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Tamura R, Chen J, De Jaeger M, Morris JF, Scott DA, Vangheluwe P, Looger LL. Genetically encoded fluorescent sensors for visualizing polyamine levels, uptake, and distribution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.21.609037. [PMID: 39229183 PMCID: PMC11370472 DOI: 10.1101/2024.08.21.609037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
Polyamines are abundant and physiologically essential biomolecules that play a role in numerous processes, but are disrupted in diseases such as cancer, and cardiovascular and neurological disorders. Despite their importance, measuring free polyamine concentrations and monitoring their metabolism and uptake in cells in real-time remains impossible due to the lack of appropriate biosensors. Here we engineered, characterized, and validated the first genetically encoded biosensors for polyamines, named iPASnFRs. We demonstrate the utility of iPASnFR for detecting polyamine import into mammalian cells, to the cytoplasm, mitochondria, and the nucleus. We demonstrate that these sensors are useful to probe the activity of polyamine transporters and to uncover biochemical pathways underlying the distribution of polyamines amongst organelles. The sensors powered a high-throughput small molecule compound library screen, revealing multiple compounds in different chemical classes that strongly modulate cellular polyamine levels. These sensors will be powerful tools to investigate the complex interplay between polyamine uptake and metabolic pathways, address open questions about their role in health and disease, and enable screening for therapeutic polyamine modulators.
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Chan YH, Liu Z, Bastard P, Khobrekar N, Hutchison KM, Yamazaki Y, Fan Q, Matuozzo D, Harschnitz O, Kerrouche N, Nakajima K, Amin P, Yatim A, Rinchai D, Chen J, Zhang P, Ciceri G, Chen J, Dobbs K, Belkaya S, Lee D, Gervais A, Aydın K, Kartal A, Hasek ML, Zhao S, Reino EG, Lee YS, Seeleuthner Y, Chaldebas M, Bailey R, Vanhulle C, Lorenzo L, Boucherit S, Rozenberg F, Marr N, Mogensen TH, Aubart M, Cobat A, Dulac O, Emiroglu M, Paludan SR, Abel L, Notarangelo L, Longnecker R, Smith G, Studer L, Casanova JL, Zhang SY. Human TMEFF1 is a restriction factor for herpes simplex virus in the brain. Nature 2024; 632:390-400. [PMID: 39048830 PMCID: PMC11306101 DOI: 10.1038/s41586-024-07745-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 06/21/2024] [Indexed: 07/27/2024]
Abstract
Most cases of herpes simplex virus 1 (HSV-1) encephalitis (HSE) remain unexplained1,2. Here, we report on two unrelated people who had HSE as children and are homozygous for rare deleterious variants of TMEFF1, which encodes a cell membrane protein that is preferentially expressed by brain cortical neurons. TMEFF1 interacts with the cell-surface HSV-1 receptor NECTIN-1, impairing HSV-1 glycoprotein D- and NECTIN-1-mediated fusion of the virus and the cell membrane, blocking viral entry. Genetic TMEFF1 deficiency allows HSV-1 to rapidly enter cortical neurons that are either patient specific or derived from CRISPR-Cas9-engineered human pluripotent stem cells, thereby enhancing HSV-1 translocation to the nucleus and subsequent replication. This cellular phenotype can be rescued by pretreatment with type I interferon (IFN) or the expression of exogenous wild-type TMEFF1. Moreover, ectopic expression of full-length TMEFF1 or its amino-terminal extracellular domain, but not its carboxy-terminal intracellular domain, impairs HSV-1 entry into NECTIN-1-expressing cells other than neurons, increasing their resistance to HSV-1 infection. Human TMEFF1 is therefore a host restriction factor for HSV-1 entry into cortical neurons. Its constitutively high abundance in cortical neurons protects these cells from HSV-1 infection, whereas inherited TMEFF1 deficiency renders them susceptible to this virus and can therefore underlie HSE.
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Affiliation(s)
- Yi-Hao Chan
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA.
| | - Zhiyong Liu
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Paul Bastard
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Paris Cité University, Imagine Institute, Paris, France
- Pediatric Hematology-Immunology and Rheumatology Unit, Necker Hospital for Sick Children, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
| | - Noopur Khobrekar
- The Center for Stem Cell Biology & Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY, USA
| | - Kennen M Hutchison
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Yasuhiro Yamazaki
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Qing Fan
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Daniela Matuozzo
- Paris Cité University, Imagine Institute, Paris, France
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
| | - Oliver Harschnitz
- The Center for Stem Cell Biology & Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY, USA
- Human Technopole, Milan, Italy
| | - Nacim Kerrouche
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Koji Nakajima
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Paris Cité University, Imagine Institute, Paris, France
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
| | - Param Amin
- The Center for Stem Cell Biology & Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY, USA
| | - Ahmad Yatim
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Darawan Rinchai
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Jie Chen
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Peng Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Gabriele Ciceri
- The Center for Stem Cell Biology & Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY, USA
| | - Jia Chen
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Kerry Dobbs
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Serkan Belkaya
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey
| | - Danyel Lee
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Paris Cité University, Imagine Institute, Paris, France
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
| | - Adrian Gervais
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Paris Cité University, Imagine Institute, Paris, France
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
| | - Kürşad Aydın
- Department of Pediatric Neurology, Faculty of Medicine, Istanbul Medipol University, Istanbul, Turkey
| | - Ayse Kartal
- Child Neurology Department, Selcuk University, Konya, Turkey
| | - Mary L Hasek
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Shuxiang Zhao
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Eduardo Garcia Reino
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Yoon Seung Lee
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Yoann Seeleuthner
- Paris Cité University, Imagine Institute, Paris, France
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
| | - Matthieu Chaldebas
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Rasheed Bailey
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | | | - Lazaro Lorenzo
- Paris Cité University, Imagine Institute, Paris, France
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
| | - Soraya Boucherit
- Paris Cité University, Imagine Institute, Paris, France
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
| | - Flore Rozenberg
- Laboratory of Virology, Assistance Publique-Hôpitaux de Paris (AP-HP), Cochin Hospital, Paris, France
| | - Nico Marr
- Research Branch, Sidra Medicine, Doha, Qatar
| | - Trine H Mogensen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
- Center for Immunology of Viral Infections, Aarhus University, Aarhus, Denmark
| | - Mélodie Aubart
- Paris Cité University, Imagine Institute, Paris, France
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- Pediatric Neurology Department, Necker Hospital for Sick Children, Paris-City University, Paris, France
| | - Aurélie Cobat
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Paris Cité University, Imagine Institute, Paris, France
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
| | - Olivier Dulac
- Department of Pediatric Neurology, Necker Hospital for Sick Children, AP-HP, Paris, France
| | - Melike Emiroglu
- Department of Pediatric Infectious Diseases, Faculty of Medicine, Selcuk University, Konya, Turkey
| | - Søren R Paludan
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Center for Immunology of Viral Infections, Aarhus University, Aarhus, Denmark
- Department of Rheumatology and Inflammation Research, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Göteborg, Sweden
| | - Laurent Abel
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Paris Cité University, Imagine Institute, Paris, France
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
| | - Luigi Notarangelo
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Richard Longnecker
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Greg Smith
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Lorenz Studer
- The Center for Stem Cell Biology & Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY, USA
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA.
- Paris Cité University, Imagine Institute, Paris, France.
- Pediatric Hematology-Immunology and Rheumatology Unit, Necker Hospital for Sick Children, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France.
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France.
- Howard Hughes Medical Institute, New York, NY, USA.
| | - Shen-Ying Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA.
- Paris Cité University, Imagine Institute, Paris, France.
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France.
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3
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Krishnan N, Priestman M, Uhía I, Charitakis N, Glegola-Madejska IT, Baer TM, Tranberg A, Faraj A, Simonsson USH, Robertson BD. A noninvasive BCG skin challenge model for assessing tuberculosis vaccine efficacy. PLoS Biol 2024; 22:e3002766. [PMID: 39159267 PMCID: PMC11361749 DOI: 10.1371/journal.pbio.3002766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 08/29/2024] [Accepted: 07/25/2024] [Indexed: 08/21/2024] Open
Abstract
We report here on the characterisation in mice of a noninvasive bacille Calmette-Guérin (BCG) skin challenge model for assessing tuberculosis (TB) vaccine efficacy. Controlled human infection models (CHIMs) are valuable tools for assessing the relevant biological activity of vaccine candidates, with the potential to accelerate TB vaccine development into the clinic. TB infection poses significant constraints on the design of a CHIM using the causative agent Mycobacterium tuberculosis (Mtb). A safer alternative is a challenge model using the attenuated vaccine agent Mycobacterium bovis BCG as a surrogate for Mtb, and intradermal (skin) challenge as an alternative to pulmonary infection. We have developed a unique noninvasive imaging system based on fluorescent reporters (FluorBCG) to quantitatively measure bacterial load over time, thereby determining a relevant biological vaccine effect. We assessed the utility of this model to measure the effectiveness of 2 TB vaccines: the currently licenced BCG and a novel subunit vaccine candidate. To assess the efficacy of the skin challenge model, a nonlinear mixed-effects models was built describing the decline of fluorescence over time. The model-based analysis identified that BCG vaccination reduced the fluorescence readout of both fluorophores compared to unvaccinated mice (p < 0.001). However, vaccination with the novel subunit candidate did not alter the fluorescence decline compared to unvaccinated mice (p > 0.05). BCG-vaccinated mice that showed the reduced fluorescent readout also had a reduced bacterial burden in the lungs when challenged with Mtb. This supports the fluorescence activity in the skin as a reflection of vaccine induced functional pulmonary immune responses. This novel noninvasive approach allows for repeated measurements from the challenge site, providing a dynamic readout of vaccine induced responses over time. This BCG skin challenge model represents an important contribution to the ongoing development of controlled challenge models for TB.
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Affiliation(s)
- Nitya Krishnan
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Miles Priestman
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Iria Uhía
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Natalie Charitakis
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Izabella T. Glegola-Madejska
- Department of Life Sciences, Centre for Bacterial Resistance Biology, Imperial College London, London, United Kingdom
| | - Thomas M. Baer
- Stanford Photonics Research Center, Stanford University, Stanford, California, United States of America
| | - Albin Tranberg
- Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - Alan Faraj
- Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - Ulrika SH Simonsson
- Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - Brian D. Robertson
- Department of Infectious Disease, Imperial College London, London, United Kingdom
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4
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Son JB, Kim S, Yang S, Ahn Y, Lee NK. Analysis of Fluorescent Proteins for Observing Single Gene Locus in a Live and Fixed Escherichia coli Cell. J Phys Chem B 2024; 128:6730-6741. [PMID: 38968413 PMCID: PMC11264270 DOI: 10.1021/acs.jpcb.4c01816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 06/21/2024] [Accepted: 06/27/2024] [Indexed: 07/07/2024]
Abstract
Fluorescent proteins (FPs) are essential tools for advanced microscopy techniques such as super-resolution imaging, single-particle tracking, and quantitative single-molecule counting. Various FPs fused to DNA-binding proteins have been used to observe the subcellular location and movement of specific gene loci in living and fixed bacterial cells. However, quantitative assessments of the properties of FPs for gene locus measurements are still lacking. Here, we assessed various FPs to observe specific gene loci in live and fixed Escherichia coli cells using a fluorescent repressor-operator binding system (FROS), tet operator-Tet repressor proteins (TetR). Tsr-fused FPs were used to assess the intensity and photostability of various FPs (five red FPs: mCherry2, FusionRed, mRFP, mCrimson3, and dKatushka; and seven yellow FPs: SYFP2, Venus, mCitrine, YPet, mClover3, mTopaz, and EYFP) at the single-molecule level in living cells. These FPs were then used for gene locus measurements using FROS. Our results indicate that TetR-mCrimson3 (red) and TetR-EYFP (yellow) had better properties for visualizing gene loci than the other TetR-FPs. Furthermore, fixation procedures affected the clustering of diffusing TetR-FPs and altered the locations of the TetR-FP foci. Fixation with formaldehyde consistently disrupted proper DNA locus observations using TetR-FPs. Notably, the foci measured using TetR-mCrimson3 remained close to their original positions in live cells after glyoxal fixation. This in vivo study provides a cell-imaging guide for the use of FPs for gene-locus observation in E. coli and a scheme for evaluating the use of FPs for other cell-imaging purposes.
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Affiliation(s)
| | | | | | - Youmin Ahn
- Department of Chemistry, Seoul
National University, 08826 Seoul, South
Korea
| | - Nam Ki Lee
- Department of Chemistry, Seoul
National University, 08826 Seoul, South
Korea
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5
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Atxabal U, Fernández A, Moure MJ, Sobczak K, Nycholat C, Almeida-Marrero V, Oyenarte I, Paulson JC, de la Escosura A, Torres T, Reichardt NC, Jiménez-Barbero J, Ereño-Orbea J. Quantifying Siglec-sialylated ligand interactions: a versatile 19F-T 2 CPMG filtered competitive NMR displacement assay. Chem Sci 2024; 15:10612-10624. [PMID: 38994400 PMCID: PMC11234860 DOI: 10.1039/d4sc01723d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 05/08/2024] [Indexed: 07/13/2024] Open
Abstract
Sialic-acid-binding immunoglobulin-like lectins (Siglecs) are integral cell surface proteins crucial for the regulation of immune responses and the maintenance of immune tolerance through interactions with sialic acids. Siglecs recognize sialic acid moieties, usually found at the end of N-glycan and O-glycan chains. However, the different Siglecs prefer diverse presentations of the recognized sialic acid, depending on the type of glycosidic linkage used to link to the contiguous Gal/GalNAc or sialic acid moieties. This fact, together with possible O- or N-substitutions at the recognized glycan epitope significantly influences their roles in various immune-related processes. Understanding the molecular details of Siglec-sialoglycan interactions is essential for unraveling their specificities and for the development of new molecules targeting these receptors. While traditional biophysical methods like isothermal titration calorimetry (ITC) have been utilized to measure binding between lectins and glycans, contemporary techniques such as surface plasmon resonance (SPR), microscale thermophoresis (MST), and biolayer interferometry (BLI) offer improved throughput. However, these methodologies require chemical modification and immobilization of at least one binding partner, which can interfere the recognition between the lectin and the ligand. Since Siglecs display a large range of dissociation constants, depending on the (bio)chemical nature of the interacting partner, a general and robust method that could monitor and quantify binding would be highly welcomed. Herein, we propose the application of an NMR-based a competitive displacement assay, grounded on 19F T2-relaxation NMR and on the design, synthesis, and use of a strategic spy molecule, to assess and quantify sialoside ligand binding to Siglecs. We show that the use of this specific approach allows the quantification of Siglec binding for natural and modified sialosides, multivalent sialosides, and sialylated glycoproteins in solution, which differ in binding affinities in more than two orders of magnitude, thus providing invaluable insights into sialoglycan-mediated interactions.
