgenic yeast and tobacco with tolerance to osmotic stress.
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Affiliation(s)
- Huining Ju
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Daxing Li
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Dequan Li
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Xinghong Yang
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, Shandong, China.
| | - Yang Liu
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, Shandong, China.
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15
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Banerjee A, Roychoudhury A. Functional and molecular characterization of fluoride exporter (FEX) from rice and its constitutive overexpression in Nicotiana benthamiana to promote fluoride tolerance. Plant Cell Rep 2021; 40:1751-1772. [PMID: 34173048 DOI: 10.1007/s00299-021-02737-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 06/10/2021] [Indexed: 06/13/2023]
Abstract
KEY MESSAGE Early induction of OsFEX was insufficient for fluoride adaptation in IR-64. Overexpression of OsFEX in yeast and Nicotiana benthamiana enhanced fluoride tolerance. The present study delineates the regulation of fluoride exporter (FEX) in the fluoride-sensitive rice cultivar, IR-64 and its efficacy in generating high fluoride tolerance in transgenic Nicotiana benthamiana. Gene and protein expression profiling revealed that OsFEX exhibited early induction during fluoride stress in the vegetative and reproductive tissues of IR-64, although the expression was suppressed upon prolonged stress treatment. Analysis of OsFEX promoter in transgenic N. benthamiana, using β-glucuronidase reporter assay confirmed its early inducible nature, since the reporter expression and activity peaked at 12 h of NaF stress, after which it was lowered. OsFEX expression was up regulated in the presence of gibberellic acid (GA) and melatonin, while it was suppressed by abscisic acid (ABA). Complementation of ΔFEX1ΔFEX2 yeast mutants with OsFEX enabled high fluoride tolerance, thus validating the functional efficiency of the transgene. Bioassay of transgenic N. benthamiana lines, expressing OsFEX either under its own promoter or under CaMV35S promoter, established that constitutive overexpression, rather than early induction of OsFEX was essential and crucial for generating fluoride tolerance in the transgenics. Overall, the suppression of OsFEX in the later growth phases of stressed IR-64 due to enhanced ABA conservation and lowered synthesis of GA, as supported by the application of the respective phytohormone biosynthetic inhibitors, such as sodium tungstate and paclobutrazol, accounted for the fluoride-hyperaccumulative nature of the rice cultivar.
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Affiliation(s)
- Aditya Banerjee
- Post Graduate Department of Biotechnology, St. Xavier's College (Autonomous), 30, Mother Teresa Sarani, Kolkata, West Bengal, 700016, India
| | - Aryadeep Roychoudhury
- Post Graduate Department of Biotechnology, St. Xavier's College (Autonomous), 30, Mother Teresa Sarani, Kolkata, West Bengal, 700016, India.
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16
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Guo Y, Nassar S, Ma L, Feng G, Li X, Chen M, Chai T, Abdel-Rahman IAM, Beuerle T, Beerhues L, Wang H, Liu B. Octaketide Synthase from Polygonum cuspidatum Implements Emodin Biosynthesis in Arabidopsis thaliana. Plant Cell Physiol 2021; 62:424-435. [PMID: 33537755 PMCID: PMC8286135 DOI: 10.1093/pcp/pcaa135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 10/18/2020] [Indexed: 06/12/2023]
Abstract
Plant anthranoids are medicinally used for their purgative properties. Their scaffold was believed to be formed by octaketide synthase (OKS), a member of the superfamily of type III polyketide synthase (PKS) enzymes. Here, a cDNA encoding OKS of Polygonum cuspidatum was isolated using a homology-based cloning strategy. When produced in Escherichia coli, P. cuspidatum octaketide synthase (PcOKS) catalyzed the condensation of eight molecules of malonyl-CoA to yield a mixture of unphysiologically folded aromatic octaketides. However, when the ORF for PcOKS was expressed in Arabidopsis thaliana, the anthranoid emodin was detected in the roots of transgenic lines. No emodin was found in the roots of wild-type A. thaliana. This result indicated that OKS is the key enzyme of plant anthranoids biosynthesis. In addition, the root growth of the transgenic A. thaliana lines was inhibited to an extent that resembled the inhibitory effect of exogenous emodin on the root growth of wild-type A. thaliana. Immunochemical studies of P. cuspidatum plants detected PcOKS mainly in roots and rhizome, in which anthranoids accumulate. Co-incubation of E. coli - produced PcOKS and cell-free extract of wild-type A. thaliana roots did not form a new product, suggesting an alternative, physiological folding of PcOKS and its possible interaction with additional factors needed for anthranoids assembling in transgenic A. thaliana. Thus, transgenic A. thaliana plants producing PcOKS provide an interesting system for elucidating the route of plant anthranoid biosynthesis.
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Affiliation(s)
- Yanwu Guo
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing 100049, China
- Institute of Botany, The Chinese Academy of Sciences, Beijing 100093, China
| | - Sara Nassar
- Institute of Pharmaceutical Biology, Technische Universität Braunschweig, Mendelssohnstrasse 1, Braunschweig 38106, Germany
| | - Lanqing Ma
- Institute of Botany, The Chinese Academy of Sciences, Beijing 100093, China
| | - Guanping Feng
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing 100049, China
- Institute of Botany, The Chinese Academy of Sciences, Beijing 100093, China
| | - Xing Li
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing 100049, China
- Institute of Botany, The Chinese Academy of Sciences, Beijing 100093, China
| | - Mo Chen
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Tuanyao Chai
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Iman A M Abdel-Rahman
- Institute of Pharmaceutical Biology, Technische Universität Braunschweig, Mendelssohnstrasse 1, Braunschweig 38106, Germany
| | - Till Beuerle
- Institute of Pharmaceutical Biology, Technische Universität Braunschweig, Mendelssohnstrasse 1, Braunschweig 38106, Germany
| | - Ludger Beerhues
- Institute of Pharmaceutical Biology, Technische Universität Braunschweig, Mendelssohnstrasse 1, Braunschweig 38106, Germany
| | - Hong Wang
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing 100049, China
- Institute of Botany, The Chinese Academy of Sciences, Beijing 100093, China
| | - Benye Liu
- Institute of Pharmaceutical Biology, Technische Universität Braunschweig, Mendelssohnstrasse 1, Braunschweig 38106, Germany
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17
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Herruzo E, Lago-Maciel A, Baztán S, Santos B, Carballo JA, San-Segundo PA. Pch2 orchestrates the meiotic recombination checkpoint from the cytoplasm. PLoS Genet 2021; 17:e1009560. [PMID: 34260586 PMCID: PMC8312941 DOI: 10.1371/journal.pgen.1009560] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 07/26/2021] [Accepted: 06/25/2021] [Indexed: 12/02/2022] Open
Abstract
During meiosis, defects in critical events trigger checkpoint activation and restrict cell cycle progression. The budding yeast Pch2 AAA+ ATPase orchestrates the checkpoint response launched by synapsis deficiency; deletion of PCH2 or mutation of the ATPase catalytic sites suppress the meiotic block of the zip1Δ mutant lacking the central region of the synaptonemal complex. Pch2 action enables adequate levels of phosphorylation of the Hop1 axial component at threonine 318, which in turn promotes activation of the Mek1 effector kinase and the ensuing checkpoint response. In zip1Δ chromosomes, Pch2 is exclusively associated to the rDNA region, but this nucleolar fraction is not required for checkpoint activation, implying that another yet uncharacterized Pch2 population must be responsible for this function. Here, we have artificially redirected Pch2 to different subcellular compartments by adding ectopic Nuclear Export (NES) or Nuclear Localization (NLS) sequences, or by trapping Pch2 in an immobile extranuclear domain, and we have evaluated the effect on Hop1 chromosomal distribution and checkpoint activity. We have also deciphered the spatial and functional impact of Pch2 regulators including Orc1, Dot1 and Nup2. We conclude that the cytoplasmic pool of Pch2 is sufficient to support the meiotic recombination checkpoint involving the subsequent Hop1-Mek1 activation on chromosomes, whereas the nuclear accumulation of Pch2 has pathological consequences. We propose that cytoplasmic Pch2 provokes a conformational change in Hop1 that poises it for its chromosomal incorporation and phosphorylation. Our discoveries shed light into the intricate regulatory network controlling the accurate balance of Pch2 distribution among different cellular compartments, which is essential for proper meiotic outcomes. During gametogenesis, the number of chromosomes is reduced by half and it returns to the normal ploidy when the two gametes fuse during fertilization. Meiosis lies at the heart of gametogenesis because it is the specialized cell division making possible the reduction in ploidy. The fidelity in this process is essential to maintain the chromosome complement characteristic of the species and to avoid aneuploidies. Meiotic cells possess an intricate surveillance network that monitors crucial meiotic events. In response to defects in synapsis and recombination, the meiotic recombination checkpoint blocks meiotic cell cycle progression, thus avoiding aberrant chromosome segregation and formation of defective gametes. The AAA+ ATPase Pch2 is an essential component of the checkpoint response triggered by the recombination defects occurring in the zip1Δ mutant lacking the central region of the synaptonemal complex. Pch2 supports proper chromosomal localization and phosphorylation of the Hop1 axial component required for the ensuing checkpoint response. We reveal here the biological relevance of a cytoplasmic population of Pch2 that is necessary for meiotic events occurring on chromosomes. Using a variety of strategies, we demonstrate that the checkpoint activating function of Pch2 takes place outside the nucleus, whereas the nuclear accumulation of Pch2 has deleterious consequences. Our work highlights the importance of nucleocytoplasmic communication for a balanced distribution of Pch2 among different subcellular compartments and how it impinges on Hop1 dynamics, which is crucial for proper completion of the meiotic program.
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Affiliation(s)
- Esther Herruzo
- Instituto de Biología Funcional y Genómica (IBFG), Consejo Superior de Investigaciones Científicas (CSIC) and University of Salamanca, Salamanca, Spain
| | - Ana Lago-Maciel
- Instituto de Biología Funcional y Genómica (IBFG), Consejo Superior de Investigaciones Científicas (CSIC) and University of Salamanca, Salamanca, Spain
| | - Sara Baztán
- Instituto de Biología Funcional y Genómica (IBFG), Consejo Superior de Investigaciones Científicas (CSIC) and University of Salamanca, Salamanca, Spain
| | - Beatriz Santos
- Instituto de Biología Funcional y Genómica (IBFG), Consejo Superior de Investigaciones Científicas (CSIC) and University of Salamanca, Salamanca, Spain
- Departamento de Microbiología y Genética, University of Salamanca, Salamanca, Spain
| | - Jesús A. Carballo
- Department of Cellular and Molecular Biology. Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Pedro A. San-Segundo
- Instituto de Biología Funcional y Genómica (IBFG), Consejo Superior de Investigaciones Científicas (CSIC) and University of Salamanca, Salamanca, Spain
- * E-mail:
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18
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Gong G, Zhang Y, Wang Z, Liu L, Shi S, Siewers V, Yuan Q, Nielsen J, Zhang X, Liu Z. GTR 2.0: gRNA-tRNA Array and Cas9-NG Based Genome Disruption and Single-Nucleotide Conversion in Saccharomyces cerevisiae. ACS Synth Biol 2021; 10:1328-1337. [PMID: 34015926 DOI: 10.1021/acssynbio.0c00560] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Targeted genome disruptions and single-nucleotide conversions with the CRISPR/Cas system have greatly facilitated the development of gene therapy, basic biological research, and synthetic biology. With vast progress in this field, there are still aspects to be optimized, including the target range, the ability to multiplex, the mutation efficiency and specificity, as well as the requirement of adjusting protospacer adjacent motifs (PAMs). Here, we report the development of a highly efficient genome disruption and single-nucleotide conversion tool with a gRNA-tRNA array and SpCas9-NG (GTR 2.0). We performed gene disruptions in yeast cells covering all 16 possible NGN PAMs and all 12 possible single-nucleotide conversions (N to N) with near 100% efficiencies. Moreover, we applied GTR 2.0 for multiplexed single-nucleotide conversions, resulting in 66.67% mutation efficiency in simultaneous generation of 4 single-nucleotide conversions in one gene, as well as 100% mutation efficiency for simultaneously generating 2 single-nucleotide conversions in two different genes. GTR 2.0 will substantially expand the scope, efficiency, and capabilities of yeast genome editing, and will be a versatile and invaluable addition to the toolbox of synthetic biology and metabolic engineering.
