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Isomeric lipid signatures reveal compartmentalized fatty acid metabolism in cancer. J Lipid Res 2022; 63:100223. [PMID: 35537528 PMCID: PMC9184569 DOI: 10.1016/j.jlr.2022.100223] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 05/03/2022] [Accepted: 05/04/2022] [Indexed: 01/18/2023] Open
Abstract
The cellular energy and biomass demands of cancer drive a complex dynamic between uptake of extracellular FAs and their de novo synthesis. Given that oxidation of de novo synthesized FAs for energy would result in net-energy loss, there is an implication that FAs from these two sources must have distinct metabolic fates; however, hitherto, all FAs have been considered part of a common pool. To probe potential metabolic partitioning of cellular FAs, cancer cells were supplemented with stable isotope-labeled FAs. Structural analysis of the resulting glycerophospholipids revealed that labeled FAs from uptake were largely incorporated to canonical (sn-) positions on the glycerol backbone. Surprisingly, labeled FA uptake also disrupted canonical isomer patterns of the unlabeled lipidome and induced repartitioning of n-3 and n-6 PUFAs into glycerophospholipid classes. These structural changes support the existence of differences in the metabolic fates of FAs derived from uptake or de novo sources and demonstrate unique signaling and remodeling behaviors usually hidden from conventional lipidomics.
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Sargsyan Y, Bickmeyer U, Gibhardt CS, Streckfuss-Bömeke K, Bogeski I, Thoms S. Peroxisomes contribute to intracellular calcium dynamics in cardiomyocytes and non-excitable cells. Life Sci Alliance 2021; 4:4/9/e202000987. [PMID: 34330788 PMCID: PMC8326789 DOI: 10.26508/lsa.202000987] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 07/09/2021] [Accepted: 07/12/2021] [Indexed: 11/24/2022] Open
Abstract
Peroxisomes communicate with other cellular compartments by transfer of various metabolites. However, whether peroxisomes are sites for calcium handling and exchange has remained contentious. Here we generated sensors for assessment of peroxisomal calcium and applied them for single cell-based calcium imaging in HeLa cells and cardiomyocytes. We found that peroxisomes in HeLa cells take up calcium upon depletion of intracellular calcium stores and upon calcium influx across the plasma membrane. Furthermore, we show that peroxisomes of neonatal rat cardiomyocytes and human induced pluripotent stem cell-derived cardiomyocytes can take up calcium. Our results indicate that peroxisomal and cytosolic calcium signals are tightly interconnected both in HeLa cells and in cardiomyocytes. Cardiac peroxisomes take up calcium on beat-to-beat basis. Hence, peroxisomes may play an important role in shaping cellular calcium dynamics of cardiomyocytes.
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Affiliation(s)
- Yelena Sargsyan
- Department of Child and Adolescent Health, University Medical Center, Göttingen, Germany
| | - Uta Bickmeyer
- Department of Child and Adolescent Health, University Medical Center, Göttingen, Germany
| | - Christine S Gibhardt
- Molecular Physiology, Institute of Cardiovascular Physiology, University Medical Center, Göttingen, Germany
| | - Katrin Streckfuss-Bömeke
- Clinic for Cardiology and Pneumology, University Medical Center, Göttingen, Germany.,Institute of Pharmacology and Toxicology, Würzburg University, Würzburg, Germany.,German Center of Cardiovascular Research (DZHK), Partner Site Göttingen, Germany
| | - Ivan Bogeski
- Molecular Physiology, Institute of Cardiovascular Physiology, University Medical Center, Göttingen, Germany
| | - Sven Thoms
- Department of Child and Adolescent Health, University Medical Center, Göttingen, Germany .,Department of Biochemistry and Molecular Medicine, Medical School, Bielefeld University, Bielefeld, Germany.,German Center of Cardiovascular Research (DZHK), Partner Site Göttingen, Germany
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Incorporation of sensing modalities into de novo designed fluorescence-activating proteins. Nat Commun 2021; 12:856. [PMID: 33558528 PMCID: PMC7870846 DOI: 10.1038/s41467-020-18911-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 08/10/2020] [Indexed: 01/07/2023] Open
Abstract
Through the efforts of many groups, a wide range of fluorescent protein reporters and sensors based on green fluorescent protein and its relatives have been engineered in recent years. Here we explore the incorporation of sensing modalities into de novo designed fluorescence-activating proteins, called mini-fluorescence-activating proteins (mFAPs), that bind and stabilize the fluorescent cis-planar state of the fluorogenic compound DFHBI. We show through further design that the fluorescence intensity and specificity of mFAPs for different chromophores can be tuned, and the fluorescence made sensitive to pH and Ca2+ for real-time fluorescence reporting. Bipartite split mFAPs enable real-time monitoring of protein-protein association and (unlike widely used split GFP reporter systems) are fully reversible, allowing direct readout of association and dissociation events. The relative ease with which sensing modalities can be incorporated and advantages in smaller size and photostability make de novo designed fluorescence-activating proteins attractive candidates for optical sensor engineering.
