1
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Kong S, Zhu M, Scarpin MR, Pan D, Jia L, Martinez RE, Alamos S, Vadde BVL, Garcia HG, Qian SB, Brunkard JO, Roeder AHK. DRMY1 promotes robust morphogenesis by sustaining the translation of cytokinin signaling inhibitor proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.04.07.536060. [PMID: 37066395 PMCID: PMC10104159 DOI: 10.1101/2023.04.07.536060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Robustness is the invariant development of phenotype despite environmental changes and genetic perturbations. In the Arabidopsis flower bud, four sepals robustly initiate and grow to constant size to enclose and protect the inner floral organs. We previously characterized the mutant development related myb-like1 ( drmy1 ), where 3-5 sepals initiate variably and grow to different sizes, compromising their protective function. The molecular mechanism underlying this loss of robustness was unclear. Here, we show that drmy1 has reduced TARGET OF RAPAMYCIN (TOR) activity, ribosomal content, and translation. Translation reduction decreases the protein level of ARABIDOPSIS RESPONSE REGULATOR7 (ARR7) and ARABIDOPSIS HISTIDINE PHOSPHOTRANSFER PROTEIN 6 (AHP6), two cytokinin signaling inhibitors that are normally rapidly produced before sepal initiation. The resultant upregulation of cytokinin signaling disrupts robust auxin patterning and sepal initiation. Our work shows that the homeostasis of translation, a ubiquitous cellular process, is crucial for the robust spatiotemporal patterning of organogenesis.
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2
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Shi Y, Huang D, Song C, Cao R, Wang Z, Wang D, Zhao L, Xu X, Lu C, Xiong F, Zhao H, Li S, Zhou Q, Luo S, Hu D, Zhang Y, Wang C, Shen Y, Su W, Wu Y, Schmitz K, Wei S, Song W. Diphthamide deficiency promotes association of eEF2 with p53 to induce p21 expression and neural crest defects. Nat Commun 2024; 15:3301. [PMID: 38671004 PMCID: PMC11053169 DOI: 10.1038/s41467-024-47670-1] [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: 12/16/2022] [Accepted: 04/08/2024] [Indexed: 04/28/2024] Open
Abstract
Diphthamide is a modified histidine residue unique for eukaryotic translation elongation factor 2 (eEF2), a key ribosomal protein. Loss of this evolutionarily conserved modification causes developmental defects through unknown mechanisms. In a patient with compound heterozygous mutations in Diphthamide Biosynthesis 1 (DPH1) and impaired eEF2 diphthamide modification, we observe multiple defects in neural crest (NC)-derived tissues. Knockin mice harboring the patient's mutations and Xenopus embryos with Dph1 depleted also display NC defects, which can be attributed to reduced proliferation in the neuroepithelium. DPH1 depletion facilitates dissociation of eEF2 from ribosomes and association with p53 to promote transcription of the cell cycle inhibitor p21, resulting in inhibited proliferation. Knockout of one p21 allele rescues the NC phenotypes in the knockin mice carrying the patient's mutations. These findings uncover an unexpected role for eEF2 as a transcriptional coactivator for p53 to induce p21 expression and NC defects, which is regulated by diphthamide modification.
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Affiliation(s)
- Yu Shi
- Department of Clinical Laboratory, Children's Hospital of Chongqing Medical University, Chongqing Key Laboratory of Child Neurodevelopment and Cognitive Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders, 136 Zhongshan 2nd Rd, Chongqing, 400014, China.
- Department of Biological Sciences, University of Delaware, Newark, DE, 19716, USA.
| | - Daochao Huang
- Department of Pediatric Research Institute, Children's Hospital of Chongqing Medical University, 136 Zhongshan 2nd Rd, Chongqing, 400014, China
| | - Cui Song
- Department of Endocrinology and Genetic Metabolism Disease, Children's Hospital of Chongqing Medical University, 136 Zhongshan 2nd Rd, Chongqing, 400014, China
| | - Ruixue Cao
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Institute of Aging, Key Laboratory of Alzheimer's Disease of Zhejiang Province, School of Mental Health and Kangning Hospital, The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Zhao Wang
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Institute of Aging, Key Laboratory of Alzheimer's Disease of Zhejiang Province, School of Mental Health and Kangning Hospital, The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Dan Wang
- Department of Pediatric Research Institute, Children's Hospital of Chongqing Medical University, 136 Zhongshan 2nd Rd, Chongqing, 400014, China
| | - Li Zhao
- Department of Pediatric Research Institute, Children's Hospital of Chongqing Medical University, 136 Zhongshan 2nd Rd, Chongqing, 400014, China
| | - Xiaolu Xu
- Department of Biological Sciences, University of Delaware, Newark, DE, 19716, USA
| | - Congyu Lu
- Department of Biological Sciences, University of Delaware, Newark, DE, 19716, USA
| | - Feng Xiong
- Department of Endocrinology and Genetic Metabolism Disease, Children's Hospital of Chongqing Medical University, 136 Zhongshan 2nd Rd, Chongqing, 400014, China
| | - Haowen Zhao
- Department of Clinical Laboratory, Children's Hospital of Chongqing Medical University, Chongqing Key Laboratory of Child Neurodevelopment and Cognitive Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders, 136 Zhongshan 2nd Rd, Chongqing, 400014, China
- Department of Pediatric Research Institute, Children's Hospital of Chongqing Medical University, 136 Zhongshan 2nd Rd, Chongqing, 400014, China
| | - Shuxiang Li
- Department of Pediatric Research Institute, Children's Hospital of Chongqing Medical University, 136 Zhongshan 2nd Rd, Chongqing, 400014, China
- Department of Endocrinology and Genetic Metabolism Disease, Children's Hospital of Chongqing Medical University, 136 Zhongshan 2nd Rd, Chongqing, 400014, China
| | - Quansheng Zhou
- Department of Pediatric Research Institute, Children's Hospital of Chongqing Medical University, 136 Zhongshan 2nd Rd, Chongqing, 400014, China
- Department of Endocrinology and Genetic Metabolism Disease, Children's Hospital of Chongqing Medical University, 136 Zhongshan 2nd Rd, Chongqing, 400014, China
| | - Shuyue Luo
- Department of Pediatric Research Institute, Children's Hospital of Chongqing Medical University, 136 Zhongshan 2nd Rd, Chongqing, 400014, China
| | - Dongjie Hu
- Department of Pediatric Research Institute, Children's Hospital of Chongqing Medical University, 136 Zhongshan 2nd Rd, Chongqing, 400014, China
| | - Yun Zhang
- Department of Radiology, Children's Hospital of Chongqing Medical University, 136 Zhongshan 2nd Rd, Chongqing, 400014, China
| | - Cui Wang
- Department of Radiology, Children's Hospital of Chongqing Medical University, 136 Zhongshan 2nd Rd, Chongqing, 400014, China
| | - Yiping Shen
- Division of Genetics and Genomics, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Weiting Su
- Kunming Institute of Zoology, Chinese Academy of Science, Kunming, 650223, Yunnan, China
| | - Yili Wu
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Institute of Aging, Key Laboratory of Alzheimer's Disease of Zhejiang Province, School of Mental Health and Kangning Hospital, The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Karl Schmitz
- Department of Biological Sciences, University of Delaware, Newark, DE, 19716, USA
| | - Shuo Wei
- Department of Biological Sciences, University of Delaware, Newark, DE, 19716, USA.
| | - Weihong Song
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Institute of Aging, Key Laboratory of Alzheimer's Disease of Zhejiang Province, School of Mental Health and Kangning Hospital, The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China.
