1
|
Kumar S, Nabet B. A chemical magnet: Approaches to guide precise protein localization. Bioorg Med Chem 2024; 102:117672. [PMID: 38461554 PMCID: PMC11064470 DOI: 10.1016/j.bmc.2024.117672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Revised: 02/26/2024] [Accepted: 03/01/2024] [Indexed: 03/12/2024]
Abstract
Small molecules that chemically induce proximity between two proteins have been widely used to precisely modulate protein levels, stability, and activity. Recently, several studies developed novel strategies that employ heterobifunctional molecules that co-opt shuttling proteins to control the spatial localization of a target protein, unlocking new potential within this domain. Together, these studies lay the groundwork for novel targeted protein relocalization modalities that can rewire the protein circuitry and interactome to influence biological outcomes.
Collapse
Affiliation(s)
- Saurav Kumar
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Behnam Nabet
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Department of Pharmacology, University of Washington, Seattle, WA 98195, USA.
| |
Collapse
|
2
|
Cau J, Toe LD, Zainu A, Baudat F, Robert T. "MeiQuant": An Integrated Tool for Analyzing Meiotic Prophase I Spread Images. Methods Mol Biol 2024; 2770:263-285. [PMID: 38351458 DOI: 10.1007/978-1-0716-3698-5_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2024]
Abstract
Immunocytochemical analysis of meiotic proteins on mouse chromosome spreads is one method of choice to study prophase I chromosome organization and homologous recombination. In recent decades, the development of microscopic approaches led to the production of a large number of images that monitor fluorescent proteins, defined as fluorescent objects, and a major challenge facing the community is the deep analysis of these fluorescent objects (measurement of object length, intensity, distance between objects, as well as foci identification, counting, and colocalization). We propose a set of tools designed from the macro language of the widely used image analysis software ImageJ (Schindelin et al., Nat Methods 9: 676-682, 2012), embedded in the "MeiQuant" macro, which are specifically designed for analyzing objects in the field of meiosis. Our aim is to propose a unified evolutive common tool for image analysis, with a specific focus on mouse prophase I meiotic events.
Collapse
Affiliation(s)
- Julien Cau
- Biocampus Montpellier, University of Montpellier, CNRS, INSERM, Montpellier, France.
| | - Laurine Dal Toe
- CBS (Centre de Biologie Structurale), Univ Montpellier, CNRS, INSERM, Montpellier, France
| | - Akbar Zainu
- Institut de Génétique Humaine, University of Montpellier, CNRS, Montpellier, France
| | - Frédéric Baudat
- Institut de Génétique Humaine, University of Montpellier, CNRS, Montpellier, France.
| | - Thomas Robert
- CBS (Centre de Biologie Structurale), Univ Montpellier, CNRS, INSERM, Montpellier, France.
| |
Collapse
|
3
|
Tsuruta A, Kanetani D, Shiiba Y, Inoki T, Yoshida Y, Matsunaga N, Koyanagi S, Ohdo S. Modulation of cell physiology by bispecific nanobodies enabling changes in the intracellular localization of organelle proteins. Biochem Pharmacol 2023; 215:115708. [PMID: 37506923 DOI: 10.1016/j.bcp.2023.115708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 07/08/2023] [Accepted: 07/25/2023] [Indexed: 07/30/2023]
Abstract
Proteins localize to their respective organelles in cells. This localization is changed by activation or repression in response to signal transduction. Therefore, the appropriate intracellular localization of proteins is important for their functions to be exerted. However, difficulties are associated with controlling the localization of endogenous proteins. In the present study, we developed a conceptually new method of controlling the intracellular localization of endogenous proteins using bispecific nanobodies (BiNbs). BiNbs recognize proteins expressed in the inner membrane, cytoskeleton, nucleus, and peroxisomes, but not in mitochondria or endoplasmic reticulum. BiNbs designed to recognize β-CATENIN and the intrinsic cytosolic protein VIMENTIN (3 × Flag β-CAT-VIM BiNbs) decreased the β-CATENIN-mediated transactivation of target genes by preventing its nuclear localization. Furthermore, 3 × Flag β-CAT-VIM BiNbs suppressed the proliferation and invasion of the VIMENTIN-expressing breast cancer cell line MDA-MB-231, but not MDA-MB-468, in which the expression of VIMENTIN was defective. The present results revealed that changes in the intracellular localization of specific proteins by BiNbs modulated the physiology and functions of cells. The development of BiNbs to recognize proteins specifically expressed in target cells may be a useful approach for eliciting cell-selective effects.
Collapse
Affiliation(s)
- Akito Tsuruta
- Department of Pharmaceutics, Faculty of Pharmaceutical Sciences, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka 812-8582, Japan; Department of Glocal Healthcare, Faculty of Pharmaceutical Sciences, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Daiki Kanetani
- Department of Pharmaceutics, Faculty of Pharmaceutical Sciences, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Yuki Shiiba
- Department of Pharmaceutics, Faculty of Pharmaceutical Sciences, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Takuto Inoki
- Department of Pharmaceutics, Faculty of Pharmaceutical Sciences, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Yuya Yoshida
- Department of Clinical Pharmacokinetics, Faculty of Pharmaceutical Sciences, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Naoya Matsunaga
- Department of Clinical Pharmacokinetics, Faculty of Pharmaceutical Sciences, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Satoru Koyanagi
- Department of Pharmaceutics, Faculty of Pharmaceutical Sciences, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka 812-8582, Japan; Department of Glocal Healthcare, Faculty of Pharmaceutical Sciences, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Shigehiro Ohdo
- Department of Pharmaceutics, Faculty of Pharmaceutical Sciences, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka 812-8582, Japan.
| |
Collapse
|
4
|
Menger KE, Nicholls TJ. Isolating Mitochondria, Mitoplasts, and mtDNA from Cultured Mammalian Cells. Methods Mol Biol 2023; 2615:17-30. [PMID: 36807781 DOI: 10.1007/978-1-0716-2922-2_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
Mitochondria are double membrane-bound eukaryotic organelles with roles in a range of cellular activities including energy conversion, apoptosis, cell signalling, and the biosynthesis of enzyme cofactors. Mitochondria contain their own genome, called mtDNA, which encodes subunits of the oxidative phosphorylation machinery as well as the rRNA and tRNA molecules required for their translation within mitochondria. The ability to isolate highly purified mitochondria from cells has been instrumental in a number of studies of mitochondrial function. Differential centrifugation is a long-established method for the isolation of mitochondria. Cells are subjected to osmotic swelling and disruption, followed by centrifugation in isotonic sucrose solutions to separate mitochondria from other cellular components. We present a method using this principle for the isolation of mitochondria from cultured mammalian cell lines. Mitochondria purified by this method can be further fractionated to investigate protein localization, or act as a starting point to purify mtDNA.
Collapse
|
5
|
Schrader TA, Carmichael RE, Schrader M. Immunolabeling for Detection of Endogenous and Overexpressed Peroxisomal Proteins in Mammalian Cells. Methods Mol Biol 2023; 2643:47-63. [PMID: 36952177 DOI: 10.1007/978-1-0716-3048-8_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/27/2023]
Abstract
Peroxisomes are dynamic subcellular organelles in mammals, playing essential roles in cellular lipid metabolism and redox homeostasis. They perform a wide spectrum of functions in human health and disease, with new roles, mechanisms, and regulatory pathways still being discovered. Recently elucidated biological roles of peroxisomes include as antiviral defense hubs, intracellular signaling platforms, immunomodulators, and protective organelles in sensory cells. Furthermore, peroxisomes are part of a complex inter-organelle interaction network, which involves metabolic cooperation and cross talk via membrane contacts. The detection of endogenous and/or overexpressed proteins within a cell by immunolabelling informs us about the organellar and even sub-organellar localization of both known and putative peroxisomal proteins. In turn, this can be exploited to characterize the effects of experimental manipulations on the morphology, distribution, and/or number of peroxisomes in a cell, which are key properties controlling peroxisome function. Here, we present a protocol used successfully in our laboratory for the immunolabelling of peroxisomal proteins in cultured mammalian cells. We present immunofluorescence and transfection techniques as well as reagents to determine the localization of endogenous and overexpressed peroxisomal proteins.
Collapse
Affiliation(s)
- Tina A Schrader
- Faculty of Health and Life Sciences, Biosciences, University of Exeter, Exeter, Devon, UK
| | - Ruth E Carmichael
- Faculty of Health and Life Sciences, Biosciences, University of Exeter, Exeter, Devon, UK
| | - Michael Schrader
- Faculty of Health and Life Sciences, Biosciences, University of Exeter, Exeter, Devon, UK.
| |
Collapse
|
6
|
Kawai H, Ono K, Eguchi T. Multiplex Immunostaining Method to Distinguish HSP Isoforms in Cancer Tissue Specimens. Methods Mol Biol 2023; 2693:281-291. [PMID: 37540442 DOI: 10.1007/978-1-0716-3342-7_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
Heat shock proteins (HSPs) are often expressed in all nucleated cells, but their expression profiles differ. In particular, HSP90α and HSP90β have high sequence identity and have not been fully examined for their individual and compensatory functions as molecular chaperones, differences in client proteins, and extracellular distributions with exosomes. Immunohistochemical staining is a technique to visualize the presence and localization of target antigens using specific antibodies, of which the multiplex immunostaining method can reveal differences in protein expression in the same tumor tissue and the localization of proteins of interest within tumor tissue or single cells. The common multiplex immunostaining method uses multiple secondary antibodies of different reacting animal species to identify and detect different antigens, thus requiring different animals to be immunized with each primary antibody. Furthermore, the fluorescent-antibody method is the predominant multiplex staining method but has the critical disadvantage that permanent specimens cannot be prepared. Here, we outline a multiplex staining method for HSP90α and HSP90β based on the enzyme-antibody method that allows permanent specimens to be prepared without the restriction of immunized animal species.
Collapse
Affiliation(s)
- Hotaka Kawai
- Department of Oral Pathology and Medicine, Faculty of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Kisho Ono
- Department of Oral and Maxillofacial Surgery, Okayama University Hospital, Okayama, Japan
| | - Takanori Eguchi
- Department of Dental Pharmacology, Faculty of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan.
| |
Collapse
|
7
|
Das H, Zografakis A, Oeljeklaus S, Warscheid B. Analysis of Yeast Peroxisomes via Spatial Proteomics. Methods Mol Biol 2023; 2643:13-31. [PMID: 36952175 DOI: 10.1007/978-1-0716-3048-8_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023]
Abstract
Peroxisomes are ubiquitous organelles with essential functions in numerous cellular processes such as lipid metabolism, detoxification of reactive oxygen species, and signaling. Knowledge of the peroxisomal proteome including multi-localized proteins and, most importantly, changes of its composition induced by altering cellular conditions or impaired peroxisome biogenesis and function is of paramount importance for a holistic view on peroxisomes and their diverse functions in a cellular context. In this chapter, we provide a spatial proteomics protocol specifically tailored to the analysis of the peroxisomal proteome of baker's yeast that enables the definition of the peroxisomal proteome under distinct conditions and to monitor dynamic changes of the proteome including the relocation of individual proteins to a different cellular compartment. The protocol comprises subcellular fractionation by differential centrifugation followed by Nycodenz density gradient centrifugation of a crude peroxisomal fraction, quantitative mass spectrometric measurements of subcellular and density gradient fractions, and advanced computational data analysis, resulting in the establishment of organellar maps on a global scale.
Collapse
Affiliation(s)
- Hirak Das
- Biochemistry II, Theodor Boveri-Institute, University of Würzburg, Würzburg, Germany
| | - Alexandros Zografakis
- Biochemistry II, Theodor Boveri-Institute, University of Würzburg, Würzburg, Germany
| | - Silke Oeljeklaus
- Biochemistry II, Theodor Boveri-Institute, University of Würzburg, Würzburg, Germany.
| | - Bettina Warscheid
- Biochemistry II, Theodor Boveri-Institute, University of Würzburg, Würzburg, Germany.
- CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany.
| |
Collapse
|
8
|
Sharma M, Klösgen RB, Bennewitz B. Fluorescent Protein-Based Approaches for Subcellular Protein Localization in Plants. Methods Mol Biol 2023; 2564:203-211. [PMID: 36107343 DOI: 10.1007/978-1-0716-2667-2_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Fluorescent proteins (FPs) remarkably advanced the study of cellular biology of plants. The most common application is their use as reporter proteins to determine the subcellular localization of a protein of interest (POI) by endogenous expression of a suitable FP-POI fusion construct in plant cells. In this chapter we describe three approaches, namely, particle bombardment, protoplast transformation, and Agrobacterium infiltration, to transiently express such fusion constructs in plant cells of different species. These approaches are versatile and can be utilized for diverse fluorescent protein-based applications.
Collapse
Affiliation(s)
- Mayank Sharma
- Institute of Molecular Plant Biology, ETH Zürich, Zürich, Switzerland.
| | - Ralf Bernd Klösgen
- Institute of Biology-Plant Physiology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Bationa Bennewitz
- Institute of Biology-Plant Physiology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| |
Collapse
|
9
|
Lobo GP, Radhakrishnan R, Leung M, Gruesen A, Knölker HJ, van Kuijk FJ, Montezuma SR. In Silico Prediction of MYO1C-Rhodopsin Interactions and Its Significance in Protein Localization and Visual Function. Adv Exp Med Biol 2023; 1415:499-505. [PMID: 37440078 DOI: 10.1007/978-3-031-27681-1_73] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/14/2023]
Abstract
Rods and cones are photoreceptor neurons in the retina that are required for visual sensation in vertebrates, where proper protein localization and compartmentalization are critical for phototransduction and visual function. In human retinal diseases, improper protein transport to the outer segment (OS) or mislocalization of proteins to the inner segment (IS) could lead to impaired visual responses and photoreceptor cell degeneration, causing a loss of visual function. We showed involvement of an unconventional motor protein, MYO1C, in the proper localization of rhodopsin to the OS, where loss of MYO1C in a mammalian model caused mislocalization of rhodopsin to IS and cell bodies, leading to progressively severe retinal phenotypes. In this study, using modeling and docking analysis, we aimed to identify the protein-protein interaction sites between MYO1C and Rhodopsin to establish a hypothesis that a physical interaction between these proteins is necessary for the proper trafficking of rhodopsin and visual function.
Collapse
Affiliation(s)
- Glenn P Lobo
- Department of Ophthalmology and Visual Neurosciences, University of Minnesota, Minneapolis, MN, USA.
| | - Rakesh Radhakrishnan
- Department of Ophthalmology and Visual Neurosciences, University of Minnesota, Minneapolis, MN, USA
| | - Matthias Leung
- Department of Ophthalmology and Visual Neurosciences, University of Minnesota, Minneapolis, MN, USA
| | - Andrew Gruesen
- Department of Ophthalmology and Visual Neurosciences, University of Minnesota, Minneapolis, MN, USA
| | | | - Frederik J van Kuijk
- Department of Ophthalmology and Visual Neurosciences, University of Minnesota, Minneapolis, MN, USA
| | - Sandra R Montezuma
- Department of Ophthalmology and Visual Neurosciences, University of Minnesota, Minneapolis, MN, USA
| |
Collapse
|
10
|
Vihinen H, Jokitalo E. Studying Golgi Structure and Function by Thin Section TEM. Methods Mol Biol 2022; 2557:141-159. [PMID: 36512215 DOI: 10.1007/978-1-0716-2639-9_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Here, we describe protocols for chemical fixation and flat embedding to study the Golgi structure by thin section transmission electron microscopy (TEM) and for 3,3'-diaminobenzidine (DAB) cytochemical staining and pre-embedding immunolabelling to localize specific Golgi proteins. Furthermore, we demonstrate how the Golgi morphology can be elucidated by classifying the Golgi membranes using Microscopy Image Browser-a software that provides anonymization, modelling, and annotation.
Collapse
Affiliation(s)
- Helena Vihinen
- Electron Microscopy Unit, Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Eija Jokitalo
- Electron Microscopy Unit, Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland.
| |
Collapse
|
11
|
LaCombe R, Cecchini A, Seibert M, Cornelison D. EphA1 receptor tyrosine kinase is localized to the nucleus in rhabdomyosarcoma from multiple species. Biol Open 2022; 11:277168. [PMID: 36214254 PMCID: PMC9581518 DOI: 10.1242/bio.059352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 09/08/2022] [Indexed: 11/20/2022] Open
Abstract
While the typical role of receptor tyrosine kinases is to receive and transmit signals at the cell surface, in some cellular contexts (particularly transformed cells) they may also act as nuclear proteins. Aberrant nuclear localization of receptor tyrosine kinases associated with transformation often enhances the transformed phenotype (i.e. nuclear ErbBs promote tumor progression in breast cancer). Rhabdomyosarcoma (RMS), the most common soft tissue tumor in children, develops to resemble immature skeletal muscle and has been proposed to derive from muscle stem/progenitor cells (satellite cells). It is an aggressive cancer with a 5-year survival rate of 33% if it has metastasized. Eph receptor tyrosine kinases have been implicated in the development and progression of many other tumor types, but there are only two published studies of Ephs localizing to the nucleus of any cell type and to date no nuclear RTKs have been identified in RMS. In a screen for protein expression of Ephs in canine RMS primary tumors as well as mouse and human RMS cell lines, we noted strong expression of EphA1 in the nucleus of interphase cells in tumors from all three species. This localization pattern changes in dividing cells, with EphA1 localizing to the nucleus or the cytoplasm depending on the phase of the cell cycle. These data represent the first case of a nuclear RTK in RMS, and the first time that EphA1 has been detected in the nucleus of any cell type.
Collapse
Affiliation(s)
- Ronnie LaCombe
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA.,Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Alessandra Cecchini
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA.,Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Morgan Seibert
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Ddw Cornelison
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA.,Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| |
Collapse
|
12
|
Pham T, Walden E, Huard S, Pezacki J, Fullerton MD, Baetz K. Fine tuning Acetyl-CoA Carboxylase 1 activity through localization: Functional genomics reveal a role for the lysine acetyltransferase NuA4 and sphingolipid metabolism in regulating Acc1 activity and localization. Genetics 2022; 221:6591204. [PMID: 35608294 PMCID: PMC9339284 DOI: 10.1093/genetics/iyac086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 05/10/2022] [Indexed: 11/29/2022] Open
Abstract
Acetyl-CoA Carboxylase 1 catalyzes the conversion of acetyl-CoA to malonyl-CoA, the committed step of de novo fatty acid synthesis. As a master regulator of lipid synthesis, acetyl-CoA carboxylase 1 has been proposed to be a therapeutic target for numerous metabolic diseases. We have shown that acetyl-CoA carboxylase 1 activity is reduced in the absence of the lysine acetyltransferase NuA4 in Saccharomyces cerevisiae. This change in acetyl-CoA carboxylase 1 activity is correlated with a change in localization. In wild-type cells, acetyl-CoA carboxylase 1 is localized throughout the cytoplasm in small punctate and rod-like structures. However, in NuA4 mutants, acetyl-CoA carboxylase 1 localization becomes diffuse. To uncover mechanisms regulating acetyl-CoA carboxylase 1 localization, we performed a microscopy screen to identify other deletion mutants that impact acetyl-CoA carboxylase 1 localization and then measured acetyl-CoA carboxylase 1 activity in these mutants through chemical genetics and biochemical assays. Three phenotypes were identified. Mutants with hyper-active acetyl-CoA carboxylase 1 form 1 or 2 rod-like structures centrally within the cytoplasm, mutants with mid-low acetyl-CoA carboxylase 1 activity displayed diffuse acetyl-CoA carboxylase 1, while the mutants with the lowest acetyl-CoA carboxylase 1 activity (hypomorphs) formed thick rod-like acetyl-CoA carboxylase 1 structures at the periphery of the cell. All the acetyl-CoA carboxylase 1 hypomorphic mutants were implicated in sphingolipid metabolism or very long-chain fatty acid elongation and in common, their deletion causes an accumulation of palmitoyl-CoA. Through exogenous lipid treatments, enzyme inhibitors, and genetics, we determined that increasing palmitoyl-CoA levels inhibits acetyl-CoA carboxylase 1 activity and remodels acetyl-CoA carboxylase 1 localization. Together this study suggests yeast cells have developed a dynamic feed-back mechanism in which downstream products of acetyl-CoA carboxylase 1 can fine-tune the rate of fatty acid synthesis.
Collapse
Affiliation(s)
- Trang Pham
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, K1H 8M5 Canada.,Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, K1H 8M5 Canada
| | - Elizabeth Walden
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, K1H 8M5 Canada.,Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, K1H 8M5 Canada
| | - Sylvain Huard
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, K1H 8M5 Canada.,Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, K1H 8M5 Canada
| | - John Pezacki
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, K1H 8M5 Canada.,Department of Chemistry and Biomolecular Sciences, Faculty of Science, University of Ottawa, Ottawa K1N6N5 Canada
| | - Morgan D Fullerton
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, K1H 8M5 Canada
| | - Kristin Baetz
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, K1H 8M5 Canada.,Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, K1H 8M5 Canada.,Department of Biological Sciences, Faculty of Science, University of Calgary, Calgary T2N 1N4, Canada
| |
Collapse
|
13
|
Hooper CM, Castleden IR, Tanz SK, Grasso SV, Millar AH. Subcellular Proteomics as a Unified Approach of Experimental Localizations and Computed Prediction Data for Arabidopsis and Crop Plants. Adv Exp Med Biol 2022; 1346:67-89. [PMID: 35113396 DOI: 10.1007/978-3-030-80352-0_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
In eukaryotic organisms, subcellular protein location is critical in defining protein function and understanding sub-functionalization of gene families. Some proteins have defined locations, whereas others have low specificity targeting and complex accumulation patterns. There is no single approach that can be considered entirely adequate for defining the in vivo location of all proteins. By combining evidence from different approaches, the strengths and weaknesses of different technologies can be estimated, and a location consensus can be built. The Subcellular Location of Proteins in Arabidopsis database ( http://suba.live/ ) combines experimental data sets that have been reported in the literature and is analyzing these data to provide useful tools for biologists to interpret their own data. Foremost among these tools is a consensus classifier (SUBAcon) that computes a proposed location for all proteins based on balancing the experimental evidence and predictions. Further tools analyze sets of proteins to define the abundance of cellular structures. Extending these types of resources to plant crop species has been complex due to polyploidy, gene family expansion and contraction, and the movement of pathways and processes within cells across the plant kingdom. The Crop Proteins of Annotated Location database ( http://crop-pal.org/ ) has developed a range of subcellular location resources including a species-specific voting consensus for 12 plant crop species that offers collated evidence and filters for current crop proteomes akin to SUBA. Comprehensive cross-species comparison of these data shows that the sub-cellular proteomes (subcellulomes) depend only to some degree on phylogenetic relationship and are more conserved in major biosynthesis than in metabolic pathways. Together SUBA and cropPAL created reference subcellulomes for plants as well as species-specific subcellulomes for cross-species data mining. These data collections are increasingly used by the research community to provide a subcellular protein location layer, inform models of compartmented cell function and protein-protein interaction network, guide future molecular crop breeding strategies, or simply answer a specific question-where is my protein of interest inside the cell?
