51
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Karthikkeyan G, Subbannayya Y, Najar MA, Mohanty V, Pinto SM, Arunachalam C, Prasad TSK, Murthy KR. Human Optic Nerve: An Enhanced Proteomic Expression Profile. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2018; 22:642-652. [PMID: 30346883 DOI: 10.1089/omi.2018.0130] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Ophthalmology and visual health are new frontiers for postgenomic research and technologies such as proteomics. In this context, the optic nerve and retina extend as the outgrowth of the brain, wherein the latter receives the optical input and the former relays the information for processing. While efforts to understand the optic nerve proteome have been made earlier, there exists a lacuna in its biochemical composition and molecular functions. We report, in this study, a high-resolution mass spectrometry-based approach using an Orbitrap Fusion Tribrid mass spectrometer to elucidate the human optic nerve proteomic profile. Raw spectra were searched against NCBI Human RefSeq 75 database using SEQUEST HT and MASCOT algorithms. We identified nearly 35,000 peptides in human optic nerve samples, corresponding to 5682 proteins, of which 3222 proteins are being reported for the first time. Label-free quantification using spectral abundance pointed out to neuronal structural proteins such as myelin basic protein, glial fibrillary acidic protein, and proteolipid protein 1 as the most abundant proteins. We also identified several neurotransmitter receptors and postsynaptic density synaptosomal scaffold proteins. Pathway analysis revealed that a majority of the proteins are structural proteins and have catalytic and binding activity. This study is one of the largest proteomic profiles of the human optic nerve and offers the research community an initial baseline optic nerve proteome for further studies. This will also help understand the protein dynamics of the human optic nerve under normal conditions.
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Affiliation(s)
- Gayathree Karthikkeyan
- 1 Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University) , Mangalore, India
| | - Yashwanth Subbannayya
- 1 Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University) , Mangalore, India
| | - Mohd Altaf Najar
- 1 Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University) , Mangalore, India
| | - Varshasnata Mohanty
- 1 Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University) , Mangalore, India
| | - Sneha M Pinto
- 1 Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University) , Mangalore, India
| | - Cynthia Arunachalam
- 2 Department of Ophthalmology, Yenepoya Medical College, Yenepoya (Deemed to be University) , Mangalore, India
| | - Thottethodi Subrahmanya Keshava Prasad
- 1 Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University) , Mangalore, India .,3 Institute of Bioinformatics , International Tech Park, Bangalore, Karnataka, India
| | - Krishna R Murthy
- 3 Institute of Bioinformatics , International Tech Park, Bangalore, Karnataka, India .,4 Vittala International Institute of Ophthalmology , Bangalore, Karnataka, India .,5 Manipal Academy of Higher Education , Manipal, Karnataka, India
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52
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Braun DA, Shril S, Sinha A, Schneider R, Tan W, Ashraf S, Hermle T, Jobst-Schwan T, Widmeier E, Majmundar AJ, Daga A, Warejko JK, Nakayama M, Schapiro D, Chen J, Airik M, Rao J, Schmidt JM, Hoogstraten CA, Hugo H, Meena J, Lek M, Laricchia KM, Bagga A, Hildebrandt F. Mutations in WDR4 as a new cause of Galloway-Mowat syndrome. Am J Med Genet A 2018; 176:2460-2465. [PMID: 30079490 DOI: 10.1002/ajmg.a.40489] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 05/19/2018] [Accepted: 07/09/2018] [Indexed: 11/05/2022]
Abstract
Galloway-Mowat syndrome (GAMOS) is a phenotypically heterogeneous disorder characterized by neurodevelopmental defects combined with renal-glomerular disease, manifesting with proteinuria. To identify additional monogenic disease causes, we here performed whole exome sequencing (WES), linkage analysis, and homozygosity mapping in three affected siblings of an Indian family with GAMOS. Applying established criteria for variant filtering, we identify a novel homozygous splice site mutation in the gene WDR4 as the likely disease-causing mutation in this family. In line with previous reports, we observe growth deficiency, microcephaly, developmental delay, and intellectual disability as phenotypic features resulting from WDR4 mutations. However, the newly identified allele additionally gives rise to proteinuria and nephrotic syndrome, a phenotype that was never reported in patients with WDR4 mutations. Our data thus expand the phenotypic spectrum of WDR4 mutations by demonstrating that, depending on the specific mutated allele, a renal phenotype may be present. This finding suggests that GAMOS may occupy a phenotypic spectrum with other microcephalic diseases. Furthermore, WDR4 is an additional example of a gene that encodes a tRNA modifying enzyme and gives rise to GAMOS, if mutated. Our findings thereby support the recent observation that, like neurons, podocytes of the renal glomerulus are particularly vulnerable to cellular defects resulting from altered tRNA modifications.
