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Yabushita A, Cheng CY, Ko YK, Kobayashi T, Iwakura I, Jimenez R. Excited State Vibrational Dynamics Reveals a Photocycle That Enhances the Photostability of the TagRFP-T Fluorescent Protein. J Phys Chem B 2024; 128:1188-1193. [PMID: 38282329 PMCID: PMC10860143 DOI: 10.1021/acs.jpcb.3c07212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 01/13/2024] [Accepted: 01/17/2024] [Indexed: 01/30/2024]
Abstract
High photostability is a desirable property of fluorescent proteins (FPs) for imaging, yet its molecular basis is poorly understood. We performed ultrafast spectroscopy on TagRFP and its 9-fold more photostable variant TagRFP-T (TagRFP S158T) to characterize their initial photoreactions. We find significant differences in their electronic and vibrational dynamics, including faster excited-state proton transfer and transient changes in the frequency of the v520 mode in the excited electronic state of TagRFP-T. The frequency of v520, which is sensitive to chromophore planarity, downshifts within 0.58 ps and recovers within 0.87 ps. This vibrational mode modulates the distance from the chromophore phenoxy to the side chain of residue N143, which we suggest can trigger cis/trans photoisomerization. In TagRFP, the dynamics of v520 is missing, and this FP therefore lacks an important channel for chromophore isomerization. These dynamics are likely to be a key mechanism differentiating the photostability of the two FPs.
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Affiliation(s)
- Atsushi Yabushita
- Department of Electrophysics, National Yang Ming Chiao Tung University, Hsinchu 300, Taiwan
- Research Institute for Engineering, Kanagawa University, Yokohama 2210802, Japan
| | - Chia-Yun Cheng
- Department of Electrophysics, National Yang Ming Chiao Tung University, Hsinchu 300, Taiwan
| | - Ying Kuan Ko
- Department of Electrophysics, National Yang Ming Chiao Tung University, Hsinchu 300, Taiwan
| | - Takayoshi Kobayashi
- Department of Electrophysics, National Yang Ming Chiao Tung University, Hsinchu 300, Taiwan
- Advanced Ultrafast Laser Research Center, The University of Electro-Communications, Chofu 1828585, Japan
| | - Izumi Iwakura
- Department of Chemistry, Faculty of Engineering, Kanagawa University, Yokohama 2218686, Japan
| | - Ralph Jimenez
- JILA, National Institute of Standards and Technology and University of Colorado Boulder, Boulder, Colorado 80309, United States
- Department of Chemistry, University of Colorado Boulder, Boulder, Colorado 80309, United States
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2
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Hu Y, Li CY, Lu Q, Kuang Y. Multiplex miRNA reporting platform for real-time profiling of living cells. Cell Chem Biol 2024; 31:150-162.e7. [PMID: 38035883 DOI: 10.1016/j.chembiol.2023.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 09/15/2023] [Accepted: 11/03/2023] [Indexed: 12/02/2023]
Abstract
Accurately characterizing cell types within complex cell structures provides invaluable information for comprehending the cellular status during biological processes. In this study, we have developed an miRNA-switch cocktail platform capable of reporting and tracking the activities of multiple miRNAs (microRNAs) at the single-cell level, while minimizing disruption to the cell culture. Drawing on the principles of traditional miRNA-sensing mRNA switches, our platform incorporates subcellular tags and employs intelligent engineering to segment three subcellular regions using two fluorescent proteins. These designs enable the quantification of multiple miRNAs within the same cell. Through our experiments, we have demonstrated the platform's ability to track marker miRNA levels during cell differentiation and provide spatial information of heterogeneity on outlier cells exhibiting extreme miRNA levels. Importantly, this platform offers real-time and in situ miRNA reporting, allowing for multidimensional evaluation of cell profile and paving the way for a comprehensive understanding of cellular events during biological processes.
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Affiliation(s)
- Yaxin Hu
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China
| | - Cheuk Yin Li
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China
| | - Qiuyu Lu
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China
| | - Yi Kuang
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China.
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3
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Vue Z, Neikirk K, Vang L, Garza-Lopez E, Christensen TA, Shao J, Lam J, Beasley HK, Marshall AG, Crabtree A, Anudokem J, Rodriguez B, Kirk B, Bacevac S, Barongan T, Shao B, Stephens DC, Kabugi K, Koh HJ, Koh A, Evans CS, Taylor B, Reddy AK, Miller-Fleming T, Actkins KV, Zaganjor E, Daneshgar N, Murray SA, Mobley BC, Damo SM, Gaddy JA, Riggs B, Wanjalla C, Kirabo A, McReynolds M, Gomez JA, Phillips MA, Exil V, Dai DF, Hinton A. Three-dimensional mitochondria reconstructions of murine cardiac muscle changes in size across aging. Am J Physiol Heart Circ Physiol 2023; 325:H965-H982. [PMID: 37624101 PMCID: PMC10977873 DOI: 10.1152/ajpheart.00202.2023] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 07/26/2023] [Accepted: 08/12/2023] [Indexed: 08/26/2023]
Abstract
With sparse treatment options, cardiac disease remains a significant cause of death among humans. As a person ages, mitochondria breakdown and the heart becomes less efficient. Heart failure is linked to many mitochondria-associated processes, including endoplasmic reticulum stress, mitochondrial bioenergetics, insulin signaling, autophagy, and oxidative stress. The roles of key mitochondrial complexes that dictate the ultrastructure, such as the mitochondrial contact site and cristae organizing system (MICOS), in aging cardiac muscle are poorly understood. To better understand the cause of age-related alteration in mitochondrial structure in cardiac muscle, we used transmission electron microscopy (TEM) and serial block facing-scanning electron microscopy (SBF-SEM) to quantitatively analyze the three-dimensional (3-D) networks in cardiac muscle samples of male mice at aging intervals of 3 mo, 1 yr, and 2 yr. Here, we present the loss of cristae morphology, the inner folds of the mitochondria, across age. In conjunction with this, the three-dimensional (3-D) volume of mitochondria decreased. These findings mimicked observed phenotypes in murine cardiac fibroblasts with CRISPR/Cas9 knockout of Mitofilin, Chchd3, Chchd6 (some members of the MICOS complex), and Opa1, which showed poorer oxidative consumption rate and mitochondria with decreased mitochondrial length and volume. In combination, these data show the need to explore if loss of the MICOS complex in the heart may be involved in age-associated mitochondrial and cristae structural changes.NEW & NOTEWORTHY This article shows how mitochondria in murine cardiac changes, importantly elucidating age-related changes. It also is the first to show that the MICOS complex may play a role in outer membrane mitochondrial structure.
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Affiliation(s)
- Zer Vue
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, United States
| | - Kit Neikirk
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, United States
| | - Larry Vang
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, United States
| | - Edgar Garza-Lopez
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa, United States
| | - Trace A Christensen
- Microscopy and Cell Analysis Core Facility, Mayo Clinic, Rochester, Minnesota, United States
| | - Jianqiang Shao
- Central Microscopy Research Facility, University of Iowa, Iowa City, Iowa, United States
| | - Jacob Lam
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa, United States
| | - Heather K Beasley
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, United States
| | - Andrea G Marshall
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, United States
| | - Amber Crabtree
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, United States
| | - Josephs Anudokem
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, United States
| | - Benjamin Rodriguez
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, United States
| | - Benjamin Kirk
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa, United States
| | - Serif Bacevac
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa, United States
| | - Taylor Barongan
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, United States
| | - Bryanna Shao
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, United States
| | - Dominique C Stephens
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, United States
- Department of Life and Physical Sciences, Fisk University, Nashville, Tennessee, United States
| | - Kinuthia Kabugi
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, United States
| | - Ho-Jin Koh
- Department of Biological Sciences, Tennessee State University, Nashville, Tennessee, United States
| | - Alice Koh
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, United States
| | - Chantell S Evans
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina, United States
| | - Brittany Taylor
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, Florida, United States
| | - Anilkumar K Reddy
- Department of Medicine, Baylor College of Medicine, Houston, Texas, United States
| | - Tyne Miller-Fleming
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States
| | - Ky'Era V Actkins
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States
| | - Elma Zaganjor
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, United States
| | - Nastaran Daneshgar
- Department of Pathology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States
| | - Sandra A Murray
- Department of Cell Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Bret C Mobley
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, United States
| | - Steven M Damo
- Department of Life and Physical Sciences, Fisk University, Nashville, Tennessee, United States
| | - Jennifer A Gaddy
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, United States
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States
- Tennessee Valley Healthcare Systems, United States Department of Veterans Affairs, Nashville, Tennessee, United States
| | - Blake Riggs
- Department of Biology at San Francisco State University, San Francisco, California, United States
| | - Celestine Wanjalla
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States
| | - Annet Kirabo
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States
| | - Melanie McReynolds
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, State College, Pennsylvania, United States
| | - Jose A Gomez
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States
| | - Mark A Phillips
- Department of Integrative Biology, Oregon State University, Corvallis, Oregon, United States
| | - Vernat Exil
- Division of Cardiology, Department of Pediatrics, St. Louis University School of Medicine, St. Louis, Missouri, United States
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States
| | - Dao-Fu Dai
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
| | - Antentor Hinton
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, United States
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4
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Cvekl A, Camerino MJ. Generation of Lens Progenitor Cells and Lentoid Bodies from Pluripotent Stem Cells: Novel Tools for Human Lens Development and Ocular Disease Etiology. Cells 2022; 11:cells11213516. [PMID: 36359912 PMCID: PMC9658148 DOI: 10.3390/cells11213516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 10/31/2022] [Accepted: 11/02/2022] [Indexed: 11/09/2022] Open
Abstract
In vitro differentiation of human pluripotent stem cells (hPSCs) into specialized tissues and organs represents a powerful approach to gain insight into those cellular and molecular mechanisms regulating human development. Although normal embryonic eye development is a complex process, generation of ocular organoids and specific ocular tissues from pluripotent stem cells has provided invaluable insights into the formation of lineage-committed progenitor cell populations, signal transduction pathways, and self-organization principles. This review provides a comprehensive summary of recent advances in generation of adenohypophyseal, olfactory, and lens placodes, lens progenitor cells and three-dimensional (3D) primitive lenses, "lentoid bodies", and "micro-lenses". These cells are produced alone or "community-grown" with other ocular tissues. Lentoid bodies/micro-lenses generated from human patients carrying mutations in crystallin genes demonstrate proof-of-principle that these cells are suitable for mechanistic studies of cataractogenesis. Taken together, current and emerging advanced in vitro differentiation methods pave the road to understand molecular mechanisms of cataract formation caused by the entire spectrum of mutations in DNA-binding regulatory genes, such as PAX6, SOX2, FOXE3, MAF, PITX3, and HSF4, individual crystallins, and other genes such as BFSP1, BFSP2, EPHA2, GJA3, GJA8, LIM2, MIP, and TDRD7 represented in human cataract patients.