Collapse
Affiliation(s)
- Cornelia M Hooper
- The Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA, Australia
| | - Ian R Castleden
- The Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA, Australia
| | - Sandra K Tanz
- The Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA, Australia
| | - Sally V Grasso
- The Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA, Australia
| | - A Harvey Millar
- The Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA, Australia.
| |
Collapse
|
14
|
Maekawa H, Otsubo M, Sato MP, Takahashi T, Mizoguchi K, Koyamatsu D, Inaba T, Ito-Inaba Y. Establishing an efficient protoplast transient expression system for investigation of floral thermogenesis in aroids. Plant Cell Rep 2022; 41:263-275. [PMID: 34704119 DOI: 10.1007/s00299-021-02806-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 10/15/2021] [Indexed: 06/13/2023]
Abstract
Floral thermogenesis is an important reproductive strategy for attracting pollinators. We developed essential biological tools for studying floral thermogenesis using two species of thermogenic aroids, Symplocarpus renifolius and Alocasia odora. Aroids contain many species with intense heat-producing abilities in their inflorescences. Several genes have been proposed to be involved in thermogenesis of these species, but biological tools for gene functional analyses are lacking. In this study, we aimed to develop a protoplast-based transient expression (PTE) system for the study of thermogenic aroids. Initially, we focused on skunk cabbage (Symplocarpus renifolius) because of its ability to produce intense as well as durable heat. In this plant, leaf protoplasts were isolated from potted and shoot tip-cultured plants with high efficiency (ca. 1.0 × 105/g fresh weight), and more than half of these protoplasts were successfully transfected. Using this PTE system, we determined the protein localization of three mitochondrial energy-dissipating proteins, SrAOX, SrUCPA, and SrNDA1, fused to green fluorescent protein (GFP). These three GFP-fused proteins were localized in MitoTracker-stained mitochondria in leaf protoplasts, although the green fluorescent particles in protoplasts expressing SrUCPA-GFP were significantly enlarged. Finally, to assess whether the PTE system established in the leaves of S. renifolius is applicable for floral tissues of thermogenic aroids, inflorescences of S. renifolius and another thermogenic aroid (Alocasia odora) were used. Although protoplasts were successfully isolated from several tissues of the inflorescences, PTE systems worked well only for the protoplasts isolated from the female parts (slightly thermogenic or nonthermogenic) of A. odora inflorescences. Our developed system has a potential to be widely used in inflorescences as well as leaves in thermogenic aroids and therefore may be a useful biological tool for investigating floral thermogenesis.
Collapse
Affiliation(s)
- Haruhiko Maekawa
- Department of Agricultural and Environmental Sciences, Faculty of Agriculture, University of Miyazaki, 1-1 Gakuenkibanadai-nishi, Miyazaki, 889-2192, Japan
| | - Miyabi Otsubo
- Department of Agricultural and Environmental Sciences, Faculty of Agriculture, University of Miyazaki, 1-1 Gakuenkibanadai-nishi, Miyazaki, 889-2192, Japan
| | - Mitsuhiko P Sato
- Department of Frontier Research and Development, Kazusa DNA Research Institute, 2-6-7 Kazusakamatari, Kisarazu, Chiba, 292-0818, Japan
| | - Tomoko Takahashi
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Shimo-Okubo 255, Sakura-ku, Saitama, 338-8570, Japan
| | - Koichiro Mizoguchi
- Department of Agricultural and Environmental Sciences, Faculty of Agriculture, University of Miyazaki, 1-1 Gakuenkibanadai-nishi, Miyazaki, 889-2192, Japan
| | - Daiki Koyamatsu
- Department of Agricultural and Environmental Sciences, Faculty of Agriculture, University of Miyazaki, 1-1 Gakuenkibanadai-nishi, Miyazaki, 889-2192, Japan
| | - Takehito Inaba
- Department of Agricultural and Environmental Sciences, Faculty of Agriculture, University of Miyazaki, 1-1 Gakuenkibanadai-nishi, Miyazaki, 889-2192, Japan
| | - Yasuko Ito-Inaba
- Department of Agricultural and Environmental Sciences, Faculty of Agriculture, University of Miyazaki, 1-1 Gakuenkibanadai-nishi, Miyazaki, 889-2192, Japan.
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, 980-8577, Japan.
| |
Collapse
|
15
|
Shelton SN, Smith SE, Jaspersen SL. Split-GFP Complementation to Study the Nuclear Membrane Proteome Using Microscopy. Methods Mol Biol 2022; 2502:205-213. [PMID: 35412240 DOI: 10.1007/978-1-0716-2337-4_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Defining the proteome of any given subcellular compartment provides insight into the activities and functions within that organelle. Understanding the composition of the nuclear envelope (NE) using traditional methods such as biochemical subcellular fractionation has been challenging due to the continuity of the NE and the endoplasmic reticulum. Here, we describe how split green fluorescent protein (split-GFP) was adapted to determine and define the NE proteome. This system is able to resolve protein topology and distinguish localization to the inner or outer nuclear membranes (INM or ONM).
Collapse
Affiliation(s)
- Shary N Shelton
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Sarah E Smith
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Sue L Jaspersen
- Stowers Institute for Medical Research, Kansas City, MO, USA.
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS, USA.
| |
Collapse
|
16
|
Jiang Y, Wang D, Yao Y, Eubel H, Künzler P, Møller IM, Xu D. MULocDeep: A deep-learning framework for protein subcellular and suborganellar localization prediction with residue-level interpretation. Comput Struct Biotechnol J 2021; 19:4825-4839. [PMID: 34522290 PMCID: PMC8426535 DOI: 10.1016/j.csbj.2021.08.027] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 08/16/2021] [Accepted: 08/16/2021] [Indexed: 12/18/2022] Open
Abstract
Prediction of protein localization plays an important role in understanding protein function and mechanisms. In this paper, we propose a general deep learning-based localization prediction framework, MULocDeep, which can predict multiple localizations of a protein at both subcellular and suborganellar levels. We collected a dataset with 44 suborganellar localization annotations in 10 major subcellular compartments—the most comprehensive suborganelle localization dataset to date. We also experimentally generated an independent dataset of mitochondrial proteins in Arabidopsis thaliana cell cultures, Solanum tuberosum tubers, and Vicia faba roots and made this dataset publicly available. Evaluations using the above datasets show that overall, MULocDeep outperforms other major methods at both subcellular and suborganellar levels. Furthermore, MULocDeep assesses each amino acid’s contribution to localization, which provides insights into the mechanism of protein sorting and localization motifs. A web server can be accessed at http://mu-loc.org.
Collapse
Affiliation(s)
- Yuexu Jiang
- Department of Electrical Engineering and Computer Science, Bond Life Sciences Center, Columbia, MO, USA
| | - Duolin Wang
- Department of Electrical Engineering and Computer Science, Bond Life Sciences Center, Columbia, MO, USA
| | - Yifu Yao
- Department of Electrical Engineering and Computer Science, Bond Life Sciences Center, Columbia, MO, USA
| | - Holger Eubel
- Institute of Plant Genetics, Leibniz University Hannover, Hannover, Germany
| | - Patrick Künzler
- Institute of Plant Genetics, Leibniz University Hannover, Hannover, Germany
| | - Ian Max Møller
- Department of Molecular Biology and Genetics, Aarhus University, Forsøgsvej 1, DK-4200 Slagelse, Denmark
| | - Dong Xu
- Department of Electrical Engineering and Computer Science, Bond Life Sciences Center, Columbia, MO, USA
| |
Collapse
|
17
|
Raghu P, Basak B, Krishnan H. Emerging perspectives on multidomain phosphatidylinositol transfer proteins. Biochim Biophys Acta Mol Cell Biol Lipids 2021; 1866:158984. [PMID: 34098114 PMCID: PMC7611342 DOI: 10.1016/j.bbalip.2021.158984] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 05/23/2021] [Accepted: 05/25/2021] [Indexed: 12/09/2022]
Abstract
The phosphatidylinositol transfer protein domain (PITPd) is an evolutionarily conserved protein that is able to transfer phosphatidylinositol between membranes in vitro and in vivo. However some animal genomes also include genes that encode proteins where the PITPd is found in cis with a number of additional domains and recent large scale genome sequencing efforts indicate that this type of multidomain architecture is widespread in the animal kingdom. In Drosophila photoreceptors, the multidomain phosphatidylinositol transfer protein RDGB is required to regulate phosphoinositide turnover during G-protein activated phospholipase C signalling. Recent studies in flies and mammalian cell culture models have begun to elucidate functions for the non-PITPd of RDGB and its vertebrate orthologs. We review emerging evidence on the genomics, functional and cell biological perspectives of these multi-domain PITPd containing proteins.
Collapse
Affiliation(s)
- Padinjat Raghu
- National Centre for Biological Sciences, TIFR-GKVK Campus, Bellary Road, Bengaluru 560065, India.
| | - Bishal Basak
- National Centre for Biological Sciences, TIFR-GKVK Campus, Bellary Road, Bengaluru 560065, India
| | - Harini Krishnan
- National Centre for Biological Sciences, TIFR-GKVK Campus, Bellary Road, Bengaluru 560065, India
| |
Collapse
|
18
|
Brock AM, Jutras BL. A simple method to detect Borrelia burgdorferi sensu lato proteins in different sub-cellular compartments by immunofluorescence. Ticks Tick Borne Dis 2021; 12:101808. [PMID: 34455142 DOI: 10.1016/j.ttbdis.2021.101808] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 07/20/2021] [Accepted: 07/28/2021] [Indexed: 01/15/2023]
Abstract
Spirochaetes constitute a unique phylum of bacteria, many of which cause severe clinical diseases. Borrelia burgdorferi sensu lato (B. burgdorferi s.l.)-the primary agent of Lyme borreliosis (LB)-is a quintessential member of this poorly understood phylum and the leading cause of tick-borne illness throughout most of the northern hemisphere. Despite its importance in human health, we lack a fundamental understanding of how B. burgdorferi s.l. is able to accomplish basic physiological tasks, such as DNA replication/segregation, and cell elongation or division. Recent advances in molecular tools to probe these essential cellular processes are great strides forward but require genetic manipulation. The latter is important since not all agents of LB are genetically tractable. Here, we describe a single method that is capable of fluorescently labeling B. burgdorferi s.l. proteins in different sub-cellular compartments. A comparative analysis of six different methods indicates that our optimized procedure outperforms all others and is the first to localize a cytoplasmic protein in B. burgdorferi s.l. by immunofluorescence. We contend that this strategy could be easily adapted to study the localization of any protein, in many Borrelia genospecies, information that will yield functional insights into the complex biology of this fascinating group of bacteria. In addition, it may provide new avenues of research in both in situ studies and in Lyme diagnostics.
Collapse
|
19
|
Fields C, Levin M. Metabolic limits on classical information processing by biological cells. Biosystems 2021; 209:104513. [PMID: 34450208 DOI: 10.1016/j.biosystems.2021.104513] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/14/2021] [Accepted: 08/14/2021] [Indexed: 01/16/2023]
Abstract
Biological information processing is generally assumed to be classical. Measured cellular energy budgets of both prokaryotes and eukaryotes, however, fall orders of magnitude short of the power required to maintain classical states of protein conformation and localization at the Å, fs scales predicted by single-molecule decoherence calculations and assumed by classical molecular dynamics models. We suggest that decoherence is limited to the immediate surroundings of the cell membrane and of intercompartmental boundaries within the cell, and that bulk cellular biochemistry implements quantum information processing. Detection of Bell-inequality violations in responses to perturbation of recently-separated sister cells would provide a sensitive test of this prediction. If it is correct, modeling both intra- and intercellular communication requires quantum theory.