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Affiliation(s)
- Unai Atxabal
- Chemical Glycobiology Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA) 48160 Derio Bizkaia Spain
| | - Andrea Fernández
- Chemical Glycobiology Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA) 48160 Derio Bizkaia Spain
- Glycotechnology Laboratory, CIC biomaGUNE Paseo Miramon 194 San Sebastian 20014 Spain
| | - Maria Jesús Moure
- Chemical Glycobiology Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA) 48160 Derio Bizkaia Spain
| | - Klaudia Sobczak
- Chemical Glycobiology Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA) 48160 Derio Bizkaia Spain
| | - Corwin Nycholat
- Departments of Molecular Medicine and Immunology & Microbiology, The Scripps Research Institute 10550 North Torrey Pines Road La Jolla California 92037 USA
| | - Verónica Almeida-Marrero
- Department of Organic Chemistry, Universidad Autónoma de Madrid C/Francisco Tomás y Valiente 7 28049 Madrid Spain
- Institute for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid C/Francisco Tomás y Valiente 7 28049 Madrid Spain
| | - Iker Oyenarte
- Chemical Glycobiology Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA) 48160 Derio Bizkaia Spain
| | - James C Paulson
- Departments of Molecular Medicine and Immunology & Microbiology, The Scripps Research Institute 10550 North Torrey Pines Road La Jolla California 92037 USA
| | - Andrés de la Escosura
- Department of Organic Chemistry, Universidad Autónoma de Madrid C/Francisco Tomás y Valiente 7 28049 Madrid Spain
- Institute for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid C/Francisco Tomás y Valiente 7 28049 Madrid Spain
| | - Tomás Torres
- Department of Organic Chemistry, Universidad Autónoma de Madrid C/Francisco Tomás y Valiente 7 28049 Madrid Spain
- Institute for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid C/Francisco Tomás y Valiente 7 28049 Madrid Spain
- Instituto Madrileño de Estudios Avanzados (IMDEA)-Nanociencia C/Faraday 9 28049 Madrid Spain
| | - Niels C Reichardt
- Glycotechnology Laboratory, CIC biomaGUNE Paseo Miramon 194 San Sebastian 20014 Spain
- CIBER-BBN Paseo Miramon 194 San Sebastian 20014 Spain
| | - Jesús Jiménez-Barbero
- Chemical Glycobiology Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA) 48160 Derio Bizkaia Spain
- Ikerbasque, Basque Foundation for Science Bilbao Spain
- Department of Organic & Inorganic Chemistry, Faculty of Science and Technology, University of the Basque Country, EHU-UPV 48940 Leioa Bizkaia Spain
- Centro de Investigacion Biomedica en Red de Enfermedades Respiratorias 28029 Madrid Spain
| | - June Ereño-Orbea
- Chemical Glycobiology Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA) 48160 Derio Bizkaia Spain
- Ikerbasque, Basque Foundation for Science Bilbao Spain
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6
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Lihanova Y, Nagel R, Jakob T, Sasso S. Characterization of activating cis-regulatory elements from the histone genes of Chlamydomonas reinhardtii. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 119:525-539. [PMID: 38693717 DOI: 10.1111/tpj.16781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 04/08/2024] [Accepted: 04/12/2024] [Indexed: 05/03/2024]
Abstract
Regulation of gene expression in eukaryotes is controlled by cis-regulatory modules (CRMs). A major class of CRMs are enhancers which are composed of activating cis-regulatory elements (CREs) responsible for upregulating transcription. To date, most enhancers and activating CREs have been studied in angiosperms; in contrast, our knowledge about these key regulators of gene expression in green algae is limited. In this study, we aimed at characterizing putative activating CREs/CRMs from the histone genes of the unicellular model alga Chlamydomonas reinhardtii. To test the activity of four candidates, reporter constructs consisting of a tetramerized CRE, an established promoter, and a gene for the mCerulean3 fluorescent protein were incorporated into the nuclear genome of C. reinhardtii, and their activity was quantified by flow cytometry. Two tested candidates, Eupstr and Ehist cons, significantly upregulated gene expression and were characterized in detail. Eupstr, which originates from highly expressed genes of C. reinhardtii, is an orientation-independent CRE capable of activating both the RBCS2 and β2-tubulin promoters. Ehist cons, which is a CRM from histone genes of angiosperms, upregulates the β2-tubulin promoter in C. reinhardtii over a distance of at least 1.5 kb. The octamer motif present in Ehist cons was identified in C. reinhardtii and the related green algae Chlamydomonas incerta, Chlamydomonas schloesseri, and Edaphochlamys debaryana, demonstrating its high evolutionary conservation. The results of this investigation expand our knowledge about the regulation of gene expression in green algae. Furthermore, the characterized activating CREs/CRMs can be applied as valuable genetic tools.
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Affiliation(s)
- Yuliia Lihanova
- Department of Plant Physiology, Institute of Biology, Leipzig University, Leipzig, Germany
| | - Raimund Nagel
- Department of Plant Physiology, Institute of Biology, Leipzig University, Leipzig, Germany
| | - Torsten Jakob
- Department of Plant Physiology, Institute of Biology, Leipzig University, Leipzig, Germany
| | - Severin Sasso
- Department of Plant Physiology, Institute of Biology, Leipzig University, Leipzig, Germany
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7
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Ding B, Wang J, Mao Y, Meng T, Luo Y, Xu X, Lv Z, Zhou M, Yang Q. Feasible and economic DIY procedures of a hand-held fluorescence detector set-FluorDetector to assist laboratory course development. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2024. [PMID: 38923792 DOI: 10.1002/bmb.21846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Revised: 06/11/2024] [Accepted: 06/14/2024] [Indexed: 06/28/2024]
Abstract
Fluorescence-related experimental techniques play an important role in biochemistry, molecular biology, and cell biology. However, fluorescence-related experiments are rarely included in the laboratory courses of most Chinese universities. This is mainly due to the conflict between large class size (50-60 students in one room) and funding/space limitations to purchase and accommodate enough fluorescence detection equipment. Here, we proposed feasible and economical Do It Yourself (DIY) procedures of a hand-held fluorescence detector set-FluorDetector to support the development of laboratory courses. Tested on several samples, clear fluorescence signals could be directly observed by FluorDetector and photographed with a smartphone. In addition, FluorDetector was able to turn a conventional stereomicroscope into a fluorescence stereomicroscope, detecting fluorescence signals with clean background. FluorDetector is easy to make with a 3D printer, with an extremely low cost ($200 each) when compared with a commercial fluorescence microscope or fluorescence stereomicroscope, and almost as sensitive as a microplate reader in measuring fluorescence. Therefore, FluorDetector is a possible strategy to solve the problem and help to integrate fluorescence-related experimental modules in laboratory courses.
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Affiliation(s)
- Bo Ding
- State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Sciences, Hubei University, Wuhan, China
| | - Ju Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Sciences, Hubei University, Wuhan, China
| | - Yaxin Mao
- State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Sciences, Hubei University, Wuhan, China
| | - Tian Meng
- State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Sciences, Hubei University, Wuhan, China
| | - Yumei Luo
- State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Sciences, Hubei University, Wuhan, China
| | - Xiaomei Xu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Sciences, Hubei University, Wuhan, China
| | - Zhanqing Lv
- Department of Applied Biology, School of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Mian Zhou
- Department of Applied Biology, School of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Qiuying Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Sciences, Hubei University, Wuhan, China
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8
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Ben-Simon Y, Hooper M, Narayan S, Daigle T, Dwivedi D, Way SW, Oster A, Stafford DA, Mich JK, Taormina MJ, Martinez RA, Opitz-Araya X, Roth JR, Allen S, Ayala A, Bakken TE, Barcelli T, Barta S, Bendrick J, Bertagnolli D, Bowlus J, Boyer G, Brouner K, Casian B, Casper T, Chakka AB, Chakrabarty R, Chance RK, Chavan S, Departee M, Donadio N, Dotson N, Egdorf T, Gabitto M, Gary A, Gasperini M, Goldy J, Gore BB, Graybuck L, Greisman N, Haeseleer F, Halterman C, Helback O, Hockemeyer D, Huang C, Huff S, Hunker A, Johansen N, Juneau Z, Kalmbach B, Khem S, Kutsal R, Larsen R, Lee C, Lee AY, Leibly M, Lenz GH, Liang E, Lusk N, Malone J, Mollenkopf T, Morin E, Newman D, Ng L, Ngo K, Omstead V, Oyama A, Pham T, Pom CA, Potekhina L, Ransford S, Rette D, Rimorin C, Rocha D, Ruiz A, Sanchez RE, Sedeno-Cortes A, Sevigny JP, Shapovalova N, Shulga L, Sigler AR, Siverts LA, Somasundaram S, Stewart K, Tieu M, Trader C, van Velthoven CT, Walker M, Weed N, Wirthlin M, Wood T, Wynalda B, Yao Z, Zhou T, Ariza J, Dee N, Reding M, Ronellenfitch K, Mufti S, Sunkin SM, Smith KA, Esposito L, Waters J, Thyagarajan B, Yao S, Lein ES, Zeng H, Levi BP, Ngai J, Ting J, Tasic B. A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.10.597244. [PMID: 38915722 PMCID: PMC11195086 DOI: 10.1101/2024.06.10.597244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
The mammalian cortex is comprised of cells with different morphological, physiological, and molecular properties that can be classified according to shared properties into cell types. Defining the contribution of each cell type to the computational and cognitive processes that are guided by the cortex is essential for understanding its function in health and disease. We use transcriptomic and epigenomic cortical cell type taxonomies from mice and humans to define marker genes and enhancers, and to build genetic tools for cortical cell types. Here, we present a large toolkit for selective targeting of cortical populations, including mouse transgenic lines and recombinant adeno-associated virus (AAV) vectors containing genomic enhancers. We report evaluation of fifteen new transgenic driver lines and over 680 different enhancer AAVs covering all major subclasses of cortical cells, with many achieving a high degree of specificity, comparable with existing transgenic lines. We find that the transgenic lines based on marker genes can provide exceptional specificity and completeness of cell type labeling, but frequently require generation of a triple-transgenic cross for best usability/specificity. On the other hand, enhancer AAVs are easy to screen and use, and can be easily modified to express diverse cargo, such as recombinases. However, their use depends on many factors, such as viral titer and route of administration. The tools reported here as well as the scaled process of tool creation provide an unprecedented resource that should enable diverse experimental strategies towards understanding mammalian cortex and brain function.
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Affiliation(s)
- Yoav Ben-Simon
- Allen Institute for Brain Science, Seattle, WA 98109
- equivalent contribution
| | - Marcus Hooper
- Allen Institute for Brain Science, Seattle, WA 98109
- equivalent contribution
| | - Sujatha Narayan
- Allen Institute for Brain Science, Seattle, WA 98109
- equivalent contribution
| | - Tanya Daigle
- Allen Institute for Brain Science, Seattle, WA 98109
- equivalent contribution
| | | | - Sharon W. Way
- Allen Institute for Brain Science, Seattle, WA 98109
| | - Aaron Oster
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | - John K. Mich
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | | | | | - Jada R. Roth
- Allen Institute for Brain Science, Seattle, WA 98109
| | - Shona Allen
- University of California, Berkeley, Berkeley, CA 94720
| | - Angela Ayala
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | | | - Stuard Barta
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | | | | | | | | | | | - Tamara Casper
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | | | | | - Sakshi Chavan
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | | | | | - Tom Egdorf
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | - Amanda Gary
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | - Jeff Goldy
- Allen Institute for Brain Science, Seattle, WA 98109
| | - Bryan B. Gore
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | - Noah Greisman
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | | | | | | | - Cindy Huang
- Allen Institute for Brain Science, Seattle, WA 98109
| | - Sydney Huff
- Allen Institute for Brain Science, Seattle, WA 98109
| | - Avery Hunker
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | - Zoe Juneau
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | - Shannon Khem
- Allen Institute for Brain Science, Seattle, WA 98109
| | - Rana Kutsal
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | - Changkyu Lee
- Allen Institute for Brain Science, Seattle, WA 98109
| | - Angus Y. Lee
- University of California, Berkeley, Berkeley, CA 94720
| | | | | | | | - Nicholas Lusk
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | | | - Elyse Morin
- Allen Institute for Brain Science, Seattle, WA 98109
| | - Dakota Newman
- Allen Institute for Brain Science, Seattle, WA 98109
| | - Lydia Ng
- Allen Institute for Brain Science, Seattle, WA 98109
| | - Kiet Ngo
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | - Alana Oyama
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | | | | | - Shea Ransford
- Allen Institute for Brain Science, Seattle, WA 98109
| | - Dean Rette
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | - Dana Rocha
- Allen Institute for Brain Science, Seattle, WA 98109
| | - Augustin Ruiz
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | | | | | | | | | - Ana R. Sigler
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | | | - Kaiya Stewart
- Allen Institute for Brain Science, Seattle, WA 98109
| | - Michael Tieu
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | | | | | - Natalie Weed
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | - Toren Wood
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | - Zizhen Yao
- Allen Institute for Brain Science, Seattle, WA 98109
| | - Thomas Zhou
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | - Nick Dee
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | | | - Shoaib Mufti
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | | | - Luke Esposito
- Allen Institute for Brain Science, Seattle, WA 98109
| | - Jack Waters
- Allen Institute for Brain Science, Seattle, WA 98109
| | | | - Shenqin Yao
- Allen Institute for Brain Science, Seattle, WA 98109
| | - Ed S. Lein
- Allen Institute for Brain Science, Seattle, WA 98109
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA 98109
| | - Boaz P. Levi
- Allen Institute for Brain Science, Seattle, WA 98109
| | - John Ngai
- University of California, Berkeley, Berkeley, CA 94720
- Present affiliation: National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892
| | - Jonathan Ting
- Allen Institute for Brain Science, Seattle, WA 98109
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9
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Jorrin B, Haskett TL, Knights HE, Martyn A, Underwood TJ, Dolliver J, Ledermann R, Poole PS. Stable, fluorescent markers for tracking synthetic communities and assembly dynamics. MICROBIOME 2024; 12:81. [PMID: 38715147 PMCID: PMC11075435 DOI: 10.1186/s40168-024-01792-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 03/09/2024] [Indexed: 05/12/2024]
Abstract
BACKGROUND After two decades of extensive microbiome research, the current forefront of scientific exploration involves moving beyond description and classification to uncovering the intricate mechanisms underlying the coalescence of microbial communities. Deciphering microbiome assembly has been technically challenging due to their vast microbial diversity but establishing a synthetic community (SynCom) serves as a key strategy in unravelling this process. Achieving absolute quantification is crucial for establishing causality in assembly dynamics. However, existing approaches are primarily designed to differentiate a specific group of microorganisms within a particular SynCom. RESULTS To address this issue, we have developed the differential fluorescent marking (DFM) strategy, employing three distinguishable fluorescent proteins in single and double combinations. Building on the mini-Tn7 transposon, DFM capitalises on enhanced stability and broad applicability across diverse Proteobacteria species. The various DFM constructions are built using the pTn7-SCOUT plasmid family, enabling modular assembly, and facilitating the interchangeability of expression and antibiotic cassettes in a single reaction. DFM has no detrimental effects on fitness or community assembly dynamics, and through the application of flow cytometry, we successfully differentiated, quantified, and tracked a diverse six-member SynCom under various complex conditions like root rhizosphere showing a different colonisation assembly dynamic between pea and barley roots. CONCLUSIONS DFM represents a powerful resource that eliminates dependence on sequencing and/or culturing, thereby opening new avenues for studying microbiome assembly. Video Abstract.
