1
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Gercke D, Lenz F, Jose J. Split-GFP complementation at the bacterial cell surface for antibody-free labeling and quantification of heterologous protein display. Enzyme Microb Technol 2024; 174:110391. [PMID: 38176324 DOI: 10.1016/j.enzmictec.2023.110391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 12/12/2023] [Accepted: 12/18/2023] [Indexed: 01/06/2024]
Abstract
The split-GFP system is a versatile tool with numerous applications, but it has been underutilized for the labeling of heterologous surface-displayed proteins. By inserting the 16 amino acid sequence of the GFP11-tag between a protein of interest and an autotransporter protein, it is possible to present a protein at the outer membrane of gram-negative bacteria and to fluorescently label it by complementation with externally added GFP1-10. The labeled cells could be clearly discerned from cells without the protein of interest using flow cytometry and the insertion of the GFP11-tag caused no significant alteration of the catalytic activity for the tested model enzyme CsBglA. Furthermore, the amount of the protein of interest on the cells could be quantified by comparing the green fluorescence resulting from the complementation to that of standards with known concentrations. This allows a precise characterization of whole-cell biocatalysts, which is difficult with existing methods. The split-GFP complementation approach was shown to be specific, in a similar manner as commercial antibodies. It is cost-efficient, minimizes the possibility of adverse effects on protein expression or solubility, and can be performed at high throughput.
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Affiliation(s)
- David Gercke
- Universität Münster, Institut für Pharmazeutische und Medizinische Chemie, PharmaCampus, Corrensstrasse 48, 48149 Münster, Germany
| | - Florian Lenz
- Universität Münster, Institut für Pharmazeutische und Medizinische Chemie, PharmaCampus, Corrensstrasse 48, 48149 Münster, Germany
| | - Joachim Jose
- Universität Münster, Institut für Pharmazeutische und Medizinische Chemie, PharmaCampus, Corrensstrasse 48, 48149 Münster, Germany.
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2
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Velappan N, Ferrara F, D’Angelo S, Close D, Naranjo L, Bolding MR, Mozden SC, Troup CB, McCullough DK, Gomez A, Kedge M, Bradbury ARM. Direct selection of functional fluorescent-protein antibody fusions by yeast display. PLoS One 2023; 18:e0280930. [PMID: 36827414 PMCID: PMC9956592 DOI: 10.1371/journal.pone.0280930] [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: 06/14/2022] [Accepted: 01/11/2023] [Indexed: 02/26/2023] Open
Abstract
Antibodies are important reagents for research, diagnostics, and therapeutics. Many examples of chimeric proteins combining the specific target recognition of antibodies with complementing functionalities such as fluorescence, toxicity or enzymatic activity have been described. However, antibodies selected solely on the basis of their binding specificities are not necessarily ideal candidates for the construction of chimeras. Here, we describe a high throughput method based on yeast display to directly select antibodies most suitable for conversion to fluorescent chimera. A library of scFv binders was converted to a fluorescent chimeric form, by cloning thermal green protein into the linker between VH and VL, and directly selecting for both binding and fluorescent functionality. This allowed us to directly identify antibodies functional in the single chain TGP format, that manifest higher protein expression, easier protein purification, and one-step binding assays.
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Affiliation(s)
- Nileena Velappan
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States of America
| | | | - Sara D’Angelo
- Specifica Inc., Santa Fe, NM, United States of America
| | - Devin Close
- Arup Laboratories, Salt Lake City, UT, United States of America
| | | | - Madeline R. Bolding
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States of America
| | - Sarah C. Mozden
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States of America
| | | | - Donna K. McCullough
- Microbiology Department, University of Tennessee, Knoxville, TN, United States of America
| | - Analyssa Gomez
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States of America
| | - Marijo Kedge
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States of America
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3
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Goelzer M, Goelzer J, Ferguson ML, Neu CP, Uzer G. Nuclear envelope mechanobiology: linking the nuclear structure and function. Nucleus 2021; 12:90-114. [PMID: 34455929 PMCID: PMC8432354 DOI: 10.1080/19491034.2021.1962610] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 07/26/2021] [Accepted: 07/27/2021] [Indexed: 01/10/2023] Open
Abstract
The nucleus, central to cellular activity, relies on both direct mechanical input as well as its molecular transducers to sense external stimuli and respond by regulating intra-nuclear chromatin organization that determines cell function and fate. In mesenchymal stem cells of musculoskeletal tissues, changes in nuclear structures are emerging as a key modulator of their differentiation and proliferation programs. In this review we will first introduce the structural elements of the nucleoskeleton and discuss the current literature on how nuclear structure and signaling are altered in relation to environmental and tissue level mechanical cues. We will focus on state-of-the-art techniques to apply mechanical force and methods to measure nuclear mechanics in conjunction with DNA, RNA, and protein visualization in living cells. Ultimately, combining real-time nuclear deformations and chromatin dynamics can be a powerful tool to study mechanisms of how forces affect the dynamics of genome function.