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Affiliation(s)
- Daniela A Braun
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Shirlee Shril
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Aditi Sinha
- Division of Nephrology, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Ronen Schneider
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Weizhen Tan
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Shazia Ashraf
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Tobias Hermle
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Tilman Jobst-Schwan
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Eugen Widmeier
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Amar J Majmundar
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Ankana Daga
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jillian K Warejko
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Makiko Nakayama
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - David Schapiro
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jing Chen
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Merlin Airik
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jia Rao
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | | | - Charlotte A Hoogstraten
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Hannah Hugo
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jitendra Meena
- Division of Nephrology, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Monkol Lek
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Kristen M Laricchia
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Arvind Bagga
- Division of Nephrology, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Friedhelm Hildebrandt
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
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53
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Hyun HS, Kim SH, Park E, Cho MH, Kang HG, Lee HS, Miyake N, Matsumoto N, Tsukaguchi H, Cheong HI. A familial case of Galloway-Mowat syndrome due to a novel TP53RK mutation: a case report. BMC MEDICAL GENETICS 2018; 19:131. [PMID: 30053862 PMCID: PMC6063015 DOI: 10.1186/s12881-018-0649-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 07/20/2018] [Indexed: 12/12/2022]
Abstract
BACKGROUND Galloway-Mowat syndrome (GAMOS) is a rare hereditary renal-neurological disease characterized by early-onset steroid-resistant nephrotic syndrome in combination with microcephaly and brain anomalies. Recently, novel causative mutations for this disease have been identified in the genes encoding the four KEOPS subunits: OSGEP, TP53RK, TPRKB, and LAGE3. CASE PRESENTATION We detected a novel homozygous TP53RK mutation (NM_033550, c.194A > T, p.Lys65Met) using whole exome sequencing in a familial case of GAMOS with three affected siblings. All three patients manifested similar phenotypes, including very early-onset nephrotic syndrome (8 days, 1 day, and 1 day after birth, respectively), microcephaly, dysmorphic faces, and early fatality (10 months, 21 days, and 25 days of age, respectively). One patient also showed hiatal hernia with gastric volvulus. Renal biopsy performed on one patient revealed focal segmental glomerulosclerosis with severe tubulo-interstitial changes. CONCLUSION We report on a familial case of GAMOS with three affected siblings carrying a novel homozygous TP53RK mutation. To our knowledge, this is only the second report on GAMOS in association with a TP53RK mutation.
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Affiliation(s)
- Hye Sun Hyun
- Department of Pediatrics, Seoul National University Children's Hospital, 101 Daehak-Ro, Jongno-Gu, Seoul, 03080, South Korea
| | - Seong Heon Kim
- Department of Pediatrics, Pusan National University Children's Hospital, Yangsan, South Korea
| | - Eujin Park
- Department of Pediatrics, Seoul National University Children's Hospital, 101 Daehak-Ro, Jongno-Gu, Seoul, 03080, South Korea
| | - Myung Hyun Cho
- Department of Pediatrics, Seoul National University Children's Hospital, 101 Daehak-Ro, Jongno-Gu, Seoul, 03080, South Korea
| | - Hee Gyung Kang
- Department of Pediatrics, Seoul National University Children's Hospital, 101 Daehak-Ro, Jongno-Gu, Seoul, 03080, South Korea.,Research Coordination Center for Rare Diseases, Seoul National University Hospital, Seoul, South Korea
| | - Hyun Soon Lee
- Renal Pathology Lab, Hankook Kidney and Diabetes Institute, Seoul, South Korea
| | - Noriko Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Hiroyasu Tsukaguchi
- Second Department of Internal Medicine, Kansai Medical University, Osaka, Japan
| | - Hae Il Cheong
- Department of Pediatrics, Seoul National University Children's Hospital, 101 Daehak-Ro, Jongno-Gu, Seoul, 03080, South Korea. .,Department of Pediatrics, Seoul National University College of Medicine, Seoul, South Korea. .,Kidney Research Institute, Medical Research Center, Seoul National University College of Medicine, Seoul, South Korea.
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54
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Pichard-Kostuch A, Zhang W, Liger D, Daugeron MC, Létoquart J, Li de la Sierra-Gallay I, Forterre P, Collinet B, van Tilbeurgh H, Basta T. Structure-function analysis of Sua5 protein reveals novel functional motifs required for the biosynthesis of the universal t 6A tRNA modification. RNA (NEW YORK, N.Y.) 2018; 24:926-938. [PMID: 29650678 PMCID: PMC6004061 DOI: 10.1261/rna.066092.118] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 04/10/2018] [Indexed: 06/08/2023]
Abstract
N6-threonyl-carbamoyl adenosine (t6A) is a universal tRNA modification found at position 37, next to the anticodon, in almost all tRNAs decoding ANN codons (where N = A, U, G, or C). t6A stabilizes the codon-anticodon interaction and hence promotes translation fidelity. The first step of the biosynthesis of t6A, the production of threonyl-carbamoyl adenylate (TC-AMP), is catalyzed by the Sua5/TsaC family of enzymes. While TsaC is a single domain protein, Sua5 enzymes are composed of the TsaC-like domain, a linker and an extra domain called SUA5 of unknown function. In the present study, we report structure-function analysis of Pyrococcus abyssi Sua5 (Pa-Sua5). Crystallographic data revealed binding sites for bicarbonate substrate and pyrophosphate product. The linker of Pa-Sua5 forms a loop structure that folds into the active site gorge and closes it. Using structure-guided mutational analysis, we established that the conserved sequence motifs in the linker and the domain-domain interface are essential for the function of Pa-Sua5. We propose that the linker participates actively in the biosynthesis of TC-AMP by binding to ATP/PPi and by stabilizing the N-carboxy-l-threonine intermediate. Hence, TsaC orthologs which lack such a linker and SUA5 domain use a different mechanism for TC-AMP synthesis.
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Affiliation(s)
- Adeline Pichard-Kostuch
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Wenhua Zhang
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Dominique Liger
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Marie-Claire Daugeron
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Juliette Létoquart
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Ines Li de la Sierra-Gallay
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Patrick Forterre
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
- Unité de Biologie Moléculaire du Gène chez les Extrêmophiles, Département de Microbiologie, Institut Pasteur, 75014 Paris, France
| | - Bruno Collinet
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Herman van Tilbeurgh
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Tamara Basta
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
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55
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Missoury S, Plancqueel S, Li de la Sierra-Gallay I, Zhang W, Liger D, Durand D, Dammak R, Collinet B, van Tilbeurgh H. The structure of the TsaB/TsaD/TsaE complex reveals an unexpected mechanism for the bacterial t6A tRNA-modification. Nucleic Acids Res 2018; 46:5850-5860. [PMID: 29741707 PMCID: PMC6009658 DOI: 10.1093/nar/gky323] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 04/09/2018] [Accepted: 04/17/2018] [Indexed: 12/25/2022] Open
Abstract
The universal N6-threonylcarbamoyladenosine (t6A) modification at position A37 of ANN-decoding tRNAs is essential for translational fidelity. In bacteria the TsaC enzyme first synthesizes an l-threonylcarbamoyladenylate (TC-AMP) intermediate. In cooperation with TsaB and TsaE, TsaD then transfers the l-threonylcarbamoyl-moiety from TC-AMP onto tRNA. We determined the crystal structure of the TsaB-TsaE-TsaD (TsaBDE) complex of Thermotoga maritima in presence of a non-hydrolysable AMPCPP. TsaE is positioned at the entrance of the active site pocket of TsaD, contacting both the TsaB and TsaD subunits and prohibiting simultaneous tRNA binding. AMPCPP occupies the ATP binding site of TsaE and is sandwiched between TsaE and TsaD. Unexpectedly, the binding of TsaE partially denatures the active site of TsaD causing loss of its essential metal binding sites. TsaE interferes in a pre- or post-catalytic step and its binding to TsaBD is regulated by ATP hydrolysis. This novel binding mode and activation mechanism of TsaE offers good opportunities for antimicrobial drug development.