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Affiliation(s)
- Beatriz Jorrin
- Molecular Plant Sciences Section, Department of Biology, University of Oxford, Oxford, OX1 3RB, UK.
| | - Timothy L Haskett
- Molecular Plant Sciences Section, Department of Biology, University of Oxford, Oxford, OX1 3RB, UK
| | - Hayley E Knights
- Molecular Plant Sciences Section, Department of Biology, University of Oxford, Oxford, OX1 3RB, UK
| | - Anna Martyn
- Molecular Plant Sciences Section, Department of Biology, University of Oxford, Oxford, OX1 3RB, UK
| | - Thomas J Underwood
- Molecular Plant Sciences Section, Department of Biology, University of Oxford, Oxford, OX1 3RB, UK
| | - Jessica Dolliver
- Molecular Plant Sciences Section, Department of Biology, University of Oxford, Oxford, OX1 3RB, UK
| | - Raphael Ledermann
- Molecular Plant Sciences Section, Department of Biology, University of Oxford, Oxford, OX1 3RB, UK
| | - Philip S Poole
- Molecular Plant Sciences Section, Department of Biology, University of Oxford, Oxford, OX1 3RB, UK
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10
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Thiele PJ, Mela-Lopez R, Blandin SA, Klug D. Let it glow: genetically encoded fluorescent reporters in Plasmodium. Malar J 2024; 23:114. [PMID: 38643106 PMCID: PMC11032601 DOI: 10.1186/s12936-024-04936-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 04/06/2024] [Indexed: 04/22/2024] Open
Abstract
The use of fluorescent proteins (FPs) in Plasmodium parasites has been key to understand the biology of this obligate intracellular protozoon. FPs like the green fluorescent protein (GFP) enabled to explore protein localization, promoter activity as well as dynamic processes like protein export and endocytosis. Furthermore, FP biosensors have provided detailed information on physiological parameters at the subcellular level, and fluorescent reporter lines greatly extended the malariology toolbox. Still, in order to achieve optimal results, it is crucial to know exactly the properties of the FP of choice and the genetic scenario in which it will be used. This review highlights advantages and disadvantages of available landing sites and promoters that have been successfully applied for the ectopic expression of FPs in Plasmodium berghei and Plasmodium falciparum. Furthermore, the properties of newly developed FPs beyond DsRed and EGFP, in the visualization of cells and cellular structures as well as in the sensing of small molecules are discussed.
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Affiliation(s)
- Pia J Thiele
- Inserm, CNRS, Université de Strasbourg, UPR9022/U1257, Mosquito Immune Responses (MIR), IBMC, F-67000, Strasbourg, France
| | - Raquel Mela-Lopez
- Inserm, CNRS, Université de Strasbourg, UPR9022/U1257, Mosquito Immune Responses (MIR), IBMC, F-67000, Strasbourg, France
| | - Stéphanie A Blandin
- Inserm, CNRS, Université de Strasbourg, UPR9022/U1257, Mosquito Immune Responses (MIR), IBMC, F-67000, Strasbourg, France
| | - Dennis Klug
- Inserm, CNRS, Université de Strasbourg, UPR9022/U1257, Mosquito Immune Responses (MIR), IBMC, F-67000, Strasbourg, France.
- Institute of Physiology and Pathophysiology, Department of Molecular Cell Physiology, Philipps University Marburg, 35037, Marburg, Germany.
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11
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Delgadillo-Guevara M, Halte M, Erhardt M, Popp PF. Fluorescent tools for the standardized work in Gram-negative bacteria. J Biol Eng 2024; 18:25. [PMID: 38589953 PMCID: PMC11003136 DOI: 10.1186/s13036-024-00420-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Accepted: 03/18/2024] [Indexed: 04/10/2024] Open
Abstract
Standardized and thoroughly characterized genetic tools are a prerequisite for studying cellular processes to ensure the reusability and consistency of experimental results. The discovery of fluorescent proteins (FPs) represents a milestone in the development of genetic reporters for monitoring transcription or protein localization in vivo. FPs have revolutionized our understanding of cellular dynamics by enabling the real-time visualization and tracking of biological processes. Despite these advancements, challenges remain in the appropriate use of FPs, specifically regarding their proper application, protein turnover dynamics, and the undesired disruption of cellular functions. Here, we systematically compared a comprehensive set of 15 FPs and assessed their performance in vivo by focusing on key parameters, such as signal over background ratios and protein stability rates, using the Gram-negative model organism Salmonella enterica as a representative host. We evaluated four protein degradation tags in both plasmid- and genome-based systems and our findings highlight the necessity of introducing degradation tags to analyze time-sensitive cellular processes. We demonstrate that the gain of dynamics mediated by the addition of degradation tags impacts the cell-to-cell heterogeneity of plasmid-based but not genome-based reporters. Finally, we probe the applicability of FPs for protein localization studies in living cells using standard and super-resolution fluorescence microscopy. In summary, our study underscores the importance of careful FP selection and paves the way for the development of improved genetic reporters to enhance the reproducibility and reliability of fluorescence-based research in Gram-negative bacteria and beyond.
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Affiliation(s)
- Mario Delgadillo-Guevara
- Institute of Biology/Molecular Microbiology, Humboldt-Universität zu Berlin, Berlin, 10115, Germany
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, Australia
| | - Manuel Halte
- Institute of Biology/Molecular Microbiology, Humboldt-Universität zu Berlin, Berlin, 10115, Germany
| | - Marc Erhardt
- Institute of Biology/Molecular Microbiology, Humboldt-Universität zu Berlin, Berlin, 10115, Germany
- Max Planck Unit for the Science of Pathogens, Berlin, 10117, Germany
| | - Philipp F Popp
- Institute of Biology/Molecular Microbiology, Humboldt-Universität zu Berlin, Berlin, 10115, Germany.
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12
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Abstract
The vesicular monoamine transporter 2 (VMAT2) is a proton-dependent antiporter responsible for loading monoamine neurotransmitters into synaptic vesicles. Dysregulation of VMAT2 can lead to several neuropsychiatric disorders including Parkinson's disease and schizophrenia. Furthermore, drugs such as amphetamine and MDMA are known to act on VMAT2, exemplifying its role in the mechanisms of actions for drugs of abuse. Despite VMAT2's importance, there remains a critical lack of mechanistic understanding, largely driven by a lack of structural information. Here, we report a 3.1 Å resolution cryo-electron microscopy (cryo-EM) structure of VMAT2 complexed with tetrabenazine (TBZ), a non-competitive inhibitor used in the treatment of Huntington's chorea. We find TBZ interacts with residues in a central binding site, locking VMAT2 in an occluded conformation and providing a mechanistic basis for non-competitive inhibition. We further identify residues critical for cytosolic and lumenal gating, including a cluster of hydrophobic residues which are involved in a lumenal gating strategy. Our structure also highlights three distinct polar networks that may determine VMAT2 conformational dynamics and play a role in proton transduction. The structure elucidates mechanisms of VMAT2 inhibition and transport, providing insights into VMAT2 architecture, function, and the design of small-molecule therapeutics.
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Affiliation(s)
- Michael P Dalton
- Department of Structural Biology, University of PittsburghPittsburghUnited States
| | - Mary Hongying Cheng
- Laufer Center for Physical and Quantitative Biology, and Department of Biochemistry and Cell Biology, School of Medicine, Stony Brook UniversityStony BrookUnited States
| | - Ivet Bahar
- Laufer Center for Physical and Quantitative Biology, and Department of Biochemistry and Cell Biology, School of Medicine, Stony Brook UniversityStony BrookUnited States
| | - Jonathan A Coleman
- Department of Structural Biology, University of PittsburghPittsburghUnited States
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13
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Baleeva NS, Bogdanova YA, Goncharuk MV, Sokolov AI, Myasnyanko IN, Kublitski VS, Smirnov AY, Gilvanov AR, Goncharuk SA, Mineev KS, Baranov MS. A Combination of Library Screening and Rational Mutagenesis Expands the Available Color Palette of the Smallest Fluorogen-Activating Protein Tag nanoFAST. Int J Mol Sci 2024; 25:3054. [PMID: 38474299 DOI: 10.3390/ijms25053054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 03/01/2024] [Accepted: 03/04/2024] [Indexed: 03/14/2024] Open
Abstract
NanoFAST is the smallest fluorogen-activating protein, consisting of only 98 amino acids, used as a genetically encoded fluorescent tag. Previously, only a single fluorogen with an orange color was revealed for this protein. In the present paper, using rational mutagenesis and in vitro screening of fluorogens libraries, we expanded the color palette of this tag. We discovered that E46Q is one of the key substitutions enabling the range of possible fluorogens to be expanded. The introduction of this and several other substitutions has made it possible to use not only orange but also red and green fluorogens with the modified protein.
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Affiliation(s)
- Nadezhda S Baleeva
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
- Laboratory of Medicinal Substances Chemistry, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Ostrovitianov 1, 117997 Moscow, Russia
| | - Yulia A Bogdanova
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Marina V Goncharuk
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Anatolii I Sokolov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
- Laboratory of Medicinal Substances Chemistry, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Ostrovitianov 1, 117997 Moscow, Russia
| | - Ivan N Myasnyanko
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
- Laboratory of Medicinal Substances Chemistry, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Ostrovitianov 1, 117997 Moscow, Russia
| | - Vadim S Kublitski
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Alexander Yu Smirnov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
- Laboratory of Medicinal Substances Chemistry, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Ostrovitianov 1, 117997 Moscow, Russia
| | - Aidar R Gilvanov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Sergey A Goncharuk
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Konstantin S Mineev
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Mikhail S Baranov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
- Laboratory of Medicinal Substances Chemistry, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Ostrovitianov 1, 117997 Moscow, Russia
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14
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Ascensao JA, Denk J, Lok K, Yu Q, Wetmore KM, Hallatschek O. Rediversification following ecotype isolation reveals hidden adaptive potential. Curr Biol 2024; 34:855-867.e6. [PMID: 38325377 PMCID: PMC10911448 DOI: 10.1016/j.cub.2024.01.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 11/09/2023] [Accepted: 01/10/2024] [Indexed: 02/09/2024]
Abstract
Microbial communities play a critical role in ecological processes, and their diversity is key to their functioning. However, little is known about whether communities can regenerate ecological diversity following ecotype removal or extinction and how the rediversified communities would compare to the original ones. Here, we show that simple two-ecotype communities from the E. coli long-term evolution experiment (LTEE) consistently rediversified into two ecotypes following the isolation of one of the ecotypes, coexisting via negative frequency-dependent selection. Communities separated by more than 30,000 generations of evolutionary time rediversify in similar ways. The rediversified ecotype appears to share a number of growth traits with the ecotype it replaces. However, the rediversified community is also different from the original community in ways relevant to the mechanism of ecotype coexistence-for example, in stationary phase response and survival. We found substantial variation in the transcriptional states between the two original ecotypes, whereas the differences within the rediversified community were comparatively smaller, although the rediversified community showed unique patterns of differential expression. Our results suggest that evolution may leave room for alternative diversification processes even in a maximally reduced community of only two strains. We hypothesize that the presence of alternative evolutionary pathways may be even more pronounced in communities of many species where there are even more potential niches, highlighting an important role for perturbations, such as species removal, in evolving ecological communities.
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Affiliation(s)
- Joao A Ascensao
- Department of Bioengineering, University of California Berkeley, Berkeley, CA, USA
| | - Jonas Denk
- Department of Physics, University of California Berkeley Berkeley, CA, USA
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA
| | - Kristen Lok
- Department of Bioengineering, University of California Berkeley, Berkeley, CA, USA
- Present affiliation: Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - QinQin Yu
- Department of Physics, University of California Berkeley Berkeley, CA, USA
- Present affiliation: Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States
| | - Kelly M Wetmore
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA
| | - Oskar Hallatschek
- Department of Physics, University of California Berkeley Berkeley, CA, USA
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA
- Peter Debye Institute for Soft Matter Physics, Leipzig University, 04103 Leipzig, Germany
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15
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Hoermann B, Dürr EM, Ludwig C, Ercan M, Köhn M. A strategy to disentangle direct and indirect effects on (de)phosphorylation by chemical modulators of the phosphatase PP1 in complex cellular contexts. Chem Sci 2024; 15:2792-2804. [PMID: 38404380 PMCID: PMC10882499 DOI: 10.1039/d3sc04746f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 01/12/2024] [Indexed: 02/27/2024] Open
Abstract
Chemical activators and inhibitors are useful probes to identify substrates and downstream effects of enzymes; however, due to the complex signaling environment within cells, it is challenging to distinguish between direct and indirect effects. This is particularly the case for phosphorylation, where a single (de)phosphorylation event can trigger rapid changes in many other phosphorylation sites. An additional complication arises when a single catalytic entity, which acts in the form of many different holoenzymes with different substrates, is activated or inhibited, as it is unclear which holoenzymes are affected, and in turn which of their substrates are (de)phosphorylated. Direct target engaging MS-based technologies to study targets of drugs do not address these challenges. Here, we tackle this by studying the modulation of protein phosphatase-1 (PP1) activity by PP1-disrupting peptides (PDPs), as well as their selectivity toward PP1, by using a combination of mass spectrometry-based experiments. By combining cellular treatment with the PDP with in vitro dephosphorylation by the enzyme, we identify high confidence substrate candidates and begin to separate direct and indirect effects. Together with experiments analyzing which holoenzymes are particularly susceptible to this treatment, we obtain insights into the effect of the modulator on the complex network of protein (de)phosphorylation. This strategy holds promise for enhancing our understanding of PP1 in particular and, due to the broad applicability of the workflow and the MS-based read-out, of chemical modulators with complex mode of action in general.
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Affiliation(s)
- Bernhard Hoermann
- Faculty of Biology, Institute of Biology III, University of Freiburg Freiburg Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg Freiburg Germany
| | - Eva-Maria Dürr
- Faculty of Biology, Institute of Biology III, University of Freiburg Freiburg Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg Freiburg Germany
| | - Christina Ludwig
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM) Freising Germany
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich (TUM) Freising Germany
| | - Melda Ercan
- Faculty of Biology, Institute of Biology III, University of Freiburg Freiburg Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg Freiburg Germany
| | - Maja Köhn
- Faculty of Biology, Institute of Biology III, University of Freiburg Freiburg Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg Freiburg Germany
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16
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Zheng R, Moynahan K, Georgomanolis T, Pavlenko E, Geissen S, Mizi A, Grimm S, Nemade H, Rehimi R, Bastigkeit J, Lackmann JW, Adam M, Rada-Iglesias A, Nuernberg P, Klinke A, Poepsel S, Baldus S, Papantonis A, Kargapolova Y. Remodeling of the endothelial cell transcriptional program via paracrine and DNA-binding activities of MPO. iScience 2024; 27:108898. [PMID: 38322992 PMCID: PMC10844825 DOI: 10.1016/j.isci.2024.108898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 12/01/2023] [Accepted: 01/09/2024] [Indexed: 02/08/2024] Open
Abstract
Myeloperoxidase (MPO) is an enzyme that functions in host defense. MPO is released into the vascular lumen by neutrophils during inflammation and may adhere and subsequently penetrate endothelial cells (ECs) coating vascular walls. We show that MPO enters the nucleus of ECs and binds chromatin independently of its enzymatic activity. MPO drives chromatin decondensation at its binding sites and enhances condensation at neighboring regions. It binds loci relevant for endothelial-to-mesenchymal transition (EndMT) and affects the migratory potential of ECs. Finally, MPO interacts with the RNA-binding factor ILF3 thereby affecting its relative abundance between cytoplasm and nucleus. This interaction leads to change in stability of ILF3-bound transcripts. MPO-knockout mice exhibit reduced number of ECs at scar sites following myocardial infarction, indicating reduced neovascularization. In summary, we describe a non-enzymatic role for MPO in coordinating EndMT and controlling the fate of endothelial cells through direct chromatin binding and association with co-factors.
