1
|
Perez-Perri JI, Ferring-Appel D, Huppertz I, Schwarzl T, Sahadevan S, Stein F, Rettel M, Galy B, Hentze MW. The RNA-binding protein landscapes differ between mammalian organs and cultured cells. Nat Commun 2023; 14:2074. [PMID: 37045843 PMCID: PMC10097726 DOI: 10.1038/s41467-023-37494-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 03/17/2023] [Indexed: 04/14/2023] Open
Abstract
System-wide approaches have unveiled an unexpected breadth of the RNA-bound proteomes of cultured cells. Corresponding information regarding RNA-binding proteins (RBPs) of mammalian organs is still missing, largely due to technical challenges. Here, we describe ex vivo enhanced RNA interactome capture (eRIC) to characterize the RNA-bound proteomes of three different mouse organs. The resulting organ atlases encompass more than 1300 RBPs active in brain, kidney or liver. Nearly a quarter (291) of these had formerly not been identified in cultured cells, with more than 100 being metabolic enzymes. Remarkably, RBP activity differs between organs independent of RBP abundance, suggesting organ-specific levels of control. Similarly, we identify systematic differences in RNA binding between animal organs and cultured cells. The pervasive RNA binding of enzymes of intermediary metabolism in organs points to tightly knit connections between gene expression and metabolism, and displays a particular enrichment for enzymes that use nucleotide cofactors. We describe a generically applicable refinement of the eRIC technology and provide an instructive resource of RBPs active in intact mammalian organs, including the brain.
Collapse
Affiliation(s)
- Joel I Perez-Perri
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Dunja Ferring-Appel
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Ina Huppertz
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany
- Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931, Cologne, Germany
| | - Thomas Schwarzl
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Sudeep Sahadevan
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Frank Stein
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Mandy Rettel
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Bruno Galy
- German Cancer Research Center (DKFZ), Division of Virus-associated Carcinogenesis, Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.
| | - Matthias W Hentze
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany.
| |
Collapse
|
2
|
Huppertz I, Perez-Perri JI, Mantas P, Sekaran T, Schwarzl T, Russo F, Ferring-Appel D, Koskova Z, Dimitrova-Paternoga L, Kafkia E, Hennig J, Neveu PA, Patil K, Hentze MW. Riboregulation of Enolase 1 activity controls glycolysis and embryonic stem cell differentiation. Mol Cell 2022; 82:2666-2680.e11. [PMID: 35709751 DOI: 10.1016/j.molcel.2022.05.019] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [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: 08/09/2021] [Revised: 02/11/2022] [Accepted: 05/17/2022] [Indexed: 10/18/2022]
Abstract
Differentiating stem cells must coordinate their metabolism and fate trajectories. Here, we report that the catalytic activity of the glycolytic enzyme Enolase 1 (ENO1) is directly regulated by RNAs leading to metabolic rewiring in mouse embryonic stem cells (mESCs). We identify RNA ligands that specifically inhibit ENO1's enzymatic activity in vitro and diminish glycolysis in cultured human cells and mESCs. Pharmacological inhibition or RNAi-mediated depletion of the protein deacetylase SIRT2 increases ENO1's acetylation and enhances its RNA binding. Similarly, induction of mESC differentiation leads to increased ENO1 acetylation, enhanced RNA binding, and inhibition of glycolysis. Stem cells expressing mutant forms of ENO1 that escape or hyper-activate this regulation display impaired germ layer differentiation. Our findings uncover acetylation-driven riboregulation of ENO1 as a physiological mechanism of glycolytic control and of the regulation of stem cell differentiation. Riboregulation may represent a more widespread principle of biological control.