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Ütkür K, Mayer K, Liu S, Brinkmann U, Schaffrath R. Functional Integrity of Radical SAM Enzyme Dph1•Dph2 Requires Non-Canonical Cofactor Motifs with Tandem Cysteines. Biomolecules 2024; 14:470. [PMID: 38672486 PMCID: PMC11048331 DOI: 10.3390/biom14040470] [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: 03/24/2024] [Revised: 04/05/2024] [Accepted: 04/09/2024] [Indexed: 04/28/2024] Open
Abstract
The Dph1•Dph2 heterodimer from yeast is a radical SAM (RS) enzyme that generates the 3-amino-3-carboxy-propyl (ACP) precursor for diphthamide, a clinically relevant modification on eukaryotic elongation factor 2 (eEF2). ACP formation requires SAM cleavage and atypical Cys-bound Fe-S clusters in each Dph1 and Dph2 subunit. Intriguingly, the first Cys residue in each motif is found next to another ill-defined cysteine that we show is conserved across eukaryotes. As judged from structural modeling, the orientation of these tandem cysteine motifs (TCMs) suggests a candidate Fe-S cluster ligand role. Hence, we generated, by site-directed DPH1 and DPH2 mutagenesis, Dph1•Dph2 variants with cysteines from each TCM replaced individually or in combination by serines. Assays diagnostic for diphthamide formation in vivo reveal that while single substitutions in the TCM of Dph2 cause mild defects, double mutations almost entirely inactivate the RS enzyme. Based on enhanced Dph1 and Dph2 subunit instability in response to cycloheximide chases, the variants with Cys substitutions in their cofactor motifs are particularly prone to protein degradation. In sum, we identify a fourth functionally cooperative Cys residue within the Fe-S motif of Dph2 and show that the Cys-based cofactor binding motifs in Dph1 and Dph2 are critical for the structural integrity of the dimeric RS enzyme in vivo.
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Affiliation(s)
- Koray Ütkür
- Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, 34132 Kassel, Germany;
| | - Klaus Mayer
- Roche Pharma Research and Early Development (pRED), Large Molecule Research, Roche Innovation Center Munich, 82377 Penzberg, Germany; (K.M.); (U.B.)
| | - Shihui Liu
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA;
| | - Ulrich Brinkmann
- Roche Pharma Research and Early Development (pRED), Large Molecule Research, Roche Innovation Center Munich, 82377 Penzberg, Germany; (K.M.); (U.B.)
| | - Raffael Schaffrath
- Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, 34132 Kassel, Germany;
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Schaffrath R, Brinkmann U. Diphthamide - a conserved modification of eEF2 with clinical relevance. Trends Mol Med 2024; 30:164-177. [PMID: 38097404 DOI: 10.1016/j.molmed.2023.11.008] [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: 09/28/2023] [Revised: 11/03/2023] [Accepted: 11/09/2023] [Indexed: 02/17/2024]
Abstract
Diphthamide, a complex modification on eukaryotic translation elongation factor 2 (eEF2), assures reading-frame fidelity during translation. Diphthamide and enzymes for its synthesis are conserved in eukaryotes and archaea. Originally identified as target for diphtheria toxin (DT) in humans, its clinical relevance now proves to be broader than the link to pathogenic bacteria. Diphthamide synthesis enzymes (DPH1 and DPH3) are associated with cancer, and DPH gene mutations can cause diphthamide deficiency syndrome (DDS). Finally, new analyses provide evidence that diphthamide may restrict propagation of viruses including SARS-CoV-2 and HIV-1, and that DPH enzymes are targeted by viruses for degradation to overcome this restriction. This review describes how diphthamide is synthesized and functions in translation, and covers its clinical relevance in human development, cancer, and infectious diseases.
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Affiliation(s)
- Raffael Schaffrath
- Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, Kassel, Germany.
| | - Ulrich Brinkmann
- Roche Pharma Research and Early Development (pRED), Large Molecule Research, Roche Innovation Center Munich, Penzberg, Germany.
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5
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Milicevic N, Jenner L, Myasnikov A, Yusupov M, Yusupova G. mRNA reading frame maintenance during eukaryotic ribosome translocation. Nature 2024; 625:393-400. [PMID: 38030725 DOI: 10.1038/s41586-023-06780-4] [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: 04/21/2023] [Accepted: 10/24/2023] [Indexed: 12/01/2023]
Abstract
One of the most critical steps of protein synthesis is coupled translocation of messenger RNA (mRNA) and transfer RNAs (tRNAs) required to advance the mRNA reading frame by one codon. In eukaryotes, translocation is accelerated and its fidelity is maintained by elongation factor 2 (eEF2)1,2. At present, only a few snapshots of eukaryotic ribosome translocation have been reported3-5. Here we report ten high-resolution cryogenic-electron microscopy (cryo-EM) structures of the elongating eukaryotic ribosome bound to the full translocation module consisting of mRNA, peptidyl-tRNA and deacylated tRNA, seven of which also contained ribosome-bound, naturally modified eEF2. This study recapitulates mRNA-tRNA2-growing peptide module progression through the ribosome, from the earliest states of eEF2 translocase accommodation until the very late stages of the process, and shows an intricate network of interactions preventing the slippage of the translational reading frame. We demonstrate how the accuracy of eukaryotic translocation relies on eukaryote-specific elements of the 80S ribosome, eEF2 and tRNAs. Our findings shed light on the mechanism of translation arrest by the anti-fungal eEF2-binding inhibitor, sordarin. We also propose that the sterically constrained environment imposed by diphthamide, a conserved eukaryotic posttranslational modification in eEF2, not only stabilizes correct Watson-Crick codon-anticodon interactions but may also uncover erroneous peptidyl-tRNA, and therefore contribute to higher accuracy of protein synthesis in eukaryotes.
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Affiliation(s)
- Nemanja Milicevic
- Institute of Genetics and Molecular and Cellular Biology (IGBMC), CNRS UMR7104, INSERM U1258, University of Strasbourg, Strasbourg, France
| | - Lasse Jenner
- Institute of Genetics and Molecular and Cellular Biology (IGBMC), CNRS UMR7104, INSERM U1258, University of Strasbourg, Strasbourg, France
| | | | - Marat Yusupov
- Institute of Genetics and Molecular and Cellular Biology (IGBMC), CNRS UMR7104, INSERM U1258, University of Strasbourg, Strasbourg, France
| | - Gulnara Yusupova
- Institute of Genetics and Molecular and Cellular Biology (IGBMC), CNRS UMR7104, INSERM U1258, University of Strasbourg, Strasbourg, France.