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Affiliation(s)
- Sophia Missoury
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS UMR 9198, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France
| | - Stéphane Plancqueel
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS UMR 9198, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France
| | - Ines Li de la Sierra-Gallay
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS UMR 9198, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France
| | - Wenhua Zhang
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS UMR 9198, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France
| | - Dominique Liger
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS UMR 9198, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France
| | - Dominique Durand
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS UMR 9198, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France
| | - Raoudha Dammak
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS UMR 9198, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France
| | - Bruno Collinet
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS UMR 9198, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, UMR7590 CNRS/Sorbonne-Université, UPMC, Paris, France
| | - Herman van Tilbeurgh
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS UMR 9198, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France
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56
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Lin H, Miyauchi K, Harada T, Okita R, Takeshita E, Komaki H, Fujioka K, Yagasaki H, Goto YI, Yanaka K, Nakagawa S, Sakaguchi Y, Suzuki T. CO 2-sensitive tRNA modification associated with human mitochondrial disease. Nat Commun 2018; 9:1875. [PMID: 29760464 PMCID: PMC5951830 DOI: 10.1038/s41467-018-04250-4] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 04/16/2018] [Indexed: 12/21/2022] Open
Abstract
It has been generally thought that tRNA modifications are stable and static, and their frequencies are rarely regulated. N6-threonylcarbamoyladenosine (t6A) occurs at position 37 of five mitochondrial (mt-)tRNA species. We show that YRDC and OSGEPL1 are responsible for t6A37 formation, utilizing L-threonine, ATP, and CO2/bicarbonate as substrates. OSGEPL1-knockout cells exhibit respiratory defects and reduced mitochondrial translation. We find low level of t6A37 in mutant mt-tRNA isolated from the MERRF-like patient’s cells, indicating that lack of t6A37 results in pathological consequences. Kinetic measurements of t6A37 formation reveal that the Km value of CO2/bicarbonate is extremely high (31 mM), suggesting that CO2/bicarbonate is a rate-limiting factor for t6A37 formation. Consistent with this, we observe a low frequency of t6A37 in mt-tRNAs isolated from human cells cultured without bicarbonate. These findings indicate that t6A37 is regulated by sensing intracellular CO2/bicarbonate concentration, implying that mitochondrial translation is modulated in a codon-specific manner under physiological conditions. Transfer RNA modifications play critical roles in protein synthesis. Here the authors reveal the t6A37 tRNA modification is dynamically regulated by sensing intracellular CO2 concentration in mitochondria, implying metabolic regulation of protein synthesis.
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Affiliation(s)
- Huan Lin
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Kenjyo Miyauchi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Tai Harada
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Ryo Okita
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Eri Takeshita
- Department of Mental Retardation and Birth Defect Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, 4-1-1 Ogawahigashi, Kodaira, Tokyo, 187-8502, Japan.,Department of Child Neurology, National Center Hospital, National Center of Neurology and Psychiatry, 4-1-1 Ogawahigashi, Kodaira, Tokyo, 187-8502, Japan
| | - Hirofumi Komaki
- Department of Mental Retardation and Birth Defect Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, 4-1-1 Ogawahigashi, Kodaira, Tokyo, 187-8502, Japan.,Department of Child Neurology, National Center Hospital, National Center of Neurology and Psychiatry, 4-1-1 Ogawahigashi, Kodaira, Tokyo, 187-8502, Japan
| | - Kaoru Fujioka
- Department of Pediatrics, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, 1110 Shimokato, Chuo, Yamanashi, Yamanashi, 409-3898, Japan
| | - Hideki Yagasaki
- Department of Pediatrics, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, 1110 Shimokato, Chuo, Yamanashi, Yamanashi, 409-3898, Japan
| | - Yu-Ichi Goto
- Department of Mental Retardation and Birth Defect Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, 4-1-1 Ogawahigashi, Kodaira, Tokyo, 187-8502, Japan.,Department of Child Neurology, National Center Hospital, National Center of Neurology and Psychiatry, 4-1-1 Ogawahigashi, Kodaira, Tokyo, 187-8502, Japan.,Medical Genome Center, National Center of Neurology and Psychiatry, 4-1-1 Ogawahigashi, Kodaira, Tokyo, 187-8502, Japan
| | - Kaori Yanaka
- RNA Biology Laboratory, RIKEN Advanced Research Institute, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Shinichi Nakagawa
- RNA Biology Laboratory, RIKEN Advanced Research Institute, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.,RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12-jo Nishi 6-chome, Kita-ku, Sapporo, 060-0812, Japan
| | - Yuriko Sakaguchi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.
