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Scherf D, Hammermeister A, Böhnert P, Burkard A, Helm M, Glatt S, Schaffrath R. tRNA binding to Kti12 is crucial for wobble uridine modification by Elongator. Nucleic Acids Res 2025; 53:gkaf296. [PMID: 40226916 PMCID: PMC11995267 DOI: 10.1093/nar/gkaf296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2024] [Revised: 03/05/2025] [Accepted: 03/28/2025] [Indexed: 04/15/2025] Open
Abstract
In yeast, tRNA modifications that are introduced by the Elongator complex are recognized by zymocin, a fungal tRNase killer toxin that cleaves the anticodon. Based on zymocin resistance conferred by mutations in KTI12, a gene coding for an Elongator interactor, we further examined the yet vaguely defined cellular role of Kti12. Guided by structural similarities between Kti12 and PSTK, a tRNA kinase involved in selenocysteine synthesis, we identified conserved basic residues in the C-terminus of Kti12, which upon site-directed mutagenesis caused progressive loss of tRNA binding in vitro. The inability of Kti12 to bind tRNA led to similar phenotypes caused by Elongator inactivation in vivo. Consistently, tRNA binding deficient kti12 mutants drastically suppressed Elongator dependent tRNA anticodon modifications and reduced the capacity of Kti12 to interact with Elongator. We further could distinguish Elongator unbound pools of Kti12 in a tRNA dependent manner from bound ones. In summary, the C-terminal domain of Kti12 is crucial for tRNA binding and Kti12 recruitment to Elongator, which are both requirements for Elongator function suggesting Kti12 is a tRNA carrier that interacts with Elongator for modification of the tRNA anticodon.
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Affiliation(s)
- David Scherf
- Institute of Biology, Division of Microbiology, University of Kassel, D-34132 Kassel, Germany
| | - Alexander Hammermeister
- Institute of Biology, Division of Microbiology, University of Kassel, D-34132 Kassel, Germany
- Małopolska Centre of Biotechnology, Jagiellonian University, 30387 Krakow, Poland
| | - Pauline Böhnert
- Institute of Biology, Division of Microbiology, University of Kassel, D-34132 Kassel, Germany
| | - Alicia Burkard
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University of Mainz, D-55128 Mainz, Germany
| | - Mark Helm
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University of Mainz, D-55128 Mainz, Germany
| | - Sebastian Glatt
- Małopolska Centre of Biotechnology, Jagiellonian University, 30387 Krakow, Poland
- Department for Biological Sciences and Pathobiology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Raffael Schaffrath
- Institute of Biology, Division of Microbiology, University of Kassel, D-34132 Kassel, Germany
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2
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Lei L, Burton ZF. Chemical Evolution of Life on Earth. Genes (Basel) 2025; 16:220. [PMID: 40004549 PMCID: PMC11854950 DOI: 10.3390/genes16020220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2025] [Revised: 02/04/2025] [Accepted: 02/08/2025] [Indexed: 02/27/2025] Open
Abstract
Background/Objectives: The origin of genes and genetics is the story of the coevolution of translation systems and the genetic code. Remarkably, the history of the origin of life on Earth was inscribed and preserved in the sequences of tRNAs. Methods: Sequence logos demonstrate the patterning of pre-life tRNA sequences. Results: The pre-life type I and type II tRNA sequences are known to the last nucleotide with only a few ambiguities. Type I and type II tRNAs evolved from ligation of three 31 nt minihelices of highly patterned and known sequence followed by closely related 9 nt internal deletion(s) within ligated acceptor stems. The D loop 17 nt core was a truncated UAGCC repeat. The anticodon and T 17 nt stem-loop-stems are homologous sequences with 5 nt stems and 7 nt U-turn loops that were selected in pre-life to resist ribozyme nucleases and to present a 3 nt anticodon with a single wobble position. The 7 nt T loop in tRNA was selected to interact with the D loop at the "elbow". The 5'-acceptor stem was based on a 7 nt truncated GCG repeat. The 3'-acceptor stem was based on a complementary 7 nt CGC repeat. In pre-life, ACCA-Gly was a primitive adapter molecule ligated to many RNAs, including tRNAs, to synthesize polyglycine. Conclusions: Analysis of sequence logos of tRNAs from an ancient Archaeon substantiates how the pre-life to life transition occurred on Earth. Polyglycine is posited to have aggregated complex molecular assemblies, including minihelices, tRNAs, cooperating molecules, and protocells, leading to the first life on Earth.
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Affiliation(s)
- Lei Lei
- School of Biological Sciences, University of New England, Biddeford, ME 04005, USA;
| | - Zachary Frome Burton
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
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3
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Abbassi NEH, Jaciuk M, Scherf D, Böhnert P, Rau A, Hammermeister A, Rawski M, Indyka P, Wazny G, Chramiec-Głąbik A, Dobosz D, Skupien-Rabian B, Jankowska U, Rappsilber J, Schaffrath R, Lin TY, Glatt S. Cryo-EM structures of the human Elongator complex at work. Nat Commun 2024; 15:4094. [PMID: 38750017 PMCID: PMC11096365 DOI: 10.1038/s41467-024-48251-y] [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: 11/10/2023] [Accepted: 04/22/2024] [Indexed: 05/18/2024] Open
Abstract
tRNA modifications affect ribosomal elongation speed and co-translational folding dynamics. The Elongator complex is responsible for introducing 5-carboxymethyl at wobble uridine bases (cm5U34) in eukaryotic tRNAs. However, the structure and function of human Elongator remain poorly understood. In this study, we present a series of cryo-EM structures of human ELP123 in complex with tRNA and cofactors at four different stages of the reaction. The structures at resolutions of up to 2.9 Å together with complementary functional analyses reveal the molecular mechanism of the modification reaction. Our results show that tRNA binding exposes a universally conserved uridine at position 33 (U33), which triggers acetyl-CoA hydrolysis. We identify a series of conserved residues that are crucial for the radical-based acetylation of U34 and profile the molecular effects of patient-derived mutations. Together, we provide the high-resolution view of human Elongator and reveal its detailed mechanism of action.
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Affiliation(s)
- Nour-El-Hana Abbassi
- Małopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow, Poland
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Marcin Jaciuk
- Małopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow, Poland
| | - David Scherf
- Institute for Biology, Department for Microbiology, University of Kassel, Kassel, Germany
| | - Pauline Böhnert
- Institute for Biology, Department for Microbiology, University of Kassel, Kassel, Germany
| | - Alexander Rau
- Bioanalytics, Institute of Biotechnology, Technical University of Berlin, Berlin, Germany
| | | | - Michał Rawski
- Małopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow, Poland
- SOLARIS National Synchrotron Radiation Centre, Jagiellonian University, Krakow, Poland
| | - Paulina Indyka
- Małopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow, Poland
- SOLARIS National Synchrotron Radiation Centre, Jagiellonian University, Krakow, Poland
| | - Grzegorz Wazny
- SOLARIS National Synchrotron Radiation Centre, Jagiellonian University, Krakow, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Krakow, Poland
| | | | - Dominika Dobosz
- Małopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow, Poland
| | | | - Urszula Jankowska
- Małopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow, Poland
| | - Juri Rappsilber
- Bioanalytics, Institute of Biotechnology, Technical University of Berlin, Berlin, Germany
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Raffael Schaffrath
- Institute for Biology, Department for Microbiology, University of Kassel, Kassel, Germany.
| | - Ting-Yu Lin
- Małopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow, Poland.
- Department of Biosciences, Durham University, Durham, UK.
| | - Sebastian Glatt
- Małopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow, Poland.
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4
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Jun SE, Cho KH, Schaffrath R, Kim GT. Evolutionary Conservation in Protein-Protein Interactions and Structures of the Elongator Sub-Complex ELP456 from Arabidopsis and Yeast. Int J Mol Sci 2024; 25:4370. [PMID: 38673955 PMCID: PMC11050213 DOI: 10.3390/ijms25084370] [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: 03/20/2024] [Revised: 04/09/2024] [Accepted: 04/12/2024] [Indexed: 04/28/2024] Open
Abstract
The Elongator complex plays a pivotal role in the wobble uridine modification of the tRNA anticodon. Comprising two sets of six distinct subunits, namely, Elongator proteins (ELP1-ELP6) and associated proteins, the holo-Elongator complex demonstrates remarkable functional and structural conservation across eukaryotes. However, the precise details of the evolutionary conservation of the holo-Elongator complex and its individual sub-complexes (i.e., ELP123; ELP456) in plants remain limited. In this study, we conducted an in vivo analysis of protein-protein interactions among Arabidopsis ELP4, ELP5, and ELP6 proteins. Additionally, we predicted their structural configurations and performed a comparative analysis with the structure of the yeast Elp456 sub-complex. Protein-protein interaction analysis revealed that AtELP4 interacts with AtELP6 but not directly with AtELP5. Furthermore, we found that the Arabidopsis Elongator-associated protein, Deformed Roots and Leaves 1 (DRL1), did not directly bind to AtELP proteins. The structural comparison of the ELP456 sub-complex between Arabidopsis and yeast demonstrated high similarity, encompassing the RecA-ATPase fold and the positions of hydrogen bonds, despite their relatively low sequence homology. Our findings suggest that Arabidopsis ELP4, ELP5, and ELP6 proteins form a heterotrimer, with ELP6 serving as a bridge, indicating high structural conservation between the ELP456 sub-complexes from Arabidopsis and yeast.
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Affiliation(s)
- Sang Eun Jun
- Department of Molecular Genetics, Dong-A University, Busan 49315, Republic of Korea (K.-H.C.)
| | - Kiu-Hyung Cho
- Department of Molecular Genetics, Dong-A University, Busan 49315, Republic of Korea (K.-H.C.)
- Gyeongbuk Institute for Bioindustry, Andong 36618, Republic of Korea
| | - Raffael Schaffrath
- Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, Heinrich-Plett-Str. 40, 34132 Kassel, Germany;
| | - Gyung-Tae Kim
- Department of Molecular Genetics, Dong-A University, Busan 49315, Republic of Korea (K.-H.C.)
