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Prakash A, Li Z, Chirasani VR, Rasquinha JA, Hewitt N, Hubbard GB, Yin G, Hawkins AT, Montore LJ, Dohlman HG, Campbell SL. Molecular and functional profiling of Gαi as an intracellular pH sensor. Nat Commun 2025; 16:3468. [PMID: 40216757 PMCID: PMC11992140 DOI: 10.1038/s41467-025-58323-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Accepted: 03/18/2025] [Indexed: 04/14/2025] Open
Abstract
Heterotrimeric G proteins (Gα, Gβ and Gγ) act downstream of G-protein-coupled receptors (GPCRs) to mediate signaling pathways that regulate various physiological processes and human disease conditions. While human Gαi and its yeast homolog Gpa1 were previously postulated to function as intracellular pH sensors, the pH-sensing capabilities of Gαi and the underlying mechanism remain to be established. Our research shows that variations in pH significantly affect the structure and stability of Gαi-GDP. Specifically, at the lower end of the physiological pH range, the protein undergoes an order-to-disorder transition due to the loss of electrostatic interactions within the Gαi Switch regions, resulting in a reduction in agonist-mediated Gαi-Gβγ release. Further, we identified key residues within the Gαi Switch regions that form the pH-sensing network. Mutation of these residues in Gαi gives rise to 'low pH mimetics' that abolish pH-dependent thermostability changes and reduce Gαi-Gβγ release. Overall, our findings suggest that pH-sensitive structural changes in Gαi impact the agonist-mediated dissociation of Gβγ, which is essential for proper signaling.
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Affiliation(s)
- Ajit Prakash
- Department of Biochemistry & Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Zijian Li
- Department of Biochemistry & Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Venkat R Chirasani
- Department of Biochemistry & Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- R. L. Juliano Structural Bioinformatics Core, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Juhi A Rasquinha
- Department of Biochemistry & Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Natalie Hewitt
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Garrett B Hubbard
- Department of Biochemistry & Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Guowei Yin
- The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518107, China
| | - Aspen T Hawkins
- Department of Biochemistry & Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Luca J Montore
- Department of Biochemistry & Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Henrik G Dohlman
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Sharon L Campbell
- Department of Biochemistry & Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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2
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Pettersen JM, McCracken O, Robinson AS. Ligand binding kinetics to evaluate the function and stability of A 2AR in nanodiscs. Biophys J 2025; 124:440-457. [PMID: 39690743 PMCID: PMC11788476 DOI: 10.1016/j.bpj.2024.12.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2024] [Revised: 11/15/2024] [Accepted: 12/13/2024] [Indexed: 12/19/2024] Open
Abstract
G-protein-coupled receptors (GPCRs) represent one of the largest classes of therapeutic targets. However, developing successful therapeutics to target GPCRs is a challenging endeavor, with many molecules failing during in vivo clinical trials due to a lack of efficacy. The in vitro identification of drug-target residence time (1/koff) has been suggested to improve predictions of in vivo success. Here, a ligand binding assay using fluorescence anisotropy was implemented to successfully determine on rates (kon) and off rates (koff) of labeled and unlabeled ligands binding to the adenosine A2A receptor (A2AR) purified into nanodiscs (A2AR-NDs). The kinetic assay was used to determine the optimal storage conditions of A2AR-NDs, where they were found to be stable for more than 6 months at -80°C. The binding assay was implemented to further understand receptor function by determining the effects of charged lipids on agonist binding kinetics, how sodium levels allosterically modulate A2AR function, and how A2AR protonation affects agonist binding.
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Affiliation(s)
- John M Pettersen
- Department of Chemical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania
| | - Olivia McCracken
- Department of Chemical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania
| | - Anne Skaja Robinson
- Department of Chemical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania.