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Affiliation(s)
- Ruiyuan Zheng
- Department III of Internal Medicine, Heart Center, Faculty of Medicine and University Hospital of Cologne, 50937 Cologne, Germany
| | - Kyle Moynahan
- Department III of Internal Medicine, Heart Center, Faculty of Medicine and University Hospital of Cologne, 50937 Cologne, Germany
| | - Theodoros Georgomanolis
- Cologne Center for Genomics (CCG), University of Cologne, 50931 Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
| | - Egor Pavlenko
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
| | - Simon Geissen
- Department III of Internal Medicine, Heart Center, Faculty of Medicine and University Hospital of Cologne, 50937 Cologne, Germany
| | - Athanasia Mizi
- Institute of Pathology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Simon Grimm
- Department III of Internal Medicine, Heart Center, Faculty of Medicine and University Hospital of Cologne, 50937 Cologne, Germany
| | - Harshal Nemade
- Department III of Internal Medicine, Heart Center, Faculty of Medicine and University Hospital of Cologne, 50937 Cologne, Germany
| | - Rizwan Rehimi
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
| | - Jil Bastigkeit
- Department III of Internal Medicine, Heart Center, Faculty of Medicine and University Hospital of Cologne, 50937 Cologne, Germany
| | - Jan-Wilm Lackmann
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
- Cluster of Excellence on Cellular Stress Responses in Age-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany
| | - Matti Adam
- Department III of Internal Medicine, Heart Center, Faculty of Medicine and University Hospital of Cologne, 50937 Cologne, Germany
| | - Alvaro Rada-Iglesias
- Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), University of Cantabria, 39011 Santander, Spain
| | - Peter Nuernberg
- Cologne Center for Genomics (CCG), University of Cologne, 50931 Cologne, Germany
| | - Anna Klinke
- Department III of Internal Medicine, Heart Center, Faculty of Medicine and University Hospital of Cologne, 50937 Cologne, Germany
| | - Simon Poepsel
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
| | - Stephan Baldus
- Department III of Internal Medicine, Heart Center, Faculty of Medicine and University Hospital of Cologne, 50937 Cologne, Germany
| | - Argyris Papantonis
- Institute of Pathology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Yulia Kargapolova
- Department III of Internal Medicine, Heart Center, Faculty of Medicine and University Hospital of Cologne, 50937 Cologne, Germany
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17
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Sanchez C, Ramirez A, Hodgson L. Unravelling molecular dynamics in living cells: Fluorescent protein biosensors for cell biology. J Microsc 2024. [PMID: 38357769 PMCID: PMC11324865 DOI: 10.1111/jmi.13270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 01/11/2024] [Accepted: 01/22/2024] [Indexed: 02/16/2024]
Abstract
Genetically encoded, fluorescent protein (FP)-based Förster resonance energy transfer (FRET) biosensors are microscopy imaging tools tailored for the precise monitoring and detection of molecular dynamics within subcellular microenvironments. They are characterised by their ability to provide an outstanding combination of spatial and temporal resolutions in live-cell microscopy. In this review, we begin by tracing back on the historical development of genetically encoded FP labelling for detection in live cells, which lead us to the development of early biosensors and finally to the engineering of single-chain FRET-based biosensors that have become the state-of-the-art today. Ultimately, this review delves into the fundamental principles of FRET and the design strategies underpinning FRET-based biosensors, discusses their diverse applications and addresses the distinct challenges associated with their implementation. We place particular emphasis on single-chain FRET biosensors for the Rho family of guanosine triphosphate hydrolases (GTPases), pointing to their historical role in driving our understanding of the molecular dynamics of this important class of signalling proteins and revealing the intricate relationships and regulatory mechanisms that comprise Rho GTPase biology in living cells.
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Affiliation(s)
- Colline Sanchez
- Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York, USA
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Andrea Ramirez
- Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York, USA
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Louis Hodgson
- Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York, USA
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, USA
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18
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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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19
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Chang J, Yuan W, Gao C, Zhang B, Liu JL, Chen G, Tan YW. Single-Molecule Fluorescence Imaging Reveals Coassembly of CTPS and P5CS. J Phys Chem B 2024; 128:949-959. [PMID: 38236746 DOI: 10.1021/acs.jpcb.3c06498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2024]
Abstract
The cellular compartmentation induced by self-assembly of natural proteins has recently attracted widespread attention due to its structural-functional significance. Among them, as a highly conserved metabolic enzyme and one of the potential targets for cancers and parasitic diseases in drug development, CTP synthase (CTPS) has also been reported to self-assemble into filamentous structures termed cytoophidia. To elucidate the dynamical mechanism of cytoophidium filamentation, we utilize single-molecule fluorescence imaging to observe the real-time self-assembly dynamics of CTPS and the coordinated assembly between CTPS and its interaction partner, Δ1-pyrroline-5-carboxylate synthase (P5CS). Significant differences exist in the direction of growth and extension when the two proteins self-assemble. The oligomer state distribution analysis of the CTPS minimum structural subunit under different conditions and the stoichiometry statistics of binding CTPS and P5CS by single-molecule fluorescence photobleach counting further confirm that the CTPS cytoophidia are mainly stacked with tetramers. CTPS can act as the nucleation core to induce the subsequent growth of the P5CS filaments. Our work not only provide evidence from the molecular level for the self-assembly and coordinated assembly (coassembly) of CTPS with its interaction partner P5CS in vitro but also offer new experimental perspectives for the dynamics research of coordinated regulation between other protein polymers.
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Affiliation(s)
- Jian Chang
- State Key Laboratory of Surface Physics, Shanghai Key Laboratory of Metasurfaces for Light Manipulation, Department of Physics, Fudan University, Shanghai 200433, China
| | - Weijie Yuan
- State Key Laboratory of Surface Physics, Shanghai Key Laboratory of Metasurfaces for Light Manipulation, Department of Physics, Fudan University, Shanghai 200433, China
| | - Chendi Gao
- The State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science, Fudan University, Shanghai 200433, China
| | - Bo Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Ji-Long Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, United Kingdom
| | - Guosong Chen
- The State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science, Fudan University, Shanghai 200433, China
| | - Yan-Wen Tan
- State Key Laboratory of Surface Physics, Shanghai Key Laboratory of Metasurfaces for Light Manipulation, Department of Physics, Fudan University, Shanghai 200433, China
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20
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Ahmad M, Imran A, Movileanu L. Overlapping characteristics of weak interactions of two transcriptional regulators with WDR5. Int J Biol Macromol 2024; 258:128969. [PMID: 38158065 PMCID: PMC10922662 DOI: 10.1016/j.ijbiomac.2023.128969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 12/18/2023] [Accepted: 12/20/2023] [Indexed: 01/03/2024]
Abstract
The WD40 repeat protein 5 (WDR5) is a nuclear hub that critically influences gene expression by interacting with transcriptional regulators. Utilizing the WDR5 binding motif (WBM) site, WDR5 interacts with the myelocytomatosis (MYC), an oncoprotein transcription factor, and the retinoblastoma-binding protein 5 (RbBP5), a scaffolding element of an epigenetic complex. Given the clinical significance of these protein-protein interactions (PPIs), there is a pressing necessity for a quantitative assessment of these processes. Here, we use biolayer interferometry (BLI) to examine interactions of WDR5 with consensus peptide ligands of MYC and RbBP5. We found that both interactions exhibit relatively weak affinities arising from a fast dissociation process. Remarkably, live-cell imaging identified distinctive WDR5 localizations in the absence and presence of full-length binding partners. Although WDR5 tends to accumulate within nucleoli, WBM-mediated interactions with MYC and RbBP5 require their localization outside nucleoli. We utilize fluorescence resonance energy transfer (FRET) microscopy to confirm these weak interactions through a low FRET efficiency of the MYC-WDR5 and RbBP5-WDR5 complexes in living cells. In addition, we evaluate the impact of peptide and small-molecule inhibitors on these interactions. These outcomes form a fundamental basis for further developments to clarify the multitasking role of the WBM binding site of WDR5.
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Affiliation(s)
- Mohammad Ahmad
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, NY 13244-1130, USA
| | - Ali Imran
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, NY 13244-1130, USA
| | - Liviu Movileanu
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, NY 13244-1130, USA; Department of Biomedical and Chemical Engineering, Syracuse University, 329 Link Hall, Syracuse, NY 13244, USA; The BioInspired Institute, Syracuse University, Syracuse, NY 13244, USA.
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21
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Dalton MP, Cheng MH, Bahar I, Coleman JA. Structural mechanisms for VMAT2 inhibition by tetrabenazine. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.05.556211. [PMID: 37732203 PMCID: PMC10508774 DOI: 10.1101/2023.09.05.556211] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
The vesicular monoamine transporter 2 (VMAT2) is a proton-dependent antiporter responsible for loading monoamine neurotransmitters into synaptic vesicles. Dysregulation of VMAT2 can lead to several neuropsychiatric disorders including Parkinson's disease and schizophrenia. Furthermore, drugs such as amphetamine and MDMA are known to act on VMAT2, exemplifying its role in the mechanisms of actions for drugs of abuse. Despite VMAT2's importance, there remains a critical lack of mechanistic understanding, largely driven by a lack of structural information. Here we report a 3.1 Å resolution cryo-EM structure of VMAT2 complexed with tetrabenazine (TBZ), a non-competitive inhibitor used in the treatment of Huntington's chorea. We find TBZ interacts with residues in a central binding site, locking VMAT2 in an occluded conformation and providing a mechanistic basis for non-competitive inhibition. We further identify residues critical for cytosolic and lumenal gating, including a cluster of hydrophobic residues which are involved in a lumenal gating strategy. Our structure also highlights three distinct polar networks that may determine VMAT2 conformational dynamics and play a role in proton transduction. The structure elucidates mechanisms of VMAT2 inhibition and transport, providing insights into VMAT2 architecture, function, and the design of small-molecule therapeutics.
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Affiliation(s)
- Michael P Dalton
- Department of Structural Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA
| | - Mary Hongying Cheng
- Laufer Center for Physical and Quantitative Biology, and Department of Biochemistry and Cell Biology, School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA
| | - Ivet Bahar
- Laufer Center for Physical and Quantitative Biology, and Department of Biochemistry and Cell Biology, School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA
| | - Jonathan A Coleman
- Department of Structural Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA
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22
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Valbuena FM, Krahn AH, Tokamov SA, Greene AC, Fehon RG, Glick BS. Yellow and oxidation-resistant derivatives of a monomeric superfolder GFP. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.25.577236. [PMID: 38328041 PMCID: PMC10849726 DOI: 10.1101/2024.01.25.577236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Fluorescent proteins (FPs) are essential tools in biology. The utility of FPs depends on their brightness, photostability, efficient folding, monomeric state, and compatibility with different cellular environments. Despite the proliferation of available FPs, derivatives of the originally identified Aequorea victoria GFP often show superior behavior as fusion tags. We recently generated msGFP2, an optimized monomeric superfolder variant of A. victoria GFP. Here, we describe two derivatives of msGFP2. The monomeric variant msYFP2 is a yellow superfolder FP with high photostability. The monomeric variant moxGFP2 lacks cysteines but retains significant folding stability, so it works well in the lumen of the secretory pathway. These new FPs are useful for common imaging applications.
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23
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Seger M, Mammadova F, Villegas-Valencia M, Bastos de Freitas B, Chang C, Isachsen I, Hemstreet H, Abualsaud F, Boring M, Lammers PJ, Lauersen KJ. Engineered ketocarotenoid biosynthesis in the polyextremophilic red microalga Cyanidioschyzon merolae 10D. Metab Eng Commun 2023; 17:e00226. [PMID: 37449053 PMCID: PMC10336515 DOI: 10.1016/j.mec.2023.e00226] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 06/03/2023] [Accepted: 06/08/2023] [Indexed: 07/18/2023] Open
Abstract
The polyextremophilic Cyanidiophyceae are eukaryotic red microalgae with promising biotechnological properties arising from their low pH and elevated temperature requirements which can minimize culture contamination at scale. Cyanidioschyzon merolae 10D is a cell wall deficient species with a fully sequenced genome that is amenable to nuclear transgene integration by targeted homologous recombination. C. merolae maintains a minimal carotenoid profile and here, we sought to determine its capacity for ketocarotenoid accumulation mediated by heterologous expression of a green algal β-carotene ketolase (BKT) and hydroxylase (CHYB). To achieve this, a synthetic transgene expression cassette system was built to integrate and express Chlamydomonas reinhardtii (Cr) sourced enzymes by fusing native C. merolae transcription, translation and chloroplast targeting signals to codon-optimized coding sequences. Chloramphenicol resistance was used to select for the integration of synthetic linear DNAs into a neutral site within the host genome. CrBKT expression caused accumulation of canthaxanthin and adonirubin as major carotenoids while co-expression of CrBKT with CrCHYB generated astaxanthin as the major carotenoid in C. merolae. Unlike green algae and plants, ketocarotenoid accumulation in C. merolae did not reduce total carotenoid contents, but chlorophyll a reduction was observed. Light intensity affected global ratios of all pigments but not individual pigment compositions and phycocyanin contents were not markedly different between parental strain and transformants. Continuous illumination was found to encourage biomass accumulation and all strains could be cultivated in simulated summer conditions from two different extreme desert environments. Our findings present the first example of carotenoid metabolic engineering in a red eukaryotic microalga and open the possibility for use of C. merolae 10D for simultaneous production of phycocyanin and ketocarotenoid pigments.
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Affiliation(s)
- Mark Seger
- Arizona Center for Algae Technology and Innovation, Arizona State University, 7418 Innovation Way South, Mesa, AZ, 85212, United States
| | - Fakhriyya Mammadova
- Arizona Center for Algae Technology and Innovation, Arizona State University, 7418 Innovation Way South, Mesa, AZ, 85212, United States
| | - Melany Villegas-Valencia
- Bioengineering Program, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Bárbara Bastos de Freitas
- Bioengineering Program, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Clarissa Chang
- Arizona Center for Algae Technology and Innovation, Arizona State University, 7418 Innovation Way South, Mesa, AZ, 85212, United States
| | - Iona Isachsen
- Arizona Center for Algae Technology and Innovation, Arizona State University, 7418 Innovation Way South, Mesa, AZ, 85212, United States
| | - Haley Hemstreet
- Arizona Center for Algae Technology and Innovation, Arizona State University, 7418 Innovation Way South, Mesa, AZ, 85212, United States
| | - Fatimah Abualsaud
- Bioengineering Program, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Malia Boring
- Arizona Center for Algae Technology and Innovation, Arizona State University, 7418 Innovation Way South, Mesa, AZ, 85212, United States
| | - Peter J. Lammers
- Arizona Center for Algae Technology and Innovation, Arizona State University, 7418 Innovation Way South, Mesa, AZ, 85212, United States
| | - Kyle J. Lauersen
- Arizona Center for Algae Technology and Innovation, Arizona State University, 7418 Innovation Way South, Mesa, AZ, 85212, United States
- Bioengineering Program, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
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24
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Wang H, Gallet B, Moriscot C, Pezet M, Chatellard C, Kleman JP, Göttlinger H, Weissenhorn W, Boscheron C. An Inducible ESCRT-III Inhibition Tool to Control HIV-1 Budding. Viruses 2023; 15:2289. [PMID: 38140530 PMCID: PMC10748027 DOI: 10.3390/v15122289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 11/14/2023] [Accepted: 11/16/2023] [Indexed: 12/24/2023] Open
Abstract
HIV-1 budding as well as many other cellular processes require the Endosomal Sorting Complex Required for Transport (ESCRT) machinery. Understanding the architecture of the native ESCRT-III complex at HIV-1 budding sites is limited due to spatial resolution and transient ESCRT-III recruitment. Here, we developed a drug-inducible transient HIV-1 budding inhibitory tool to enhance the ESCRT-III lifetime at budding sites. We generated autocleavable CHMP2A, CHMP3, and CHMP4B fusion proteins with the hepatitis C virus NS3 protease. We characterized the CHMP-NS3 fusion proteins in the absence and presence of protease inhibitor Glecaprevir with regard to expression, stability, localization, and HIV-1 Gag VLP budding. Immunoblotting experiments revealed rapid and stable accumulation of CHMP-NS3 fusion proteins. Notably, upon drug administration, CHMP2A-NS3 and CHMP4B-NS3 fusion proteins substantially decrease VLP release while CHMP3-NS3 exerted no effect but synergized with CHMP2A-NS3. Localization studies demonstrated the relocalization of CHMP-NS3 fusion proteins to the plasma membrane, endosomes, and Gag VLP budding sites. Through the combined use of transmission electron microscopy and video-microscopy, we unveiled drug-dependent accumulation of CHMP2A-NS3 and CHMP4B-NS3, causing a delay in HIV-1 Gag-VLP release. Our findings provide novel insight into the functional consequences of inhibiting ESCRT-III during HIV-1 budding and establish new tools to decipher the role of ESCRT-III at HIV-1 budding sites and other ESCRT-catalyzed cellular processes.