- Graduate School of Applied Bioscience, Dong-A University, Busan 49315, Republic of Korea
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5
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Moody JD, Hill S, Lundahl MN, Saxton AJ, Galambas A, Broderick WE, Lawrence CM, Broderick JB. Computational engineering of previously crystallized pyruvate formate-lyase activating enzyme reveals insights into SAM binding and reductive cleavage. J Biol Chem 2023; 299:104791. [PMID: 37156396 PMCID: PMC10267522 DOI: 10.1016/j.jbc.2023.104791] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 04/21/2023] [Accepted: 04/23/2023] [Indexed: 05/10/2023] Open
Abstract
Radical S-adenosyl-l-methionine (SAM) enzymes are ubiquitous in nature and carry out a broad variety of difficult chemical transformations initiated by hydrogen atom abstraction. Although numerous radical SAM (RS) enzymes have been structurally characterized, many prove recalcitrant to crystallization needed for atomic-level structure determination using X-ray crystallography, and even those that have been crystallized for an initial study can be difficult to recrystallize for further structural work. We present here a method for computationally engineering previously observed crystallographic contacts and employ it to obtain more reproducible crystallization of the RS enzyme pyruvate formate-lyase activating enzyme (PFL-AE). We show that the computationally engineered variant binds a typical RS [4Fe-4S]2+/+ cluster that binds SAM, with electron paramagnetic resonance properties indistinguishable from the native PFL-AE. The variant also retains the typical PFL-AE catalytic activity, as evidenced by the characteristic glycyl radical electron paramagnetic resonance signal observed upon incubation of the PFL-AE variant with reducing agent, SAM, and PFL. The PFL-AE variant was also crystallized in the [4Fe-4S]2+ state with SAM bound, providing a new high-resolution structure of the SAM complex in the absence of substrate. Finally, by incubating such a crystal in a solution of sodium dithionite, the reductive cleavage of SAM is triggered, providing us with a structure in which the SAM cleavage products 5'-deoxyadenosine and methionine are bound in the active site. We propose that the methods described herein may be useful in the structural characterization of other difficult-to-resolve proteins.
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Affiliation(s)
- James D Moody
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, USA; Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Sarah Hill
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Maike N Lundahl
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Aubrianna J Saxton
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, USA
| | - Amanda Galambas
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - William E Broderick
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - C Martin Lawrence
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Joan B Broderick
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA.
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6
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Jaciuk M, Scherf D, Kaszuba K, Gaik M, Rau A, Kościelniak A, Krutyhołowa R, Rawski M, Indyka P, Graziadei A, Chramiec-Głąbik A, Biela A, Dobosz D, Lin TY, Abbassi NEH, Hammermeister A, Rappsilber J, Kosinski J, Schaffrath R, Glatt S. Cryo-EM structure of the fully assembled Elongator complex. Nucleic Acids Res 2023; 51:2011-2032. [PMID: 36617428 PMCID: PMC10018365 DOI: 10.1093/nar/gkac1232] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 11/22/2022] [Accepted: 12/09/2022] [Indexed: 01/10/2023] Open
Abstract
Transfer RNA (tRNA) molecules are essential to decode messenger RNA codons during protein synthesis. All known tRNAs are heavily modified at multiple positions through post-transcriptional addition of chemical groups. Modifications in the tRNA anticodons are directly influencing ribosome decoding and dynamics during translation elongation and are crucial for maintaining proteome integrity. In eukaryotes, wobble uridines are modified by Elongator, a large and highly conserved macromolecular complex. Elongator consists of two subcomplexes, namely Elp123 containing the enzymatically active Elp3 subunit and the associated Elp456 hetero-hexamer. The structure of the fully assembled complex and the function of the Elp456 subcomplex have remained elusive. Here, we show the cryo-electron microscopy structure of yeast Elongator at an overall resolution of 4.3 Å. We validate the obtained structure by complementary mutational analyses in vitro and in vivo. In addition, we determined various structures of the murine Elongator complex, including the fully assembled mouse Elongator complex at 5.9 Å resolution. Our results confirm the structural conservation of Elongator and its intermediates among eukaryotes. Furthermore, we complement our analyses with the biochemical characterization of the assembled human Elongator. Our results provide the molecular basis for the assembly of Elongator and its tRNA modification activity in eukaryotes.
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Affiliation(s)
- Marcin Jaciuk
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow 30-387, Poland
| | - David Scherf
- Institute for Biology, Department for Microbiology, University of Kassel, Kassel 34132, Germany
| | - Karol Kaszuba
- European Molecular Biology Laboratory Hamburg, Hamburg 22607, Germany
- Centre for Structural Systems Biology (CSSB), Hamburg 22607, Germany
| | - Monika Gaik
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow 30-387, Poland
| | - Alexander Rau
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin 13355, Germany
| | - Anna Kościelniak
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow 30-387, Poland
| | - Rościsław Krutyhołowa
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow 30-387, Poland
| | - Michał Rawski
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow 30-387, Poland
- National Synchrotron Radiation Centre SOLARIS, Jagiellonian University, Krakow 30-387, Poland
| | - Paulina Indyka
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow 30-387, Poland
- National Synchrotron Radiation Centre SOLARIS, Jagiellonian University, Krakow 30-387, Poland
| | - Andrea Graziadei
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin 13355, Germany
| | | | - Anna Biela
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow 30-387, Poland
| | - Dominika Dobosz
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow 30-387, Poland
| | - Ting-Yu Lin
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow 30-387, Poland
| | - Nour-el-Hana Abbassi
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow 30-387, Poland
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warsaw 02-091, Poland
| | - Alexander Hammermeister
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow 30-387, Poland
- Institute for Biology, Department for Microbiology, University of Kassel, Kassel 34132, Germany
| | - Juri Rappsilber
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin 13355, Germany
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Jan Kosinski
- European Molecular Biology Laboratory Hamburg, Hamburg 22607, Germany
- Centre for Structural Systems Biology (CSSB), Hamburg 22607, Germany
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Raffael Schaffrath
- Institute for Biology, Department for Microbiology, University of Kassel, Kassel 34132, Germany
| | - Sebastian Glatt
- To whom correspondence should be addressed. Tel: +48 12 664 6321; Fax: +48 12 664 6902;
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7
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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: 15] [Impact Index Per Article: 7.5] [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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8
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A novel ELP1 mutation impairs the function of the Elongator complex and causes a severe neurodevelopmental phenotype. J Hum Genet 2023. [PMID: 36864284 DOI: 10.1038/s10038-023-01135-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
BACKGROUND Neurodevelopmental disorders (NDDs) are heterogeneous, debilitating conditions that include motor and cognitive disability and social deficits. The genetic factors underlying the complex phenotype of NDDs remain to be elucidated. Accumulating evidence suggest that the Elongator complex plays a role in NDDs, given that patient-derived mutations in its ELP2, ELP3, ELP4 and ELP6 subunits have been associated with these disorders. Pathogenic variants in its largest subunit ELP1 have been previously found in familial dysautonomia and medulloblastoma, with no link to NDDs affecting primarily the central nervous system. METHODS Clinical investigation included patient history and physical, neurological and magnetic resonance imaging (MRI) examination. A novel homozygous likely pathogenic ELP1 variant was identified by whole-genome sequencing. Functional studies included in silico analysis of the mutated ELP1 in the context of the holo-complex, production and purification of the ELP1 harbouring the identified mutation and in vitro analyses using microscale thermophoresis for tRNA binding assay and acetyl-CoA hydrolysis assay. Patient fibroblasts were harvested for tRNA modification analysis using HPLC coupled to mass spectrometry. RESULTS We report a novel missense mutation in the ELP1 identified in two siblings with intellectual disability and global developmental delay. We show that the mutation perturbs the ability of ELP123 to bind tRNAs and compromises the function of the Elongator in vitro and in human cells. CONCLUSION Our study expands the mutational spectrum of ELP1 and its association with different neurodevelopmental conditions and provides a specific target for genetic counselling.
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9
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Functional Characterization of the GNAT Family Histone Acetyltransferase Elp3 and GcnE in Aspergillus fumigatus. Int J Mol Sci 2023; 24:ijms24032179. [PMID: 36768506 PMCID: PMC9916960 DOI: 10.3390/ijms24032179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/12/2023] [Accepted: 01/20/2023] [Indexed: 01/25/2023] Open
Abstract
Post-translational modifications of chromatin structure by histone acetyltransferase (HATs) play a pivotal role in the regulation of gene expression and diverse biological processes. However, the function of GNAT family HATs, especially Elp3, in the opportunistic human pathogenic fungus Aspergillus fumigatus is largely unknown. To investigate the roles of the GNAT family HATs Elp3 and GcnE in the A. fumigatus, we have generated and characterized individual null Δelp3 and ΔgcnE mutants. The radial growth of fungal colonies was significantly decreased by the loss of elp3 or gcnE, and the number of asexual spores (conidia) in the ΔgcnE mutant was significantly reduced. Moreover, the mRNA levels of the key asexual development regulators were also significantly low in the ΔgcnE mutant compared to wild type (WT). Whereas both the Δelp3 and ΔgcnE mutants were markedly impaired in the formation of adherent biofilms, the ΔgcnE mutant showed a complete loss of surface structure and of intercellular matrix. The ΔgcnE mutant responded differently to oxidative stressors and showed significant susceptibility to triazole antifungal agents. Furthermore, Elp3 and GcnE function oppositely in the production of secondary metabolites, and the ΔgcnE mutant showed attenuated virulence. In conclusion, Elp3 and GcnE are associated with diverse biological processes and can be potential targets for controlling the pathogenic fungus.
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10
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Chramiec-Głąbik A, Rawski M, Glatt S, Lin TY. Electrophoretic Mobility Shift Assay (EMSA) and Microscale Thermophoresis (MST) Methods to Measure Interactions Between tRNAs and Their Modifying Enzymes. Methods Mol Biol 2023; 2666:29-53. [PMID: 37166655 DOI: 10.1007/978-1-0716-3191-1_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The Elongator complex is a unique tRNA acetyltransferase; it was initially annotated as a protein acetyltransferase, but in-depth biochemical analyses revealed its genuine function as a tRNA modifier. The substrate recognition and binding of the Elongator is mainly mediated by its catalytic Elp3 subunit. In this chapter, we describe protocols to generate fluorescently labeled RNAs and outline the principles underlying electrophoretic mobility shift assays (EMSA) and microscale thermophoresis (MST). These two methods allow qualitative and quantitative examinations of the binding affinity of various tRNAs toward the homologs of Elp3 from various organisms. The rather qualitative results from EMSA analyses can be nicely complemented by MST measurements allowing precise determination of the dissociation constant (KD). We also provide detailed notes for users to mitigate potential ambiguities and technical pitfalls during the procedures.
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Affiliation(s)
| | - Michał Rawski
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow, Poland
| | - Sebastian Glatt
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow, Poland.
| | - Ting-Yu Lin
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow, Poland.