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3
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Timsit Y, Sergeant-Perthuis G, Bennequin D. The role of ribosomal protein networks in ribosome dynamics. Nucleic Acids Res 2025; 53:gkae1308. [PMID: 39788545 PMCID: PMC11711686 DOI: 10.1093/nar/gkae1308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 12/12/2024] [Accepted: 01/02/2025] [Indexed: 01/12/2025] Open
Abstract
Accurate protein synthesis requires ribosomes to integrate signals from distant functional sites and execute complex dynamics. Despite advances in understanding ribosome structure and function, two key questions remain: how information is transmitted between these distant sites, and how ribosomal movements are synchronized? We recently highlighted the existence of ribosomal protein networks, likely evolved to participate in ribosome signaling. Here, we investigate the relationship between ribosomal protein networks and ribosome dynamics. Our findings show that major motion centers in the bacterial ribosome interact specifically with r-proteins, and that ribosomal RNA exhibits high mobility around each r-protein. This suggests that periodic electrostatic changes in the context of negatively charged residues (Glu and Asp) induce RNA-protein 'distance-approach' cycles, controlling key ribosomal movements during translocation. These charged residues play a critical role in modulating electrostatic repulsion between RNA and proteins, thus coordinating ribosomal dynamics. We propose that r-protein networks synchronize ribosomal dynamics through an 'electrostatic domino' effect, extending the concept of allostery to the regulation of movements within supramolecular assemblies.
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Affiliation(s)
- Youri Timsit
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM110, 163 avenue de Luminy 13288 Marseille, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 3 Rue Michel-Ange, 75016 Paris, France
| | - Grégoire Sergeant-Perthuis
- Laboratory of Computational and Quantitative Biology (LCQB), Sorbonne Université, 4 Place Jussieu, 75005 Paris, France
| | - Daniel Bennequin
- Institut de Mathématiques de Jussieu - Paris Rive Gauche (IMJ-PRG), UMR 7586, CNRS, Université Paris Diderot, 8, Pace Aurélie Nemours, 75013 Paris, France
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4
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Fu M, He J, Zhu D, Zhang Q, Jiang Z, Yang G. Promising therapeutic targets for tumor treatment: Cleaved activation of receptors in the nucleus. Drug Discov Today 2024; 29:104192. [PMID: 39332484 DOI: 10.1016/j.drudis.2024.104192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2024] [Revised: 09/11/2024] [Accepted: 09/21/2024] [Indexed: 09/29/2024]
Abstract
A new fate of cell surface receptors, cleaved activation in the nucleus, is summarized. The intracellular domain (ICD) of cell surface receptors, cleaved by enzymes like γ-secretase, translocates to the nucleus to form transcriptional complexes participating in the onset and development of tumors. The fate is clinically significant, as inhibitors of cleavage enzymes have shown effectiveness in treating advanced tumors by reducing tumorigenic ICDs. Additionally, the construction of synthetic receptors also conforms with the fate mechanism. This review details each step of cleaved activation in the nucleus, elucidates tumorigenic mechanisms, explores application in antitumor therapy, and scrutinizes possible limitations.
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Affiliation(s)
- Mengdie Fu
- The Affiliated Hospital of Stomatology, School of Stomatology, Zhejiang University School of Medicine, and Key Laboratory of Oral Biomedical Research of Zhejiang Province, Hangzhou, Zhejiang, 310006, China
| | - Jin He
- The Affiliated Hospital of Stomatology, School of Stomatology, Zhejiang University School of Medicine, and Key Laboratory of Oral Biomedical Research of Zhejiang Province, Hangzhou, Zhejiang, 310006, China
| | - Danji Zhu
- The Affiliated Hospital of Stomatology, School of Stomatology, Zhejiang University School of Medicine, and Key Laboratory of Oral Biomedical Research of Zhejiang Province, Hangzhou, Zhejiang, 310006, China
| | - Qinmeng Zhang
- The Affiliated Hospital of Stomatology, School of Stomatology, Zhejiang University School of Medicine, and Key Laboratory of Oral Biomedical Research of Zhejiang Province, Hangzhou, Zhejiang, 310006, China
| | - Zhiwei Jiang
- The Affiliated Hospital of Stomatology, School of Stomatology, Zhejiang University School of Medicine, and Key Laboratory of Oral Biomedical Research of Zhejiang Province, Hangzhou, Zhejiang, 310006, China.
| | - Guoli Yang
- The Affiliated Hospital of Stomatology, School of Stomatology, Zhejiang University School of Medicine, and Key Laboratory of Oral Biomedical Research of Zhejiang Province, Hangzhou, Zhejiang, 310006, China.