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6
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Ren M, Fan B, Cao G, Zong R, Feng L, Sun H. Exploration and validation of a combined Hypoxia and m6A/m5C/m1A regulated gene signature for prognosis prediction of liver cancer. BMC Genomics 2023; 24:776. [PMID: 38097948 PMCID: PMC10722758 DOI: 10.1186/s12864-023-09876-3] [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: 10/24/2023] [Accepted: 12/06/2023] [Indexed: 12/17/2023] Open
Abstract
BACKGROUND It is widely acknowledged that hypoxia and m6A/m5C/m1A RNA modifications promote the occurrence and development of tumors by regulating the tumor microenvironment. This study aimed to establish a novel liver cancer risk signature based on hypoxia and m6A/m5C/m1A modifications. METHODS We collected data from The Cancer Genome Atlas (TCGA-LIHC), the National Omics Data Encyclopedia (NODE-HCC), the International Cancer Genome Consortium (ICGC), and the Gene Expression Omnibus (GEO) databases for our study (GSE59729, GSE41666). Using Cox regression and least absolute shrinkage and selection operator (LASSO) method, we developed a risk signature for liver cancer based on differentially expressed genes related to hypoxia and genes regulated by m6A/m5C/m1A modifications. We stratified patients into high- and low-risk groups and assessed differences between these groups in terms of gene mutations, copy number variations, pathway enrichment, stemness scores, immune infiltration, and predictive capabilities of the model for immunotherapy and chemotherapy efficacy. RESULTS Our analysis revealed a significantly correlated between hypoxia and methylation as well as m6A/m5C/m1A RNA methylation. The three-gene prognosis signature (CEP55, DPH2, SMS) combining hypoxia and m6A/m5C/m1A regulated genes exhibited strong predictive performance in TCGA-LIHC, NODE-HCC, and ICGC-LIHC-JP cohorts. The low-risk group demonstrated a significantly better overall survival compared to the high-risk group (p < 0.0001 in TCGA, p = 0.0043 in NODE, p = 0.0015 in ICGC). The area under the curve (AUC) values for survival at 1, 2, and 3 years are all greater than 0.65 in the three cohorts. Univariate and Multivariate Cox regression analyses of the three datasets indicated that the signature could serve as an independent prognostic predictor (p < 0.001 in the three cohorts). The high-risk group exhibited more genome changes and higher homologous recombination deficiency scores and stemness scores. Analysis of immune infiltration and immune activation confirmed that the signature was associated with various immune microenvironment characteristics. Finally, patients in the high-risk group experienced a more favorable response to immunotherapy, and various common chemotherapy drugs. CONCLUSION Our prognostic signature which integrates hypoxia and m6A/m5C/m1A-regulated genes, provides valuable insights for clinical prediction and treatment guidance for liver cancer patients.
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Affiliation(s)
- Min Ren
- College of Life Science, Yan'an University, 716000, Yan'an, China
| | - Bei Fan
- College of Life Science, Yan'an University, 716000, Yan'an, China
| | - Guangcai Cao
- The First Clinical Medical College, Yan'an University, 716000, Yan'an, China
| | - Rongrong Zong
- College of Life Science, Yan'an University, 716000, Yan'an, China
| | - Liaoliao Feng
- College of Life Science, Yan'an University, 716000, Yan'an, China
| | - Huiru Sun
- College of Life Science, Yan'an University, 716000, Yan'an, China.
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7
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Ütkür K, Schmidt S, Mayer K, Klassen R, Brinkmann U, Schaffrath R. DPH1 Gene Mutations Identify a Candidate SAM Pocket in Radical Enzyme Dph1•Dph2 for Diphthamide Synthesis on EF2. Biomolecules 2023; 13:1655. [PMID: 38002337 PMCID: PMC10669111 DOI: 10.3390/biom13111655] [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: 10/24/2023] [Revised: 11/10/2023] [Accepted: 11/13/2023] [Indexed: 11/26/2023] Open
Abstract
In eukaryotes, the Dph1•Dph2 dimer is a non-canonical radical SAM enzyme. Using iron-sulfur (FeS) clusters, it cleaves the cosubstrate S-adenosyl-methionine (SAM) to form a 3-amino-3-carboxy-propyl (ACP) radical for the synthesis of diphthamide. The latter decorates a histidine residue on elongation factor 2 (EF2) conserved from archaea to yeast and humans and is important for accurate mRNA translation and protein synthesis. Guided by evidence from archaeal orthologues, we searched for a putative SAM-binding pocket in Dph1•Dph2 from Saccharomyces cerevisiae. We predict an SAM-binding pocket near the FeS cluster domain that is conserved across eukaryotes in Dph1 but not Dph2. Site-directed DPH1 mutagenesis and functional characterization through assay diagnostics for the loss of diphthamide reveal that the SAM pocket is essential for synthesis of the décor on EF2 in vivo. Further evidence from structural modeling suggests particularly critical residues close to the methionine moiety of SAM. Presumably, they facilitate a geometry specific for SAM cleavage and ACP radical formation that distinguishes Dph1•Dph2 from classical radical SAM enzymes, which generate canonical 5'-deoxyadenosyl (dAdo) radicals.
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Affiliation(s)
- Koray Ütkür
- Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, 34132 Kassel, Germany; (K.Ü.); (S.S.); (R.K.)
| | - Sarina Schmidt
- Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, 34132 Kassel, Germany; (K.Ü.); (S.S.); (R.K.)
| | - Klaus Mayer
- Roche Pharma Research and Early Development (pRED), Large Molecule Research, Roche Innovation Center Munich, 82377 Penzberg, Germany; (K.M.); (U.B.)
| | - Roland Klassen
- Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, 34132 Kassel, Germany; (K.Ü.); (S.S.); (R.K.)
| | - Ulrich Brinkmann
- Roche Pharma Research and Early Development (pRED), Large Molecule Research, Roche Innovation Center Munich, 82377 Penzberg, Germany; (K.M.); (U.B.)
| | - Raffael Schaffrath
- Roche Pharma Research and Early Development (pRED), Large Molecule Research, Roche Innovation Center Munich, 82377 Penzberg, Germany; (K.M.); (U.B.)
