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Sakai A, Jonker AJ, Nelissen FHT, Kalb EM, van Sluijs B, Heus HA, Adamala KP, Glass JI, Huck WTS. Cell-Free Expression System Derived from a Near-Minimal Synthetic Bacterium. ACS Synth Biol 2023; 12:1616-1623. [PMID: 37278603 PMCID: PMC10278164 DOI: 10.1021/acssynbio.3c00114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Indexed: 06/07/2023]
Abstract
Cell-free expression (CFE) systems are fundamental to reconstituting metabolic pathways in vitro toward the construction of a synthetic cell. Although an Escherichia coli-based CFE system is well-established, simpler model organisms are necessary to understand the principles behind life-like behavior. Here, we report the successful creation of a CFE system derived from JCVI-syn3A (Syn3A), the minimal synthetic bacterium. Previously, high ribonuclease activity in Syn3A lysates impeded the establishment of functional CFE systems. Now, we describe how an unusual cell lysis method (nitrogen decompression) yielded Syn3A lysates with reduced ribonuclease activity that supported in vitro expression. To improve the protein yields in the Syn3A CFE system, we optimized the Syn3A CFE reaction mixture using an active machine learning tool. The optimized reaction mixture improved the CFE 3.2-fold compared to the preoptimized condition. This is the first report of a functional CFE system derived from a minimal synthetic bacterium, enabling further advances in bottom-up synthetic biology.
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Affiliation(s)
- Andrei Sakai
- Institute
for Molecules and Materials, Radboud University, Nijmegen 6525AJ, The Netherlands
| | - Aafke J. Jonker
- Institute
for Molecules and Materials, Radboud University, Nijmegen 6525AJ, The Netherlands
| | - Frank H. T. Nelissen
- Institute
for Molecules and Materials, Radboud University, Nijmegen 6525AJ, The Netherlands
| | - Evan M. Kalb
- Department
of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Bob van Sluijs
- Institute
for Molecules and Materials, Radboud University, Nijmegen 6525AJ, The Netherlands
| | - Hans A. Heus
- Institute
for Molecules and Materials, Radboud University, Nijmegen 6525AJ, The Netherlands
| | - Katarzyna P. Adamala
- Department
of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - John I. Glass
- Synthetic
Biology & Bioenergy, J. Craig Venter
Institute, La Jolla, California 92037, United States
| | - Wilhelm T. S. Huck
- Institute
for Molecules and Materials, Radboud University, Nijmegen 6525AJ, The Netherlands
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2
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Harvey B, Fu X, Li L, Neupane KR, Anand N, Kolesar JM, Richards CI. Dendritic Cell Membrane-Derived Nanovesicles for Targeted T Cell Activation. ACS OMEGA 2022; 7:46222-46233. [PMID: 36570199 PMCID: PMC9773342 DOI: 10.1021/acsomega.2c04420] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 11/14/2022] [Indexed: 06/17/2023]
Abstract
T cells play an integral role in the generation of an effective immune response and are responsible for clearing foreign microbes that have bypassed innate immune system defenses and possess cognate antigens. The immune response can be directed toward a desired target through the selective priming and activation of T cells. Due to their ability to activate a T cell response, dendritic cells and endogenous vesicles from dendritic cells are being developed for cancer immunotherapy treatment. However, current platforms, such as exosomes and synthetic nanoparticles, are limited by their production methods and application constraints. Here, we engineer nanovesicles derived from dendritic cell membranes with similar properties as dendritic cell exosomes via nitrogen cavitation. These cell-derived nanovesicles are capable of activating antigen-specific T cells through direct and indirect mechanisms. Additionally, these nanovesicles can be produced in large yields, overcoming production constraints that limit clinical application of alternative immunomodulatory vesicle or nanoparticle-based methods. Thus, dendritic cell-derived nanovesicles generated by nitrogen cavitation show potential as an immunotherapy platform to stimulate and direct T cell response.
