1
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Perlinska AP, Sikora M, Sulkowska JI. Everything AlphaFold tells us about protein knots. J Mol Biol 2024; 436:168715. [PMID: 39029890 DOI: 10.1016/j.jmb.2024.168715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 06/29/2024] [Accepted: 07/14/2024] [Indexed: 07/21/2024]
Abstract
Recent advances in Machine Learning methods in structural biology opened up new perspectives for protein analysis. Utilizing these methods allows us to go beyond the limitations of empirical research, and take advantage of the vast amount of generated data. We use a complete set of potentially knotted protein models identified in all high-quality predictions from the AlphaFold Database to search for any common trends that describe them. We show that the vast majority of knotted proteins have 31 knot and that the presence of knots is preferred in neither Bacteria, Eukaryota, or Archaea domains. On the contrary, the percentage of knotted proteins in any given proteome is around 0.4%, regardless of the taxonomical group. We also verified that the organism's living conditions do not impact the number of knotted proteins in its proteome, as previously expected. We did not encounter an organism without a single knotted protein. What is more, we found four universally present families of knotted proteins in Bacteria, consisting of SAM synthase, and TrmD, TrmH, and RsmE methyltransferases.
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Affiliation(s)
- Agata P Perlinska
- Centre of New Technologies, University of Warsaw, Banacha 2c, Warsaw 02-097, Poland
| | - Maciej Sikora
- Centre of New Technologies, University of Warsaw, Banacha 2c, Warsaw 02-097, Poland
| | - Joanna I Sulkowska
- Centre of New Technologies, University of Warsaw, Banacha 2c, Warsaw 02-097, Poland.
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2
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Wang Z, Xu X, Li X, Fang J, Huang Z, Zhang M, Liu J, Qiu X. Investigations of Single-Subunit tRNA Methyltransferases from Yeast. J Fungi (Basel) 2023; 9:1030. [PMID: 37888286 PMCID: PMC10608323 DOI: 10.3390/jof9101030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/13/2023] [Accepted: 10/13/2023] [Indexed: 10/28/2023] Open
Abstract
tRNA methylations, including base modification and 2'-O-methylation of ribose moiety, play critical roles in the structural stabilization of tRNAs and the fidelity and efficiency of protein translation. These modifications are catalyzed by tRNA methyltransferases (TRMs). Some of the TRMs from yeast can fully function only by a single subunit. In this study, after performing the primary bioinformatic analyses, the progress of the studies of yeast single-subunit TRMs, as well as the studies of their homologues from yeast and other types of eukaryotes and the corresponding TRMs from other types of organisms was systematically reviewed, which will facilitate the understanding of the evolutionary origin of functional diversity of eukaryotic single-subunit TRM.
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Affiliation(s)
- Zhongyuan Wang
- Ministry of Education Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ningbo 315800, China; (Z.W.); (X.L.); (J.F.); (Z.H.); (M.Z.); (J.L.)
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China;
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Centre, Ningbo University, Ningbo 315800, China
| | - Xiangbin Xu
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China;
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Centre, Ningbo University, Ningbo 315800, China
| | - Xinhai Li
- Ministry of Education Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ningbo 315800, China; (Z.W.); (X.L.); (J.F.); (Z.H.); (M.Z.); (J.L.)
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China;
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Centre, Ningbo University, Ningbo 315800, China
| | - Jiaqi Fang
- Ministry of Education Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ningbo 315800, China; (Z.W.); (X.L.); (J.F.); (Z.H.); (M.Z.); (J.L.)
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China;
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Centre, Ningbo University, Ningbo 315800, China
| | - Zhenkuai Huang
- Ministry of Education Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ningbo 315800, China; (Z.W.); (X.L.); (J.F.); (Z.H.); (M.Z.); (J.L.)
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China;
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Centre, Ningbo University, Ningbo 315800, China
| | - Mengli Zhang
- Ministry of Education Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ningbo 315800, China; (Z.W.); (X.L.); (J.F.); (Z.H.); (M.Z.); (J.L.)
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China;
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Centre, Ningbo University, Ningbo 315800, China
| | - Jiameng Liu
- Ministry of Education Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ningbo 315800, China; (Z.W.); (X.L.); (J.F.); (Z.H.); (M.Z.); (J.L.)
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China;
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Centre, Ningbo University, Ningbo 315800, China
| | - Xiaoting Qiu
- Ministry of Education Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ningbo 315800, China; (Z.W.); (X.L.); (J.F.); (Z.H.); (M.Z.); (J.L.)
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China;
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Centre, Ningbo University, Ningbo 315800, China
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3
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Yang J, Son Y, Kang M, Park W. AamA-mediated epigenetic control of genome-wide gene expression and phenotypic traits in Acinetobacter baumannii ATCC 17978. Microb Genom 2023; 9:mgen001093. [PMID: 37589545 PMCID: PMC10483419 DOI: 10.1099/mgen.0.001093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 08/03/2023] [Indexed: 08/18/2023] Open
Abstract
Individual deletions of three genes encoding orphan DNA methyltransferases resulted in the occurrence of growth defect only in the aamA (encoding AcinetobacterAdenine Methylase A) mutant of A. baumannii strain ATCC 17978. Our single-molecule real-time sequencing-based methylome analysis revealed multiple AamA-mediated DNA methylation sites and proposed a potent census target motif (TTTRAATTYAAA). Loss of Dam led to modulation of genome-wide gene expression, and several Dam-target sites including the promoter region of the trmD operon (rpsP, rimM, trmD, and rplS) were identified through our methylome and transcriptome analyses. AamA methylation also appeared to control the expression of many genes linked to membrane functions (lolAB, lpxO), replication (dnaA) and protein synthesis (trmD operon) in the strain ATCC 17978. Interestingly, cellular resistance against several antibiotics and ethidium bromide through functions of efflux pumps diminished in the absence of the aamA gene, and the complementation of aamA gene restored the wild-type phenotypes. Other tested phenotypic traits such as outer-membrane vesicle production, biofilm formation and virulence were also affected in the aamA mutant. Collectively, our data indicated that epigenetic regulation through AamA-mediated DNA methylation of novel target sites mostly in the regulatory regions could contribute significantly to changes in multiple phenotypic traits in A. baumannii ATCC 17978.
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Affiliation(s)
- Jihye Yang
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, Republic of Korea
| | - Yongjun Son
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, Republic of Korea
| | - Mingyeong Kang
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, Republic of Korea
| | - Woojun Park
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, Republic of Korea
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4
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Lyu Z, Wilson C, Ling J. Translational Fidelity during Bacterial Stresses and Host Interactions. Pathogens 2023; 12:383. [PMID: 36986305 PMCID: PMC10057733 DOI: 10.3390/pathogens12030383] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 02/22/2023] [Accepted: 02/24/2023] [Indexed: 03/05/2023] Open
Abstract
Translational fidelity refers to accuracy during protein synthesis and is maintained in all three domains of life. Translational errors occur at base levels during normal conditions and may rise due to mutations or stress conditions. In this article, we review our current understanding of how translational fidelity is perturbed by various environmental stresses that bacterial pathogens encounter during host interactions. We discuss how oxidative stress, metabolic stresses, and antibiotics affect various types of translational errors and the resulting effects on stress adaption and fitness. We also discuss the roles of translational fidelity during pathogen-host interactions and the underlying mechanisms. Many of the studies covered in this review will be based on work with Salmonella enterica and Escherichia coli, but other bacterial pathogens will also be discussed.
