1
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Walker RV, Yao Q, Xu H, Maranto A, Swaney KF, Ramachandran S, Li R, Cassina L, Polster BM, Outeda P, Boletta A, Watnick T, Qian F. Fibrocystin/Polyductin releases a C-terminal fragment that translocates into mitochondria and suppresses cystogenesis. Nat Commun 2023; 14:6513. [PMID: 37845212 PMCID: PMC10579373 DOI: 10.1038/s41467-023-42196-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 10/03/2023] [Indexed: 10/18/2023] Open
Abstract
Fibrocystin/Polyductin (FPC), encoded by PKHD1, is associated with autosomal recessive polycystic kidney disease (ARPKD), yet its precise role in cystogenesis remains unclear. Here we show that FPC undergoes complex proteolytic processing in developing kidneys, generating three soluble C-terminal fragments (ICDs). Notably, ICD15, contains a novel mitochondrial targeting sequence at its N-terminus, facilitating its translocation into mitochondria. This enhances mitochondrial respiration in renal epithelial cells, partially restoring impaired mitochondrial function caused by FPC loss. FPC inactivation leads to abnormal ultrastructural morphology of mitochondria in kidney tubules without cyst formation. Moreover, FPC inactivation significantly exacerbates renal cystogenesis and triggers severe pancreatic cystogenesis in a Pkd1 mouse mutant Pkd1V/V in which cleavage of Pkd1-encoded Polycystin-1 at the GPCR Proteolysis Site is blocked. Deleting ICD15 enhances renal cystogenesis without inducing pancreatic cysts in Pkd1V/V mice. These findings reveal a direct link between FPC and a mitochondrial pathway through ICD15 cleavage, crucial for cystogenesis mechanisms.
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Affiliation(s)
- Rebecca V Walker
- Division of Nephrology, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Qin Yao
- Division of Nephrology, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
- Laboratory of Clinical Investigation, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Hangxue Xu
- Division of Nephrology, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Anthony Maranto
- Division of Nephrology, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Kristen F Swaney
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sreekumar Ramachandran
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Rong Li
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Mechanobiology Institute and Department of Biological Sciences, National University of Singapore, Singapore, 117411, Singapore
| | - Laura Cassina
- Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Brian M Polster
- Department of Anesthesiology and Center for Shock, Trauma, and Anesthesiology Research, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Patricia Outeda
- Division of Nephrology, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Alessandra Boletta
- Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Terry Watnick
- Division of Nephrology, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Feng Qian
- Division of Nephrology, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA.
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2
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Morleo M, Vieira HL, Pennekamp P, Palma A, Bento-Lopes L, Omran H, Lopes SS, Barral DC, Franco B. Crosstalk between cilia and autophagy: implication for human diseases. Autophagy 2023; 19:24-43. [PMID: 35613303 PMCID: PMC9809938 DOI: 10.1080/15548627.2022.2067383] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Macroautophagy/autophagy is a self-degradative process necessary for cells to maintain their energy balance during development and in response to nutrient deprivation. Autophagic processes are tightly regulated and have been found to be dysfunctional in several pathologies. Increasing experimental evidence points to the existence of an interplay between autophagy and cilia. Cilia are microtubule-based organelles protruding from the cell surface of mammalian cells that perform a variety of motile and sensory functions and, when dysfunctional, result in disorders known as ciliopathies. Indeed, selective autophagic degradation of ciliary proteins has been shown to control ciliogenesis and, conversely, cilia have been reported to control autophagy. Moreover, a growing number of players such as lysosomal and mitochondrial proteins are emerging as actors of the cilia-autophagy interplay. However, some of the published data on the cilia-autophagy axis are contradictory and indicate that we are just starting to understand the underlying molecular mechanisms. In this review, the current knowledge about this axis and challenges are discussed, as well as the implication for ciliopathies and autophagy-associated disorders.