Collapse
|
20
|
Manina G, Dhar N. Single-Cell Analysis of Mycobacteria Using Microfluidics and Time-Lapse Microscopy. Methods Mol Biol 2021; 2314:205-29. [PMID: 34235654 DOI: 10.1007/978-1-0716-1460-0_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Studies on cell-to-cell phenotypic variation in microbial populations, with individuals sharing the same genetic background, provide insights not only on bacterial behavior but also on the adaptive spectrum of the population. Phenotypic variation is an innate property of microbial populations, and this can be further amplified under stressful conditions, providing a fitness advantage. Furthermore, phenotypic variation may also precede a latter step of genetic-based diversification, resulting in the transmission of the most beneficial phenotype to the progeny. While population-wide studies provide a measure of the collective average behavior, single-cell studies, which have expanded over the last decade, delve into the behavior of smaller subpopulations that would otherwise remain concealed. In this chapter, we describe approaches to carry out spatiotemporal analysis of individual mycobacterial cells using time-lapse microscopy. Our method encompasses the fabrication of a microfluidic device; the assembly of a microfluidic system suitable for long-term imaging of mycobacteria; and the quantitative analysis of single-cell behavior under varying growth conditions. Phenotypic variation is conceivably associated to the resilience and endurance of mycobacterial cells. Therefore, shedding light on the dynamics of this phenomenon, on the transience or stability of the given phenotype, on its molecular bases and its functional consequences, offers new scope for intervention.
Collapse
|
21
|
Wolpe AG, Ruddiman CA, Hall PJ, Isakson BE. Polarized Proteins in Endothelium and Their Contribution to Function. J Vasc Res 2021; 58:65-91. [PMID: 33503620 DOI: 10.1159/000512618] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 10/27/2020] [Indexed: 12/11/2022] Open
Abstract
Protein localization in endothelial cells is tightly regulated to create distinct signaling domains within their tight spatial restrictions including luminal membranes, abluminal membranes, and interendothelial junctions, as well as caveolae and calcium signaling domains. Protein localization in endothelial cells is also determined in part by the vascular bed, with differences between arteries and veins and between large and small arteries. Specific protein polarity and localization is essential for endothelial cells in responding to various extracellular stimuli. In this review, we examine protein localization in the endothelium of resistance arteries, with occasional references to other vessels for contrast, and how that polarization contributes to endothelial function and ultimately whole organism physiology. We highlight the protein localization on the luminal surface, discussing important physiological receptors and the glycocalyx. The protein polarization to the abluminal membrane is especially unique in small resistance arteries with the presence of the myoendothelial junction, a signaling microdomain that regulates vasodilation, feedback to smooth muscle cells, and ultimately total peripheral resistance. We also discuss the interendothelial junction, where tight junctions, adherens junctions, and gap junctions all convene and regulate endothelial function. Finally, we address planar cell polarity, or axial polarity, and how this is regulated by mechanosensory signals like blood flow.
Collapse
Affiliation(s)
- Abigail G Wolpe
- Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, Virginia, USA.,Department of Cell Biology, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Claire A Ruddiman
- Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, Virginia, USA.,Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Phillip J Hall
- Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Brant E Isakson
- Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, Virginia, USA, .,Department of Molecular Physiology and Biophysics, University of Virginia School of Medicine, Charlottesville, Virginia, USA,
| |
Collapse
|
22
|
Suzuki S, Hatano Y, Yoshii T, Tsukiji S. Chemogenetic Control of Protein Localization and Mammalian Cell Signaling by SLIPT. Methods Mol Biol 2021; 2312:237-251. [PMID: 34228294 DOI: 10.1007/978-1-0716-1441-9_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Chemical control of protein localization is a powerful approach for manipulating mammalian cellular processes. Self-localizing ligand-induced protein translocation (SLIPT) is an emerging platform that enables control of protein localization in living mammalian cells using synthetic self-localizing ligands (SLs). We recently established a chemogenetic SLIPT system, in which any protein of interest fused to an engineered variant of Escherichia coli dihydrofolate reductase, DHFRiK6, can be rapidly and specifically translocated from the cytoplasm to the inner leaflet of the plasma membrane (PM) using a trimethoprim (TMP)-based PM-targeting SL, mDcTMP. The mDcTMP-mediated PM recruitment of DHFRiK6-fusion proteins can be efficiently returned to the cytoplasm by subsequent addition of free TMP, enabling temporal and reversible control over the protein localization. Here we describe the use of this mDcTMP/DHFRiK6-based SLIPT system for inducing (1) reversible protein translocation and (2) synthetic activation of the Raf/ERK pathway. This system provides a simple and versatile tool in mammalian synthetic biology for temporally manipulating various signaling molecules and pathways at the PM.
Collapse
Affiliation(s)
- Sachio Suzuki
- Department of Nanopharmaceutical Sciences, Nagoya Institute of Technology, Showa-ku, Nagoya, Japan
| | - Yuka Hatano
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya, Japan
| | - Tatsuyuki Yoshii
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya, Japan
- PRESTO, Japan Science and Technology Agency (JST), Kawaguchi, Saitama, Japan
| | - Shinya Tsukiji
- Department of Nanopharmaceutical Sciences, Nagoya Institute of Technology, Showa-ku, Nagoya, Japan.
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya, Japan.
| |
Collapse
|
23
|
Sagar S, Deepika, Biswas DK, Chandrasekar R, Singh A. Genome-wide identification, structure analysis and expression profiling of phospholipases D under hormone and abiotic stress treatment in chickpea (Cicer arietinum). Int J Biol Macromol 2020; 169:264-273. [PMID: 33338528 DOI: 10.1016/j.ijbiomac.2020.12.102] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 12/09/2020] [Accepted: 12/13/2020] [Indexed: 12/19/2022]
Abstract
Phospholipases D (PLDs) are phospholipid hydrolyzing enzymes and crucial components of lipid signaling in plants. PLDs are implicated in stress responses in different plants however, characterization of PLDs in chickpea is missing. Here, we identify 13 PLD genes in the chickpea genome. PLD family could be divided into α, β, δ, ε and ζ isoforms based on sequence and structure. Protein remodeling described that chickpea PLDs are composed of defined arrangements of α-helix, β-sheets and short loops. Phylogenetic analysis suggested evolutionary conservation of chickpea PLD family with dicots. In-planta subcellular localization showed the plasma membrane localization of chickpea PLDs. All PLD promoters had hormone and stress related cis-regulatory elements, which suggested overlapping function of PLDs in hormone and abiotic stress signaling. The qRT-PCR expression analysis revealed that most PLD genes are differentially expressed in multiple abiotic stresses (drought, salt and cold stress). Moreover, several PLD genes had overlapping expression in abiotic stress and ABA and JA treatment. These observations indicate the involvement of PLD gene family in cross-talk of phytohormone and abiotic stress signaling in chickpea. Thus, present study opens new avenues of utilizing PLD related information for understanding hormone-regulated abiotic stress signaling in legume crops.
Collapse
Affiliation(s)
- Sushma Sagar
- National Institute of Plant Genome Research, New Delhi 110067, India
| | - Deepika
- National Institute of Plant Genome Research, New Delhi 110067, India
| | | | | | - Amarjeet Singh
- National Institute of Plant Genome Research, New Delhi 110067, India.
| |
Collapse
|
24
|
Waite JM, Collum TD, Dardick C. AtDRO1 is nuclear localized in root tips under native conditions and impacts auxin localization. Plant Mol Biol 2020; 103:197-210. [PMID: 32130643 PMCID: PMC7170825 DOI: 10.1007/s11103-020-00984-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 02/20/2020] [Indexed: 05/19/2023]
Abstract
DEEPER ROOTING 1 (DRO1) contributes to the downward gravitropic growth trajectory of roots upstream of lateral auxin transport in monocots and dicots. Loss of DRO1 function leads to horizontally oriented lateral roots and altered gravitropic set point angle, while loss of all three DRO family members results in upward, vertical root growth. Here, we attempt to dissect the roles of AtDRO1 by analyzing expression, protein localization, auxin gradient formation, and auxin responsiveness in the atdro1 mutant. Current evidence suggests AtDRO1 is predominantly a membrane-localized protein. Here we show that VENUS-tagged AtDRO1 driven by the native AtDRO1 promoter complemented an atdro1 Arabidopsis mutant and the protein was localized in root tips and detectable in nuclei. atdro1 primary and lateral roots showed impairment in establishing an auxin gradient upon gravistimulation as visualized with DII-VENUS, a sensor for auxin signaling and proxy for relative auxin distribution. Additionally, PIN3 domain localization was not significantly altered upon gravistimulation in atdro1 primary and lateral roots. RNA-sequencing revealed differential expression of known root development-related genes in atdro1 mutants. atdro1 lateral roots were able to respond to exogenous auxin and AtDRO1 gene expression levels in root tips were unaffected by the addition of auxin. Collectively, the data suggest that nuclear localization may be important for AtDRO1 function and suggests a more nuanced role for DRO1 in regulating auxin-mediated changes in lateral branch angle. KEY MESSAGE: DEEPER ROOTING 1 (DRO1) when expressed from its native promoter is predominately localized in Arabidopsis root tips, detectable in nuclei, and impacts auxin gradient formation.
Collapse
Affiliation(s)
- Jessica M Waite
- Washington State University Tree Fruit Research and Extension Center, Wenatchee, WA, 98801, USA
- USDA-ARS Appalachian Fruit Research Station, Kearneysville, WV, 25430, USA
| | - Tamara D Collum
- USDA-ARS Appalachian Fruit Research Station, Kearneysville, WV, 25430, USA
| | - Chris Dardick
- USDA-ARS Appalachian Fruit Research Station, Kearneysville, WV, 25430, USA.
| |
Collapse
|
25
|
Gao Y, Wilson GR, Stephenson SEM, Oulad-Abdelghani M, Charlet-Berguerand N, Bozaoglu K, McLean CA, Thomas PQ, Finkelstein DI, Lockhart PJ. Distribution of Parkinson's disease associated RAB39B in mouse brain tissue. Mol Brain 2020; 13:52. [PMID: 32228644 PMCID: PMC7106796 DOI: 10.1186/s13041-020-00584-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 03/10/2020] [Indexed: 12/22/2022] Open
Abstract
Pathogenic variants in the gene encoding the small GTPase Ras analogue in Brain 39b (RAB39B) are associated with early-onset parkinsonism. In this study we investigated the expression and localization of RAB39B (RNA and protein) in mouse brain tissue to gain a better understanding of its normal physiological function(s) and role in disease. We developed novel resources, including monoclonal antibodies directed against RAB39B and mice with Rab39b knockout, and performed real-time PCR and western blot analysis on whole brain lysates. To determine the spatial localization of Rab39b RNA and protein, we performed in-situ hybridization and immunohistochemistry on fresh frozen and fixed brain tissue. Our results show that RAB39B is localized throughout the cortex, hippocampus and substantia nigra of mice throughout postnatal life. We found high levels of RAB39B within MAP2 positive cortical and hippocampal neurons, and TH positive dopaminergic neurons in the substantia nigra pars compacta. Our studies support and extend current knowledge of the localization of RAB39B. We validate RAB39B as a neuron-enriched protein and demonstrate that it is present throughout the mouse cortex and hippocampus. Further, we observe high levels in the substantia nigra pars compacta, the brain region most affected in Parkinson’s disease pathology. The distribution of Rab39b is consistent with human disease associations with parkinsonism and cognitive impairment. We also describe and validate novel resources, including monoclonal antibodies directed against RAB39B and mice with Rab39b knockout, both of which are valuable tools for future studies of the molecular function of RAB39B.