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Affiliation(s)
- Aleš Cvekl
- Departments Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Correspondence: ; Tel.: +1-718-430-3217; Fax: +1-718-430-8778
| | - Michael John Camerino
- Departments Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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5
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Pathological mitophagy disrupts mitochondrial homeostasis in Leber's hereditary optic neuropathy. Cell Rep 2022; 40:111124. [PMID: 35858578 PMCID: PMC9314546 DOI: 10.1016/j.celrep.2022.111124] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 03/27/2022] [Accepted: 06/29/2022] [Indexed: 01/18/2023] Open
Abstract
Leber’s hereditary optic neuropathy (LHON), a disease associated with a mitochondrial DNA mutation, is characterized by blindness due to degeneration of retinal ganglion cells (RGCs) and their axons, which form the optic nerve. We show that a sustained pathological autophagy and compartment-specific mitophagy activity affects LHON patient-derived cells and cybrids, as well as induced pluripotent-stem-cell-derived neurons. This is variably counterbalanced by compensatory mitobiogenesis. The aberrant quality control disrupts mitochondrial homeostasis as reflected by defective bioenergetics and excessive reactive oxygen species production, a stress phenotype that ultimately challenges cell viability by increasing the rate of apoptosis. We counteract this pathological mechanism by using autophagy regulators (clozapine and chloroquine) and redox modulators (idebenone), as well as genetically activating mitochondrial biogenesis (PGC1-α overexpression). This study substantially advances our understanding of LHON pathophysiology, providing an integrated paradigm for pathogenesis of mitochondrial diseases and druggable targets for therapy. Autophagy and mitophagy are abnormally activated in samples carrying LHON mutations Autophagy and mitophagy affect LHON cells’ viability Therapeutic approaches targeting autophagy reverts LHON cells’ apoptotic death
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6
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Short O-GlcNAcase Is Targeted to the Mitochondria and Regulates Mitochondrial Reactive Oxygen Species Level. Cells 2022; 11:cells11111827. [PMID: 35681522 PMCID: PMC9180253 DOI: 10.3390/cells11111827] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 05/18/2022] [Accepted: 05/26/2022] [Indexed: 02/01/2023] Open
Abstract
O-GlcNAcylation is a reversible post-translational modification involved in the regulation of cytosolic, nuclear, and mitochondrial proteins. Only two enzymes, OGT (O-GlcNAc transferase) and OGA (O-GlcNAcase), control the attachment and removal of O-GlcNAc on proteins, respectively. Whereas a variant OGT (mOGT) has been proposed as the main isoform that O-GlcNAcylates proteins in mitochondria, identification of a mitochondrial OGA has not been performed yet. Two splice variants of OGA (short and long isoforms) have been described previously. In this work, using cell fractionation experiments, we show that short-OGA is preferentially recovered in mitochondria-enriched fractions from HEK-293T cells and RAW 264.7 cells, as well as mouse embryonic fibroblasts. Moreover, fluorescent microscopy imaging confirmed that GFP-tagged short-OGA is addressed to mitochondria. In addition, using a Bioluminescence Resonance Energy Transfer (BRET)-based mitochondrial O-GlcNAcylation biosensor, we show that co-transfection of short-OGA markedly reduced O-GlcNAcylation of the biosensor, whereas long-OGA had no significant effect. Finally, using genetically encoded or chemical fluorescent mitochondrial probes, we show that short-OGA overexpression increases mitochondrial ROS levels, whereas long-OGA has no significant effect. Together, our work reveals that the short-OGA isoform is targeted to the mitochondria where it regulates ROS homoeostasis.
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7
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Pócsi I, Szigeti ZM, Emri T, Boczonádi I, Vereb G, Szöllősi J. Use of red, far-red, and near-infrared light in imaging of yeasts and filamentous fungi. Appl Microbiol Biotechnol 2022; 106:3895-3912. [PMID: 35599256 PMCID: PMC9200671 DOI: 10.1007/s00253-022-11967-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 05/02/2022] [Accepted: 05/07/2022] [Indexed: 11/30/2022]
Abstract
Abstract While phototoxicity can be a useful therapeutic modality not only for eliminating malignant cells but also in treating fungal infections, mycologists aiming to observe morphological changes or molecular events in fungi, especially when long observation periods or high light fluxes are warranted, encounter problems owed to altered regulatory pathways or even cell death caused by various photosensing mechanisms. Consequently, the ever expanding repertoire of visible fluorescent protein toolboxes and high-resolution microscopy methods designed to investigate fungi in vitro and in vivo need to comply with an additional requirement: to decrease the unwanted side effects of illumination. In addition to optimizing exposure, an obvious solution is red-shifted illumination, which, however, does not come without compromises. This review summarizes the interactions of fungi with light and the various molecular biology and technology approaches developed for exploring their functions on the molecular, cellular, and in vivo microscopic levels, and outlines the progress towards reducing phototoxicity through applying far-red and near-infrared light. Key points • Fungal biological processes alter upon illumination, also under the microscope • Red shifted fluorescent protein toolboxes decrease interference by illumination • Innovations like two-photon, lightsheet, and near IR microscopy reduce phototoxicity
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Affiliation(s)
- István Pócsi
- Department of Molecular Biotechnology and Microbiology, Institute of Biotechnology, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, 4032, Debrecen, Hungary.
| | - Zsuzsa M Szigeti
- Department of Molecular Biotechnology and Microbiology, Institute of Biotechnology, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, 4032, Debrecen, Hungary
| | - Tamás Emri
- Department of Molecular Biotechnology and Microbiology, Institute of Biotechnology, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, 4032, Debrecen, Hungary
| | - Imre Boczonádi
- Department of Molecular Biotechnology and Microbiology, Institute of Biotechnology, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, 4032, Debrecen, Hungary
| | - György Vereb
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, 4032, Debrecen, Hungary.,MTA-DE Cell Biology and Signaling Research Group, Faculty of Medicine, University of Debrecen, Egyetem tér 1, 4032, Debrecen, Hungary.,Faculty of Pharmacy, University of Debrecen, Egyetem tér 1, 4032, Debrecen, Hungary
| | - János Szöllősi
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, 4032, Debrecen, Hungary.,MTA-DE Cell Biology and Signaling Research Group, Faculty of Medicine, University of Debrecen, Egyetem tér 1, 4032, Debrecen, Hungary
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8
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First biphotochromic fluorescent protein moxSAASoti stabilized for oxidizing environment. Sci Rep 2022; 12:7862. [PMID: 35551209 PMCID: PMC9098843 DOI: 10.1038/s41598-022-11249-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 04/19/2022] [Indexed: 11/08/2022] Open
Abstract
Biphotochromic proteins simultaneously possess reversible photoswitching (on-to-off) and irreversible photoconversion (green-to-red). High photochemical reactivity of cysteine residues is one of the reasons for the development of "mox"-monomeric and oxidation resistant proteins. Based on site-saturated simultaneous two-point C105 and C117 mutagenesis, we chose C21N/C71G/C105G/C117T/C175A as the moxSAASoti variant. Since its on-to-off photoswitching rate is higher, off-to-on recovery is more complete and photoconversion rates are higher than those of mSAASoti. We analyzed the conformational behavior of the F177 side chain by classical MD simulations. The conformational flexibility of the F177 side chain is mainly responsible for the off-to-on conversion rate changes and can be further utilized as a measure of the conversion rate. Point mutations in mSAASoti mainly affect the pKa values of the red form and off-to-on switching. We demonstrate that the microscopic measure of the observed pKa value is the C-O bond length in the phenyl fragment of the neutral chromophore. According to molecular dynamics simulations with QM/MM potentials, larger C-O bond lengths are found for proteins with larger pKa. This feature can be utilized for prediction of the pKa values of red fluorescent proteins.
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9
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Demange P, Joly E, Marcoux J, Zanon PRA, Listunov D, Rullière P, Barthes C, Noirot C, Izquierdo JB, Rozié A, Pradines K, Hee R, de Brito MV, Marcellin M, Serre RF, Bouchez O, Burlet-Schiltz O, Oliveira MCF, Ballereau S, Bernardes-Génisson V, Maraval V, Calsou P, Hacker SM, Génisson Y, Chauvin R, Britton S. SDR enzymes oxidize specific lipidic alkynylcarbinols into cytotoxic protein-reactive species. eLife 2022; 11:73913. [PMID: 35535493 PMCID: PMC9090334 DOI: 10.7554/elife.73913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 04/19/2022] [Indexed: 11/21/2022] Open
Abstract
Hundreds of cytotoxic natural or synthetic lipidic compounds contain chiral alkynylcarbinol motifs, but the mechanism of action of those potential therapeutic agents remains unknown. Using a genetic screen in haploid human cells, we discovered that the enantiospecific cytotoxicity of numerous terminal alkynylcarbinols, including the highly cytotoxic dialkynylcarbinols, involves a bioactivation by HSD17B11, a short-chain dehydrogenase/reductase (SDR) known to oxidize the C-17 carbinol center of androstan-3-alpha,17-beta-diol to the corresponding ketone. A similar oxidation of dialkynylcarbinols generates dialkynylketones, that we characterize as highly protein-reactive electrophiles. We established that, once bioactivated in cells, the dialkynylcarbinols covalently modify several proteins involved in protein-quality control mechanisms, resulting in their lipoxidation on cysteines and lysines through Michael addition. For some proteins, this triggers their association to cellular membranes and results in endoplasmic reticulum stress, unfolded protein response activation, ubiquitin-proteasome system inhibition and cell death by apoptosis. Finally, as a proof-of-concept, we show that generic lipidic alkynylcarbinols can be devised to be bioactivated by other SDRs, including human RDH11 and HPGD/15-PGDH. Given that the SDR superfamily is one of the largest and most ubiquitous, this unique cytotoxic mechanism-of-action could be widely exploited to treat diseases, in particular cancer, through the design of tailored prodrugs.
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Affiliation(s)
- Pascal Demange
- Institut de Pharmacologie et de Biologie Structurale, IPBS, CNRS, Université de Toulouse, Toulouse, France
| | - Etienne Joly
- Institut de Pharmacologie et de Biologie Structurale, IPBS, CNRS, Université de Toulouse, Toulouse, France
| | - Julien Marcoux
- Institut de Pharmacologie et de Biologie Structurale, IPBS, CNRS, Université de Toulouse, Toulouse, France
| | - Patrick R A Zanon
- Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands.,Department of Chemistry, Technical University of Munich, Garching, Germany
| | - Dymytrii Listunov
- SPCMIB, UMR5068, CNRS, Université de Toulouse, UPS, Toulouse, France.,LCC-CNRS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Pauline Rullière
- SPCMIB, UMR5068, CNRS, Université de Toulouse, UPS, Toulouse, France
| | - Cécile Barthes
- LCC-CNRS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Céline Noirot
- INRAE, UR 875 Unité de Mathématique et Informatique Appliquées, Genotoul Bioinfo Auzeville, Castanet-Tolosan, France
| | - Jean-Baptiste Izquierdo
- Institut de Pharmacologie et de Biologie Structurale, IPBS, CNRS, Université de Toulouse, Toulouse, France
| | - Alexandrine Rozié
- Institut de Pharmacologie et de Biologie Structurale, IPBS, CNRS, Université de Toulouse, Toulouse, France.,Equipe labellisée la Ligue contre le Cancer 2018, Toulouse, France
| | - Karen Pradines
- Institut de Pharmacologie et de Biologie Structurale, IPBS, CNRS, Université de Toulouse, Toulouse, France.,Equipe labellisée la Ligue contre le Cancer 2018, Toulouse, France
| | - Romain Hee
- Institut de Pharmacologie et de Biologie Structurale, IPBS, CNRS, Université de Toulouse, Toulouse, France.,Equipe labellisée la Ligue contre le Cancer 2018, Toulouse, France
| | - Maria Vieira de Brito
- LCC-CNRS, Université de Toulouse, CNRS, UPS, Toulouse, France.,Department of Organic and Inorganic Chemistry, Science Center, Federal University of Ceará, Fortaleza, Brazil
| | - Marlène Marcellin
- Institut de Pharmacologie et de Biologie Structurale, IPBS, CNRS, Université de Toulouse, Toulouse, France
| | | | | | - Odile Burlet-Schiltz
- Institut de Pharmacologie et de Biologie Structurale, IPBS, CNRS, Université de Toulouse, Toulouse, France
| | | | | | | | - Valérie Maraval
- LCC-CNRS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Patrick Calsou
- Institut de Pharmacologie et de Biologie Structurale, IPBS, CNRS, Université de Toulouse, Toulouse, France.,Equipe labellisée la Ligue contre le Cancer 2018, Toulouse, France
| | - Stephan M Hacker
- Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands.,Department of Chemistry, Technical University of Munich, Garching, Germany
| | - Yves Génisson
- SPCMIB, UMR5068, CNRS, Université de Toulouse, UPS, Toulouse, France
| | - Remi Chauvin
- LCC-CNRS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Sébastien Britton
- Institut de Pharmacologie et de Biologie Structurale, IPBS, CNRS, Université de Toulouse, Toulouse, France.,Equipe labellisée la Ligue contre le Cancer 2018, Toulouse, France
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10
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Guerra P, Vuillemenot LA, Rae B, Ladyhina V, Milias-Argeitis A. Systematic In Vivo Characterization of Fluorescent Protein Maturation in Budding Yeast. ACS Synth Biol 2022; 11:1129-1141. [PMID: 35180343 PMCID: PMC8938947 DOI: 10.1021/acssynbio.1c00387] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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Fluorescent protein
(FP) maturation can limit the accuracy with
which dynamic intracellular processes are captured and reduce the in vivo brightness of a given FP in fast-dividing cells.