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Affiliation(s)
| | | | - Jiqiang Ling
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, MD 20742, USA
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5
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Modopathies Caused by Mutations in Genes Encoding for Mitochondrial RNA Modifying Enzymes: Molecular Mechanisms and Yeast Disease Models. Int J Mol Sci 2023; 24:ijms24032178. [PMID: 36768505 PMCID: PMC9917222 DOI: 10.3390/ijms24032178] [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: 12/28/2022] [Revised: 01/17/2023] [Accepted: 01/20/2023] [Indexed: 01/25/2023] Open
Abstract
In eukaryotes, mitochondrial RNAs (mt-tRNAs and mt-rRNAs) are subject to specific nucleotide modifications, which are critical for distinct functions linked to the synthesis of mitochondrial proteins encoded by mitochondrial genes, and thus for oxidative phosphorylation. In recent years, mutations in genes encoding for mt-RNAs modifying enzymes have been identified as being causative of primary mitochondrial diseases, which have been called modopathies. These latter pathologies can be caused by mutations in genes involved in the modification either of tRNAs or of rRNAs, resulting in the absence of/decrease in a specific nucleotide modification and thus on the impairment of the efficiency or the accuracy of the mitochondrial protein synthesis. Most of these mutations are sporadic or private, thus it is fundamental that their pathogenicity is confirmed through the use of a model system. This review will focus on the activity of genes that, when mutated, are associated with modopathies, on the molecular mechanisms through which the enzymes introduce the nucleotide modifications, on the pathological phenotypes associated with mutations in these genes and on the contribution of the yeast Saccharomyces cerevisiae to confirming the pathogenicity of novel mutations and, in some cases, for defining the molecular defects.
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6
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Finger V, Kufa M, Soukup O, Castagnolo D, Roh J, Korabecny J. Pyrimidine derivatives with antitubercular activity. Eur J Med Chem 2023; 246:114946. [PMID: 36459759 DOI: 10.1016/j.ejmech.2022.114946] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/17/2022] [Accepted: 11/18/2022] [Indexed: 11/23/2022]
Abstract
Small molecules with antitubercular activity containing the pyrimidine motif in their structure have gained more attention after three drugs, namely GSK 2556286 (GSK-286), TBA-7371 and SPR720, have entered clinical trials. This review provides an overview of recent advances in the hit-to-lead drug discovery studies of antitubercular pyrimidine-containing compounds with the aim to highlight their structural diversity. In the first part, the review discusses the pyrimidine compounds according to their targets, pinpointing the structure-activity relationships of each pyrimidine family. The second part of this review is concentrated on antitubercular pyrimidine derivatives with a yet unexplored or speculative target, dividing the compounds according to their structural types.
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Affiliation(s)
- Vladimir Finger
- Faculty of Pharmacy in Hradec Kralove, Charles University, Akademika Heyrovskeho 1203, 50005 Hradec Kralove, Czech Republic; Biomedical Research Center, University Hospital Hradec Kralove, Sokolska 581, 500 05, Hradec, Kralove, Czech Republic
| | - Martin Kufa
- Faculty of Pharmacy in Hradec Kralove, Charles University, Akademika Heyrovskeho 1203, 50005 Hradec Kralove, Czech Republic; Biomedical Research Center, University Hospital Hradec Kralove, Sokolska 581, 500 05, Hradec, Kralove, Czech Republic
| | - Ondrej Soukup
- Biomedical Research Center, University Hospital Hradec Kralove, Sokolska 581, 500 05, Hradec, Kralove, Czech Republic
| | - Daniele Castagnolo
- Department of Chemistry, University College London, 20 Gordon Street, WC1H 0AJ, London, United Kingdom
| | - Jaroslav Roh
- Faculty of Pharmacy in Hradec Kralove, Charles University, Akademika Heyrovskeho 1203, 50005 Hradec Kralove, Czech Republic.
| | - Jan Korabecny
- Biomedical Research Center, University Hospital Hradec Kralove, Sokolska 581, 500 05, Hradec, Kralove, Czech Republic.
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7
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Strassler SE, Bowles IE, Dey D, Jackman JE, Conn GL. Tied up in knots: Untangling substrate recognition by the SPOUT methyltransferases. J Biol Chem 2022; 298:102393. [PMID: 35988649 PMCID: PMC9508554 DOI: 10.1016/j.jbc.2022.102393] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 08/10/2022] [Accepted: 08/11/2022] [Indexed: 10/25/2022] Open
Abstract
The SpoU-TrmD (SPOUT) methyltransferase superfamily was designated when structural similarity was identified between the transfer RNA-modifying enzymes TrmH (SpoU) and TrmD. SPOUT methyltransferases are found in all domains of life and predominantly modify transfer RNA or ribosomal RNA substrates, though one instance of an enzyme with a protein substrate has been reported. Modifications placed by SPOUT methyltransferases play diverse roles in regulating cellular processes such as ensuring translational fidelity, altering RNA stability, and conferring bacterial resistance to antibiotics. This large collection of S-adenosyl-L-methionine-dependent methyltransferases is defined by a unique α/β fold with a deep trefoil knot in their catalytic (SPOUT) domain. Herein, we describe current knowledge of SPOUT enzyme structure, domain architecture, and key elements of catalytic function, including S-adenosyl-L-methionine co-substrate binding, beginning with a new sequence alignment that divides the SPOUT methyltransferase superfamily into four major clades. Finally, a major focus of this review will be on our growing understanding of how these diverse enzymes accomplish the molecular feat of specific substrate recognition and modification, as highlighted by recent advances in our knowledge of protein-RNA complex structures and the discovery of the dependence of one SPOUT methyltransferase on metal ion binding for catalysis. Considering the broad biological roles of RNA modifications, developing a deeper understanding of the process of substrate recognition by the SPOUT enzymes will be critical for defining many facets of fundamental RNA biology with implications for human disease.
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Affiliation(s)
- Sarah E Strassler
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA; Graduate Program in Biochemistry, Cell and Developmental Biology, Graduate Division of Biological and Biomedical Sciences, Emory University, Atlanta, Georgia, USA
| | - Isobel E Bowles
- Department of Chemistry and Biochemistry, Center for RNA Biology and Ohio State Biochemistry Program, Columbus, Ohio, USA
| | - Debayan Dey
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Jane E Jackman
- Department of Chemistry and Biochemistry, Center for RNA Biology and Ohio State Biochemistry Program, Columbus, Ohio, USA.
| | - Graeme L Conn
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA; Graduate Program in Biochemistry, Cell and Developmental Biology, Graduate Division of Biological and Biomedical Sciences, Emory University, Atlanta, Georgia, USA.
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8
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Clifton BE, Fariz MA, Uechi GI, Laurino P. Evolutionary repair reveals an unexpected role of the tRNA modification m1G37 in aminoacylation. Nucleic Acids Res 2021; 49:12467-12485. [PMID: 34761260 PMCID: PMC8643618 DOI: 10.1093/nar/gkab1067] [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: 07/26/2021] [Revised: 10/13/2021] [Accepted: 10/20/2021] [Indexed: 11/13/2022] Open
Abstract
The tRNA modification m1G37, introduced by the tRNA methyltransferase TrmD, is thought to be essential for growth in bacteria because it suppresses translational frameshift errors at proline codons. However, because bacteria can tolerate high levels of mistranslation, it is unclear why loss of m1G37 is not tolerated. Here, we addressed this question through experimental evolution of trmD mutant strains of Escherichia coli. Surprisingly, trmD mutant strains were viable even if the m1G37 modification was completely abolished, and showed rapid recovery of growth rate, mainly via duplication or mutation of the proline-tRNA ligase gene proS. Growth assays and in vitro aminoacylation assays showed that G37-unmodified tRNAPro is aminoacylated less efficiently than m1G37-modified tRNAPro, and that growth of trmD mutant strains can be largely restored by single mutations in proS that restore aminoacylation of G37-unmodified tRNAPro. These results show that inefficient aminoacylation of tRNAPro is the main reason for growth defects observed in trmD mutant strains and that proS may act as a gatekeeper of translational accuracy, preventing the use of error-prone unmodified tRNAPro in translation. Our work shows the utility of experimental evolution for uncovering the hidden functions of essential genes and has implications for the development of antibiotics targeting TrmD.