Collapse
Affiliation(s)
- Yujing Gao
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Children's Research Institute, 50 Flemington Road, Parkville, Victoria, 3052, Australia.,Department of Paediatrics, The University of Melbourne, 30 Royal Parade, Parkville, Victoria, 3052, Australia
| | - Gabrielle R Wilson
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Children's Research Institute, 50 Flemington Road, Parkville, Victoria, 3052, Australia.,Department of Paediatrics, The University of Melbourne, 30 Royal Parade, Parkville, Victoria, 3052, Australia
| | - Sarah E M Stephenson
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Children's Research Institute, 50 Flemington Road, Parkville, Victoria, 3052, Australia.,Department of Paediatrics, The University of Melbourne, 30 Royal Parade, Parkville, Victoria, 3052, Australia
| | - Mustapha Oulad-Abdelghani
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U964, CNRS UMR7104, Strasbourg University, 67400, Illkirch, France
| | - Nicolas Charlet-Berguerand
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U964, CNRS UMR7104, Strasbourg University, 67400, Illkirch, France
| | - Kiymet Bozaoglu
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Children's Research Institute, 50 Flemington Road, Parkville, Victoria, 3052, Australia.,Department of Paediatrics, The University of Melbourne, 30 Royal Parade, Parkville, Victoria, 3052, Australia
| | - Catriona A McLean
- Anatomical Pathology, Alfred Hospital, Melbourne, Victoria, 3004, Australia
| | - Paul Q Thomas
- Robinson Research Institute and School of Medicine, University of Adelaide, Adelaide, SA, 5005, Australia
| | - David I Finkelstein
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, 30 Royal Parade, Parkville, Victoria, 3052, Australia
| | - Paul J Lockhart
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Children's Research Institute, 50 Flemington Road, Parkville, Victoria, 3052, Australia. .,Department of Paediatrics, The University of Melbourne, 30 Royal Parade, Parkville, Victoria, 3052, Australia.
| |
Collapse
|
26
|
Abstract
Background Understanding cellular responses via signal transduction is a core focus in systems biology. Tools to automatically reconstruct signaling pathways from protein-protein interactions (PPIs) can help biologists generate testable hypotheses about signaling. However, automatic reconstruction of signaling pathways suffers from many interactions with the same confidence score leading to many equally good candidates. Further, some reconstructions are biologically misleading due to ignoring protein localization information. Results We propose LocPL, a method to improve the automatic reconstruction of signaling pathways from PPIs by incorporating information about protein localization in the reconstructions. The method relies on a dynamic program to ensure that the proteins in a reconstruction are localized in cellular compartments that are consistent with signal transduction from the membrane to the nucleus. LocPL and existing reconstruction algorithms are applied to two PPI networks and assessed using both global and local definitions of accuracy. LocPL produces more accurate and biologically meaningful reconstructions on a versatile set of signaling pathways. Conclusion LocPL is a powerful tool to automatically reconstruct signaling pathways from PPIs that leverages cellular localization information about proteins. The underlying dynamic program and signaling model are flexible enough to study cellular signaling under different settings of signaling flow across the cellular compartments.
Collapse
Affiliation(s)
- Ibrahim Youssef
- Biomedical Engineering Department, Cairo University, Giza, 12613, Egypt.,Biology Department, Reed College, Portland, OR 97202, USA
| | - Jeffrey Law
- Genetics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, VA 24061, USA
| | - Anna Ritz
- Biology Department, Reed College, Portland, OR 97202, USA.
| |
Collapse
|
27
|
Kurotani A, Tokmakov AA, Sato KI, Stefanov VE, Yamada Y, Sakurai T. Localization-specific distributions of protein pI in human proteome are governed by local pH and membrane charge. BMC Mol Cell Biol 2019; 20:36. [PMID: 31429701 DOI: 10.1186/s12860-019-0221-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 08/08/2019] [Indexed: 11/10/2022] Open
Abstract
Background Whole-proteome distributions of protein isoelectric point (pI) values in different organisms are bi- or trimodal with some variations. It was suggested that the observed multimodality of the proteome-wide pI distributions is associated with subcellular localization-specific differences in the local pI distributions. However, the factors responsible for variation of the intracellular localization-specific pI profiles have not been investigated in detail. Results In this work, we explored proteome-wide pI distributions of 32,138 human proteins predicted to reside in 10 subcellular compartments, as well as the pI distributions of experimentally observed lysosomal and Golgi proteins. The distributions were found to differ significantly, although all of them adhered to the major recurrent bimodal pattern. Grossly, acid-biased and alkaline-biased patterns with various minor statistical features were observed at different subcellular locations. Bioinformatics analysis revealed the existence of strong statistically significant correlations between protein pI and subcellular localization. Most markedly, protein pI was found to correlate positively with nuclear and mitochondrial locations and negatively with cytoskeletal, cytoplasmic, lysosomal and peroxisomal environment. Further analysis demonstrated that subcellular compartment-specific pI distributions are greatly influenced by local pH and organelle membrane charge. Multiple nonlinear regression analysis identified a polynomial function of the two variables that best fitted the mean pI values of the localization-specific pI distributions. A high coefficient of determination calculated for this regression (R2 = 0.98) suggests that local pH and organelle membrane charge are the major factors responsible for variation of the intracellular localization-specific pI profiles. Conclusions Our study demonstrates that strong correlations exist between protein pI and subcellular localization. The specific pI distributions at different subcellular locations are defined by local environment. Predominantly, it is the local pH and membrane charge that shape the organelle-specific protein pI patterns. These findings expand our understanding of spatial organization of the human proteome. Electronic supplementary material The online version of this article (10.1186/s12860-019-0221-4) contains supplementary material, which is available to authorized users.
Collapse
|
28
|
Luo J, Liu H, Luan S, Li Z. Guidance of circular RNAs to proteins' behavior as binding partners. Cell Mol Life Sci 2019; 76:4233-4243. [PMID: 31270581 DOI: 10.1007/s00018-019-03216-z] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 06/08/2019] [Accepted: 06/28/2019] [Indexed: 12/20/2022]
Abstract
Circular RNAs (circRNAs) are single-stranded and covalently closed back-splicing products of pre-mRNAs. They can be derived from exons, introns, or exons with intron retained between exons of transcripts, as well as antisense transcripts. CircRNAs have been reported to function as microRNA sponges, regulate gene transcription mediated by RNA polymerase II, and modulate the splicing or stability of mRNA. However, emerging studies demonstrate that they affect the behavior of proteins via direct interactions with them. Here, we summarize that by binding directly with proteins; circRNAs can facilitate their nuclear or cytoplasmic localizations, regulate their functions or stability, promote or inhibit the interactions between them, or influence the interactions between them and DNA. Furthermore, these circRNA-binding proteins contain transcription factors, RNA processing proteins, proteases, and some other RNA-binding proteins. As a consequence, circRNAs are involved in the regulation of multiple physiological or pathological processes, including tumorigenesis, atherosclerosis, wound repair, cardiac senescence, myocardial ischemia/reperfusion injury, and so forth. Nonetheless, it is worthwhile to further explore more types of proteins that interact with circRNAs, which would be helpful in revealing other unknown biological functions of circRNAs that guide the variation in behavior of cellular proteins.
Collapse
Affiliation(s)
- Junyun Luo
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha, 410082, Hunan, China
| | - Hui Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha, 410082, Hunan, China
| | - Siyu Luan
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha, 410082, Hunan, China
| | - Zhaoyong Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha, 410082, Hunan, China.
| |
Collapse
|
29
|
Bodensohn US, Simm S, Fischer K, Jäschke M, Groß LE, Kramer K, Ehmann C, Rensing SA, Ladig R, Schleiff E. The intracellular distribution of the components of the GET system in vascular plants. Biochim Biophys Acta Mol Cell Res 2019; 1866:1650-1662. [PMID: 31233800 DOI: 10.1016/j.bbamcr.2019.06.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Revised: 06/17/2019] [Accepted: 06/19/2019] [Indexed: 12/16/2022]
Abstract
The guided entry of tail-anchored proteins (GET) pathway facilitates targeting and insertion of tail-anchored proteins into membranes. In plants, such a protein insertion machinery for the endoplasmic reticulum as well as constituents within mitochondrial and chloroplasts were discovered. Previous phylogenetic analysis revealed that Get3 sequences of Embryophyta form two clades representing cytosolic ("a") and organellar ("bc") GET3 homologs, respectively. Cellular fractionation of Arabidopsis thaliana seedlings and usage of the self-assembly GFP system in protoplasts verified the cytosolic (ATGet3a), plastidic (ATGet3b) and mitochondrial (ATGet3c) localization of the different homologs. The identified plant homologs of Get1 and Get4 in A. thaliana are localized in ER and cytosol, respectively, implicating a degree of conservation of the GET pathway in A. thaliana. Transient expression of Get3 homologs of Solanum lycopersicum, Medicago × varia or Physcomitrella patens with the self-assembly GFP technique in homologous and heterologous systems verified that multiple Get3 homologs with differing subcellular localizations are common in plants. Chloroplast localized Get3 homologs were detected in all tested plant systems. In contrast, mitochondrial localized Get3 homologs were not identified in S. lycopersicum, or P. patens, while we confirmed on the example of A. thaliana proteins that mitochondrial localized Get3 proteins are properly targeted in S. lycopersicum as well.
Collapse
Affiliation(s)
- Uwe S Bodensohn
- Institute for Molecular Biosciences, Goethe University Frankfurt am Main, Max-von-Laue Str. 9, D-60438 Frankfurt, Germany
| | - Stefan Simm
- Institute for Molecular Biosciences, Goethe University Frankfurt am Main, Max-von-Laue Str. 9, D-60438 Frankfurt, Germany; Frankfurt Institute of Advanced Studies, Ruth-Moufang-Straße 1, D-60438 Frankfurt, Germany
| | - Ken Fischer
- Institute for Molecular Biosciences, Goethe University Frankfurt am Main, Max-von-Laue Str. 9, D-60438 Frankfurt, Germany
| | - Michelle Jäschke
- Institute for Molecular Biosciences, Goethe University Frankfurt am Main, Max-von-Laue Str. 9, D-60438 Frankfurt, Germany
| | - Lucia E Groß
- Institute for Molecular Biosciences, Goethe University Frankfurt am Main, Max-von-Laue Str. 9, D-60438 Frankfurt, Germany
| | - Katharina Kramer
- Institute for Molecular Biosciences, Goethe University Frankfurt am Main, Max-von-Laue Str. 9, D-60438 Frankfurt, Germany
| | - Christian Ehmann
- Institute for Molecular Biosciences, Goethe University Frankfurt am Main, Max-von-Laue Str. 9, D-60438 Frankfurt, Germany
| | - Stefan A Rensing
- Faculty of Biology, University of Marburg, Karl-von-Frisch-Str. 8, D-35043 Marburg, Germany
| | - Roman Ladig
- Institute for Molecular Biosciences, Goethe University Frankfurt am Main, Max-von-Laue Str. 9, D-60438 Frankfurt, Germany
| | - Enrico Schleiff
- Institute for Molecular Biosciences, Goethe University Frankfurt am Main, Max-von-Laue Str. 9, D-60438 Frankfurt, Germany; Buchman Institute for Molecular Life Sciences, Goethe University Frankfurt am Main, Max-von-Laue Str. 15, D-60438 Frankfurt, Germany; Frankfurt Institute of Advanced Studies, Ruth-Moufang-Straße 1, D-60438 Frankfurt, Germany.