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Chornyi S, IJlst L, van Roermund CWT, Wanders RJA, Waterham HR. Peroxisomal Metabolite and Cofactor Transport in Humans. Front Cell Dev Biol 2021; 8:613892. [PMID: 33505966 PMCID: PMC7829553 DOI: 10.3389/fcell.2020.613892] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Accepted: 12/10/2020] [Indexed: 12/20/2022] Open
Abstract
Peroxisomes are membrane-bound organelles involved in many metabolic pathways and essential for human health. They harbor a large number of enzymes involved in the different pathways, thus requiring transport of substrates, products and cofactors involved across the peroxisomal membrane. Although much progress has been made in understanding the permeability properties of peroxisomes, there are still important gaps in our knowledge about the peroxisomal transport of metabolites and cofactors. In this review, we discuss the different modes of transport of metabolites and essential cofactors, including CoA, NAD+, NADP+, FAD, FMN, ATP, heme, pyridoxal phosphate, and thiamine pyrophosphate across the peroxisomal membrane. This transport can be mediated by non-selective pore-forming proteins, selective transport proteins, membrane contact sites between organelles, and co-import of cofactors with proteins. We also discuss modes of transport mediated by shuttle systems described for NAD+/NADH and NADP+/NADPH. We mainly focus on current knowledge on human peroxisomal metabolite and cofactor transport, but also include knowledge from studies in plants, yeast, fruit fly, zebrafish, and mice, which has been exemplary in understanding peroxisomal transport mechanisms in general.
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Affiliation(s)
- Serhii Chornyi
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC Location AMC, University of Amsterdam, Amsterdam, Netherlands
| | - Lodewijk IJlst
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC Location AMC, University of Amsterdam, Amsterdam, Netherlands
| | - Carlo W T van Roermund
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC Location AMC, University of Amsterdam, Amsterdam, Netherlands
| | - Ronald J A Wanders
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC Location AMC, University of Amsterdam, Amsterdam, Netherlands
| | - Hans R Waterham
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC Location AMC, University of Amsterdam, Amsterdam, Netherlands
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Rajendran M, Claywell B, Haynes EP, Scales U, Henning CK, Tantama M. Imaging pH Dynamics Simultaneously in Two Cellular Compartments Using a Ratiometric pH-Sensitive Mutant of mCherry. ACS OMEGA 2018; 3:9476-9486. [PMID: 30197999 PMCID: PMC6120727 DOI: 10.1021/acsomega.8b00655] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 08/06/2018] [Indexed: 05/09/2023]
Abstract
The regulation of pH is essential for proper organelle function, and organelle-specific changes in pH often reflect the dynamics of physiological signaling and metabolism. For example, mitochondrial energy production depends on the proton gradient maintained between the alkaline mitochondrial matrix and neutral cytosol. However, we still lack a quantitative understanding of how pH dynamics are coupled between compartments and how pH gradients are regulated at organelle boundaries. Genetically encoded pH sensors are well suited to address this problem because they can be targeted to specific subcellular locations and they facilitate live, single-cell analysis. However, most of these pH sensors are derivatives of green and yellow fluorescent proteins that are not spectrally compatible for dual-compartment imaging. Therefore, there is a need for ratiometric red fluorescent protein pH sensors that enable quantitative multicolor imaging of spatially resolved pH dynamics. In this work, we demonstrate that the I158E/Q160A mutant of the red fluorescent protein mCherry is an effective ratiometric pH sensor. It has a pKa of 7.3 and a greater than 3-fold change in ratio signal. To demonstrate its utility in cells, we measured activity and metabolism-dependent pH dynamics in cultured primary neurons and neuroblastoma cells. Furthermore, we were able to image pH changes simultaneously in the cytosol and mitochondria by using the mCherryEA mutant together with the green fluorescent pH sensor, ratiometric-pHluorin. Our results demonstrate the feasibility of studying interorganelle pH dynamics in live cells over time and the broad applicability of these sensors in studying the role of pH regulation in metabolism and signaling.
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Affiliation(s)
- Megha Rajendran
- Department
of Chemistry, Institute for Integrative Neuroscience, and Institute of Inflammation, Immunology,
and Infectious Disease, Purdue University, 560 Oval Drive,
P.O. Box 68, West Lafayette, Indiana 47907, United States
| | - Benjamin Claywell
- Department
of Chemistry, Institute for Integrative Neuroscience, and Institute of Inflammation, Immunology,
and Infectious Disease, Purdue University, 560 Oval Drive,
P.O. Box 68, West Lafayette, Indiana 47907, United States
| | - Emily P. Haynes
- Department
of Chemistry, Institute for Integrative Neuroscience, and Institute of Inflammation, Immunology,
and Infectious Disease, Purdue University, 560 Oval Drive,
P.O. Box 68, West Lafayette, Indiana 47907, United States
| | - Umi Scales
- Department
of Chemistry, Institute for Integrative Neuroscience, and Institute of Inflammation, Immunology,
and Infectious Disease, Purdue University, 560 Oval Drive,
P.O. Box 68, West Lafayette, Indiana 47907, United States
| | - Chace K. Henning
- Department
of Chemistry, Institute for Integrative Neuroscience, and Institute of Inflammation, Immunology,
and Infectious Disease, Purdue University, 560 Oval Drive,
P.O. Box 68, West Lafayette, Indiana 47907, United States
| | - Mathew Tantama
- Department
of Chemistry, Institute for Integrative Neuroscience, and Institute of Inflammation, Immunology,
and Infectious Disease, Purdue University, 560 Oval Drive,
P.O. Box 68, West Lafayette, Indiana 47907, United States
- E-mail: . Phone: 765-494-5312
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