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5
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Didan Y, Ghomlaghi M, Nguyen LK, Ng DCH. Stress pathway outputs are encoded by pH-dependent clustering of kinase components. Nat Commun 2024; 15:6614. [PMID: 39103333 DOI: 10.1038/s41467-024-50638-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Accepted: 07/10/2024] [Indexed: 08/07/2024] Open
Abstract
Signal processing by intracellular kinases controls near all biological processes but how signal pathway functions evolve with changed cellular context is poorly understood. Functional specificity of c-Jun N-terminal Kinases (JNK) are partly encoded by signal strength. Here we reveal that intracellular pH (pHi) is a significant component of the JNK network and defines signal response to specific stimuli. We show pHi regulates JNK activity in response to cell stress, with the relationship between pHi and JNK activity dependent on specific stimuli and upstream kinases activated. Using the optogenetic clustering tag CRY2, we show that an increase in pHi promotes the light-induced phase transition of ASK1 to augment JNK activation. While increased pHi similarly promoted CRY2-tagged JNK2 to form light-induced condensates, this attenuated JNK activity. Mathematical modelling of feedback signalling incorporating pHi and differential contributions by ASK1 and JNK2 condensates was sufficient to delineate signal responses to specific stimuli. Taking pHi and ASK1/JNK2 signal contributions into consideration may delineate oncogenic versus tumour suppressive JNK functions and cancer cell drug responses.
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Affiliation(s)
- Yuliia Didan
- School of Biomedical Science, Faculty of Medicine, University of Queensland; St Lucia, Brisbane, Australia
| | - Milad Ghomlaghi
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Australia
- Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Lan K Nguyen
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Australia
- Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Dominic C H Ng
- School of Biomedical Science, Faculty of Medicine, University of Queensland; St Lucia, Brisbane, Australia.
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6
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Kapolka NJ, Taghon GJ, Isom DG. Advances in yeast synthetic biology for human G protein-coupled receptor biology and pharmacology. Curr Opin Biotechnol 2024; 88:103176. [PMID: 39079313 DOI: 10.1016/j.copbio.2024.103176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 06/04/2024] [Accepted: 07/12/2024] [Indexed: 08/11/2024]
Abstract
G protein-coupled receptors (GPCRs) are the largest family of transmembrane receptors in humans. Over 800 GPCRs regulate the (patho)biology of every organ, tissue, and cell type. Consequently, GPCRs are the most prominent therapeutic targets in medicine. Although over 30% of current U.S. Food and Drug Administration-approved drugs target GPCR signaling, most receptors remain understudied and therapeutically underutilized. Challenges include an incomplete understanding of GPCR signaling, pharmacology, structural biology, and the multiplicity of endogenous GPCR ligands, in addition to a scarcity of biological and pharmacological tools for elucidating GPCR-mediated cellular processes beyond initial signaling events. Various mammalian, insect, and yeast cell models currently address some of these needs. Here, we review recent advances in yeast synthetic biology that are helping to catalyze new and unexpected conceptual and technical breakthroughs in GPCR-based medicine and biotechnology.
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Affiliation(s)
- Nicholas J Kapolka
- Department of Pharmacology, University of North Carolina, Chapel Hill, USA
| | - Geoffrey J Taghon
- National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Daniel G Isom
- Department of Molecular and Cellular Pharmacology, University of Miami School of Medicine, USA; Sylvester Comprehensive Cancer Center, Tumor Biology Program, USA; Frost Institute for Data Science and Computing, USA
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7
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Prakash A, Li Z, Chirasani VR, Rasquinha JA, Valentin NH, Hubbard GB, Yin G, Dohlman HG, Campbell SL. Molecular and Functional Profiling of Gαi as an Intracellular pH Sensor. RESEARCH SQUARE 2024:rs.3.rs-4203924. [PMID: 38746411 PMCID: PMC11092800 DOI: 10.21203/rs.3.rs-4203924/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Heterotrimeric G proteins (Gα, Gβ and Gγ) act downstream of G-protein-coupled receptors (GPCRs) to mediate signaling pathways that regulate various physiological processes and human disease conditions. Previously, human Gαi and its yeast homolog Gpa1 have been reported to function as intracellular pH sensors, yet the pH sensing capabilities of Gαi and the underlying mechanism remain to be established. Herein, we identify a pH sensing network within Gαi, and evaluate the consequences of pH modulation on the structure and stability of the G-protein. We find that changes over the physiological pH range significantly alter the structure and stability of Gαi-GDP, with the protein undergoing a disorder-to-order transition as the pH is raised from 6.8 to 7.5. Further, we find that modulation of intracellular pH in HEK293 cells regulates Gαi-Gβγ release. Identification of key residues in the pH-sensing network allowed the generation of low pH mimetics that attenuate Gαi-Gβγ release. Our findings, taken together, indicate that pH-dependent structural changes in Gαi alter the agonist-mediated Gβγ dissociation necessary for proper signaling.