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11
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Jun SE, Cho KH, Manzoor MA, Hwang TY, Kim YS, Schaffrath R, Kim GT. AtELP4 a subunit of the Elongator complex in Arabidopsis, mediates cell proliferation and dorsoventral polarity during leaf morphogenesis. FRONTIERS IN PLANT SCIENCE 2022; 13:1033358. [PMID: 36340367 PMCID: PMC9634574 DOI: 10.3389/fpls.2022.1033358] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 09/20/2022] [Indexed: 06/16/2023]
Abstract
The Elongator complex in eukaryotes has conserved tRNA modification functions and contributes to various physiological processes such as transcriptional control, DNA replication and repair, and chromatin accessibility. ARABIDOPSIS ELONGATOR PROTEIN 4 (AtELP4) is one of the six subunits (AtELP1-AtELP6) in Arabidopsis Elongator. In addition, there is an Elongator-associated protein, DEFORMED ROOTS AND LEAVES 1 (DRL1), whose homolog in yeast (Kti12) binds tRNAs. In this study, we explored the functions of AtELP4 in plant-specific aspects such as leaf morphogenesis and evolutionarily conserved ones between yeast and Arabidopsis. ELP4 comparison between yeast and Arabidopsis revealed that plant ELP4 possesses not only a highly conserved P-loop ATPase domain but also unknown plant-specific motifs. ELP4 function is partially conserved between Arabidopsis and yeast in the growth sensitivity toward caffeine and elevated cultivation temperature. Either single Atelp4 or drl1-102 mutants and double Atelp4 drl1-102 mutants exhibited a reduction in cell proliferation and changed the adaxial-abaxial polarity of leaves. In addition, the single Atelp4 and double Atelp4 drl1-102 mutants showed remarkable downward curling at the whole part of leaf blades in contrast to wild-type leaf blades. Furthermore, our genetic study revealed that AtELP4 might epistatically act on DRL1 in the regulation of cell proliferation and dorsoventral polarity in leaves. Taken together, we suggest that AtELP4 as part of the plant Elongator complex may act upstream of a regulatory pathway for adaxial-abaxial polarity and cell proliferation during leaf development.
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Affiliation(s)
- Sang Eun Jun
- Department of Molecular Genetics, Dong-A University, Busan, South Korea
| | - Kiu-Hyung Cho
- Department of Molecular Genetics, Dong-A University, Busan, South Korea
| | | | - Tae Young Hwang
- Graduate School of Applied Bioscience, Dong-A University, Busan, South Korea
| | - Youn Soo Kim
- Graduate School of Applied Bioscience, Dong-A University, Busan, South Korea
| | - Raffael Schaffrath
- Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, Kassel, Germany
| | - Gyung-Tae Kim
- Department of Molecular Genetics, Dong-A University, Busan, South Korea
- Graduate School of Applied Bioscience, Dong-A University, Busan, South Korea
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12
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Boutoual R, Jo H, Heckenbach I, Tiwari R, Kasler H, Lerner CA, Shah S, Schilling B, Calvanese V, Rardin MJ, Scheibye-Knudsen M, Verdin E. A novel splice variant of Elp3/Kat9 regulates mitochondrial tRNA modification and function. Sci Rep 2022; 12:14804. [PMID: 36045139 PMCID: PMC9433433 DOI: 10.1038/s41598-022-18114-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 08/05/2022] [Indexed: 12/03/2022] Open
Abstract
Post-translational modifications, such as lysine acetylation, regulate the activity of diverse proteins across many cellular compartments. Protein deacetylation in mitochondria is catalyzed by the enzymatic activity of the NAD+-dependent deacetylase sirtuin 3 (SIRT3), however it remains unclear whether corresponding mitochondrial acetyltransferases exist. We used a bioinformatics approach to search for mitochondrial proteins with an acetyltransferase catalytic domain, and identified a novel splice variant of ELP3 (mt-ELP3) of the elongator complex, which localizes to the mitochondrial matrix in mammalian cells. Unexpectedly, mt-ELP3 does not mediate mitochondrial protein acetylation but instead induces a post-transcriptional modification of mitochondrial-transfer RNAs (mt-tRNAs). Overexpression of mt-ELP3 leads to the protection of mt-tRNAs against the tRNA-specific RNase angiogenin, increases mitochondrial translation, and furthermore increases expression of OXPHOS complexes. This study thus identifies mt-ELP3 as a non-canonical mt-tRNA modifying enzyme.
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Affiliation(s)
- Rachid Boutoual
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA, 94945, USA.
| | - Hyunsun Jo
- Gladstone Institutes and University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Indra Heckenbach
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA, 94945, USA.,Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Ritesh Tiwari
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA, 94945, USA
| | - Herbert Kasler
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA, 94945, USA
| | - Chad A Lerner
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA, 94945, USA
| | - Samah Shah
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA, 94945, USA
| | | | - Vincenzo Calvanese
- Gladstone Institutes and University of California, San Francisco, San Francisco, CA, 94158, USA
| | | | - Morten Scheibye-Knudsen
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Eric Verdin
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA, 94945, USA. .,Gladstone Institutes and University of California, San Francisco, San Francisco, CA, 94158, USA.
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13
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Boswinkle K, McKinney J, Allen KD. Highlighting the Unique Roles of Radical S-Adenosylmethionine Enzymes in Methanogenic Archaea. J Bacteriol 2022; 204:e0019722. [PMID: 35880875 PMCID: PMC9380564 DOI: 10.1128/jb.00197-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Radical S-adenosylmethionine (SAM) enzymes catalyze an impressive variety of difficult biochemical reactions in various pathways across all domains of life. These metalloenzymes employ a reduced [4Fe-4S] cluster and SAM to generate a highly reactive 5'-deoxyadenosyl radical that is capable of initiating catalysis on otherwise unreactive substrates. Interestingly, the genomes of methanogenic archaea encode many unique radical SAM enzymes with underexplored or completely unknown functions. These organisms are responsible for the yearly production of nearly 1 billion tons of methane, a potent greenhouse gas as well as a valuable energy source. Thus, understanding the details of methanogenic metabolism and elucidating the functions of essential enzymes in these organisms can provide insights into strategies to decrease greenhouse gas emissions as well as inform advances in bioenergy production processes. This minireview provides an overview of the current state of the field regarding the functions of radical SAM enzymes in methanogens and discusses gaps in knowledge that should be addressed.
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Affiliation(s)
- Kaleb Boswinkle
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
| | - Justin McKinney
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
| | - Kylie D. Allen
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
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14
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Iron–sulfur clusters as inhibitors and catalysts of viral replication. Nat Chem 2022; 14:253-266. [DOI: 10.1038/s41557-021-00882-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 12/15/2021] [Indexed: 12/11/2022]
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15
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“Superwobbling” and tRNA-34 Wobble and tRNA-37 Anticodon Loop Modifications in Evolution and Devolution of the Genetic Code. Life (Basel) 2022; 12:life12020252. [PMID: 35207539 PMCID: PMC8879553 DOI: 10.3390/life12020252] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 01/25/2022] [Accepted: 02/01/2022] [Indexed: 11/17/2022] Open
Abstract
The genetic code evolved around the reading of the tRNA anticodon on the primitive ribosome, and tRNA-34 wobble and tRNA-37 modifications coevolved with the code. We posit that EF-Tu, the closing mechanism of the 30S ribosomal subunit, methylation of wobble U34 at the 5-carbon and suppression of wobbling at the tRNA-36 position were partly redundant and overlapping functions that coevolved to establish the code. The genetic code devolved in evolution of mitochondria to reduce the size of the tRNAome (all of the tRNAs of an organism or organelle). “Superwobbling” or four-way wobbling describes a major mechanism for shrinking the mitochondrial tRNAome. In superwobbling, unmodified wobble tRNA-U34 can recognize all four codon wobble bases (A, G, C and U), allowing a single unmodified tRNA-U34 to read a 4-codon box. During code evolution, to suppress superwobbling in 2-codon sectors, U34 modification by methylation at the 5-carbon position appears essential. As expected, at the base of code evolution, tRNA-37 modifications mostly related to the identity of the adjacent tRNA-36 base. TRNA-37 modifications help maintain the translation frame during elongation.
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16
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Prediction of the Iron–Sulfur Binding Sites in Proteins Using the Highly Accurate Three-Dimensional Models Calculated by AlphaFold and RoseTTAFold. INORGANICS 2021. [DOI: 10.3390/inorganics10010002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
AlphaFold and RoseTTAFold are deep learning-based approaches that predict the structure of proteins from their amino acid sequences. Remarkable success has recently been achieved in the prediction accuracy of not only the fold of the target protein but also the position of its amino acid side chains. In this article, I question the accuracy of these methods to predict iron–sulfur binding sites. I analyze three-dimensional models calculated by AlphaFold and RoseTTAFold of Fe–S–dependent enzymes, for which no structure of a homologous protein has been solved experimentally. In all cases, the amino acids that presumably coordinate the cluster were gathered together and facing each other, which led to a quite accurate model of the Fe–S cluster binding site. Yet, cysteine candidates were often involved in intramolecular disulfide bonds, and the number and identity of the protein amino acids that should ligate the cluster were not always clear. The experimental structure determination of the protein with its Fe–S cluster and in complex with substrate/inhibitor/product is still needed to unambiguously visualize the coordination state of the cluster and understand the conformational changes occurring during catalysis.
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17
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Cameron B, Lehrmann E, Chih T, Walters J, Buksch R, Snyder S, Goffena J, Lefcort F, Becker KG, George L. Loss of Elp1 perturbs histone H2A.Z and the Notch signaling pathway. Biol Open 2021; 10:272332. [PMID: 34590699 PMCID: PMC8496692 DOI: 10.1242/bio.058979] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 08/17/2021] [Indexed: 12/12/2022] Open
Abstract
Elongator dysfunction is increasingly recognized as a contributor to multiple neurodevelopmental and neurodegenerative disorders including familial dysautonomia, intellectual disability, amyotrophic lateral sclerosis, and autism spectrum disorder. Although numerous cellular processes are perturbed in the context of Elongator loss, converging evidence from multiple studies has resolved Elongator's primary function in the cell to the modification of tRNA wobble uridines and the translational regulation of codon-biased genes. Here we characterize H2a.z, encoding the variant H2a histone H2A.Z, as an indirect Elongator target. We further show that canonical Notch signaling, a pathway directed by H2A.Z, is perturbed as a consequence of Elp1 loss. Finally, we demonstrate that hyperacetylation of H2A.Z and other histones via exposure to the histone deacetylase inhibitor Trichostatin A during neurogenesis corrects the expression of Notch3 and rescues the development of sensory neurons in embryos lacking the Elp1 Elongator subunit. Summary: The maldevelopment of sensory neurons in Elongator knockout embryos is associated with elevated H2A.Z and perturbed Notch signaling that can be rescued by Trichostatin A.