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Affiliation(s)
- Haiyan Wang
- University Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 38000 Grenoble, France; (H.W.); (B.G.); (C.C.); (J.-P.K.)
| | - Benoit Gallet
- University Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 38000 Grenoble, France; (H.W.); (B.G.); (C.C.); (J.-P.K.)
| | | | - Mylène Pezet
- University Grenoble Alpes, INSERM, IAB, 38000 Grenoble, France;
| | - Christine Chatellard
- University Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 38000 Grenoble, France; (H.W.); (B.G.); (C.C.); (J.-P.K.)
| | - Jean-Philippe Kleman
- University Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 38000 Grenoble, France; (H.W.); (B.G.); (C.C.); (J.-P.K.)
| | - Heinrich Göttlinger
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA;
| | - Winfried Weissenhorn
- University Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 38000 Grenoble, France; (H.W.); (B.G.); (C.C.); (J.-P.K.)
| | - Cécile Boscheron
- University Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 38000 Grenoble, France; (H.W.); (B.G.); (C.C.); (J.-P.K.)
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25
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Allen J, Flanagan M, Pathak S, Emenecker S, Emenecker R, Strader L. An Improved Toolkit of Gateway- and Gibson Assembly-Compatible Vectors for Protoplast Transfection and Agrobacterium-Mediated Plant Transformation. RESEARCH SQUARE 2023:rs.3.rs-3558280. [PMID: 37986897 PMCID: PMC10659543 DOI: 10.21203/rs.3.rs-3558280/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Objective Understanding the regulation and function of plant genes is essential for addressing the challenges faced by modern agriculture. Plant transformation, in conjunction with fluorescence microscopy, offers a powerful approach to investigate the dynamic behavior of plant genes and the proteins they encode. We previously developed a set of Gateway-compatible tissue-specific plant transformation vectors. In this paper we aim to expand the toolkit of vectors available for Agrobacterium-mediated plant transformation and protoplast transfection. Results Here, we introduce new Agrobacterium-mediated plant transformation vectors by introducing additional fluorophores to create the pJRA vector series. Additionally, we introduce the pLCS series of vectors, a new set of modular Gateway- and Gibson assembly-compatible vectors designed for protoplast transfection. All described vectors are available from Addgene to serve as a resource for the plant research community.
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26
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Wang H, Gallet B, Moriscot C, Pezet M, Chatellard C, Kleman JP, Göttlinger H, Weissenhorn W, Boscheron C. An inducible ESCRT-III inhibition tool to control HIV-1 budding. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.16.562494. [PMID: 37905063 PMCID: PMC10614826 DOI: 10.1101/2023.10.16.562494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
HIV-1 budding as well as many other cellular processes require the Endosomal Sorting Complex Required for Transport (ESCRT) machinery. Understanding the architecture of the native ESCRT-III complex at HIV-1 budding sites is limited due to spatial resolution and transient ESCRT-III recruitment. Here, we developed a drug-inducible transient HIV-1 budding inhibitory tool to enhance the ESCRT-III lifetime at budding sites. We generated auto-cleavable CHMP2A, CHMP3, and CHMP4B fusion proteins with the hepatitis C virus NS3 protease. We characterized the CHMP-NS3 fusion proteins in the absence and presence of protease inhibitor Glecaprevir with regard to expression, stability, localization and HIV-1 Gag VLP budding. Immunoblotting experiments revealed rapid and stable accumulation of CHMP-NS3 fusion proteins with variable modification of Gag VLP budding upon drug administration. Notably, CHMP2A-NS3 and CHMP4B-NS3 fusion proteins substantially decrease VLP release while CHMP3-NS3 exerted a minor effect and synergized with CHMP2A-NS3. Localization studies demonstrated the re-localization of CHMP-NS3 fusion proteins to the plasma membrane, endosomes, and Gag VLP budding sites. Through the combined use of transmission electron microscopy and video-microscopy, we unveiled drug-dependent accumulation of CHMP2A-NS3 and CHMP4B-NS3, causing a delay in HIV-1 Gag-VLP release. Our findings provide novel insight into the functional consequences of inhibiting ESCRT-III during HIV-1 budding and establish new tools to decipher the role of ESCRT-III at HIV-1 budding sites and other ESCRT-catalyzed cellular processes.
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Coucke Q, Parveen N, Fernández GS, Qian C, Hofkens J, Debyser Z, Hendrix J. Particle-based phasor-FLIM-FRET resolves protein-protein interactions inside single viral particles. BIOPHYSICAL REPORTS 2023; 3:100122. [PMID: 37649577 PMCID: PMC10463199 DOI: 10.1016/j.bpr.2023.100122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 08/07/2023] [Indexed: 09/01/2023]
Abstract
Fluorescence lifetime imaging microscopy (FLIM) is a popular modality to create additional contrast in fluorescence images. By carefully analyzing pixel-based nanosecond lifetime patterns, FLIM allows studying complex molecular populations. At the single-molecule or single-particle level, however, image series often suffer from low signal intensities per pixel, rendering it difficult to quantitatively disentangle different lifetime species, such as during Förster resonance energy transfer (FRET) analysis in the presence of a significant donor-only fraction. In this article we investigate whether an object localization strategy and the phasor approach to FLIM have beneficial effects when carrying out FRET analyses of single particles. Using simulations, we first showed that an average of ∼300 photons, spread over the different pixels encompassing single fluorescing particles and without background, is enough to determine a correct phasor signature (SD < 5% for a 4-ns lifetime). For immobilized single- or double-labeled dsDNA molecules, we next validated that particle-based phasor-FLIM-FRET readily allows estimating fluorescence lifetimes and FRET from single molecules. Thirdly, we applied particle-based phasor-FLIM-FRET to investigate protein-protein interactions in subdiffraction HIV-1 viral particles. To do this, we first quantitatively compared the fluorescence brightness, lifetime, and photostability of different popular fluorescent protein-based FRET probes when genetically fused to the HIV-1 integrase enzyme in viral particles, and conclude that eGFP, mTurquoise2, and mScarlet perform best. Finally, for viral particles coexpressing FRET-donor/acceptor-labeled IN, we determined the absolute FRET efficiency of IN oligomers. Available in a convenient open-source graphical user interface, we believe that particle-based phasor-FLIM-FRET is a promising tool to provide detailed insights in samples suffering from low overall signal intensities.
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Affiliation(s)
- Quinten Coucke
- Molecular Imaging and Photonics Division, Department of Chemistry, KU Leuven, Leuven, Belgium
| | - Nagma Parveen
- Molecular Imaging and Photonics Division, Department of Chemistry, KU Leuven, Leuven, Belgium
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
| | - Guillermo Solís Fernández
- Molecular Imaging and Photonics Division, Department of Chemistry, KU Leuven, Leuven, Belgium
- UFIEC, National Institute of Health Carlos III, Madrid, Spain
| | - Chen Qian
- Department of Chemistry, Center for Nano Science (CENS), Center for Integrated Protein Science Munich (CIPSM), and Nanosystems Initiative Munich (NIM), Ludwig Maximilians-Universität München, Munich, Germany
| | - Johan Hofkens
- Molecular Imaging and Photonics Division, Department of Chemistry, KU Leuven, Leuven, Belgium
- Max Planck Institute for Polymer Research, Mainz, Germany
| | - Zeger Debyser
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
| | - Jelle Hendrix
- Molecular Imaging and Photonics Division, Department of Chemistry, KU Leuven, Leuven, Belgium
- Dynamic Bioimaging Lab, Advanced Optical Microscopy Centre and Biomedical Research Institute, Hasselt University, Hasselt, Belgium
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28
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Kuehner F, Wong M, Straub E, Doorbar J, Iftner T, Roden RBS, Stubenrauch F. Mus musculus papillomavirus 1 E8^E2 represses expression of late protein E4 in basal-like keratinocytes via NCoR/SMRT-HDAC3 co-repressor complexes to enable wart formation in vivo. mBio 2023; 14:e0069623. [PMID: 37382436 PMCID: PMC10470772 DOI: 10.1128/mbio.00696-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 05/22/2023] [Indexed: 06/30/2023] Open
Abstract
High-risk human papillomaviruses (PV) account for approximately 600,000 new cancers per year. The early protein E8^E2 is a conserved repressor of PV replication, whereas E4 is a late protein that arrests cells in G2 and collapses keratin filaments to facilitate virion release. While inactivation of the Mus musculus PV1 (MmuPV1) E8 start codon (E8-) increases viral gene expression, surprisingly, it prevents wart formation in FoxN1nu/nu mice. To understand this surprising phenotype, the impact of additional E8^E2 mutations was characterized in tissue culture and mice. MmuPV1 and HPV E8^E2 similarly interact with cellular NCoR/SMRT-HDAC3 co-repressor complexes. Disruption of the splice donor sequence used to generate the E8^E2 transcript or E8^E2 mutants (mt) with impaired binding to NCoR/SMRT-HDAC3 activates MmuPV1 transcription in murine keratinocytes. These MmuPV1 E8^E2 mt genomes also fail to induce warts in mice. The phenotype of E8^E2 mt genomes in undifferentiated cells resembles productive PV replication in differentiated keratinocytes. Consistent with this, E8^E2 mt genomes induced aberrant E4 expression in undifferentiated keratinocytes. In line with observations for HPV, MmuPV1 E4-positive cells displayed a shift to the G2 phase of the cell cycle. In summary, we propose that in order to enable both expansion of infected cells and wart formation in vivo, MmuPV1 E8^E2 inhibits E4 protein expression in the basal keratinocytes that would otherwise undergo E4-mediated cell cycle arrest. IMPORTANCE Human papillomaviruses (PVs) initiate productive replication, which is characterized by genome amplification and expression of E4 protein strictly within suprabasal, differentiated keratinocytes. Mus musculus PV1 mutants that disrupt splicing of the E8^E2 transcript or abolish the interaction of E8^E2 with cellular NCoR/SMRT-HDAC3 co-repressor complexes display increased gene expression in tissue culture but are unable to form warts in vivo. This confirms that the repressor activity of E8^E2 is required for tumor formation and genetically defines a conserved E8 interaction domain. E8^E2 prevents expression of E4 protein in basal-like, undifferentiated keratinocytes and thereby their arrest in G2 phase. Since binding of E8^E2 to NCoR/SMRT-HDAC3 co-repressor is required to enable expansion of infected cells in the basal layer and wart formation in vivo, this interaction represents a novel, conserved, and potentially druggable target.
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Affiliation(s)
- Franziska Kuehner
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tuebingen, Eberhard-Karls University Tuebingen, Tuebingen, Germany
| | - Margaret Wong
- Department of Pathology, The Johns Hopkins University, Baltimore, Maryland, USA
| | - Elke Straub
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tuebingen, Eberhard-Karls University Tuebingen, Tuebingen, Germany
| | - John Doorbar
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Thomas Iftner
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tuebingen, Eberhard-Karls University Tuebingen, Tuebingen, Germany
| | - Richard B. S. Roden
- Department of Pathology, The Johns Hopkins University, Baltimore, Maryland, USA
| | - Frank Stubenrauch
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tuebingen, Eberhard-Karls University Tuebingen, Tuebingen, Germany
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29
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McCarthy M, Dodd WB, Lu X, Pritko DJ, Patel ND, Haskell CV, Sanabria H, Blenner MA, Birtwistle MR. Theory for High-Throughput Genetic Interaction Screening. ACS Synth Biol 2023; 12:2290-2300. [PMID: 37463472 PMCID: PMC10443530 DOI: 10.1021/acssynbio.2c00627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Indexed: 07/20/2023]
Abstract
Systematic, genome-scale genetic screens have been instrumental for elucidating genotype-phenotype relationships, but approaches for probing genetic interactions have been limited to at most ∼100 pre-selected gene combinations in mammalian cells. Here, we introduce a theory for high-throughput genetic interaction screens. The theory extends our recently developed Multiplexing using Spectral Imaging and Combinatorics (MuSIC) approach to propose ∼105 spectrally unique, genetically encoded MuSIC barcodes from 18 currently available fluorescent proteins. Simulation studies based on constraints imposed by spectral flow cytometry equipment suggest that genetic interaction screens at the human genome-scale may be possible if MuSIC barcodes can be paired to guide RNAs. While experimental testing of this theory awaits, it offers transformative potential for genetic perturbation technology and knowledge of genetic function. More broadly, the availability of a genome-scale spectral barcode library for non-destructive identification of single cells could find more widespread applications such as traditional genetic screening and high-dimensional lineage tracing.
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Affiliation(s)
- Madeline
E. McCarthy
- Department
of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29631, United States
| | - William B. Dodd
- Department
of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29631, United States
| | - Xiaoming Lu
- Department
of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29631, United States
| | - Daniel J. Pritko
- Department
of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29631, United States
| | - Nishi D. Patel
- Department
of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29631, United States
| | - Charlotte V. Haskell
- Department
of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29631, United States
| | - Hugo Sanabria
- Department
of Physics and Astronomy, Clemson University, Clemson, South Carolina 29631, United States
| | - Mark A. Blenner
- Department
of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29631, United States
- Department
of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Marc R. Birtwistle
- Department
of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29631, United States
- Department
of Bioengineering, Clemson University, Clemson, South Carolina 29631, United States
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30
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Ahmad M, Movileanu L. Multiplexed imaging for probing RAS-RAF interactions in living cells. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2023; 1865:184173. [PMID: 37211322 PMCID: PMC10330472 DOI: 10.1016/j.bbamem.2023.184173] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 04/18/2023] [Accepted: 05/08/2023] [Indexed: 05/23/2023]
Abstract
GTP-bound RAS interacts with its protein effectors in response to extracellular stimuli, leading to chemical inputs for downstream pathways. Significant progress has been made in measuring these reversible protein-protein interactions (PPIs) in various cell-free environments. Yet, acquiring high sensitivity in heterogeneous solutions remains challenging. Here, using an intermolecular fluorescence resonance energy transfer (FRET) biosensing approach, we develop a method to visualize and localize HRAS-CRAF interactions in living cells. We demonstrate that the EGFR activation and the HRAS-CRAF complex formation can be concurrently probed in a single cell. This biosensing strategy discriminates EGF-stimulated HRAS-CRAF interactions at the cell and organelle membranes. In addition, we provide quantitative FRET measurements for assessing these transient PPIs in a cell-free environment. Finally, we prove the utility of this approach by showing that an EGFR-binding compound is a potent inhibitor of HRAS-CRAF interactions. The outcomes of this work form a fundamental basis for further explorations of the spatiotemporal dynamics of various signaling networks.
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Affiliation(s)
- Mohammad Ahmad
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, USA
| | - Liviu Movileanu
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, USA; Department of Biomedical and Chemical Engineering, Syracuse University, 329 Link Hall, Syracuse, NY 13244, USA; The BioInspired Institute, Syracuse University, Syracuse, NY 13244, USA.