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Affiliation(s)
- Ben E Clifton
- Protein Engineering and Evolution Unit, Okinawa Institute of Science and Technology, Onna, Okinawa 904-0495, Japan
| | - Muhammad A Fariz
- Protein Engineering and Evolution Unit, Okinawa Institute of Science and Technology, Onna, Okinawa 904-0495, Japan
| | - Gen-Ichiro Uechi
- Protein Engineering and Evolution Unit, Okinawa Institute of Science and Technology, Onna, Okinawa 904-0495, Japan
| | - Paola Laurino
- Protein Engineering and Evolution Unit, Okinawa Institute of Science and Technology, Onna, Okinawa 904-0495, Japan
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9
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Structure based design, synthesis and evaluation of new thienopyrimidine derivatives as anti-bacterial agents. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130168] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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10
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Pereira J. GCsnap: Interactive Snapshots for the Comparison of Protein-Coding Genomic Contexts. J Mol Biol 2021; 433:166943. [PMID: 33737026 DOI: 10.1016/j.jmb.2021.166943] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 02/09/2021] [Accepted: 03/09/2021] [Indexed: 12/30/2022]
Abstract
The biological function and evolutionary history of protein-coding genes are not only written in their nucleotide sequences. The comparison of genomic contexts throughout different lineages may highlight genomic mechanisms in the generation of new protein families, while the conservation of gene clusters may unravel, for instance, metabolic pathways. Various tools and databases exist that allow for the analysis and comparison of genomic contexts, but each has its own limitations. Online databases allow for quick comparisons, but only for those genomes for which data were pre-calculated. More advanced tools may allow for the comparison of any genome, but are often limited to a given phylogenetic kingdom or provide only a snapshot of the genomic contexts without further information about the genes involved. Here, we introduce GCsnap, a flexible Python-based tool that allows for the interactive comparison of the genomic contexts of protein-coding genes from any genome at any taxonomic level, integrating them with functional and structural information. By connecting the output to different protein databases, users can navigate through the different genomic contexts from a simple interactive platform, facilitating the further analysis of the contexts found. GCsnap is not limited to a single input format, can perform batch jobs and accepts protein classification maps. Results are stored in detailed, human and machine-readable files, and customizable, publication-ready figures. GCsnap is freely available from https://github.com/JoanaMPereira/GCsnap and can be set up easily on any computer.
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Affiliation(s)
- Joana Pereira
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
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11
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Edwards AM, Addo MA, Dos Santos PC. Extracurricular Functions of tRNA Modifications in Microorganisms. Genes (Basel) 2020; 11:genes11080907. [PMID: 32784710 PMCID: PMC7466049 DOI: 10.3390/genes11080907] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 07/29/2020] [Accepted: 08/02/2020] [Indexed: 12/29/2022] Open
Abstract
Transfer RNAs (tRNAs) are essential adaptors that mediate translation of the genetic code. These molecules undergo a variety of post-transcriptional modifications, which expand their chemical reactivity while influencing their structure, stability, and functionality. Chemical modifications to tRNA ensure translational competency and promote cellular viability. Hence, the placement and prevalence of tRNA modifications affects the efficiency of aminoacyl tRNA synthetase (aaRS) reactions, interactions with the ribosome, and transient pairing with messenger RNA (mRNA). The synthesis and abundance of tRNA modifications respond directly and indirectly to a range of environmental and nutritional factors involved in the maintenance of metabolic homeostasis. The dynamic landscape of the tRNA epitranscriptome suggests a role for tRNA modifications as markers of cellular status and regulators of translational capacity. This review discusses the non-canonical roles that tRNA modifications play in central metabolic processes and how their levels are modulated in response to a range of cellular demands.
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12
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Jaroensuk J, Wong YH, Zhong W, Liew CW, Maenpuen S, Sahili AE, Atichartpongkul S, Chionh YH, Nah Q, Thongdee N, McBee ME, Prestwich EG, DeMott MS, Chaiyen P, Mongkolsuk S, Dedon PC, Lescar J, Fuangthong M. Crystal structure and catalytic mechanism of the essential m 1G37 tRNA methyltransferase TrmD from Pseudomonas aeruginosa. RNA (NEW YORK, N.Y.) 2019; 25:1481-1496. [PMID: 31399541 PMCID: PMC6795141 DOI: 10.1261/rna.066746.118] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Accepted: 07/28/2019] [Indexed: 06/10/2023]
Abstract
The tRNA (m1G37) methyltransferase TrmD catalyzes m1G formation at position 37 in many tRNA isoacceptors and is essential in most bacteria, which positions it as a target for antibiotic development. In spite of its crucial role, little is known about TrmD in Pseudomonas aeruginosa (PaTrmD), an important human pathogen. Here we present detailed structural, substrate, and kinetic properties of PaTrmD. The mass spectrometric analysis confirmed the G36G37-containing tRNAs Leu(GAG), Leu(CAG), Leu(UAG), Pro(GGG), Pro(UGG), Pro(CGG), and His(GUG) as PaTrmD substrates. Analysis of steady-state kinetics with S-adenosyl-l-methionine (SAM) and tRNALeu(GAG) showed that PaTrmD catalyzes the two-substrate reaction by way of a ternary complex, while isothermal titration calorimetry revealed that SAM and tRNALeu(GAG) bind to PaTrmD independently, each with a dissociation constant of 14 ± 3 µM. Inhibition by the SAM analog sinefungin was competitive with respect to SAM (Ki = 0.41 ± 0.07 µM) and uncompetitive for tRNA (Ki = 6.4 ± 0.8 µM). A set of crystal structures of the homodimeric PaTrmD protein bound to SAM and sinefungin provide the molecular basis for enzyme competitive inhibition and identify the location of the bound divalent ion. These results provide insights into PaTrmD as a potential target for the development of antibiotics.
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Affiliation(s)
- Juthamas Jaroensuk
- Applied Biological Sciences Program, Chulabhorn Graduate Institute, Chulabhorn Royal Academy, Bangkok 10210, Thailand
- Singapore-MIT Alliance for Research and Technology Antimicrobial Resistance and Infectious Disease Interdisciplinary Research Groups, 138602 Singapore
| | - Yee Hwa Wong
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, 636921 Singapore
| | - Wenhe Zhong
- Singapore-MIT Alliance for Research and Technology Antimicrobial Resistance and Infectious Disease Interdisciplinary Research Groups, 138602 Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, 636921 Singapore
| | - Chong Wai Liew
- NTU Institute of Structural Biology, Nanyang Technological University, 636921 Singapore
| | - Somchart Maenpuen
- Department of Biochemistry, Faculty of Science, Burapha University, Chonburi 20131, Thailand
| | - Abbas E Sahili
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, 636921 Singapore
| | | | - Yok Hian Chionh
- Singapore-MIT Alliance for Research and Technology Antimicrobial Resistance and Infectious Disease Interdisciplinary Research Groups, 138602 Singapore
| | - Qianhui Nah
- Singapore-MIT Alliance for Research and Technology Antimicrobial Resistance and Infectious Disease Interdisciplinary Research Groups, 138602 Singapore
| | - Narumon Thongdee
- Applied Biological Sciences Program, Chulabhorn Graduate Institute, Chulabhorn Royal Academy, Bangkok 10210, Thailand
| | - Megan E McBee
- Singapore-MIT Alliance for Research and Technology Antimicrobial Resistance and Infectious Disease Interdisciplinary Research Groups, 138602 Singapore
| | - Erin G Prestwich
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Michael S DeMott
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Pimchai Chaiyen
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong 21210, Thailand
| | - Skorn Mongkolsuk
- Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok 10210, Thailand
- Department of Biotechnology, Faculty of Sciences, Mahidol University, Bangkok 10400, Thailand
- Center of Excellence on Environmental Health and Toxicology (EHT), Bangkok 10400, Thailand
| | - Peter C Dedon
- Singapore-MIT Alliance for Research and Technology Antimicrobial Resistance and Infectious Disease Interdisciplinary Research Groups, 138602 Singapore
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Julien Lescar
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, 636921 Singapore
| | - Mayuree Fuangthong
- Applied Biological Sciences Program, Chulabhorn Graduate Institute, Chulabhorn Royal Academy, Bangkok 10210, Thailand
- Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok 10210, Thailand
- Center of Excellence on Environmental Health and Toxicology (EHT), Bangkok 10400, Thailand
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13
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Li Y, Zhong W, Koay AZ, Ng HQ, Nah Q, Wong YH, Hill J, Lescar J, Dedon PC, Kang C. Backbone resonance assignment for the full length tRNA-(N 1G37) methyltransferase of Pseudomonas aeruginosa. BIOMOLECULAR NMR ASSIGNMENTS 2019; 13:327-332. [PMID: 31175551 DOI: 10.1007/s12104-019-09900-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 05/31/2019] [Indexed: 06/09/2023]
Abstract
Bacterial tRNA (guanine37-N1)-methyltransferase (TrmD) plays important roles in translation, making it an important target for the development of new antibacterial compounds. TrmD comprises two domains with the N-terminal domain binding to the S-adenosyl-L-methionine (SAM) cofactor and the C-terminal domain critical for tRNA binding. Bacterial TrmD is functional as a dimer. Here we report the backbone NMR resonance assignments for the full length TrmD protein of Pseudomonas aeruginosa. Most resonances were assigned and the secondary structure for each amino acid was determined according to the assigned backbone resonances. The availability of the assignment will be valuable for exploring molecular interactions of TrmD with ligands, inhibitors and tRNA.