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Affiliation(s)
- BreAnna Cameron
- Department of Biological and Physical Sciences, Montana State University Billings, Billings, MT 59101, USA
| | - Elin Lehrmann
- Computational Biology & Genomics Core (CBGC), Laboratory of Genetics and Genomics (LGG), Department of Health and Human Services (DHHS), National Institute on Aging, Intramural Research Program (NIA IRP), National Institutes of Health (NIH), Biomedical Research Center, Baltimore, MD 21224, USA
| | - Tien Chih
- Department of Biological and Physical Sciences, Montana State University Billings, Billings, MT 59101, USA
| | - Joseph Walters
- Department of Biological and Physical Sciences, Montana State University Billings, Billings, MT 59101, USA
| | - Richard Buksch
- Department of Biological and Physical Sciences, Montana State University Billings, Billings, MT 59101, USA
| | - Sara Snyder
- Department of Biological and Physical Sciences, Montana State University Billings, Billings, MT 59101, USA
| | - Joy Goffena
- Department of Biological and Physical Sciences, Montana State University Billings, Billings, MT 59101, USA
| | - Frances Lefcort
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | - Kevin G Becker
- Gene Expression and Genomics Unit, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Lynn George
- Department of Biological and Physical Sciences, Montana State University Billings, Billings, MT 59101, USA
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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: 7] [Impact Index Per Article: 1.8] [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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19
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Kojic M, Gawda T, Gaik M, Begg A, Salerno-Kochan A, Kurniawan ND, Jones A, Drożdżyk K, Kościelniak A, Chramiec-Głąbik A, Hediyeh-Zadeh S, Kasherman M, Shim WJ, Sinniah E, Genovesi LA, Abrahamsen RK, Fenger CD, Madsen CG, Cohen JS, Fatemi A, Stark Z, Lunke S, Lee J, Hansen JK, Boxill MF, Keren B, Marey I, Saenz MS, Brown K, Alexander SA, Mureev S, Batzilla A, Davis MJ, Piper M, Bodén M, Burne THJ, Palpant NJ, Møller RS, Glatt S, Wainwright BJ. Elp2 mutations perturb the epitranscriptome and lead to a complex neurodevelopmental phenotype. Nat Commun 2021; 12:2678. [PMID: 33976153 PMCID: PMC8113450 DOI: 10.1038/s41467-021-22888-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 03/24/2021] [Indexed: 02/03/2023] Open
Abstract
Intellectual disability (ID) and autism spectrum disorder (ASD) are the most common neurodevelopmental disorders and are characterized by substantial impairment in intellectual and adaptive functioning, with their genetic and molecular basis remaining largely unknown. Here, we identify biallelic variants in the gene encoding one of the Elongator complex subunits, ELP2, in patients with ID and ASD. Modelling the variants in mice recapitulates the patient features, with brain imaging and tractography analysis revealing microcephaly, loss of white matter tract integrity and an aberrant functional connectome. We show that the Elp2 mutations negatively impact the activity of the complex and its function in translation via tRNA modification. Further, we elucidate that the mutations perturb protein homeostasis leading to impaired neurogenesis, myelin loss and neurodegeneration. Collectively, our data demonstrate an unexpected role for tRNA modification in the pathogenesis of monogenic ID and ASD and define Elp2 as a key regulator of brain development.
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Affiliation(s)
- Marija Kojic
- The University of Queensland Diamantina Institute, Translational Research Institute, The University of Queensland, Brisbane, QLD, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Tomasz Gawda
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Monika Gaik
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Alexander Begg
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Anna Salerno-Kochan
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
- Postgraduate School of Molecular Medicine, Warsaw, Poland
| | - Nyoman D Kurniawan
- Centre for Advanced Imaging, The University of Queensland, Brisbane, QLD, Australia
| | - Alun Jones
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Katarzyna Drożdżyk
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Anna Kościelniak
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | | | - Soroor Hediyeh-Zadeh
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC, Australia
| | - Maria Kasherman
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Woo Jun Shim
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Enakshi Sinniah
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Laura A Genovesi
- The University of Queensland Diamantina Institute, Translational Research Institute, The University of Queensland, Brisbane, QLD, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Rannvá K Abrahamsen
- Department of Epilepsy Genetics and Personalized Medicine, Danish Epilepsy Centre, Dianalund, Denmark
| | - Christina D Fenger
- Department of Epilepsy Genetics and Personalized Medicine, Danish Epilepsy Centre, Dianalund, Denmark
| | - Camilla G Madsen
- Centre for Functional and Diagnostic Imaging and Research, Hvidovre Hospital, Hvidovre, Denmark
| | - Julie S Cohen
- Department of Neurology and Developmental Medicine, Division of Neurogenetics, Kennedy Krieger Institute, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ali Fatemi
- Department of Neurology and Developmental Medicine, Division of Neurogenetics, Kennedy Krieger Institute, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Zornitza Stark
- Department of Paediatrics, The University of Melbourne, Melbourne, VIC, Australia
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia
- Australian Genomics Health Alliance, Parkville, VIC, Australia
| | - Sebastian Lunke
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia
- Australian Genomics Health Alliance, Parkville, VIC, Australia
- The University of Melbourne, Melbourne, VIC, Australia
| | - Joy Lee
- Department of Paediatrics, The University of Melbourne, Melbourne, VIC, Australia
- Department of Metabolic Medicine, Royal Children's Hospital, Parkville, VIC, Australia
| | - Jonas K Hansen
- Department of Paediatrics, Regional Hospital Viborg, Viborg, Denmark
| | - Martin F Boxill
- Department of Paediatrics, Regional Hospital Viborg, Viborg, Denmark
| | - Boris Keren
- Department of Genetics, Pitié-Salpêtrière Hospital, AP-HP, Paris, France
| | - Isabelle Marey
- Department of Genetics, Pitié-Salpêtrière Hospital, AP-HP, Paris, France
| | - Margarita S Saenz
- The University of Colorado Anschutz, Children's Hospital Colorado, Aurora, CO, USA
| | - Kathleen Brown
- The University of Colorado Anschutz, Children's Hospital Colorado, Aurora, CO, USA
| | - Suzanne A Alexander
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
- Queensland Centre for Mental Health Research, The Park Centre for Mental Health, Brisbane, QLD, Australia
| | - Sergey Mureev
- CSIRO-QUT Synthetic Biology Alliance, Centre for Tropical Crops and Bio-commodities, Queensland University of Technology, Brisbane, QLD, Australia
| | - Alina Batzilla
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
- The Ruprecht Karl University of Heidelberg, Heidelberg, Germany
| | - Melissa J Davis
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC, Australia
- Department of Clinical Pathology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC, Australia
| | - Michael Piper
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Mikael Bodén
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Thomas H J Burne
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
- Queensland Centre for Mental Health Research, The Park Centre for Mental Health, Brisbane, QLD, Australia
| | - Nathan J Palpant
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Rikke S Møller
- Department of Epilepsy Genetics and Personalized Medicine, Danish Epilepsy Centre, Dianalund, Denmark
- Department for Regional Health Research, The University of Southern Denmark, Odense, Denmark
| | - Sebastian Glatt
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.
| | - Brandon J Wainwright
- The University of Queensland Diamantina Institute, Translational Research Institute, The University of Queensland, Brisbane, QLD, Australia.
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia.
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20
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Abbassi NEH, Biela A, Glatt S, Lin TY. How Elongator Acetylates tRNA Bases. Int J Mol Sci 2020; 21:E8209. [PMID: 33152999 PMCID: PMC7663514 DOI: 10.3390/ijms21218209] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 10/29/2020] [Accepted: 10/30/2020] [Indexed: 12/13/2022] Open
Abstract
Elp3, the catalytic subunit of the eukaryotic Elongator complex, is a lysine acetyltransferase that acetylates the C5 position of wobble-base uridines (U34) in transfer RNAs (tRNAs). This Elongator-dependent RNA acetylation of anticodon bases affects the ribosomal translation elongation rates and directly links acetyl-CoA metabolism to both protein synthesis rates and the proteome integrity. Of note, several human diseases, including various cancers and neurodegenerative disorders, correlate with the dysregulation of Elongator's tRNA modification activity. In this review, we focus on recent findings regarding the structure of Elp3 and the role of acetyl-CoA during its unique modification reaction.
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Affiliation(s)
- Nour-el-Hana Abbassi
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland; (N.-e.-H.A.); (A.B.)
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, 02-091 Warsaw, Poland
| | - Anna Biela
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland; (N.-e.-H.A.); (A.B.)
| | - Sebastian Glatt
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland; (N.-e.-H.A.); (A.B.)
| | - Ting-Yu Lin
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland; (N.-e.-H.A.); (A.B.)
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21
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Schäck MA, Jablonski KP, Gräf S, Klassen R, Schaffrath R, Kellner S, Hammann C. Eukaryotic life without tQCUG: the role of Elongator-dependent tRNA modifications in Dictyostelium discoideum. Nucleic Acids Res 2020; 48:7899-7913. [PMID: 32609816 PMCID: PMC7430636 DOI: 10.1093/nar/gkaa560] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 06/16/2020] [Accepted: 06/18/2020] [Indexed: 12/23/2022] Open
Abstract
In the Elongator-dependent modification pathway, chemical modifications are introduced at the wobble uridines at position 34 in transfer RNAs (tRNAs), which serve to optimize codon translation rates. Here, we show that this three-step modification pathway exists in Dictyostelium discoideum, model of the evolutionary superfamily Amoebozoa. Not only are previously established modifications observable by mass spectrometry in strains with the most conserved genes of each step deleted, but also additional modifications are detected, indicating a certain plasticity of the pathway in the amoeba. Unlike described for yeast, D. discoideum allows for an unconditional deletion of the single tQCUG gene, as long as the Elongator-dependent modification pathway is intact. In gene deletion strains of the modification pathway, protein amounts are significantly reduced as shown by flow cytometry and Western blotting, using strains expressing different glutamine leader constructs fused to GFP. Most dramatic are these effects, when the tQCUG gene is deleted, or Elp3, the catalytic component of the Elongator complex is missing. In addition, Elp3 is the most strongly conserved protein of the modification pathway, as our phylogenetic analysis reveals. The implications of this observation are discussed with respect to the evolutionary age of the components acting in the Elongator-dependent modification pathway.