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Affiliation(s)
- Ajit Prakash
- Department of Biochemistry & Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Zijian Li
- Department of Biochemistry & Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Venkata R. Chirasani
- Department of Biochemistry & Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Juhi A. Rasquinha
- Department of Biochemistry & Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Natalie H. Valentin
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Garrett B. Hubbard
- Department of Biochemistry & Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Guowei Yin
- The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518107, China
| | - Henrik G. Dohlman
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Sharon L. Campbell
- Department of Biochemistry & Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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8
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Klauer MJ, Willette BKA, Tsvetanova NG. Functional diversification of cell signaling by GPCR localization. J Biol Chem 2024; 300:105668. [PMID: 38272232 PMCID: PMC10882132 DOI: 10.1016/j.jbc.2024.105668] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 11/13/2023] [Accepted: 11/29/2023] [Indexed: 01/27/2024] Open
Abstract
G protein-coupled receptors (GPCRs) are the largest family of cell surface receptors and a critical class of regulators of mammalian physiology. Also known as seven transmembrane receptors (7TMs), GPCRs are ubiquitously expressed and versatile, detecting a diverse set of endogenous stimuli, including odorants, neurotransmitters, hormones, peptides, and lipids. Accordingly, GPCRs have emerged as the largest class of drug targets, accounting for upward of 30% of all prescription drugs. The view that ligand-induced GPCR responses originate exclusively from the cell surface has evolved to reflect accumulating evidence that receptors can elicit additional waves of signaling from intracellular compartments. These events in turn shape unique cellular and physiological outcomes. Here, we discuss our current understanding of the roles and regulation of compartmentalized GPCR signaling.
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Affiliation(s)
- Matthew J Klauer
- Department of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina, USA
| | - Blair K A Willette
- Department of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina, USA
| | - Nikoleta G Tsvetanova
- Department of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina, USA.
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9
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Hoch-Schneider EE, Saleski T, Jensen ED, Jensen MK. Rational engineering approaches for establishing insect olfaction reporters in yeast. BIOTECHNOLOGY NOTES (AMSTERDAM, NETHERLANDS) 2023; 4:90-99. [PMID: 39416924 PMCID: PMC11446376 DOI: 10.1016/j.biotno.2023.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 10/26/2023] [Accepted: 11/12/2023] [Indexed: 10/19/2024]
Abstract
Insect olfaction directly impacts insect behavior and thus is an important consideration in the development of smart farming tools and in integrated pest management strategies. Insect olfactory receptors (ORs) have been traditionally studied using Drosophila empty neuron systems or with expression and functionalization in HEK293 cells or Xenopus laevis oocytes. Recently, the yeast Saccharomyces cerevisiae (S. cerevisiae) has emerged as a promising chassis for the functional expression of heterologous seven transmembrane receptors. S. cerevisiae provides a platform for the cheap and high throughput study of these receptors and potential deorphanization. In this study, we explore the foundations of a scalable yeast-based platform for the functional expression of insect olfactory receptors by employing a genetically encoded calcium sensor for quantitative evaluation of fluorescence and optimized experimental parameters for enhanced functionality. While the co-receptor of insect olfactory receptors remains non-functional in our yeast-based system, we thoroughly evaluated various experimental variables and identified future research directions for establishing an OR platform in S. cerevisiae.