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Affiliation(s)
- Manuela Morleo
- Telethon Institute of Genetics and Medicine (TIGEM), 80078, Pozzuoli, Italy,Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Naples, Italy
| | - Helena L.A. Vieira
- CEDOC, NOVA Medical School, NMS, Universidade NOVA de Lisboa, Lisboa1169-056, Portugal,UCIBIO, Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal,Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Petra Pennekamp
- Department of General Pediatrics, University Hospital Münster, University of Münster, Münster48149, Germany,Member of the European Reference Networks ERN-LUNG, Lisbon, Portugal
| | - Alessandro Palma
- Department of Onco-hematology, Gene and Cell Therapy, Bambino Gesù Children’s Hospital - IRCCS, Rome, Italy
| | - Liliana Bento-Lopes
- CEDOC, NOVA Medical School, NMS, Universidade NOVA de Lisboa, Lisboa1169-056, Portugal
| | - Heymut Omran
- Department of General Pediatrics, University Hospital Münster, University of Münster, Münster48149, Germany,Member of the European Reference Networks ERN-LUNG, Lisbon, Portugal
| | - Susana S. Lopes
- CEDOC, NOVA Medical School, NMS, Universidade NOVA de Lisboa, Lisboa1169-056, Portugal,Member of the European Reference Networks ERN-LUNG, Lisbon, Portugal
| | - Duarte C. Barral
- CEDOC, NOVA Medical School, NMS, Universidade NOVA de Lisboa, Lisboa1169-056, Portugal
| | - Brunella Franco
- Telethon Institute of Genetics and Medicine (TIGEM), 80078, Pozzuoli, Italy,Medical Genetics, Department of Translational Medical Science, University of Naples “Federico II”, Naples, Italy,Scuola Superiore Meridionale, School for Advanced Studies, Naples, Italy,CONTACT Brunella Franco CEDOC, NOVA Medical School, NMS, Universidade NOVA de Lisboa, Lisboa1169-056, Portugal
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3
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Dow JAT, Simons M, Romero MF. Drosophila melanogaster: a simple genetic model of kidney structure, function and disease. Nat Rev Nephrol 2022; 18:417-434. [PMID: 35411063 DOI: 10.1038/s41581-022-00561-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/07/2022] [Indexed: 12/27/2022]
Abstract
Although the genetic basis of many kidney diseases is being rapidly elucidated, their experimental study remains problematic owing to the lack of suitable models. The fruitfly Drosophila melanogaster provides a rapid, ethical and cost-effective model system of the kidney. The unique advantages of D. melanogaster include ease and low cost of maintenance, comprehensive availability of genetic mutants and powerful transgenic technologies, and less onerous regulation, as compared with mammalian systems. Renal and excretory functions in D. melanogaster reside in three main tissues - the transporting renal (Malpighian) tubules, the reabsorptive hindgut and the endocytic nephrocytes. Tubules contain multiple cell types and regions and generate a primary urine by transcellular transport rather than filtration, which is then subjected to selective reabsorption in the hindgut. By contrast, the nephrocytes are specialized for uptake of macromolecules and equipped with a filtering slit diaphragm resembling that of podocytes. Many genes with key roles in the human kidney have D. melanogaster orthologues that are enriched and functionally relevant in fly renal tissues. This similarity has allowed investigations of epithelial transport, kidney stone formation and podocyte and proximal tubule function. Furthermore, a range of unique quantitative phenotypes are available to measure function in both wild type and disease-modelling flies.