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Affiliation(s)
- Manfred A Schäck
- Ribogenetics Biochemistry Lab, Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, DE 28759 Bremen, Germany
| | - Kim Philipp Jablonski
- Ribogenetics Biochemistry Lab, Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, DE 28759 Bremen, Germany
| | - Stefan Gräf
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Roland Klassen
- Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, Heinrich-Plett-Str. 40, 34132 Kassel, Germany
| | - Raffael Schaffrath
- Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, Heinrich-Plett-Str. 40, 34132 Kassel, Germany
| | - Stefanie Kellner
- Department of Chemistry and Pharmacy, Ludwig-Maximilians University Munich, Butenandtstr. 5-13, 81377 Munich, Germany
| | - Christian Hammann
- Ribogenetics Biochemistry Lab, Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, DE 28759 Bremen, Germany
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22
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Plant Elongator-Protein Complex of Diverse Activities Regulates Growth, Development, and Immune Responses. Int J Mol Sci 2020; 21:ijms21186912. [PMID: 32971769 PMCID: PMC7555253 DOI: 10.3390/ijms21186912] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 09/16/2020] [Accepted: 09/18/2020] [Indexed: 12/23/2022] Open
Abstract
Contrary to the conserved Elongator composition in yeast, animals, and plants, molecular functions and catalytic activities of the complex remain controversial. Elongator was identified as a component of elongating RNA polymerase II holoenzyme in yeast, animals, and plants. Furthermore, it was suggested that Elonagtor facilitates elongation of transcription via histone acetyl transferase activity. Accordingly, phenotypes of Arabidopsis elo mutants, which show development, growth, or immune response defects, correlate with transcriptional downregulation and the decreased histone acetylation in the coding regions of crucial genes. Plant Elongator was also implicated in other processes: transcription and processing of miRNA, regulation of DNA replication by histone acetylation, and acetylation of alpha-tubulin. Moreover, tRNA modification, discovered first in yeast and confirmed in plants, was claimed as the main activity of Elongator, leading to specificity in translation that might also result indirectly in a deficiency in transcription. Heterologous overexpression of individual Arabidopsis Elongator subunits and their respective phenotypes suggest that single Elongator subunits might also have another function next to being a part of the complex. In this review, we shall present the experimental evidence of all molecular mechanisms and catalytic activities performed by Elongator in nucleus and cytoplasm of plant cells, which might explain how Elongator regulates growth, development, and immune responses.
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23
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Karambelkar S, Udupa S, Gowthami VN, Ramachandra SG, Swapna G, Nagaraja V. Emergence of a novel immune-evasion strategy from an ancestral protein fold in bacteriophage Mu. Nucleic Acids Res 2020; 48:5294-5305. [PMID: 32369169 PMCID: PMC7261163 DOI: 10.1093/nar/gkaa319] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 04/17/2020] [Accepted: 04/21/2020] [Indexed: 01/21/2023] Open
Abstract
The broad host range bacteriophage Mu employs a novel 'methylcarbamoyl' modification to protect its DNA from diverse restriction systems of its hosts. The DNA modification is catalyzed by a phage-encoded protein Mom, whose mechanism of action is a mystery. Here, we characterized the co-factor and metal-binding properties of Mom and provide a molecular mechanism to explain 'methylcarbamoyl'ation of DNA by Mom. Computational analyses revealed a conserved GNAT (GCN5-related N-acetyltransferase) fold in Mom. We demonstrate that Mom binds to acetyl CoA and identify the active site. We discovered that Mom is an iron-binding protein, with loss of Fe2+/3+-binding associated with loss of DNA modification activity. The importance of Fe2+/3+ is highlighted by the colocalization of Fe2+/3+ with acetyl CoA within the Mom active site. Puzzlingly, acid-base mechanisms employed by >309,000 GNAT members identified so far, fail to support methylcarbamoylation of adenine using acetyl CoA. In contrast, free-radical chemistry catalyzed by transition metals like Fe2+/3+ can explain the seemingly challenging reaction, accomplished by collaboration between acetyl CoA and Fe2+/3+. Thus, binding to Fe2+/3+, a small but unprecedented step in the evolution of Mom, allows a giant chemical leap from ordinary acetylation to a novel methylcarbamoylation function, while conserving the overall protein architecture.
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Affiliation(s)
- Shweta Karambelkar
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India.,Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India
| | - Shubha Udupa
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Vykuntham Naga Gowthami
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | | | - Ganduri Swapna
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Valakunja Nagaraja
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India.,Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India
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24
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Krutyhołowa R, Reinhardt-Tews A, Chramiec-Głąbik A, Breunig KD, Glatt S. Fungal Kti12 proteins display unusual linker regions and unique ATPase p-loops. Curr Genet 2020; 66:823-833. [PMID: 32236652 PMCID: PMC7363723 DOI: 10.1007/s00294-020-01070-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 03/13/2020] [Accepted: 03/19/2020] [Indexed: 12/24/2022]
Abstract
Kti12 (Kluyveromyces lactis toxin insensitive 12) is an evolutionary highly conserved ATPase, crucial for the tRNA-modification activity of the eukaryotic Elongator complex. The protein consists of an N-terminal ATPase and a C-terminal tRNA-binding domain, which are connected by a flexible linker. The precise role of the linker region and its involvement in the communication between the two domains and their activities remain elusive. Here, we analyzed all available Kti12 protein sequences and report the discovery of a subset of Kti12 proteins with abnormally long linker regions. These Kti12 proteins are characterized by a co-occurring lysine to leucine substitution in their Walker A motif, previously thought to be invariable. We show that the K14L substitution lowers the affinity to ATP, but does not affect the catalytic activity of Kti12 at high ATP concentrations. We compare the activity of mutated variants of Kti12 in vitro with complementation assays in vivo in yeast. Ultimately, we compared Kti12 to other known p-loop ATPase family members known to carry a similar deviant Walker A motif. Our data establish Kti12 of Eurotiomycetes as an example of eukaryotic ATPase harboring a significantly deviating but still functional Walker A motif.
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Affiliation(s)
- Rościsław Krutyhołowa
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow, Poland.,Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | | | | | - Karin D Breunig
- Institut für Biologie, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany.
| | - Sebastian Glatt
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow, Poland.
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25
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Krutyhołowa R, Hammermeister A, Zabel R, Abdel-Fattah W, Reinhardt-Tews A, Helm M, Stark MJR, Breunig KD, Schaffrath R, Glatt S. Kti12, a PSTK-like tRNA dependent ATPase essential for tRNA modification by Elongator. Nucleic Acids Res 2019; 47:4814-4830. [PMID: 30916349 PMCID: PMC6511879 DOI: 10.1093/nar/gkz190] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 02/14/2019] [Accepted: 03/11/2019] [Indexed: 01/08/2023] Open
Abstract
Posttranscriptional RNA modifications occur in all domains of life. Modifications of anticodon bases are of particular importance for ribosomal decoding and proteome homeostasis. The Elongator complex modifies uridines in the wobble position and is highly conserved in eukaryotes. Despite recent insights into Elongator's architecture, the structure and function of its regulatory factor Kti12 have remained elusive. Here, we present the crystal structure of Kti12′s nucleotide hydrolase domain trapped in a transition state of ATP hydrolysis. The structure reveals striking similarities to an O-phosphoseryl-tRNA kinase involved in the selenocysteine pathway. Both proteins employ similar mechanisms of tRNA binding and show tRNASec-dependent ATPase activity. In addition, we demonstrate that Kti12 binds directly to Elongator and that ATP hydrolysis is crucial for Elongator to maintain proper tRNA anticodon modification levels in vivo. In summary, our data reveal a hitherto uncharacterized link between two translational control pathways that regulate selenocysteine incorporation and affect ribosomal tRNA selection via specific tRNA modifications.
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Affiliation(s)
- Rościsław Krutyhołowa
- Max Planck Research Group at the Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.,Department of Cell Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | | | - Rene Zabel
- Institut für Biologie, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
| | - Wael Abdel-Fattah
- Institut für Biologie, FG Mikrobiologie, Universität Kassel, Kassel, Germany
| | | | - Mark Helm
- Institut für Pharmazie und Biochemie, Universität Mainz, Mainz, Germany
| | - Michael J R Stark
- Centre for Gene Regulation & Expression, University of Dundee, Dundee, UK
| | - Karin D Breunig
- Institut für Biologie, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
| | - Raffael Schaffrath
- Institut für Biologie, FG 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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26
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tRNA wobble-uridine modifications as amino acid sensors and regulators of cellular metabolic state. Curr Genet 2019; 66:475-480. [PMID: 31758251 DOI: 10.1007/s00294-019-01045-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 11/10/2019] [Accepted: 11/13/2019] [Indexed: 12/24/2022]
Abstract
Cells must appropriately sense available nutrients and accordingly regulate their metabolic outputs, to survive. This mini-review considers the idea that conserved chemical modifications of wobble (U34) position tRNA uridines enable cells to sense nutrients and regulate their metabolic state. tRNA wobble uridines are chemically modified at the 2- and 5- positions, with a thiol (s2), and (commonly) a methoxycarbonylmethyl (mcm5) modification, respectively. These modifications reflect sulfur amino acid (methionine and cysteine) availability. The loss of these modifications has minor translation defects. However, they result in striking phenotypes consistent with an altered metabolic state. Using yeast, we recently discovered that the s2 modification regulates overall carbon and nitrogen metabolism, dependent on methionine availability. The loss of this modification results in rewired carbon (glucose) metabolism. Cells have reduced carbon flux towards the pentose phosphate pathway and instead increased flux towards storage carbohydrates-primarily trehalose, along with reduced nucleotide synthesis, and perceived amino acid starvation signatures. Remarkably, this metabolic rewiring in the s2U mutants is caused by mechanisms leading to intracellular phosphate limitation. Thus this U34 tRNA modification responds to methionine availability and integratively regulates carbon and nitrogen homeostasis, wiring cells to a 'growth' state. We interpret the importance of U34 modifications in the context of metabolic sensing and anabolism, emphasizing their intimate coupling to methionine metabolism.
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27
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Biosynthetic capacity, metabolic variety and unusual biology in the CPR and DPANN radiations. Nat Rev Microbiol 2019; 16:629-645. [PMID: 30181663 DOI: 10.1038/s41579-018-0076-2] [Citation(s) in RCA: 251] [Impact Index Per Article: 41.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Candidate phyla radiation (CPR) bacteria and DPANN (an acronym of the names of the first included phyla) archaea are massive radiations of organisms that are widely distributed across Earth's environments, yet we know little about them. Initial indications are that they are consistently distinct from essentially all other bacteria and archaea owing to their small cell and genome sizes, limited metabolic capacities and often episymbiotic associations with other bacteria and archaea. In this Analysis, we investigate their biology and variations in metabolic capacities by analysis of approximately 1,000 genomes reconstructed from several metagenomics-based studies. We find that they are not monolithic in terms of metabolism but rather harbour a diversity of capacities consistent with a range of lifestyles and degrees of dependence on other organisms. Notably, however, certain CPR and DPANN groups seem to have exceedingly minimal biosynthetic capacities, whereas others could potentially be free living. Understanding of these microorganisms is important from the perspective of evolutionary studies and because their interactions with other organisms are likely to shape natural microbiome function.