The knowledge of maturation timescales can therefore help users determine
the appropriate FP for each application. However, in vivo maturation rates can greatly deviate from in vitro estimates that are mostly available. In this work, we present the
first systematic study of in vivo maturation for
12 FPs in budding yeast. To overcome the technical limitations of
translation inhibitors commonly used to study FP maturation, we implemented
a new approach based on the optogenetic stimulations of FP expression
in cells grown under constant nutrient conditions. Combining the rapid
and orthogonal induction of FP transcription with a mathematical model
of expression and maturation allowed us to accurately estimate maturation
rates from microscopy data in a minimally invasive manner. Besides
providing a useful resource for the budding yeast community, we present
a new joint experimental and computational approach for characterizing
FP maturation, which is applicable to a wide range of organisms.
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Affiliation(s)
- Paolo Guerra
- Molecular Systems Biology, Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG Groningen, Netherlands
| | - Luc-Alban Vuillemenot
- Molecular Systems Biology, Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG Groningen, Netherlands
| | - Brady Rae
- Molecular Systems Biology, Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG Groningen, Netherlands
| | - Valeriia Ladyhina
- Molecular Systems Biology, Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG Groningen, Netherlands
| | - Andreas Milias-Argeitis
- Molecular Systems Biology, Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG Groningen, Netherlands
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11
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Methods to Monitor Mitophagy and Mitochondrial Quality: Implications in Cancer, Neurodegeneration, and Cardiovascular Diseases. Methods Mol Biol 2021; 2310:113-159. [PMID: 34096002 DOI: 10.1007/978-1-0716-1433-4_9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Mitochondria are dynamic organelles that participate in a broad array of molecular functions within the cell. They are responsible for maintaining the appropriate energetic levels and control the cellular homeostasis throughout the generation of intermediary metabolites. Preserving a healthy and functional mitochondrial population is of fundamental importance throughout the life of the cells under pathophysiological conditions. Hence, cells have evolved fine-tuned mechanisms of quality control that help to preserve the right amount of functional mitochondria to meet the demand of the cell. The specific recycling of mitochondria by autophagy, termed mitophagy, represents the primary contributor to mitochondrial quality control. During this process, damaged or unnecessary mitochondria are recognized and selectively degraded. In the past few years, the knowledge in mitophagy has seen rapid progress, and a growing body of evidence confirms that mitophagy holds a central role in controlling cellular functions and the progression of various human diseases.In this chapter, we will discuss the pathophysiological roles of mitophagy and provide a general overview of the current methods used to monitor and quantify mitophagy. We will also outline the main established approaches to investigate the mitochondrial function, metabolism, morphology, and protein damage.
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12
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Bakholdina SI, Stenkova AM, Bystritskaya EP, Sidorin EV, Kim NY, Menchinskaya ES, Gorpenchenko TY, Aminin DL, Shved NA, Solov’eva TF. Studies on the Structure and Properties of Membrane Phospholipase A 1 Inclusion Bodies Formed at Low Growth Temperatures Using GFP Fusion Strategy. Molecules 2021; 26:molecules26133936. [PMID: 34203222 PMCID: PMC8271855 DOI: 10.3390/molecules26133936] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 06/08/2021] [Accepted: 06/22/2021] [Indexed: 11/23/2022] Open
Abstract
The effect of cultivation temperatures (37, 26, and 18 °C) on the conformational quality of Yersinia pseudotuberculosis phospholipase A1 (PldA) in inclusion bodies (IBs) was studied using green fluorescent protein (GFP) as a folding reporter. GFP was fused to the C-terminus of PldA to form the PldA-GFP chimeric protein. It was found that the maximum level of fluorescence and expression of the chimeric protein is observed in cells grown at 18 °C, while at 37 °C no formation of fluorescently active forms of PldA-GFP occurs. The size, stability in denaturant solutions, and enzymatic and biological activity of PldA-GFP IBs expressed at 18 °C, as well as the secondary structure and arrangement of protein molecules inside the IBs, were studied. Solubilization of the chimeric protein from IBs in urea and SDS is accompanied by its denaturation. The obtained data show the structural heterogeneity of PldA-GFP IBs. It can be assumed that compactly packed, properly folded, proteolytic resistant, and structurally less organized, susceptible to proteolysis polypeptides can coexist in PldA-GFP IBs. The use of GFP as a fusion partner improves the conformational quality of PldA, but negatively affects its enzymatic activity. The PldA-GFP IBs are not toxic to eukaryotic cells and have the property to penetrate neuroblastoma cells. Data presented in the work show that the GFP-marker can be useful not only as target protein folding indicator, but also as a tool for studying the molecular organization of IBs, their morphology, and localization in E. coli, as well as for visualization of IBs interactions with eukaryotic cells.
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Affiliation(s)
- Svetlana I. Bakholdina
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch of the Russian Academy of Sciences, Prospekt 100-let Vladivostoku 159, 690022 Vladivostok, Russia; (E.P.B.); (E.V.S.); (N.Y.K.); (E.S.M.); (D.L.A.)
- Correspondence: (S.I.B.); (T.F.S.); Tel.: +7-423-231-11-58 (S.I.B. & T.F.S.); Fax: +7-423-231-40-50 (S.I.B. & T.F.S.)
| | - Anna M. Stenkova
- Department of Medical Biology and Biotechnology, FEFU Campus, School of Biomedicine, Far Eastern Federal University, Russky Island Ajax Bay 10, 690922 Vladivostok, Russia; (A.M.S.); (N.A.S.)
| | - Evgenia P. Bystritskaya
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch of the Russian Academy of Sciences, Prospekt 100-let Vladivostoku 159, 690022 Vladivostok, Russia; (E.P.B.); (E.V.S.); (N.Y.K.); (E.S.M.); (D.L.A.)
| | - Evgeniy V. Sidorin
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch of the Russian Academy of Sciences, Prospekt 100-let Vladivostoku 159, 690022 Vladivostok, Russia; (E.P.B.); (E.V.S.); (N.Y.K.); (E.S.M.); (D.L.A.)
| | - Natalya Yu. Kim
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch of the Russian Academy of Sciences, Prospekt 100-let Vladivostoku 159, 690022 Vladivostok, Russia; (E.P.B.); (E.V.S.); (N.Y.K.); (E.S.M.); (D.L.A.)
| | - Ekaterina S. Menchinskaya
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch of the Russian Academy of Sciences, Prospekt 100-let Vladivostoku 159, 690022 Vladivostok, Russia; (E.P.B.); (E.V.S.); (N.Y.K.); (E.S.M.); (D.L.A.)
| | - Tatiana Yu. Gorpenchenko
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, Prospect 100-let Vladivostoku, 159, 690022 Vladivostok, Russia;
| | - Dmitry L. Aminin
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch of the Russian Academy of Sciences, Prospekt 100-let Vladivostoku 159, 690022 Vladivostok, Russia; (E.P.B.); (E.V.S.); (N.Y.K.); (E.S.M.); (D.L.A.)
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, 100, Shih-Chuan 1st Road, Kaohsiung 80708, Taiwan
| | - Nikita A. Shved
- Department of Medical Biology and Biotechnology, FEFU Campus, School of Biomedicine, Far Eastern Federal University, Russky Island Ajax Bay 10, 690922 Vladivostok, Russia; (A.M.S.); (N.A.S.)
| | - Tamara F. Solov’eva
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch of the Russian Academy of Sciences, Prospekt 100-let Vladivostoku 159, 690022 Vladivostok, Russia; (E.P.B.); (E.V.S.); (N.Y.K.); (E.S.M.); (D.L.A.)
- Correspondence: (S.I.B.); (T.F.S.); Tel.: +7-423-231-11-58 (S.I.B. & T.F.S.); Fax: +7-423-231-40-50 (S.I.B. & T.F.S.)
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13
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Heinrich R, Hussein W, Berlin S. Photo-transformable genetically-encoded optical probes for functional highlighting in vivo. J Neurosci Methods 2021; 355:109129. [PMID: 33711357 DOI: 10.1016/j.jneumeth.2021.109129] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 03/02/2021] [Accepted: 03/04/2021] [Indexed: 12/13/2022]
Abstract
Studying the brain requires knowledge about both structure (i.e., connectome) and function of its constituents (neurons and glia alike). This need has prompted the development of novel tools and techniques, in particular optical techniques to examine cells remotely. Early works (1900's) led to the development of novel cell-staining techniques that, when combined with the use of a very simple light microscope, visualized individual neurons and their subcellular compartments in fixed tissues. Today, highlighting of structure and function can be performed on live cells, notably in vivo, owing to discovery of GFP and subsequent development of genetically encoded fluorescent optical tools. In this review, we focus our attention on a subset of optical biosensors, namely probes whose emission can be modified by light. We designate them photo-transformable genetically encoded probes. The family of photo-transformable probes embraces current probes that undergo photoactivation (PA), photoconversion (PC) or photoswitching (PS). We argue that these are particularly suited for studying multiple features of neurons, such as structure, connectivity and function concomitantly, for functional highlighting of neurons in vivo.
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Affiliation(s)
- Ronit Heinrich
- Department of Neuroscience, The Ruth and Bruce Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
| | - Wessal Hussein
- Department of Neuroscience, The Ruth and Bruce Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
| | - Shai Berlin
- Department of Neuroscience, The Ruth and Bruce Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel.
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14
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Aras S, Purandare N, Gladyck S, Somayajulu-Nitu M, Zhang K, Wallace DC, Grossman LI. Mitochondrial Nuclear Retrograde Regulator 1 (MNRR1) rescues the cellular phenotype of MELAS by inducing homeostatic mechanisms. Proc Natl Acad Sci U S A 2020; 117:32056-32065. [PMID: 33257573 PMCID: PMC7749287 DOI: 10.1073/pnas.2005877117] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
MNRR1 (CHCHD2) is a bi-organellar regulator of mitochondrial function that directly activates cytochrome c oxidase in the mitochondria and functions in the nucleus as a transcriptional activator for hundreds of genes. Since MNRR1 depletion contains features of a mitochondrial disease phenotype, we evaluated the effects of forced expression of MNRR1 on the mitochondrial disease MELAS (mitochondrial encephalomyopathy, lactic acidosis and stroke-like episodes) syndrome. MELAS is a multisystem encephalomyopathy disorder that can result from a heteroplasmic mutation in the mitochondrial DNA (mtDNA; m.3243A > G) at heteroplasmy levels of ∼50 to 90%. Since cybrid cell lines with 73% m.3243A > G heteroplasmy (DW7) display a significant reduction in MNRR1 levels compared to the wild type (0% heteroplasmy) (CL9), we evaluated the effects of MNRR1 levels on mitochondrial functioning. Overexpression of MNRR1 in DW7 cells induces the mitochondrial unfolded protein response (UPRmt), autophagy, and mitochondrial biogenesis, thereby rescuing the mitochondrial phenotype. It does so primarily as a transcription activator, revealing this function to be a potential therapeutic target. The role of MNRR1 in stimulating UPRmt, which is blunted in MELAS cells, was surprising and further investigation uncovered that under conditions of stress the import of MNRR1 into the mitochondria was blocked, allowing the protein to accumulate in the nucleus to enhance its transcription function. In the mammalian system, ATF5, has been identified as a mediator of UPRmt MNRR1 knockout cells display an ∼40% reduction in the protein levels of ATF5, suggesting that MNRR1 plays an important role upstream of this known mediator of UPRmt.