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8
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Pinilla M, Mazars R, Vergé R, Gorse L, Paradis M, Suire B, Santoni K, Robinson KS, Toh GA, Prouvensier L, Leon-Icaza SA, Hessel A, Péricat D, Murris M, Guet-Revillet H, Henras A, Buyck J, Ravet E, Zhong FL, Cougoule C, Planès R, Meunier E. EEF2-inactivating toxins engage the NLRP1 inflammasome and promote epithelial barrier disruption. J Exp Med 2023; 220:e20230104. [PMID: 37642996 PMCID: PMC10465324 DOI: 10.1084/jem.20230104] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 06/02/2023] [Accepted: 07/14/2023] [Indexed: 08/31/2023] Open
Abstract
Human airway and corneal epithelial cells, which are critically altered during chronic infections mediated by Pseudomonas aeruginosa, specifically express the inflammasome sensor NLRP1. Here, together with a companion study, we report that the NLRP1 inflammasome detects exotoxin A (EXOA), a ribotoxin released by P. aeruginosa type 2 secretion system (T2SS), during chronic infection. Mechanistically, EXOA-driven eukaryotic elongation factor 2 (EEF2) ribosylation and covalent inactivation promote ribotoxic stress and subsequent NLRP1 inflammasome activation, a process shared with other EEF2-inactivating toxins, diphtheria toxin and cholix toxin. Biochemically, irreversible EEF2 inactivation triggers ribosome stress-associated kinases ZAKα- and P38-dependent NLRP1 phosphorylation and subsequent proteasome-driven functional degradation. Finally, cystic fibrosis cells from patients exhibit exacerbated P38 activity and hypersensitivity to EXOA-induced ribotoxic stress-dependent NLRP1 inflammasome activation, a process inhibited by the use of ZAKα inhibitors. Altogether, our results show the importance of P. aeruginosa virulence factor EXOA at promoting NLRP1-dependent epithelial damage and identify ZAKα as a critical sensor of virulence-inactivated EEF2.
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Affiliation(s)
- Miriam Pinilla
- Institute of Pharmacology and Structural Biology, University of Toulouse, CNRS, Toulouse, France
| | - Raoul Mazars
- Institute of Pharmacology and Structural Biology, University of Toulouse, CNRS, Toulouse, France
| | - Romain Vergé
- Institute of Pharmacology and Structural Biology, University of Toulouse, CNRS, Toulouse, France
| | - Leana Gorse
- Institute of Pharmacology and Structural Biology, University of Toulouse, CNRS, Toulouse, France
| | - Margaux Paradis
- Institute of Pharmacology and Structural Biology, University of Toulouse, CNRS, Toulouse, France
| | - Bastien Suire
- Institute of Pharmacology and Structural Biology, University of Toulouse, CNRS, Toulouse, France
| | - Karin Santoni
- Institute of Pharmacology and Structural Biology, University of Toulouse, CNRS, Toulouse, France
| | - Kim Samirah Robinson
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Skin Research Institute of Singapore, Singapore, Singapore
| | - Gee Ann Toh
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Skin Research Institute of Singapore, Singapore, Singapore
| | - Laure Prouvensier
- UFR Medicine and Pharmacy, INSERM U1070, University of Poitiers, Poitiers, France
| | | | - Audrey Hessel
- Institute of Pharmacology and Structural Biology, University of Toulouse, CNRS, Toulouse, France
| | - David Péricat
- Institute of Pharmacology and Structural Biology, University of Toulouse, CNRS, Toulouse, France
| | - Marlène Murris
- Department of Pneumology, Hospital Larrey, Toulouse, France
- University Hospital of Toulouse, Toulouse, France
| | | | - Anthony Henras
- Center of Integrative Biology, University of Toulouse, CNRS, Toulouse, France
| | - Julien Buyck
- UFR Medicine and Pharmacy, INSERM U1070, University of Poitiers, Poitiers, France
| | | | - Franklin L. Zhong
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Skin Research Institute of Singapore, Singapore, Singapore
| | - Céline Cougoule
- Institute of Pharmacology and Structural Biology, University of Toulouse, CNRS, Toulouse, France
| | - Rémi Planès
- Institute of Pharmacology and Structural Biology, University of Toulouse, CNRS, Toulouse, France
- Invivogen, Toulouse, France
| | - Etienne Meunier
- Institute of Pharmacology and Structural Biology, University of Toulouse, CNRS, Toulouse, France
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Arend M, Ütkür K, Hawer H, Mayer K, Ranjan N, Adrian L, Brinkmann U, Schaffrath R. Yeast gene KTI13 (alias DPH8) operates in the initiation step of diphthamide synthesis on elongation factor 2. MICROBIAL CELL (GRAZ, AUSTRIA) 2023; 10:195-203. [PMID: 37662670 PMCID: PMC10468694 DOI: 10.15698/mic2023.09.804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 07/31/2023] [Accepted: 08/07/2023] [Indexed: 09/05/2023]
Abstract
In yeast, Elongator-dependent tRNA modifications are regulated by the Kti11•Kti13 dimer and hijacked for cell killing by zymocin, a tRNase ribotoxin. Kti11 (alias Dph3) also controls modification of elongation factor 2 (EF2) with diphthamide, the target for lethal ADP-ribosylation by diphtheria toxin (DT). Diphthamide formation on EF2 involves four biosynthetic steps encoded by the DPH1-DPH7 network and an ill-defined KTI13 function. On further examining the latter gene in yeast, we found that kti13Δ null-mutants maintain unmodified EF2 able to escape ADP-ribosylation by DT and to survive EF2 inhibition by sordarin, a diphthamide-dependent antifungal. Consistently, mass spectrometry shows kti13Δ cells are blocked in proper formation of amino-carboxyl-propyl-EF2, the first diphthamide pathway intermediate. Thus, apart from their common function in tRNA modification, both Kti11/Dph3 and Kti13 share roles in the initiation step of EF2 modification. We suggest an alias KTI13/DPH8 nomenclature indicating dual-functionality analogous to KTI11/DPH3.
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Affiliation(s)
- Meike Arend
- Institute of Biology, Division of Microbiology, University of Kassel, Heinrich-Plett-Str. 40, 34132 Kassel, Germany
| | - Koray Ütkür
- Institute of Biology, Division of Microbiology, University of Kassel, Heinrich-Plett-Str. 40, 34132 Kassel, Germany
| | - Harmen Hawer
- Institute of Biology, Division of Microbiology, University of Kassel, Heinrich-Plett-Str. 40, 34132 Kassel, Germany
| | - Klaus Mayer
- Roche Pharma Research & Early Development, Large Molecule Research, Roche Innovation Center München, Nonnenwald 2, 82377 Penzberg, Germany
| | - Namit Ranjan
- Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Lorenz Adrian
- Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, 04318 Leipzig, Germany
| | - Ulrich Brinkmann
- Roche Pharma Research & Early Development, Large Molecule Research, Roche Innovation Center München, Nonnenwald 2, 82377 Penzberg, Germany
| | - Raffael Schaffrath
- Institute of Biology, Division of Microbiology, University of Kassel, Heinrich-Plett-Str. 40, 34132 Kassel, Germany
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10
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Ütkür K, Mayer K, Khan M, Manivannan T, Schaffrath R, Brinkmann U. DPH1 and DPH2 variants that confer susceptibility to diphthamide deficiency syndrome in human cells and yeast models. Dis Model Mech 2023; 16:dmm050207. [PMID: 37675463 PMCID: PMC10538292 DOI: 10.1242/dmm.050207] [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: 03/28/2023] [Accepted: 08/21/2023] [Indexed: 09/08/2023] Open
Abstract
The autosomal-recessive diphthamide deficiency syndrome presents as intellectual disability with developmental abnormalities, seizures, craniofacial and additional morphological phenotypes. It is caused by reduced activity of proteins that synthesize diphthamide on human translation elongation factor 2. Diphthamide synthesis requires seven proteins (DPH1-DPH7), with clinical deficiency described for DPH1, DPH2 and DPH5. A limited set of variant alleles from syndromic patients has been functionally analyzed, but databases (gnomAD) list additional so far uncharacterized variants in human DPH1 and DPH2. Because DPH enzymes are conserved among eukaryotes, their functionality can be assessed in yeast and mammalian cells. Our experimental assessment of known and uncharacterized DPH1 and DPH2 missense alleles showed that six variants are tolerated despite inter-species conservation. Ten additional human DPH1 (G113R, A114T, H132P, H132R, S136R, C137F, L138P, Y152C, S221P, H240R) and two DPH2 (H105P, C341Y) variants showed reduced functionality and hence are deficiency-susceptibility alleles. Some variants locate close to the active enzyme center and may affect catalysis, while others may impact on enzyme activation. In sum, our study has identified functionally compromised alleles of DPH1 and DPH2 genes that likely cause diphthamide deficiency syndrome.