Collapse
Affiliation(s)
- Ina Huppertz
- European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Joel I Perez-Perri
- European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Panagiotis Mantas
- European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Thileepan Sekaran
- European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Thomas Schwarzl
- European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Francesco Russo
- European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Dunja Ferring-Appel
- European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Zuzana Koskova
- European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany
| | | | - Eleni Kafkia
- European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Janosch Hennig
- European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Pierre A Neveu
- European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Kiran Patil
- European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Matthias W Hentze
- European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany.
| |
Collapse
|
3
|
Kovac S, Böser P, Cui Y, Ferring-Appel D, Casarrubea D, Huang L, Fung E, Popp A, Mueller BK, Hentze MW. Anti-hemojuvelin antibody corrects anemia caused by inappropriately high hepcidin levels. Haematologica 2016; 101:e173-6. [PMID: 26944476 DOI: 10.3324/haematol.2015.140772] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
- Suzana Kovac
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | | | - Yifang Cui
- Abbvie Deutschland GmbH & Co KG, Ludwigshafen, Germany
| | | | | | - Lili Huang
- Abbvie Bioresearch Center, Worcester, USA
| | - Emma Fung
- Abbvie Bioresearch Center, Worcester, USA
| | - Andreas Popp
- Abbvie Deutschland GmbH & Co KG, Ludwigshafen, Germany
| | | | | |
Collapse
|
4
|
Nairz M, Ferring-Appel D, Casarrubea D, Sonnweber T, Viatte L, Schroll A, Haschka D, Fang FC, Hentze MW, Weiss G, Galy B. Iron Regulatory Proteins Mediate Host Resistance to Salmonella Infection. Cell Host Microbe 2015; 18:254-61. [PMID: 26190773 DOI: 10.1016/j.chom.2015.06.017] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Revised: 05/26/2015] [Accepted: 06/19/2015] [Indexed: 01/01/2023]
Abstract
Macrophages are essential for systemic iron recycling, and also control iron availability to pathogens. Iron metabolism in mammalian cells is orchestrated posttranscriptionally by iron-regulatory proteins (IRP)-1 and -2. Here, we generated mice with selective and combined ablation of both IRPs in macrophages to investigate the role of IRPs in controlling iron availability. These animals are hyperferritinemic but otherwise display normal clinical iron parameters. However, mutant mice rapidly succumb to systemic infection with Salmonella Typhimurium, a pathogenic bacterium that multiplies within macrophages, with increased bacterial burdens in liver and spleen. Ex vivo infection experiments indicate that IRP function restricts bacterial access to iron via the EntC and Feo bacterial iron-acquisition systems. Further, IRPs contain Salmonella by promoting the induction of lipocalin 2, a host antimicrobial factor that inhibits bacterial uptake of iron-laden siderophores, and by suppressing the ferritin iron pool. This work reveals the importance of the IRPs in innate immunity.
Collapse
Affiliation(s)
- Manfred Nairz
- Department of Internal Medicine VI, Infectious Diseases, Immunology, Rheumatology, and Pneumology, Medical University of Innsbruck, Anichstrasse 35, A-6020 Innsbruck, Austria
| | - Dunja Ferring-Appel
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Daniela Casarrubea
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Thomas Sonnweber
- Department of Internal Medicine VI, Infectious Diseases, Immunology, Rheumatology, and Pneumology, Medical University of Innsbruck, Anichstrasse 35, A-6020 Innsbruck, Austria
| | - Lydie Viatte
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Andrea Schroll
- Department of Internal Medicine VI, Infectious Diseases, Immunology, Rheumatology, and Pneumology, Medical University of Innsbruck, Anichstrasse 35, A-6020 Innsbruck, Austria
| | - David Haschka
- Department of Internal Medicine VI, Infectious Diseases, Immunology, Rheumatology, and Pneumology, Medical University of Innsbruck, Anichstrasse 35, A-6020 Innsbruck, Austria
| | - Ferric C Fang
- Department of Laboratory Medicine, University of Washington, Seattle, WA 98195-7735, USA; Department of Microbiology, University of Washington, Seattle, WA 98195-7735, USA
| | - Matthias W Hentze
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
| | - Guenter Weiss
- Department of Internal Medicine VI, Infectious Diseases, Immunology, Rheumatology, and Pneumology, Medical University of Innsbruck, Anichstrasse 35, A-6020 Innsbruck, Austria.