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Affiliation(s)
- Yan Li
- Experimental Drug Development Centre, 10 Biopolis Road, #05-01, Singapore, 138670, Singapore
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, 430030, Hubei, People's Republic of China
| | - Wenhe Zhong
- Infectious Disease and Antimicrobial Resistance Interdisciplinary Research Groups, Singapore-MIT Alliance for Research and Technology, 1 CREATE Way, Singapore, 138602, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore, 636921, Singapore
| | - Ann Zhufang Koay
- Experimental Drug Development Centre, 10 Biopolis Road, #05-01, Singapore, 138670, Singapore
| | - Hui Qi Ng
- Experimental Drug Development Centre, 10 Biopolis Road, #05-01, Singapore, 138670, Singapore
| | - Qianhui Nah
- Infectious Disease and Antimicrobial Resistance Interdisciplinary Research Groups, Singapore-MIT Alliance for Research and Technology, 1 CREATE Way, Singapore, 138602, Singapore
| | - Yee Hwa Wong
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore, 636921, Singapore
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Jeffrey Hill
- Experimental Drug Development Centre, 10 Biopolis Road, #05-01, Singapore, 138670, Singapore
| | - Julien Lescar
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore, 636921, Singapore.
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
| | - Peter C Dedon
- Infectious Disease and Antimicrobial Resistance Interdisciplinary Research Groups, Singapore-MIT Alliance for Research and Technology, 1 CREATE Way, Singapore, 138602, Singapore.
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| | - CongBao Kang
- Experimental Drug Development Centre, 10 Biopolis Road, #05-01, Singapore, 138670, Singapore.
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14
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Zhong W, Pasunooti KK, Balamkundu S, Wong YH, Nah Q, Gadi V, Gnanakalai S, Chionh YH, McBee ME, Gopal P, Lim SH, Olivier N, Buurman ET, Dick T, Liu CF, Lescar J, Dedon PC. Thienopyrimidinone Derivatives That Inhibit Bacterial tRNA (Guanine37- N1)-Methyltransferase (TrmD) by Restructuring the Active Site with a Tyrosine-Flipping Mechanism. J Med Chem 2019; 62:7788-7805. [PMID: 31442049 PMCID: PMC6748665 DOI: 10.1021/acs.jmedchem.9b00582] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
![]()
Among the >120
modified ribonucleosides in the prokaryotic epitranscriptome,
many tRNA modifications are critical to bacterial survival, which
makes their synthetic enzymes ideal targets for antibiotic development.
Here we performed a structure-based design of inhibitors of tRNA-(N1G37) methyltransferase, TrmD, which is an essential enzyme
in many bacterial pathogens. On the basis of crystal structures of
TrmDs from Pseudomonas aeruginosa and Mycobacterium tuberculosis, we synthesized a series
of thienopyrimidinone derivatives with nanomolar potency against TrmD
in vitro and discovered a novel active site conformational change
triggered by inhibitor binding. This tyrosine-flipping mechanism is
uniquely found in P. aeruginosa TrmD
and renders the enzyme inaccessible to the cofactor S-adenosyl-l-methionine (SAM) and probably to the substrate
tRNA. Biophysical and biochemical structure–activity relationship
studies provided insights into the mechanisms underlying the potency
of thienopyrimidinones as TrmD inhibitors, with several derivatives
found to be active against Gram-positive and mycobacterial pathogens.
These results lay a foundation for further development of TrmD inhibitors
as antimicrobial agents.
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Affiliation(s)
- Wenhe Zhong
- Infectious Disease and Antimicrobial Resistance Interdisciplinary Research Groups , Singapore-MIT Alliance for Research and Technology , 1 CREATE Way , 138602 Singapore.,NTU Institute of Structural Biology , Nanyang Technological University , 636921 Singapore
| | - Kalyan Kumar Pasunooti
- Infectious Disease and Antimicrobial Resistance Interdisciplinary Research Groups , Singapore-MIT Alliance for Research and Technology , 1 CREATE Way , 138602 Singapore
| | - Seetharamsing Balamkundu
- Infectious Disease and Antimicrobial Resistance Interdisciplinary Research Groups , Singapore-MIT Alliance for Research and Technology , 1 CREATE Way , 138602 Singapore
| | - Yee Hwa Wong
- School of Biological Sciences , Nanyang Technological University , 60 Nanyang Drive , 637551 Singapore.,NTU Institute of Structural Biology , Nanyang Technological University , 636921 Singapore
| | - Qianhui Nah
- Infectious Disease and Antimicrobial Resistance Interdisciplinary Research Groups , Singapore-MIT Alliance for Research and Technology , 1 CREATE Way , 138602 Singapore
| | - Vinod Gadi
- Infectious Disease and Antimicrobial Resistance Interdisciplinary Research Groups , Singapore-MIT Alliance for Research and Technology , 1 CREATE Way , 138602 Singapore
| | - Shanmugavel Gnanakalai
- Infectious Disease and Antimicrobial Resistance Interdisciplinary Research Groups , Singapore-MIT Alliance for Research and Technology , 1 CREATE Way , 138602 Singapore
| | - Yok Hian Chionh
- Infectious Disease and Antimicrobial Resistance Interdisciplinary Research Groups , Singapore-MIT Alliance for Research and Technology , 1 CREATE Way , 138602 Singapore
| | - Megan E McBee
- Infectious Disease and Antimicrobial Resistance Interdisciplinary Research Groups , Singapore-MIT Alliance for Research and Technology , 1 CREATE Way , 138602 Singapore
| | - Pooja Gopal
- Yong Loo Lin School of Medicine , National University of Singapore , 117597 Singapore
| | - Siau Hoi Lim
- School of Biological Sciences , Nanyang Technological University , 60 Nanyang Drive , 637551 Singapore
| | | | | | - Thomas Dick
- Yong Loo Lin School of Medicine , National University of Singapore , 117597 Singapore
| | - Chuan Fa Liu
- School of Biological Sciences , Nanyang Technological University , 60 Nanyang Drive , 637551 Singapore
| | - Julien Lescar
- School of Biological Sciences , Nanyang Technological University , 60 Nanyang Drive , 637551 Singapore.,NTU Institute of Structural Biology , Nanyang Technological University , 636921 Singapore
| | - Peter C Dedon
- Infectious Disease and Antimicrobial Resistance Interdisciplinary Research Groups , Singapore-MIT Alliance for Research and Technology , 1 CREATE Way , 138602 Singapore.,Department of Biological Engineering , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
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15
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Li Y, Zhong W, Koay AZ, Ng HQ, Koh-Stenta X, Nah Q, Lim SH, Larsson A, Lescar J, Hill J, Dedon PC, Kang C. Backbone resonance assignment for the N-terminal region of bacterial tRNA-(N 1G37) methyltransferase. BIOMOLECULAR NMR ASSIGNMENTS 2019; 13:49-53. [PMID: 30298375 DOI: 10.1007/s12104-018-9849-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 09/15/2018] [Indexed: 06/08/2023]
Abstract
Bacterial tRNA (guanine37-N1)-methyltransferase (TrmD) is an important antibacterial target due to its essential role in translation. TrmD has two domains connected with a flexible linker. The N-terminal domain (NTD) of TrmD contains the S-adenosyl-L-methionine (SAM) cofactor binding site and the C-terminal domain is critical for tRNA binding. Here we report the backbone NMR resonance assignments for NTD of Pseudomonas aeruginosa TrmD. Its secondary structure was determined based on the assigned resonances. Relaxation analysis revealed that NTD existed as dimers in solution. NTD also exhibited thermal stability in solution. Its interactions with SAM and other compounds suggest it can be used for evaluating SAM competitive inhibitors by NMR.
