1
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Alperovich N, Scott BM, Ross D. Automation protocol for high-efficiency and high-quality genomic DNA extraction from Saccharomyces cerevisiae. PLoS One 2023; 18:e0292401. [PMID: 37847718 PMCID: PMC10581484 DOI: 10.1371/journal.pone.0292401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 09/19/2023] [Indexed: 10/19/2023] Open
Abstract
Although many protocols have been previously developed for genomic DNA (gDNA) extraction from S. cerevisiae, to take advantage of recent advances in laboratory automation and DNA-barcode sequencing, there is a need for automated methods that can provide high-quality gDNA at high efficiency. Here, we describe and demonstrate a fully automated protocol that includes five basic steps: cell wall and RNA digestion, cell lysis, DNA binding to magnetic beads, washing with ethanol, and elution. Our protocol avoids the use of hazardous reagents (e.g., phenol, chloroform), glass beads for mechanical cell disruption, or incubation of samples at 100°C (i.e., boiling). We show that our protocol can extract gDNA with high efficiency both from cells grown in liquid culture and from colonies grown on agar plates. We also show results from gel electrophoresis that demonstrate that the resulting gDNA is of high quality.
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Affiliation(s)
- Nina Alperovich
- National Institute of Standards and Technology, Gaithersburg, MD, United States of America
| | - Benjamin M. Scott
- National Institute of Standards and Technology, Gaithersburg, MD, United States of America
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, United States of America
| | - David Ross
- National Institute of Standards and Technology, Gaithersburg, MD, United States of America
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2
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Patel A, Peralta-Yahya P. Olfactory Receptors as an Emerging Chemical Sensing Scaffold. Biochemistry 2022; 62:187-195. [PMID: 36318941 PMCID: PMC9850922 DOI: 10.1021/acs.biochem.2c00486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Chemical biosensors are an increasingly ubiquitous part of our lives. Beyond enzyme-coupled assays, recent synthetic biology advances now allow us to hijack more complex biosensing systems to respond to difficult to detect analytes, such as chemical small molecules. Here, we briefly overview recent advances in the biosensing of small molecules, including nucleic acid aptamers, allosteric transcription factors, and two-component systems. We then look more closely at a recently developed chemical sensing system, G protein-coupled receptor (GPCR)-based sensors. Finally, we consider the chemical sensing capabilities of the largest GPCR subfamily, olfactory receptors (ORs). We examine ORs' role in nature, their potential as a biomedical target, and their ability to detect compounds not amenable for detection using other biological scaffolds. We conclude by evaluating the current challenges, opportunities, and future applications of GPCR- and OR-based sensors.
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Affiliation(s)
- Amisha Patel
- School
of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Pamela Peralta-Yahya
- School
of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States,School
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30332, United States,E-mail:
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3
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Miettinen K, Leelahakorn N, Almeida A, Zhao Y, Hansen LR, Nikolajsen IE, Andersen JB, Givskov M, Staerk D, Bak S, Kampranis SC. A GPCR-based yeast biosensor for biomedical, biotechnological, and point-of-use cannabinoid determination. Nat Commun 2022; 13:3664. [PMID: 35760809 PMCID: PMC9237071 DOI: 10.1038/s41467-022-31357-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 06/15/2022] [Indexed: 11/09/2022] Open
Abstract
Eukaryotic cells use G-protein coupled receptors to sense diverse signals, ranging from chemical compounds to light. Here, we exploit the remarkable sensing capacity of G-protein coupled receptors to construct yeast-based biosensors for real-life applications. To establish proof-of-concept, we focus on cannabinoids because of their neuromodulatory and immunomodulatory activities. We construct a CB2 receptor-based biosensor, optimize it to achieve high sensitivity and dynamic range, and prove its effectiveness in three applications of increasing difficulty. First, we screen a compound library to discover agonists and antagonists. Second, we analyze 54 plants to discover a new phytocannabinoid, dugesialactone. Finally, we develop a robust portable device, analyze body-fluid samples, and confidently detect designer drugs like JWH-018. These examples demonstrate the potential of yeast-based biosensors to enable diverse applications that can be implemented by non-specialists. Taking advantage of the extensive sensing repertoire of G-protein coupled receptors, this technology can be extended to detect numerous compounds. GPCRs are used for diverse sensing in eukaryotes. Here the authors use GPCRs to construct yeast-based biosensors, focussing on cannabinoids, and use these to screen agonists and antagonists, as well as generate a portable detection device.