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Affiliation(s)
- Siddhesh Aras
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201
| | - Neeraja Purandare
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201
| | - Stephanie Gladyck
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201
| | - Mallika Somayajulu-Nitu
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201
| | - Kezhong Zhang
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201
| | - Douglas C Wallace
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104;
- Department of Pediatrics, Division of Human Genetics, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Lawrence I Grossman
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201;
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15
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Singhal NS, Bai M, Lee EM, Luo S, Cook KR, Ma DK. Cytoprotection by a naturally occurring variant of ATP5G1 in Arctic ground squirrel neural progenitor cells. eLife 2020; 9:55578. [PMID: 33050999 PMCID: PMC7671683 DOI: 10.7554/elife.55578] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 10/08/2020] [Indexed: 02/06/2023] Open
Abstract
Many organisms in nature have evolved mechanisms to tolerate severe hypoxia or ischemia, including the hibernation-capable Arctic ground squirrel (AGS). Although hypoxic or ischemia tolerance in AGS involves physiological adaptations, little is known about the critical cellular mechanisms underlying intrinsic AGS cell resilience to metabolic stress. Through cell survival-based cDNA expression screens in neural progenitor cells, we identify a genetic variant of AGS Atp5g1 that confers cell resilience to metabolic stress. Atp5g1 encodes a subunit of the mitochondrial ATP synthase. Ectopic expression in mouse cells and CRISPR/Cas9 base editing of endogenous AGS loci revealed causal roles of one AGS-specific amino acid substitution in mediating cytoprotection by AGS ATP5G1. AGS ATP5G1 promotes metabolic stress resilience by modulating mitochondrial morphological change and metabolic functions. Our results identify a naturally occurring variant of ATP5G1 from a mammalian hibernator that critically contributes to intrinsic cytoprotection against metabolic stress. When animals hibernate, they lower their body temperature and metabolism to conserve the energy they need to withstand cold harsh winters. One such animal is the Arctic ground squirrel, an extreme hibernator that can drop its body temperatures to below 0°C. This hibernation ability means the cells of Arctic ground squirrels can survive severe shortages of blood and oxygen. But, it is unclear how their cells are able to endure this metabolic stress. To answer this question, Singhal, Bai et al. studied the cells of Arctic ground squirrels for unique features that might make them more durable to stress. Examining the genetic code of these resilient cells revealed that Arctic ground squirrels may have a variant form of a protein called ATP5G1. This protein is found in a cellular compartment called the mitochondria, which is responsible for supplying energy to the rest of the cell and therefore plays an important role in metabolic processes. Singhal, Bai et al. found that when this variant form of ATP5G1 was introduced into the cells of mice, their mitochondria was better at coping with stress conditions, such as low oxygen, low temperature and poisoning. Using a gene editing tool to selectively substitute some of the building blocks, also known as amino acids, that make up the ATP5G1 protein revealed that improvements to the mitochondria were caused by switching specific amino acids. However, swapping these amino acids, which presumably affects the role of ATP5G1, did not completely remove the cells’ resilience to stress. This suggests that variants of other genes and proteins may also be involved in providing protection. These findings provide the first evidence of a protein variant that is responsible for protecting cells during the metabolic stress conditions caused by hibernation. The approach taken by Singhal, Bai et al. could be used to identify and study other proteins that increase resilience to metabolic stress. These findings could help develop new treatments for diseases caused by a limited blood supply to human organs, such as a stroke or heart attack.
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Affiliation(s)
- Neel S Singhal
- Department of Neurology, University of California-San Francisco, San Francisco, United States
| | - Meirong Bai
- Cardiovascular Research Institute, University of California-San Francisco, San Francisco, United States.,Department of Physiology, University of California-San Francisco, San Francisco, United States
| | - Evan M Lee
- Cardiovascular Research Institute, University of California-San Francisco, San Francisco, United States.,Department of Physiology, University of California-San Francisco, San Francisco, United States
| | - Shuo Luo
- Cardiovascular Research Institute, University of California-San Francisco, San Francisco, United States.,Department of Physiology, University of California-San Francisco, San Francisco, United States
| | - Kayleigh R Cook
- Cardiovascular Research Institute, University of California-San Francisco, San Francisco, United States.,Department of Physiology, University of California-San Francisco, San Francisco, United States
| | - Dengke K Ma
- Cardiovascular Research Institute, University of California-San Francisco, San Francisco, United States.,Department of Physiology, University of California-San Francisco, San Francisco, United States.,Innovative Genomics Institute, Berkeley, United States
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16
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Liang JR, Lingeman E, Luong T, Ahmed S, Muhar M, Nguyen T, Olzmann JA, Corn JE. A Genome-wide ER-phagy Screen Highlights Key Roles of Mitochondrial Metabolism and ER-Resident UFMylation. Cell 2020; 180:1160-1177.e20. [PMID: 32160526 DOI: 10.1016/j.cell.2020.02.017] [Citation(s) in RCA: 153] [Impact Index Per Article: 38.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 11/04/2019] [Accepted: 02/07/2020] [Indexed: 12/13/2022]
Abstract
Selective autophagy of organelles is critical for cellular differentiation, homeostasis, and organismal health. Autophagy of the ER (ER-phagy) is implicated in human neuropathy but is poorly understood beyond a few autophagosomal receptors and remodelers. By using an ER-phagy reporter and genome-wide CRISPRi screening, we identified 200 high-confidence human ER-phagy factors. Two pathways were unexpectedly required for ER-phagy. First, reduced mitochondrial metabolism represses ER-phagy, which is opposite of general autophagy and is independent of AMPK. Second, ER-localized UFMylation is required for ER-phagy to repress the unfolded protein response via IRE1α. The UFL1 ligase is brought to the ER surface by DDRGK1 to UFMylate RPN1 and RPL26 and preferentially targets ER sheets for degradation, analogous to PINK1-Parkin regulation during mitophagy. Our data provide insight into the cellular logic of ER-phagy, reveal parallels between organelle autophagies, and provide an entry point to the relatively unexplored process of degrading the ER network.
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Affiliation(s)
- Jin Rui Liang
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Emily Lingeman
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Thao Luong
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Saba Ahmed
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Matthias Muhar
- Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Truc Nguyen
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - James A Olzmann
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Jacob E Corn
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Biology, ETH Zürich, 8093 Zürich, Switzerland.
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17
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Schwerk J, Soveg FW, Ryan AP, Thomas KR, Hatfield LD, Ozarkar S, Forero A, Kell AM, Roby JA, So L, Hyde JL, Gale M, Daugherty MD, Savan R. RNA-binding protein isoforms ZAP-S and ZAP-L have distinct antiviral and immune resolution functions. Nat Immunol 2019; 20:1610-1620. [PMID: 31740798 DOI: 10.1038/s41590-019-0527-6] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 09/26/2019] [Indexed: 12/22/2022]
Abstract
The initial response to viral infection is anticipatory, with host antiviral restriction factors and pathogen sensors constantly surveying the cell to rapidly mount an antiviral response through the synthesis and downstream activity of interferons. After pathogen clearance, the host's ability to resolve this antiviral response and return to homeostasis is critical. Here, we found that isoforms of the RNA-binding protein ZAP functioned as both a direct antiviral restriction factor and an interferon-resolution factor. The short isoform of ZAP bound to and mediated the degradation of several host interferon messenger RNAs, and thus acted as a negative feedback regulator of the interferon response. In contrast, the long isoform of ZAP had antiviral functions and did not regulate interferon. The two isoforms contained identical RNA-targeting domains, but differences in their intracellular localization modulated specificity for host versus viral RNA, which resulted in disparate effects on viral replication during the innate immune response.
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Affiliation(s)
- Johannes Schwerk
- Department of Immunology, School of Medicine, University of Washington, Seattle, WA, USA
| | - Frank W Soveg
- Department of Immunology, School of Medicine, University of Washington, Seattle, WA, USA
| | - Andrew P Ryan
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Kerri R Thomas
- Department of Immunology, School of Medicine, University of Washington, Seattle, WA, USA
| | - Lauren D Hatfield
- Department of Immunology, School of Medicine, University of Washington, Seattle, WA, USA
| | - Snehal Ozarkar
- Department of Immunology, School of Medicine, University of Washington, Seattle, WA, USA
| | - Adriana Forero
- Department of Immunology, School of Medicine, University of Washington, Seattle, WA, USA
| | - Alison M Kell
- Department of Immunology, School of Medicine, University of Washington, Seattle, WA, USA
| | - Justin A Roby
- Department of Immunology, School of Medicine, University of Washington, Seattle, WA, USA
| | - Lomon So
- Department of Immunology, School of Medicine, University of Washington, Seattle, WA, USA.,Immunology Program, Benaroya Research Institute at Virginia Mason, Seattle, WA, USA
| | - Jennifer L Hyde
- Department of Microbiology, School of Medicine, University of Washington, Seattle, WA, USA
| | - Michael Gale
- Department of Immunology, School of Medicine, University of Washington, Seattle, WA, USA.,Center for Innate Immunity and Immune Disease, University of Washington, Seattle, WA, USA
| | - Matthew D Daugherty
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA.
| | - Ram Savan
- Department of Immunology, School of Medicine, University of Washington, Seattle, WA, USA. .,Center for Innate Immunity and Immune Disease, University of Washington, Seattle, WA, USA.
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18
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Ko PJ, Woodrow C, Dubreuil MM, Martin BR, Skouta R, Bassik MC, Dixon SJ. A ZDHHC5-GOLGA7 Protein Acyltransferase Complex Promotes Nonapoptotic Cell Death. Cell Chem Biol 2019; 26:1716-1724.e9. [PMID: 31631010 DOI: 10.1016/j.chembiol.2019.09.014] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 08/29/2019] [Accepted: 09/26/2019] [Indexed: 12/11/2022]
Abstract
Lethal small molecules are useful probes to discover and characterize novel cell death pathways and biochemical mechanisms. Here we report that the synthetic oxime-containing small molecule caspase-independent lethal 56 (CIL56) induces an unconventional form of nonapoptotic cell death distinct from necroptosis, ferroptosis, and other pathways. CIL56-induced cell death requires a catalytically active protein S-acyltransferase complex comprising the enzyme ZDHHC5 and an accessory subunit GOLGA7. The ZDHHC5-GOLGA7 complex is mutually stabilizing and localizes to the plasma membrane. CIL56 inhibits anterograde protein transport from the Golgi apparatus, which may be lethal in the context of ongoing ZDHHC5-GOLGA7 complex-dependent retrograde protein trafficking from the plasma membrane to internal sites. Other oxime-containing small molecules, structurally distinct from CIL56, may trigger cell death through the same pathway. These results define an unconventional form of nonapoptotic cell death regulated by protein S-acylation.
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Affiliation(s)
- Pin-Joe Ko
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Claire Woodrow
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Michael M Dubreuil
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Brent R Martin
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Rachid Skouta
- Department of Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Michael C Bassik
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Scott J Dixon
- Department of Biology, Stanford University, Stanford, CA 94305, USA.
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19
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Kostyuk AI, Demidovich AD, Kotova DA, Belousov VV, Bilan DS. Circularly Permuted Fluorescent Protein-Based Indicators: History, Principles, and Classification. Int J Mol Sci 2019; 20:E4200. [PMID: 31461959 PMCID: PMC6747460 DOI: 10.3390/ijms20174200] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 08/22/2019] [Accepted: 08/24/2019] [Indexed: 12/28/2022] Open
Abstract
Genetically encoded biosensors based on fluorescent proteins (FPs) are a reliable tool for studying the various biological processes in living systems. The circular permutation of single FPs led to the development of an extensive class of biosensors that allow the monitoring of many intracellular events. In circularly permuted FPs (cpFPs), the original N- and C-termini are fused using a peptide linker, while new termini are formed near the chromophore. Such a structure imparts greater mobility to the FP than that of the native variant, allowing greater lability of the spectral characteristics. One of the common principles of creating genetically encoded biosensors is based on the integration of a cpFP into a flexible region of a sensory domain or between two interacting domains, which are selected according to certain characteristics. Conformational rearrangements of the sensory domain associated with ligand interaction or changes in the cellular parameter are transferred to the cpFP, changing the chromophore environment. In this review, we highlight the basic principles of such sensors, the history of their creation, and a complete classification of the available biosensors.