| |
Collapse
|
30
|
Luz JS, Caneguim BH, Baggio A, Santoni MM, Helbing CC, Valentini SR, Sasso-Cerri E, Oliveira CC. Differential expression of RNA exosome subunits in the amphibian Lithobates catesbeianus during reproductive and non-reproductive periods. BMC Res Notes 2019; 12:46. [PMID: 30665462 PMCID: PMC6341637 DOI: 10.1186/s13104-019-4077-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 01/11/2019] [Indexed: 11/20/2022] Open
Abstract
Objective The RNA exosome is an evolutionarily conserved 3′–5′ exoribonucleolytic protein complex involved in processing and degradation of different classes of nuclear and cytoplasmic RNAs, and, therefore, important for the posttranscriptional control of gene expression. Despite the extensive in vivo functional studies and the structural data on the RNA exosome, few studies have been performed on the localization and expression of exosome subunits during gametogenesis, process during which gene expression is largely controlled at the posttranscriptional level. Results We report the identification of exosome subunits in Lithobates catesbeianus and analysis of the differential subcellular localization of RNA exosome core and catalytic subunits in testis cells. In addition, we show seasonal differences in the expression levels of four exosome subunits in different organs. In addition to being part of the RNA exosome complex, its subunits might participate independently of the complex in the control of gene expression during seasonal variation in bullfrog tissues. These results may be relevant for other eukaryotic species. Electronic supplementary material The online version of this article (10.1186/s13104-019-4077-7) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- J S Luz
- School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara, Brazil
| | - B H Caneguim
- Department of Morphology and Genetics, Federal University of São Paulo (UNIFESP), São Paulo, Brazil.,Federal University of Triângulo Mineiro (UFTM)-Iturama University Campus (UFTM-CIT), Iturama, Brazil
| | - A Baggio
- School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara, Brazil
| | - M M Santoni
- School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara, Brazil
| | - C C Helbing
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - S R Valentini
- School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara, Brazil
| | - E Sasso-Cerri
- Department of Morphology, Dental School of São Paulo State University, Araraquara, Brazil
| | - C C Oliveira
- Department of Biochemistry, Chemistry Institute, University of São Paulo, São Paulo, Brazil.
| |
Collapse
|
31
|
Abstract
The subcellular localization of proteins is a posttranslational modification of paramount importance. The ability to study subcellular and organelle proteomes improves our understanding of cellular homeostasis and cellular dynamics. In this chapter, we describe a protocol for the unbiased and high-throughput study of protein subcellular localization in the yeast Saccharomyces cerevisiae: hyperplexed localization of organelle proteins by isotope tagging (hyperLOPIT), which involves biochemical fractionation of Saccharomyces cerevisiae and high resolution mass spectrometry-based protein quantitation using TMT 10-plex isobaric tags. This protocol enables the determination of the subcellular localizations of thousands of proteins in parallel in a single experiment and thereby deep sampling and high-resolution mapping of the spatial proteome.
Collapse
Affiliation(s)
- Daniel J H Nightingale
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, UK
- Cambridge Systems Biology Centre, Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Stephen G Oliver
- Cambridge Systems Biology Centre, Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Kathryn S Lilley
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, UK.
- Cambridge Systems Biology Centre, Department of Biochemistry, University of Cambridge, Cambridge, UK.
| |
Collapse
|
32
|
Weill U, Krieger G, Avihou Z, Milo R, Schuldiner M, Davidi D. Assessment of GFP Tag Position on Protein Localization and Growth Fitness in Yeast. J Mol Biol 2018; 431:636-641. [PMID: 30550779 DOI: 10.1016/j.jmb.2018.12.004] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 11/05/2018] [Accepted: 12/05/2018] [Indexed: 11/30/2022]
Abstract
While protein tags are ubiquitously utilized in molecular biology, they harbor the potential to interfere with functional traits of their fusion counterparts. Systematic evaluation of the effect of protein tags on function would promote accurate use of tags in experimental setups. Here we examine the effect of green fluorescent protein tagging at either the N or C terminus of budding yeast proteins on subcellular localization and functionality. We use a competition-based approach to decipher the relative fitness of two strains tagged on the same protein but on opposite termini and from that infer the correct, physiological localization for each protein and the optimal position for tagging. Our study provides a first of a kind systematic assessment of the effect of tags on the functionality of proteins and provides a step toward broad investigation of protein fusion libraries.
Collapse
Affiliation(s)
- Uri Weill
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Gat Krieger
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Zohar Avihou
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ron Milo
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Dan Davidi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel.
| |
Collapse
|
33
|
Lu AX, Handfield LF, Moses AM. Extracting and Integrating Protein Localization Changes from Multiple Image Screens of Yeast Cells. Bio Protoc 2018; 8:e3022. [PMID: 34395810 DOI: 10.21769/bioprotoc.3022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 08/30/2018] [Accepted: 09/11/2018] [Indexed: 11/02/2022] Open
Abstract
The evaluation of protein localization changes in cells under diverse chemical and genetic perturbations is now possible due to the increasing quantity of screens that systematically image thousands of proteins in an organism. Integrating information from different screens provides valuable contextual information about the protein function. For example, proteins that change localization in response to many different stressful environmental perturbations may have different roles than those that only change in response to a few. We developed, to our knowledge, the first protocol that permits the quantitative comparison and clustering of protein localization changes across multiple screens. Our analysis allows for the exploratory analysis of proteins according to their pattern of localization changes across many different perturbations, potentially discovering new roles by association.
Collapse
Affiliation(s)
- Alex X Lu
- Department of Computer Science, University of Toronto, Toronto, Canada
| | | | - Alan M Moses
- Department of Computer Science, University of Toronto, Toronto, Canada.,Department of Cells and System Biology, University of Toronto, Toronto, Canada.,Center for Analysis of Genome Evolution and Function, University of Toronto, Toronto, Canada
| |
Collapse
|
34
|
Ravindran R, Polk P, Robinson LC, Tatchell K. New ubiquitin-dependent mechanisms regulating the Aurora B-protein phosphatase 1 balance in Saccharomyces cerevisiae. J Cell Sci 2018; 131:jcs.217620. [PMID: 30054382 DOI: 10.1242/jcs.217620] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 07/11/2018] [Indexed: 12/25/2022] Open
Abstract
Protein ubiquitylation regulates many cellular processes, including cell division. We report here a novel mutation altering the Saccharomyces cerevisiae E1 ubiquitin-activating enzyme (uba1-W928R) that suppresses the temperature sensitivity and chromosome loss phenotype of a well-characterized Aurora B mutant (ip1-2). The uba1-W928R mutation increases histone H3-S10 phosphorylation in the ipl1-2 strain, indicating that uba1-W928R acts by increasing Ipl1 activity and/or reducing the opposing protein phosphatase 1 (PP1; Glc7 in S. cerevisiae) phosphatase activity. Consistent with this hypothesis, Ipl1 protein levels and stability are elevated in the uba1-W928R mutant, likely mediated via the E2 enzymes Ubc4 and Cdc34. In contrast, the uba1-W928R mutation does not affect Glc7 stability, but exhibits synthetic lethality with several glc7 mutations. Moreover, uba1-W928R cells have an altered subcellular distribution of Glc7 and form nuclear Glc7 foci. These effects are likely mediated via the E2 enzymes Rad6 and Cdc34. Our new UBA1 allele reveals new roles for ubiquitylation in regulating the Ipl1-Glc7 balance in budding yeast. While ubiquitylation likely regulates Ipl1 protein stability via the canonical proteasomal degradation pathway, a non-canonical ubiquitin-dependent pathway maintains normal Glc7 localization and activity.This article has an associated First Person interview with the first author of the paper.
Collapse
Affiliation(s)
- Rini Ravindran
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, Shreveport, LA 71130, USA
| | - Paula Polk
- Research Core Facility Genomics Core, Louisiana State University Health Sciences Center, Shreveport, LA 71130, USA
| | - Lucy C Robinson
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, Shreveport, LA 71130, USA
| | - Kelly Tatchell
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, Shreveport, LA 71130, USA
| |
Collapse
|
35
|
Hoseini ASH, Mirzarezaee M. Prediction of Protein Sub-Mitochondria Locations Using Protein Interaction Networks. Iran J Biotechnol 2018; 16:e1933. [PMID: 31457027 PMCID: PMC6697825 DOI: 10.15171/ijb.1933] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 01/11/2018] [Accepted: 01/13/2018] [Indexed: 01/09/2023]
Abstract
Background Prediction of the protein localization is among the most important issues in the bioinformatics that is used for the prediction of the proteins in the cells and organelles such as mitochondria. In this study, several machine learning algorithms are applied for the prediction of the intracellular protein locations. These algorithms use the features extracted from protein sequences. In contrast, protein interactions have been less investigated. Objectives As protein interactions usually occur in the same or adjacent places, using this feature to find the location would be efficient and impressive. This study did not aim at increasing the total accuracy of the conducted research. The study has focused on the features of the proteins’ interaction and their employment which lead to a higher accuracy. Materials and Methods In this study, we have examined the protein interaction network as one of the features for prediction of the protein localization and its effects on the prediction results. In this regards, we have gathered some of the most common features including Amino Acid Composition, Dipeptide Compositions, Pseudo Amino Acid Compositions (PseAAC), Position Specific Scoring Matrix (PSSM), Functional Domain, Gene Ontology information, and the Pair-wise sequence alignment. The results of the classification are compared to the ones using protein interactions. For achieving this goal different machine learning algorithms were tested. Results The best-obtained results of using single feature set obtained using SVM classifier for PseAAC feature. The accuracy of combining all features with PPI data, using the Decision Tree and Random Forest classifiers, was 82.49% and 83.35%, respectively. In another experiment, using just protein interaction data with the different cutting points resulted in obtaining an accuracy of 93.035% for the protein location prediction. Conclusion In total, it was shown that protein(s) interaction has a significant impact on the prediction of the mitochondrial proteins’ location. This feature can separately distinguish the locations well. Using this feature the accuracy of the results is raised up to 5%.
Collapse
Affiliation(s)
| | - Mitra Mirzarezaee
- Department of Computer Engineering, Science and Research branch, Islamic Azad University, Tehran, Iran.,School of Biological Science, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran
| |
Collapse
|
36
|
Abstract
Peroxisomes in fungi are involved in a huge number of different metabolic processes. In addition, non-metabolic functions have also been identified. The proteins that are present in a particular peroxisome determine its metabolic function, whether they are the matrix localized enzymes of the different metabolic pathways or the membrane proteins involved in transport of metabolites across the peroxisomal membrane. Other peroxisomal proteins play a role in organelle biogenesis and dynamics, such as fission, transport and inheritance. Hence, obtaining a complete overview of which proteins are present in peroxisomes at a given time or under a given growth condition provides invaluable insights into peroxisome biology. Bottom up approaches are ideal to follow one or a few proteins at a time but they are not able to give a global view of the content of peroxisomes. To gain such information, top down approaches are required and one that has provided valuable insights into peroxisome function is mass spectrometry based organellar proteomics. Here, we discuss the findings of several such studies in yeast and filamentous fungi and outline new insights into peroxisomal function that were gained from these studies.
Collapse
Affiliation(s)
- Xin Chen
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747AG, Groningen, The Netherlands
| | - Chris Williams
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747AG, Groningen, The Netherlands.
| |
Collapse
|
37
|
Abstract
C. elegans is widely used to investigate biological processes related to health and disease. To study protein localization, fluorescently-tagged proteins can be used in vivo or immunohistochemistry can be performed in whole worms. Here, we describe a technique to localize a protein of interest at a subcellular level in C. elegans lysates, which can give insight into the location, function and/or toxicity of proteins.