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31
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Ashworth EK, Dezalay J, Ryan CRM, Ieritano C, Hopkins WS, Chambrier I, Cammidge AN, Stockett MH, Noble JA, Bull JN. Protomers of the green and cyan fluorescent protein chromophores investigated using action spectroscopy. Phys Chem Chem Phys 2023. [PMID: 37465988 DOI: 10.1039/d3cp02661b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
The photophysics of biochromophore ions often depends on the isomeric or protomeric distribution, yet this distribution, and the individual isomer contributions to an action spectrum, can be difficult to quantify. Here, we use two separate photodissociation action spectroscopy instruments to record electronic spectra for protonated forms of the green (pHBDI+) and cyan (Cyan+) fluorescent protein chromophores. One instrument allows for cryogenic (T = 40 ± 10 K) cooling of the ions, while the other offers the ability to perform protomer-selective photodissociation spectroscopy. We show that both chromophores are generated as two protomers when using electrospray ionisation, and that the protomers have partially overlapping absorption profiles associated with the S1 ← S0 transition. The action spectra for both species span the 340-460 nm range, although the spectral onset for the pHBDI+ protomer with the proton residing on the carbonyl oxygen is red-shifted by ≈40 nm relative to the lower-energy imine protomer. Similarly, the imine and carbonyl protomers are the lowest energy forms of Cyan+, with the main band for the carbonyl protomer red-shifted by ≈60 nm relative to the lower-energy imine protomer. The present strategy for investigating protomers can be applied to a wide range of other biochromophore ions.
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Affiliation(s)
- Eleanor K Ashworth
- School of Chemistry, Norwich Research Park, University of East Anglia, Norwich NR4 7TJ, UK.
| | - Jordan Dezalay
- Department of Physics, Stockholm University, SE-10691 Stockholm, Sweden
| | | | - Christian Ieritano
- Department of Chemistry, University of Waterloo, Waterloo N2L 3G1, Canada
| | - W Scott Hopkins
- Department of Chemistry, University of Waterloo, Waterloo N2L 3G1, Canada
| | - Isabelle Chambrier
- School of Chemistry, Norwich Research Park, University of East Anglia, Norwich NR4 7TJ, UK.
| | - Andrew N Cammidge
- School of Chemistry, Norwich Research Park, University of East Anglia, Norwich NR4 7TJ, UK.
| | - Mark H Stockett
- Department of Physics, Stockholm University, SE-10691 Stockholm, Sweden
| | | | - James N Bull
- School of Chemistry, Norwich Research Park, University of East Anglia, Norwich NR4 7TJ, UK.
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32
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Perozeni F, Baier T. Current Nuclear Engineering Strategies in the Green Microalga Chlamydomonas reinhardtii. Life (Basel) 2023; 13:1566. [PMID: 37511941 PMCID: PMC10381326 DOI: 10.3390/life13071566] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 07/07/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
The green model microalga Chlamydomonas reinhardtii recently emerged as a sustainable production chassis for the efficient biosynthesis of recombinant proteins and high-value metabolites. Its capacity for scalable, rapid and light-driven growth in minimal salt solutions, its simplicity for genetic manipulation and its "Generally Recognized As Safe" (GRAS) status are key features for its application in industrial biotechnology. Although nuclear transformation has typically resulted in limited transgene expression levels, recent developments now allow the design of powerful and innovative bioproduction concepts. In this review, we summarize the main obstacles to genetic engineering in C. reinhardtii and describe all essential aspects in sequence adaption and vector design to enable sufficient transgene expression from the nuclear genome. Several biotechnological examples of successful engineering serve as blueprints for the future establishment of C. reinhardtii as a green cell factory.
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Affiliation(s)
- Federico Perozeni
- Department of Biotechnology, University of Verona, 37134 Verona, Italy
| | - Thomas Baier
- Algae Biotechnology and Bioenergy, Faculty of Biology, Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany
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33
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Mahlandt EK, Palacios Martínez S, Arts JJG, Tol S, van Buul JD, Goedhart J. Opto-RhoGEFs, an optimized optogenetic toolbox to reversibly control Rho GTPase activity on a global to subcellular scale, enabling precise control over vascular endothelial barrier strength. eLife 2023; 12:RP84364. [PMID: 37449837 PMCID: PMC10393062 DOI: 10.7554/elife.84364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023] Open
Abstract
The inner layer of blood vessels consists of endothelial cells, which form the physical barrier between blood and tissue. This vascular barrier is tightly regulated and is defined by cell-cell contacts through adherens and tight junctions. To investigate the signaling that regulates vascular barrier strength, we focused on Rho GTPases, regulators of the actin cytoskeleton and known to control junction integrity. To manipulate Rho GTPase signaling in a temporal and spatial manner we applied optogenetics. Guanine-nucleotide exchange factor (GEF) domains from ITSN1, TIAM1, and p63RhoGEF, activating Cdc42, Rac, and Rho, respectively, were integrated into the optogenetic recruitment tool improved light-induced dimer (iLID). This tool allows for Rho GTPase activation at the subcellular level in a reversible and non-invasive manner by recruiting a GEF to a specific area at the plasma membrane, The membrane tag of iLID was optimized and a HaloTag was applied to gain more flexibility for multiplex imaging. The resulting optogenetically recruitable RhoGEFs (Opto-RhoGEFs) were tested in an endothelial cell monolayer and demonstrated precise temporal control of vascular barrier strength by a cell-cell overlap-dependent, VE-cadherin-independent, mechanism. Furthermore, Opto-RhoGEFs enabled precise optogenetic control in endothelial cells over morphological features such as cell size, cell roundness, local extension, and cell contraction. In conclusion, we have optimized and applied the optogenetic iLID GEF recruitment tool, that is Opto-RhoGEFs, to study the role of Rho GTPases in the vascular barrier of the endothelium and found that membrane protrusions at the junction region can rapidly increase barrier integrity independent of VE-cadherin.
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Affiliation(s)
- Eike K Mahlandt
- Swammerdam Institute for Life Sciences, Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, University of Amsterdam, Amsterdam, Netherlands
| | - Sebastián Palacios Martínez
- Swammerdam Institute for Life Sciences, Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, University of Amsterdam, Amsterdam, Netherlands
| | - Janine J G Arts
- Swammerdam Institute for Life Sciences, Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, University of Amsterdam, Amsterdam, Netherlands
- Molecular Cell Biology Lab at Dept. Molecular Hematology, Sanquin Research and Landsteiner Laboratory, Amsterdam, Netherlands
| | - Simon Tol
- Molecular Cell Biology Lab at Dept. Molecular Hematology, Sanquin Research and Landsteiner Laboratory, Amsterdam, Netherlands
| | - Jaap D van Buul
- Swammerdam Institute for Life Sciences, Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, University of Amsterdam, Amsterdam, Netherlands
- Molecular Cell Biology Lab at Dept. Molecular Hematology, Sanquin Research and Landsteiner Laboratory, Amsterdam, Netherlands
| | - Joachim Goedhart
- Swammerdam Institute for Life Sciences, Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, University of Amsterdam, Amsterdam, Netherlands
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34
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Steinberger S, Adler J, Shaul Y. Method of Monitoring 26S Proteasome in Cells Revealed the Crucial Role of PSMA3 C-Terminus in 26S Integrity. Biomolecules 2023; 13:992. [PMID: 37371572 DOI: 10.3390/biom13060992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 06/11/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023] Open
Abstract
Proteasomes critically regulate proteostasis via protein degradation. Proteasomes are multi-subunit complexes composed of the 20S proteolytic core particle (20S CP) that, in association with one or two 19S regulatory particles (19S RPs), generates the 26S proteasome, which is the major proteasomal complex in cells. Native gel protocols are used to investigate the 26S/20S ratio. However, a simple method for detecting these proteasome complexes in cells is missing. To this end, using CRISPR technology, we YFP-tagged the endogenous PSMB6 (β1) gene, a 20S CP subunit, and co-tagged endogenous PSMD6 (Rpn7), a 19S RP subunit, with the mScarlet fluorescent protein. We observed the colocalization of the YFP and mScarlet fluorescent proteins in the cells, with higher nuclear accumulation. Nuclear proteasomal granules are formed under osmotic stress, and all were positive for YFP and mScarlet. Previously, we have reported that PSMD1 knockdown, one of the 19 RP subunits, gives rise to a high level of "free" 20S CPs. Intriguingly, under this condition, the 20S-YFP remained nuclear, whereas the PSMD6-mScarlet was mostly in cytoplasm, demonstrating the distinct subcellular distribution of uncapped 20S CPs. Lately, we have shown that the PSMA3 (α7) C-terminus, a 20S CP subunit, binds multiple intrinsically disordered proteins (IDPs). Remarkably, the truncation of the PSMA3 C-terminus is phenotypically reminiscent of PSMD1 knockdown. These data suggest that the PSMA3 C-terminal region is critical for 26S proteasome integrity.
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Affiliation(s)
- Shirel Steinberger
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Julia Adler
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yosef Shaul
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
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35
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Lenza MP, Egia-Mendikute L, Antoñana-Vildosola A, Soares CO, Coelho H, Corzana F, Bosch A, Manisha P, Quintana JI, Oyenarte I, Unione L, Moure MJ, Azkargorta M, Atxabal U, Sobczak K, Elortza F, Sutherland JD, Barrio R, Marcelo F, Jiménez-Barbero J, Palazon A, Ereño-Orbea J. Structural insights into Siglec-15 reveal glycosylation dependency for its interaction with T cells through integrin CD11b. Nat Commun 2023; 14:3496. [PMID: 37311743 DOI: 10.1038/s41467-023-39119-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 05/26/2023] [Indexed: 06/15/2023] Open
Abstract
Sialic acid-binding Ig-like lectin 15 (Siglec-15) is an immune modulator and emerging cancer immunotherapy target. However, limited understanding of its structure and mechanism of action restrains the development of drug candidates that unleash its full therapeutic potential. In this study, we elucidate the crystal structure of Siglec-15 and its binding epitope via co-crystallization with an anti-Siglec-15 blocking antibody. Using saturation transfer-difference nuclear magnetic resonance (STD-NMR) spectroscopy and molecular dynamics simulations, we reveal Siglec-15 binding mode to α(2,3)- and α(2,6)-linked sialic acids and the cancer-associated sialyl-Tn (STn) glycoform. We demonstrate that binding of Siglec-15 to T cells, which lack STn expression, depends on the presence of α(2,3)- and α(2,6)-linked sialoglycans. Furthermore, we identify the leukocyte integrin CD11b as a Siglec-15 binding partner on human T cells. Collectively, our findings provide an integrated understanding of the structural features of Siglec-15 and emphasize glycosylation as a crucial factor in controlling T cell responses.
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Affiliation(s)
- Maria Pia Lenza
- Chemical Glycobiology lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160, Derio, Bizkaia, Spain
| | - Leire Egia-Mendikute
- Cancer Immunology and Immunotherapy Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Bizkaia, Spain
| | - Asier Antoñana-Vildosola
- Cancer Immunology and Immunotherapy Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Bizkaia, Spain
| | - Cátia O Soares
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, NOVA School of Science and Technology, Caparica campus, 2829-516, Caparica, Portugal
- UCIBIO, Department of Chemistry, NOVA School of Science and Technology, Caparica campus, 2829-516, Caparica, Portugal
| | - Helena Coelho
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, NOVA School of Science and Technology, Caparica campus, 2829-516, Caparica, Portugal
- UCIBIO, Department of Chemistry, NOVA School of Science and Technology, Caparica campus, 2829-516, Caparica, Portugal
| | - Francisco Corzana
- Department of Chemistry, University of La Rioja, The Center for Research in Chemical Synthesis, Madre de Dios 53, E-26006, Logroño, Spain
| | - Alexandre Bosch
- Cancer Immunology and Immunotherapy Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Bizkaia, Spain
| | - Prodhi Manisha
- Cancer Immunology and Immunotherapy Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Bizkaia, Spain
| | - Jon Imanol Quintana
- Chemical Glycobiology lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160, Derio, Bizkaia, Spain
| | - Iker Oyenarte
- Chemical Glycobiology lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160, Derio, Bizkaia, Spain
| | - Luca Unione
- Chemical Glycobiology lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160, Derio, Bizkaia, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - María Jesús Moure
- Chemical Glycobiology lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160, Derio, Bizkaia, Spain
| | - Mikel Azkargorta
- Proteomics Platform, CIC bioGUNE, CIBERehd, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160, Derio, Spain
| | - Unai Atxabal
- Chemical Glycobiology lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160, Derio, Bizkaia, Spain
| | - Klaudia Sobczak
- Chemical Glycobiology lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160, Derio, Bizkaia, Spain
| | - Felix Elortza
- Proteomics Platform, CIC bioGUNE, CIBERehd, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160, Derio, Spain
| | - James D Sutherland
- Ubiquitin-likes and Development Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Bizkaia, Spain
| | - Rosa Barrio
- Ubiquitin-likes and Development Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Bizkaia, Spain
| | - Filipa Marcelo
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, NOVA School of Science and Technology, Caparica campus, 2829-516, Caparica, Portugal
- UCIBIO, Department of Chemistry, NOVA School of Science and Technology, Caparica campus, 2829-516, Caparica, Portugal
| | - Jesús Jiménez-Barbero
- Chemical Glycobiology lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160, Derio, Bizkaia, Spain.
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain.
- Department of Organic & Inorganic Chemistry, Faculty of Science and Technology, University of the Basque Country, EHU-UPV, 48940, Leioa, Bizkaia, Spain.
- Centro de Investigacion Biomedica En Red de Enfermedades Respiratorias, 28029, Madrid, Spain.
| | - Asis Palazon
- Cancer Immunology and Immunotherapy Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Bizkaia, Spain.
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain.
| | - June Ereño-Orbea
- Chemical Glycobiology lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160, Derio, Bizkaia, Spain.
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain.
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36
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Rocha RA, Esquirol L, Rolland V, Hands P, Speight RE, Scott C. Non-covalent binding tags for batch and flow biocatalysis. Enzyme Microb Technol 2023; 169:110268. [PMID: 37300919 DOI: 10.1016/j.enzmictec.2023.110268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 05/31/2023] [Accepted: 06/02/2023] [Indexed: 06/12/2023]
Abstract
Enzyme immobilization offers considerable advantage for biocatalysis in batch and continuous flow reactions. However, many currently available immobilization methods require that the surface of the carrier is chemically modified to allow site specific interactions with their cognate enzymes, which requires specific processing steps and incurs associated costs. Two carriers (cellulose and silica) were investigated here, initially using fluorescent proteins as models to study binding, followed by assessment of industrially relevant enzyme performance (transaminases and an imine reductase/glucose oxidoreductase fusion). Two previously described binding tags, the 17 amino acid long silica-binding peptide from the Bacillus cereus CotB protein and the cellulose binding domain from the Clostridium thermocellum, were fused to a range of proteins without impairing their heterologous expression. When fused to a fluorescent protein both tags conferred high avidity specific binding with their respective carriers (low nanomolar Kd values). The CotB peptide (CotB1p) induced protein aggregation in the transaminase and imine reductase/glucose oxidoreductase fusions when incubated with the silica carrier. The Clostridium thermocellum cellulose binding domain (CBDclos) allowed immobilization of all the proteins tested, but immobilization led to loss of enzymatic activity in the transaminases (< 2-fold) and imine reductase/glucose oxidoreductase fusion (> 80%). A transaminase-CBDclos fusion was then successfully used to demonstrate the application of the binding tag in repetitive batch and a continuous-flow reactor.