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Affiliation(s)
- Alexander I Kostyuk
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
- Pirogov Russian National Research Medical University, Moscow 117997, Russia
| | | | - Daria A Kotova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
| | - Vsevolod V Belousov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
- Pirogov Russian National Research Medical University, Moscow 117997, Russia
- Institute for Cardiovascular Physiology, Georg August University Göttingen, D-37073 Göttingen, Germany
| | - Dmitry S Bilan
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia.
- Pirogov Russian National Research Medical University, Moscow 117997, Russia.
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20
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Liu K, Jones S, Minis A, Rodriguez J, Molina H, Steller H. PI31 Is an Adaptor Protein for Proteasome Transport in Axons and Required for Synaptic Development. Dev Cell 2019; 50:509-524.e10. [PMID: 31327739 DOI: 10.1016/j.devcel.2019.06.009] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 04/18/2019] [Accepted: 06/14/2019] [Indexed: 12/13/2022]
Abstract
Protein degradation by the ubiquitin-proteasome system is critical for neuronal function. Neurons utilize microtubule-dependent molecular motors to allocate proteasomes to synapses, but how proteasomes are coupled to motors and how this is regulated to meet changing demand for protein breakdown remain largely unknown. We show that the conserved proteasome-binding protein PI31 serves as an adaptor to couple proteasomes with dynein light chain proteins (DYNLL1/2). The inactivation of PI31 inhibited proteasome motility in axons and disrupted synaptic proteostasis, structure, and function. Moreover, phosphorylation of PI31 by p38 MAPK enhanced binding to DYNLL1/2 and promoted the directional movement of proteasomes in axons, suggesting a mechanism to regulate loading of proteasomes onto motors. Inactivation of PI31 in mouse neurons attenuated proteasome movement in axons, indicating this process is conserved. Because mutations affecting PI31 activity are associated with human neurodegenerative diseases, impairment of PI31-mediated axonal transport of proteasomes may contribute to these disorders.
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Affiliation(s)
- Kai Liu
- Strang Laboratory of Apoptosis and Cancer Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Sandra Jones
- Strang Laboratory of Apoptosis and Cancer Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Adi Minis
- Strang Laboratory of Apoptosis and Cancer Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Jose Rodriguez
- Strang Laboratory of Apoptosis and Cancer Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Henrik Molina
- Proteomics Resource Center, The Rockefeller University, New York, NY 10065, USA
| | - Hermann Steller
- Strang Laboratory of Apoptosis and Cancer Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
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21
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Wang Y, Metz J, Costello JL, Passmore J, Schrader M, Schultz C, Islinger M. Intracellular redistribution of neuronal peroxisomes in response to ACBD5 expression. PLoS One 2018; 13:e0209507. [PMID: 30589881 PMCID: PMC6307868 DOI: 10.1371/journal.pone.0209507] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 12/06/2018] [Indexed: 12/21/2022] Open
Abstract
Peroxisomes can be frequently found in proximity to other subcellular organelles such as the endoplasmic reticulum (ER), mitochondria or lysosomes. The tail-anchored protein ACBD5 was recently identified as part of a tethering complex at peroxisome-ER contact sites, interacting with the ER resident protein VAPB. Contact site disruption was found to significantly increase peroxisome motility, apparently interfering with intracellular positioning systems. Unlike other somatic cells, neurons have to distribute organelles across relatively long distances in order to maintain their extraordinary cellular polarity. Using confocal live imaging microscopy in cultured hippocampal neurons we observed that peroxisomes and mitochondria show a strikingly similar motility with approximately 10% performing microtubule-driven long range movements. In order to investigate if ER contacts influence overall peroxisome motility and cellular distribution patterns, hippocampal neurons were transfected with plasmids encoding ACBD5 to stimulate peroxisome-ER interactions. Overexpression of ACBD5 reduced peroxisomal long range movements in the neurites of the hippocampal cells by 70%, implying that ER attachment counteracts microtubule-driven peroxisome transport, while mitochondrial motility was unaffected. Moreover, the analyses of peroxisome distribution in fixed neurons unveiled a significant redistribution of peroxisomes towards the periphery of the perikaryon underneath the plasma membrane and into neurites, where peroxisomes are frequently found in close proximity to mitochondria. Surprisingly, further analysis of peroxisome and VAPB distribution upon ACBD5 expression did not reveal a substantial colocalization, implying this effect may be independent of VAPB. In line with these findings, expression of an ACBD5 variant unable to bind to VAPB still altered the localization of peroxisomes in the same way as the wild-type ACBD5. Thus, we conclude, that the VAPB-ACBD5 facilitated peroxisome-ER interaction is not responsible for the observed organelle redistribution in neurons. Rather, we suggest that additional ACBD5-binding proteins in neurons may tether peroxisomes to contact sites at or near the plasma membrane of neurons.
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Affiliation(s)
- Yunhong Wang
- Institute of Neuroanatomy, Center for Biomedicine & Medical Technology Mannheim, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Jeremy Metz
- Biosciences, University of Exeter, Exeter, United Kingdom
| | | | | | | | - Christian Schultz
- Institute of Neuroanatomy, Center for Biomedicine & Medical Technology Mannheim, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Markus Islinger
- Institute of Neuroanatomy, Center for Biomedicine & Medical Technology Mannheim, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
- * E-mail:
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22
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Chronic Energy Depletion due to Iron Deficiency Impairs Dendritic Mitochondrial Motility during Hippocampal Neuron Development. J Neurosci 2018; 39:802-813. [PMID: 30523068 DOI: 10.1523/jneurosci.1504-18.2018] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 10/25/2018] [Accepted: 11/25/2018] [Indexed: 11/21/2022] Open
Abstract
During development, neurons require highly integrated metabolic machinery to meet the large energy demands of growth, differentiation, and synaptic activity within their complex cellular architecture. Dendrites/axons require anterograde trafficking of mitochondria for local ATP synthesis to support these processes. Acute energy depletion impairs mitochondrial dynamics, but how chronic energy insufficiency affects mitochondrial trafficking and quality control during neuronal development is unknown. Because iron deficiency impairs mitochondrial respiration/ATP production, we treated mixed-sex embryonic mouse hippocampal neuron cultures with the iron chelator deferoxamine (DFO) to model chronic energetic insufficiency and its effects on mitochondrial dynamics during neuronal development. At 11 days in vitro (DIV), DFO reduced average mitochondrial speed by increasing the pause frequency of individual dendritic mitochondria. Time spent in anterograde motion was reduced; retrograde motion was spared. The average size of moving mitochondria was reduced, and the expression of fusion and fission genes was altered, indicating impaired mitochondrial quality control. Mitochondrial density was not altered, suggesting that respiratory capacity and not location is the key factor for mitochondrial regulation of early dendritic growth/branching. At 18 DIV, the overall density of mitochondria within terminal dendritic branches was reduced in DFO-treated neurons, which may contribute to the long-term deficits in connectivity and synaptic function following early-life iron deficiency. The study provides new insights into the cross-regulation between energy production and dendritic mitochondrial dynamics during neuronal development and may be particularly relevant to neuropsychiatric and neurodegenerative diseases, many of which are characterized by impaired brain iron homeostasis, energy metabolism and mitochondrial trafficking.SIGNIFICANCE STATEMENT This study uses a primary neuronal culture model of iron deficiency to address a gap in understanding of how dendritic mitochondrial dynamics are regulated when energy depletion occurs during a critical period of neuronal maturation. At the beginning of peak dendritic growth/branching, iron deficiency reduces mitochondrial speed through increased pause frequency, decreases mitochondrial size, and alters fusion/fission gene expression. At this stage, mitochondrial density in terminal dendrites is not altered, suggesting that total mitochondrial oxidative capacity and not trafficking is the main mechanism underlying dendritic complexity deficits in iron-deficient neurons. Our findings provide foundational support for future studies exploring the mechanistic role of developmental mitochondrial dysfunction in neurodevelopmental, psychiatric, and neurodegenerative disorders characterized by mitochondrial energy production and trafficking deficits.
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23
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Abuaita BH, Schultz TL, O'Riordan MX. Mitochondria-Derived Vesicles Deliver Antimicrobial Reactive Oxygen Species to Control Phagosome-Localized Staphylococcus aureus. Cell Host Microbe 2018; 24:625-636.e5. [PMID: 30449314 DOI: 10.1016/j.chom.2018.10.005] [Citation(s) in RCA: 142] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 08/10/2018] [Accepted: 10/05/2018] [Indexed: 12/20/2022]
Abstract
Pathogenic bacteria taken up into the macrophage phagosome are the target of many anti-microbial mechanisms. Although mitochondria-derived antimicrobial effectors like reactive oxygen species (mROS) aid in bacterial killing, it is unclear how these effectors reach bacteria within the phagosomal lumen. We show here that endoplasmic reticulum stress triggered upon methicillin-resistant Staphylococcus aureus (MRSA) infection induces mROS that are delivered to bacteria-containing phagosomes via mitochondria-derived vesicles (MDVs). The endoplasmic reticulum stress sensor IRE1α induces mROS, specifically hydrogen peroxide (mH2O2), upon MRSA infection. MRSA infection also stimulates the generation of MDVs, which require the mitochondrial stress response factor Parkin, and contributes to mH2O2 accumulation in bacteria-containing phagosomes. Accumulation of phagosomal H2O2 requires Toll-like receptor signaling and the mitochondrial enzyme superoxide dismutase-2 (Sod2), which is delivered to phagosomes by MDVs. Sod2 depletion compromises mH2O2 production and bacterial killing. Thus, mitochondrial redox capacity enhances macrophage antimicrobial function by delivering mitochondria-derived effector molecules into bacteria-containing phagosomes.
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Affiliation(s)
- Basel H Abuaita
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Tracey L Schultz
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Mary X O'Riordan
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
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24
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Soleja N, Manzoor O, Khan I, Ahmad A, Mohsin M. Role of green fluorescent proteins and their variants in development of FRET-based sensors. J Biosci 2018. [DOI: 10.1007/s12038-018-9783-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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25
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Harwig MC, Viana MP, Egner JM, Harwig JJ, Widlansky ME, Rafelski SM, Hill RB. Methods for imaging mammalian mitochondrial morphology: A prospective on MitoGraph. Anal Biochem 2018; 552:81-99. [PMID: 29505779 DOI: 10.1016/j.ab.2018.02.022] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 02/06/2018] [Accepted: 02/22/2018] [Indexed: 12/22/2022]
Abstract
Mitochondria are found in a variety of shapes, from small round punctate structures to a highly interconnected web. This morphological diversity is important for function, but complicates quantification. Consequently, early quantification efforts relied on various qualitative descriptors that understandably reduce the complexity of the network leading to challenges in consistency across the field. Recent application of state-of-the-art computational tools have resulted in more quantitative approaches. This prospective highlights the implementation of MitoGraph, an open-source image analysis platform for measuring mitochondrial morphology initially optimized for use with Saccharomyces cerevisiae. Here Mitograph was assessed on five different mammalian cells types, all of which were accurately segmented by MitoGraph analysis. MitoGraph also successfully differentiated between distinct mitochondrial morphologies that ranged from entirely fragmented to hyper-elongated. General recommendations are also provided for confocal imaging of labeled mitochondria (using mito-YFP, MitoTracker dyes and immunostaining parameters). Widespread adoption of MitoGraph will help achieve a long-sought goal of consistent and reproducible quantification of mitochondrial morphology.