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Affiliation(s)
- Julian A T Dow
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK.
| | - Matias Simons
- INSERM UMR1163, Laboratory of Epithelial Biology and Disease, Imagine Institute, Université de Paris, Hôpital Necker-Enfants Malades, Paris, France
- Institute of Human Genetics, University Hospital Heidelberg, Heidelberg, Germany
| | - Michael F Romero
- Department of Physiology and Biomedical Engineering, Division of Nephrology and Hypertension, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
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4
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Cantero MDR, Cantiello HF. Polycystin-2 (TRPP2): Ion channel properties and regulation. Gene 2022; 827:146313. [PMID: 35314260 DOI: 10.1016/j.gene.2022.146313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 01/19/2022] [Accepted: 02/08/2022] [Indexed: 12/01/2022]
Abstract
Polycystin-2 (TRPP2, PKD2, PC2) is the product of the PKD2 gene, whose mutations cause Autosomal Dominant Polycystic Kidney Disease (ADPKD). PC2 belongs to the superfamily of TRP (Transient Receptor Potential) proteins that generally function as Ca2+-permeable nonselective cation channels implicated in Ca2+ signaling. PC2 localizes to various cell domains with distinct functions that likely depend on interactions with specific channel partners. Functions include receptor-operated, nonselective cation channel activity in the plasma membrane, intracellular Ca2+ release channel activity in the endoplasmic reticulum (ER), and mechanosensitive channel activity in the primary cilium of renal epithelial cells. Here we summarize our current understanding of the properties of PC2 and how other transmembrane and cytosolic proteins modulate this activity, providing functional diversity and selective regulatory mechanisms to its role in the control of cellular Ca2+ homeostasis.
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Affiliation(s)
- María Del Rocío Cantero
- Laboratorio de Canales Iónicos, Instituto Multidisciplinario de Salud, Tecnología y Desarrollo (IMSaTeD, CONICET-UNSE), El Zanjón, Santiago del Estero 4206, Argentina.
| | - Horacio F Cantiello
- Laboratorio de Canales Iónicos, Instituto Multidisciplinario de Salud, Tecnología y Desarrollo (IMSaTeD, CONICET-UNSE), El Zanjón, Santiago del Estero 4206, Argentina
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5
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A pair of transporters controls mitochondrial Zn 2+ levels to maintain mitochondrial homeostasis. Protein Cell 2021; 13:180-202. [PMID: 34687432 PMCID: PMC8901913 DOI: 10.1007/s13238-021-00881-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 09/02/2021] [Indexed: 12/15/2022] Open
Abstract
Zn2+ is required for the activity of many mitochondrial proteins, which regulate mitochondrial dynamics, apoptosis and mitophagy. However, it is not understood how the proper mitochondrial Zn2+ level is achieved to maintain mitochondrial homeostasis. Using Caenorhabditis elegans, we reveal here that a pair of mitochondrion-localized transporters controls the mitochondrial level of Zn2+. We demonstrate that SLC-30A9/ZnT9 is a mitochondrial Zn2+ exporter. Loss of SLC-30A9 leads to mitochondrial Zn2+ accumulation, which damages mitochondria, impairs animal development and shortens the life span. We further identify SLC-25A25/SCaMC-2 as an important regulator of mitochondrial Zn2+ import. Loss of SLC-25A25 suppresses the abnormal mitochondrial Zn2+ accumulation and defective mitochondrial structure and functions caused by loss of SLC-30A9. Moreover, we reveal that the endoplasmic reticulum contains the Zn2+ pool from which mitochondrial Zn2+ is imported. These findings establish the molecular basis for controlling the correct mitochondrial Zn2+ levels for normal mitochondrial structure and functions.