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Affiliation(s)
- Koray Ütkür
- Institut für Biologie,Fachgebiet Mikrobiologie, Universität Kassel, 34132 Kassel, Germany
| | - Klaus Mayer
- Roche Pharma Research and Early Development (pRED), Large Molecule Research, Roche Innovation Center Munich, 82377 Penzberg, Germany
| | - Maliha Khan
- Institut für Biologie,Fachgebiet Mikrobiologie, Universität Kassel, 34132 Kassel, Germany
| | - Thirishika Manivannan
- Institut für Biologie,Fachgebiet Mikrobiologie, Universität Kassel, 34132 Kassel, Germany
| | - Raffael Schaffrath
- Institut für Biologie,Fachgebiet Mikrobiologie, Universität Kassel, 34132 Kassel, Germany
| | - Ulrich Brinkmann
- Roche Pharma Research and Early Development (pRED), Large Molecule Research, Roche Innovation Center Munich, 82377 Penzberg, Germany
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11
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Doering L, Cornean A, Thumberger T, Benjaminsen J, Wittbrodt B, Kellner T, Hammouda OT, Gorenflo M, Wittbrodt J, Gierten J. CRISPR-based knockout and base editing confirm the role of MYRF in heart development and congenital heart disease. Dis Model Mech 2023; 16:dmm049811. [PMID: 37584388 PMCID: PMC10445736 DOI: 10.1242/dmm.049811] [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: 08/01/2022] [Accepted: 07/21/2023] [Indexed: 08/17/2023] Open
Abstract
High-throughput DNA sequencing studies increasingly associate DNA variants with congenital heart disease (CHD). However, functional modeling is a crucial prerequisite for translating genomic data into clinical care. We used CRISPR-Cas9-mediated targeting of 12 candidate genes in the vertebrate model medaka (Oryzias latipes), five of which displayed a novel cardiovascular phenotype spectrum in F0 (crispants): mapre2, smg7, cdc42bpab, ankrd11 and myrf, encoding a transcription factor recently linked to cardiac-urogenital syndrome. Our myrf mutant line showed particularly prominent embryonic cardiac defects recapitulating phenotypes of pediatric patients, including hypoplastic ventricle. Mimicking human mutations, we edited three sites to generate specific myrf single-nucleotide variants via cytosine and adenine base editors. The Glu749Lys missense mutation in the conserved intramolecular chaperon autocleavage domain fully recapitulated the characteristic myrf mutant phenotype with high penetrance, underlining the crucial function of this protein domain. The efficiency and scalability of base editing to model specific point mutations accelerate gene validation studies and the generation of human-relevant disease models.
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Affiliation(s)
- Lino Doering
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
- Department of Pediatric Cardiology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Alex Cornean
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
- Heidelberg Biosciences International Graduate School, Heidelberg University, 69120 Heidelberg, Germany
| | - Thomas Thumberger
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Joergen Benjaminsen
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Beate Wittbrodt
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Tanja Kellner
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Omar T. Hammouda
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Matthias Gorenflo
- Department of Pediatric Cardiology, University Hospital Heidelberg, 69120 Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Heidelberg/Mannheim, 69120 Heidelberg, Germany
| | - Joachim Wittbrodt
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Heidelberg/Mannheim, 69120 Heidelberg, Germany
| | - Jakob Gierten
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
- Department of Pediatric Cardiology, University Hospital Heidelberg, 69120 Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Heidelberg/Mannheim, 69120 Heidelberg, Germany
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12
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Baik AH, Haribowo AG, Chen X, Queliconi BB, Barrios AM, Garg A, Maishan M, Campos AR, Matthay MA, Jain IH. Oxygen toxicity causes cyclic damage by destabilizing specific Fe-S cluster-containing protein complexes. Mol Cell 2023; 83:942-960.e9. [PMID: 36893757 PMCID: PMC10148707 DOI: 10.1016/j.molcel.2023.02.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 01/12/2023] [Accepted: 02/14/2023] [Indexed: 03/11/2023]
Abstract
Oxygen is toxic across all three domains of life. Yet, the underlying molecular mechanisms remain largely unknown. Here, we systematically investigate the major cellular pathways affected by excess molecular oxygen. We find that hyperoxia destabilizes a specific subset of Fe-S cluster (ISC)-containing proteins, resulting in impaired diphthamide synthesis, purine metabolism, nucleotide excision repair, and electron transport chain (ETC) function. Our findings translate to primary human lung cells and a mouse model of pulmonary oxygen toxicity. We demonstrate that the ETC is the most vulnerable to damage, resulting in decreased mitochondrial oxygen consumption. This leads to further tissue hyperoxia and cyclic damage of the additional ISC-containing pathways. In support of this model, primary ETC dysfunction in the Ndufs4 KO mouse model causes lung tissue hyperoxia and dramatically increases sensitivity to hyperoxia-mediated ISC damage. This work has important implications for hyperoxia pathologies, including bronchopulmonary dysplasia, ischemia-reperfusion injury, aging, and mitochondrial disorders.
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Affiliation(s)
- Alan H Baik
- Department of Medicine, Division of Cardiology, University of California, San Francisco, San Francisco, CA 94143, USA; Gladstone Institutes, San Francisco, CA 94158, USA
| | - Augustinus G Haribowo
- Gladstone Institutes, San Francisco, CA 94158, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Xuewen Chen
- Gladstone Institutes, San Francisco, CA 94158, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Bruno B Queliconi
- Gladstone Institutes, San Francisco, CA 94158, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Alec M Barrios
- Gladstone Institutes, San Francisco, CA 94158, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Ankur Garg
- Gladstone Institutes, San Francisco, CA 94158, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Mazharul Maishan
- Cardiovascular Research Institute, UCSF, San Francisco, CA 94143, USA
| | - Alexandre R Campos
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Michael A Matthay
- Cardiovascular Research Institute, UCSF, San Francisco, CA 94143, USA; Departments of Medicine and Anesthesia, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Isha H Jain
- Gladstone Institutes, San Francisco, CA 94158, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA.