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57
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Jung Y, Goldman D. Role of RNA modifications in brain and behavior. GENES, BRAIN, AND BEHAVIOR 2018; 17:e12444. [PMID: 29244246 PMCID: PMC6233296 DOI: 10.1111/gbb.12444] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 03/07/2018] [Indexed: 12/23/2022]
Abstract
Much progress in our understanding of RNA metabolism has been made since the first RNA nucleoside modification was identified in 1957. Many of these modifications are found in noncoding RNAs but recent interest has focused on coding RNAs. Here, we summarize current knowledge of cellular consequences of RNA modifications, with a special emphasis on neuropsychiatric disorders. We present evidence for the existence of an "RNA code," similar to the histone code, that fine-tunes gene expression in the nervous system by using combinations of different RNA modifications. Unlike the relatively stable genetic code, this combinatorial RNA epigenetic code, or epitranscriptome, may be dynamically reprogrammed as a cause or consequence of psychiatric disorders. We discuss potential mechanisms linking disregulation of the epitranscriptome with brain disorders and identify potential new avenues of research.
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Affiliation(s)
- Y. Jung
- Laboratory of Neurogenetics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Rockville, Maryland
| | - D. Goldman
- Laboratory of Neurogenetics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Rockville, Maryland
- Office of the Clinical Director, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Rockville, Maryland
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58
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Luthra A, Swinehart W, Bayooz S, Phan P, Stec B, Iwata-Reuyl D, Swairjo MA. Structure and mechanism of a bacterial t6A biosynthesis system. Nucleic Acids Res 2018; 46:1395-1411. [PMID: 29309633 PMCID: PMC5814804 DOI: 10.1093/nar/gkx1300] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Revised: 12/13/2017] [Accepted: 12/19/2017] [Indexed: 11/12/2022] Open
Abstract
The universal N(6)-threonylcarbamoyladenosine (t6A) modification at position 37 of ANN-decoding tRNAs is central to translational fidelity. In bacteria, t6A biosynthesis is catalyzed by the proteins TsaB, TsaC/TsaC2, TsaD and TsaE. Despite intense research, the molecular mechanisms underlying t6A biosynthesis are poorly understood. Here, we report biochemical and biophysical studies of the t6A biosynthesis system from Thermotoga maritima. Small angle X-ray scattering analysis reveals a symmetric 2:2 stoichiometric complex of TsaB and TsaD (TsaB2D2), as well as 2:2:2 complex (TsaB2D2E2), in which TsaB acts as a dimerization module, similar to the role of Pcc1 in the archaeal system. The TsaB2D2 complex is the minimal platform for the binding of one tRNA molecule, which can then accommodate a single TsaE subunit. Kinetic data demonstrate that TsaB2D2 alone, and a TsaB2D2E1 complex with TsaE mutants deficient in adenosine triphosphatase (ATPase) activity, can catalyze only a single cycle of t6A synthesis, while gel shift experiments provide evidence that the role of TsaE-catalyzed ATP hydrolysis occurs after the release of product tRNA. Based on these results, we propose a model for t6A biosynthesis in bacteria.
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Affiliation(s)
- Amit Luthra
- Department of Chemistry and Biochemistry, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182, USA
| | - William Swinehart
- Department of Chemistry, PO Box 751 Portland State University, Portland, OR 97207, USA
| | - Susan Bayooz
- Department of Chemistry and Biochemistry, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182, USA
| | - Phuc Phan
- Department of Chemistry and Biochemistry, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182, USA
| | - Boguslaw Stec
- Department of Chemistry and Biochemistry, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182, USA
| | - Dirk Iwata-Reuyl
- Department of Chemistry, PO Box 751 Portland State University, Portland, OR 97207, USA
| | - Manal A Swairjo
- Department of Chemistry and Biochemistry, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182, USA
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59
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Kapur M, Ackerman SL. mRNA Translation Gone Awry: Translation Fidelity and Neurological Disease. Trends Genet 2018; 34:218-231. [PMID: 29352613 DOI: 10.1016/j.tig.2017.12.007] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 12/04/2017] [Accepted: 12/11/2017] [Indexed: 10/18/2022]
Abstract
Errors during mRNA translation can lead to a reduction in the levels of functional proteins and an increase in deleterious molecules. Advances in next-generation sequencing have led to the discovery of rare genetic disorders, many caused by mutations in genes encoding the mRNA translation machinery, as well as to a better understanding of translational dynamics through ribosome profiling. We discuss here multiple neurological disorders that are linked to errors in tRNA aminoacylation and ribosome decoding. We draw on studies from genetic models, including yeast and mice, to enhance our understanding of the translational defects observed in these diseases. Finally, we emphasize the importance of tRNA, their associated enzymes, and the inextricable link between accuracy and efficiency in the maintenance of translational fidelity.
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Affiliation(s)
- Mridu Kapur
- Howard Hughes Medical Institute, Department of Cellular and Molecular Medicine, Section of Neurobiology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Susan L Ackerman
- Howard Hughes Medical Institute, Department of Cellular and Molecular Medicine, Section of Neurobiology, University of California, San Diego, La Jolla, CA 92093, USA.
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60
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Sokołowski M, Klassen R, Bruch A, Schaffrath R, Glatt S. Cooperativity between different tRNA modifications and their modification pathways. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2017; 1861:409-418. [PMID: 29222069 DOI: 10.1016/j.bbagrm.2017.12.003] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 11/30/2017] [Accepted: 12/03/2017] [Indexed: 12/11/2022]
Abstract
Ribonucleotide modifications perform a wide variety of roles in synthesis, turnover and functionality of tRNA molecules. The presence of particular chemical moieties can refine the internal interaction network within a tRNA molecule, influence its thermodynamic stability, contribute novel chemical properties and affect its decoding behavior during mRNA translation. As the lack of specific modifications in the anticodon stem and loop causes disrupted proteome homeostasis, diminished response to stress conditions, and the onset of human diseases, the underlying modification cascades have recently gained particular scientific and clinical interest. Nowadays, a complicated but conclusive image of the interconnectivity between different enzymatic modification cascades and their resulting tRNA modifications emerges. Here we summarize the current knowledge in the field, focusing on the known instances of cross talk among the enzymatic tRNA modification pathways and the consequences on the dynamic regulation of the tRNA modificome by various factors. This article is part of a Special Issue entitled: SI: Regulation of tRNA synthesis and modification in physiological conditions and disease edited by Dr. Boguta Magdalena.