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Affiliation(s)
- Raquel A Rocha
- School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology (QUT), Brisbane, Qld 4000, Australia; CSIRO Environment, Black Mountain Science and Innovation Park, Canberra, ACT 2601, Australia
| | - Lygie Esquirol
- CSIRO Environment, Black Mountain Science and Innovation Park, Canberra, ACT 2601, Australia
| | - Vivien Rolland
- CSIRO Agriculture and Food, Black Mountain Science and Innovation Park, Canberra, ACT 2601, Australia
| | - Philip Hands
- CSIRO Agriculture and Food, Black Mountain Science and Innovation Park, Canberra, ACT 2601, Australia
| | - Robert E Speight
- School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology (QUT), Brisbane, Qld 4000, Australia; ARC Centre of Excellence in Synthetic Biology, Queensland University of Technology (QUT), Brisbane, Qld 4000, Australia
| | - Colin Scott
- CSIRO Environment, Black Mountain Science and Innovation Park, Canberra, ACT 2601, Australia.
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37
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Yahya RZ, Wellman GB, Overmans S, Lauersen KJ. Engineered production of isoprene from the model green microalga Chlamydomonas reinhardtii. Metab Eng Commun 2023; 16:e00221. [PMID: 37006831 PMCID: PMC10063407 DOI: 10.1016/j.mec.2023.e00221] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 02/23/2023] [Accepted: 03/16/2023] [Indexed: 03/30/2023] Open
Abstract
Isoprene is a clear, colorless, volatile 5-carbon hydrocarbon that is one monomer of all cellular isoprenoids and a platform chemical with multiple applications in industry. Many plants have evolved isoprene synthases (IspSs) with the capacity to liberate isoprene from dimethylallyl diphosphate (DMADP) as part of cellular thermotolerance mechanisms. Isoprene is hydrophobic and volatile, rapidly leaves plant tissues and is one of the main carbon emission sources from vegetation globally. The universality of isoprenoid metabolism allows volatile isoprene production from microbes expressing heterologous IspSs. Here, we compared heterologous overexpression from the nuclear genome and localization into the plastid of four plant terpene synthases (TPs) in the green microalga Chlamydomonas reinhardtii. Using sealed vial mixotrophic cultivation, direct quantification of isoprene production was achieved from the headspace of living cultures, with the highest isoprene production observed in algae expressing the Ipomoea batatas IspS. Perturbations of the downstream carotenoid pathway through keto carotenoid biosynthesis enhanced isoprene titers, which could be further enhanced by increasing flux towards DMADP through heterologous co-expression of a yeast isopentenyl-DP delta isomerase. Multiplexed controlled-environment testing revealed that cultivation temperature, rather than illumination intensity, was the main factor affecting isoprene yield from the engineered alga. This is the first report of heterologous isoprene production from a eukaryotic alga and sets a foundation for further exploration of carbon conversion to this commodity chemical.
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38
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Saldanha DJ, Cai A, Dorval Courchesne NM. The Evolving Role of Proteins in Wearable Sweat Biosensors. ACS Biomater Sci Eng 2023; 9:2020-2047. [PMID: 34491052 DOI: 10.1021/acsbiomaterials.1c00699] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Sweat is an increasingly popular biological medium for fitness monitoring and clinical diagnostics. It contains an abundance of biological information and is available continuously and noninvasively. Sweat-sensing devices often employ proteins in various capacities to create skin-friendly matrices that accurately extract valuable and time-sensitive information from sweat. Proteins were first used in sensors as biorecognition elements in the form of enzymes and antibodies, which are now being tuned to operate at ranges relevant for sweat. In addition, a range of structural proteins, sometimes assembled in conjunction with polymers, can provide flexible and compatible matrices for skin sensors. Other proteins also naturally possess a range of functionalities─as adhesives, charge conductors, fluorescence emitters, and power generators─that can make them useful components in wearable devices. Here, we examine the four main components of wearable sweat sensors─the biorecognition element, the transducer, the scaffold, and the adhesive─and the roles that proteins have played so far, or promise to play in the future, in each component. On a case-by-case basis, we analyze the performance characteristics of existing protein-based devices, their applicable ranges of detection, their transduction mechanism and their mechanical properties. Thereby, we review and compare proteins that can readily be used in sweat sensors and others that will require further efforts to overcome design, stability or scalability challenges. Incorporating proteins in one or multiple components of sweat sensors could lead to the development and deployment of tunable, greener, and safer biosourced devices.
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Affiliation(s)
- Dalia Jane Saldanha
- Department of Chemical Engineering, McGill University, Montréal, Québec, Canada H3A 0C5
| | - Anqi Cai
- Department of Chemical Engineering, McGill University, Montréal, Québec, Canada H3A 0C5
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39
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Ascensao JA, Denk J, Lok K, Yu Q, Wetmore KM, Hallatschek O. Rediversification Following Ecotype Isolation Reveals Hidden Adaptive Potential. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.03.539206. [PMID: 37205326 PMCID: PMC10187175 DOI: 10.1101/2023.05.03.539206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Microbial communities play a critical role in ecological processes, and their diversity is key to their functioning. However, little is known about if communities can regenerate ecological diversity following species removal or extinction, and how the rediversified communities would compare to the original ones. Here we show that simple two-ecotype communities from the E. coli Long Term Evolution Experiment (LTEE) consistently rediversified into two ecotypes following the isolation of one of the ecotypes, coexisting via negative frequency-dependent selection. Communities separated by more than 30,000 generations of evolutionary time rediversify in similar ways. The rediversified ecotype appears to share a number of growth traits with the ecotype it replaces. However, the rediversified community is also different compared to the original community in ways relevant to the mechanism of ecotype coexistence, for example in stationary phase response and survival. We found substantial variation in the transcriptional states between the two original ecotypes, whereas the differences within the rediversified community were comparatively smaller, but with unique patterns of differential expression. Our results suggest that evolution may leave room for alternative diversification processes even in a maximally reduced community of only two strains. We hypothesize that the presence of alternative evolutionary pathways may be even more pronounced in communities of many species, highlighting an important role for perturbations, such as species removal, in evolving ecological communities.
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Affiliation(s)
- Joao A Ascensao
- Department of Bioengineering, University of California Berkeley, Berkeley, CA, USA
| | - Jonas Denk
- Department of Physics, University of California Berkeley Berkeley, CA, USA
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA
| | - Kristen Lok
- Department of Bioengineering, University of California Berkeley, Berkeley, CA, USA
| | - QinQin Yu
- Department of Physics, University of California Berkeley Berkeley, CA, USA
- Present affiliation: Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States
| | - Kelly M Wetmore
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA
| | - Oskar Hallatschek
- Department of Physics, University of California Berkeley Berkeley, CA, USA
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA
- Peter Debye Institute for Soft Matter Physics, Leipzig University, 04103 Leipzig, Germany
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40
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Thouvenel L, Rech J, Guilhot C, Bouet JY, Chalut C. In vivo imaging of MmpL transporters reveals distinct subcellular locations for export of mycolic acids and non-essential trehalose polyphleates in the mycobacterial outer membrane. Sci Rep 2023; 13:7045. [PMID: 37120636 PMCID: PMC10148836 DOI: 10.1038/s41598-023-34315-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 04/27/2023] [Indexed: 05/01/2023] Open
Abstract
The mycobacterial cell envelope consists of a typical plasma membrane, surrounded by a complex cell wall and a lipid-rich outer membrane. The biogenesis of this multilayer structure is a tightly regulated process requiring the coordinated synthesis and assembly of all its constituents. Mycobacteria grow by polar extension and recent studies showed that cell envelope incorporation of mycolic acids, the major constituent of the cell wall and outer membrane, is coordinated with peptidoglycan biosynthesis at the cell poles. However, there is no information regarding the dynamics of incorporation of other families of outer membrane lipids during cell elongation and division. Here, we establish that the translocation of non-essential trehalose polyphleates (TPP) occurs at different subcellular locations than that of the essential mycolic acids. Using fluorescence microscopy approaches, we investigated the subcellular localization of MmpL3 and MmpL10, respectively involved in the export of mycolic acids and TPP, in growing cells and their colocalization with Wag31, a protein playing a critical role in regulating peptidoglycan biosynthesis in mycobacteria. We found that MmpL3, like Wag31, displays polar localization and preferential accumulation at the old pole whereas MmpL10 is more homogenously distributed in the plasma membrane and slightly accumulates at the new pole. These results led us to propose a model in which insertion of TPP and mycolic acids into the mycomembrane is spatially uncoupled.
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Affiliation(s)
- Laurie Thouvenel
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, Toulouse, France
- de Duve Institute, UCLouvain, Brussels, Belgium
| | - Jérôme Rech
- Laboratoire de Microbiologie et Génétique Moléculaires, Centre de Biologie Intégrative de Toulouse, CNRS, Université de Toulouse, UPS, Toulouse, France
| | - Christophe Guilhot
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Jean-Yves Bouet
- Laboratoire de Microbiologie et Génétique Moléculaires, Centre de Biologie Intégrative de Toulouse, CNRS, Université de Toulouse, UPS, Toulouse, France
| | - Christian Chalut
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, Toulouse, France.
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41
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Kotera Y, Komori H, Tasaki K, Takagi K, Imano S, Katou S. The Peroxisomal β-Oxidative Pathway and Benzyl Alcohol O-Benzoyltransferase HSR201 Cooperatively Contribute to the Biosynthesis of Salicylic Acid. PLANT & CELL PHYSIOLOGY 2023:pcad034. [PMID: 37098219 DOI: 10.1093/pcp/pcad034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 04/17/2023] [Accepted: 04/21/2023] [Indexed: 06/19/2023]
Abstract
The phytohormone salicylic acid (SA) regulates plant defense responses against pathogens. Previous studies have suggested that SA is mainly produced from trans-cinnamic acid (CA) in tobacco, but the underlying mechanisms remain largely unknown. SA synthesis is activated by wounding in tobacco plants in which the expression of WIPK and SIPK, two mitogen-activated protein kinases, is suppressed. Using this phenomenon, we previously revealed that HSR201 encoding benzyl alcohol O-benzoyltransferase is required for pathogen signal-induced SA synthesis. In this study, we further analyzed the transcriptomes of wounded WIPK/SIPK-suppressed plants and found that the expression of NtCNL, NtCHD and NtKAT1, homologous to cinnamate-coenzyme A (CoA) ligase (CNL), cinnamoyl-CoA hydratase/dehydrogenase (CHD) and 3-ketoacyl-CoA thiolase (KAT), respectively, is associated with SA biosynthesis. CNL, CHD and KAT constitute a β-oxidative pathway in the peroxisomes and produce benzoyl-CoA, a precursor of benzenoid compounds in petunia flowers. Subcellular localization analysis showed that NtCNL, NtCHD and NtKAT1 localize in the peroxisomes. Recombinant NtCNL catalyzed the formation of CoA esters of CA, whereas recombinant NtCHD and NtKAT1 proteins converted cinnamoyl-CoA to benzoyl-CoA, a substrate of HSR201. Virus-induced gene silencing of any one of NtCNL, NtCHD and NtKAT1 homologs compromised SA accumulation induced by a pathogen-derived elicitor in Nicotiana benthamiana leaves. Transient overexpression of NtCNL in N. benthamiana leaves resulted in SA accumulation, which was enhanced by co-expression of HSR201, although overexpression of HSR201 alone did not cause SA accumulation. These results suggested that the peroxisomal β-oxidative pathway and HSR201 cooperatively contribute to SA biosynthesis in tobacco and N. benthamiana.
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Affiliation(s)
- Yu Kotera
- Graduate School of Science and Technology, Shinshu University, Minamiminowa 8304, Nagano 399-4598, Japan
| | - Hirotomo Komori
- Graduate School of Science and Technology, Shinshu University, Minamiminowa 8304, Nagano 399-4598, Japan
| | - Kosuke Tasaki
- Graduate School of Science and Technology, Shinshu University, Minamiminowa 8304, Nagano 399-4598, Japan
| | - Kumiko Takagi
- Graduate School of Science and Technology, Shinshu University, Minamiminowa 8304, Nagano 399-4598, Japan
| | - Sayaka Imano
- Faculty of Agriculture, Shinshu University, Minamiminowa 8304, Nagano 399-4598, Japan
| | - Shinpei Katou
- Graduate School of Science and Technology, Shinshu University, Minamiminowa 8304, Nagano 399-4598, Japan
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42
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Chuntharpursat-Bon E, Povstyan OV, Ludlow MJ, Carrier DJ, Debant M, Shi J, Gaunt HJ, Bauer CC, Curd A, Simon Futers T, Baxter PD, Peckham M, Muench SP, Adamson A, Humphreys N, Tumova S, Bon RS, Cubbon R, Lichtenstein L, Beech DJ. PIEZO1 and PECAM1 interact at cell-cell junctions and partner in endothelial force sensing. Commun Biol 2023; 6:358. [PMID: 37005489 PMCID: PMC10067937 DOI: 10.1038/s42003-023-04706-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 03/14/2023] [Indexed: 04/04/2023] Open
Abstract
Two prominent concepts for the sensing of shear stress by endothelium are the PIEZO1 channel as a mediator of mechanically activated calcium ion entry and the PECAM1 cell adhesion molecule as the apex of a triad with CDH5 and VGFR2. Here, we investigated if there is a relationship. By inserting a non-disruptive tag in native PIEZO1 of mice, we reveal in situ overlap of PIEZO1 with PECAM1. Through reconstitution and high resolution microscopy studies we show that PECAM1 interacts with PIEZO1 and directs it to cell-cell junctions. PECAM1 extracellular N-terminus is critical in this, but a C-terminal intracellular domain linked to shear stress also contributes. CDH5 similarly drives PIEZO1 to junctions but unlike PECAM1 its interaction with PIEZO1 is dynamic, increasing with shear stress. PIEZO1 does not interact with VGFR2. PIEZO1 is required in Ca2+-dependent formation of adherens junctions and associated cytoskeleton, consistent with it conferring force-dependent Ca2+ entry for junctional remodelling. The data suggest a pool of PIEZO1 at cell junctions, the coming together of PIEZO1 and PECAM1 mechanisms and intimate cooperation of PIEZO1 and adhesion molecules in tailoring junctional structure to mechanical requirement.
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Affiliation(s)
| | | | | | - David J Carrier
- School of Medicine, University of Leeds, Leeds, LS2 9JT, UK
- School of Biomedical Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | | | - Jian Shi
- School of Medicine, University of Leeds, Leeds, LS2 9JT, UK
| | - Hannah J Gaunt
- School of Medicine, University of Leeds, Leeds, LS2 9JT, UK
| | | | - Alistair Curd
- School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - T Simon Futers
- School of Medicine, University of Leeds, Leeds, LS2 9JT, UK
| | - Paul D Baxter
- School of Medicine, University of Leeds, Leeds, LS2 9JT, UK
| | - Michelle Peckham
- School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Stephen P Muench
- School of Biomedical Sciences, University of Leeds, Leeds, LS2 9JT, UK
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Antony Adamson
- Faculty of Biology, Medicine and Health, University of Manchester, AV Hill Building, Manchester, M13 9PT, UK
| | - Neil Humphreys
- Faculty of Biology, Medicine and Health, University of Manchester, AV Hill Building, Manchester, M13 9PT, UK
| | - Sarka Tumova
- School of Medicine, University of Leeds, Leeds, LS2 9JT, UK
| | - Robin S Bon
- School of Medicine, University of Leeds, Leeds, LS2 9JT, UK
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Richard Cubbon
- School of Medicine, University of Leeds, Leeds, LS2 9JT, UK
| | | | - David J Beech
- School of Medicine, University of Leeds, Leeds, LS2 9JT, UK.