| | - Bruno Galy
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| |
Collapse
|
5
|
Galy B, Ferring-Appel D, Becker C, Gretz N, Gröne HJ, Schümann K, Hentze MW. Iron regulatory proteins control a mucosal block to intestinal iron absorption. Cell Rep 2013; 3:844-57. [PMID: 23523353 DOI: 10.1016/j.celrep.2013.02.026] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Revised: 02/11/2013] [Accepted: 02/22/2013] [Indexed: 12/21/2022] Open
Abstract
Mammalian iron metabolism is regulated systemically by the hormone hepcidin and cellularly by iron regulatory proteins (IRPs) that orchestrate a posttranscriptional regulatory network. Through ligand-inducible genetic ablation of both IRPs in the gut epithelium of adult mice, we demonstrate that IRP deficiency impairs iron absorption and promotes mucosal iron retention via a ferritin-mediated "mucosal block." We show that IRP deficiency does not interfere with intestinal sensing of body iron loading and erythropoietic iron need, but rather alters the basal expression of the iron-absorption machinery. IRPs thus secure sufficient iron transport across absorptive enterocytes by restricting the ferritin "mucosal block" and define a basal set point for iron absorption upon which IRP-independent systemic regulatory inputs are overlaid.
Collapse
Affiliation(s)
- Bruno Galy
- European Molecular Biology Laboratory, Meyerhofstrasse 1, Heidelberg 69117, Germany.
| | | | | | | | | | | | | |
Collapse
|
6
|
Galy B, Ferring-Appel D, Sauer SW, Kaden S, Lyoumi S, Puy H, Kölker S, Gröne HJ, Hentze MW. Iron regulatory proteins secure mitochondrial iron sufficiency and function. Cell Metab 2010; 12:194-201. [PMID: 20674864 DOI: 10.1016/j.cmet.2010.06.007] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/09/2009] [Revised: 04/06/2010] [Accepted: 06/02/2010] [Indexed: 12/20/2022]
Abstract
Mitochondria supply cells with ATP, heme, and iron sulfur clusters (ISC), and mitochondrial energy metabolism involves both heme- and ISC-dependent enzymes. Here, we show that mitochondrial iron supply and function require iron regulatory proteins (IRP), cytosolic RNA-binding proteins that control mRNA translation and stability. Mice lacking both IRP1 and IRP2 in their hepatocytes suffer from mitochondrial iron deficiency and dysfunction associated with alterations of the ISC and heme biosynthetic pathways, leading to liver failure and death. These results uncover a major role of the IRPs in cell biology: to ensure adequate iron supply to the mitochondrion for proper function of this critical organelle.
Collapse
Affiliation(s)
- Bruno Galy
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | | | | | | | | | | | | | | | | |
Collapse
|
7
|
Galy B, Ferring-Appel D, Kaden S, Gröne HJ, Hentze MW. Iron regulatory proteins are essential for intestinal function and control key iron absorption molecules in the duodenum. Cell Metab 2008; 7:79-85. [PMID: 18177727 DOI: 10.1016/j.cmet.2007.10.006] [Citation(s) in RCA: 129] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2007] [Revised: 09/24/2007] [Accepted: 10/12/2007] [Indexed: 12/25/2022]
Abstract
Iron regulatory proteins (IRPs) orchestrate the posttranscriptional regulation of critical iron metabolism proteins at the cellular level. Redundancy between IRP1 and IRP2 associated with embryonic lethality of doubly IRP-deficient mice has precluded the study of IRP function in vivo. Here we use Cre/Lox technology to generate viable organisms lacking IRP expression in a single tissue, the intestine. Mice lacking intestinal IRP expression develop intestinal malabsorption and dehydration postnatally and die within 4 weeks of birth. We demonstrate that IRPs control the expression of divalent metal transporter 1 (DMT1) mRNA and protein, a limiting intestinal iron importer. IRPs are also shown to be critically important to secure physiological levels of the basolateral iron exporter ferroportin. IRPs are thus essential for intestinal function and organismal survival and coordinate the synthesis of key iron metabolism proteins in the duodenum.
Collapse
Affiliation(s)
- Bruno Galy
- European Molecular Biology Laboratory, Meyerhofstrasse 1, Heidelberg, Germany
| | | | | | | | | |
Collapse
|