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28
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Sheikh BN, Akhtar A. The many lives of KATs - detectors, integrators and modulators of the cellular environment. Nat Rev Genet 2019; 20:7-23. [PMID: 30390049 DOI: 10.1038/s41576-018-0072-4] [Citation(s) in RCA: 112] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Research over the past three decades has firmly established lysine acetyltransferases (KATs) as central players in regulating transcription. Recent advances in genomic sequencing, metabolomics, animal models and mass spectrometry technologies have uncovered unexpected new roles for KATs at the nexus between the environment and transcriptional regulation. Thousands of reversible acetylation sites have been mapped in the proteome that respond dynamically to the cellular milieu and maintain major processes such as metabolism, autophagy and stress response. Concurrently, researchers are continuously uncovering how deregulation of KAT activity drives disease, including cancer and developmental syndromes characterized by severe intellectual disability. These novel findings are reshaping our view of KATs away from mere modulators of chromatin to detectors of the cellular environment and integrators of diverse signalling pathways with the ability to modify cellular phenotype.
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Affiliation(s)
- Bilal N Sheikh
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
| | - Asifa Akhtar
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany.
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29
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Dauden MI, Jaciuk M, Weis F, Lin TY, Kleindienst C, Abbassi NEH, Khatter H, Krutyhołowa R, Breunig KD, Kosinski J, Müller CW, Glatt S. Molecular basis of tRNA recognition by the Elongator complex. SCIENCE ADVANCES 2019; 5:eaaw2326. [PMID: 31309145 PMCID: PMC6620098 DOI: 10.1126/sciadv.aaw2326] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 06/03/2019] [Indexed: 05/17/2023]
Abstract
The highly conserved Elongator complex modifies transfer RNAs (tRNAs) in their wobble base position, thereby regulating protein synthesis and ensuring proteome stability. The precise mechanisms of tRNA recognition and its modification reaction remain elusive. Here, we show cryo-electron microscopy structures of the catalytic subcomplex of Elongator and its tRNA-bound state at resolutions of 3.3 and 4.4 Å. The structures resolve details of the catalytic site, including the substrate tRNA, the iron-sulfur cluster, and a SAM molecule, which are all validated by mutational analyses in vitro and in vivo. tRNA binding induces conformational rearrangements, which precisely position the targeted anticodon base in the active site. Our results provide the molecular basis for substrate recognition of Elongator, essential to understand its cellular function and role in neurodegenerative diseases and cancer.
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Affiliation(s)
- Maria I. Dauden
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Marcin Jaciuk
- Max Planck Research Group at the Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
| | - Felix Weis
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Ting-Yu Lin
- Max Planck Research Group at the Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
| | - Carolin Kleindienst
- Institute of Biology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Nour El Hana Abbassi
- Max Planck Research Group at the Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
- Postgraduate School of Molecular Medicine, Warsaw, Poland
| | - Heena Khatter
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Rościsław Krutyhołowa
- Max Planck Research Group at the Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
- Department of Cell Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Karin D. Breunig
- Institute of Biology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Jan Kosinski
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
- Centre for Structural Systems Biology (CSSB), DESY and European Molecular Biology Laboratory Hamburg, Hamburg, Germany
| | - Christoph W. Müller
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Sebastian Glatt
- Max Planck Research Group at the Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
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30
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Charging the code - tRNA modification complexes. Curr Opin Struct Biol 2019; 55:138-146. [PMID: 31102979 DOI: 10.1016/j.sbi.2019.03.014] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 03/08/2019] [Indexed: 02/06/2023]
Abstract
All types of cellular RNAs are post-transcriptionally modified, constituting the so called 'epitranscriptome'. In particular, tRNAs and their anticodon stem loops represent major modification hotspots. The attachment of small chemical groups at the heart of the ribosomal decoding machinery can directly affect translational rates, reading frame maintenance, co-translational folding dynamics and overall proteome stability. The variety of tRNA modification patterns is driven by the activity of specialized tRNA modifiers and large modification complexes. Notably, the absence or dysfunction of these cellular machines is correlated with several human pathophysiologies. In this review, we aim to highlight the most recent scientific progress and summarize currently available structural information of the most prominent eukaryotic tRNA modifiers.
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31
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The Elongator subunit Elp3 is a non-canonical tRNA acetyltransferase. Nat Commun 2019; 10:625. [PMID: 30733442 PMCID: PMC6367351 DOI: 10.1038/s41467-019-08579-2] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 01/18/2019] [Indexed: 11/19/2022] Open
Abstract
The Elongator complex catalyzes posttranscriptional tRNA modifications by attaching carboxy-methyl (cm5) moieties to uridine bases located in the wobble position. The catalytic subunit Elp3 is highly conserved and harbors two individual subdomains, a radical S-adenosyl methionine (rSAM) and a lysine acetyltransferase (KAT) domain. The details of its modification reaction cycle and particularly the substrate specificity of its KAT domain remain elusive. Here, we present the co-crystal structure of bacterial Elp3 (DmcElp3) bound to an acetyl-CoA analog and compare it to the structure of a monomeric archaeal Elp3 from Methanocaldococcus infernus (MinElp3). Furthermore, we identify crucial active site residues, confirm the importance of the extended N-terminus for substrate recognition and uncover the specific induction of acetyl-CoA hydrolysis by different tRNA species. In summary, our results establish the clinically relevant Elongator subunit as a non-canonical acetyltransferase and genuine tRNA modification enzyme. Elp3 is the catalytic subunit of the eukaryotic Elongator complex that catalyzes posttranscriptional tRNA modifications. Here the authors present the crystal structures of an acetyl-CoA analog bound bacterial Elp3 and a monomeric archaeal Elp3 and show that Elp3 functions as a tRNA modification enzyme in all domains of life.
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32
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Roles of Elongator Dependent tRNA Modification Pathways in Neurodegeneration and Cancer. Genes (Basel) 2018; 10:genes10010019. [PMID: 30597914 PMCID: PMC6356722 DOI: 10.3390/genes10010019] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 12/18/2018] [Accepted: 12/20/2018] [Indexed: 02/07/2023] Open
Abstract
Transfer RNA (tRNA) is subject to a multitude of posttranscriptional modifications which can profoundly impact its functionality as the essential adaptor molecule in messenger RNA (mRNA) translation. Therefore, dynamic regulation of tRNA modification in response to environmental changes can tune the efficiency of gene expression in concert with the emerging epitranscriptomic mRNA regulators. Several of the tRNA modifications are required to prevent human diseases and are particularly important for proper development and generation of neurons. In addition to the positive role of different tRNA modifications in prevention of neurodegeneration, certain cancer types upregulate tRNA modification genes to sustain cancer cell gene expression and metastasis. Multiple associations of defects in genes encoding subunits of the tRNA modifier complex Elongator with human disease highlight the importance of proper anticodon wobble uridine modifications (xm⁵U34) for health. Elongator functionality requires communication with accessory proteins and dynamic phosphorylation, providing regulatory control of its function. Here, we summarized recent insights into molecular functions of the complex and the role of Elongator dependent tRNA modification in human disease.
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33
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Vasilieva EN, Laptev IG, Sergiev PV, Dontsova OA. The Common Partner of Several Methyltransferases Modifying the Components of The Eukaryotic Translation Apparatus. Mol Biol 2018. [DOI: 10.1134/s0026893318060171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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34
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van Tran N, Muller L, Ross RL, Lestini R, Létoquart J, Ulryck N, Limbach PA, de Crécy-Lagard V, Cianférani S, Graille M. Evolutionary insights into Trm112-methyltransferase holoenzymes involved in translation between archaea and eukaryotes. Nucleic Acids Res 2018; 46:8483-8499. [PMID: 30010922 PMCID: PMC6144793 DOI: 10.1093/nar/gky638] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 06/25/2018] [Accepted: 07/04/2018] [Indexed: 12/22/2022] Open
Abstract
Protein synthesis is a complex and highly coordinated process requiring many different protein factors as well as various types of nucleic acids. All translation machinery components require multiple maturation events to be functional. These include post-transcriptional and post-translational modification steps and methylations are the most frequent among these events. In eukaryotes, Trm112, a small protein (COG2835) conserved in all three domains of life, interacts and activates four methyltransferases (Bud23, Trm9, Trm11 and Mtq2) that target different components of the translation machinery (rRNA, tRNAs, release factors). To clarify the function of Trm112 in archaea, we have characterized functionally and structurally its interaction network using Haloferax volcanii as model system. This led us to unravel that methyltransferases are also privileged Trm112 partners in archaea and that this Trm112 network is much more complex than anticipated from eukaryotic studies. Interestingly, among the identified enzymes, some are functionally orthologous to eukaryotic Trm112 partners, emphasizing again the similarity between eukaryotic and archaeal translation machineries. Other partners display some similarities with bacterial methyltransferases, suggesting that Trm112 is a general partner for methyltransferases in all living organisms.
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Affiliation(s)
- Nhan van Tran
- Laboratoire de Biochimie, Ecole polytechnique, CNRS, Université Paris-Saclay, F-91128 Palaiseau cedex, France
| | - Leslie Muller
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), Université de Strasbourg, CNRS, IPHC UMR 7178, F-67000 Strasbourg, France
| | - Robert L Ross
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, P.O. Box 210172, Cincinnati, OH 45221-0172, USA
| | - Roxane Lestini
- Laboratoire d’Optique et Biosciences, Ecole Polytechnique, CNRS UMR7645-INSERM U1182 91128, Palaiseau Cedex, France
| | - Juliette Létoquart
- Laboratoire de Biochimie, Ecole polytechnique, CNRS, Université Paris-Saclay, F-91128 Palaiseau cedex, France
| | - Nathalie Ulryck
- Laboratoire de Biochimie, Ecole polytechnique, CNRS, Université Paris-Saclay, F-91128 Palaiseau cedex, France
| | - Patrick A Limbach
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, P.O. Box 210172, Cincinnati, OH 45221-0172, USA
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), Université de Strasbourg, CNRS, IPHC UMR 7178, F-67000 Strasbourg, France
| | - Marc Graille
- Laboratoire de Biochimie, Ecole polytechnique, CNRS, Université Paris-Saclay, F-91128 Palaiseau cedex, France
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35
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Elongator mutation in mice induces neurodegeneration and ataxia-like behavior. Nat Commun 2018; 9:3195. [PMID: 30097576 PMCID: PMC6086839 DOI: 10.1038/s41467-018-05765-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 07/05/2018] [Indexed: 12/14/2022] Open
Abstract
Cerebellar ataxias are severe neurodegenerative disorders with an early onset and progressive and inexorable course of the disease. Here, we report a single point mutation in the gene encoding Elongator complex subunit 6 causing Purkinje neuron degeneration and an ataxia-like phenotype in the mutant wobbly mouse. This mutation destabilizes the complex and compromises its function in translation regulation, leading to protein misfolding, proteotoxic stress, and eventual neuronal death. In addition, we show that substantial microgliosis is triggered by the NLRP3 inflammasome pathway in the cerebellum and that blocking NLRP3 function in vivo significantly delays neuronal degeneration and the onset of ataxia in mutant animals. Our data provide a mechanistic insight into the pathophysiology of a cerebellar ataxia caused by an Elongator mutation, substantiating the increasing body of evidence that alterations of this complex are broadly implicated in the onset of a number of diverse neurological disorders. Elp6 is a component of the Elongator complex that regulates tRNAs and translation. Here the authors identify a mutation in the Elp6 gene that contributes to the cerebellar ataxia-like phenotype in a mutant mouse.