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Affiliation(s)
- Guiping Gong
- College of Life Science and Technology, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Lab of Bioprocess, National Energy R&D Center for Biorefinery, State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Yueping Zhang
- College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Zibai Wang
- College of Life Science and Technology, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Lab of Bioprocess, National Energy R&D Center for Biorefinery, State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Luo Liu
- College of Life Science and Technology, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Lab of Bioprocess, National Energy R&D Center for Biorefinery, State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Shuobo Shi
- College of Life Science and Technology, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Lab of Bioprocess, National Energy R&D Center for Biorefinery, State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Verena Siewers
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg SE412 96, Sweden
- BioInnovation Institute, Ole Maaløes Vej 3, Copenhagen N DK2200, Denmark
| | - Qipeng Yuan
- College of Life Science and Technology, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Lab of Bioprocess, National Energy R&D Center for Biorefinery, State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Jens Nielsen
- College of Life Science and Technology, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Lab of Bioprocess, National Energy R&D Center for Biorefinery, State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg SE412 96, Sweden
- BioInnovation Institute, Ole Maaløes Vej 3, Copenhagen N DK2200, Denmark
| | - Xu Zhang
- College of Life Science and Technology, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Lab of Bioprocess, National Energy R&D Center for Biorefinery, State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Zihe Liu
- College of Life Science and Technology, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Lab of Bioprocess, National Energy R&D Center for Biorefinery, State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
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Abstract
Growth feedback, the inherent coupling between the synthetic gene circuit and the host cell growth, could significantly change the circuit behaviors. Previously, a diverse array of emergent behaviors, such as growth bistability, enhanced ultrasensitivity, and topology-dependent memory loss, were reported to be induced by growth feedback. However, the influence of the growth feedback on the circuit functions remains underexplored. Here, we reported an unexpected damped oscillatory behavior of a self-activation gene circuit induced by nutrient-modulating growth feedback. Specifically, after dilution of the activated self-activation switch into the fresh medium with moderate nutrients, its gene expression first decreases as the cell grows and then shows a significant overshoot before it reaches the steady state, leading to damped oscillation dynamics. Fitting the data with a coarse-grained model suggests a nonmonotonic growth-rate regulation on gene production rate. The underlying mechanism of the oscillation was demonstrated by a molecular mathematical model, which includes the ribosome allocation toward gene production, cell growth, and cell maintenance. Interestingly, the model predicted a counterintuitive dependence of oscillation amplitude on the nutrition level, where the highest peak was found in the medium with moderate nutrients, but was not observed in rich nutrients. We experimentally verified this prediction by tuning the nutrient level in the culture medium. We did not observe significant oscillatory behavior for the toggle switch, suggesting that the emergence of damped oscillatory behavior depends on circuit network topology. Our results demonstrated a new nonlinear emergent behavior mediated by growth feedback, which depends on the ribosome allocation between gene circuit and cell growth.
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Affiliation(s)
- Juan Melendez-Alvarez
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona 85281, United States
| | - Changhan He
- School of Mathematical and Statistical Sciences, Arizona State University, Tempe, Arizona 85281, United States
| | - Rong Zhang
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona 85281, United States
| | - Yang Kuang
- School of Mathematical and Statistical Sciences, Arizona State University, Tempe, Arizona 85281, United States
| | - Xiao-Jun Tian
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona 85281, United States
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20
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Haase S, Condron M, Miller D, Cherkaoui D, Jordan S, Gulbis JM, Baum J. Identification and characterisation of a phospholipid scramblase in the malaria parasite Plasmodium falciparum. Mol Biochem Parasitol 2021; 243:111374. [PMID: 33974939 PMCID: PMC8202325 DOI: 10.1016/j.molbiopara.2021.111374] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 04/27/2021] [Accepted: 05/06/2021] [Indexed: 02/07/2023]
Abstract
Identification of a phospholipid scramblase in P. falciparum (PfPLSCR). PfPLSCR is conserved across the genus and in closely related unicellular algae. Recombinant PfPLSCR shows metal-ion dependent phospholipid translocase activity. PfPLSCR is expressed in asexual stages and membrane associated. PfPLSCR is shown to be non-essential for asexual parasite development.
Recent studies highlight the emerging role of lipids as important messengers in malaria parasite biology. In an attempt to identify interacting proteins and regulators of these dynamic and versatile molecules, we hypothesised the involvement of phospholipid translocases and their substrates in the infection of the host erythrocyte by the malaria parasite Plasmodium spp. Here, using a data base searching approach of the Plasmodium Genomics Resources (www.plasmodb.org), we have identified a putative phospholipid (PL) scramblase in P. falciparum (PfPLSCR) that is conserved across the genus and in closely related unicellular algae. By reconstituting recombinant PfPLSCR into liposomes, we demonstrate metal ion dependent PL translocase activity and substrate preference, confirming PfPLSCR as a bona fide scramblase. We show that PfPLSCR is expressed during asexual and sexual parasite development, localising to different membranous compartments of the parasite throughout the intra-erythrocytic life cycle. Two different gene knockout approaches, however, suggest that PfPLSCR is not essential for erythrocyte invasion and asexual parasite development, pointing towards a possible role in other stages of the parasite life cycle.
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Affiliation(s)
- Silvia Haase
- Department of Life Sciences, Imperial College London, Sir Alexander Fleming Building, Exhibition Road, South Kensington, London, UK.
| | - Melanie Condron
- Division of Infection and Immunity, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
| | - David Miller
- Division of Structural Biology, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
| | - Dounia Cherkaoui
- Department of Life Sciences, Imperial College London, Sir Alexander Fleming Building, Exhibition Road, South Kensington, London, UK
| | - Sarah Jordan
- Department of Life Sciences, Imperial College London, Sir Alexander Fleming Building, Exhibition Road, South Kensington, London, UK
| | - Jacqueline M Gulbis
- Division of Structural Biology, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia; Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Jake Baum
- Department of Life Sciences, Imperial College London, Sir Alexander Fleming Building, Exhibition Road, South Kensington, London, UK.
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21
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Guo L, Zhao M, Tang Y, Han J, Gui Y, Ge J, Jiang S, Dai Q, Zhang W, Lin M, Zhou Z, Wang J. Modular Assembly of Ordered Hydrophilic Proteins Improve Salinity Tolerance in Escherichia coli. Int J Mol Sci 2021; 22:ijms22094482. [PMID: 33923104 PMCID: PMC8123400 DOI: 10.3390/ijms22094482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/20/2021] [Accepted: 04/23/2021] [Indexed: 11/24/2022] Open
Abstract
Most late embryogenesis abundant group 3 (G3LEA) proteins are highly hydrophilic and disordered, which can be transformed into ordered α-helices to play an important role in responding to diverse stresses in numerous organisms. Unlike most G3LEA proteins, DosH derived from Dinococcus radiodurans is a naturally ordered G3LEA protein, and previous studies have found that the N-terminal domain (position 1–103) of DosH protein is the key region for its folding into an ordered secondary structure. Synthetic biology provides the possibility for artificial assembling ordered G3LEA proteins or their analogues. In this report, we used the N-terminal domain of DosH protein as module A (named DS) and the hydrophilic domains (DrHD, BnHD, CeHD, and YlHD) of G3LEA protein from different sources as module B, and artificially assembled four non-natural hydrophilic proteins, named DS + DrHD, DS + BnHD, DS + CeHD, and DS + YlHD, respectively. Circular dichroism showed that the four hydrophile proteins were highly ordered proteins, in which the α-helix contents were DS + DrHD (56.1%), DS + BnHD (53.7%), DS + CeHD (49.1%), and DS + YLHD (64.6%), respectively. Phenotypic analysis showed that the survival rate of recombinant Escherichia coli containing ordered hydrophilic protein was more than 10% after 4 h treatment with 1.5 M NaCl, which was much higher than that of the control group. Meanwhile, in vivo enzyme activity results showed that they had higher activities of superoxide dismutase, catalase, lactate dehydrogenase and less malondialdehyde production. Based on these results, the N-terminal domain of DosH protein can be applied in synthetic biology due to the fact that it can change the order of hydrophilic domains, thus increasing stress resistance.
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Affiliation(s)
- Leizhou Guo
- College of Life Science and Engineering, Southwest University of Science and Technology, Mianyang 621000, China; (L.G.); (Y.T.); (Y.G.); (S.J.); (Q.D.)
| | - Mingming Zhao
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (M.Z.); (J.H.); (J.G.); (W.Z.); (M.L.)
| | - Yin Tang
- College of Life Science and Engineering, Southwest University of Science and Technology, Mianyang 621000, China; (L.G.); (Y.T.); (Y.G.); (S.J.); (Q.D.)
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (M.Z.); (J.H.); (J.G.); (W.Z.); (M.L.)
| | - Jiahui Han
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (M.Z.); (J.H.); (J.G.); (W.Z.); (M.L.)
| | - Yuan Gui
- College of Life Science and Engineering, Southwest University of Science and Technology, Mianyang 621000, China; (L.G.); (Y.T.); (Y.G.); (S.J.); (Q.D.)
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (M.Z.); (J.H.); (J.G.); (W.Z.); (M.L.)
| | - Jiaming Ge
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (M.Z.); (J.H.); (J.G.); (W.Z.); (M.L.)
| | - Shijie Jiang
- College of Life Science and Engineering, Southwest University of Science and Technology, Mianyang 621000, China; (L.G.); (Y.T.); (Y.G.); (S.J.); (Q.D.)
| | - Qilin Dai
- College of Life Science and Engineering, Southwest University of Science and Technology, Mianyang 621000, China; (L.G.); (Y.T.); (Y.G.); (S.J.); (Q.D.)
| | - Wei Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (M.Z.); (J.H.); (J.G.); (W.Z.); (M.L.)
| | - Min Lin
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (M.Z.); (J.H.); (J.G.); (W.Z.); (M.L.)
| | - Zhengfu Zhou
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (M.Z.); (J.H.); (J.G.); (W.Z.); (M.L.)
- Correspondence: (Z.Z.); (J.W.)
| | - Jin Wang
- College of Life Science and Engineering, Southwest University of Science and Technology, Mianyang 621000, China; (L.G.); (Y.T.); (Y.G.); (S.J.); (Q.D.)