Collapse
Affiliation(s)
| | - Olga Sin
- Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany.,Cells-in-Motion Cluster of Excellence, University of Münster, Münster, Germany
| | - Renée I Seinstra
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
| | - Ellen A A Nollen
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
| |
Collapse
|
38
|
Carqueijeiro I, Sepúlveda LJ, Mosquera A, Payne R, Corbin C, Papon N, de Bernonville TD, Besseau S, Lanoue A, Glévarec G, Clastre M, St-Pierre B, Atehortùa L, Giglioli-Guivarc'h N, O'Connor SE, Oudin A, Courdavault V. Vacuole-Targeted Proteins: Ins and Outs of Subcellular Localization Studies. Methods Mol Biol 2018; 1789:33-54. [PMID: 29916070 DOI: 10.1007/978-1-4939-7856-4_4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Accurate and efficient demonstrations of protein localizations to the vacuole or tonoplast remain strict prerequisites to decipher the role of vacuoles in the whole plant cell biology and notably in defence processes. In this chapter, we describe a reliable procedure of protein subcellular localization study through transient transformations of Catharanthus roseus or onion cells and expression of fusions with fluorescent proteins allowing minimizing artefacts of targeting.
Collapse
Affiliation(s)
- Inês Carqueijeiro
- EA2106 "Biomolécules et Biotechnologies Végétales", UFR Sciences et Techniques, Université François-Rabelais de Tours, Tours, France
| | - Liuda J Sepúlveda
- EA2106 "Biomolécules et Biotechnologies Végétales", UFR Sciences et Techniques, Université François-Rabelais de Tours, Tours, France.,Laboratorio de Biotecnología, Sede de Investigación Universitaria, Universidad de Antioquia, Medellin, Colombia
| | - Angela Mosquera
- EA2106 "Biomolécules et Biotechnologies Végétales", UFR Sciences et Techniques, Université François-Rabelais de Tours, Tours, France.,Laboratorio de Biotecnología, Sede de Investigación Universitaria, Universidad de Antioquia, Medellin, Colombia
| | - Richard Payne
- Department of Biological Chemistry, The John Innes Centre, Norwich Research Park, Norwich, UK
| | - Cyrielle Corbin
- EA2106 "Biomolécules et Biotechnologies Végétales", UFR Sciences et Techniques, Université François-Rabelais de Tours, Tours, France
| | - Nicolas Papon
- EA3142 "Groupe d'Etude des Interactions Hôte-Pathogène", Université d'Angers, Angers, France
| | - Thomas Dugé de Bernonville
- EA2106 "Biomolécules et Biotechnologies Végétales", UFR Sciences et Techniques, Université François-Rabelais de Tours, Tours, France
| | - Sébastien Besseau
- EA2106 "Biomolécules et Biotechnologies Végétales", UFR Sciences et Techniques, Université François-Rabelais de Tours, Tours, France
| | - Arnaud Lanoue
- EA2106 "Biomolécules et Biotechnologies Végétales", UFR Sciences et Techniques, Université François-Rabelais de Tours, Tours, France
| | - Gaëlle Glévarec
- EA2106 "Biomolécules et Biotechnologies Végétales", UFR Sciences et Techniques, Université François-Rabelais de Tours, Tours, France
| | - Marc Clastre
- EA2106 "Biomolécules et Biotechnologies Végétales", UFR Sciences et Techniques, Université François-Rabelais de Tours, Tours, France
| | - Benoit St-Pierre
- EA2106 "Biomolécules et Biotechnologies Végétales", UFR Sciences et Techniques, Université François-Rabelais de Tours, Tours, France
| | - Lucia Atehortùa
- Laboratorio de Biotecnología, Sede de Investigación Universitaria, Universidad de Antioquia, Medellin, Colombia
| | - Nathalie Giglioli-Guivarc'h
- EA2106 "Biomolécules et Biotechnologies Végétales", UFR Sciences et Techniques, Université François-Rabelais de Tours, Tours, France
| | - Sarah E O'Connor
- Department of Biological Chemistry, The John Innes Centre, Norwich Research Park, Norwich, UK
| | - Audrey Oudin
- EA2106 "Biomolécules et Biotechnologies Végétales", UFR Sciences et Techniques, Université François-Rabelais de Tours, Tours, France
| | - Vincent Courdavault
- EA2106 "Biomolécules et Biotechnologies Végétales", UFR Sciences et Techniques, Université François-Rabelais de Tours, Tours, France.
| |
Collapse
|
39
|
Walton PA, Brees C, Lismont C, Apanasets O, Fransen M. The peroxisomal import receptor PEX5 functions as a stress sensor, retaining catalase in the cytosol in times of oxidative stress. Biochim Biophys Acta Mol Cell Res 2017; 1864:1833-1843. [PMID: 28760655 DOI: 10.1016/j.bbamcr.2017.07.013] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2017] [Revised: 07/03/2017] [Accepted: 07/27/2017] [Indexed: 02/08/2023]
Abstract
Accumulating evidence indicates that peroxisome functioning, catalase localization, and cellular oxidative balance are intimately interconnected. Nevertheless, it remains largely unclear why modest increases in the cellular redox state especially interfere with the subcellular localization of catalase, the most abundant peroxisomal antioxidant enzyme. This study aimed at gaining more insight into this phenomenon. Therefore, we first established a simple and powerful approach to study peroxisomal protein import and protein-protein interactions in living cells in response to changes in redox state. By employing this approach, we confirm and extend previous observations that Cys-11 of human PEX5, the shuttling import receptor for peroxisomal matrix proteins containing a C-terminal peroxisomal targeting signal (PTS1), functions as a redox switch that modulates the protein's activity in response to intracellular oxidative stress. In addition, we show that oxidative stress affects the import of catalase, a non-canonical PTS1-containing protein, more than the import of a reporter protein containing a canonical PTS1. Furthermore, we demonstrate that changes in the local redox state do not affect PEX5-substrate binding and that human PEX5 does not oligomerize in cellulo, not even when the cells are exposed to oxidative stress. Finally, we present evidence that catalase retained in the cytosol can protect against H2O2-mediated redox changes in a manner that peroxisomally targeted catalase does not. Together, these findings lend credit to the idea that inefficient catalase import, when coupled with the role of PEX5 as a redox-regulated import receptor, constitutes a cellular defense mechanism to combat oxidative insults of extra-peroxisomal origin.
Collapse
Affiliation(s)
- Paul A Walton
- Laboratory of Lipid Biochemistry and Protein Interactions, Department of Cellular and Molecular Medicine, KU Leuven - University of Leuven, Herestraat 49, Box 601, B-3000 Leuven, Belgium; Department of Anatomy and Cell Biology, University of Western Ontario, 474 Medical Sciences Building, London, Ontario ON N6A 3K7, Canada
| | - Chantal Brees
- Laboratory of Lipid Biochemistry and Protein Interactions, Department of Cellular and Molecular Medicine, KU Leuven - University of Leuven, Herestraat 49, Box 601, B-3000 Leuven, Belgium
| | - Celien Lismont
- Laboratory of Lipid Biochemistry and Protein Interactions, Department of Cellular and Molecular Medicine, KU Leuven - University of Leuven, Herestraat 49, Box 601, B-3000 Leuven, Belgium
| | - Oksana Apanasets
- Laboratory of Lipid Biochemistry and Protein Interactions, Department of Cellular and Molecular Medicine, KU Leuven - University of Leuven, Herestraat 49, Box 601, B-3000 Leuven, Belgium
| | - Marc Fransen
- Laboratory of Lipid Biochemistry and Protein Interactions, Department of Cellular and Molecular Medicine, KU Leuven - University of Leuven, Herestraat 49, Box 601, B-3000 Leuven, Belgium.
| |
Collapse
|
40
|
Ishimoto K, Hayase A, Kumagai F, Kawai M, Okuno H, Hino N, Okada Y, Kawamura T, Tanaka T, Hamakubo T, Sakai J, Kodama T, Tachibana K, Doi T. Degradation of human Lipin-1 by BTRC E3 ubiquitin ligase. Biochem Biophys Res Commun 2017; 488:159-164. [PMID: 28483528 DOI: 10.1016/j.bbrc.2017.04.159] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 04/18/2017] [Indexed: 10/19/2022]
Abstract
Lipin-1 has dual functions in the regulation of lipid and energy metabolism according to its subcellular localization, which is tightly controlled. However, it is unclear how Lipin-1 degradation is regulated. Here, we demonstrate that Lipin-1 is degraded through its DSGXXS motif. We show that Lipin-1 interacts with either of two E3 ubiquitin ligases, BTRC or FBXW11, and that this interaction is DSGXXS-dependent and mediates the attachment of polyubiquitin chains. Further, we demonstrate that degradation of Lipin-1 is regulated by BTRC in the cytoplasm and on membranes. These novel insights into the regulation of human Lipin-1 stability will be useful in planning further studies to elucidate its metabolic processes.
Collapse
Affiliation(s)
- Kenji Ishimoto
- Laboratory of Molecular Medicine, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Ayaka Hayase
- Laboratory of Molecular Medicine, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Fumiko Kumagai
- Laboratory of Molecular Medicine, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Megumi Kawai
- Laboratory of Molecular Medicine, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Hiroko Okuno
- Laboratory of Molecular Medicine, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Nobumasa Hino
- Laboratory of Molecular Medicine, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yoshiaki Okada
- Laboratory of Molecular Medicine, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Takeshi Kawamura
- Isotope Science Center, The University of Tokyo, 2-11-16 Yayoi, Bunkyo, Tokyo 113-0032, Japan
| | - Toshiya Tanaka
- Laboratory for System Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8904, Japan
| | - Takao Hamakubo
- Department of Quantitative Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8904, Japan
| | - Juro Sakai
- Division of Metabolic Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8904, Japan
| | - Tatsuhiko Kodama
- Laboratory for System Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8904, Japan
| | - Keisuke Tachibana
- Laboratory of Molecular Medicine, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Takefumi Doi
- Laboratory of Molecular Medicine, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
| |
Collapse
|
41
|
Belardinelli JM, Jackson M. Green Fluorescent Protein as a protein localization and topological reporter in mycobacteria. Tuberculosis (Edinb) 2017; 105:13-17. [PMID: 28610783 DOI: 10.1016/j.tube.2017.04.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 04/04/2017] [Accepted: 04/07/2017] [Indexed: 11/29/2022]
Abstract
The cell envelope-associated proteins of Mycobacterium species play critical functions in the physiology and pathogenicity of these microorganisms. Because the determination of their subcellular localization and transmembrane topology is often critical to the understanding of their function, we investigated whether the Green Fluorescent Protein (GFP) could be used as a reporter to probe protein localization and map the topology of inner membrane proteins directly in intact mycobacterial cells. To this end, two GFP-based mycobacterial reporter plasmids were engineered and their functionality validated using a variety of membrane-associated, exported and cytosolic proteins.
Collapse
Affiliation(s)
- Juan Manuel Belardinelli
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523-1682, USA
| | - Mary Jackson
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523-1682, USA.
| |
Collapse
|
42
|
Poersch A, Maria AG, Palma CS, Grassi ML, Albuquerque D, Thomé CH, Faça VM. Profiling Cell Lines Nuclear Sub-proteome. Methods Mol Biol 2017; 1550:35-46. [PMID: 28188521 DOI: 10.1007/978-1-4939-6747-6_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Proteins are very dynamic within the cell and their localization and trafficking between subcellular compartments are critical for their correct function. Indeed, the abnormal localization of a protein might lead to the pathogenesis of several diseases. The association of cell fractionation methods and mass spectrometry based proteomic methods allow both the localization and quantification of proteins in different sub-compartments. Here we present a detailed protocol for enrichment, identification, and quantitation of the nuclear proteome in cell lines combining nuclear subproteome enrichment by differential centrifugation and high-throughput proteomics.
Collapse
|
43
|
Abstract
Immunohistochemistry (IHC) is a powerful immunology-based method that is used to study the location of proteins in cells and tissues. There have been numerous advancements in IHC technology that continually increase the sensitivity and specificity through which this method can be used to generate new discoveries. Similarly, Alpha-1 Antitrypsin (AAT) IHC can be used to study AAT protein expression within the human liver or exogenous AAT that is delivered through gene therapy. Here, we describe a highly sensitive method to detect the AAT antigen in formalin-fixed paraffin-embedded human or mouse tissues.