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43
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Alamos S, Reimer A, Westrum C, Turner MA, Talledo P, Zhao J, Luu E, Garcia HG. Minimal synthetic enhancers reveal control of the probability of transcriptional engagement and its timing by a morphogen gradient. Cell Syst 2023; 14:220-236.e3. [PMID: 36696901 PMCID: PMC10125799 DOI: 10.1016/j.cels.2022.12.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 09/03/2022] [Accepted: 12/21/2022] [Indexed: 01/26/2023]
Abstract
How enhancers interpret morphogen gradients to generate gene expression patterns is a central question in developmental biology. Recent studies have proposed that enhancers can dictate whether, when, and at what rate promoters engage in transcription, but the complexity of endogenous enhancers calls for theoretical models with too many free parameters to quantitatively dissect these regulatory strategies. To overcome this limitation, we established a minimal promoter-proximal synthetic enhancer in embryos of Drosophila melanogaster. Here, a gradient of the Dorsal activator is read by a single Dorsal DNA binding site. Using live imaging to quantify transcriptional activity, we found that a single binding site can regulate whether promoters engage in transcription in a concentration-dependent manner. By modulating the binding-site affinity, we determined that a gene's decision to transcribe and its transcriptional onset time can be explained by a simple model where the promoter traverses multiple kinetic barriers before transcription can ensue.
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Affiliation(s)
- Simon Alamos
- Department of Plant and Microbial Biology, University of California at Berkeley, Berkeley, CA, USA
| | - Armando Reimer
- Biophysics Graduate Group, University of California at Berkeley, Berkeley, CA, USA
| | - Clay Westrum
- Department of Physics, University of California at Berkeley, Berkeley, CA, USA
| | - Meghan A Turner
- Department of Plant and Microbial Biology, University of California at Berkeley, Berkeley, CA, USA
| | - Paul Talledo
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA
| | - Jiaxi Zhao
- Department of Physics, University of California at Berkeley, Berkeley, CA, USA
| | - Emma Luu
- Department of Physics, University of California at Berkeley, Berkeley, CA, USA
| | - Hernan G Garcia
- Biophysics Graduate Group, University of California at Berkeley, Berkeley, CA, USA; Department of Physics, University of California at Berkeley, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA; Institute for Quantitative Biosciences-QB3, University of California at Berkeley, Berkeley, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA.
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44
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Fukui A, Maruzuru Y, Takeshima K, Koyanagi N, Kato A, Kawaguchi Y. Establishment of a system to quantify wild-type herpes simplex virus-induced cell-cell fusion reveals a role of N-glycosylation of HSV-1 envelope glycoprotein B in cell-cell fusion. Microbiol Immunol 2023; 67:114-119. [PMID: 36606601 DOI: 10.1111/1348-0421.13050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 12/29/2022] [Accepted: 01/04/2023] [Indexed: 01/07/2023]
Abstract
Wild-type herpes simplex virus (HSV) strains infrequently mediate cell-cell fusion in cell cultures and barely induce large multinucleated cells. In this study, we established a system to quantify infrequent cell-cell fusion induced by wild-type HSV strains. The established system clarified that the HSV-1 envelope glycoprotein B and its N-glycosylation at asparagine at position 141 were required for efficient cell-cell fusion. This study provides a link between cell-cell fusion induced by wild-type HSV-1 and viral pathogenesis in vivo.
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Affiliation(s)
- Ayano Fukui
- Division of Molecular Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.,Department of Infectious Disease Control, International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yuhei Maruzuru
- Division of Molecular Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.,Department of Infectious Disease Control, International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.,Research Center for Asian Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Kosuke Takeshima
- Division of Molecular Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.,Department of Infectious Disease Control, International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Naoto Koyanagi
- Division of Molecular Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.,Department of Infectious Disease Control, International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.,Research Center for Asian Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Akihisa Kato
- Division of Molecular Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.,Department of Infectious Disease Control, International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.,Research Center for Asian Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yasushi Kawaguchi
- Division of Molecular Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.,Department of Infectious Disease Control, International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.,Research Center for Asian Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
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45
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Ishikawa K, Kobayashi M, Kusano M, Numata K, Kodama Y. Using the organelle glue technique to engineer the plant cell metabolome. PLANT CELL REPORTS 2023; 42:599-607. [PMID: 36705704 DOI: 10.1007/s00299-023-02982-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 01/11/2023] [Indexed: 06/18/2023]
Abstract
By using the organelle glue technique, we artificially manipulated organelle interactions and controlled the plant metabolome at the pathway level. Plant cell metabolic activity changes with fluctuating environmental conditions, in part via adjustments in the arrangement and interaction of organelles. This hints at the potential for designing plants with desirable metabolic activities for food and pharmaceutical industries by artificially controlling the interaction of organelles through genetic modification. We previously developed a method called the organelle glue technique, in which chloroplast-chloroplast adhesion is induced in plant cells using the multimerization properties of split fluorescent proteins. Here, we generated transgenic Arabidopsis (Arabidopsis thaliana) plants in which chloroplasts adhere to each other and performed metabolome analysis to examine the metabolic changes in these lines. In plant cells expressing a construct encoding the red fluorescent protein mCherry targeted to the chloroplast outer envelope by fusion with a signal sequence (cTP-mCherry), chloroplasts adhered to each other and formed chloroplast aggregations. Mitochondria and peroxisomes were embedded in the aggregates, suggesting that normal interactions between chloroplasts and these organelles were also affected. Metabolome analysis of the cTP-mCherry-expressing Arabidopsis shoots revealed significantly higher levels of glycine, serine, and glycerate compared to control plants. Notably, these are photorespiratory metabolites that are normally transported between chloroplasts, mitochondria, and peroxisomes. Together, our data indicate that chloroplast-chloroplast adhesion alters organellar interactions with mitochondria and peroxisomes and disrupts photorespiratory metabolite transport. These results highlight the possibility of controlling plant metabolism at the pathway level by manipulating organelle interactions.
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Affiliation(s)
- Kazuya Ishikawa
- Center for Bioscience Research and Education, Utsunomiya University, Utsunomiya, Tochigi, Japan
- Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Makoto Kobayashi
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan
| | - Miyako Kusano
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
- Tsukuba-Plant Innovation Research Center, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Keiji Numata
- Department of Material Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
- Biomacromolecules Research Team, Center for Sustainable Resource Science, RIKEN, Wako, Saitama, Japan
| | - Yutaka Kodama
- Center for Bioscience Research and Education, Utsunomiya University, Utsunomiya, Tochigi, Japan.
- Biomacromolecules Research Team, Center for Sustainable Resource Science, RIKEN, Wako, Saitama, Japan.
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Abstract
The genetically encoded fluorescent sensors convert chemical and physical signals into light. They are powerful tools for the visualisation of physiological processes in living cells and freely moving animals. The fluorescent protein is the reporter module of a genetically encoded biosensor. In this study, we first review the history of the fluorescent protein in full emission spectra on a structural basis. Then, we discuss the design of the genetically encoded biosensor. Finally, we briefly review several major types of genetically encoded biosensors that are currently widely used based on their design and molecular targets, which may be useful for the future design of fluorescent biosensors.
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Affiliation(s)
- Minji Wang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, No. 3663 Zhong Shan Road North, Shanghai, 200062, China
| | - Yifan Da
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, No. 3663 Zhong Shan Road North, Shanghai, 200062, China
| | - Yang Tian
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, No. 3663 Zhong Shan Road North, Shanghai, 200062, China
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47
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Henke K, Farmer DT, Niu X, Kraus JM, Galloway JL, Youngstrom DW. Genetically engineered zebrafish as models of skeletal development and regeneration. Bone 2023; 167:116611. [PMID: 36395960 PMCID: PMC11080330 DOI: 10.1016/j.bone.2022.116611] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 11/01/2022] [Accepted: 11/08/2022] [Indexed: 11/16/2022]
Abstract
Zebrafish (Danio rerio) are aquatic vertebrates with significant homology to their terrestrial counterparts. While zebrafish have a centuries-long track record in developmental and regenerative biology, their utility has grown exponentially with the onset of modern genetics. This is exemplified in studies focused on skeletal development and repair. Herein, the numerous contributions of zebrafish to our understanding of the basic science of cartilage, bone, tendon/ligament, and other skeletal tissues are described, with a particular focus on applications to development and regeneration. We summarize the genetic strengths that have made the zebrafish a powerful model to understand skeletal biology. We also highlight the large body of existing tools and techniques available to understand skeletal development and repair in the zebrafish and introduce emerging methods that will aid in novel discoveries in skeletal biology. Finally, we review the unique contributions of zebrafish to our understanding of regeneration and highlight diverse routes of repair in different contexts of injury. We conclude that zebrafish will continue to fill a niche of increasing breadth and depth in the study of basic cellular mechanisms of skeletal biology.
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Affiliation(s)
- Katrin Henke
- Department of Orthopaedics, Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA.
| | - D'Juan T Farmer
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095, USA; Department of Orthopaedic Surgery, University of California, Los Angeles, CA 90095, USA.
| | - Xubo Niu
- Center for Regenerative Medicine, Department of Orthopaedic Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
| | - Jessica M Kraus
- Department of Orthopaedic Surgery, University of Connecticut Health Center, Farmington, CT 06030, USA.
| | - Jenna L Galloway
- Center for Regenerative Medicine, Department of Orthopaedic Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
| | - Daniel W Youngstrom
- Department of Orthopaedic Surgery, University of Connecticut Health Center, Farmington, CT 06030, USA.
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48
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Characterization of Galectin Fusion Proteins with Glycoprotein Affinity Columns and Binding Assays. Molecules 2023; 28:molecules28031054. [PMID: 36770718 PMCID: PMC9919667 DOI: 10.3390/molecules28031054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/11/2023] [Accepted: 01/15/2023] [Indexed: 01/21/2023] Open
Abstract
Galectins are β-galactosyl-binding proteins that fulfill essential physiological functions. In the biotechnological field, galectins are versatile tools, such as in the development of biomaterial coatings or the early-stage diagnosis of cancer diseases. Recently, we introduced galectin-1 (Gal-1) and galectin-3 (Gal-3) as fusion proteins of a His6-tag, a SNAP-tag, and a fluorescent protein. We characterized their binding in ELISA-type assays and their application in cell-surface binding. In the present study, we have constructed further fusion proteins of galectins with fluorescent protein color code. The fusion proteins of Gal-1, Gal-3, and Gal-8 were purified by affinity chromatography. For this, we have prepared glycoprotein affinity resins based on asialofetuin (ASF) and fetuin and combined this in a two-step purification with Immobilized Metal Affinity chromatography (IMAC) to get pure and active galectins. Purified galectin fractions were analyzed by size-exclusion chromatography. The binding characteristics to ASF of solely His6-tagged galectins and galectin fusion proteins were compared. As an example, we demonstrate a 1.6-3-fold increase in binding efficiency for HSYGal-3 (His6-SNAP-yellow fluorescent protein-Gal-3) compared to the HGal-3 (His6-Gal-3). Our results reveal an apparent higher binding efficiency for galectin SNAP-tag fusion proteins compared to His6-tagged galectins, which are independent of the purification mode. This is also demonstrated by the binding of galectin fusion proteins to extracellular glycoconjugates laminin, fibronectin, and collagen IV. Our results indicate the probable involvement of the SNAP-tag in apparently higher binding signals, which we discuss in this study.
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Lim B, Kim J, Desai MS, Wu W, Chae I, Lee SW. Elastic Fluorescent Protein-Based Down-Converting Optical Films for Flexible Display. Biomacromolecules 2023; 24:118-131. [PMID: 36507771 DOI: 10.1021/acs.biomac.2c00957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Protein-based material design provides great advantages to developing smart biomaterials with tunable structures and desired functions. They have been widely used in many biomedical applications including tissue engineering and drug delivery. However, protein-based materials are not yet widely used in optoelectronic materials despite their excellent optical and tunable mechanical properties. Here, we synthesized engineered fluorescent proteins (FPs) fused with elastic protein for the development of optoelectrical down-converting optical filters for flexible display materials. We synthesized sequence-specific FPs to tune blue, green, yellow, and red colors and fused them with elastic protein to tune mechanical properties. We fabricated flexible self-supporting film materials and characterized mechanical properties and down-converting optical properties. We also fabricated a hybrid light-emitting diode (LED) to down convert blue to desired green, red, and white colors. Furthermore, we constructed a flexible white LED using organic LED as a flexible substrate. Our modular synthesis approach of tunable bio-optoelectrical material approaches will be useful to design future biocompatible and flexible display materials and technologies.
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Affiliation(s)
- Butaek Lim
- Department of Bioengineering, University of California, Berkeley, Berkeley, California94720, United States.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California94720, United States
| | - Jinyeong Kim
- Samsung Display Co Ltd, 1 Samsung-ro, Giheung-gu, Yongin-si17113, Republic of Korea
| | - Malav S Desai
- Department of Bioengineering, University of California, Berkeley, Berkeley, California94720, United States.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California94720, United States
| | - Weiyu Wu
- Department of Bioengineering, University of California, Berkeley, Berkeley, California94720, United States
| | - Inseok Chae
- Department of Bioengineering, University of California, Berkeley, Berkeley, California94720, United States.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California94720, United States
| | - Seung-Wuk Lee
- Department of Bioengineering, University of California, Berkeley, Berkeley, California94720, United States.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California94720, United States
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50
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Singer M, Simon K, Forné I, Meissner M. A central CRMP complex essential for invasion in Toxoplasma gondii. PLoS Biol 2023; 21:e3001937. [PMID: 36602948 PMCID: PMC9815656 DOI: 10.1371/journal.pbio.3001937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 11/29/2022] [Indexed: 01/06/2023] Open
Abstract
Apicomplexa are obligate intracellular parasites. While most species are restricted to specific hosts and cell types, Toxoplasma gondii can invade every nucleated cell derived from warm-blooded animals. This broad host range suggests that this parasite can recognize multiple host cell ligands or structures, leading to the activation of a central protein complex, which should be conserved in all apicomplexans. During invasion, the unique secretory organelles (micronemes and rhoptries) are sequentially released and several micronemal proteins have been suggested to be required for host cell recognition and invasion. However, to date, only few micronemal proteins have been demonstrated to be essential for invasion, suggesting functional redundancy that might allow such a broad host range. Cysteine Repeat Modular Proteins (CRMPs) are a family of apicomplexan-specific proteins. In T. gondii, two CRMPs are present in the genome, CRMPA (TGGT1_261080) and CRMPB (TGGT1_292020). Here, we demonstrate that both proteins form a complex that contains the additional proteins MIC15 and the thrombospondin type 1 domain-containing protein (TSP1). Disruption of this complex results in a block of rhoptry secretion and parasites being unable to invade the host cell. In conclusion, this complex is a central invasion complex conserved in all apicomplexans.
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Affiliation(s)
- Mirko Singer
- Faculty of Veterinary Medicine, Experimental Parasitology, Ludwig-Maximilians-University (LMU) Munich, Germany
- Integrative Parasitology, Center for Infectious Diseases, Heidelberg University Medical School, Heidelberg, Germany
- * E-mail: (MS); (MM)
| | - Kathrin Simon
- Faculty of Veterinary Medicine, Experimental Parasitology, Ludwig-Maximilians-University (LMU) Munich, Germany
| | - Ignasi Forné
- Faculty of Medicine, Protein Analysis Unit, Biomedical Center (BMC), Ludwig-Maximilians-University (LMU) Munich, Martinsried, Germany
| | - Markus Meissner
- Faculty of Veterinary Medicine, Experimental Parasitology, Ludwig-Maximilians-University (LMU) Munich, Germany
- * E-mail: (MS); (MM)
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