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Affiliation(s)
- Megan C Harwig
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, 53226, United States
| | - Matheus P Viana
- Visual Analytics and Comprehension Group, IBM Research, Brazil; Department of Developmental and Cell Biology and Center for Complex Biological Systems, University of California Irvine, Irvine, CA, 92697, United States
| | - John M Egner
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, 53226, United States
| | | | - Michael E Widlansky
- Division of Cardiovascular Medicine, Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, 53226, United States
| | - Susanne M Rafelski
- Department of Developmental and Cell Biology and Center for Complex Biological Systems, University of California Irvine, Irvine, CA, 92697, United States; Assay Development, Allen Institute for Cell Science, Seattle, WA, 98109, United States
| | - R Blake Hill
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, 53226, United States.
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26
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Spacova I, Lievens E, Verhoeven T, Steenackers H, Vanderleyden J, Lebeer S, Petrova MI. Expression of fluorescent proteins in Lactobacillus rhamnosus to study host-microbe and microbe-microbe interactions. Microb Biotechnol 2018; 11:317-331. [PMID: 29027368 PMCID: PMC5812243 DOI: 10.1111/1751-7915.12872] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 08/12/2017] [Accepted: 08/25/2017] [Indexed: 12/28/2022] Open
Abstract
Probiotic Lactobacillus strains are widely used to benefit human and animal health, although the exact mechanisms behind their interactions with the host and the microbiota are largely unknown. Fluorescent tagging of live probiotic cells is an important tool to unravel their modes of action. In this study, the implementation of different heterologously expressed fluorescent proteins for the labelling of the model probiotic strains Lactobacillus rhamnosusGG (gastrointestinal) and Lactobacillus rhamnosusGR-1 (vaginal) was explored. Heterologous expression of mTagBFP2 and mCherry resulted in long-lasting fluorescence of L. rhamnosusGG and GR-1 cells, using the nisin-controlled expression (NICE) system. These novel fluorescent strains were then used to study in vitro aspects of their microbe-microbe and microbe-host interactions. Lactobacillus rhamnosusGG and L. rhamnosusGR-1 expressing mTagBFP2 and mCherry could be visualized in mixed-species biofilms, where they inhibited biofilm formation by Salmonella Typhimurium-gfpmut3 expressing the green fluorescent protein. Likewise, fluorescent L. rhamnosusGG and L. rhamnosusGR-1 were implemented for the visualization of their adhesion patterns to intestinal epithelial cell cultures. The fluorescent L. rhamnosus strains developed in this study can therefore serve as novel tools for the study of probiotic interactions with their environment.
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Affiliation(s)
- Irina Spacova
- Centre of Microbial and Plant GeneticsKU LeuvenHeverleeBelgium
- Department of Bioscience EngineeringUniversity of AntwerpAntwerpBelgium
| | - Elke Lievens
- Centre of Microbial and Plant GeneticsKU LeuvenHeverleeBelgium
- Department of Bioscience EngineeringUniversity of AntwerpAntwerpBelgium
| | - Tine Verhoeven
- Centre of Microbial and Plant GeneticsKU LeuvenHeverleeBelgium
| | | | | | - Sarah Lebeer
- Centre of Microbial and Plant GeneticsKU LeuvenHeverleeBelgium
- Department of Bioscience EngineeringUniversity of AntwerpAntwerpBelgium
| | - Mariya I. Petrova
- Centre of Microbial and Plant GeneticsKU LeuvenHeverleeBelgium
- Department of Bioscience EngineeringUniversity of AntwerpAntwerpBelgium
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27
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SensorFRET: A Standardless Approach to Measuring Pixel-based Spectral Bleed-through and FRET Efficiency using Spectral Imaging. Sci Rep 2017; 7:15609. [PMID: 29142199 PMCID: PMC5688180 DOI: 10.1038/s41598-017-15411-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 10/25/2017] [Indexed: 12/03/2022] Open
Abstract
Fluorescence microscopy of FRET-based biosensors allow nanoscale interactions to be probed in living cells. This paper describes a novel approach to spectrally resolved fluorescence microscopy, termed sensorFRET, that enables quantitative measurement of FRET efficiency. This approach is an improvement on existing methods (FLIM, sRET, luxFRET, pFRET), as it does not require single fluorophore standards to be measured with every experiment and the acquisition is intensity independent, allowing the laser power to be optimized for varying levels of fluorophore expression. Additionally, it was found that all spectral based methods, including sensorFRET, fail at specific fluorophore-excitation wavelength combinations. These combinations can be determined a priori using sensorFRET, whereas other methods would give no indication of inaccuracies. This method was thoroughly validated and compared to existing methods using simulated spectra, Fluorescein and TAMRA dye mixtures as a zero FRET control, and Cerulean-Venus FRET standards as positive FRET controls. Simulations also provided a means of quantifying the uncertainty in each measurement by relating the fit residual of noisy spectra to the standard deviation of the measured FRET efficiency. As an example application, Teal-Venus force sensitive biosensors integrated into E-cadherin were used to resolve piconewton scale forces along different parts of an individual cell junction.
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28
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Axton RA, Haideri SS, Lopez-Yrigoyen M, Taylor HA, Forrester LM. SplitAx: A novel method to assess the function of engineered nucleases. PLoS One 2017; 12:e0171698. [PMID: 28212417 PMCID: PMC5315338 DOI: 10.1371/journal.pone.0171698] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 01/24/2017] [Indexed: 12/29/2022] Open
Abstract
Engineered nucleases have been used to generate knockout or reporter cell lines and a range of animal models for human disease. These new technologies also hold great promise for therapeutic genome editing. Current methods to evaluate the activity of these nucleases are time consuming, require extensive optimization and are hampered by readouts with low signals and high background. We have developed a simple and easy to perform method (SplitAx) that largely addresses these issues and provides a readout of nuclease activity. The assay involves splitting the N-terminal (amino acid 1-158) coding region of GFP and an out-of-frame of C-terminal region with a nuclease binding site sequence. Following exposure to the test nuclease, cutting and repair by error prone non-homologous end joining (NHEJ) restores the reading frame resulting in the production of a full length fluorescent GFP protein. Fluorescence can also be restored by complementation between the N-terminal and C-terminal coding sequences in trans. We demonstrate successful use of the SplitAx assay to assess the function of zinc finger nucleases, CRISPR hCAS9 and TALENS. We also test the activity of multiple gRNAs in CRISPR/hCas9/D10A systems. The zinc finger nucleases and guide RNAs that showed functional activity in the SplitAx assay were then used successfully to target the endogenous AAVS1, SOX6 and Cfms loci. This simple method can be applied to other unrelated proteins such as ZsGreen1 and provides a test system that does not require complex optimization.
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Affiliation(s)
- Richard A. Axton
- MRC Centre for Regenerative Medicine, SCRM Building, The University of Edinburgh, Edinburgh bioQuarter, 5 Little France Drive, Edinburgh, United Kingdom
| | - Sharmin S. Haideri
- MRC Centre for Regenerative Medicine, SCRM Building, The University of Edinburgh, Edinburgh bioQuarter, 5 Little France Drive, Edinburgh, United Kingdom
| | - Martha Lopez-Yrigoyen
- MRC Centre for Regenerative Medicine, SCRM Building, The University of Edinburgh, Edinburgh bioQuarter, 5 Little France Drive, Edinburgh, United Kingdom
| | - Helen A. Taylor
- MRC Centre for Regenerative Medicine, SCRM Building, The University of Edinburgh, Edinburgh bioQuarter, 5 Little France Drive, Edinburgh, United Kingdom
| | - Lesley M. Forrester
- MRC Centre for Regenerative Medicine, SCRM Building, The University of Edinburgh, Edinburgh bioQuarter, 5 Little France Drive, Edinburgh, United Kingdom
- * E-mail:
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29
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Wang H, Hahn KM. LOVTRAP: A Versatile Method to Control Protein Function with Light. ACTA ACUST UNITED AC 2016; 73:21.10.1-21.10.14. [PMID: 27906450 DOI: 10.1002/cpcb.12] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We describe a detailed procedure for the use of LOVTRAP, an approach to reversibly sequester and release proteins from cellular membranes using light. In the application described here, proteins that act at the plasma membrane are held at mitochondria in the dark, and reversibly released by irradiation. The technique relies on binding of an engineered Zdk domain to a LOV2 domain, with affinity <30 nM in the dark and >500 nM upon irradiation between 400 and 500 nm. LOVTRAP can be applied to diverse proteins, as it requires attaching only one member of the Zdk/LOV2 pair to the target protein, and the other to the membrane where the target protein is to be sequestered. Light-induced protein release occurs in less than a second, and the half-life of return can be adjusted using LOV point mutations (∼2 to 500 sec). © 2016 by John Wiley & Sons, Inc.
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Affiliation(s)
- Hui Wang
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Klaus M Hahn
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
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30
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Rodilla AM, Korrodi-Gregório L, Hernando E, Manuel-Manresa P, Quesada R, Pérez-Tomás R, Soto-Cerrato V. Synthetic tambjamine analogues induce mitochondrial swelling and lysosomal dysfunction leading to autophagy blockade and necrotic cell death in lung cancer. Biochem Pharmacol 2016; 126:23-33. [PMID: 27890727 DOI: 10.1016/j.bcp.2016.11.022] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 11/22/2016] [Indexed: 01/05/2023]
Abstract
Current pharmacological treatments for lung cancer show very poor clinical outcomes, therefore, the development of novel anticancer agents with innovative mechanisms of action is urgently needed. Cancer cells have a reversed pH gradient compared to normal cells, which favours cancer progression by promoting proliferation, metabolic adaptation and evasion of apoptosis. In this regard, the use of ionophores to modulate intracellular pH appears as a promising new therapeutic strategy. Indeed, there is a growing body of evidence supporting ionophores as novel antitumour drugs. Despite this, little is known about the implications of pH deregulation and homeostasis imbalance triggered by ionophores at the cellular level. In this work, we deeply analyse for the first time the anticancer effects of tambjamine analogues, a group of highly effective anion selective ionophores, at the cellular and molecular levels. First, their effects on cell viability were determined in several lung cancer cell lines and patient-derived cancer stem cells, demonstrating their potent cytotoxic effects. Then, we have characterized the induced lysosomal deacidification, as well as, the massive cytoplasmic vacuolization observed after treatment with these compounds, which is consistent with mitochondrial swelling. Finally, the activation of several proteins involved in stress response, autophagy and apoptosis was also detected, although they were not significantly responsible for the cell death induced. Altogether, these evidences suggest that tambjamine analogues provoke an imbalance in cellular ion homeostasis that triggers mitochondrial dysfunction and lysosomal deacidification leading to a potent cytotoxic effect through necrosis in lung cancer cell lines and cancer stem cells.
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Affiliation(s)
- Ananda M Rodilla
- Cancer Cell Biology Research Group, Department of Pathology and Experimental Therapeutics, Faculty of Medicine, University of Barcelona, Barcelona, Spain.
| | - Luís Korrodi-Gregório
- Cancer Cell Biology Research Group, Department of Pathology and Experimental Therapeutics, Faculty of Medicine, University of Barcelona, Barcelona, Spain; Laboratory of Signal Transduction, Department of Medical Sciences, Institute for Research in Biomedicine - iBiMED, Health Sciences Program, University of Aveiro, Aveiro, Portugal.
| | - Elsa Hernando
- Department of Chemistry, University of Burgos, Burgos, Spain.
| | - Pilar Manuel-Manresa
- Cancer Cell Biology Research Group, Department of Pathology and Experimental Therapeutics, Faculty of Medicine, University of Barcelona, Barcelona, Spain.
| | - Roberto Quesada
- Department of Chemistry, University of Burgos, Burgos, Spain.
| | - Ricardo Pérez-Tomás
- Cancer Cell Biology Research Group, Department of Pathology and Experimental Therapeutics, Faculty of Medicine, University of Barcelona, Barcelona, Spain.
| | - Vanessa Soto-Cerrato
- Cancer Cell Biology Research Group, Department of Pathology and Experimental Therapeutics, Faculty of Medicine, University of Barcelona, Barcelona, Spain.