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Affiliation(s)
- Mikołaj Sokołowski
- Max Planck Research Group at the Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland; Postgraduate School of Molecular Medicine, Warsaw, Poland
| | - Roland Klassen
- Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, Kassel, Germany
| | - Alexander Bruch
- Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, Kassel, Germany
| | - Raffael Schaffrath
- Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, Kassel, Germany.
| | - Sebastian Glatt
- Max Planck Research Group at the Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.
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61
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Kapur M, Monaghan CE, Ackerman SL. Regulation of mRNA Translation in Neurons-A Matter of Life and Death. Neuron 2017; 96:616-637. [PMID: 29096076 DOI: 10.1016/j.neuron.2017.09.057] [Citation(s) in RCA: 138] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 09/20/2017] [Accepted: 09/28/2017] [Indexed: 12/14/2022]
Abstract
Dynamic regulation of mRNA translation initiation and elongation is essential for the survival and function of neural cells. Global reductions in translation initiation resulting from mutations in the translational machinery or inappropriate activation of the integrated stress response may contribute to pathogenesis in a subset of neurodegenerative disorders. Aberrant proteins generated by non-canonical translation initiation may be a factor in the neuron death observed in the nucleotide repeat expansion diseases. Dysfunction of central components of the elongation machinery, such as the tRNAs and their associated enzymes, can cause translational infidelity and ribosome stalling, resulting in neurodegeneration. Taken together, dysregulation of mRNA translation is emerging as a unifying mechanism underlying the pathogenesis of many neurodegenerative disorders.
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Affiliation(s)
- Mridu Kapur
- Howard Hughes Medical Institute, Department of Cellular and Molecular Medicine, Section of Neurobiology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Caitlin E Monaghan
- Howard Hughes Medical Institute, Department of Cellular and Molecular Medicine, Section of Neurobiology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Susan L Ackerman
- Howard Hughes Medical Institute, Department of Cellular and Molecular Medicine, Section of Neurobiology, University of California, San Diego, La Jolla, CA 92093, USA.
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62
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Bacusmo JM, Orsini SS, Hu J, DeMott M, Thiaville PC, Elfarash A, Paulines MJ, Rojas-Benítez D, Meineke B, Deutsch C, Iwata-Reuyl D, Limbach PA, Dedon PC, Rice KC, Shuman S, Crécy-Lagard VD. The t 6A modification acts as a positive determinant for the anticodon nuclease PrrC, and is distinctively nonessential in Streptococcus mutans. RNA Biol 2017; 15:508-517. [PMID: 28726545 DOI: 10.1080/15476286.2017.1353861] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Endoribonuclease toxins (ribotoxins) are produced by bacteria and fungi to respond to stress, eliminate non-self competitor species, or interdict virus infection. PrrC is a bacterial ribotoxin that targets and cleaves tRNALysUUU in the anticodon loop. In vitro studies suggested that the post-transcriptional modification threonylcarbamoyl adenosine (t6A) is required for PrrC activity but this prediction had never been validated in vivo. Here, by using t6A-deficient yeast derivatives, it is shown that t6A is a positive determinant for PrrC proteins from various bacterial species. Streptococcus mutans is one of the few bacteria where the t6A synthesis gene tsaE (brpB) is dispensable and its genome encodes a PrrC toxin. We had previously shown using an HPLC-based assay that the S. mutans tsaE mutant was devoid of t6A. However, we describe here a novel and a more sensitive hybridization-based t6A detection method (compared to HPLC) that showed t6A was still present in the S. mutans ΔtsaE, albeit at greatly reduced levels (93% reduced compared with WT). Moreover, mutants in 2 other S. mutans t6A synthesis genes (tsaB and tsaC) were shown to be totally devoid of the modification thus confirming its dispensability in this organism. Furthermore, analysis of t6A modification ratios and of t6A synthesis genes mRNA levels in S. mutans suggest they may be regulated by growth phase.
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Affiliation(s)
- Jo Marie Bacusmo
- a Department of Microbiology and Cell Science, IFAS , University of Florida , Gainesville , FL , USA
| | - Silvia S Orsini
- a Department of Microbiology and Cell Science, IFAS , University of Florida , Gainesville , FL , USA
| | - Jennifer Hu
- b Center for Environmental Health Sciences, Department of Biological Engineering , Massachusetts Institute of Technology , Cambridge , MA , USA
| | - Michael DeMott
- b Center for Environmental Health Sciences, Department of Biological Engineering , Massachusetts Institute of Technology , Cambridge , MA , USA
| | - Patrick C Thiaville
- a Department of Microbiology and Cell Science, IFAS , University of Florida , Gainesville , FL , USA.,c Genetics and Genomics Graduate Program , University of Florida , Gainesville , USA.,d University of Florida Genetics Institute, University of Florida , Gainesville , FL , USA
| | - Ameer Elfarash
- a Department of Microbiology and Cell Science, IFAS , University of Florida , Gainesville , FL , USA.,e Genetic Department, Faculty of Agriculture , Assiut University , Assuit , Egypt
| | - Mellie June Paulines
- f Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry , University of Cincinnati , Cincinnati OH , USA
| | - Diego Rojas-Benítez
- g Centro de Regulación del Genoma. Facultad de Ciencias - Universidad de Chile , Santiago , Chile
| | - Birthe Meineke
- h Molecular Biology Program , Sloan-Kettering Institute , New York , NY , USA
| | - Chris Deutsch
- i Department of Chemistry , Portland State University , Portland , OR , USA
| | - Dirk Iwata-Reuyl
- i Department of Chemistry , Portland State University , Portland , OR , USA
| | - Patrick A Limbach
- f Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry , University of Cincinnati , Cincinnati OH , USA
| | - Peter C Dedon