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Affiliation(s)
- Yan Li
- Experimental Therapeutics Centre, 31 Biopolis Way, #03-01 Nanos, Singapore, 138669, Singapore
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, Hubei, 430030, People's Republic of China
| | - Wenhe Zhong
- Infectious Disease and Antimicrobial Resistance Interdisciplinary Research Groups, Singapore-MIT Alliance for Research and Technology, 1 CREATE Way, Singapore, 138602, Singapore
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, 1 CREATE Way, Singapore, 138602, Singapore
| | - Ann Zhufang Koay
- Experimental Therapeutics Centre, 31 Biopolis Way, #03-01 Nanos, Singapore, 138669, Singapore
| | - Hui Qi Ng
- Experimental Therapeutics Centre, 31 Biopolis Way, #03-01 Nanos, Singapore, 138669, Singapore
| | - Xiaoying Koh-Stenta
- Experimental Therapeutics Centre, 31 Biopolis Way, #03-01 Nanos, Singapore, 138669, Singapore
| | - Qianhui Nah
- Infectious Disease and Antimicrobial Resistance Interdisciplinary Research Groups, Singapore-MIT Alliance for Research and Technology, 1 CREATE Way, Singapore, 138602, Singapore
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, 1 CREATE Way, Singapore, 138602, Singapore
| | - Siau Hoi Lim
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
- Experimental Biotherapeutics Centre, 30 Biopolis Street, #08-01 Matrix, Singapore, 138671, Singapore
| | - Andreas Larsson
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Julien Lescar
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore, 636921, Singapore
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Jeffrey Hill
- Experimental Therapeutics Centre, 31 Biopolis Way, #03-01 Nanos, Singapore, 138669, Singapore.
| | - Peter C Dedon
- Infectious Disease and Antimicrobial Resistance Interdisciplinary Research Groups, Singapore-MIT Alliance for Research and Technology, 1 CREATE Way, Singapore, 138602, Singapore.
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, 1 CREATE Way, Singapore, 138602, Singapore.
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| | - CongBao Kang
- Experimental Therapeutics Centre, 31 Biopolis Way, #03-01 Nanos, Singapore, 138669, Singapore.
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16
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Zhong W, Koay A, Ngo A, Li Y, Nah Q, Wong YH, Chionh YH, Ng HQ, Koh-Stenta X, Poulsen A, Foo K, McBee M, Choong ML, El Sahili A, Kang C, Matter A, Lescar J, Hill J, Dedon P. Targeting the Bacterial Epitranscriptome for Antibiotic Development: Discovery of Novel tRNA-(N 1G37) Methyltransferase (TrmD) Inhibitors. ACS Infect Dis 2019; 5:326-335. [PMID: 30682246 DOI: 10.1021/acsinfecdis.8b00275] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Bacterial tRNA modification synthesis pathways are critical to cell survival under stress and thus represent ideal mechanism-based targets for antibiotic development. One such target is the tRNA-(N1G37) methyltransferase (TrmD), which is conserved and essential in many bacterial pathogens. Here we developed and applied a widely applicable, radioactivity-free, bioluminescence-based high-throughput screen (HTS) against 116350 compounds from structurally diverse small-molecule libraries to identify inhibitors of Pseudomonas aeruginosa TrmD ( PaTrmD). Of 285 compounds passing primary and secondary screens, a total of 61 TrmD inhibitors comprised of more than 12 different chemical scaffolds were identified, all showing submicromolar to low micromolar enzyme inhibitor constants, with binding affinity confirmed by thermal stability and surface plasmon resonance. S-Adenosyl-l-methionine (SAM) competition assays suggested that compounds in the pyridine-pyrazole-piperidine scaffold were substrate SAM-competitive inhibitors. This was confirmed in structural studies, with nuclear magnetic resonance analysis and crystal structures of PaTrmD showing pyridine-pyrazole-piperidine compounds bound in the SAM-binding pocket. Five hits showed cellular activities against Gram-positive bacteria, including mycobacteria, while one compound, a SAM-noncompetitive inhibitor, exhibited broad-spectrum antibacterial activity. The results of this HTS expand the repertoire of TrmD-inhibiting molecular scaffolds that show promise for antibiotic development.
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Affiliation(s)
- Wenhe Zhong
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, 1 CREATE Way, 138602 Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, 636921 Singapore
| | - Ann Koay
- Experimental Therapeutics Centre, 31 Biopolis Way, #03-01 Nanos, 138669 Singapore
| | - Anna Ngo
- Experimental Therapeutics Centre, 31 Biopolis Way, #03-01 Nanos, 138669 Singapore
| | - Yan Li
- Experimental Therapeutics Centre, 31 Biopolis Way, #03-01 Nanos, 138669 Singapore
| | - Qianhui Nah
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, 1 CREATE Way, 138602 Singapore
| | - Yee Hwa Wong
- NTU Institute of Structural Biology, Nanyang Technological University, 636921 Singapore
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
| | - Yok Hian Chionh
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, 1 CREATE Way, 138602 Singapore
| | - Hui Qi Ng
- Experimental Therapeutics Centre, 31 Biopolis Way, #03-01 Nanos, 138669 Singapore
| | - Xiaoying Koh-Stenta
- Experimental Therapeutics Centre, 31 Biopolis Way, #03-01 Nanos, 138669 Singapore
| | - Anders Poulsen
- Experimental Therapeutics Centre, 31 Biopolis Way, #03-01 Nanos, 138669 Singapore
| | - Klement Foo
- Experimental Therapeutics Centre, 31 Biopolis Way, #03-01 Nanos, 138669 Singapore
| | - Megan McBee
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, 1 CREATE Way, 138602 Singapore
| | - Meng Ling Choong
- Experimental Therapeutics Centre, 31 Biopolis Way, #03-01 Nanos, 138669 Singapore
| | - Abbas El Sahili
- NTU Institute of Structural Biology, Nanyang Technological University, 636921 Singapore
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
| | - Congbao Kang
- Experimental Therapeutics Centre, 31 Biopolis Way, #03-01 Nanos, 138669 Singapore
| | - Alex Matter
- Experimental Therapeutics Centre, 31 Biopolis Way, #03-01 Nanos, 138669 Singapore
| | - Julien Lescar
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, 1 CREATE Way, 138602 Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, 636921 Singapore
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
| | - Jeffrey Hill
- Experimental Therapeutics Centre, 31 Biopolis Way, #03-01 Nanos, 138669 Singapore
| | - Peter Dedon
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, 1 CREATE Way, 138602 Singapore
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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17
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Transfer RNA methyltransferases with a SpoU-TrmD (SPOUT) fold and their modified nucleosides in tRNA. Biomolecules 2017; 7:biom7010023. [PMID: 28264529 PMCID: PMC5372735 DOI: 10.3390/biom7010023] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2017] [Accepted: 02/23/2017] [Indexed: 11/22/2022] Open
Abstract
The existence of SpoU-TrmD (SPOUT) RNA methyltransferase superfamily was first predicted by bioinformatics. SpoU is the previous name of TrmH, which catalyzes the 2’-O-methylation of ribose of G18 in tRNA; TrmD catalyzes the formation of N1-methylguanosine at position 37 in tRNA. Although SpoU (TrmH) and TrmD were originally considered to be unrelated, the bioinformatics study suggested that they might share a common evolution origin and form a single superfamily. The common feature of SPOUT RNA methyltransferases is the formation of a deep trefoil knot in the catalytic domain. In the past decade, the SPOUT RNA methyltransferase superfamily has grown; furthermore, knowledge concerning the functions of their modified nucleosides in tRNA has also increased. Some enzymes are potential targets in the design of anti-bacterial drugs. In humans, defects in some genes may be related to carcinogenesis. In this review, recent findings on the tRNA methyltransferases with a SPOUT fold and their methylated nucleosides in tRNA, including classification of tRNA methyltransferases with a SPOUT fold; knot structures, domain arrangements, subunit structures and reaction mechanisms; tRNA recognition mechanisms, and functions of modified nucleosides synthesized by this superfamily, are summarized. Lastly, the future perspective for studies on tRNA modification enzymes are considered.