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Affiliation(s)
- Karel Miettinen
- Biochemical Engineering Group, Plant Biochemistry Section, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Nattawat Leelahakorn
- Biochemical Engineering Group, Plant Biochemistry Section, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Aldo Almeida
- Biochemical Engineering Group, Plant Biochemistry Section, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark.,Bioremediation Laboratory, Faculty of Biological Sciences, Autonomous University of Coahuila, Carretera Torreón-Matamoros km. 7.5, Torreón, Coahuila, 27000, Mexico
| | - Yong Zhao
- Biochemical Engineering Group, Plant Biochemistry Section, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Lukas R Hansen
- Biochemical Engineering Group, Plant Biochemistry Section, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Iben E Nikolajsen
- Biochemical Engineering Group, Plant Biochemistry Section, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Jens B Andersen
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Michael Givskov
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Dan Staerk
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100, Copenhagen, Denmark
| | - Søren Bak
- Biochemical Engineering Group, Plant Biochemistry Section, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Sotirios C Kampranis
- Biochemical Engineering Group, Plant Biochemistry Section, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark.
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4
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Yang C, Georgiou M, Atkinson R, Collin J, Al-Aama J, Nagaraja-Grellscheid S, Johnson C, Ali R, Armstrong L, Mozaffari-Jovin S, Lako M. Pre-mRNA Processing Factors and Retinitis Pigmentosa: RNA Splicing and Beyond. Front Cell Dev Biol 2021; 9:700276. [PMID: 34395430 PMCID: PMC8355544 DOI: 10.3389/fcell.2021.700276] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 07/09/2021] [Indexed: 12/20/2022] Open
Abstract
Retinitis pigmentosa (RP) is the most common inherited retinal disease characterized by progressive degeneration of photoreceptors and/or retinal pigment epithelium that eventually results in blindness. Mutations in pre-mRNA processing factors (PRPF3, 4, 6, 8, 31, SNRNP200, and RP9) have been linked to 15–20% of autosomal dominant RP (adRP) cases. Current evidence indicates that PRPF mutations cause retinal specific global spliceosome dysregulation, leading to mis-splicing of numerous genes that are involved in a variety of retina-specific functions and/or general biological processes, including phototransduction, retinol metabolism, photoreceptor disk morphogenesis, retinal cell polarity, ciliogenesis, cytoskeleton and tight junction organization, waste disposal, inflammation, and apoptosis. Importantly, additional PRPF functions beyond RNA splicing have been documented recently, suggesting a more complex mechanism underlying PRPF-RPs driven disease pathogenesis. The current review focuses on the key RP-PRPF genes, depicting the current understanding of their roles in RNA splicing, impact of their mutations on retinal cell’s transcriptome and phenome, discussed in the context of model species including yeast, zebrafish, and mice. Importantly, information on PRPF functions beyond RNA splicing are discussed, aiming at a holistic investigation of PRPF-RP pathogenesis. Finally, work performed in human patient-specific lab models and developing gene and cell-based replacement therapies for the treatment of PRPF-RPs are thoroughly discussed to allow the reader to get a deeper understanding of the disease mechanisms, which we believe will facilitate the establishment of novel and better therapeutic strategies for PRPF-RP patients.