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (M.Z.); (J.H.); (J.G.); (W.Z.); (M.L.)
- Correspondence: (Z.Z.); (J.W.)
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22
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Wu JJ, Mu LL, Kang WN, Ze LJ, Shen CH, Jin L, Anjum AA, Li GQ. RNA interference targeting ecdysone receptor blocks the larval-pupal transition in Henosepilachna vigintioctopunctata. Insect Sci 2021; 28:419-429. [PMID: 32162469 DOI: 10.1111/1744-7917.12777] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 02/19/2020] [Accepted: 03/08/2020] [Indexed: 05/10/2023]
Abstract
Henosepilachna vigintioctopunctata is a serious insect pest which attacks a large number of nightshades and cucurbits in Asian countries, Brazil and Australia. Prolonged application of traditional pesticides has caused environmental pollution and exerted deleterious effects on human health. Finding new approaches with high target specificity and low environmental contamination has become an urgent task. RNA interference (RNAi) induced by double-stranded RNA (dsRNA) is expected to be applicable to managing this pest. Here we evaluated the effects of Escherichia coli-expressed dsRNAs targeting ecdysone receptor (EcR) gene via dietary delivery in laboratory and foliar spraying in a greenhouse. The target transcript was successfully knocked down when the 4th-instar larvae had fed on potato foliage dipped with dsEcR in a laboratory bioassay. Around 85% of the HvEcR RNAi larvae remained as prepupae or became abnormal pupae, and failed to emerge into adults. Ingestion of dsEcR-immersed foliage by the 3rd-instar larvae effectuated a comparable RNAi response and brought about more severe defects: all the resultant larvae arrested development, remained as prepupae and finally died. For assay in the greenhouse, a dsEcR-contained E. coli suspension was directly sprayed to the foliage of greenhouse-growing potato plants and the 3rd- and 4th-instar larvae were transferred to the leaves. High RNAi efficacy was obtained and identical RNAi phenotypes were observed in treated larvae. In addition, spraying dsEcR reduced leaf damage. Our results indicate a possibility of practical application of dsEcR as an environmentally friendly RNA pesticide to control H. vigintioctopunctata larvae.
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Affiliation(s)
- Jian-Jian Wu
- Education Ministry Key Laboratory of Integrated Management of Crop Diseases and Pests, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Li-Li Mu
- Education Ministry Key Laboratory of Integrated Management of Crop Diseases and Pests, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Wei-Nan Kang
- Education Ministry Key Laboratory of Integrated Management of Crop Diseases and Pests, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Long-Ji Ze
- Education Ministry Key Laboratory of Integrated Management of Crop Diseases and Pests, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Chen-Hui Shen
- Education Ministry Key Laboratory of Integrated Management of Crop Diseases and Pests, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Lin Jin
- Education Ministry Key Laboratory of Integrated Management of Crop Diseases and Pests, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Ahmad Ali Anjum
- Education Ministry Key Laboratory of Integrated Management of Crop Diseases and Pests, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Guo-Qing Li
- Education Ministry Key Laboratory of Integrated Management of Crop Diseases and Pests, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
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Shimizu T, Hayashi Y, Arai M, McGlynn SE, Masuda T, Masuda S. Repressor Activity of SqrR, a Master Regulator of Persulfide-Responsive Genes, Is Regulated by Heme Coordination. Plant Cell Physiol 2021; 62:100-110. [PMID: 33169162 DOI: 10.1093/pcp/pcaa144] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Accepted: 11/03/2020] [Indexed: 06/11/2023]
Abstract
Reactive sulfur species (RSS) are involved in bioactive regulation via persulfidation of proteins. However, how cells regulate RSS-based signaling and RSS metabolism is poorly understood, despite the importance of universal regulation systems in biology. We previously showed that the persulfide-responsive transcriptional factor SqrR acts as a master regulator of sulfide-dependent photosynthesis in proteobacteria. Here, we demonstrated that SqrR also binds heme at a near one-to-one ratio with a binding constant similar to other heme-binding proteins. Heme does not change the DNA-binding pattern of SqrR to the target gene promoter region; however, DNA-binding affinity of SqrR is reduced by the binding of heme, altering its regulatory activity. Circular dichroism spectroscopy clearly showed secondary structural changes in SqrR by the heme binding. Incremental change in the intracellular heme concentration is associated with small, but significant reduction in the transcriptional repression by SqrR. Overall, these results indicate that SqrR has an ability to bind heme to modulate its DNA-binding activity, which may be important for the precise regulation of RSS metabolism in vivo.
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Affiliation(s)
- Takayuki Shimizu
- Department of Life Science and Technology, Tokyo Institute of Technology, Kanagawa, Japan
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
- Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Yuuki Hayashi
- Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Munehito Arai
- Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
- Department of Physics, The University of Tokyo, Tokyo, Japan
| | - Shawn E McGlynn
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
| | - Tatsuru Masuda
- Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Shinji Masuda
- Department of Life Science and Technology, Tokyo Institute of Technology, Kanagawa, Japan
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
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24
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Gonzalez-Perez D, Ratcliffe J, Tan SK, Wong MCM, Yee YP, Nyabadza N, Xu JH, Wong TS, Tee KL. Random and combinatorial mutagenesis for improved total production of secretory target protein in Escherichia coli. Sci Rep 2021; 11:5290. [PMID: 33674702 PMCID: PMC7935960 DOI: 10.1038/s41598-021-84859-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 02/22/2021] [Indexed: 11/17/2022] Open
Abstract
Signal peptides and secretory carrier proteins are commonly used to secrete heterologous recombinant protein in Gram-negative bacteria. The Escherichia coli osmotically-inducible protein Y (OsmY) is a carrier protein that secretes a target protein extracellularly, and we have previously applied it in the Bacterial Extracellular Protein Secretion System (BENNY) to accelerate directed evolution. In this study, we reported the first application of random and combinatorial mutagenesis on a carrier protein to enhance total secretory target protein production. After one round of random mutagenesis followed by combining the mutations found, OsmY(M3) (L6P, V43A, S154R, V191E) was identified as the best carrier protein. OsmY(M3) produced 3.1 ± 0.3 fold and 2.9 ± 0.8 fold more secretory Tfu0937 β-glucosidase than its wildtype counterpart in E. coli strains BL21(DE3) and C41(DE3), respectively. OsmY(M3) also produced more secretory Tfu0937 at different cultivation temperatures (37 °C, 30 °C and 25 °C) compared to the wildtype. Subcellular fractionation of the expressed protein confirmed the essential role of OsmY in protein secretion. Up to 80.8 ± 12.2% of total soluble protein was secreted after 15 h of cultivation. When fused to a red fluorescent protein or a lipase from Bacillus subtillis, OsmY(M3) also produced more secretory protein compared to the wildtype. In this study, OsmY(M3) variant improved the extracellular production of three proteins originating from diverse organisms and with diverse properties, clearly demonstrating its wide-ranging applications. The use of random and combinatorial mutagenesis on the carrier protein demonstrated in this work can also be further extended to evolve other signal peptides or carrier proteins for secretory protein production in E. coli.
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Affiliation(s)
- David Gonzalez-Perez
- Department of Chemical and Biological Engineering, The University of Sheffield, Sir Robert Hadfield Building, Mappin Street, Sheffield, S1 3JD, UK
- Department of Drug Discovery, Moffitt Cancer Center & Research Institute, Stabile Research Building, 12902 Magnolia Dr, Tampa, FL, 33612, USA
| | - James Ratcliffe
- Department of Chemical and Biological Engineering, The University of Sheffield, Sir Robert Hadfield Building, Mappin Street, Sheffield, S1 3JD, UK
| | - Shu Khan Tan
- Department of Chemical and Biological Engineering, The University of Sheffield, Sir Robert Hadfield Building, Mappin Street, Sheffield, S1 3JD, UK
| | - Mary Chen May Wong
- Department of Chemical and Biological Engineering, The University of Sheffield, Sir Robert Hadfield Building, Mappin Street, Sheffield, S1 3JD, UK
| | - Yi Pei Yee
- Department of Chemical and Biological Engineering, The University of Sheffield, Sir Robert Hadfield Building, Mappin Street, Sheffield, S1 3JD, UK
| | - Natsai Nyabadza
- Department of Chemical and Biological Engineering, The University of Sheffield, Sir Robert Hadfield Building, Mappin Street, Sheffield, S1 3JD, UK
| | - Jian-He Xu
- Laboratory of Biocatalysis and Bioprocessing, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, People's Republic of China
| | - Tuck Seng Wong
- Department of Chemical and Biological Engineering, The University of Sheffield, Sir Robert Hadfield Building, Mappin Street, Sheffield, S1 3JD, UK.
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Khlong Luang, 12120, Pathum Thani, Thailand.
| | - Kang Lan Tee
- Department of Chemical and Biological Engineering, The University of Sheffield, Sir Robert Hadfield Building, Mappin Street, Sheffield, S1 3JD, UK.
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25
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Wang X, Han JN, Zhang X, Ma YY, Lin Y, Wang H, Li DJ, Zheng TR, Wu FQ, Ye JW, Chen GQ. Reversible thermal regulation for bifunctional dynamic control of gene expression in Escherichia coli. Nat Commun 2021; 12:1411. [PMID: 33658500 PMCID: PMC7930084 DOI: 10.1038/s41467-021-21654-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 02/03/2021] [Indexed: 11/08/2022] Open
Abstract
Genetically programmed circuits allowing bifunctional dynamic regulation of enzyme expression have far-reaching significances for various bio-manufactural purposes. However, building a bio-switch with a post log-phase response and reversibility during scale-up bioprocesses is still a challenge in metabolic engineering due to the lack of robustness. Here, we report a robust thermosensitive bio-switch that enables stringent bidirectional control of gene expression over time and levels in living cells. Based on the bio-switch, we obtain tree ring-like colonies with spatially distributed patterns and transformer cells shifting among spherical-, rod- and fiber-shapes of the engineered Escherichia coli. Moreover, fed-batch fermentations of recombinant E. coli are conducted to obtain ordered assembly of tailor-made biopolymers polyhydroxyalkanoates including diblock- and random-copolymer, composed of 3-hydroxybutyrate and 4-hydroxybutyrate with controllable monomer molar fraction. This study demonstrates the possibility of well-organized, chemosynthesis-like block polymerization on a molecular scale by reprogrammed microbes, exemplifying the versatility of thermo-response control for various practical uses.
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Affiliation(s)
- Xuan Wang
- Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Jia-Ning Han
- Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Xu Zhang
- Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yue-Yuan Ma
- Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yina Lin
- Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Huan Wang
- Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Dian-Jie Li
- School of Physics, Peking University, Beijing, China
| | - Tao-Ran Zheng
- Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Fu-Qing Wu
- Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
- MOE Key Lab of Industrial Biocatalysts, Department of Chemical Engineering, Tsinghua University, Beijing, China
| | - Jian-Wen Ye
- Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China.
- MOE Key Lab of Industrial Biocatalysts, Department of Chemical Engineering, Tsinghua University, Beijing, China.
- Center for Materials Synthetic Biology, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
| | - Guo-Qiang Chen
- Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China.
- Tsinghua-Peking Center for Life Sciences, Beijing, China.