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13
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Ma X, Li L, Li Z, Huang Z, Yang Y, Liu P, Guo D, Li Y, Wu T, Luo R, Xu J, Ye W, Jiang B, Shi L. eEF2 in the prefrontal cortex promotes excitatory synaptic transmission and social novelty behavior. EMBO Rep 2022; 23:e54543. [PMID: 35993189 PMCID: PMC9535807 DOI: 10.15252/embr.202154543] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 07/22/2022] [Accepted: 08/03/2022] [Indexed: 08/24/2023] Open
Abstract
Regulation of mRNA translation is essential for brain development and function. Translation elongation factor eEF2 acts as a molecular hub orchestrating various synaptic signals to protein synthesis control and participates in hippocampus-dependent cognitive functions. However, whether eEF2 regulates other behaviors in different brain regions has been unknown. Here, we construct a line of Eef2 heterozygous (HET) mice, which show a reduction in eEF2 and protein synthesis mainly in excitatory neurons of the prefrontal cortex. The mice also show lower spine density, reduced excitability, and AMPAR-mediated synaptic transmission in pyramidal neurons of the medial prefrontal cortex (mPFC). While HET mice exhibit normal learning and memory, they show defective social behavior and elevated anxiety. Knockdown of Eef2 in excitatory neurons of the mPFC specifically is sufficient to impair social novelty preference. Either chemogenetic activation of excitatory neurons in the mPFC or mPFC local infusion of the AMPAR potentiator PF-4778574 corrects the social novelty deficit of HET mice. Collectively, we identify a novel role for eEF2 in promoting prefrontal AMPAR-mediated synaptic transmission underlying social novelty behavior.
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Affiliation(s)
- Xuanyue Ma
- JNU‐HKUST Joint Laboratory for Neuroscience and Innovative Drug Research, College of PharmacyJinan UniversityGuangzhouChina
| | - Liuren Li
- JNU‐HKUST Joint Laboratory for Neuroscience and Innovative Drug Research, College of PharmacyJinan UniversityGuangzhouChina
| | - Ziming Li
- Guangdong Province Key Laboratory of Brain Function and Disease, Zhongshan School of MedicineSun Yat‐sen UniversityGuangzhouChina
| | - Zhengyi Huang
- JNU‐HKUST Joint Laboratory for Neuroscience and Innovative Drug Research, College of PharmacyJinan UniversityGuangzhouChina
| | - Yaorong Yang
- JNU‐HKUST Joint Laboratory for Neuroscience and Innovative Drug Research, College of PharmacyJinan UniversityGuangzhouChina
| | - Peng Liu
- JNU‐HKUST Joint Laboratory for Neuroscience and Innovative Drug Research, College of PharmacyJinan UniversityGuangzhouChina
| | - Daji Guo
- JNU‐HKUST Joint Laboratory for Neuroscience and Innovative Drug Research, College of PharmacyJinan UniversityGuangzhouChina
- Clinical Neuroscience InstituteThe First Affiliated Hospital of Jinan UniversityGuangzhouChina
| | - Yueyao Li
- JNU‐HKUST Joint Laboratory for Neuroscience and Innovative Drug Research, College of PharmacyJinan UniversityGuangzhouChina
| | - Tianying Wu
- JNU‐HKUST Joint Laboratory for Neuroscience and Innovative Drug Research, College of PharmacyJinan UniversityGuangzhouChina
| | - Ruixiang Luo
- JNU‐HKUST Joint Laboratory for Neuroscience and Innovative Drug Research, College of PharmacyJinan UniversityGuangzhouChina
| | - Junyu Xu
- Department of Neurobiology and Department of Rehabilitation of the Children's HospitalZhejiang University School of MedicineHangzhouChina
| | - Wen‐Cai Ye
- JNU‐HKUST Joint Laboratory for Neuroscience and Innovative Drug Research, College of PharmacyJinan UniversityGuangzhouChina
- Center for Bioactive Natural Molecules and Innovative Drugs Research, College of PharmacyJinan UniversityGuangzhouChina
- Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, College of PharmacyJinan UniversityGuangzhouChina
| | - Bin Jiang
- Guangdong Province Key Laboratory of Brain Function and Disease, Zhongshan School of MedicineSun Yat‐sen UniversityGuangzhouChina
| | - Lei Shi
- JNU‐HKUST Joint Laboratory for Neuroscience and Innovative Drug Research, College of PharmacyJinan UniversityGuangzhouChina
- Center for Bioactive Natural Molecules and Innovative Drugs Research, College of PharmacyJinan UniversityGuangzhouChina
- Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, College of PharmacyJinan UniversityGuangzhouChina
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14
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Farache D, Antine SP, Lee ASY. Moonlighting translation factors: multifunctionality drives diverse gene regulation. Trends Cell Biol 2022; 32:762-772. [PMID: 35466028 PMCID: PMC9378348 DOI: 10.1016/j.tcb.2022.03.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 03/16/2022] [Accepted: 03/18/2022] [Indexed: 12/09/2022]
Abstract
Translation factors have traditionally been viewed as proteins that drive ribosome function and ensure accurate mRNA translation. Recent discoveries have highlighted that these factors can also moonlight in gene regulation, but through functions distinct from their canonical roles in protein synthesis. Notably, the additional functions that translation factors encode are diverse, ranging from transcriptional control and extracellular signaling to RNA binding, and are highly regulated in response to external cues and the intrinsic cellular state. Thus, this multifunctionality of translation factors provides an additional mechanism for exquisite control of gene expression.
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Affiliation(s)
- Dorian Farache
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA; Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sadie P Antine
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA; Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Amy S Y Lee
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA; Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA.