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Affiliation(s)
- Emma Elise Hoch-Schneider
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Tatyana Saleski
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Emil D. Jensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Michael Krogh Jensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
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10
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Lešnik S, Bren U, Domratcheva T, Bondar AN. Fentanyl and the Fluorinated Fentanyl Derivative NFEPP Elicit Distinct Hydrogen-Bond Dynamics of the Opioid Receptor. J Chem Inf Model 2023; 63:4732-4748. [PMID: 37498626 DOI: 10.1021/acs.jcim.3c00197] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2023]
Abstract
The development of safe therapeutics to manage pain is of central interest for biomedical applications. The fluorinated fentanyl derivative N-(3-fluoro-1-phenethylpiperidin-4-yl)-N-phenylpropionamide (NFEPP) is potentially a safer alternative to fentanyl because unlike fentanyl─which binds to the μ-opioid receptor (MOR) at both physiological and acidic pH─NFEPP might bind to the MOR only at acidic pH typical of inflamed tissue. Knowledge of the protonation-coupled dynamics of the receptor-drug interactions is thus required to understand the molecular mechanism by which receptor activation initiates cell signaling to silence pain. To this end, here we have carried out extensive atomistic simulations of the MOR in different protonation states, in the absence of opioid drugs, and in the presence of fentanyl vs NFEPP. We used graph-based analyses to characterize internal hydrogen-bond networks that could contribute to the activation of the MOR. We find that fentanyl and NFEPP prefer distinct binding poses and that, in their binding poses, fentanyl and NFEPP partake in distinct internal hydrogen-bond networks, leading to the cytoplasmic G-protein-binding region. Moreover, the protonation state of functionally important aspartic and histidine side chains impacts hydrogen-bond networks that extend throughout the receptor, such that the ligand-bound MOR presents at its cytoplasmic G-protein-binding side, a hydrogen-bonding environment where dynamics depend on whether fentanyl or NFEPP is bound, and on the protonation state of specific MOR groups. The exquisite sensitivity of the internal protein-water hydrogen-bond network to the protonation state and to details of the drug binding could enable the MOR to elicit distinct pH- and opioid-dependent responses at its cytoplasmic G-protein-binding site.
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Affiliation(s)
- Samo Lešnik
- Faculty of Chemistry and Chemical Engineering, Laboratory of Physical Chemistry and Chemical Thermodynamics, University of Maribor, Smetanova ulica 17, SI-2000 Maribor, Slovenia
- Institute for Environmental Protection and Sensors, Beloruska ulica 7, 2000 Maribor, Slovenia
| | - Urban Bren
- Faculty of Chemistry and Chemical Engineering, Laboratory of Physical Chemistry and Chemical Thermodynamics, University of Maribor, Smetanova ulica 17, SI-2000 Maribor, Slovenia
- Institute for Environmental Protection and Sensors, Beloruska ulica 7, 2000 Maribor, Slovenia
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, SI-6000 Koper, Slovenia
| | - Tatiana Domratcheva
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
- Department of Biomolecular Mechanisms, Max-Plank-Institute fur Medizinische Forschung, D-69120 Heidelberg, Germany
| | - Ana-Nicoleta Bondar
- Faculty of Physics, University of Bucharest, Atomiştilor 405, 077125 Măgurele, Romania
- Institute of Computational Biomedicine, IAS-5/INM-9, Forschungszentrum Jülich, Wilhelm-Johnen Straße, 5428 Jülich, Germany
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11
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Shaw WM, Zhang Y, Lu X, Khalil AS, Ladds G, Luo X, Ellis T. Screening microbially produced Δ 9-tetrahydrocannabinol using a yeast biosensor workflow. Nat Commun 2022; 13:5509. [PMID: 36127350 PMCID: PMC9489785 DOI: 10.1038/s41467-022-33207-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 09/07/2022] [Indexed: 12/03/2022] Open
Abstract
Microbial production of cannabinoids promises to provide a consistent, cheaper, and more sustainable supply of these important therapeutic molecules. However, scaling production to compete with traditional plant-based sources is challenging. Our ability to make strain variants greatly exceeds our capacity to screen and identify high producers, creating a bottleneck in metabolic engineering efforts. Here, we present a yeast-based biosensor for detecting microbially produced Δ9-tetrahydrocannabinol (THC) to increase throughput and lower the cost of screening. We port five human cannabinoid G protein-coupled receptors (GPCRs) into yeast, showing the cannabinoid type 2 receptor, CB2R, can couple to the yeast pheromone response pathway and report on the concentration of a variety of cannabinoids over a wide dynamic and operational range. We demonstrate that our cannabinoid biosensor can detect THC from microbial cell culture and use this as a tool for measuring relative production yields from a library of Δ9-tetrahydrocannabinol acid synthase (THCAS) mutants. Microbial production of cannabinoids promises a cheaper and more sustainable route to these important therapeutic molecules, but strain improvement and screening is challenging. Here, the authors develop a yeast-based Δ9-tetrahydrocannabinol (THC) biosensor for screening microbial mutant libraries.