- MOE Key Lab of Industrial Biocatalysts, Department of Chemical Engineering, Tsinghua University, Beijing, China.
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26
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Lee BC, Tsai JC, Lin CY, Hung CW, Sheu JC, Tsai HJ. Using Bacillus subtilis as a Host Cell to Express an Antimicrobial Peptide from the Marine Chordate Ciona intestinalis. Mar Drugs 2021; 19:md19020111. [PMID: 33673287 PMCID: PMC7918927 DOI: 10.3390/md19020111] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 02/08/2021] [Accepted: 02/08/2021] [Indexed: 11/30/2022] Open
Abstract
Ciona molecule against microbes-A24 (CiMAM) isolated from the marine chordate Ciona intestinalis is an antimicrobial peptide. To generate CiMAM-expressing transgenic Bacillus subtilis, we constructed a plasmid expressing recombinant CiMAM (rCiMAM) and introduced it into B. subtilis. Transgenic strains C117 and C166 were selected since they were able to highly and stably express rCiMAM. We studied the bactericidal activity of pepsin-digested extracts from rCiMAM-expressing strains against freshwater and euryhaline pathogens that commonly occur in aquaculture ponds and found no difference from that of lactoferricin-expressing strains. The bactericidal activity of 1-μL aliquot from a total 5.5 mL extracted from 5 mL of cultured C117 (1.45 × 108 CFU·mL−1) and C166 (2.17 × 108 CFU·mL−1) against halophilic bacteria was equivalent to the efficacy of 57.06 and 32.35 ng of Tetracycline against Vibrio natriegens, 47.07 and 25.2 ng against V. parahaemolyticus, and 58.17 and 36.55 ng against V. alginolyticus, respectively, indicating higher bactericidal activity of pepsin-extracts from rCiMAM-containing strains against halophilic bacteria compared to that from lactoferricin-containing strains. Since the antibacterial activity of rCiMAM-expressing B. subtilis strains shows higher competence against halophilic pathogens compared to that against freshwater and euryhaline pathogens, these strains are promising candidates to protect marine fish and shellfish from halophilic bacterial infection.
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Affiliation(s)
- Bing-Chang Lee
- Institute of Biomedical Sciences, Mackay Medical College, New Taipei City 25245, Taiwan; (B.-C.L.); (C.-Y.L.)
| | - Jui-Che Tsai
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei 10617, Taiwan; (J.-C.T.); (C.-W.H.)
| | - Cheng-Yung Lin
- Institute of Biomedical Sciences, Mackay Medical College, New Taipei City 25245, Taiwan; (B.-C.L.); (C.-Y.L.)
| | - Chun-Wei Hung
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei 10617, Taiwan; (J.-C.T.); (C.-W.H.)
| | - Jin-Chuan Sheu
- Liver Disease Prevention and Treatment Research Foundation, Taipei 10047, Taiwan;
| | - Huai-Jen Tsai
- Institute of Biomedical Sciences, Mackay Medical College, New Taipei City 25245, Taiwan; (B.-C.L.); (C.-Y.L.)
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei 10617, Taiwan; (J.-C.T.); (C.-W.H.)
- Department of Life Science, Fu Jen Catholic University, New Taipei 20206, Taiwan
- Correspondence:
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27
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Chen J, Ruan JW, Ye JX, Cheng ZW, Chen DZ. Removal of gaseous tetrahydrofuran via a three-phase airlift bioreactor loaded with immobilized cells of GFP-tagged Pseudomonas oleovorans GDT4. Chemosphere 2020; 258:127148. [PMID: 32535434 DOI: 10.1016/j.chemosphere.2020.127148] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 05/01/2020] [Accepted: 05/18/2020] [Indexed: 06/11/2023]
Abstract
Tetrahydrofuran (THF) is a common highly toxic cyclic aliphatic ether that frequently exists in waste gases. Removal of gaseous THF is a serious issue with important environmental ramifications. A novel three-phase airlift bioreactor (TPAB) loaded with immobilized cells was developed for efficient THF removal from gas streams. An effective THF-degrading transformant, Pseudomonas oleovorans GDT4, which contains the pTn-Mod-OTc-gfp plasmid and was tagged with a green fluorescent protein (GFP), was constructed. Continuous treatment of THF-containing waste gases was succeeded by the GFP-labelled cells immobilized with calcium alginate and activated carbon fiber in the TPAB for 60 days with >90% removal efficiency. The number of fluorescent cells in the beads reached 1.7 × 1011 cells·g-1 of bead on day 10, accounting for 83.3% of the total number of cells. The amount further increased to 3.0 × 1011 cells·g-1 of bead on day 40. However, it decreased to 2.5 × 1011 cells·g-1 of bead with a substantial increase in biomass in the liquid because of cell leakage and hydraulic shock. PCR-DGGE revealed that P. oleovorans was the dominant microorganism throughout the entire operation. The maximum elimination capacity was affected by empty bed residence time (EBRT). The capacity was only 25.9 g m-3·h-1 at EBRT of 80 s, whereas it reached 37.8 g m-3·h-1 at EBRT of 140 s. This work provides an alternative method for full-scale removal of gaseous THF and presents a useful tool for determining the biomass of a specific degrader in immobilized beads.
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Affiliation(s)
- Jing Chen
- College of Food and Pharmacy, Zhejiang Ocean University, Zhoushan, 316004, China
| | - Jing-Wen Ruan
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, China
| | - Jie-Xu Ye
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, China
| | - Zhuo-Wei Cheng
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, China
| | - Dong-Zhi Chen
- College of Petrochemical and Environment, Zhejiang Ocean University, Zhoushan, 316004, China; College of Environment, Zhejiang University of Technology, Hangzhou, 310032, China.
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28
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Liang K, Liu Q, Kong Q. New technologies in developing recombinant-attenuated bacteria for cancer therapy. Biotechnol Bioeng 2020; 118:513-530. [PMID: 33038015 DOI: 10.1002/bit.27596] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 09/12/2020] [Accepted: 10/06/2020] [Indexed: 12/12/2022]
Abstract
Cancer has always been a global problem, with more cases of cancer patients being diagnosed every year. Conventional cancer treatments, including radiotherapy, chemotherapy, and surgery, are still unable to bypass their obvious limitations, and developing effective targeted therapies is still required. More than one century ago, the doctor William B. Coley discovered that cancer patients had tumor regression by injection of Streptococcus bacteria. The studies of cancer therapy using bacterial microorganisms are now very widespread. In particular, the facultative anaerobic bacteria Salmonella typhimurium is widely investigated as it can selectively colonize different types of tumors, locally deliver various antitumor drugs, and inhibit tumor growth. The exciting antitumor efficacy and safety observed in animal tumor models prompted the well-known attenuated Salmonella bacterial strain VNP20009 to be tested in human clinical trials in the early 21st century. Regrettably, no patients showed significant therapeutic effects and even bacterial colonization in tumor tissue was undetectable in most patients. Salmonella bacteria are still considered as a promising agent or vehicle for cancer therapy. Recent efforts have been focused on the generation of attenuated bacterial strains with higher targeting for tumor tissue, and optimization of the delivery of therapeutic antitumor cargoes into the tumor microenvironment. This review will summarize new technologies or approaches that may improve bacteria-mediated cancer therapy.
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Affiliation(s)
- Kang Liang
- College of Veterinary Medicine, Southwest University, Chongqing, China
| | - Qing Liu
- College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Qingke Kong
- College of Veterinary Medicine, Southwest University, Chongqing, China
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29
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Fei X, Zhang Y, Ding L, Li Y, Deng X. Controlling the development of the dengue vector Aedes aegypti using HR3 RNAi transgenic Chlamydomonas. PLoS One 2020; 15:e0240223. [PMID: 33052930 PMCID: PMC7556462 DOI: 10.1371/journal.pone.0240223] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 09/23/2020] [Indexed: 11/29/2022] Open
Abstract
The Aedes aegypti mosquito plays an important role in the spread of diseases, including epidemic ones, such as dengue fever, Zika virus disease, yellow fever, and chikungunya disease. To control the population of Ae.aegypti, we transferred an HR3 RNAi fragment into the microalgae Chlamydomonas, which serves as food for Ae.aegypti larvae. Results showed that the HR3 RNAi transgenic algal strains were lethal to Ae.aegypti. The integumentary system of larvae fed with HR3 RNAi transgenic algal strains was severely damaged. Muscles of the larvae were unevenly distributed and disordered, and their midgut showed disintegration of the intestinal cavity. RNA-Seq results demonstrated that on the 4th day of inoculation with the transgenic algae, the abundance of early expressed genes in the 20E signal transduction pathway of larvae fed with the HR3 RNAi transgenic algal strain significantly reduced. These genes include E74, E75, E93, and 20E receptor complex EcR/USP and FTZ-F1 gene regulated by HR3. In later experiments, a scale test of 300 Ae.aegypti eggs per group was carried out for 30 days, and the survival rate of Ae.aegypti fed with the HR3 RNAi transgenic strain was only 1.3%. These results indicate that the HR3 RNAi transgenic strain exerts obvious insecticidal effect.
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Affiliation(s)
- Xiaowen Fei
- Department of Biochemistry and Molecular Biology, Hainan Medical College, Haikou, China
| | - Yang Zhang
- Department of Biochemistry and Molecular Biology, Hainan Medical College, Haikou, China
| | - Lili Ding
- Department of Biochemistry and Molecular Biology, Hainan Medical College, Haikou, China
| | - Yajun Li
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Science, Haikou, China
- Hainan Provincial Key Laboratory for Functional Components Research and Utilization of Marine Bio-resources, Haikou, China
| | - Xiaodong Deng
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Science, Haikou, China
- Hainan Provincial Key Laboratory for Functional Components Research and Utilization of Marine Bio-resources, Haikou, China
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Chang JD, Huang S, Yamaji N, Zhang W, Ma JF, Zhao FJ. OsNRAMP1 transporter contributes to cadmium and manganese uptake in rice. Plant Cell Environ 2020; 43:2476-2491. [PMID: 32666540 DOI: 10.1111/pce.13843] [Citation(s) in RCA: 135] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 07/07/2020] [Accepted: 07/07/2020] [Indexed: 05/23/2023]
Abstract
Rice is a major dietary source of the toxic metal, cadmium (Cd). Previous studies reported that the rice transporter, OsNRAMP1, (Natural resistance-associated macrophage protein 1) could transport iron (Fe), Cd and arsenic (As) in heterologous yeast assays. However, the in planta function of OsNRAMP1 remains unknown. Here, we showed that OsNRAMP1 was able to transport Cd and manganese (Mn) when expressed in yeast, but did not transport Fe or As. OsNRAMP1 was mainly expressed in roots and leaves and encoded a plasma membrane-localized protein. OsNRAMP1 expression was induced by Cd treatment and Fe deficiency. Immunostaining showed that OsNRAMP1 was localized in all root cells, except the central vasculature, and in leaf mesophyll cells. The knockout of OsNRAMP1 resulted in significant decreases in root uptake of Cd and Mn and their accumulation in rice shoots and grains, and increased sensitivity to Mn deficiency. The knockout of OsNRAMP1 had smaller effects on Cd and Mn uptake than knockout of OsNRAMP5, while knockout of both genes resulted in large decreases in the uptake of the two metals. Taken together, OsNRAMP1 contributes significantly to the uptake of Mn and Cd in rice, and the functions of OsNRAMP1 and OsNRAMP5 are similar but not redundant.