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Affiliation(s)
- Matthew Goelzer
- Materials Science and Engineering, Boise State University, Boise, ID, US
| | | | - Matthew L. Ferguson
- Biomolecular Science, Boise State University, Boise, ID, US
- Physics, Boise State University, Boise, ID, US
| | - Corey P. Neu
- Paul M. Rady Department of Mechanical Engineering, University of Colorado, Boulder, CO, US
| | - Gunes Uzer
- Mechanical and Biomedical Engineering, Boise State University, Boise, ID, US
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4
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Velappan N, Close D, Hung LW, Naranjo L, Hemez C, DeVore N, McCullough DK, Lillo AM, Waldo GS, Bradbury ARM. Construction, characterization and crystal structure of a fluorescent single-chain Fv chimera. Protein Eng Des Sel 2021; 34:gzaa029. [PMID: 33586761 PMCID: PMC7901706 DOI: 10.1093/protein/gzaa029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 12/21/2020] [Accepted: 12/24/2020] [Indexed: 11/12/2022] Open
Abstract
In vitro display technologies based on phage and yeast have a successful history of selecting single-chain variable fragment (scFv) antibodies against various targets. However, single-chain antibodies are often unstable and poorly expressed in Escherichia coli. Here, we explore the feasibility of converting scFv antibodies to an intrinsically fluorescent format by inserting the monomeric, stable fluorescent protein named thermal green, between the light- and heavy-chain variable regions. Our results show that the scTGP format maintains the affinity and specificity of the antibodies, improves expression levels, allows one-step fluorescent assay for detection of binding and is a suitable reagent for epitope binning. We also report the crystal structure of an scTGP construct that recognizes phosphorylated tyrosine on FcεR1 receptor of the allergy pathway.
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Affiliation(s)
- Nileena Velappan
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
- Microbiology Department, University of Tennessee, Knoxville, TN 37996, USA
| | - Devin Close
- ARUP Laboratories, Institute for Clinical and Experimental Pathology, Salt Lake City, UT 84108, USA
- Microbiology Department, University of Tennessee, Knoxville, TN 37996, USA
| | - Li-Wei Hung
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
- Microbiology Department, University of Tennessee, Knoxville, TN 37996, USA
| | - Leslie Naranjo
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
- Specifica Inc., Santa Fe, NM 87505, USA
| | - Colin Hemez
- Graduate Program in Biophysics, Harvard University, Boston, MA 02115 USA
| | - Natasha DeVore
- Chemistry Department, Missouri State University, Springfield, MO 65897, USA
| | - Donna K McCullough
- Microbiology Department, University of Tennessee, Knoxville, TN 37996, USA
| | - Antonietta M Lillo
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Geoffrey S Waldo
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
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5
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Deng H, Yan S, Huang Y, Lei C, Nie Z. Design strategies for fluorescent proteins/mimics and their applications in biosensing and bioimaging. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2019.115757] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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6
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Ferreira AV, Antunes E, Ribeiro A, Matamá T, Azoia NG, Cunha J, Cavaco-Paulo A. Design of a chromogenic substrate for elastase based on split GFP system-Proof of concept for colour switch sensors. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2019; 22:e00324. [PMID: 31049301 PMCID: PMC6479270 DOI: 10.1016/j.btre.2019.e00324] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 02/15/2019] [Accepted: 03/15/2019] [Indexed: 06/09/2023]
Abstract
Recent studies have demonstrated that human neutrophil elastase (HNE) can be used as marker for inflammation/infection of chronic wounds since it was found to be present in high concentration in exudate collected from chronic wounds. Biosensors used in wound care benefit from a chromogenic signalling due to the readiness of signal interpretation, but the most common use faint yellow chromogenic molecules such as p-nitroaniline (pNa). In addition, if to be converted into smart dressings, the colour of the detection system should not be masked by the exudate's colour. In this work, we designed a chromogenic substrate for HNE aiming to be incorporated in a smart dressing as a colour switch sensor. The substrate was developed using the GFP-like chromoprotein ultramarine (UM), following the split GFP technology. The cleavage sequence for HNE (Ala-Ala-Pro-Val) was embedded into the sensing moiety of the substrate corresponding to the 11th β-sheet. In the presence of HNE, the 11th β-sheet is able to interact to the signalling moiety composed of the β1-β10 incomplete barrel, allowing the re-establishment of the chromophore environment and, hence, the colour production. Structural homology and molecular dynamics simulations were conducted to aid on the disclosure of the structural changes that are the base of the mechanism of action of this HNE switch substrate. Our findings explore the possible application of GFP-like chromogenic sensors in point-of-care devices for the evaluation of the wounds status, representing a major step in the medical field.