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Affiliation(s)
- William M Shaw
- Biological Design Center, Boston University, Boston, MA, 02215, USA.,Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA.,Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK.,Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK
| | - Yunfeng Zhang
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Xinyu Lu
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK.,Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK
| | - Ahmad S Khalil
- Biological Design Center, Boston University, Boston, MA, 02215, USA.,Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA
| | - Graham Ladds
- Department of Pharmacology, University of Cambridge, Cambridge, CB2 1PD, UK
| | - Xiaozhou Luo
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Tom Ellis
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK. .,Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK.
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12
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Schmoll M, Hinterdobler W. Tools for adapting to a complex habitat: G-protein coupled receptors in Trichoderma. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2022; 193:65-97. [PMID: 36357080 DOI: 10.1016/bs.pmbts.2022.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Sensing the environment and interpretation of the received signals are crucial competences of living organisms in order to properly adapt to their habitat, succeed in competition and to reproduce. G-protein coupled receptors (GPCRs) are members of a large family of sensors for extracellular signals and represent the starting point of complex signaling cascades regulating a plethora of intracellular physiological processes and output pathways in fungi. In Trichoderma spp. current research involves a wide range of topics from enzyme production, light response and secondary metabolism to sexual and asexual development as well as biocontrol, all of which require delicate balancing of resources in response to the environmental challenges or biotechnological needs at hand, which are crucially impacted by the surroundings of the fungi and their intercellular signaling cascades triggering a precisely tailored response. In this review we summarize recent findings on sensing by GPCRs in Trichoderma, including the function of pheromone receptors, glucose sensing by CSG1 and CSG2, regulation of secondary metabolism by GPR8 and impacts on mycoparasitism by GPR1. Additionally, we provide an overview on structural determinants, posttranslational modifications and interactions for regulation, activation and signal termination of GPCRs in order to inspire future in depth analyses of their function and to understand previous regulatory outcomes of natural and biotechnological processes modulated or enabled by GPCRs.
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Affiliation(s)
- Monika Schmoll
- Department of Microbiology and Ecosystem Science, Division of Terrestrial Ecosystem Research, University of Vienna, Vienna, Austria.
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13
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Lengger B, Hoch-Schneider EE, Jensen CN, Jakočiu̅nas T, Petersen AA, Frimurer TM, Jensen ED, Jensen MK. Serotonin G Protein-Coupled Receptor-Based Biosensing Modalities in Yeast. ACS Sens 2022; 7:1323-1335. [PMID: 35452231 PMCID: PMC9150182 DOI: 10.1021/acssensors.1c02061] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 03/17/2022] [Indexed: 11/29/2022]
Abstract
Serotonin is a key neurotransmitter involved in numerous physiological processes and serves as an important precursor for manufacturing bioactive indoleamines and alkaloids used in the treatment of human pathologies. In humans, serotonin sensing and signaling can occur by 12 G protein-coupled receptors (GPCRs) coupled to Gα proteins. In yeast, human serotonin GPCRs coupled to Gα proteins have previously been shown to function as whole-cell biosensors of serotonin. However, systematic characterization of serotonin biosensing modalities between variant serotonin GPCRs and application thereof for high-resolution serotonin quantification is still awaiting. To systematically assess GPCR signaling in response to serotonin, we characterized reporter gene expression at two different pHs of a 144-sized library encoding all 12 human serotonin GPCRs in combination with 12 different Gα proteins engineered in yeast. From this screen, we observed changes in the biosensor sensitivities of >4 orders of magnitude. Furthermore, adopting optimal biosensing designs and pH conditions enabled high-resolution high-performance liquid chromatography-validated sensing of serotonin produced in yeast. Lastly, we used the yeast platform to characterize 19 serotonin GPCR polymorphisms found in human populations. While major differences in signaling were observed among the individual polymorphisms when studied in yeast, a cross-comparison of selected variants in mammalian cells showed both similar and disparate results. Taken together, our study highlights serotonin biosensing modalities of relevance to both biotechnological and potential human health applications.