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Affiliation(s)
- Jia-Dong Chang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Sheng Huang
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Naoki Yamaji
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Wenwen Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Jian Feng Ma
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Fang-Jie Zhao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
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Akintade D, Chaudhuri B. The effect of copy number on α-synuclein's toxicity and its protective role in Bax-induced apoptosis, in yeast. Biosci Rep 2020; 40:BSR20201912. [PMID: 32794578 PMCID: PMC7468099 DOI: 10.1042/bsr20201912] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 07/24/2020] [Accepted: 07/27/2020] [Indexed: 12/14/2022] Open
Abstract
Apoptosis is a form of programmed cell death which is essential for the growth of dividing human cells whereas, in contrast, it is deleterious for post-mitotic cells such as neurons. Bax and α-synuclein are two human proteins which play a role in the induction of neuronal apoptosis in neurodegenerative diseases like Alzheimer's and Parkinson's. Human Bax and α-synuclein also induce cell death when expressed in baker's yeast, Saccharomyces cerevisiae. Quite unexpectedly, the human α-synuclein gene had been identified as an inhibitor of pro-apoptotic Bax using a yeast-based screen of a human hippocampal cDNA library. Plasmids were constructed with different promoters, which allow expression of wildtype and Parkinson's disease (PD)-related mutant α-synuclein genes, from (i) multi-copy 2µ (episomal) plasmids and (ii) integrative plasmids that compel expression of genes from chromosomal sites in varying copy numbers (1-3). All α-synuclein-containing plasmids were introduced, through transformation, into a yeast strain which already contained a chromosomally integrated copy of Bax. It is for the first time that it was observed that, depending on gene dosage, only wildtype α-synuclein is anti-apoptotic while mutant α-synuclein is not. The results also indicate that wildtype α-synuclein has a remarkable ability to manifest two contrasting effects depending on its level of expression: (i) normally, it would negate apoptosis but (ii) when overexpressed, it tends to induce apoptosis which is probably what happens in PD.
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Affiliation(s)
- Damilare D. Akintade
- School of Life Sciences, Medical School, University of Nottingham, Nottingham, NG7 2UH, U.K
- Leicester School of Pharmacy, De Montfort University, Leicester LE1 9BH, U.K
| | - Bhabatosh Chaudhuri
- Leicester School of Pharmacy, De Montfort University, Leicester LE1 9BH, U.K
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32
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Keep S, Britton P, Bickerton E. Transient Dominant Selection for the Modification and Generation of Recombinant Infectious Bronchitis Coronaviruses. Methods Mol Biol 2020; 2203:147-165. [PMID: 32833211 DOI: 10.1007/978-1-0716-0900-2_12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
We have developed a reverse genetics system for the avian coronavirus infectious bronchitis virus (IBV) in which a full-length cDNA corresponding to the IBV genome is inserted into the vaccinia virus genome under the control of a T7 promoter sequence. Vaccinia virus as a vector for the full-length IBV cDNA has the advantage that modifications can be introduced into the IBV cDNA using homologous recombination, a method frequently used to insert and delete sequences from the vaccinia virus genome. Here, we describe the use of transient dominant selection as a method for introducing modifications into the IBV cDNA that has been successfully used for the substitution of specific nucleotides, deletion of genomic regions, and the exchange of complete genes. Infectious recombinant IBVs are generated in situ following the transfection of vaccinia virus DNA, containing the modified IBV cDNA, into cells infected with a recombinant fowlpox virus expressing T7 DNA-dependent RNA polymerase.
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33
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Pan X, Yu J, Du Q, Zeng S, Liu J, Jiao Q, Zhang H. Efficient synthesis of γ-glutamyl compounds by co-expression of γ-glutamylmethylamide synthetase and polyphosphate kinase in engineered Escherichia coli. J Ind Microbiol Biotechnol 2020; 47:573-583. [PMID: 32885332 DOI: 10.1007/s10295-020-02305-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 08/25/2020] [Indexed: 12/22/2022]
Abstract
γ-Glutamyl compounds have unveiled their importance as active substances or precursors of pharmaceuticals. In this research, an approach for enzymatic synthesis of γ-glutamyl compounds was developed using γ-glutamylmethylamide synthetase (GMAS) from Methylovorus mays and polyphosphate kinase (PPK) from Corynebacterium glutamicum. GMAS and PPK were co-recombined in pETDuet-1 plasmid and co-expressed in E. coli BL21 (DE3), and the enzymatic properties of GMAS and PPK were investigated, respectively. Under the catalysis of the co-expression system, L-theanine was synthesized with 89.8% conversion when the substrate molar ratio of sodium glutamate and ethylamine (1:1.4) and only 2 mM ATP were used. A total of 14 γ-glutamyl compounds were synthesized by this one-pot method and purified by cation exchange resin and isoelectric point crystallization with a yield range from 22.3 to 72.7%. This study provided an efficient approach for the synthesis of γ-glutamyl compounds by GMAS and PPK co-expression system.
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Affiliation(s)
- Xinru Pan
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, Jiangsu, China
| | - Jinhai Yu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, Jiangsu, China
| | - Qinglin Du
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, Jiangsu, China
| | - Shuiyun Zeng
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, Jiangsu, China
| | - Junzhong Liu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, Jiangsu, China.
| | - Qingcai Jiao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, Jiangsu, China.
| | - Hongjuan Zhang
- School of Pharmacy, Nanjing Medical University, Nanjing, 210029, Jiangsu, China.
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Kemppainen M, Chowdhury J, Lundberg-Felten J, Pardo A. Fluorescent protein expression in the ectomycorrhizal fungus Laccaria bicolor: a plasmid toolkit for easy use of fluorescent markers in basidiomycetes. Curr Genet 2020; 66:791-811. [PMID: 32170354 DOI: 10.1007/s00294-020-01060-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 01/22/2020] [Accepted: 02/04/2020] [Indexed: 10/24/2022]
Abstract
For long time, studies on ectomycorrhiza (ECM) have been limited by inefficient expression of fluorescent proteins (FPs) in the fungal partner. To convert this situation, we have evaluated the basic requirements of FP expression in the model ECM homobasidiomycete Laccaria bicolor and established eGFP and mCherry as functional FP markers. Comparison of intron-containing and intronless FP-expression cassettes confirmed that intron-processing is indispensable for efficient FP expression in Laccaria. Nuclear FP localization was obtained via in-frame fusion of FPs between the intron-containing genomic gene sequences of Laccaria histone H2B, while cytosolic FP expression was produced by incorporating the intron-containing 5' fragment of the glyceraldehyde-3-phosphate dehydrogenase encoding gene. In addition, we have characterized the consensus Kozak sequence of strongly expressed genes in Laccaria and demonstrated its boosting effect on transgene mRNA accumulation. Based on these results, an Agrobacterium-mediated transformation compatible plasmid set was designed for easy use of FPs in Laccaria. The four cloning plasmids presented here allow fast and highly flexible construction of C-terminal in-frame fusions between the sequences of interest and the two FPs, expressed either from the endogenous gene promoter, allowing thus evaluation of the native regulation modes of the gene under study, or alternatively, from the constitutive Agaricus bisporus gpdII promoter for enhanced cellular protein localization assays. The molecular tools described here for cell-biological studies in Laccaria can also be exploited in studies of other biotrophic or saprotrophic basidiomycete species susceptible to genetic transformation.
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Affiliation(s)
- Minna Kemppainen
- Laboratory of Molecular Mycology, Institute of Basic and Applied Microbiology, Department of Science and Technology, Nacional University of Quilmes and CONICET, Bernal, Buenos Aires, Argentina.
| | - Jamil Chowdhury
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, 901 83, Umeå, Sweden
| | - Judith Lundberg-Felten
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, 901 83, Umeå, Sweden
| | - Alejandro Pardo
- Laboratory of Molecular Mycology, Institute of Basic and Applied Microbiology, Department of Science and Technology, Nacional University of Quilmes and CONICET, Bernal, Buenos Aires, Argentina
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35
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Barry MA, Rubin JD, Lu SC. Retargeting adenoviruses for therapeutic applications and vaccines. FEBS Lett 2020; 594:1918-1946. [PMID: 31944286 PMCID: PMC7311308 DOI: 10.1002/1873-3468.13731] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Revised: 12/02/2019] [Accepted: 12/03/2019] [Indexed: 12/29/2022]
Abstract
Adenoviruses (Ads) are robust vectors for therapeutic applications and vaccines, but their use can be limited by differences in their in vitro and in vivo pharmacologies. This review emphasizes that there is not just one Ad, but a whole virome of diverse viruses that can be used as therapeutics. It discusses that true vector targeting involves not only retargeting viruses, but importantly also detargeting the viruses from off-target cells.
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Affiliation(s)
- Michael A Barry
- Department of Medicine, Division of Infectious Diseases, Department of Immunology, Department of Molecular Medicine, Mayo Clinic, Rochester, MN, USA
| | - Jeffrey D Rubin
- Virology and Gene Therapy Graduate Program, Mayo Graduate School, Mayo Clinic, Rochester, MN, USA
| | - Shao-Chia Lu
- Virology and Gene Therapy Graduate Program, Mayo Graduate School, Mayo Clinic, Rochester, MN, USA
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36
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Schuster BS, Dignon GL, Tang WS, Kelley FM, Ranganath AK, Jahnke CN, Simpkins AG, Regy RM, Hammer DA, Good MC, Mittal J. Identifying sequence perturbations to an intrinsically disordered protein that determine its phase-separation behavior. Proc Natl Acad Sci U S A 2020; 117:11421-11431. [PMID: 32393642 PMCID: PMC7261017 DOI: 10.1073/pnas.2000223117] [Citation(s) in RCA: 160] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Phase separation of intrinsically disordered proteins (IDPs) commonly underlies the formation of membraneless organelles, which compartmentalize molecules intracellularly in the absence of a lipid membrane. Identifying the protein sequence features responsible for IDP phase separation is critical for understanding physiological roles and pathological consequences of biomolecular condensation, as well as for harnessing phase separation for applications in bioinspired materials design. To expand our knowledge of sequence determinants of IDP phase separation, we characterized variants of the intrinsically disordered RGG domain from LAF-1, a model protein involved in phase separation and a key component of P granules. Based on a predictive coarse-grained IDP model, we identified a region of the RGG domain that has high contact probability and is highly conserved between species; deletion of this region significantly disrupts phase separation in vitro and in vivo. We determined the effects of charge patterning on phase behavior through sequence shuffling. We designed sequences with significantly increased phase separation propensity by shuffling the wild-type sequence, which contains well-mixed charged residues, to increase charge segregation. This result indicates the natural sequence is under negative selection to moderate this mode of interaction. We measured the contributions of tyrosine and arginine residues to phase separation experimentally through mutagenesis studies and computationally through direct interrogation of different modes of interaction using all-atom simulations. Finally, we show that despite these sequence perturbations, the RGG-derived condensates remain liquid-like. Together, these studies advance our fundamental understanding of key biophysical principles and sequence features important to phase separation.