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Affiliation(s)
- Chunbo Yang
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Maria Georgiou
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Robert Atkinson
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Joseph Collin
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Jumana Al-Aama
- Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | - Colin Johnson
- Leeds Institute of Molecular Medicine, University of Leeds, Leeds, United Kingdom
| | - Robin Ali
- King's College London, London, United Kingdom
| | - Lyle Armstrong
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Sina Mozaffari-Jovin
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.,Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Majlinda Lako
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
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5
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Lengger B, Jensen MK. Engineering G protein-coupled receptor signalling in yeast for biotechnological and medical purposes. FEMS Yeast Res 2021; 20:5673487. [PMID: 31825496 PMCID: PMC6977407 DOI: 10.1093/femsyr/foz087] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [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: 10/02/2019] [Accepted: 12/09/2019] [Indexed: 12/13/2022] Open
Abstract
G protein-coupled receptors (GPCRs) comprise the largest class of membrane proteins in the human genome, with a common denominator of seven-transmembrane domains largely conserved among eukaryotes. Yeast is naturally armoured with three different GPCRs for pheromone and sugar sensing, with the pheromone pathway being extensively hijacked for characterising heterologous GPCR signalling in a model eukaryote. This review focusses on functional GPCR studies performed in yeast and on the elucidated hotspots for engineering, and discusses both endogenous and heterologous GPCR signalling. Key emphasis will be devoted to studies describing important engineering parameters to consider for successful coupling of GPCRs to the yeast mating pathway. We also review the various means of applying yeast for studying GPCRs, including the use of yeast armed with heterologous GPCRs as a platform for (i) deorphanisation of orphan receptors, (ii) metabolic engineering of yeast for production of bioactive products and (iii) medical applications related to pathogen detection and drug discovery. Finally, this review summarises the current challenges related to expression of functional membrane-bound GPCRs in yeast and discusses the opportunities to continue capitalising on yeast as a model chassis for functional GPCR signalling studies.
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Affiliation(s)
- Bettina Lengger
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, Kgs. Lyngby, 2800, Denmark
| | - Michael K Jensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, Kgs. Lyngby, 2800, Denmark
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6
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Wang X, van Westen GJP, Heitman LH, IJzerman AP. G protein-coupled receptors expressed and studied in yeast. The adenosine receptor as a prime example. Biochem Pharmacol 2020; 187:114370. [PMID: 33338473 DOI: 10.1016/j.bcp.2020.114370] [Citation(s) in RCA: 3] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 12/11/2020] [Accepted: 12/11/2020] [Indexed: 11/25/2022]
Abstract
G protein-coupled receptors (GPCRs) are the largest class of membrane proteins with around 800 members in the human genome/proteome. Extracellular signals such as hormones and neurotransmitters regulate various biological processes via GPCRs, with GPCRs being the bodily target of 30-40% of current drugs on the market. Complete identification and understanding of GPCR functionality will provide opportunities for novel drug discovery. Yeast expresses three different endogenous GPCRs regulating pheromone and sugar sensing, with the pheromone pathway offering perspectives for the characterization of heterologous GPCR signaling. Moreover, yeast offers a ''null" background for studies on mammalian GPCRs, including GPCR activation and signaling, ligand identification, and characterization of disease-related mutations. This review focuses on modifications of the yeast pheromone signaling pathway for functional GPCR studies, and on opportunities and usage of the yeast system as a platform for human GPCR studies. Finally, this review discusses in some further detail studies of adenosine receptors heterologously expressed in yeast, and what Geoff Burnstock thought of this approach.
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Affiliation(s)
- Xuesong Wang
- Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Gerard J P van Westen
- Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Laura H Heitman
- Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Einsteinweg 55, 2333 CC Leiden, The Netherlands; Oncode Institute, Leiden, The Netherlands
| | - Adriaan P IJzerman
- Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Einsteinweg 55, 2333 CC Leiden, The Netherlands
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7
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Jaakola VP, Scalise M. Membrane Proteins: New Approaches to Probes, Technologies, and Drug Design, Part II. SLAS Discov 2019; 24:941-942. [PMID: 31746681 DOI: 10.1177/2472555219881666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Affiliation(s)
| | - Mariafrancesca Scalise
- Department BEST (Biologia, Ecologia, Scienze della Terra), University of Calabria, Arcavacata di Rende (CS), Italy
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