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6
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Jabalameli MR, Fitzpatrick FM, Colombo R, Howles SA, Leggatt G, Walker V, Wiberg A, Kunji ERS, Ennis S. Exome sequencing identifies a disease variant of the mitochondrial ATP-Mg/Pi carrier SLC25A25 in two families with kidney stones. Mol Genet Genomic Med 2021; 9:e1749. [PMID: 34346195 PMCID: PMC8683635 DOI: 10.1002/mgg3.1749] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 05/13/2021] [Accepted: 07/01/2021] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Calcium kidney stones are common and recurrences are often not preventable by available empiric remedies. Their etiology is multifactorial and polygenic, and an increasing number of genes are implicated. Their identification will enable improved management. METHODS DNA from three stone-formers in a Southampton family (UK) and two from an Italian family were analyzed independently by whole exome sequencing and selected variants were genotyped across all available members of both pedigrees. A disease variant of SLC25A25 (OMIM 608745), encoding the mitochondrial ATP-Mg/Pi carrier 3 (APC3) was identified, and analyzed structurally and functionally with respect to its calcium-regulated transport activity. RESULTS All five patients had a heterozygous dominant SLC25A25 variant (rs140777921; GRCh37.p13: chr 9 130868670 G>C; p.Gln349His; Reference Sequence NM_001006641.3). Non-stone formers also carried the variant indicating incomplete penetrance. Modeling suggests that the variant lacks a conserved polar interaction, which may cause structural instability. Calcium-regulated ATP transport was reduced to ~20% of the wild type, showing a large reduction in function. CONCLUSION The transporter is important in regulating mitochondrial ATP production. This rare variant may increase urine lithogenicity through impaired provision of ATP for solute transport processes in the kidney, and/or for purinergic signaling. Variants found in other genes may compound this abnormality.
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Affiliation(s)
- M Reza Jabalameli
- Department of Human Genetics and Genomic Medicine, University of Southampton, Southampton, UK
| | - Fiona M Fitzpatrick
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Roberto Colombo
- Faculty of Medicine 'Agostino Gemelli', Catholic University of the Sacred Heart, Rome, Italy.,Center for the Study of Rare Inherited Diseases, Niguarda Ca´Granda Metropolitan Hospital, Milan, Italy
| | - Sarah A Howles
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK.,Academic Endocrine Unit, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Gary Leggatt
- Department of Human Genetics and Genomic Medicine, University of Southampton, Southampton, UK.,Wessex Kidney Centre, Queen Alexandra Hospital, Portsmouth, UK
| | - Valerie Walker
- Department of Clinical Biochemistry, University Hospital Southampton, Southampton, UK
| | - Akira Wiberg
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Edmund R S Kunji
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Sarah Ennis
- Department of Human Genetics and Genomic Medicine, University of Southampton, Southampton, UK
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7
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Identification of pathological transcription in autosomal dominant polycystic kidney disease epithelia. Sci Rep 2021; 11:15139. [PMID: 34301992 PMCID: PMC8302622 DOI: 10.1038/s41598-021-94442-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 07/08/2021] [Indexed: 11/09/2022] Open
Abstract
Autosomal dominant polycystic kidney disease (ADPKD) affects more than 12 million people worldwide. Mutations in PKD1 and PKD2 cause cyst formation through unknown mechanisms. To unravel the pathogenic mechanisms in ADPKD, multiple studies have investigated transcriptional mis-regulation in cystic kidneys from patients and mouse models, and numerous dysregulated genes and pathways have been described. Yet, the concordance between studies has been rather limited. Furthermore, the cellular and genetic diversity in cystic kidneys has hampered the identification of mis-expressed genes in kidney epithelial cells with homozygous PKD mutations, which are critical to identify polycystin-dependent pathways. Here we performed transcriptomic analyses of Pkd1- and Pkd2-deficient mIMCD3 kidney epithelial cells followed by a meta-analysis to integrate all published ADPKD transcriptomic data sets. Based on the hypothesis that Pkd1 and Pkd2 operate in a common pathway, we first determined transcripts that are differentially regulated by both genes. RNA sequencing of genome-edited ADPKD kidney epithelial cells identified 178 genes that are concordantly regulated by Pkd1 and Pkd2. Subsequent integration of existing transcriptomic studies confirmed 31 previously described genes and identified 61 novel genes regulated by Pkd1 and Pkd2. Cluster analyses then linked Pkd1 and Pkd2 to mRNA splicing, specific factors of epithelial mesenchymal transition, post-translational protein modification and epithelial cell differentiation, including CD34, CDH2, CSF2RA, DLX5, HOXC9, PIK3R1, PLCB1 and TLR6. Taken together, this model-based integrative analysis of transcriptomic alterations in ADPKD annotated a conserved core transcriptomic profile and identified novel candidate genes for further experimental studies.