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15
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Tu WL, Chih YC, Shih YT, Yu YR, You LR, Chen CM. Context-specific roles of diphthamide deficiency in hepatocellular carcinogenesis. J Pathol 2022; 258:149-163. [PMID: 35781884 DOI: 10.1002/path.5986] [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: 02/18/2022] [Revised: 06/13/2022] [Accepted: 07/01/2022] [Indexed: 11/07/2022]
Abstract
Diphthamide biosynthesis protein 1 (DPH1) is biochemically involved in the first step of diphthamide biosynthesis, a post-translational modification of eukaryotic elongation factor 2 (EEF2). Earlier studies showed that DPH1, also known as ovarian cancer-associated gene 1 (OVCA1), is involved in ovarian carcinogenesis. However, the role of DPH1 in hepatocellular carcinoma (HCC) remains unclear. To investigate the impact of DPH1 in hepatocellular carcinogenesis, we have performed data mining from The Cancer Genome Atlas Liver Hepatocellular Carcinoma (TCGA-LIHC) dataset. We found that reduced DPH1 levels were associated with advanced stages and poor survival of patients with HCC. Also, we generated hepatocyte-specific Dph1 deficient mice and showed that diphthamide deficient EEF2 resulted in a reduced translation elongation rate in the hepatocytes and let to mild liver damage with fatty accumulation. After N-diethylnitrosamine (DEN) -induced acute liver injury, p53-mediated pericentral hepatocyte death was increased, and compensatory proliferation was reduced in Dph1-deficient mice. Consistent with these effects, Dph1 deficiency decreased the incidence of DEN-induced pericentral-derived HCC and revealed a protective effect against p53 loss. In contrast, Dph1 deficiency combined with Trp53- or Trp53/Pten-deficient hepatocytes led to increased tumor loads associated with KRT19 (K19)-positive periportal-like cell expansion in mice. Further gene set enrichment analysis also revealed that HCC patients with lower levels of DPH1 and TP53 expression had enriched gene-sets related to the cell cycle and K19-upregulated HCC. Additionally, liver tumor organoids obtained from 6-month-old Pten/Trp53/Dph1-triple-mutant mice had a higher frequency of organoid re-initiation cells and higher proliferative index compared with those of the Pten/Trp53-double-mutant. Pten/Trp53/Dph1-triple-mutant liver tumor organoids showed expression of genes associated with stem/progenitor phenotypes, including Krt19 and Prominin-1 (Cd133) progenitor markers, combined with low hepatocyte-expressed fibrinogen genes. These findings indicate that diphthamide deficiency differentially regulates hepatocellular carcinogenesis, which inhibits pericentral hepatocytes-derived tumor and promotes periportal progenitors-associated liver tumors. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Wei-Ling Tu
- Department of Life Sciences and Institute of Genome Sciences, National Yang Ming, Chiao Tung University, Taipei, Taiwan
| | - Yu-Chan Chih
- Department of Life Sciences and Institute of Genome Sciences, National Yang Ming, Chiao Tung University, Taipei, Taiwan
| | - Ya-Tung Shih
- Department of Life Sciences and Institute of Genome Sciences, National Yang Ming, Chiao Tung University, Taipei, Taiwan
| | - Yi-Ru Yu
- Department of Life Sciences and Institute of Genome Sciences, National Yang Ming, Chiao Tung University, Taipei, Taiwan
| | - Li-Ru You
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, Taipei, Taiwan.,Cancer Progression Research Center, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Chun-Ming Chen
- Department of Life Sciences and Institute of Genome Sciences, National Yang Ming, Chiao Tung University, Taipei, Taiwan.,Cancer Progression Research Center, National Yang Ming Chiao Tung University, Taipei, Taiwan
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16
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Shankar SP, Grimsrud K, Lanoue L, Egense A, Willis B, Hörberg J, AlAbdi L, Mayer K, Ütkür K, Monaghan KG, Krier J, Stoler J, Alnemer M, Shankar PR, Schaffrath R, Alkuraya FS, Brinkmann U, Eriksson LA, Lloyd K, Rauen KA. A novel DPH5-related diphthamide-deficiency syndrome causing embryonic lethality or profound neurodevelopmental disorder. Genet Med 2022; 24:1567-1582. [PMID: 35482014 DOI: 10.1016/j.gim.2022.03.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 03/16/2022] [Accepted: 03/16/2022] [Indexed: 11/15/2022] Open
Abstract
PURPOSE Diphthamide is a post-translationally modified histidine essential for messenger RNA translation and ribosomal protein synthesis. We present evidence for DPH5 as a novel cause of embryonic lethality and profound neurodevelopmental delays (NDDs). METHODS Molecular testing was performed using exome or genome sequencing. A targeted Dph5 knockin mouse (C57BL/6Ncrl-Dph5em1Mbp/Mmucd) was created for a DPH5 p.His260Arg homozygous variant identified in 1 family. Adenosine diphosphate-ribosylation assays in DPH5-knockout human and yeast cells and in silico modeling were performed for the identified DPH5 potential pathogenic variants. RESULTS DPH5 variants p.His260Arg (homozygous), p.Asn110Ser and p.Arg207Ter (heterozygous), and p.Asn174LysfsTer10 (homozygous) were identified in 3 unrelated families with distinct overlapping craniofacial features, profound NDDs, multisystem abnormalities, and miscarriages. Dph5 p.His260Arg homozygous knockin was embryonically lethal with only 1 subviable mouse exhibiting impaired growth, craniofacial dysmorphology, and multisystem dysfunction recapitulating the human phenotype. Adenosine diphosphate-ribosylation assays showed absent to decreased function in DPH5-knockout human and yeast cells. In silico modeling of the variants showed altered DPH5 structure and disruption of its interaction with eEF2. CONCLUSION We provide strong clinical, biochemical, and functional evidence for DPH5 as a novel cause of embryonic lethality or profound NDDs with multisystem involvement and expand diphthamide-deficiency syndromes and ribosomopathies.
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Affiliation(s)
- Suma P Shankar
- Division of Genomic Medicine, UC Davis Health MIND Institute, Department of Pediatrics, UC Davis Health, University of California, Davis, Sacramento, CA; Department of Ophthalmology and Vision Science, UC Davis Health, University of California, Davis, Sacramento, CA.
| | - Kristin Grimsrud
- Department of Pathology and Laboratory Medicine, UC Davis Health, University of California, Davis, Sacramento, CA; UC Davis Mouse Biology Program, University of California, Davis, Davis, CA
| | - Louise Lanoue
- UC Davis Mouse Biology Program, University of California, Davis, Davis, CA
| | - Alena Egense
- Division of Genomic Medicine, UC Davis Health MIND Institute, Department of Pediatrics, UC Davis Health, University of California, Davis, Sacramento, CA
| | - Brandon Willis
- UC Davis Mouse Biology Program, University of California, Davis, Davis, CA
| | - Johanna Hörberg
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Lama AlAbdi
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia; Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Klaus Mayer
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Munich (RICM), Penzberg, Germany
| | - Koray Ütkür
- Division of Microbiology, Institute of Biology, University of Kassel, Kassel, Germany
| | | | - Joel Krier
- Division of Genetics, Brigham and Women's Hospital, Boston, MA; Undiagnosed Diseases Network
| | - Joan Stoler
- Undiagnosed Diseases Network; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA
| | - Maha Alnemer
- Department of Obstetrics & Gynecology, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Prabhu R Shankar
- Division of Health Informatics, Department of Public Health Sciences, School of Medicine, University of California, Davis, Sacramento, CA
| | - Raffael Schaffrath
- Division of Microbiology, Institute of Biology, University of Kassel, Kassel, Germany
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Ulrich Brinkmann
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Munich (RICM), Penzberg, Germany
| | - Leif A Eriksson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Kent Lloyd