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Affiliation(s)
- Brock
T. Harvey
- Department
of Chemistry, College of Arts and Sciences, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Xu Fu
- Light
Microscopy Facility, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Lan Li
- Department
of Chemistry, College of Arts and Sciences, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Khaga R. Neupane
- Department
of Chemistry, College of Arts and Sciences, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Namrata Anand
- Department
of Pharmacy and Practice, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Jill M. Kolesar
- Department
of Pharmacy and Practice, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Christopher I. Richards
- Department
of Chemistry, College of Arts and Sciences, University of Kentucky, Lexington, Kentucky 40506, United States
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Ahearn IM, Court HR, Siddiqui F, Abankwa D, Philips MR. NRAS is unique among RAS proteins in requiring ICMT for trafficking to the plasma membrane. Life Sci Alliance 2021; 4:4/5/e202000972. [PMID: 33579760 PMCID: PMC7893820 DOI: 10.26508/lsa.202000972] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 01/26/2021] [Accepted: 01/27/2021] [Indexed: 12/17/2022] Open
Abstract
Among the RAS isoforms, NRAS uniquely requires carboxyl methylation by ICMT for delivery to the plasma membrane because of having only a single palmitoylation as a second targeting signal. Isoprenylcysteine carboxyl methyltransferase (ICMT) is the third of three enzymes that sequentially modify the C-terminus of CaaX proteins, including RAS. Although all four RAS proteins are substrates for ICMT, each traffics to membranes differently by virtue of their hypervariable regions that are differentially palmitoylated. We found that among RAS proteins, NRAS was unique in requiring ICMT for delivery to the PM, a consequence of having only a single palmitoylation site as its secondary affinity module. Although not absolutely required for palmitoylation, acylation was diminished in the absence of ICMT. Photoactivation and FRAP of GFP-NRAS revealed increase flux at the Golgi, independent of palmitoylation, in the absence of ICMT. Association of NRAS with the prenyl-protein chaperone PDE6δ also required ICMT and promoted anterograde trafficking from the Golgi. We conclude that carboxyl methylation of NRAS is required for efficient palmitoylation, PDE6δ binding, and homeostatic flux through the Golgi, processes that direct delivery to the plasma membrane.
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Affiliation(s)
- Ian M Ahearn
- The Ronald O Perelman Department of Dermatology, New York University Grossman School of Medicine, New York, NY, USA .,The Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY, USA.,Veterans Affairs New York Harbor Healthcare System, Manhattan Campus, New York, NY, USA
| | - Helen R Court
- The Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY, USA
| | - Farid Siddiqui
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Daniel Abankwa
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland.,Cancer Cell Biology and Drug Discovery Group, Department of Life Sciences and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Mark R Philips
- The Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY, USA
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Scaffold association factor B (SAFB) is required for expression of prenyltransferases and RAS membrane association. Proc Natl Acad Sci U S A 2020; 117:31914-31922. [PMID: 33257571 DOI: 10.1073/pnas.2005712117] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Inhibiting membrane association of RAS has long been considered a rational approach to anticancer therapy, which led to the development of farnesyltransferase inhibitors (FTIs). However, FTIs proved ineffective against KRAS-driven tumors. To reveal alternative therapeutic strategies, we carried out a genome-wide CRISPR-Cas9 screen designed to identify genes required for KRAS4B membrane association. We identified five enzymes in the prenylation pathway and SAFB, a nuclear protein with both DNA and RNA binding domains. Silencing SAFB led to marked mislocalization of all RAS isoforms as well as RAP1A but not RAB7A, a pattern that phenocopied silencing FNTA, the prenyltransferase α subunit shared by farnesyltransferase and geranylgeranyltransferase type I. We found that SAFB promoted RAS membrane association by controlling FNTA expression. SAFB knockdown decreased GTP loading of RAS, abrogated alternative prenylation, and sensitized RAS-mutant cells to growth inhibition by FTI. Our work establishes the prenylation pathway as paramount in KRAS membrane association, reveals a regulator of prenyltransferase expression, and suggests that reduction in FNTA expression may enhance the efficacy of FTIs.