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Affiliation(s)
| | | | | | | | | | | | - Artur Cavaco-Paulo
- Centre of Biological Engineering (CEB), University of Minho, Campus of Gualtar, 4710-057, Braga, Portugal
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7
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Islam J, Riley BT, Fercher C, Jones ML, Buckle AM, Howard CB, Cox RP, Bell TDM, Mahler S, Corrie SR. Wavelength-Dependent Fluorescent Immunosensors via Incorporation of Polarity Indicators near the Binding Interface of Antibody Fragments. Anal Chem 2019; 91:7631-7638. [DOI: 10.1021/acs.analchem.9b00445] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jiaul Islam
- Department of Chemical Engineering, ARC Centre of Excellence in Convergent BioNano Science and Technology, Monash University, Clayton VIC 3800, Australia
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St Lucia QLD 4072, Australia
| | - Blake T. Riley
- Dept. of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton VIC 3800, Australia
| | - Christian Fercher
- Department of Chemical Engineering, ARC Centre of Excellence in Convergent BioNano Science and Technology, Monash University, Clayton VIC 3800, Australia
- ARC Training Centre for Biopharmaceutical Innovation, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St Lucia QLD 4072, Australia
| | - Martina L. Jones
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St Lucia QLD 4072, Australia
- ARC Training Centre for Biopharmaceutical Innovation, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St Lucia QLD 4072, Australia
| | - Ashley M. Buckle
- Dept. of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton VIC 3800, Australia
| | - Christopher B. Howard
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St Lucia QLD 4072, Australia
- ARC Training Centre for Biopharmaceutical Innovation, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St Lucia QLD 4072, Australia
| | - Rosalind P. Cox
- School of Chemistry, Monash University, Clayton VIC 3800, Australia
| | - Toby D. M. Bell
- School of Chemistry, Monash University, Clayton VIC 3800, Australia
| | - Stephen Mahler
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St Lucia QLD 4072, Australia
- ARC Training Centre for Biopharmaceutical Innovation, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St Lucia QLD 4072, Australia
| | - Simon R. Corrie
- Department of Chemical Engineering, ARC Centre of Excellence in Convergent BioNano Science and Technology, Monash University, Clayton VIC 3800, Australia
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St Lucia QLD 4072, Australia
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8
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Knapp A, Ripphahn M, Volkenborn K, Skoczinski P, Jaeger KE. Activity-independent screening of secreted proteins using split GFP. J Biotechnol 2017; 258:110-116. [PMID: 28619616 DOI: 10.1016/j.jbiotec.2017.05.024] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 05/31/2017] [Accepted: 05/31/2017] [Indexed: 01/16/2023]
Abstract
The large-scale industrial production of proteins requires efficient secretion, as provided, for instance, by the Sec system of Gram-positive bacteria. Protein engineering approaches to optimize secretion often involve the screening of large libraries, e.g. comprising a target protein fused to many different signal peptides. Respective high-throughput screening methods are usually based on photometric or fluorimetric assays enabling fast and simple determination of enzymatic activities. Here, we report on an alternative method for quantification of secreted proteins based on the split GFP assay. We analyzed the secretion by Bacillus subtilis of a homologous lipase and a heterologous cutinase by determination of GFP fluorescence and enzyme activity assays. Furthermore, we identified from a signal peptide library a variant of the biotechnologically relevant B. subtilis protein swollenin EXLX1 with up to 5-fold increased secretion. Our results demonstrate that the split GFP assay can be used to monitor secretion of enzymatic and non-enzymatic proteins in B. subtilis in a high-throughput manner.