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Affiliation(s)
- Benjamin S Schuster
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104
- Department of Chemical and Biochemical Engineering, Rutgers University, Piscataway, NJ 08854
| | - Gregory L Dignon
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, PA 18015
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794
| | - Wai Shing Tang
- Department of Physics, Brown University, Providence, RI 02912
| | - Fleurie M Kelley
- Department of Chemical and Biochemical Engineering, Rutgers University, Piscataway, NJ 08854
| | | | - Craig N Jahnke
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA 19104
| | - Alison G Simpkins
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA 19104
| | - Roshan Mammen Regy
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, PA 18015
| | - Daniel A Hammer
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA 19104
| | - Matthew C Good
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104
| | - Jeetain Mittal
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, PA 18015;
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Abstract
Efficient microbial synthesis of chemicals requires the coordinated supply of precursors and cofactors to maintain cell growth and product formation. Substrates with different entry points into the metabolic network have different energetic and redox statuses. Generally, substrate cofeeding could bypass the lengthy and highly regulated native metabolism and facilitates high carbon conversion rate. Aiming to efficiently synthesize the high-value rose-smell 2-phenylethanol (2-PE) in Y. lipolytica, we analyzed the stoichiometric constraints of the Ehrlich pathway and identified that the selectivity of the Ehrlich pathway and the availability of 2-oxoglutarate are the rate-limiting factors. Stepwise refactoring of the Ehrlich pathway led us to identify the optimal catalytic modules consisting of l-phenylalanine permease, ketoacid aminotransferase, phenylpyruvate decarboxylase, phenylacetaldehyde reductase, and alcohol dehydrogenase. On the other hand, mitochondrial compartmentalization of 2-oxoglutarate inherently creates a bottleneck for efficient assimilation of l-phenylalanine, which limits 2-PE production. To improve 2-oxoglutarate (aKG) trafficking across the mitochondria membrane, we constructed a cytosolic aKG source pathway by coupling a bacterial aconitase with a native isocitrate dehydrogenase (ylIDP2). Additionally, we also engineered dicarboxylic acid transporters to further improve the 2-oxoglutarate availability. Furthermore, by blocking the precursor-competing pathways and mitigating fatty acid synthesis, the engineered strain produced 2669.54 mg/L of 2-PE in shake flasks, a 4.16-fold increase over the starting strain. The carbon conversion yield reaches 0.702 g/g from l-phenylalanine, 95.0% of the theoretical maximal. The reported work expands our ability to harness the Ehrlich pathway for production of high-value aromatics in oleaginous yeast species.
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Affiliation(s)
- Yang Gu
- Department
of Chemical, Biochemical and Environmental Engineering, University of Maryland, Baltimore County, Baltimore, Maryland 21250, United States
- Key
Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of
Education, Jiangnan University, Wuxi 214122, China
| | - Jingbo Ma
- Department
of Chemical, Biochemical and Environmental Engineering, University of Maryland, Baltimore County, Baltimore, Maryland 21250, United States
| | - Yonglian Zhu
- Key
Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of
Education, Jiangnan University, Wuxi 214122, China
| | - Peng Xu
- Department
of Chemical, Biochemical and Environmental Engineering, University of Maryland, Baltimore County, Baltimore, Maryland 21250, United States
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Abstract
Bacteria generally live in species-rich communities, such as the gut microbiota. Yet little is known about bacterial evolution in natural ecosystems. Here, we followed the long-term evolution of commensal Escherichia coli in the mouse gut. We observe the emergence of mutation rate polymorphism, ranging from wild-type levels to 1,000-fold higher. By combining experiments, whole-genome sequencing, and in silico simulations, we identify the molecular causes and explore the evolutionary conditions allowing these hypermutators to emerge and coexist within the microbiota. The hypermutator phenotype is caused by mutations in DNA polymerase III proofreading and catalytic subunits, which increase mutation rate by approximately 1,000-fold and stabilise hypermutator fitness, respectively. Strong mutation rate variation persists for >1,000 generations, with coexistence between lineages carrying 4 to >600 mutations. The in vivo molecular evolution pattern is consistent with fitness effects of deleterious mutations sd ≤ 10−4/generation, assuming a constant effect or exponentially distributed effects with a constant mean. Such effects are lower than typical in vitro estimates, leading to a low mutational load, an inference that is observed in in vivo and in vitro competitions. Despite large numbers of deleterious mutations, we identify multiple beneficial mutations that do not reach fixation over long periods of time. This indicates that the dynamics of beneficial mutations are not shaped by constant positive Darwinian selection but could be explained by other evolutionary mechanisms that maintain genetic diversity. Thus, microbial evolution in the gut is likely characterised by partial sweeps of beneficial mutations combined with hitchhiking of slightly deleterious mutations, which take a long time to be purged because they impose a low mutational load. The combination of these two processes could allow for the long-term maintenance of intraspecies genetic diversity, including mutation rate polymorphism. These results are consistent with the pattern of genetic polymorphism that is emerging from metagenomics studies of the human gut microbiota, suggesting that we have identified key evolutionary processes shaping the genetic composition of this community. Weak-effect deleterious mutations and negative frequency–dependent selection, acting on beneficial mutations, shape the dynamics of molecular evolution within the mouse gut microbiota.
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Affiliation(s)
- Ricardo S. Ramiro
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
- * E-mail: (RSR); (IG)
| | - Paulo Durão
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Claudia Bank
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Isabel Gordo
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
- * E-mail: (RSR); (IG)
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Knoot CJ, Biswas S, Pakrasi HB. Tunable Repression of Key Photosynthetic Processes Using Cas12a CRISPR Interference in the Fast-Growing Cyanobacterium Synechococcus sp. UTEX 2973. ACS Synth Biol 2020; 9:132-143. [PMID: 31829621 DOI: 10.1021/acssynbio.9b00417] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Cyanobacteria are photoautotrophic prokaryotes that serve as key model organisms to study basic photosynthetic processes and are potential carbon-negative production chassis for commodity and high-value chemicals. The development of new synthetic biology tools and improvement of current ones is a requisite for furthering these organisms as models and production vehicles. CRISPR interference (CRISPRi) allows for targeted gene repression using a DNase-dead Cas nuclease ("dCas"). Here, we describe a titratable dCas12a (dCpf1) CRISPRi system and apply it to repress key photosynthetic processes in the fast-growing cyanobacterium Synechococcus sp. UTEX 2973 (S2973). The system relies on a lac repressor system that retains tight regulation in the absence of inducer (0-10% repression) while maintaining the capability for >90% repression of high-abundance gene targets. We determined that dCas12a is less toxic than dCas9. We tested the efficacy of the system toward eYFP and three native targets in S2973: the phycobilisome antenna, glycogen synthesis, and photosystem I (PSI), an essential part of the photosynthetic electron transport chain in oxygenic photoautotrophs. PSI was knocked down indirectly by repressing the protein factor BtpA involved in stabilizing core PSI proteins. We could reduce cellular PSI titer by 87% under photoautotrophic conditions, and we characterized these cells to gain insights into the response of the strain to the low PSI content. The ability to tightly regulate and time the (de)repression of essential genes in trans will allow for the study of photosynthetic processes that are not accessible using knockout mutants.
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Affiliation(s)
- Cory J Knoot
- Department of Biology , Washington University , St. Louis , Missouri United States
| | - Sandeep Biswas
- Department of Biology , Washington University , St. Louis , Missouri United States
| | - Himadri B Pakrasi
- Department of Biology , Washington University , St. Louis , Missouri United States
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Orf GS, Redding KE. Expression and purification of affinity-tagged variants of the photochemical reaction center from Heliobacterium modesticaldum. Photosynth Res 2019; 142:335-348. [PMID: 31542861 DOI: 10.1007/s11120-019-00672-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 09/05/2019] [Indexed: 06/10/2023]
Abstract
The heliobacterial photochemical reaction center (HbRC) from the chlorophototrophic Firmicutes bacterium Heliobacterium modesticaldum is the only homodimeric type I RC whose structure is known. Using genetic techniques recently established in our lab, we have developed a rapid heterologous expression system for the HbRC core polypeptide PshA. Our system relies on rescue of the non-chlorophototrophic ∆pshA::cbp2p-aph3 strain of Hbt. modesticaldum by expression of a heterologous pshA gene from a replicating shuttle vector. In addition, we constructed two tagged variants of PshA, one with an N-terminal octahistidine tag and one with an internal hexahistidine tag, which facilitate rapid purification of pure, active HbRC cores in milligram quantities. We constructed a suite of shuttle vectors bearing untagged or tagged versions of pshA driven by various promoters. Surprisingly, we found that the eno and gapDH_2 promoters from Clostridium thermocellum drive better expression of pshA than fragments of DNA derived from the region upstream of the pshA locus on the Hbt. modesticaldum genome. This "pshA rescue" strategy also provided a useful window into how Hbt. modesticaldum regulates pigment synthesis and growth rate when chlorophototrophic output decreases.
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Affiliation(s)
- Gregory S Orf
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
- Center for Bioenergy and Photosynthesis, Arizona State University, Tempe, AZ, 85287, USA
| | - Kevin E Redding
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA.
- Center for Bioenergy and Photosynthesis, Arizona State University, Tempe, AZ, 85287, USA.
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Abstract
We develop a method for completing the genetics of natural living systems by which the absence of expected future discoveries can be established. We demonstrate the method using bacteriophage øX174, the first DNA genome to be sequenced. Like many well-studied natural organisms, closely related genome sequences are available-23 Bullavirinae genomes related to øX174. Using bioinformatic tools, we first identified 315 potential open reading frames (ORFs) within the genome, including the 11 established essential genes and 82 highly conserved ORFs that have no known gene products or assigned functions. Using genome-scale design and synthesis, we made a mutant genome in which all 11 essential genes are simultaneously disrupted, leaving intact only the 82 conserved but cryptic ORFs. The resulting genome is not viable. Cell-free gene expression followed by mass spectrometry revealed only a single peptide expressed from both the cryptic ORF and wild-type genomes, suggesting a potential new gene. A second synthetic genome in which 71 conserved cryptic ORFs were simultaneously disrupted is viable but with ∼50% reduced fitness relative to the wild type. However, rather than finding any new genes, repeated evolutionary adaptation revealed a single point mutation that modulates expression of gene H, a known essential gene, and fully suppresses the fitness defect. Taken together, we conclude that the annotation of currently functional ORFs for the øX174 genome is formally complete. More broadly, we show that sequencing and bioinformatics followed by synthesis-enabled reverse genomics, proteomics, and evolutionary adaptation can definitely establish the sufficiency and completeness of natural genome annotations.