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18
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Abstract
Methyl transfer from S-adenosyl methionine (abbreviated as AdoMet) to biologically active molecules such as mRNAs and tRNAs is one of the most fundamental and widespread reactions in nature, occurring in all three domains of life. The measurement of kinetic constants of AdoMet-dependent methyl transfer is therefore important for understanding the reaction mechanism in the context of biology. When kinetic constants of methyl transfer are measured in steady state over multiple rounds of turnover, the meaning of these constants is difficult to define and is often limited by non-chemical steps of the reaction, such as product release after each turnover. Here, the measurement of kinetic constants of methyl transfer by tRNA methyltransferases in rapid equilibrium binding condition for one methyl transfer is described. The advantage of such a measurement is that the meaning of kinetic constants can be directly assigned to the steps associated with the chemistry of methyl transfer, including the substrate binding affinity to the methyltransferase, the pre-chemistry re-arrangement of the active site, and the chemical step of methyl transfer. An additional advantage is that kinetic constants measured for one methyl transfer can be correlated with structural information of the methyltransferase to gain direct insight into its reaction mechanism.
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19
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Abstract
Transfer RNA (tRNA) from all organisms on this planet contains modified nucleosides, which are derivatives of the four major nucleosides. tRNA from Escherichia coli/Salmonella enterica contains 31 different modified nucleosides, which are all, except for one (Queuosine[Q]), synthesized on an oligonucleotide precursor, which through specific enzymes later matures into tRNA. The corresponding structural genes for these enzymes are found in mono- and polycistronic operons, the latter of which have a complex transcription and translation pattern. The syntheses of some of them (e.g.,several methylated derivatives) are catalyzed by one enzyme, which is position and base specific, but synthesis of some have a very complex biosynthetic pathway involving several enzymes (e.g., 2-thiouridines, N6-threonyladenosine [t6A],and Q). Several of the modified nucleosides are essential for viability (e.g.,lysidin, t6A, 1-methylguanosine), whereas deficiency in others induces severe growth defects. However, some have no or only a small effect on growth at laboratory conditions. Modified nucleosides that are present in the anticodon loop or stem have a fundamental influence on the efficiency of charging the tRNA, reading cognate codons, and preventing missense and frameshift errors. Those, which are present in the body of the tRNA, have a primarily stabilizing effect on the tRNA. Thus, the ubiquitouspresence of these modified nucleosides plays a pivotal role in the function of the tRNA by their influence on the stability and activity of the tRNA.
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20
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Gamper HB, Masuda I, Frenkel-Morgenstern M, Hou YM. The UGG Isoacceptor of tRNAPro Is Naturally Prone to Frameshifts. Int J Mol Sci 2015; 16:14866-83. [PMID: 26140378 PMCID: PMC4519876 DOI: 10.3390/ijms160714866] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 06/23/2015] [Accepted: 06/24/2015] [Indexed: 11/16/2022] Open
Abstract
Native tRNAs often contain post-transcriptional modifications to the wobble position to expand the capacity of reading the genetic code. Some of these modifications, due to the ability to confer imperfect codon-anticodon pairing at the wobble position, can induce a high propensity for tRNA to shift into alternative reading frames. An example is the native UGG isoacceptor of E. coli tRNAPro whose wobble nucleotide U34 is post-transcriptionally modified to cmo5U34 to read all four proline codons (5ʹ-CCA, 5ʹ-CCC, 5ʹ-CCG, and 5ʹ-CCU). Because the pairing of the modified anticodon to CCC codon is particularly weak relative to CCA and CCG codons, this tRNA can readily shift into both the +1 and +2-frame on the slippery mRNA sequence CCC-CG. We show that the shift to the +2-frame is more dominant, driven by the higher stability of the codon-anticodon pairing at the wobble position. Kinetic analysis suggests that both types of shifts can occur during stalling of the tRNA in a post-translocation complex or during translocation from the A to the P-site. Importantly, while the +1-frame post complex is active for peptidyl transfer, the +2-frame complex is a poor peptidyl donor. Together with our recent work, we draw a mechanistic distinction between +1 and +2-frameshifts, showing that while the +1-shifts are suppressed by the additional post-transcriptionally modified m1G37 nucleotide in the anticodon loop, the +2-shifts are suppressed by the ribosome, supporting a role of the ribosome in the overall quality control of reading-frame maintenance.
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Affiliation(s)
- Howard B Gamper
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA.
| | - Isao Masuda
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA.
| | | | - Ya-Ming Hou
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA.
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21
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Abstract
Transfer RNAs (tRNAs) are central players in the protein translation machinery and as such are prominent targets for a large number of natural and synthetic antibiotics. This review focuses on the role of tRNAs in bacterial antibiosis. We will discuss examples of antibiotics that target multiple stages in tRNA biology from tRNA biogenesis and modification, mature tRNAs, aminoacylation of tRNA as well as prevention of proper tRNA function by small molecules binding to the ribosome. Finally, the role of deacylated tRNAs in the bacterial “stringent response” mechanism that can lead to bacteria displaying antibiotic persistence phenotypes will be discussed.
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22
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Gu C, Begley TJ, Dedon PC. tRNA modifications regulate translation during cellular stress. FEBS Lett 2014; 588:4287-96. [PMID: 25304425 DOI: 10.1016/j.febslet.2014.09.038] [Citation(s) in RCA: 119] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Revised: 09/29/2014] [Accepted: 09/29/2014] [Indexed: 12/20/2022]
Abstract
The regulation of gene expression in response to stress is an essential cellular protection mechanism. Recent advances in tRNA modification analysis and genome-based codon bias analytics have facilitated studies that lead to a novel model for translational control, with translation elongation dynamically regulated during stress responses. Stress-induced increases in specific anticodon wobble bases are required for the optimal translation of stress response transcripts that are significantly biased in the use of degenerate codons keyed to these modified tRNA bases. These findings led us to introduce the notion of tRNA modification tunable transcripts (MoTTs - transcripts whose translation is regulated by tRNA modifications), which are identifiable using genome-wide codon counting algorithms. In support of this general model of translational control of stress response, studies making use of detailed measures of translation, tRNA methyltransferase mutants, and computational and mass spectrometry approaches reveal that stress reprograms tRNA modifications to translationally regulate MoTTs linked to arginine and leucine codons, which helps cells survive insults by damaging agents. These studies highlight how tRNA methyltransferase activities and MoTTs are key components of the cellular stress response.
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Affiliation(s)
- Chen Gu
- Department of Biological Engineering and Center for Environmental Health Science, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Thomas J Begley
- State University of New York - College of Nanoscale Science and Engineering, Albany, NY, United States; The RNA Institute at the University at Albany, Albany, NY, United States.
| | - Peter C Dedon
- Department of Biological Engineering and Center for Environmental Health Science, Massachusetts Institute of Technology, Cambridge, MA, United States; Singapore-MIT Alliance for Research and Technology, Singapore, Singapore.