Collapse
Affiliation(s)
- Dongtao A Fu
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, 1395 Center Drive, Gainesville, FL, 32610, USA
| | - Martha Campbell-Thompson
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, 1395 Center Drive, Gainesville, FL, 32610, USA.
| |
Collapse
|
44
|
Mardakheh FK. Mass Spectrometry Analysis of Spatial Protein Networks by Colocalization Analysis (COLA). Methods Mol Biol 2017; 1636:337-352. [PMID: 28730490 DOI: 10.1007/978-1-4939-7154-1_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2024]
Abstract
A major challenge in systems biology is comprehensive mapping of protein interaction networks. Crucially, such interactions are often dynamic in nature, necessitating methods that can rapidly mine the interactome across varied conditions and treatments to reveal change in the interaction networks. Recently, we described a fast mass spectrometry-based method to reveal functional interactions in mammalian cells on a global scale, by revealing spatial colocalizations between proteins (COLA) (Mardakheh et al., Mol Biosyst 13:92-105, 2017). As protein localization and function are inherently linked, significant colocalization between two proteins is a strong indication for their functional interaction. COLA uses rapid complete subcellular fractionation, coupled with quantitative proteomics to generate a subcellular localization profile for each protein quantified by the mass spectrometer. Robust clustering is then applied to reveal significant similarities in protein localization profiles, indicative of colocalization.
Collapse
Affiliation(s)
- Faraz K Mardakheh
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ, UK.
| |
Collapse
|
45
|
Schwelberger HG, Feurle J, Houen G. Monoclonal antibodies for human and porcine histamine N-methyltransferase (HMT) facilitate protein expression and localization studies. Inflamm Res 2016; 66:67-77. [PMID: 27632021 PMCID: PMC5209425 DOI: 10.1007/s00011-016-0987-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 08/09/2016] [Accepted: 09/02/2016] [Indexed: 01/11/2023] Open
Abstract
Objective The lack of suitable antibodies for the histamine inactivating enzyme histamine N-methyltransferase (HMT) has so far prevented the direct analysis of HMT proteins in man and other mammals. Methods A series of monoclonal antibodies was produced by immunizing mice with human and porcine HMT expressed in vitro. Antibodies were characterized by immunoblotting and immunohistochemical staining. Results Six different monoclonal antibodies specific for human HMT and four different monoclonal antibodies specific for porcine HMT were obtained that can detect HMT with up to tenfold greater sensitivity than the most sensitive enzymatic assays currently available. Using these antibodies allowed us to confirm the expression and cellular localization of HMT in various human and porcine tissues, where the presence of the enzyme had previously been deduced from activity measurement and HMT mRNA analysis. Immunohistochemical staining of human and porcine tissue sections clearly showed that HMT is a cytosolic protein, which is localized in specific cells of most mammalian tissues. Conclusions The new monoclonal antibodies not only allow a comprehensive quantitative evaluation of the expression of HMT at the cellular level in man and other mammals but will also facilitate sensitive analyses of disease-associated alterations of this protein.
Collapse
Affiliation(s)
- Hubert G Schwelberger
- Molecular Biology Laboratory, Department of Visceral, Transplant and Thoracic Surgery, Medical University Innsbruck, Schöpfstraße 41, 6020, Innsbruck, Austria.
| | - Johannes Feurle
- Molecular Biology Laboratory, Department of Visceral, Transplant and Thoracic Surgery, Medical University Innsbruck, Schöpfstraße 41, 6020, Innsbruck, Austria
| | - Gunnar Houen
- Statens Serum Institut, Artillerivej 5, 2300, Copenhagen, Denmark
| |
Collapse
|
46
|
Leyton-Puig D, Kedziora KM, Isogai T, van den Broek B, Jalink K, Innocenti M. PFA fixation enables artifact-free super-resolution imaging of the actin cytoskeleton and associated proteins. Biol Open 2016; 5:1001-9. [PMID: 27378434 PMCID: PMC4958280 DOI: 10.1242/bio.019570] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 06/01/2016] [Indexed: 01/22/2023] Open
Abstract
Super-resolution microscopy (SRM) allows precise localization of proteins in cellular organelles and structures, including the actin cytoskeleton. Yet sample preparation protocols for SRM are rather anecdotal and still being optimized. Thus, SRM-based imaging of the actin cytoskeleton and associated proteins often remains challenging and poorly reproducible. Here, we show that proper paraformaldehyde (PFA)-based sample preparation preserves the architecture of the actin cytoskeleton almost as faithfully as gold-standard glutaraldehyde fixation. We show that this fixation is essential for proper immuno-based localization of actin-binding and actin-regulatory proteins involved in the formation of lamellipodia and ruffles, such as mDia1, WAVE2 and clathrin heavy chain, and provide detailed guidelines for the execution of our method. In summary, proper PFA-based sample preparation increases the multi-color possibilities and the reproducibility of SRM of the actin cytoskeleton and its associated proteins.
Collapse
Affiliation(s)
- Daniela Leyton-Puig
- Division of Cell Biology I, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam 1066 CX, The Netherlands
| | - Katarzyna M Kedziora
- Division of Cell Biology I, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam 1066 CX, The Netherlands
| | - Tadamoto Isogai
- Division of Molecular Genetics, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam 1066 CX, The Netherlands
| | - Bram van den Broek
- Division of Cell Biology I, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam 1066 CX, The Netherlands
| | - Kees Jalink
- Division of Cell Biology I, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam 1066 CX, The Netherlands
| | - Metello Innocenti
- Division of Molecular Genetics, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam 1066 CX, The Netherlands
| |
Collapse
|
47
|
Abstract
Septins are highly conserved and essential eukaryotic cytoskeletal proteins that interact with the inner plasma membrane. They are involved in essential functions requiring cell membrane remodeling and compartmentalization, such as cell division and dendrite morphogenesis, and have been implicated in numerous diseases. Depending on the organisms and on the type of tissue, a specific set of septins genes are expressed, ranging from 2 to 13. Septins self-assemble into linear, symmetric rods that can further organize into linear filaments several microns in length. Only a subset of human septins has been described at high resolution by X-ray crystallography (Sirajuddin et al., 2007). Electron microscopy (EM) has proven to be a method of choice for analyzing the molecular organization of septins. It is possible to localize each septin subunit within the rod complex using genetic tags, such as maltose-binding protein or green fluorescent protein, to generate a visible label of a specific septin subunit in EM images that are processed using single-particle EM methodology. In this chapter we present, in detail, the methods that we have used to analyze the molecular organization of budding yeast septins (Bertin et al., 2008). These methods include purification of septin complexes, sample preparation for EM, and image processing procedures. Such methods can be generalized to analyze the organization of septins from any organism.
Collapse
|
48
|
Söhnel AC, Kohl W, Gregor I, Enderlein J, Rieger B, Busch KB. Probing of protein localization and shuttling in mitochondrial microcompartments by FLIM with sub-diffraction resolution. Biochim Biophys Acta 2016; 1857:1290-9. [PMID: 27016377 DOI: 10.1016/j.bbabio.2016.03.021] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 03/17/2016] [Accepted: 03/18/2016] [Indexed: 12/31/2022]
Abstract
The cell is metabolically highly compartmentalized. Especially, mitochondria host many vital reactions in their different microcompartments. However, due to their small size, these microcompartments are not accessible by conventional microscopy. Here, we demonstrate that time-correlated single-photon counting (TCSPC) fluorescence lifetime-imaging microscopy (FLIM) classifies not only mitochondria, but different microcompartments inside mitochondria. Sensor proteins in the matrix had a different lifetime than probes at membrane proteins. Localization in the outer and inner mitochondrial membrane could be distinguished by significant differences in the lifetime. The method was sensitive enough to monitor shifts in protein location within mitochondrial microcompartments. Macromolecular crowding induced by changes in the protein content significantly affected the lifetime, while oxidizing conditions or physiological pH changes had only marginal effects. We suggest that FLIM is a versatile and completive method to monitor spatiotemporal events in mitochondria. The sensitivity in the time domain allows for gaining substantial information about sub-mitochondrial localization overcoming diffraction limitation. This article is part of a Special Issue entitled 'EBEC 2016: 19th European Bioenergetics Conference, Riva del Garda, Italy, July 2-6, 2016', edited by Prof. Paolo Bernardi.
Collapse
|
49
|
Kilaru S, Schuster M, Studholme D, Soanes D, Lin C, Talbot NJ, Steinberg G. A codon-optimized green fluorescent protein for live cell imaging in Zymoseptoria tritici. Fungal Genet Biol 2016; 79:125-31. [PMID: 26092799 PMCID: PMC4502462 DOI: 10.1016/j.fgb.2015.03.022] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 03/12/2015] [Accepted: 03/17/2015] [Indexed: 11/24/2022]
Abstract
Fluorescent proteins (FPs) are powerful tools to investigate intracellular dynamics and protein localization. Cytoplasmic expression of FPs in fungal pathogens allows greater insight into invasion strategies and the host-pathogen interaction. Detection of their fluorescent signal depends on the right combination of microscopic setup and signal brightness. Slow rates of photo-bleaching are pivotal for in vivo observation of FPs over longer periods of time. Here, we test green-fluorescent proteins, including Aequorea coerulescens GFP (AcGFP), enhanced GFP (eGFP) from Aequorea victoria and a novel Zymoseptoria tritici codon-optimized eGFP (ZtGFP), for their usage in conventional and laser-enhanced epi-fluorescence, and confocal laser-scanning microscopy. We show that eGFP, expressed cytoplasmically in Z. tritici, is significantly brighter and more photo-stable than AcGFP. The codon-optimized ZtGFP performed even better than eGFP, showing significantly slower bleaching and a 20-30% further increase in signal intensity. Heterologous expression of all GFP variants did not affect pathogenicity of Z. tritici. Our data establish ZtGFP as the GFP of choice to investigate intracellular protein dynamics in Z. tritici, but also infection stages of this wheat pathogen inside host tissue.
Collapse
Affiliation(s)
- S Kilaru
- Biosciences, University of Exeter, Exeter EX4 4QD, UK
| | - M Schuster
- Biosciences, University of Exeter, Exeter EX4 4QD, UK
| | - D Studholme
- Biosciences, University of Exeter, Exeter EX4 4QD, UK
| | - D Soanes
- Biosciences, University of Exeter, Exeter EX4 4QD, UK
| | - C Lin
- Mathematics, University of Exeter, Exeter EX4 3QF, UK
| | - N J Talbot
- Biosciences, University of Exeter, Exeter EX4 4QD, UK
| | - G Steinberg
- Biosciences, University of Exeter, Exeter EX4 4QD, UK.
| |
Collapse
|
50
|
Pratt EP, Owens JL, Hockerman GH, Hu CD. Bimolecular Fluorescence Complementation (BiFC) Analysis of Protein-Protein Interactions and Assessment of Subcellular Localization in Live Cells. Methods Mol Biol 2016; 1474:153-70. [PMID: 27515079 DOI: 10.1007/978-1-4939-6352-2_9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Bimolecular fluorescence complementation (BiFC) is a fluorescence imaging technique used to visualize protein-protein interactions (PPIs) in live cells and animals. One unique application of BiFC is to reveal subcellular localization of PPIs. The superior signal-to-noise ratio of BiFC in comparison with fluorescence resonance energy transfer or bioluminescence resonance energy transfer enables its wide applications. Here, we describe how confocal microscopy can be used to detect and quantify PPIs and their subcellular localization. We use basic leucine zipper transcription factor proteins as an example to provide a step-by-step BiFC protocol using a Nikon A1 confocal microscope and NIS-Elements imaging software. The protocol given below can be readily adapted for use with other confocal microscopes or imaging software.
Collapse
|