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Affiliation(s)
- Paul R Jaschke
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia;
| | | | - Kay S Hung
- Bioengineering Department, Stanford University, Stanford, CA 94305
| | - Diane Liu
- Bioengineering Department, Stanford University, Stanford, CA 94305
| | - Drew Endy
- Bioengineering Department, Stanford University, Stanford, CA 94305
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Ren J, Karna S, Lee HM, Yoo SM, Na D. Artificial transformation methodologies for improving the efficiency of plasmid DNA transformation and simplifying its use. Appl Microbiol Biotechnol 2019; 103:9205-9215. [PMID: 31650193 DOI: 10.1007/s00253-019-10173-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 10/03/2019] [Accepted: 10/08/2019] [Indexed: 01/23/2023]
Abstract
The uptake of exogenous DNA materials through the cell membrane by bacteria, known as transformation, is essential for the genetic manipulation of bacteria and, thus, plays key roles in biotechnological and biological research. The efficiency of natural transformation is very low; therefore, various artificial transformation methods have been developed for simple and efficient bacterial transformation. The basic bacterial transformation method is based on chemical, physical, and electrical processes and other means to permeabilize the bacterial cell membrane to allow plasmid DNA uptake. With the introduction of novel chemicals, materials, and devices and the optimization of protocols, new transformation methods have become simpler, cheaper, and more reproducible for use in diverse bacterial species compared with conventional methods. In this review, artificial transformation methods have been classified according to the membrane-permeabilizing mechanisms employed by them. Their influential factors, transformation efficiency, advantages, disadvantages, and practical applications are briefly illustrated. Finally, physicochemical transformation as a new bacterial transformation technique has also been described.
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Affiliation(s)
- Jun Ren
- School of Integrative Engineering, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Sandeep Karna
- School of Integrative Engineering, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Hyang-Mi Lee
- School of Integrative Engineering, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Seung Min Yoo
- School of Integrative Engineering, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Dokyun Na
- School of Integrative Engineering, Chung-Ang University, Seoul, 06974, Republic of Korea.
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López-Yglesias AH, Lu CC, Zhao X, Chou T, VandenBos T, Strong RK, Smith KD. FliC's Hypervariable D3 Domain Is Required for Robust Anti-Flagellin Primary Antibody Responses. Immunohorizons 2019; 3:422-432. [PMID: 31488506 DOI: 10.4049/immunohorizons.1800061] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 08/13/2019] [Indexed: 11/19/2022] Open
Abstract
Bacterial flagellin is a well-known agonist of the innate immune system that induces proinflammatory responses through the TLR5 and Naip5/6 recognition pathways. Several clinical trials investigating flagellin fusion proteins have demonstrated promising results for inducing protective immunity toward influenza virus, which has been largely attributed to flagellin's ability to activate TLR5. Our laboratory previously demonstrated that the Salmonella enterica serovar Typhimurium flagellin protein, FliC, induces Ab responses in mice through a third pathway that is independent of TLR5, Casp1/11, and MyD88. In this study, we further define the structural features of FliC that contribute to this unknown third pathway. By destroying the Naip5/6 and TLR5 recognition sites, we demonstrate that neither were required for the TLR5-, inflammasome- and MyD88-independent Ab responses toward FliC. In contrast, deletion of FliC's D3 or D0/D1 domains eliminated primary anti-flagellin Ab responses. For optimal primary and secondary anti-flagellin Ab responses we show that TLR5, inflammasome recognition, and the D3 domain of FliC are essential for flagellin's robust immunogenicity. Our data demonstrate that the D3 domain of FliC influences immunogenicity independent of the known innate recognition sites in the D0/D1 domains to augment Ab production. Our results suggest full-length FliC is critical for optimal immunogenicity and Ab responses in flagellin-based vaccines.
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Affiliation(s)
| | - Chun-Chi Lu
- Department of Pathology, University of Washington, Seattle, WA 98195; and
| | - Xiaodan Zhao
- Department of Pathology, University of Washington, Seattle, WA 98195; and
| | - Tiffany Chou
- Department of Pathology, University of Washington, Seattle, WA 98195; and
| | - Tim VandenBos
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109
| | - Roland K Strong
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109
| | - Kelly D Smith
- Department of Pathology, University of Washington, Seattle, WA 98195; and
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Tounsi S, Feki K, Kamoun Y, Saïdi MN, Jemli S, Ghorbel M, Alcon C, Brini F. Highlight on the expression and the function of a novel MnSOD from diploid wheat (T. monococcum) in response to abiotic stress and heavy metal toxicity. Plant Physiol Biochem 2019; 142:384-394. [PMID: 31401434 DOI: 10.1016/j.plaphy.2019.08.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 07/09/2019] [Accepted: 08/02/2019] [Indexed: 06/10/2023]
Abstract
Superoxide dismutases (SODs) play a pivotal role in improving abiotic stress tolerance in plant cells. A novel manganese superoxide dismutase gene, denoted as TmMnSOD, was identified from Triticum monococcum. The encoded protein displayed high sequence identity with MnSOD family members and was highly homologous to TdMnSOD from durum wheat. Furthermore, the 3D structure analysis revealed that TmMnSOD displayed homotetramer subunit organization, incorporating four Mn2+ ions. Notably, TmMnSOD structure contains predominantly alpha helices with three beta sheets. On the other hand, under stress conditions, TmMnSOD transcript level was significantly up-regulated by salt, oxidative and heavy metal stresses. At the functional level, TmMnSOD imparts tolerance of yeast and E. coli cells under diverse stresses. Promoter analysis of TmMnSOD gene showed the presence of a great number of salt and pathogen-responsive cis-regulatory elements, highlighting the interest of this gene in breeding programs towards improved tolerance to salt stress in wheat.
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Affiliation(s)
- Sana Tounsi
- Biotechnology and Plant Improvement Laboratory, Centre of Biotechnology of Sfax (CBS)/University of Sfax, B.P ''1177'', 3018, Sfax, Tunisia
| | - Kaouthar Feki
- Laboratory of Legumes, Centre of Biotechnology Bordj Cedria, BP 901, 2050, Hammam Lif, Tunisia
| | - Yosra Kamoun
- Laboratory of Molecular Biotechnology of Eukaryotes, Centre of Biotechnology of Sfax, B.P ''1177'', 3018, Sfax, Tunisia
| | - Mohamed Najib Saïdi
- Biotechnology and Plant Improvement Laboratory, Centre of Biotechnology of Sfax (CBS)/University of Sfax, B.P ''1177'', 3018, Sfax, Tunisia
| | - Sonia Jemli
- Laboratory of Microbial Biotechnology and Enzymes Engineering, Centre of Biotechnology of Sfax, B.P ''1177'', 3018, Sfax, Tunisia
| | - Mouna Ghorbel
- Biotechnology and Plant Improvement Laboratory, Centre of Biotechnology of Sfax (CBS)/University of Sfax, B.P ''1177'', 3018, Sfax, Tunisia
| | - Carine Alcon
- Biochimie & Physiologie Moléculaire des plantes, PHIV platform, UMR 5004 CNRS/386 INRA/Supagro Montpellier / Université Montpellier 2, Campus Supagro-INRA, 34060, Montpellier Cedex 2, France
| | - Faiçal Brini
- Biotechnology and Plant Improvement Laboratory, Centre of Biotechnology of Sfax (CBS)/University of Sfax, B.P ''1177'', 3018, Sfax, Tunisia.
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Wróblewska JP, van der Klei IJ. Peroxisome Maintenance Depends on De Novo Peroxisome Formation in Yeast Mutants Defective in Peroxisome Fission and Inheritance. Int J Mol Sci 2019; 20:ijms20164023. [PMID: 31426544 PMCID: PMC6719073 DOI: 10.3390/ijms20164023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 08/13/2019] [Accepted: 08/15/2019] [Indexed: 01/15/2023] Open
Abstract
There is an ongoing debate on how peroxisomes form: by growth and fission of pre-existing peroxisomes or de novo from another membrane. It has been proposed that, in wild type yeast cells, peroxisome fission and careful segregation of the organelles over mother cells and buds is essential for organelle maintenance. Using live cell imaging we observed that cells of the yeast Hansenula polymorpha, lacking the peroxisome fission protein Pex11, still show peroxisome fission and inheritance. Also, in cells of mutants without the peroxisome inheritance protein Inp2 peroxisome segregation can still occur. In contrast, peroxisome fission and inheritance were not observed in cells of a pex11 inp2 double deletion strain. In buds of cells of this double mutant, new organelles likely appear de novo. Growth of pex11 inp2 cells on methanol, a growth substrate that requires functional peroxisomes, is retarded relative to the wild type control. Based on these observations we conclude that in H. polymorpha de novo peroxisome formation is a rescue mechanism, which is less efficient than organelle fission and inheritance to maintain functional peroxisomes.
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Affiliation(s)
- Justyna P Wróblewska
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute (BBA), University of Groningen, PO Box 11103, 9300 CC Groningen, The Netherlands
| | - Ida J van der Klei
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute (BBA), University of Groningen, PO Box 11103, 9300 CC Groningen, The Netherlands.
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Pedro AQ, Queiroz JA, Passarinha LA. Smoothing membrane protein structure determination by initial upstream stage improvements. Appl Microbiol Biotechnol 2019; 103:5483-5500. [PMID: 31127356 PMCID: PMC7079970 DOI: 10.1007/s00253-019-09873-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 04/25/2019] [Accepted: 04/26/2019] [Indexed: 12/14/2022]
Abstract
Membrane proteins (MP) constitute 20–30% of all proteins encoded by the genome of various organisms and perform a wide range of essential biological functions. However, despite they represent the largest class of protein drug targets, a relatively small number high-resolution 3D structures have been obtained yet. Membrane protein biogenesis is more complex than that of the soluble proteins and its recombinant biosynthesis has been a major drawback, thus delaying their further structural characterization. Indeed, the major limitation in structure determination of MP is the low yield achieved in recombinant expression, usually coupled to low functionality, pinpointing the optimization target in recombinant MP research. Recently, the growing attention that have been dedicated to the upstream stage of MP bioprocesses allowed great advances, permitting the evolution of the number of MP solved structures. In this review, we analyse and discuss effective solutions and technical advances at the level of the upstream stage using prokaryotic and eukaryotic organisms foreseeing an increase in expression yields of correctly folded MP and that may facilitate the determination of their three-dimensional structure. A section on techniques used to protein quality control and further structure determination of MP is also included. Lastly, a critical assessment of major factors contributing for a good decision-making process related to the upstream stage of MP is presented.
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Affiliation(s)
- Augusto Quaresma Pedro
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, 6201-001, Covilhã, Portugal
- CICECO - Aveiro Institute of Materials, Department of Chemistry, Universidade de Aveiro, 3810-193, Aveiro, Portugal
| | - João António Queiroz
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, 6201-001, Covilhã, Portugal
| | - Luís António Passarinha
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, 6201-001, Covilhã, Portugal.
- UCIBIO@REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal.