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Affiliation(s)
- Andreas Knapp
- Institute of Molecular Enzyme Technology, Heinrich -Heine -University Düsseldorf, Forschungszentrum Jülich, D-52426 Jülich, Germany
| | - Myriam Ripphahn
- Institute of Molecular Enzyme Technology, Heinrich -Heine -University Düsseldorf, Forschungszentrum Jülich, D-52426 Jülich, Germany
| | - Kristina Volkenborn
- Institute of Molecular Enzyme Technology, Heinrich -Heine -University Düsseldorf, Forschungszentrum Jülich, D-52426 Jülich, Germany
| | - Pia Skoczinski
- Institute of Molecular Enzyme Technology, Heinrich -Heine -University Düsseldorf, Forschungszentrum Jülich, D-52426 Jülich, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich -Heine -University Düsseldorf, Forschungszentrum Jülich, D-52426 Jülich, Germany; Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, D-52428 Jülich, Germany.
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9
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Specific cell surface labeling of GPCRs using split GFP. Sci Rep 2016; 6:20568. [PMID: 26857153 PMCID: PMC4746647 DOI: 10.1038/srep20568] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 01/07/2016] [Indexed: 01/13/2023] Open
Abstract
Specific cell surface labeling is essential for visualizing the internalization processes of G-protein coupled receptors (GPCRs) and for gaining mechanistic insight of GPCR functions. Here we present a rapid, specific, and versatile labeling scheme for GPCRs at living-cell membrane with the use of a split green fluorescent protein (GFP). Demonstrated with two GPCRs, GPR17 and CysLT2R, we show that two β-stands (β-stands 10 and 11) derived from a superfolder GFP (sfGFP) can be engineered to one of the three extracellular loop of a GPCR. The complementary fragment of sfGFP has nine β-strands (β-stands 1-9) that carries the mature fluorophore, and can be proteolytically derived from the full-length sfGFP. Separately the GFP fragments are non-fluorescent, but become fluorescent upon assembly, thus allowing specific labeling of the target proteins. The two GFP fragments rapidly assemble and the resulting complex is extremely tight under non-denaturing conditions, which allows real-time and quantitative assessment of the internalized GPCRs. We envision that this labeling scheme will be of great use for labeling other membrane proteins in various biological and pharmacological applications.
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10
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Jha RK, Gaiotto T, Bradbury ARM, Strauss CEM. An improved Protein G with higher affinity for human/rabbit IgG Fc domains exploiting a computationally designed polar network. Protein Eng Des Sel 2014; 27:127-34. [PMID: 24632761 DOI: 10.1093/protein/gzu005] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Protein G is an IgG binding protein that has been widely exploited for biotechnological purposes. Rosetta protein modeling identified a set of favorable polar mutations in Protein G, at its binding interface with the Fc domain of Immunoglobulin G, that were predicted to increase the stability and tighten the binding relative to native Protein G, with only a minor perturbation of the binding mode seen in the crystal structure. This triple mutant was synthesized and evaluated experimentally. Relative to the native protein G, the mutant showed a 3.5-fold enhancement in display level on the surface of yeast and a 5-fold tighter molar affinity for rabbit and human IgG. We attribute the improved affinity to a network of hydrogen bonds exploiting specific polar groups on human and rabbit Fc. The relative specificity increased as well since there was little affinity enhancement for goat and mouse Fc, while the affinity for rat Fc was poorer by half. This designed Protein G will be useful in biotechnological applications as a recombinant protein, where its improved affinity, display and specificity will increase antibody capture sensitivity and capacity. Furthermore, the display of this protein on the surface of yeast introduces the concept of the use of yeast as an affinity matrix.