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Affiliation(s)
- Bettina Lengger
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Emma E. Hoch-Schneider
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Christina N. Jensen
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Tadas Jakočiu̅nas
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Anja A. Petersen
- Novo
Nordisk Foundation Center for Basic Metabolic Research, Faculty of
Health and Medical Sciences, University
of Copenhagen, Maersk
Tower, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
| | - Thomas M. Frimurer
- Novo
Nordisk Foundation Center for Basic Metabolic Research, Faculty of
Health and Medical Sciences, University
of Copenhagen, Maersk
Tower, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
| | - Emil D. Jensen
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Michael K. Jensen
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
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14
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Imenez Silva PH, Wagner CA. Physiological relevance of proton-activated GPCRs. Pflugers Arch 2022; 474:487-504. [PMID: 35247105 PMCID: PMC8993716 DOI: 10.1007/s00424-022-02671-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 02/07/2022] [Accepted: 02/08/2022] [Indexed: 12/12/2022]
Abstract
The detection of H+ concentration variations in the extracellular milieu is accomplished by a series of specialized and non-specialized pH-sensing mechanisms. The proton-activated G protein-coupled receptors (GPCRs) GPR4 (Gpr4), TDAG8 (Gpr65), and OGR1 (Gpr68) form a subfamily of proteins capable of triggering intracellular signaling in response to alterations in extracellular pH around physiological values, i.e., in the range between pH 7.5 and 6.5. Expression of these receptors is widespread for GPR4 and OGR1 with particularly high levels in endothelial cells and vascular smooth muscle cells, respectively, while expression of TDAG8 appears to be more restricted to the immune compartment. These receptors have been linked to several well-studied pH-dependent physiological activities including central control of respiration, renal adaption to changes in acid-base status, secretion of insulin and peripheral responsiveness to insulin, mechanosensation, and cellular chemotaxis. Their role in pathological processes such as the genesis and progression of several inflammatory diseases (asthma, inflammatory bowel disease), and tumor cell metabolism and invasiveness, is increasingly receiving more attention and makes these receptors novel and interesting targets for therapy. In this review, we cover the role of these receptors in physiological processes and will briefly discuss some implications for disease processes.
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Affiliation(s)
- Pedro H Imenez Silva
- Institute of Physiology, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland.
- National Center of Competence in Research NCCR Kidney.CH, Zurich, Switzerland.
| | - Carsten A Wagner
- Institute of Physiology, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland.
- National Center of Competence in Research NCCR Kidney.CH, Zurich, Switzerland.
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15
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Richardson K. Genes and knowledge: Response to Baverstock, K. the gene an appraisal. https://doi.org/10.1016/j.pbiomolbio.2021.04.005. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2021; 167:12-17. [PMID: 34736965 DOI: 10.1016/j.pbiomolbio.2021.10.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 09/21/2021] [Accepted: 10/26/2021] [Indexed: 06/13/2023]
Abstract
This response aims to expand on some of the issues raised by Keith Baverstock's The Gene: An Appraisal, especially on the evolution and nature of knowledge in living things. In contrast to the simple associationism envisaged in "genetic information", it emphasises the dynamic complexity and changeability of most natural environments, and, therefore, predictability based on underlying statistical structures. That seems to be the basis of the "cognitive" functions increasingly being reported about cellular, as well as more evolved, functions, and of the autonomous agency of organisms thriving creatively in complex environments.
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