- b Center for Environmental Health Sciences, Department of Biological Engineering , Massachusetts Institute of Technology , Cambridge , MA , USA
| | - Kelly C Rice
- a Department of Microbiology and Cell Science, IFAS , University of Florida , Gainesville , FL , USA
| | - Stewart Shuman
- h Molecular Biology Program , Sloan-Kettering Institute , New York , NY , USA
| | - Valérie de Crécy-Lagard
- a Department of Microbiology and Cell Science, IFAS , University of Florida , Gainesville , FL , USA.,d University of Florida Genetics Institute, University of Florida , Gainesville , FL , USA
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63
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Braun DA, Rao J, Mollet G, Schapiro D, Daugeron MC, Tan W, Gribouval O, Boyer O, Revy P, Jobst-Schwan T, Schmidt JM, Lawson JA, Schanze D, Ashraf S, Ullmann JFP, Hoogstraten CA, Boddaert N, Collinet B, Martin G, Liger D, Lovric S, Furlano M, Guerrera IC, Sanchez-Ferras O, Hu JF, Boschat AC, Sanquer S, Menten B, Vergult S, De Rocker N, Airik M, Hermle T, Shril S, Widmeier E, Gee HY, Choi WI, Sadowski CE, Pabst WL, Warejko JK, Daga A, Basta T, Matejas V, Scharmann K, Kienast SD, Behnam B, Beeson B, Begtrup A, Bruce M, Ch'ng GS, Lin SP, Chang JH, Chen CH, Cho MT, Gaffney PM, Gipson PE, Hsu CH, Kari JA, Ke YY, Kiraly-Borri C, Lai WM, Lemyre E, Littlejohn RO, Masri A, Moghtaderi M, Nakamura K, Ozaltin F, Praet M, Prasad C, Prytula A, Roeder ER, Rump P, Schnur RE, Shiihara T, Sinha MD, Soliman NA, Soulami K, Sweetser DA, Tsai WH, Tsai JD, Topaloglu R, Vester U, Viskochil DH, Vatanavicharn N, Waxler JL, Wierenga KJ, Wolf MTF, Wong SN, Leidel SA, Truglio G, Dedon PC, Poduri A, Mane S, Lifton RP, Bouchard M, Kannu P, Chitayat D, Magen D, Callewaert B, van Tilbeurgh H, Zenker M, Antignac C, Hildebrandt F. Mutations in KEOPS-complex genes cause nephrotic syndrome with primary microcephaly. Nat Genet 2017; 49:1529-1538. [PMID: 28805828 DOI: 10.1038/ng.3933] [Citation(s) in RCA: 141] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2016] [Accepted: 07/20/2017] [Indexed: 12/19/2022]
Abstract
Galloway-Mowat syndrome (GAMOS) is an autosomal-recessive disease characterized by the combination of early-onset nephrotic syndrome (SRNS) and microcephaly with brain anomalies. Here we identified recessive mutations in OSGEP, TP53RK, TPRKB, and LAGE3, genes encoding the four subunits of the KEOPS complex, in 37 individuals from 32 families with GAMOS. CRISPR-Cas9 knockout in zebrafish and mice recapitulated the human phenotype of primary microcephaly and resulted in early lethality. Knockdown of OSGEP, TP53RK, or TPRKB inhibited cell proliferation, which human mutations did not rescue. Furthermore, knockdown of these genes impaired protein translation, caused endoplasmic reticulum stress, activated DNA-damage-response signaling, and ultimately induced apoptosis. Knockdown of OSGEP or TP53RK induced defects in the actin cytoskeleton and decreased the migration rate of human podocytes, an established intermediate phenotype of SRNS. We thus identified four new monogenic causes of GAMOS, describe a link between KEOPS function and human disease, and delineate potential pathogenic mechanisms.
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Affiliation(s)
- Daniela A Braun
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Jia Rao
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Geraldine Mollet
- Laboratory of Hereditary Kidney Diseases, INSERM UMR1163, Imagine Institute, Paris, France.,Université Paris Descartes-Sorbonne Paris Cité, Imagine Institute, Paris, France
| | - David Schapiro
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Marie-Claire Daugeron
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Weizhen Tan
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Olivier Gribouval
- Laboratory of Hereditary Kidney Diseases, INSERM UMR1163, Imagine Institute, Paris, France.,Université Paris Descartes-Sorbonne Paris Cité, Imagine Institute, Paris, France
| | - Olivia Boyer
- Laboratory of Hereditary Kidney Diseases, INSERM UMR1163, Imagine Institute, Paris, France.,Université Paris Descartes-Sorbonne Paris Cité, Imagine Institute, Paris, France.,Department of Pediatric Nephrology, Necker Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Patrick Revy
- Université Paris Descartes-Sorbonne Paris Cité, Imagine Institute, Paris, France.,INSERM, U1163, Imagine Institute, Laboratory of Genome Dynamics in the Immune system, Paris, France
| | - Tilman Jobst-Schwan
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Johanna Magdalena Schmidt
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Jennifer A Lawson
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Denny Schanze
- Institute of Human Genetics, University Hospital Magdeburg, Magdeburg, Germany
| | - Shazia Ashraf
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Jeremy F P Ullmann
- Epilepsy Genetics Program and F.M. Kirby Neurobiology Center, Department of Neurology, Boston Children's Hospital, Boston, Massachusetts, USA.,Department of Neurology, Harvard Medical School, Boston, Massachusetts, USA
| | - Charlotte A Hoogstraten
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Nathalie Boddaert
- Université Paris Descartes-Sorbonne Paris Cité, Imagine Institute, Paris, France.,INSERM, U1163, Imagine Institute, Laboratory of Molecular and Pathophysiological Bases of Cognitive Disorders, and INSERM U1000, Paris, France.,Department of Pediatric Radiology, Necker Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Bruno Collinet
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France.,Sorbonne Universités UPMC, UFR 927, Sciences de la Vie, Paris, France.,Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie UMR 7590, Sorbonne Universités, UPMC, Université Paris 06, Paris, France
| | - Gaëlle Martin
- Laboratory of Hereditary Kidney Diseases, INSERM UMR1163, Imagine Institute, Paris, France.,Université Paris Descartes-Sorbonne Paris Cité, Imagine Institute, Paris, France
| | - Dominique Liger
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Svjetlana Lovric
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Monica Furlano
- Laboratory of Hereditary Kidney Diseases, INSERM UMR1163, Imagine Institute, Paris, France.,Université Paris Descartes-Sorbonne Paris Cité, Imagine Institute, Paris, France.,Nephrology Department, Fundació Puigvert, IIB Sant Pau, Universitat Autònoma de Barcelona and REDINREN, Barcelona, Spain