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23
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Kuiper EG, Conn GL. Binding induced RNA conformational changes control substrate recognition and catalysis by the thiostrepton resistance methyltransferase (Tsr). J Biol Chem 2014; 289:26189-26200. [PMID: 25086036 DOI: 10.1074/jbc.m114.574780] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Ribosomal RNA (rRNA) post-transcriptional modifications are essential for ribosome maturation, translational fidelity, and are one mechanism used by both antibiotic-producing and pathogenic bacteria to resist the effects of antibiotics that target the ribosome. The thiostrepton producer Streptomyces azureus prevents self-intoxication by expressing the thiostrepton-resistance methyltransferase (Tsr), which methylates the 2'-hydroxyl of 23 S rRNA nucleotide adenosine 1067 within the thiostrepton binding site. Tsr is a homodimer with each protomer containing an L30e-like amino-terminal domain (NTD) and a SPOUT methyltransferase family catalytic carboxyl-terminal domain (CTD). We show that both enzyme domains are required for high affinity RNA substrate binding. The Tsr-CTD has intrinsic, weak RNA affinity that is necessary to direct the specific high-affinity Tsr-RNA interaction via NTDs, which have no detectable RNA affinity in isolation. RNA structure probing experiments identify the Tsr footprint on the RNA and structural changes in the substrate, induced specifically upon NTD binding, which are necessary for catalysis by the CTD. Additionally, we identify a key amino acid in each domain responsible for CTD-RNA binding and the observed NTD-dependent RNA structural changes. These studies allow us to develop a model for Tsr-RNA interaction in which the coordinated substrate recognition of each Tsr structural domain is an obligatory pre-catalytic recognition event. Our findings underscore the complexity of substrate recognition by RNA modification enzymes and the potential for direct involvement of the RNA substrate in controlling the process of its modification.
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Affiliation(s)
- Emily G Kuiper
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322
| | - Graeme L Conn
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322.
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24
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Mosquera-Rendón J, Cárdenas-Brito S, Pineda JD, Corredor M, Benítez-Páez A. Evolutionary and sequence-based relationships in bacterial AdoMet-dependent non-coding RNA methyltransferases. BMC Res Notes 2014; 7:440. [PMID: 25012753 PMCID: PMC4119055 DOI: 10.1186/1756-0500-7-440] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Accepted: 07/02/2014] [Indexed: 12/12/2022] Open
Abstract
Background RNA post-transcriptional modification is an exciting field of research that has evidenced this editing process as a sophisticated epigenetic mechanism to fine tune the ribosome function and to control gene expression. Although tRNA modifications seem to be more relevant for the ribosome function and cell physiology as a whole, some rRNA modifications have also been seen to play pivotal roles, essentially those located in central ribosome regions. RNA methylation at nucleobases and ribose moieties of nucleotides appear to frequently modulate its chemistry and structure. RNA methyltransferases comprise a superfamily of highly specialized enzymes that accomplish a wide variety of modifications. These enzymes exhibit a poor degree of sequence similarity in spite of using a common reaction cofactor and modifying the same substrate type. Results Relationships and lineages of RNA methyltransferases have been extensively discussed, but no consensus has been reached. To shed light on this topic, we performed amino acid and codon-based sequence analyses to determine phylogenetic relationships and molecular evolution. We found that most Class I RNA MTases are evolutionarily related to protein and cofactor/vitamin biosynthesis methyltransferases. Additionally, we found that at least nine lineages explain the diversity of RNA MTases. We evidenced that RNA methyltransferases have high content of polar and positively charged amino acid, which coincides with the electrochemistry of their substrates. Conclusions After studying almost 12,000 bacterial genomes and 2,000 patho-pangenomes, we revealed that molecular evolution of Class I methyltransferases matches the different rates of synonymous and non-synonymous substitutions along the coding region. Consequently, evolution on Class I methyltransferases selects against amino acid changes affecting the structure conformation.
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Affiliation(s)
| | | | | | | | - Alfonso Benítez-Páez
- Bioinformatics Analysis Group - GABi, Centro de Investigación y Desarrollo en Biotecnología - CIDBIO, 111221 Bogotá, D,C, Colombia.
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25
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Hori H. Methylated nucleosides in tRNA and tRNA methyltransferases. Front Genet 2014; 5:144. [PMID: 24904644 PMCID: PMC4033218 DOI: 10.3389/fgene.2014.00144] [Citation(s) in RCA: 141] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 05/04/2014] [Indexed: 12/26/2022] Open
Abstract
To date, more than 90 modified nucleosides have been found in tRNA and the biosynthetic pathways of the majority of tRNA modifications include a methylation step(s). Recent studies of the biosynthetic pathways have demonstrated that the availability of methyl group donors for the methylation in tRNA is important for correct and efficient protein synthesis. In this review, I focus on the methylated nucleosides and tRNA methyltransferases. The primary functions of tRNA methylations are linked to the different steps of protein synthesis, such as the stabilization of tRNA structure, reinforcement of the codon-anticodon interaction, regulation of wobble base pairing, and prevention of frameshift errors. However, beyond these basic functions, recent studies have demonstrated that tRNA methylations are also involved in the RNA quality control system and regulation of tRNA localization in the cell. In a thermophilic eubacterium, tRNA modifications and the modification enzymes form a network that responses to temperature changes. Furthermore, several modifications are involved in genetic diseases, infections, and the immune response. Moreover, structural, biochemical, and bioinformatics studies of tRNA methyltransferases have been clarifying the details of tRNA methyltransferases and have enabled these enzymes to be classified. In the final section, the evolution of modification enzymes is discussed.
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Affiliation(s)
- Hiroyuki Hori
- Department of Materials Science and Biotechnology, Applied Chemistry, Graduate School of Science and Engineering, Ehime University Matsuyama, Japan
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Björk GR, Hagervall TG. Transfer RNA Modification: Presence, Synthesis, and Function. EcoSal Plus 2014; 6. [PMID: 26442937 DOI: 10.1128/ecosalplus.esp-0007-2013] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Indexed: 06/05/2023]
Abstract
Transfer RNA (tRNA) from all organisms on this planet contains modified nucleosides, which are derivatives of the four major nucleosides. tRNA from Escherichia coli/Salmonella enterica serovar Typhimurium contains 33 different modified nucleosides, which are all, except one (Queuosine [Q]), synthesized on an oligonucleotide precursor, which by specific enzymes later matures into tRNA. The structural genes for these enzymes are found in mono- and polycistronic operons, the latter of which have a complex transcription and translation pattern. The synthesis of the tRNA-modifying enzymes is not regulated similarly, and it is not coordinated to that of their substrate, the tRNA. The synthesis of some of them (e.g., several methylated derivatives) is catalyzed by one enzyme, which is position and base specific, whereas synthesis of some has a very complex biosynthetic pathway involving several enzymes (e.g., 2-thiouridines, N 6-cyclicthreonyladenosine [ct6A], and Q). Several of the modified nucleosides are essential for viability (e.g., lysidin, ct6A, 1-methylguanosine), whereas the deficiency of others induces severe growth defects. However, some have no or only a small effect on growth at laboratory conditions. Modified nucleosides that are present in the anticodon loop or stem have a fundamental influence on the efficiency of charging the tRNA, reading cognate codons, and preventing missense and frameshift errors. Those that are present in the body of the tRNA primarily have a stabilizing effect on the tRNA. Thus, the ubiquitous presence of these modified nucleosides plays a pivotal role in the function of the tRNA by their influence on the stability and activity of the tRNA.