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Abstract
The most frequently mutated oncogene in cancer is KRAS, which utilizes alternative fourth exons to generate two gene products, KRAS4A and KRAS4B, that differ only in their C-terminal membrane-targeting region 1. Because oncogenic mutations occur in exons 2 or 3, when KRAS is activated by mutation two constitutively active KRAS proteins are encoded, each capable of transforming cells 2. No functional distinctions among the splice variants have been established. Oncogenic KRAS alters tumor metabolism 3. Among these alterations is increased glucose uptake and glycolysis, even in the presence of abundant oxygen 4 (the Warburg Effect). Whereas these metabolic effects of oncogenic KRAS have been explained by transcriptional upregulation of glucose transporters and glycolytic enzymes 3–5, direct regulation of metabolic enzymes has not been examined. We report a direct, GTP-dependent interaction between KRAS4A and hexokinase 1 (HK1) that alters the activity of the kinase, establishing HK1 as an effector of KRAS4A. The interaction is unique to KRAS4A because the palmitoylation/depalmitoylation cycle of this RAS isoform permits co-localization with HK1 on the outer mitochondrial membrane (OMM). KRAS4A expression in cancer may drive unique metabolic vulnerabilities that can be exploited therapeutically.
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Boucher D. Isolation of Neutrophil Nuclei for Use in NETosis Assays. Bio Protoc 2019; 9:e3357. [PMID: 33654856 DOI: 10.21769/bioprotoc.3357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 08/28/2019] [Accepted: 08/28/2019] [Indexed: 11/02/2022] Open
Abstract
Neutrophils are critical immune cells that protect our body against invading pathogens. They generate antibacterial DNA structures called neutrophil extracellular traps (NET). Recently we identified a new mechanism that enables NET formation. We observed that following recognition of lipopolysaccharides, inflammatory caspases cleave Gasdermin D and enable NET generation ( Chen et al., 2018 ). This protocol describes how we purify neutrophil nuclei to visualize NET formation by live microscopy. After neutrophil purification from murine bone marrow, neutrophils are lysed in a hypotonic buffer using a nitrogen cavitation device to prevent lysis of neutrophil granules and subsequent contamination by granules proteases. Lysed neutrophils are then centrifuged, and nuclei are counted. The protocol described here is straightforward and enables the study of early changes happening in the nuclei of neutrophils undergoing NETosis with limited contamination by granule proteases.
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Affiliation(s)
- Dave Boucher
- Institut de Biochimie, Université de Lausanne, Epalinges, Switzerland
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Rahman MH, Xiao Q, Zhao S, Qu F, Chang C, Wei AC, Ho YP. Demarcating the membrane damage for the extraction of functional mitochondria. MICROSYSTEMS & NANOENGINEERING 2018; 4:39. [PMID: 31057927 PMCID: PMC6311452 DOI: 10.1038/s41378-018-0037-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Revised: 09/11/2018] [Accepted: 10/19/2018] [Indexed: 05/02/2023]
Abstract
Defective mitochondria have been linked to several critical human diseases such as neurodegenerative disorders, cancers and cardiovascular disease. However, the detailed characterization of mitochondria has remained relatively unexplored, largely due to the lack of effective extraction methods that may sufficiently retain the functionality of mitochondria, particularly when limited amount of sample is considered. In this study, we explore the possibility of modulating hydrodynamic stress through a cross-junction geometry at microscale to selectively disrupt the cellular membrane while mitochondrial membrane is secured. The operational conditions are empirically optimized to effectively shred the cell membranes while keeping mitochondria intact for the model mammalian cell lines, namely human embryonic kidney cells, mouse muscle cells and neuroblastoma cells. Unsurprisingly, the disruption of cell membranes with higher elastic moduli (neuroblastoma) requires elevated stress. This study also presents a comparative analysis of total protein yield and concentrations of extracted functional mitochondria with two commercially available mitochondria extraction approaches, the Dounce Homogenizer and the Qproteome® Mitochondria Isolation Kit, in a range of cell concentrations. Our findings show that the proposed "microscale cell shredder" yields at least 40% more functional mitochondria than the two other approaches and is able to preserve the morphological integrity of extracted mitochondria, particularly at low cell concentrations (5-20 × 104 cells/mL). Characterized by its capability of rapidly processing a limited quantity of samples (200 μL), demarcating the membrane damage through the proposed microscale cell shredder represents a novel strategy to extract subcellular organelles from clinical samples.
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Affiliation(s)
- Md Habibur Rahman
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Qinru Xiao
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Shun Hing Institute of Advanced Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Shirui Zhao
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Shun Hing Institute of Advanced Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Fuyang Qu
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Chen Chang
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University,
| | - An-Chi Wei
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University,
| | - Yi-Ping Ho
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- Shun Hing Institute of Advanced Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
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