| | - I Chiara Guerrera
- Proteomics platform 3P5-Necker, Université Paris Descartes-Structure Fédérative de Recherche Necker, INSERM US24/CNRS UMS3633, Paris, France
| | - Oraly Sanchez-Ferras
- Goodman Cancer Research Centre and Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Jennifer F Hu
- Departments of Chemistry and Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | | | - Sylvia Sanquer
- Department of Metabolomic and Proteomic Biochemistry, Necker Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France.,INSERM UMR-S1124, Paris Descartes-Sorbonne Paris Cité University, Paris, France
| | - Björn Menten
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Sarah Vergult
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Nina De Rocker
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Merlin Airik
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Tobias Hermle
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Shirlee Shril
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Eugen Widmeier
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Department of Medicine, Renal Division, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Heon Yung Gee
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Department of Pharmacology, Brain Korea 21 PLUS Project for Medical Sciences, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Won-Il Choi
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Carolin E Sadowski
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Werner L Pabst
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Jillian K Warejko
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Ankana Daga
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Tamara Basta
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Verena Matejas
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Karin Scharmann
- Max Planck Institute for Molecular Biomedicine, Muenster, Germany.,Cells-in-Motion Cluster of Excellence, University of Muenster, Muenster, Germany
| | - Sandra D Kienast
- Max Planck Institute for Molecular Biomedicine, Muenster, Germany.,Cells-in-Motion Cluster of Excellence, University of Muenster, Muenster, Germany
| | - Babak Behnam
- Department of Medical Genetics and Molecular Biology, Iran University of Medical Sciences (IUMS), Tehran, Iran.,Medical Genetics Branch, National Human Genome Research Institute (NHGRI), Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, Maryland, USA
| | - Brendan Beeson
- Department of Diagnostic Imaging, Princess Margaret and King Edward Memorial Hospitals, Perth, Western Australia, Australia
| | | | - Malcolm Bruce
- Department of Diagnostic Imaging, Princess Margaret and King Edward Memorial Hospitals, Perth, Western Australia, Australia
| | - Gaik-Siew Ch'ng
- Department of Genetics, Kuala Lumpur Hospital, Kuala Lumpur, Malaysia
| | - Shuan-Pei Lin
- Department of Pediatric Genetics, MacKay Children's Hospital, Taipei, Taiwan.,Department of Medicine, MacKay Medical College, New Taipei City, Taiwan
| | - Jui-Hsing Chang
- Department of Pediatrics, MacKay Children's Hospital, Taipei, Taiwan
| | - Chao-Huei Chen
- Department of Pediatrics, Taichung Veterans General Hospital, Taichung, Taiwan
| | | | - Patrick M Gaffney
- Department of Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Patrick E Gipson
- Internal Medicine and Pediatrics Divisions of Adult and Pediatric Nephrology, University of Michigan, Ann Arbor, Michigan, USA
| | - Chyong-Hsin Hsu
- Department of Pediatrics, MacKay Children's Hospital, Taipei, Taiwan
| | - Jameela A Kari
- Pediatric Nephrology Center of Excellence and Pediatric Department, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Yu-Yuan Ke
- Department of Pediatrics, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Cathy Kiraly-Borri
- Genetic Services of Western Australia, Princess Margaret Hospital for Children and King Edward Memorial Hospital for Women, Subiaco, Western Australia, Australia
| | - Wai-Ming Lai
- Department of Paediatrics and Adolescent Medicine, Princess Margaret Hospital, Hong Kong, China
| | - Emmanuelle Lemyre
- Service de Génétique Médicale, Département de Pédiatrie, CHU Sainte-Justine, Université de Montréal, Montréal, Québec, Canada
| | - Rebecca Okashah Littlejohn
- Department of Pediatrics, Baylor College of Medicine, San Antonio, Texas, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Amira Masri
- Department of Pediatrics, Division of Child Neurology, Faculty of Medicine, University of Jordan, Amman, Jordan
| | - Mastaneh Moghtaderi
- Chronic Kidney Disease Research Center, Tehran University of Medical Science, Tehran, Iran
| | - Kazuyuki Nakamura
- Department of Pediatrics, Yamagata University School of Medicine, Yamagata, Japan
| | - Fatih Ozaltin
- Department of Pediatric Nephrology, Hacettepe University Faculty of Medicine, Hacettepe University, Ankara, Turkey.,Nephrogenetics Laboratory, Hacettepe University Faculty of Medicine, Hacettepe University, Ankara, Turkey.,Hacettepe University Center for Biobanking and Genomics, Hacettepe University, Ankara, Turkey
| | - Marleen Praet
- Department of Pathology, Ghent University Hospital, Ghent, Belgium
| | - Chitra Prasad
- Department of Genetics, Metabolism and Pediatrics, Western University, London Health Sciences Centre, London, Ontario, Canada
| | | | - Elizabeth R Roeder
- Department of Pediatrics, Baylor College of Medicine, San Antonio, Texas, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Patrick Rump
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | | | - Takashi Shiihara
- Department of Pediatrics, Yamagata University School of Medicine, Yamagata, Japan
| | - Manish D Sinha
- Department of Paediatric Nephrology, Kings College London, Evelina London Children's Hospital, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Neveen A Soliman
- Department of Pediatrics, Center of Pediatric Nephrology &Transplantation, Kasr Al Ainy School of Medicine, Cairo University, Cairo, Egypt.,Egyptian Group for Orphan Renal Diseases, Cairo, Egypt
| | - Kenza Soulami
- Department of Nephrology, Ibn Rochd University Hospital, Casablanca, Morocco
| | - David A Sweetser
- Division of Medical Genetics, Massachusetts General Hospital for Children, Boston, Massachusetts, USA
| | - Wen-Hui Tsai