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8
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Kunji ERS, King MS, Ruprecht JJ, Thangaratnarajah C. The SLC25 Carrier Family: Important Transport Proteins in Mitochondrial Physiology and Pathology. Physiology (Bethesda) 2021; 35:302-327. [PMID: 32783608 PMCID: PMC7611780 DOI: 10.1152/physiol.00009.2020] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Members of the mitochondrial carrier family (SLC25) transport a variety of compounds across the inner membrane of mitochondria. These transport steps provide building blocks for the cell and link the pathways of the mitochondrial matrix and cytosol. An increasing number of diseases and pathologies has been associated with their dysfunction. In this review, the molecular basis of these diseases is explained based on our current understanding of their transport mechanism.
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Affiliation(s)
- Edmund R S Kunji
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, United Kingdom
| | - Martin S King
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, United Kingdom
| | - Jonathan J Ruprecht
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, United Kingdom
| | - Chancievan Thangaratnarajah
- Groningen Biomolecular Sciences and Biotechnology Institute, Membrane Enzymology, University of Groningen, Groningen, The Netherlands
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9
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Ca 2+-regulated mitochondrial carriers of ATP-Mg 2+/Pi: Evolutionary insights in protozoans. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2021; 1868:119038. [PMID: 33839167 DOI: 10.1016/j.bbamcr.2021.119038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/30/2021] [Accepted: 03/31/2021] [Indexed: 11/23/2022]
Abstract
In addition to its uptake across the Ca2+ uniporter, intracellular calcium signals can stimulate mitochondrial metabolism activating metabolite exchangers of the inner mitochondrial membrane belonging to the mitochondrial carrier family (SLC25). One of these Ca2+-regulated mitochondrial carriers (CaMCs) are the reversible ATP-Mg2+/Pi transporters, or SCaMCs, required for maintaining optimal adenine nucleotide (AdN) levels in the mitochondrial matrix representing an alternative transporter to the ADP/ATP translocases (AAC). This CaMC has a distinctive Calmodulin-like (CaM-like) domain fused to the carrier domain that makes its transport activity strictly dependent on cytosolic Ca2+ signals. Here we investigate about its origin analysing its distribution and features in unicellular eukaryotes. Unexpectedly, we find two types of ATP-Mg2+/Pi carriers, the canonical ones and shortened variants lacking the CaM-like domain. Phylogenetic analysis shows that both SCaMC variants have a common origin, unrelated to AACs, suggesting in turn that recurrent losses of the regulatory module have occurred in the different phyla. They are excluding variants that show a more limited distribution and less conservation than AACs. Interestingly, these truncated variants of SCaMC are found almost exclusively in parasitic protists, such as apicomplexans, kinetoplastides or animal-patogenic oomycetes, and in green algae, suggesting that its lost could be related to certain life-styles. In addition, we find an intricate structural diversity in these variants that may be associated with their pathogenicity. The consequences on SCaMC functions of these new SCaMC-b variants are discussed.