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36
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Imashimizu M, Takahashi M, Amano R, Nakamura Y. Single-round isolation of diverse RNA aptamers from a random sequence pool. Biol Methods Protoc 2018; 3:bpy004. [PMID: 32161798 PMCID: PMC6994090 DOI: 10.1093/biomethods/bpy004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 04/02/2018] [Accepted: 04/10/2018] [Indexed: 01/09/2023] Open
Abstract
Aptamers are oligonucleotide ligands with specific binding affinity to target molecules. Generally, RNA aptamers are selected from an RNA pool with random sequences, using the technique termed SELEX, in which the target-binding RNA molecules are repeatedly isolated and exponentially amplified. Despite several advantages, SELEX often produces uncertain results during the iterative amplifications of the rare target-binding RNA molecules. Here, we develop a non-repeated, primer-less and target immobilization-free isolation method for generating RNA aptamers, which is robust to experimental noise. Uniquely, this method focuses on finding and removal of non-aptamer sequences from the RNA pool by RNase digestion leaving target-bound aptamer molecules, and thus is independent of aptamer types. The undigested RNA sequences remaining are so few in number that they must be mixed with a large excess of a known sequence for further manipulations and this sequence is then removed by restriction digestion followed by high-throughput sequencing analysis to identify aptamers. Using this method, we generated multiple RNA aptamers targeting α-thrombin and TGFβ1 proteins, independently. This method potentially generates thousands of sequences as aptamer candidates, which may enable us to predict a common average sequence or structural property of these aptamers that is different from input RNA.
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Affiliation(s)
- Masahiko Imashimizu
- Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo, 108-8639, Japan
| | - Masaki Takahashi
- Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo, 108-8639, Japan
| | - Ryo Amano
- Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo, 108-8639, Japan
| | - Yoshikazu Nakamura
- Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo, 108-8639, Japan.,RIBOMIC Inc., Minato-ku, Tokyo, 108-0071, Japan
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37
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Dalwadi U, Yip CK. Structural insights into the function of Elongator. Cell Mol Life Sci 2018; 75:1613-1622. [PMID: 29332244 PMCID: PMC11105301 DOI: 10.1007/s00018-018-2747-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 12/09/2017] [Accepted: 01/08/2018] [Indexed: 12/13/2022]
Abstract
Conserved from yeast to humans, Elongator is a protein complex implicated in multiple processes including transcription regulation, α-tubulin acetylation, and tRNA modification, and its defects have been shown to cause human diseases such as familial dysautonomia. Elongator consists of two copies of six core subunits (Elp1, Elp2, Elp3, Elp4, Elp5, and Elp6) that are organized into two subcomplexes: Elp1/2/3 and Elp4/5/6 and form a stable assembly of ~ 850 kDa in size. Although the catalytic subunit of Elongator is Elp3, which contains a radical S-adenosyl-L-methionine (SAM) domain and a putative histone acetyltransferase domain, the Elp4/5/6 subcomplex also possesses ATP-modulated tRNA binding activity. How at the molecular level, Elongator performs its multiple functions and how the different subunits regulate Elongator's activities remains poorly understood. Here, we provide an overview of the proposed functions of Elongator and describe how recent structural studies provide new insights into the mechanism of action of this multifunctional complex.
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Affiliation(s)
- Udit Dalwadi
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Calvin K Yip
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, BC, V6T 1Z3, Canada.
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38
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Yu D, Tan Y, Chakraborty M, Tomchik S, Davis RL. Elongator complex is required for long-term olfactory memory formation in Drosophila. Learn Mem 2018; 25:183-196. [PMID: 29545390 PMCID: PMC5855525 DOI: 10.1101/lm.046557.117] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 01/12/2018] [Indexed: 12/13/2022]
Abstract
The evolutionarily conserved Elongator Complex associates with RNA polymerase II for transcriptional elongation. Elp3 is the catalytic subunit, contains histone acetyltransferase activity, and is associated with neurodegeneration in humans. Elp1 is a scaffolding subunit and when mutated causes familial dysautonomia. Here, we show that elp3 and elp1 are required for aversive long-term olfactory memory in Drosophila RNAi knockdown of elp3 in adult mushroom bodies impairs long-term memory (LTM) without affecting earlier forms of memory. RNAi knockdown with coexpression of elp3 cDNA reverses the impairment. Similarly, RNAi knockdown of elp1 impairs LTM and coexpression of elp1 cDNA reverses this phenotype. The LTM deficit in elp3 and elp1 knockdown flies is accompanied by the abolishment of a LTM trace, which is registered as increased calcium influx in response to the CS+ odor in the α-branch of mushroom body neurons. Coexpression of elp1 or elp3 cDNA rescues the memory trace in parallel with LTM. These data show that the Elongator complex is required in adult mushroom body neurons for long-term behavioral memory and the associated long-term memory trace.
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Affiliation(s)
- Dinghui Yu
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas 77030, USA
| | - Ying Tan
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Molee Chakraborty
- Department of Neuroscience, Scripps Research Institute Florida, Jupiter, Florida 33458, USA
| | - Seth Tomchik
- Department of Neuroscience, Scripps Research Institute Florida, Jupiter, Florida 33458, USA
| | - Ronald L Davis
- Department of Neuroscience, Scripps Research Institute Florida, Jupiter, Florida 33458, USA
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Fernandes N, Eshleman N, Buchan JR. Stress Granules and ALS: A Case of Causation or Correlation? ADVANCES IN NEUROBIOLOGY 2018; 20:173-212. [PMID: 29916020 DOI: 10.1007/978-3-319-89689-2_7] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Amyotrophic Lateral Sclerosis (ALS) is a fatal neurodegenerative disease characterized by cytoplasmic protein aggregates within motor neurons. These aggregates are linked to ALS pathogenesis. Recent evidence has suggested that stress granules may aid the formation of ALS protein aggregates. Here, we summarize current understanding of stress granules, focusing on assembly and clearance. We also assess the evidence linking alterations in stress granule formation and dynamics to ALS protein aggregates and disease pathology.
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Affiliation(s)
- Nikita Fernandes
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, USA
| | - Nichole Eshleman
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, USA
| | - J Ross Buchan
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, USA.
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40
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He M, Han Z, Liu L, Zheng YG. Untersuchung der epigenetischen Funktionen von Lysin‐Acetyltransferasen mit Methoden der chemischen Biologie. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201704745] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Maomao He
- Department of Pharmaceutical and Biochemical Sciences and Department of Statistics University of Georgia Athens Georgia 30602 USA
| | - Zhen Han
- Department of Pharmaceutical and Biochemical Sciences and Department of Statistics University of Georgia Athens Georgia 30602 USA
| | - Liang Liu
- Department of Pharmaceutical and Biochemical Sciences and Department of Statistics University of Georgia Athens Georgia 30602 USA
| | - Y. George Zheng
- Department of Pharmaceutical and Biochemical Sciences and Department of Statistics University of Georgia Athens Georgia 30602 USA
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41
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He M, Han Z, Liu L, Zheng YG. Chemical Biology Approaches for Investigating the Functions of Lysine Acetyltransferases. Angew Chem Int Ed Engl 2017; 57:1162-1184. [PMID: 28786225 DOI: 10.1002/anie.201704745] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Indexed: 12/20/2022]
Abstract
The side-chain acetylation of lysine residues in histones and non-histone proteins catalyzed by lysine acetyltransferases (KATs) represents a widespread posttranslational modification (PTM) in the eukaryotic cells. Lysine acetylation plays regulatory roles in major cellular pathways inside and outside the nucleus. In particular, KAT-mediated histone acetylation has an effect on all DNA-templated epigenetic processes. Aberrant expression and activation of KATs are commonly observed in human diseases, especially cancer. In recent years, the study of KAT functions in biology and disease has greatly benefited from chemical biology tools and strategies. In this Review, we present the past and current accomplishments in the design of chemical biology approaches for the interrogation of KAT activity and function. These methods and probes are classified according to their mechanisms of action and respective applications, with both strengths and limitations discussed.
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Affiliation(s)
- Maomao He
- Department of Pharmaceutical and Biochemical Sciences and Department of Statistics, University of Georgia, Athens, Georgia, 30602 (U, SA
| | - Zhen Han
- Department of Pharmaceutical and Biochemical Sciences and Department of Statistics, University of Georgia, Athens, Georgia, 30602 (U, SA
| | - Liang Liu
- Department of Pharmaceutical and Biochemical Sciences and Department of Statistics, University of Georgia, Athens, Georgia, 30602 (U, SA
| | - Y George Zheng
- Department of Pharmaceutical and Biochemical Sciences and Department of Statistics, University of Georgia, Athens, Georgia, 30602 (U, SA
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42
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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: 5.3] [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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43
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Johansson MJO, Xu F, Byström AS. Elongator-a tRNA modifying complex that promotes efficient translational decoding. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2017; 1861:401-408. [PMID: 29170010 DOI: 10.1016/j.bbagrm.2017.11.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 11/19/2017] [Indexed: 12/22/2022]
Abstract
Naturally occurring modifications of the nucleosides in the anticodon region of tRNAs influence their translational decoding properties. Uridines present at the wobble position in eukaryotic cytoplasmic tRNAs often contain a 5-carbamoylmethyl (ncm(5)) or 5-methoxycarbonylmethyl (mcm(5)) side-chain and sometimes also a 2-thio or 2'-O-methyl group. The first step in the formation of the ncm(5) and mcm(5) side-chains requires the conserved six-subunit Elongator complex. Although Elongator has been implicated in several different cellular processes, accumulating evidence suggests that its primary, and possibly only, cellular function is to promote modification of tRNAs. In this review, we discuss the biosynthesis and function of modified wobble uridines in eukaryotic cytoplasmic tRNAs, focusing on the in vivo role of Elongator-dependent modifications in Saccharomyces cerevisiae. 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)
| | - Fu Xu
- Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden
| | - Anders S Byström
- Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden.