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31
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Shokrollahi N, Shahbazzadeh D, Pooshang-Bagheri K, Habibi-Anbouhi M, Jahanian-Najafabadi A, Behdani M. A Model to Study the Phenotypic Changes of Insect Cell Transfection by Copepod Super Green Fluorescent Protein (cop-GFP) in Baculovirus Expression System. IRANIAN BIOMEDICAL JOURNAL 2016; 20:182-6. [PMID: 26518237 PMCID: PMC4949983 DOI: 10.7508/ibj.2016.03.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Background: Baculovirus expression system is one of the most attractive and powerful eukaryotic expression systems for the production of recombinant proteins. The presence of a biomarker is required to monitor transfection efficiency or protein expression levels in insect cells. Methods: The aim of this study was to construct a baculovirus expression vector encoding a copepod super green fluorescent protein (copGFP). In this light, the resultant vector was constructed and used for transfection of Spodoptera frugiperda cells. Results: Expression of the copGFP protein in insect cells was confirmed by fluorescent microscopy and Western-blot analysis. Conclusion: The application of copGFP control bacmid can be considered as an appropriate control for insect cell transfection.
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Affiliation(s)
- Narjes Shokrollahi
- Biotechnology Research Center, Venom and Biotherapeutics Molecules Lab, Pasteur Institute of Iran, Tehran, Iran
| | - Delavar Shahbazzadeh
- Biotechnology Research Center, Venom and Biotherapeutics Molecules Lab, Pasteur Institute of Iran, Tehran, Iran
| | - Kamran Pooshang-Bagheri
- Biotechnology Research Center, Venom and Biotherapeutics Molecules Lab, Pasteur Institute of Iran, Tehran, Iran
| | | | - Ali Jahanian-Najafabadi
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Isfahan University of Medical Sciences and Health Services, Isfahan, Iran
| | - Mahdi Behdani
- Biotechnology Research Center, Venom and Biotherapeutics Molecules Lab, Pasteur Institute of Iran, Tehran, Iran
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32
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Norris SR, Núñez MF, Verhey KJ. Influence of fluorescent tag on the motility properties of kinesin-1 in single-molecule assays. Biophys J 2016; 108:1133-43. [PMID: 25762325 DOI: 10.1016/j.bpj.2015.01.031] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Revised: 01/15/2015] [Accepted: 01/28/2015] [Indexed: 12/26/2022] Open
Abstract
Molecular motors such as kinesin and dynein use the energy derived from ATP hydrolysis to walk processively along microtubule tracks and transport various cargoes inside the cell. Recent advancements in fluorescent protein (FP) research enable motors to be fluorescently labeled such that single molecules can be visualized inside cells in multiple colors. The performance of these fluorescent tags can vary depending on their spectral properties and a natural tendency for oligomerization. Here we present a survey of different fluorescent tags fused to kinesin-1 and studied by single-molecule motility assays of mammalian cell lysates. We tested eight different FP tags and found that seven of them display sufficient fluorescence intensity and photostability to visualize motility events. Although none of the FP tags interfere with the enzymatic properties of the motor, four of the tags (EGFP, monomeric EGFP, tagRFPt, and mApple) cause aberrantly long motor run lengths. This behavior is unlikely to be due to electrostatic interactions and is probably caused by tag-dependent oligomerization events that appear to be facilitated by fusion to the dimeric kinesin-1. We also compared the single-molecule performance of various fluorescent SNAP and HALO ligands. We found that although both green and red SNAP ligands provide sufficient fluorescent signal, only the tetramethyl rhodamine (TMR) HALO ligand provides sufficient signal for detection in these assays. This study will serve as a valuable reference for choosing fluorescent labels for single-molecule motility assays.
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Affiliation(s)
- Stephen R Norris
- Department of Biophysics, University of Michigan, Ann Arbor, Michigan; Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan
| | - Marcos F Núñez
- Department of Biophysics, University of Michigan, Ann Arbor, Michigan
| | - Kristen J Verhey
- Department of Biophysics, University of Michigan, Ann Arbor, Michigan; Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan.
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Cell type-dependent ROS and mitophagy response leads to apoptosis or necroptosis in neuroblastoma. Oncogene 2015; 35:3839-53. [PMID: 26640148 DOI: 10.1038/onc.2015.455] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 10/05/2015] [Indexed: 02/06/2023]
Abstract
A limiting factor in the therapeutic outcome of children with high-risk neuroblastoma is the intrinsic and acquired resistance to common chemotherapeutic treatments. Here we investigated the molecular mechanisms by which the hemisynthetic cardiac glycoside UNBS1450 overcomes this limitation and induces differential cell death modalities in both neuroblastic and stromal neuroblastoma through stimulation of a cell-type-specific autophagic response eventually leading to apoptosis or necroptosis. In neuroblastic SH-SY5Y cells, we observed a time-dependent production of reactive oxygen species that affects lysosomal integrity inducing lysosome-associated membrane protein 2 degradation and cathepsin B and L activation. Subsequent mitochondrial membrane depolarization and accumulation of mitochondria in phagophores occurred after 8h of UNBS1450 treatment. Results were confirmed by mitochondrial mass analysis, electron microscopy and co-localization of mitochondria with GFP-LC3, suggesting the impaired clearance of damaged mitochondria. Thus, a stress-induced defective autophagic flux and the subsequent lack of clearance of damaged mitochondria sensitized SH-SY5Y cells to UNBS1450-induced apoptosis. Inhibition of autophagy with small inhibitory RNAs against ATG5, ATG7 and Beclin-1 protected SH-SY5Y cells against the cytotoxic effect of UNBS1450 by inhibiting apoptosis. In contrast, autophagy progression towards the catabolic state was observed in stromal SK-N-AS cells: here reactive oxygen species (ROS) generation remained undetectable preserving intact lysosomes and engulfing damaged mitochondria after UNBS1450 treatment. Moreover, autophagy inhibition determined sensitization of SK-N-AS to apoptosis. We identified efficient mitophagy as the key mechanism leading to failure of activation of the apoptotic pathway that increased resistance of SK-N-AS to UNBS1450, triggering rather necroptosis at higher doses. Altogether we characterize here the differential modulation of ROS and mitophagy as a main determinant of neuroblastoma resistance with potential relevance for personalized anticancer therapeutic approaches.
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Hochreiter B, Garcia AP, Schmid JA. Fluorescent proteins as genetically encoded FRET biosensors in life sciences. SENSORS 2015; 15:26281-314. [PMID: 26501285 PMCID: PMC4634415 DOI: 10.3390/s151026281] [Citation(s) in RCA: 118] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Accepted: 10/08/2015] [Indexed: 12/11/2022]
Abstract
Fluorescence- or Förster resonance energy transfer (FRET) is a measurable physical energy transfer phenomenon between appropriate chromophores, when they are in sufficient proximity, usually within 10 nm. This feature has made them incredibly useful tools for many biomedical studies on molecular interactions. Furthermore, this principle is increasingly exploited for the design of biosensors, where two chromophores are linked with a sensory domain controlling their distance and thus the degree of FRET. The versatility of these FRET-biosensors made it possible to assess a vast amount of biological variables in a fast and standardized manner, allowing not only high-throughput studies but also sub-cellular measurements of biological processes. In this review, we aim at giving an overview over the recent advances in genetically encoded, fluorescent-protein based FRET-biosensors, as these represent the largest and most vividly growing group of FRET-based sensors. For easy understanding, we are grouping them into four categories, depending on their molecular mechanism. These are based on: (a) cleavage; (b) conformational-change; (c) mechanical force and (d) changes in the micro-environment. We also address the many issues and considerations that come with the development of FRET-based biosensors, as well as the possibilities that are available to measure them.
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Affiliation(s)
- Bernhard Hochreiter
- Institute for Vascular Biology and Thrombosis Research, Medical University Vienna, Schwarzspanierstraße17, Vienna A-1090, Austria.
| | - Alan Pardo Garcia
- Institute for Vascular Biology and Thrombosis Research, Medical University Vienna, Schwarzspanierstraße17, Vienna A-1090, Austria.
| | - Johannes A Schmid
- Institute for Vascular Biology and Thrombosis Research, Medical University Vienna, Schwarzspanierstraße17, Vienna A-1090, Austria.
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35
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Chou KF, Dennis AM. Förster Resonance Energy Transfer between Quantum Dot Donors and Quantum Dot Acceptors. SENSORS 2015; 15:13288-325. [PMID: 26057041 PMCID: PMC4507609 DOI: 10.3390/s150613288] [Citation(s) in RCA: 182] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 05/29/2015] [Accepted: 06/01/2015] [Indexed: 01/27/2023]
Abstract
Förster (or fluorescence) resonance energy transfer amongst semiconductor quantum dots (QDs) is reviewed, with particular interest in biosensing applications. The unique optical properties of QDs provide certain advantages and also specific challenges with regards to sensor design, compared to other FRET systems. The brightness and photostability of QDs make them attractive for highly sensitive sensing and long-term, repetitive imaging applications, respectively, but the overlapping donor and acceptor excitation signals that arise when QDs serve as both the donor and acceptor lead to high background signals from direct excitation of the acceptor. The fundamentals of FRET within a nominally homogeneous QD population as well as energy transfer between two distinct colors of QDs are discussed. Examples of successful sensors are highlighted, as is cascading FRET, which can be used for solar harvesting.
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Affiliation(s)
- Kenny F Chou
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA.
| | - Allison M Dennis
- Department of Biomedical Engineering and Division of Materials Science and Engineering, Boston University, Boston, MA 02215, USA.
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36
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Long AH, Haso WM, Shern JF, Wanhainen KM, Murgai M, Ingaramo M, Smith JP, Walker AJ, Kohler ME, Venkateshwara VR, Kaplan RN, Patterson GH, Fry TJ, Orentas RJ, Mackall CL. 4-1BB costimulation ameliorates T cell exhaustion induced by tonic signaling of chimeric antigen receptors. Nat Med 2015; 21:581-90. [PMID: 25939063 PMCID: PMC4458184 DOI: 10.1038/nm.3838] [Citation(s) in RCA: 1202] [Impact Index Per Article: 133.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 03/13/2015] [Indexed: 02/07/2023]
Abstract
Chimeric antigen receptors (CARs) targeting CD19 have mediated dramatic antitumor responses in hematologic malignancies, but tumor regression has rarely occurred using CARs targeting other antigens. It remains unknown whether the impressive effects of CD19 CARs relate to greater susceptibility of hematologic malignancies to CAR therapies, or superior functionality of the CD19 CAR itself. We show that tonic CAR CD3-ζ phosphorylation, triggered by antigen-independent clustering of CAR single-chain variable fragments, can induce early exhaustion of CAR T cells that limits antitumor efficacy. Such activation is present to varying degrees in all CARs studied, except the highly effective CD19 CAR. We further determine that CD28 costimulation augments, whereas 4-1BB costimulation reduces, exhaustion induced by persistent CAR signaling. Our results provide biological explanations for the antitumor effects of CD19 CARs and for the observations that CD19 CAR T cells incorporating the 4-1BB costimulatory domain are more persistent than those incorporating CD28 in clinical trials.
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Affiliation(s)
- Adrienne H Long
- 1] Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA. [2] Department of Microbiology and Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Waleed M Haso
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Jack F Shern
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Kelsey M Wanhainen
- 1] Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA. [2] Department of Biology, Colgate University, Hamilton, New York, USA
| | - Meera Murgai
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Maria Ingaramo
- Section on Biophotonics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, USA
| | - Jillian P Smith
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Alec J Walker
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - M Eric Kohler
- 1] Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA. [2] Department of Pediatrics, Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - Vikas R Venkateshwara
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Rosandra N Kaplan
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - George H Patterson
- Section on Biophotonics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, USA
| | - Terry J Fry
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Rimas J Orentas
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Crystal L Mackall
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
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Ausili A, Staiano M, Marabotti A, D'Auria G, Gómez-Fernández JC, Torrecillas A, Ortiz A, D'Auria S. Correlation between fluorescence and structure in the orange-emitting GFP-like protein, monomeric Kusabira Orange. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2014; 138:223-229. [PMID: 24980638 DOI: 10.1016/j.jphotobiol.2014.04.028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Accepted: 04/23/2014] [Indexed: 06/03/2023]
Abstract
The mKO is the monomeric version of Kusabira Orange, a GFP-like protein emitting bright orange fluorescence at 559 nm. This protein shows the characteristic β-barrel motif typical of the fluorescent protein family which it belongs to, similar spectral properties to the tetrameric form and an exceptional photo-stability to pH changes. Here, we demonstrate that mKO in solution at physiological pH exhibits a secondary structure analogue to that of the crystal. Moreover, we describe the thermal unfolding, revealing an outstanding structural stability with a denaturation temperature close to 90 °C and identifying the existence of a thermodynamic intermediate. The denaturation process of mKO results to be absolutely irreversible because of the complete lost of the native structure and the consequent aggregation, while the presence of the intermediate state is most likely due to coexistence of two different species of mKO, with protonated and deprotonated chromophore respectively, that affects the fluorescence properties and the structural stability of the protein.