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10
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Transcriptome-wide analysis of PGC-1α-binding RNAs identifies genes linked to glucagon metabolic action. Proc Natl Acad Sci U S A 2020; 117:22204-22213. [PMID: 32848060 DOI: 10.1073/pnas.2000643117] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC-1α) is a transcriptional coactivator that controls expression of metabolic/energetic genes, programming cellular responses to nutrient and environmental adaptations such as fasting, cold, or exercise. Unlike other coactivators, PGC-1α contains protein domains involved in RNA regulation such as serine/arginine (SR) and RNA recognition motifs (RRMs). However, the RNA targets of PGC-1α and how they pertain to metabolism are unknown. To address this, we performed enhanced ultraviolet (UV) cross-linking and immunoprecipitation followed by sequencing (eCLIP-seq) in primary hepatocytes induced with glucagon. A large fraction of RNAs bound to PGC-1α were intronic sequences of genes involved in transcriptional, signaling, or metabolic function linked to glucagon and fasting responses, but were not the canonical direct transcriptional PGC-1α targets such as OXPHOS or gluconeogenic genes. Among the top-scoring RNA sequences bound to PGC-1α were Foxo1, Camk1δ, Per1, Klf15, Pln4, Cluh, Trpc5, Gfra1, and Slc25a25 PGC-1α depletion decreased a fraction of these glucagon-induced messenger RNA (mRNA) transcript levels. Importantly, knockdown of several of these genes affected glucagon-dependent glucose production, a PGC-1α-regulated metabolic pathway. These studies show that PGC-1α binds to intronic RNA sequences, some of them controlling transcript levels associated with glucagon action.
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11
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Abstract
Saccharomyces cerevisiae is one of the most popular expression systems for eukaryotic membrane proteins. Here, we describe protocols for the expression and purification of mitochondrial membrane proteins developed in our laboratory during the last 15 years. To optimize their expression in a functional form, different promoter systems as well as codon-optimization and complementation strategies were established. Purification approaches were developed which remove the membrane protein from the affinity column by specific proteolytic cleavage rather than by elution. This strategy has several important advantages, most notably improving the purity of the sample, as contaminants stay bound to the column, thus eliminating the need for a secondary purification step, such as size exclusion chromatography. This strategy also avoids dilution of the sample, which would occur as a consequence of elution, precluding the need for concentration steps, and thus preventing detergent concentration.
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Affiliation(s)
- Martin S King
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Edmund R S Kunji
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK.
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12
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Rothé B, Gagnieux C, Leal-Esteban LC, Constam DB. Role of the RNA-binding protein Bicaudal-C1 and interacting factors in cystic kidney diseases. Cell Signal 2019; 68:109499. [PMID: 31838063 DOI: 10.1016/j.cellsig.2019.109499] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 12/09/2019] [Accepted: 12/10/2019] [Indexed: 01/03/2023]
Abstract
Polycystic kidneys frequently associate with mutations in individual components of cilia, basal bodies or centriolar satellites that perturb complex protein networks. In this review, we focus on the RNA-binding protein Bicaudal-C1 (BICC1) which was found mutated in renal cystic dysplasia, and on its interactions with the ankyrin repeat and sterile α motif (SAM)-containing proteins ANKS3 and ANKS6 and associated kinases and their partially overlapping ciliopathy phenotypes. After reviewing BICC1 homologs in model organisms and their functions in mRNA and cell metabolism during development and in renal tubules, we discuss recent insights from cell-based assays and from structure analysis of the SAM domains, and how SAM domain oligomerization might influence multivalent higher order complexes that are implicated in ciliary signal transduction.
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Affiliation(s)
- Benjamin Rothé
- Ecole Polytechnique Fédérale de Lausanne (EPFL) SV ISREC, Station 19, CH-1015 Lausanne, Switzerland
| | - Céline Gagnieux
- Ecole Polytechnique Fédérale de Lausanne (EPFL) SV ISREC, Station 19, CH-1015 Lausanne, Switzerland
| | - Lucia Carolina Leal-Esteban
- Ecole Polytechnique Fédérale de Lausanne (EPFL) SV ISREC, Station 19, CH-1015 Lausanne, Switzerland; Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Daniel B Constam
- Ecole Polytechnique Fédérale de Lausanne (EPFL) SV ISREC, Station 19, CH-1015 Lausanne, Switzerland.