- Division of Genetics and Metabolism, Department of Pediatrics, Chi Mei Medical Center, Tainan, Taiwan
| | - Jeng-Daw Tsai
- Department of Medicine, MacKay Medical College, New Taipei City, Taiwan.,Department of Pediatrics, MacKay Children's Hospital, Taipei, Taiwan.,Department of Pediatrics, Taipei Medical University Hospital, Taipei, Taiwan.,Department of Pediatrics, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Rezan Topaloglu
- Department of Pediatric Nephrology, Hacettepe University Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Udo Vester
- Department of Pediatrics II, University Hospital Essen, Essen, Germany
| | - David H Viskochil
- Department of Pediatrics, Division of Medical Genetics, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Nithiwat Vatanavicharn
- Division of Medical Genetics, Department of Pediatrics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Jessica L Waxler
- Division of Medical Genetics, Massachusetts General Hospital for Children, Boston, Massachusetts, USA
| | - Klaas J Wierenga
- Department of Pediatrics, Oklahoma University Health Sciences Center (OUHSC), Oklahoma City, Oklahoma, USA
| | - Matthias T F Wolf
- Division of Pediatric Nephrology, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Sik-Nin Wong
- Department of Pediatrics and Adolescent Medicine, Tuen Mun Hospital, Tuen Mun, Hong Kong, China
| | - Sebastian A Leidel
- Max Planck Institute for Molecular Biomedicine, Muenster, Germany.,Cells-in-Motion Cluster of Excellence, University of Muenster, Muenster, Germany.,Medical Faculty, University of Muenster, Muenster, Germany
| | - Gessica Truglio
- Epilepsy Genetics Program and F.M. Kirby Neurobiology Center, Department of Neurology, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Peter C Dedon
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Singapore-MIT Alliance for Research and Technology, Infectious Disease IRG, Singapore
| | - Annapurna Poduri
- Epilepsy Genetics Program and F.M. Kirby Neurobiology Center, Department of Neurology, Boston Children's Hospital, Boston, Massachusetts, USA.,Department of Neurology, Harvard Medical School, Boston, Massachusetts, USA
| | - Shrikant Mane
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Richard P Lifton
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA.,Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, New York, USA
| | - Maxime Bouchard
- Goodman Cancer Research Centre and Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Peter Kannu
- Department of Pediatrics, Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - David Chitayat
- Department of Pediatrics, Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Daniella Magen
- Pediatric Nephrology Institute, Rambam Health Care Campus, Haifa, Israel
| | - Bert Callewaert
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Herman van Tilbeurgh
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Martin Zenker
- Institute of Human Genetics, University Hospital Magdeburg, Magdeburg, Germany
| | - Corinne Antignac
- Laboratory of Hereditary Kidney Diseases, INSERM UMR1163, Imagine Institute, Paris, France.,Université Paris Descartes-Sorbonne Paris Cité, Imagine Institute, Paris, France.,Department of Genetics, Necker Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Friedhelm Hildebrandt
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
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64
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Bednářová A, Hanna M, Durham I, VanCleave T, England A, Chaudhuri A, Krishnan N. Lost in Translation: Defects in Transfer RNA Modifications and Neurological Disorders. Front Mol Neurosci 2017; 10:135. [PMID: 28536502 PMCID: PMC5422465 DOI: 10.3389/fnmol.2017.00135] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 04/20/2017] [Indexed: 11/13/2022] Open
Abstract
Transfer RNAs (tRNAs) are key molecules participating in protein synthesis. To augment their functionality they undergo extensive post-transcriptional modifications and, as such, are subject to regulation at multiple levels including transcription, transcript processing, localization and ribonucleoside base modification. Post-transcriptional enzyme-catalyzed modification of tRNA occurs at a number of base and sugar positions and influences specific anticodon-codon interactions and regulates translation, its efficiency and fidelity. This phenomenon of nucleoside modification is most remarkable and results in a rich structural diversity of tRNA of which over 100 modified nucleosides have been characterized. Most often these hypermodified nucleosides are found in the wobble position of tRNAs, where they play a direct role in codon recognition as well as in maintaining translational efficiency and fidelity, etc. Several recent studies have pointed to a link between defects in tRNA modifications and human diseases including neurological disorders. Therefore, defects in tRNA modifications in humans need intensive characterization at the enzymatic and mechanistic level in order to pave the way to understand how lack of such modifications are associated with neurological disorders with the ultimate goal of gaining insights into therapeutic interventions.
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Affiliation(s)
- Andrea Bednářová
- Department of Biochemistry and Physiology, Institute of Entomology, Biology Centre, Academy of SciencesČeské Budějovice, Czechia.,Laboratory of Molecular Biology and Biochemistry, Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State UniversityMississippi State, MS, USA
| | - Marley Hanna
- Molecular Biosciences Program, Arkansas State UniversityJonesboro, AR, USA
| | - Isabella Durham
- Department of Wildlife, Fisheries and Aquaculture, Mississippi State UniversityMississippi State, MS, USA
| | - Tara VanCleave
- Laboratory of Molecular Biology and Biochemistry, Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State UniversityMississippi State, MS, USA
| | - Alexis England
- Laboratory of Molecular Biology and Biochemistry, Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State UniversityMississippi State, MS, USA
| | | | - Natraj Krishnan
- Laboratory of Molecular Biology and Biochemistry, Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State UniversityMississippi State, MS, USA
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