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Liu Y, Zhu A, Tan H, Cao L, Zhang R. Engineering banana endosphere microbiome to improve Fusarium wilt resistance in banana. Microbiome 2019; 7:74. [PMID: 31092296 PMCID: PMC6521393 DOI: 10.1186/s40168-019-0690-x] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 05/05/2019] [Indexed: 05/04/2023]
Abstract
BACKGROUND Plant microbiome highlights the importance of endosphere microbiome for growth and health of the host plant. Microbial community analysis represents an elegant way to identify keystone microbial species that have a more central position in the community. The aim of this study was to access the interactions between the keystone bacterial species and plants during banana Fusarium wilt process, by comparing the endophytic bacterial and fungal community in banana roots and shoot tips during growth and wilting processes. The keystone bacterial species were isolated and further engineered to improve banana wilt resistance. RESULTS Banana endosphere microbiome structure varied during plant growth and wilting processes. Bacterial and fungal diversity in the shoot tips and roots increased with the development of the banana plantlets. The bacterial groups belonging to the Enterobacteriaceae family with different relative abundances were detected in all the samples. The Klebsiella spp. might be the keystone bacteria during the growth of banana plantlets. The relative abundance of Fusarium associated with the wilt disease did not increase during the wilting process. The endophytic Enterobacteriaceae strains Enterobacter sp. E5, Kosakonia sp. S1, and Klebsiella sp. Kb were isolated on Enterobacteriaceae selective medium and further engineered by expressing 1-aminocyclopropane-1-carboxylate (ACC) deaminase on the bacterial cell walls (designated as E5P, S1P, and KbP, respectively). Pot experiments suggested that plants inoculated with strains E5, E5P, S1, and S1P increased resistance to the Fusarium wilt disease compared with the controls without inoculation, whereas the Klebsiella inoculation (Kb and KbP) did not increase the wilt resistance. Compared with the inoculation with the wild strains E5 and S1, the inoculation with engineered strains E5P and S1P significantly increased wilt resistance and promoted plant growth, respectively. The results illustrated that the keystone species in the banana microbiome may not be dominant in numbers and the functional role of keystone species should be involved in the wilt resistance. CONCLUSION The ACC deaminase activity of engineered bacteria was essential to the Fusarium wilt resistance and growth promotion of banana plants. Engineering keystone bacteria in plant microbiome with ACC deaminase on the cell walls should be a promising method to improve plant growth and disease resistance.
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Affiliation(s)
- Yupei Liu
- School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, China
| | - Aiping Zhu
- School of Life Sciences, Guangdong Provincial Key Laboratory for Climate Change and Natural Disaster Studies, Sun Yat-sen University, Guangzhou, China
| | - Hongming Tan
- School of Life Sciences, Guangdong Provincial Key Laboratory for Climate Change and Natural Disaster Studies, Sun Yat-sen University, Guangzhou, China
| | - Lixiang Cao
- School of Life Sciences, Guangdong Provincial Key Laboratory for Climate Change and Natural Disaster Studies, Sun Yat-sen University, Guangzhou, China.
| | - Renduo Zhang
- School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, China.
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Gbesemete D, Laver JR, de Graaf H, Ibrahim M, Vaughan A, Faust S, Gorringe A, Read RC. Protocol for a controlled human infection with genetically modified Neisseria lactamica expressing the meningococcal vaccine antigen NadA: a potent new technique for experimental medicine. BMJ Open 2019; 9:e026544. [PMID: 31048443 PMCID: PMC6501966 DOI: 10.1136/bmjopen-2018-026544] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
INTRODUCTION Neisseria lactamica is a commensal organism found in the human nasopharynx and is closely related to the pathogen N. meningitidis (meningococcus). Carriage of N. lactamica is associated with reduced meningococcal carriage and disease. We summarise an ethically approved protocol for an experimental human challenge study using a genetically modified strain of N. lactamica that expresses the meningococcal antigen NadA. We aim to develop a model to study the role of specific bacterial antigens in nasopharyngeal carriage and immunity, to evaluate vaccines for their efficacy in preventing colonisation and to provide a proof of principle for the development of bacterial medicines. METHODS AND ANALYSIS Healthy adult volunteers aged 18-45 years will receive an intranasal inoculation of either the NadA containing strain of N. lactamica or a genetically modified, but wild-type equivalent control strain. These challenge volunteers will be admitted for 4.5 days observation following inoculation and will then be discharged with strict infection control rules. Bedroom contacts of the challenge volunteers will also be enrolled as contact volunteers. Safety, colonisation, shedding, transmission and immunogenicity will be assessed over 90 days after which carriage will be terminated with antibiotic eradication therapy. ETHICS AND DISSEMINATION This study has been approved by the Department for Environment, Food and Rural Affairs and South Central Oxford A Research Ethics Committee (reference: 18/SC/0133). Findings will be published in peer-reviewed open-access journals as soon as possible. TRIAL REGISTRATION NUMBER NCT03630250; Pre-results.
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Affiliation(s)
- Diane Gbesemete
- NIHR Clinical Research Facility, University Hospital Southampton NHS Foundation Trust, Southampton, UK
- Faculty of Medicine, University of Southampton, Southampton, UK
| | - Jay Robert Laver
- Clinical and Experimental Sciences, University of Southampton, Southampton, UK
| | - Hans de Graaf
- NIHR Clinical Research Facility, University Hospital Southampton NHS Foundation Trust, Southampton, UK
- Faculty of Medicine, University of Southampton, Southampton, UK
| | - Muktar Ibrahim
- Clinical and Experimental Sciences, University of Southampton, Southampton, UK
| | - Andrew Vaughan
- Clinical and Experimental Sciences, University of Southampton, Southampton, UK
| | - Saul Faust
- NIHR Clinical Research Facility, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Andrew Gorringe
- Research, Public Health England Porton, Salisbury, Wiltshire, UK
| | - Robert Charles Read
- Clinical and Experimental Sciences, University of Southampton, Southampton, UK
- NIHR Southampton Biomedical Research Centre, Southampton, UK
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He L, Jing Y, Shen J, Li X, Liu H, Geng Z, Wang M, Li Y, Chen D, Gao J, Zhang W. Mitochondrial Pyruvate Carriers Prevent Cadmium Toxicity by Sustaining the TCA Cycle and Glutathione Synthesis. Plant Physiol 2019; 180:198-211. [PMID: 30770461 PMCID: PMC6501077 DOI: 10.1104/pp.18.01610] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 02/05/2019] [Indexed: 05/20/2023]
Abstract
Cadmium (Cd) is a major heavy metal pollutant, and Cd toxicity is a serious cause of abiotic stress in the environment. Plants protect themselves against Cd stress through a variety of pathways. In a recent study, we found that mitochondrial pyruvate carriers (MPCs) are involved in Cd tolerance in Arabidopsis (Arabidopsis thaliana). Following the identification of MPCs in yeast (Saccharomyces cerevisiae) in 2012, most studies have focused on the function of MPCs in animals, as a possible approach to reduce the risk of cancer developing. The results of this study show that AtMPC protein complexes are required for Cd tolerance and prevention of Cd accumulation in Arabidopsis. AtMPC complexes are composed of two elements, AtMPC1 and AtMPC2 (AtNRGA1 or AtMPC3). When the formation of AtMPCs was interrupted by the loss of AtMPC1, glutamate could supplement the synthesis of acetyl-coenzyme A and sustain the TCA cycle. With the up-regulation of glutathione synthesis following exposure to Cd stress, the supplementary pathway could not efficiently drive the tricarboxylic acid cycle without AtMPC. The ATP content decreased concomitantly with the deletion of tricarboxylic acid activity, which led to Cd accumulation in Arabidopsis. More importantly, ScMPCs were also required for Cd tolerance in yeast. Our results suggest that the mechanism of Cd tolerance may be similar in other species.
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Affiliation(s)
- Lilong He
- Key Laboratory of Plant Development and Environmental Adaption Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao 266237, China
- Shandong Key Laboratory of Greenhouse Vegetable Biology, Institute of Vegetables and Flowers, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Ying Jing
- Key Laboratory of Plant Development and Environmental Adaption Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao 266237, China
| | - Jianlin Shen
- Key Laboratory of Plant Development and Environmental Adaption Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao 266237, China
| | - Xining Li
- Key Laboratory of Plant Development and Environmental Adaption Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao 266237, China
| | - Huiping Liu
- Key Laboratory of Plant Development and Environmental Adaption Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao 266237, China
| | - Zilong Geng
- Key Laboratory of Plant Development and Environmental Adaption Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao 266237, China
| | - Mei Wang
- Key Laboratory of Plant Development and Environmental Adaption Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao 266237, China
| | - Yongqing Li
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Donghua Chen
- Key Laboratory of Plant Development and Environmental Adaption Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao 266237, China
| | - Jianwei Gao
- Key Laboratory of Plant Development and Environmental Adaption Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao 266237, China
- Shandong Key Laboratory of Greenhouse Vegetable Biology, Institute of Vegetables and Flowers, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Wei Zhang
- Key Laboratory of Plant Development and Environmental Adaption Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao 266237, China
- Shandong Key Laboratory of Greenhouse Vegetable Biology, Institute of Vegetables and Flowers, Shandong Academy of Agricultural Sciences, Jinan 250100, China
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Xu J, Xing S, Sun Q, Zhan C, Liu X, Zhang S, Wang X. The expression of a tubby-like protein from Malus domestica (MdTLP7) enhances abiotic stress tolerance in Arabidopsis. BMC Plant Biol 2019; 19:60. [PMID: 30727953 PMCID: PMC6366083 DOI: 10.1186/s12870-019-1662-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 01/24/2019] [Indexed: 05/23/2023]
Abstract
BACKGROUND Tubby-like proteins (TLPs), characterized by a signature tubby domain, are widespread in plants and animals. To date, only plant TLPs involved in multifarious stress responses and male gametophyte development have been identified. However, studies on the molecular functions of plant TLPs are largely unknown. RESULTS In this investigation, the roles of a TLP from Malus domestica (MdTLP7) in response to abiotic stresses were characterized by expressing it in Arabidopsis. The expression of wild-type full-length MdTLP7 (FL) significantly increased the stress tolerance of Arabidopsis seedlings to osmotic, salt, cold and heat stress, while the expression of truncated MdTLP7 containing only the tubby domain (Tub) also showed some function. Located on a central α helix surrounded by 12 anti-parallel β strands in the tubby domain, the K190/R192 site may be involved in fixation to the plasma membrane, as shown by 3D homology modelling with animal TLPs. This site might play a crucial role in anti-stress functions since site-directed mutagenesis of MdTLP7 reduced stress tolerance. Subcellular localization showed that MdTLP7 was mainly localized in the plasma membrane in plant cells, suggesting that it might participate in the transduction of stress signals. CONCLUSIONS The results of this study showed that MdTLP7 could improve abiotic stress tolerance not only in bacteria but also in plants. The K190/R192 residues in the tubby domain were not only the plasma membrane binding site of MdTLP7 but also played a key role in stress tolerance. These results may provide a basis for further exploring the mechanism of anti-stress functioning and downstream target genes of plant TLPs.
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Affiliation(s)
- Jianing Xu
- College of Life Science, State Key Laboratory of Crop Biology, Shandong Agricultural University, Shandong Taian, 271018 People’s Republic of China
| | - Shanshan Xing
- College of Life Science, State Key Laboratory of Crop Biology, Shandong Agricultural University, Shandong Taian, 271018 People’s Republic of China
| | - Qinghua Sun
- College of Life Science, State Key Laboratory of Crop Biology, Shandong Agricultural University, Shandong Taian, 271018 People’s Republic of China
| | - Chunyan Zhan
- College of Life Science, State Key Laboratory of Crop Biology, Shandong Agricultural University, Shandong Taian, 271018 People’s Republic of China
| | - Xin Liu
- College of Life Science, State Key Laboratory of Crop Biology, Shandong Agricultural University, Shandong Taian, 271018 People’s Republic of China
| | - Shizhong Zhang
- College of Life Science, State Key Laboratory of Crop Biology, Shandong Agricultural University, Shandong Taian, 271018 People’s Republic of China
| | - Xiaoyun Wang
- College of Life Science, State Key Laboratory of Crop Biology, Shandong Agricultural University, Shandong Taian, 271018 People’s Republic of China
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