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13
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Podrini C, Cassina L, Boletta A. Metabolic reprogramming and the role of mitochondria in polycystic kidney disease. Cell Signal 2019; 67:109495. [PMID: 31816397 DOI: 10.1016/j.cellsig.2019.109495] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 12/04/2019] [Accepted: 12/04/2019] [Indexed: 01/24/2023]
Abstract
Autosomal Dominant Polycystic Kidney Disease (ADPKD) is a slowly progressive disease characterized by the relentless growth of renal cysts throughout the life of affected individuals. Early evidence suggested that the epithelia lining the cysts share neoplastic features, leading to the definition of PKD as a "neoplasm in disguise". Recent work from our and other laboratories has identified a profound metabolic reprogramming in PKD, similar to the one reported in cancer and consistent with the reported increased proliferation. Multiple lines of evidence suggest that aerobic glycolysis (a Warburg-like effect) is present in the disease, along with other metabolic dysfunctions such as an increase in the pentose phosphate pathway, in glutamine anaplerosis and fatty acid biosynthesis, while fatty acid oxidation and oxidative phosphorylation (OXPHOS) are decreased. In addition to glutamine, other amino acid-related pathways appear altered, including asparagine and arginine. The precise origin of the metabolic alterations is not entirely clear, but two hypotheses can be formulated, not mutually exclusive. First, the polycystins have been recently shown to regulate directly mitochondrial function and structure either by regulating Ca2+ uptake in mitochondria at the Mitochondria Associated Membranes (MAMs) of the Endoplasmic Reticulum, or by a direct translocation of a small fragment of the protein into the matrix of mitochondria. One alternative possibility is that metabolic and mitochondrial dysfunctions in ADPKD are secondary to the de-regulation of proliferation, driven by the multiple signaling pathways identified in the disease, which include mTORC1 and AMPK among the most relevant. While the precise mechanisms underlying these novel alterations identified in ADPKD will need further investigation, it is evident that they offer a great opportunity for novel interventions in the disease.
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Affiliation(s)
- Christine Podrini
- Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele Scientific Institute, Milan, Italy
| | - Laura Cassina
- Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele Scientific Institute, Milan, Italy
| | - Alessandra Boletta
- Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele Scientific Institute, Milan, Italy.
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14
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Ogunbona OB, Claypool SM. Emerging Roles in the Biogenesis of Cytochrome c Oxidase for Members of the Mitochondrial Carrier Family. Front Cell Dev Biol 2019; 7:3. [PMID: 30766870 PMCID: PMC6365663 DOI: 10.3389/fcell.2019.00003] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 01/10/2019] [Indexed: 12/11/2022] Open
Abstract
The mitochondrial carrier family (MCF) is a group of transport proteins that are mostly localized to the inner mitochondrial membrane where they facilitate the movement of various solutes across the membrane. Although these carriers represent potential targets for therapeutic application and are repeatedly associated with human disease, research on the MCF has not progressed commensurate to their physiologic and pathophysiologic importance. Many of the 53 MCF members in humans are orphans and lack known transport substrates. Even for the relatively well-studied members of this family, such as the ADP/ATP carrier and the uncoupling protein, there exist fundamental gaps in our understanding of their biological roles including a clear rationale for the existence of multiple isoforms. Here, we briefly review this important family of mitochondrial carriers, provide a few salient examples of their diverse metabolic roles and disease associations, and then focus on an emerging link between several distinct MCF members, including the ADP/ATP carrier, and cytochrome c oxidase biogenesis. As the ADP/ATP carrier is regarded as the paradigm of the entire MCF, its newly established role in regulating translation of the mitochondrial genome highlights that we still have a lot to learn about these metabolite transporters.
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Affiliation(s)
- Oluwaseun B. Ogunbona
- Department of Physiology, School of Medicine, Johns Hopkins University, Baltimore, MD, United States
- Department of Pathology & Laboratory Medicine, School of Medicine, Emory University, Atlanta, GA, United States
| | - Steven M. Claypool
- Department of Physiology, School of Medicine, Johns Hopkins University, Baltimore, MD, United States
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