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Affiliation(s)
- Ramesh K Jha
- Bioscience Division, MS M888, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
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11
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Wang Z, Chen Y, Li S, Cheng Y, Zhao H, Jia M, Luo Z, Tang Y. Successful construction and stable expression of an anti-CD45RA scFv–EGFP fusion protein in Chinese hamster ovary cells. Protein Expr Purif 2014; 94:1-6. [DOI: 10.1016/j.pep.2013.10.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2013] [Revised: 10/22/2013] [Accepted: 10/25/2013] [Indexed: 10/26/2022]
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12
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Dezfouli M, Vickovic S, Iglesias MJ, Nilsson P, Schwenk JM, Ahmadian A. Magnetic bead assisted labeling of antibodies at nanogram scale. Proteomics 2013; 14:14-8. [PMID: 24307663 DOI: 10.1002/pmic.201300283] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Revised: 10/01/2013] [Accepted: 10/16/2013] [Indexed: 12/19/2022]
Abstract
There are currently several initiatives that aim to produce binding reagents for proteome-wide analysis. To enable protein detection, visualization, and target quantification, covalent coupling of reporter molecules to antibodies is essential. However, current labeling protocols recommend considerable amount of antibodies, require antibody purity and are not designed for automation. Given that small amounts of antibodies are often sufficient for downstream analysis, we developed a labeling protocol that combines purification and modification of antibodies at submicrogram quantities. With the support of magnetic microspheres, automated labeling of antibodies in parallel using biotin or fluorescent dyes was achieved.
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Affiliation(s)
- Mahya Dezfouli
- Science for Life Laboratory, Division of Gene Technology, School of Biotechnology, Royal Institute of Technology (KTH), Solna, Sweden
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13
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Close DW, Ferrara F, Dichosa AEK, Kumar S, Daughton AR, Daligault HE, Reitenga KG, Velappan N, Sanchez TC, Iyer S, Kiss C, Han CS, Bradbury ARM. Using phage display selected antibodies to dissect microbiomes for complete de novo genome sequencing of low abundance microbes. BMC Microbiol 2013; 13:270. [PMID: 24279426 PMCID: PMC3907030 DOI: 10.1186/1471-2180-13-270] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2013] [Accepted: 11/21/2013] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Single cell genomics has revolutionized microbial sequencing, but complete coverage of genomes in complex microbiomes is imperfect due to enormous variation in organismal abundance and amplification bias. Empirical methods that complement rapidly improving bioinformatic tools will improve characterization of microbiomes and facilitate better genome coverage for low abundance microbes. METHODS We describe a new approach to sequencing individual species from microbiomes that combines antibody phage display against intact bacteria with fluorescence activated cell sorting (FACS). Single chain (scFv) antibodies are selected using phage display against a bacteria or microbial community, resulting in species-specific antibodies that can be used in FACS for relative quantification of an organism in a community, as well as enrichment or depletion prior to genome sequencing. RESULTS We selected antibodies against Lactobacillus acidophilus and demonstrate a FACS-based approach for identification and enrichment of the organism from both laboratory-cultured and commercially derived bacterial mixtures. The ability to selectively enrich for L. acidophilus when it is present at a very low abundance (<0.2%) leads to complete (>99.8%) de novo genome coverage whereas the standard single-cell sequencing approach is incomplete (<68%). We show that specific antibodies can be selected against L. acidophilus when the monoculture is used as antigen as well as when a community of 10 closely related species is used demonstrating that in principal antibodies can be generated against individual organisms within microbial communities. CONCLUSIONS The approach presented here demonstrates that phage-selected antibodies against bacteria enable identification, enrichment of rare species, and depletion of abundant organisms making it tractable to virtually any microbe or microbial community. Combining antibody specificity with FACS provides a new approach for characterizing and manipulating microbial communities prior to genome sequencing.
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Affiliation(s)
- Devin W Close
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA.
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14
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Wiesemann K, Groß LE, Sommer M, Schleiff E, Sommer MS. self-assembling GFP: a versatile tool for plant (membrane) protein analyses. Methods Mol Biol 2013; 1033:131-144. [PMID: 23996175 DOI: 10.1007/978-1-62703-487-6_9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The investigation of cellular processes on the molecular level is important to understand the functional network within plant cells. self-assembling GFP has evolved to be a versatile tool for (membrane) protein analyses. Based on the autocatalytical reassembling property of the nonfluorescent strands 1-10 and 11, protein distribution and membrane protein topology can be analyzed in vivo. Here, we provide basic protocols to determine membrane protein topology in Arabidopsis thaliana protoplasts.
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Affiliation(s)
- Katharina Wiesemann
- Cluster of Excellence Frankfurt, Center for Membrane Proteomics, Department of Biosciences, Molecular Cell Biology, Goethe University, Frankfurt, Germany
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