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44
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Tuorto F, Lyko F. Genome recoding by tRNA modifications. Open Biol 2017; 6:rsob.160287. [PMID: 27974624 PMCID: PMC5204126 DOI: 10.1098/rsob.160287] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 11/14/2016] [Indexed: 11/12/2022] Open
Abstract
RNA modifications are emerging as an additional regulatory layer on top of the primary RNA sequence. These modifications are particularly enriched in tRNAs where they can regulate not only global protein translation, but also protein translation at the codon level. Modifications located in or in the vicinity of tRNA anticodons are highly conserved in eukaryotes and have been identified as potential regulators of mRNA decoding. Recent studies have provided novel insights into how these modifications orchestrate the speed and fidelity of translation to ensure proper protein homeostasis. This review highlights the prominent modifications in the tRNA anticodon loop: queuosine, inosine, 5-methoxycarbonylmethyl-2-thiouridine, wybutosine, threonyl-carbamoyl-adenosine and 5-methylcytosine. We discuss the functional relevance of these modifications in protein translation and their emerging role in eukaryotic genome recoding during cellular adaptation and disease.
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Affiliation(s)
- Francesca Tuorto
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Frank Lyko
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
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45
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Benjdia A, Balty C, Berteau O. Radical SAM Enzymes in the Biosynthesis of Ribosomally Synthesized and Post-translationally Modified Peptides (RiPPs). Front Chem 2017; 5:87. [PMID: 29167789 PMCID: PMC5682303 DOI: 10.3389/fchem.2017.00087] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 10/11/2017] [Indexed: 11/13/2022] Open
Abstract
Ribosomally-synthesized and post-translationally modified peptides (RiPPs) are a large and diverse family of natural products. They possess interesting biological properties such as antibiotic or anticancer activities, making them attractive for therapeutic applications. In contrast to polyketides and non-ribosomal peptides, RiPPs derive from ribosomal peptides and are post-translationally modified by diverse enzyme families. Among them, the emerging superfamily of radical SAM enzymes has been shown to play a major role. These enzymes catalyze the formation of a wide range of post-translational modifications some of them having no counterparts in living systems or synthetic chemistry. The investigation of radical SAM enzymes has not only illuminated unprecedented strategies used by living systems to tailor peptides into complex natural products but has also allowed to uncover novel RiPP families. In this review, we summarize the current knowledge on radical SAM enzymes catalyzing RiPP post-translational modifications and discuss their mechanisms and growing importance notably in the context of the human microbiota.
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Affiliation(s)
- Alhosna Benjdia
- Micalis Institute, ChemSyBio, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Clémence Balty
- Micalis Institute, ChemSyBio, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Olivier Berteau
- Micalis Institute, ChemSyBio, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
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46
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Dauden MI, Jaciuk M, Müller CW, Glatt S. Structural asymmetry in the eukaryotic Elongator complex. FEBS Lett 2017; 592:502-515. [DOI: 10.1002/1873-3468.12865] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 09/08/2017] [Accepted: 09/24/2017] [Indexed: 12/28/2022]
Affiliation(s)
- Maria I. Dauden
- Structural and Computational Biology Unit European Molecular Biology Laboratory Heidelberg Germany
| | - Marcin Jaciuk
- Max Planck Research Group at the Malopolska Centre of Biotechnology Jagiellonian University Krakow Poland
| | - Christoph W. Müller
- Structural and Computational Biology Unit European Molecular Biology Laboratory Heidelberg Germany
| | - Sebastian Glatt
- Max Planck Research Group at the Malopolska Centre of Biotechnology Jagiellonian University Krakow Poland
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47
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Mehlgarten C, Prochaska H, Hammermeister A, Abdel-Fattah W, Wagner M, Krutyhołowa R, Jun SE, Kim GT, Glatt S, Breunig KD, Stark MJR, Schaffrath R. Use of a Yeast tRNase Killer Toxin to Diagnose Kti12 Motifs Required for tRNA Modification by Elongator. Toxins (Basel) 2017; 9:E272. [PMID: 28872616 PMCID: PMC5618205 DOI: 10.3390/toxins9090272] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 08/29/2017] [Accepted: 09/03/2017] [Indexed: 01/23/2023] Open
Abstract
Saccharomyces cerevisiae cells are killed by zymocin, a tRNase ribotoxin complex from Kluyveromyces lactis, which cleaves anticodons and inhibits protein synthesis. Zymocin's action requires specific chemical modification of uridine bases in the anticodon wobble position (U34) by the Elongator complex (Elp1-Elp6). Hence, loss of anticodon modification in mutants lacking Elongator or related KTI (K. lactis Toxin Insensitive) genes protects against tRNA cleavage and confers resistance to the toxin. Here, we show that zymocin can be used as a tool to genetically analyse KTI12, a gene previously shown to code for an Elongator partner protein. From a kti12 mutant pool of zymocin survivors, we identify motifs in Kti12 that are functionally directly coupled to Elongator activity. In addition, shared requirement of U34 modifications for nonsense and missense tRNA suppression (SUP4; SOE1) strongly suggests that Kti12 and Elongator cooperate to assure proper tRNA functioning. We show that the Kti12 motifs are conserved in plant ortholog DRL1/ELO4 from Arabidopsis thaliana and seem to be involved in binding of cofactors (e.g., nucleotides, calmodulin). Elongator interaction defects triggered by mutations in these motifs correlate with phenotypes typical for loss of U34 modification. Thus, tRNA modification by Elongator appears to require physical contact with Kti12, and our preliminary data suggest that metabolic signals may affect proper communication between them.
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Affiliation(s)
- Constance Mehlgarten
- Institut für Biologie, Martin Luther Universität Halle-Wittenberg, Weinbergweg 10, 06120 Halle/Saale, Germany.
| | - Heike Prochaska
- Institut für Biologie, Martin Luther Universität Halle-Wittenberg, Weinbergweg 10, 06120 Halle/Saale, Germany.
| | - Alexander Hammermeister
- Institut für Biologie, FG Mikrobiologie, Universität Kassel, Heirich-Plett-Str. 40, 34132 Kassel, Germany.
| | - Wael Abdel-Fattah
- Institut für Biologie, FG Mikrobiologie, Universität Kassel, Heirich-Plett-Str. 40, 34132 Kassel, Germany.
| | - Melanie Wagner
- Institut für Biologie, Martin Luther Universität Halle-Wittenberg, Weinbergweg 10, 06120 Halle/Saale, Germany.
| | - Rościsław Krutyhołowa
- Max Planck Research Group at the Malopolska Centre of Biotechnology, Jagiellonian University, 31-007 Krakow, Poland.
- Department of Cell Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 31-007 Krakow, Poland.
| | - Sang Eun Jun
- Department of Molecular Biotechnology, Dong-A University, Busan 604-714, Korea.
| | - Gyung-Tae Kim
- Department of Molecular Biotechnology, Dong-A University, Busan 604-714, Korea.
| | - Sebastian Glatt
- Max Planck Research Group at the Malopolska Centre of Biotechnology, Jagiellonian University, 31-007 Krakow, Poland.
| | - Karin D Breunig
- Institut für Biologie, Martin Luther Universität Halle-Wittenberg, Weinbergweg 10, 06120 Halle/Saale, Germany.
| | - Michael J R Stark
- Centre for Gene Regulation & Expression, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK.
| | - Raffael Schaffrath
- Institut für Biologie, Martin Luther Universität Halle-Wittenberg, Weinbergweg 10, 06120 Halle/Saale, Germany.
- Institut für Biologie, FG Mikrobiologie, Universität Kassel, Heirich-Plett-Str. 40, 34132 Kassel, Germany.
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48
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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: 54] [Impact Index Per Article: 6.8] [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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49
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Abstract
Wobble uridines (U34) are generally modified in all species. U34 modifications can be essential in metazoans but are not required for viability in fungi. In this review, we provide an overview on the types of modifications and how they affect the physico-chemical properties of wobble uridines. We describe the molecular machinery required to introduce these modifications into tRNA posttranscriptionally and discuss how posttranslational regulation may affect the activity of the modifying enzymes. We highlight the activity of anticodon specific RNases that target U34 containing tRNA. Finally, we discuss how defects in wobble uridine modifications lead to phenotypes in different species. Importantly, this review will mainly focus on the cytoplasmic tRNAs of eukaryotes. A recent review has extensively covered their bacterial and mitochondrial counterparts.1
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Affiliation(s)
- Raffael Schaffrath
- a Institut für Biologie, FG Mikrobiologie , Universität Kassel , Germany
| | - Sebastian A Leidel
- b Max Planck Institute for Molecular Biomedicine , Germany.,c Cells-in-Motion Cluster of Excellence , University of Münster , Münster , Germany.,d Medical Faculty , University of Münster , Albert-Schweitzer-Campus 1, Münster , Germany
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50
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Sulfur Modifications of the Wobble U 34 in tRNAs and their Intracellular Localization in Eukaryotic Cells. Biomolecules 2017; 7:biom7010017. [PMID: 28218716 PMCID: PMC5372729 DOI: 10.3390/biom7010017] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 02/08/2017] [Accepted: 02/08/2017] [Indexed: 12/21/2022] Open
Abstract
The wobble uridine (U34) of transfer RNAs (tRNAs) for two-box codon recognition, i.e., tRNALysUUU, tRNAGluUUC, and tRNAGlnUUG, harbor a sulfur- (thio-) and a methyl-derivative structure at the second and fifth positions of U34, respectively. Both modifications are necessary to construct the proper anticodon loop structure and to enable them to exert their functions in translation. Thio-modification of U34 (s2U34) is found in both cytosolic tRNAs (cy-tRNAs) and mitochondrial tRNAs (mt-tRNAs). Although l-cysteine desulfurase is required in both cases, subsequent sulfur transfer pathways to cy-tRNAs and mt-tRNAs are different due to their distinct intracellular locations. The s2U34 formation in cy-tRNAs involves a sulfur delivery system required for the biosynthesis of iron-sulfur (Fe/S) clusters and certain resultant Fe/S proteins. This review addresses presumed sulfur delivery pathways for the s2U34 formation in distinct intracellular locations, especially that for cy-tRNAs in comparison with that for mt-tRNAs.
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