- UC Davis Mouse Biology Program, University of California, Davis, Davis, CA; Department of Surgery, UC Davis Health, University of California, Davis, Sacramento, CA
| | - Katherine A Rauen
- Division of Genomic Medicine, UC Davis Health MIND Institute, Department of Pediatrics, UC Davis Health, University of California, Davis, Sacramento, CA
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- Undiagnosed Diseases Network
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17
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Hengel H, Hannan SB, Dyack S, MacKay SB, Schatz U, Fleger M, Kurringer A, Balousha G, Ghanim Z, Alkuraya FS, Alzaidan H, Alsaif HS, Mitani T, Bozdogan S, Pehlivan D, Lupski JR, Gleeson JJ, Dehghani M, Mehrjardi MY, Sherr EH, Parks KC, Argilli E, Begtrup A, Galehdari H, Balousha O, Shariati G, Mazaheri N, Malamiri RA, Pagnamenta AT, Kingston H, Banka S, Jackson A, Osmond M, Rieß A, Haack TB, Nägele T, Schuster S, Hauser S, Admard J, Casadei N, Velic A, Macek B, Ossowski S, Houlden H, Maroofian R, Schöls L, Maroofian R, Schöls L. Bi-allelic loss-of-function variants in BCAS3 cause a syndromic neurodevelopmental disorder. Am J Hum Genet 2021; 108:1069-1082. [PMID: 34022130 PMCID: PMC8206390 DOI: 10.1016/j.ajhg.2021.04.024] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 04/29/2021] [Indexed: 12/27/2022] Open
Abstract
BCAS3 microtubule-associated cell migration factor (BCAS3) is a large, highly conserved cytoskeletal protein previously proposed to be critical in angiogenesis and implicated in human embryogenesis and tumorigenesis. Here, we established BCAS3 loss-of-function variants as causative for a neurodevelopmental disorder. We report 15 individuals from eight unrelated families with germline bi-allelic loss-of-function variants in BCAS3. All probands share a global developmental delay accompanied by pyramidal tract involvement, microcephaly, short stature, strabismus, dysmorphic facial features, and seizures. The human phenotype is less severe compared with the Bcas3 knockout mouse model and cannot be explained by angiogenic defects alone. Consistent with being loss-of-function alleles, we observed absence of BCAS3 in probands' primary fibroblasts. By comparing the transcriptomic and proteomic data based on probands' fibroblasts with those of the knockout mouse model, we identified similar dysregulated pathways resulting from over-representation analysis, while the dysregulation of some proposed key interactors could not be confirmed. Together with the results from a tissue-specific Drosophila loss-of-function model, we demonstrate a vital role for BCAS3 in neural tissue development.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Reza Maroofian
- Department of Neuromuscular Disorders, Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK.
| | - Ludger Schöls
- Department of Neurology and Hertie-Institute for Clinical Brain Research, University of Tübingen, 72076 Tübingen, Germany; German Center of Neurodegenerative Diseases, 72076 Tübingen, Germany.
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18
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Iron in Translation: From the Beginning to the End. Microorganisms 2021; 9:microorganisms9051058. [PMID: 34068342 PMCID: PMC8153317 DOI: 10.3390/microorganisms9051058] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/10/2021] [Accepted: 05/11/2021] [Indexed: 12/16/2022] Open
Abstract
Iron is an essential element for all eukaryotes, since it acts as a cofactor for many enzymes involved in basic cellular functions, including translation. While the mammalian iron-regulatory protein/iron-responsive element (IRP/IRE) system arose as one of the first examples of translational regulation in higher eukaryotes, little is known about the contribution of iron itself to the different stages of eukaryotic translation. In the yeast Saccharomyces cerevisiae, iron deficiency provokes a global impairment of translation at the initiation step, which is mediated by the Gcn2-eIF2α pathway, while the post-transcriptional regulator Cth2 specifically represses the translation of a subgroup of iron-related transcripts. In addition, several steps of the translation process depend on iron-containing enzymes, including particular modifications of translation elongation factors and transfer RNAs (tRNAs), and translation termination by the ATP-binding cassette family member Rli1 (ABCE1 in humans) and the prolyl hydroxylase Tpa1. The influence of these modifications and their correlation with codon bias in the dynamic control of protein biosynthesis, mainly in response to stress, is emerging as an interesting focus of research. Taking S. cerevisiae as a model, we hereby discuss the relevance of iron in the control of global and specific translation steps.
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Nabais Sá MJ, Olson AN, Yoon G, Nimmo GAM, Gomez CM, Willemsen MA, Millan F, Schneider A, Pfundt R, de Brouwer APM, Dinman JD, de Vries BBA. De Novo variants in EEF2 cause a neurodevelopmental disorder with benign external hydrocephalus. Hum Mol Genet 2020; 29:3892-3899. [PMID: 33355653 DOI: 10.1093/hmg/ddaa270] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 12/06/2020] [Accepted: 12/07/2020] [Indexed: 11/15/2022] Open
Abstract
Eukaryotic translation elongation factor 2 (eEF2) is a key regulatory factor in gene expression that catalyzes the elongation stage of translation. A functionally impaired eEF2, due to a heterozygous missense variant in the EEF2 gene, was previously reported in one family with spinocerebellar ataxia-26 (SCA26), an autosomal dominant adult-onset pure cerebellar ataxia. Clinical exome sequencing identified de novo EEF2 variants in three unrelated children presenting with a neurodevelopmental disorder (NDD). Individuals shared a mild phenotype comprising motor delay and relative macrocephaly associated with ventriculomegaly. Populational data and bioinformatic analysis underscored the pathogenicity of all de novo missense variants. The eEF2 yeast model strains demonstrated that patient-derived variants affect cellular growth, sensitivity to translation inhibitors and translational fidelity. Consequently, we propose that pathogenic variants in the EEF2 gene, so far exclusively associated with late-onset SCA26, can cause a broader spectrum of neurologic disorders, including childhood-onset NDDs and benign external hydrocephalus.
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Affiliation(s)
- Maria J Nabais Sá
- Department of Human Genetics, Radboud University Medical Center and Donders Institute for Brain, Cognition and Behavior, 6525 GA Nijmegen, The Netherlands.,Unit for Multidisciplinary Research in Biomedicine, Instituto de Ciências Biomédicas Abel Salazar/Universidade do Porto, 4050-313 Porto, Portugal
| | - Alexandra N Olson
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Grace Yoon
- Division of Clinical and Metabolic Genetics and Division of Neurology, The Hospital for Sick Children, University of Toronto, Toronto, ON M5G 1X8, Canada
| | - Graeme A M Nimmo
- Fred A Litwin Family Centre for Genetic Medicine, University Health Network/Mount Sinai Hospital, Toronto, ON M5T 3L9, Canada
| | | | - Michèl A Willemsen
- Department of Pediatric Neurology, Radboud University Medical Center and Donders Institute for Brain, Cognition and Behavior, Amalia Children's Hospital, 6525 GA Nijmegen, The Netherlands
| | | | - Alexandra Schneider
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Rolph Pfundt
- Department of Human Genetics, Radboud University Medical Center and Donders Institute for Brain, Cognition and Behavior, 6525 GA Nijmegen, The Netherlands
| | - Arjan P M de Brouwer
- Department of Human Genetics, Radboud University Medical Center and Donders Institute for Brain, Cognition and Behavior, 6525 GA Nijmegen, The Netherlands
| | - Jonathan D Dinman
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Bert B A de Vries
- Department of Human Genetics, Radboud University Medical Center and Donders Institute for Brain, Cognition and Behavior, 6525 GA Nijmegen, The Netherlands
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