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Affiliation(s)
- A Ausili
- Laboratory for Molecular Sensing, IBP-CNR, Naples, Italy.
| | - M Staiano
- Laboratory for Molecular Sensing, IBP-CNR, Naples, Italy
| | - A Marabotti
- Department of Chemistry and Biology, University of Salerno, Fisciano (SA), Italy
| | - G D'Auria
- Laboratory for Molecular Sensing, IBP-CNR, Naples, Italy; Department of Chemistry and Biology, University of Salerno, Fisciano (SA), Italy
| | - J C Gómez-Fernández
- Departamento de Bioquimica y Biologia Molecular-A, University of Murcia, Spain
| | - A Torrecillas
- Departamento de Bioquimica y Biologia Molecular-A, University of Murcia, Spain
| | - A Ortiz
- Departamento de Bioquimica y Biologia Molecular-A, University of Murcia, Spain
| | - S D'Auria
- Laboratory for Molecular Sensing, IBP-CNR, Naples, Italy.
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38
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Roura S, Gálvez-Montón C, Bayes-Genis A. Bioluminescence imaging: a shining future for cardiac regeneration. J Cell Mol Med 2013; 17:693-703. [PMID: 23402217 PMCID: PMC3823173 DOI: 10.1111/jcmm.12018] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Accepted: 12/28/2012] [Indexed: 12/28/2022] Open
Abstract
Advances in bioanalytical techniques have become crucial for both basic research and medical practice. One example, bioluminescence imaging (BLI), is based on the application of natural reactants with light-emitting capabilities (photoproteins and luciferases) isolated from a widespread group of organisms. The main challenges in cardiac regeneration remain unresolved, but a vast number of studies have harnessed BLI with the discovery of aequorin and green fluorescent proteins. First described in the luminous hydromedusan Aequorea victoria in the early 1960s, bioluminescent proteins have greatly contributed to the design and initiation of ongoing cell-based clinical trials on cardiovascular diseases. In conjunction with advances in reporter gene technology, BLI provides valuable information about the location and functional status of regenerative cells implanted into numerous animal models of disease. The purpose of this review was to present the great potential of BLI, among other existing imaging modalities, to refine effectiveness and underlying mechanisms of cardiac cell therapy. We recount the first discovery of natural primary compounds with light-emitting capabilities, and follow their applications to bioanalysis. We also illustrate insights and perspectives on BLI to illuminate current efforts in cardiac regeneration, where the future is bright.
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Affiliation(s)
- Santiago Roura
- ICREC Research Program, Fundació Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Badalona, Spain
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Broussard JA, Rappaz B, Webb DJ, Brown CM. Fluorescence resonance energy transfer microscopy as demonstrated by measuring the activation of the serine/threonine kinase Akt. Nat Protoc 2013; 8:265-81. [PMID: 23306460 DOI: 10.1038/nprot.2012.147] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
This protocol describes procedures for performing fluorescence resonance energy transfer (FRET) microscopy analysis by three different methods: acceptor photobleaching, sensitized emission and spectral imaging. We also discuss anisotropy and fluorescence lifetime imaging microscopy-based FRET techniques. By using the specific example of the FRET probe Akind (Akt indicator), which is a version of Akt modified such that FRET occurs when the probe is activated by phosphorylation, indicating Akt activation. The protocol provides a detailed step-by-step description of sample preparation, image acquisition and analysis, including control samples, image corrections and the generation of quantitative FRET/CFP ratio images for both sensitized emission and spectral imaging. The sample preparation takes 2 d, equipment setup takes 2-3 h and image acquisition and analysis take 6-8 h.
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Affiliation(s)
- Joshua A Broussard
- Department of Biological Sciences and Vanderbilt Kennedy Center for Research on Human Development, Vanderbilt University, Nashville, Tennessee, USA
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40
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Telford WG, Hawley T, Subach F, Verkhusha V, Hawley RG. Flow cytometry of fluorescent proteins. Methods 2012; 57:318-30. [PMID: 22293036 DOI: 10.1016/j.ymeth.2012.01.003] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2011] [Accepted: 01/16/2012] [Indexed: 11/30/2022] Open
Abstract
Fluorescent proteins are now a critical tool in all areas of biomedical research. In this article, we review the techniques required to use fluorescent proteins for flow cytometry, concentrating specifically on the excitation and emission requirements for each protein, and the specific equipment required for optimal use.
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Affiliation(s)
- William G Telford
- Experimental Transplantation and Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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41
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Penzkofer A, Stierl M, Hegemann P, Kateriya S. Absorption and fluorescence characteristics of photo-activated adenylate cyclase nano-clusters from the amoeboflagellate Naegleria gruberi NEG-M strain. Chem Phys 2012. [DOI: 10.1016/j.chemphys.2011.09.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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42
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Wang Y, Pan Y, Price A, Martin LJ. Generation and characterization of transgenic mice expressing mitochondrial targeted red fluorescent protein selectively in neurons: modeling mitochondriopathy in excitotoxicity and amyotrophic lateral sclerosis. Mol Neurodegener 2011; 6:75. [PMID: 22047141 PMCID: PMC3227596 DOI: 10.1186/1750-1326-6-75] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2011] [Accepted: 11/02/2011] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Mitochondria have roles or appear to have roles in the pathogenesis of several chronic age-related and acute neurological disorders, including Charcot-Marie-Tooth disease, amyotrophic lateral sclerosis, Parkinson's disease, and cerebral ischemia, and could be critical targets for development of rational mechanism-based, disease-modifying therapeutics for treating these disorders effectively. A deeper understanding of neural tissue mitochondria pathobiologies as definitive mediators of neural injury, disease, and cell death merits further study, and the development of additional tools to study neural mitochondria will help achieve this unmet need. RESULTS We created transgenic mice that express the coral (Discosoma sp.) red fluorescent protein DsRed2 specifically in mitochondria of neurons using a construct engineered with a Thy1 promoter, specific for neuron expression, to drive expression of a fusion protein of DsRed2 with a mitochondrial targeting sequence. The biochemical and histological characterization of these mice shows the expression of mitochondrial-targeted DsRed2 to be specific for mitochondria and concentrated in distinct CNS regions, including cerebral cortex, hippocampus, thalamus, brainstem, and spinal cord. Red fluorescent mitochondria were visualized in cerebral cortical and hippocampal pyramidal neurons, ventrobasal thalamic neurons, subthalamic neurons, and spinal motor neurons. For the purpose of proof of principle application, these mice were used in excitotoxicity paradigms and double transgenic mice were generated by crossing Thy1-mitoDsRed2 mice with transgenic mice expressing enhanced-GFP (eGFP) under the control of the Hlxb9 promoter that drives eGFP expression specifically in motor neurons and by crossing Thy1-mitoDsRed2 mice to amyotrophic lateral sclerosis (ALS) mice expressing human mutant superoxide dismutase-1. CONCLUSIONS These novel transgenic mice will be a useful tool for better understanding the biology of mitochondria in mouse and cellular models of human neurological disorders as exemplified by the mitochondrial swelling and fission seen in excitotoxicity and mouse ALS.
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Affiliation(s)
- Yi Wang
- Department of Pathology, Division of Neuropathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, MD 21205, USA
| | - Yan Pan
- Department of Pathology, Division of Neuropathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, MD 21205, USA
| | - Ann Price
- Department of Pathology, Division of Neuropathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, MD 21205, USA
| | - Lee J Martin
- Department of Pathology, Division of Neuropathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, MD 21205, USA
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Don Paul C, Traore DAK, Byres E, Rossjohn J, Devenish RJ, Kiss C, Bradbury A, Wilce MCJ, Prescott M. Expression, purification, crystallization and preliminary X-ray analysis of eCGP123, an extremely stable monomeric green fluorescent protein with reversible photoswitching properties. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:1266-8. [PMID: 22102044 DOI: 10.1107/s1744309111028156] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2011] [Accepted: 07/13/2011] [Indexed: 11/10/2022]
Abstract
Enhanced consensus green protein variant 123 (eCGP123) is an extremely thermostable green fluorescent protein (GFP) that exhibits useful negative reversible photoswitching properties. eCGP123 was derived by the application of both a consensus engineering approach and a recursive evolutionary process. Diffraction-quality crystals of recombinant eCGP123 were obtained by the hanging-drop vapour-diffusion method using PEG 3350 as the precipitant. The eCGP123 crystal diffracted X-rays to 2.10 Å resolution. The data were indexed in space group P1, with unit-cell parameters a = 74.63, b = 75.38, c = 84.51 Å, α = 90.96, β = 89.92, γ = 104.03°. The Matthews coefficient (V(M) = 2.26 Å(3) Da(-1)) and a solvent content of 46% indicated that the asymmetric unit contained eight eCGP123 molecules.
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Affiliation(s)
- Craig Don Paul
- Department of Biochemistry and Molecular Biology, School of Biomedical Science, Monash University, Clayton Campus, Melbourne, Victoria 3800, Australia
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44
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Chen SX, Osipovich AB, Ustione A, Potter LA, Hipkens S, Gangula R, Yuan W, Piston DW, Magnuson MA. Quantification of factors influencing fluorescent protein expression using RMCE to generate an allelic series in the ROSA26 locus in mice. Dis Model Mech 2011; 4:537-47. [PMID: 21324933 PMCID: PMC3124063 DOI: 10.1242/dmm.006569] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2010] [Accepted: 12/22/2010] [Indexed: 11/20/2022] Open
Abstract
Fluorescent proteins (FPs) have great utility in identifying specific cell populations and in studying cellular dynamics in the mouse. To quantify the factors that determine both the expression and relative brightness of FPs in mouse embryonic stem cells (mESCs) and in mice, we generated eight different FP-expressing ROSA26 alleles using recombinase-mediated cassette exchange (RMCE). These alleles enabled us to analyze the effects on FP expression of a translational enhancer and different 3'-intronic and/or polyadenylation sequences, as well as the relative brightness of five different FPs, without the confounding position and copy number effects that are typically associated with randomly inserted transgenes. We found that the expression of a given FP can vary threefold or more depending on the genetic features present in the allele. The optimal FP expression cassette contained both a translational enhancer sequence in the 5'-untranslated region (UTR) and an intron-containing rabbit β-globin sequence within the 3'-UTR. The relative expressed brightness of individual FPs varied up to tenfold. Of the five different monomeric FPs tested, Citrine (YFP) was the brightest, followed by Apple, eGFP, Cerulean (CFP) and Cherry. Generation of a line of Cherry-expressing mice showed that there was a 30-fold variation of Cherry expression among different tissues and that there was a punctate expression pattern within cells of all tissues examined. This study should help investigators make better-informed design choices when expressing FPs in mESCs and mice.
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Affiliation(s)
| | | | - Alessandro Ustione
- Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, TN 37232-0494, USA
| | - Leah A. Potter
- Center for Stem Cell Biology and
- Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, TN 37232-0494, USA
| | | | | | | | - David W. Piston
- Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, TN 37232-0494, USA
| | - Mark A. Magnuson
- Center for Stem Cell Biology and
- Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, TN 37232-0494, USA
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