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Affiliation(s)
- Glenn R Björk
- Department of Molecular Biology, Umeå University, S-90187 Umeå, Sweden
| | - Tord G Hagervall
- Department of Molecular Biology, Umeå University, S-90187 Umeå, Sweden
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Hill PJ, Abibi A, Albert R, Andrews B, Gagnon MM, Gao N, Grebe T, Hajec LI, Huang J, Livchak S, Lahiri SD, McKinney DC, Thresher J, Wang H, Olivier N, Buurman ET. Selective Inhibitors of Bacterial t-RNA-(N1G37) Methyltransferase (TrmD) That Demonstrate Novel Ordering of the Lid Domain. J Med Chem 2013; 56:7278-88. [DOI: 10.1021/jm400718n] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Pamela J. Hill
- Departments of Chemistry, ‡Biosciences and §Discovery Sciences, Infection Innovative Medicines Unit, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Ayome Abibi
- Departments of Chemistry, ‡Biosciences and §Discovery Sciences, Infection Innovative Medicines Unit, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Robert Albert
- Departments of Chemistry, ‡Biosciences and §Discovery Sciences, Infection Innovative Medicines Unit, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Beth Andrews
- Departments of Chemistry, ‡Biosciences and §Discovery Sciences, Infection Innovative Medicines Unit, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Moriah M. Gagnon
- Departments of Chemistry, ‡Biosciences and §Discovery Sciences, Infection Innovative Medicines Unit, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Ning Gao
- Departments of Chemistry, ‡Biosciences and §Discovery Sciences, Infection Innovative Medicines Unit, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Tyler Grebe
- Departments of Chemistry, ‡Biosciences and §Discovery Sciences, Infection Innovative Medicines Unit, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Laurel I. Hajec
- Departments of Chemistry, ‡Biosciences and §Discovery Sciences, Infection Innovative Medicines Unit, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Jian Huang
- Departments of Chemistry, ‡Biosciences and §Discovery Sciences, Infection Innovative Medicines Unit, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Stephania Livchak
- Departments of Chemistry, ‡Biosciences and §Discovery Sciences, Infection Innovative Medicines Unit, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Sushmita D. Lahiri
- Departments of Chemistry, ‡Biosciences and §Discovery Sciences, Infection Innovative Medicines Unit, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - David C. McKinney
- Departments of Chemistry, ‡Biosciences and §Discovery Sciences, Infection Innovative Medicines Unit, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Jason Thresher
- Departments of Chemistry, ‡Biosciences and §Discovery Sciences, Infection Innovative Medicines Unit, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Hongming Wang
- Departments of Chemistry, ‡Biosciences and §Discovery Sciences, Infection Innovative Medicines Unit, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Nelson Olivier
- Departments of Chemistry, ‡Biosciences and §Discovery Sciences, Infection Innovative Medicines Unit, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Ed T. Buurman
- Departments of Chemistry, ‡Biosciences and §Discovery Sciences, Infection Innovative Medicines Unit, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
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Masuda I, Sakaguchi R, Liu C, Gamper H, Hou YM. The temperature sensitivity of a mutation in the essential tRNA modification enzyme tRNA methyltransferase D (TrmD). J Biol Chem 2013; 288:28987-96. [PMID: 23986443 DOI: 10.1074/jbc.m113.485797] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Conditional temperature-sensitive (ts) mutations are important reagents to study essential genes. Although it is commonly assumed that the ts phenotype of a specific mutation arises from thermal denaturation of the mutant enzyme, the possibility also exists that the mutation decreases the enzyme activity to a certain level at the permissive temperature and aggravates the negative effect further upon temperature upshifts. Resolving these possibilities is important for exploiting the ts mutation for studying the essential gene. The trmD gene is essential for growth in bacteria, encoding the enzyme for converting G37 to m(1)G37 on the 3' side of the tRNA anticodon. This conversion involves methyl transfer from S-adenosyl methionine and is critical to minimize tRNA frameshift errors on the ribosome. Using the ts-S88L mutation of Escherichia coli trmD as an example, we show that although the mutation confers thermal lability to the enzyme, the effect is relatively minor. In contrast, the mutation decreases the catalytic efficiency of the enzyme to 1% at the permissive temperature, and at the nonpermissive temperature, it renders further deterioration of activity to 0.1%. These changes are accompanied by losses of both the quantity and quality of tRNA methylation, leading to the potential of cellular pleiotropic effects. This work illustrates the principle that the ts phenotype of an essential gene mutation can be closely linked to the catalytic defect of the gene product and that such a mutation can provide a useful tool to study the mechanism of catalytic inactivation.
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Affiliation(s)
- Isao Masuda
- From the Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107
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29
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Liu RJ, Zhou M, Fang ZP, Wang M, Zhou XL, Wang ED. The tRNA recognition mechanism of the minimalist SPOUT methyltransferase, TrmL. Nucleic Acids Res 2013; 41:7828-42. [PMID: 23804755 PMCID: PMC3763551 DOI: 10.1093/nar/gkt568] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Unlike other transfer RNAs (tRNA)-modifying enzymes from the SPOUT methyltransferase superfamily, the tRNA (Um34/Cm34) methyltransferase TrmL lacks the usual extension domain for tRNA binding and consists only of a SPOUT domain. Both the catalytic and tRNA recognition mechanisms of this enzyme remain elusive. By using tRNAs purified from an Escherichia coli strain with the TrmL gene deleted, we found that TrmL can independently catalyze the methyl transfer from S-adenosyl-L-methionine to and isoacceptors without the involvement of other tRNA-binding proteins. We have solved the crystal structures of TrmL in apo form and in complex with S-adenosyl-homocysteine and identified the cofactor binding site and a possible active site. Methyltransferase activity and tRNA-binding affinity of TrmL mutants were measured to identify residues important for tRNA binding of TrmL. Our results suggest that TrmL functions as a homodimer by using the conserved C-terminal half of the SPOUT domain for catalysis, whereas residues from the less-conserved N-terminal half of the other subunit participate in tRNA recognition.
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Affiliation(s)
- Ru-Juan Liu
- Center for RNA research, State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, The Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
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30
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Abstract
Transfer RNA (tRNA) molecules play the key role in adapting the genetic code sequences with amino acids. The execution of this key role is highly dependent on the presence of modified nucleotides in tRNA, each of which performs a distinct function. To better understand how individual modifications modulate tRNA function, a method to isolate and purify a site-specifically modified tRNA is essential. This chapter describes an enzymatic method to synthesize a site-specifically modified tRNA, followed by purification of this tRNA away from unmodified tRNA using a selective oligonucleotide-based hybridization approach. This method is broadly applicable to site-specific tRNA modifications that interfere with nucleic-acid base-pairing principles.
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Affiliation(s)
- Ya-Ming Hou
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, BLSB, Philadelphia, PA, USA.
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31
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Sakaguchi R, Giessing A, Dai Q, Lahoud G, Liutkeviciute Z, Klimasauskas S, Piccirilli J, Kirpekar F, Hou YM. Recognition of guanosine by dissimilar tRNA methyltransferases. RNA (NEW YORK, N.Y.) 2012; 18:1687-1701. [PMID: 22847817 PMCID: PMC3425783 DOI: 10.1261/rna.032029.111] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Accepted: 06/16/2012] [Indexed: 06/01/2023]
Abstract
Guanosines are important for biological activities through their specific functional groups that are recognized for RNA or protein interactions. One example is recognition of N(1) of G37 in tRNA by S-adenosyl-methionine (AdoMet)-dependent tRNA methyltransferases to synthesize m(1)G37-tRNA, which is essential for translational fidelity in all biological domains. Synthesis of m(1)G37-tRNA is catalyzed by TrmD in bacteria and by Trm5 in eukarya and archaea, using unrelated and dissimilar structural folds. This raises the question of how dissimilar proteins recognize the same guanosine. Here we probe the mechanism of discrimination among functional groups of guanosine by TrmD and Trm5. Guanosine analogs were systematically introduced into tRNA through a combination of chemical and enzymatic synthesis. Single turnover kinetic assays and thermodynamic analysis of the effect of each analog on m(1)G37-tRNA synthesis reveal that TrmD and Trm5 discriminate functional groups differently. While both recognize N(1) and O(6) of G37, TrmD places a much stronger emphasis on these functional groups than Trm5. While the exocyclic 2-amino group of G37 is important for TrmD, it is dispensable for Trm5. In addition, while an adjacent G36 is obligatory for TrmD, it is nonessential for Trm5. These results depict a more rigid requirement of guanosine functional groups for TrmD than for Trm5. However, the sensitivity of both enzymes to analog substitutions, together with an experimental revelation of their low cellular concentrations relative to tRNA substrates, suggests a model in which these enzymes rapidly screen tRNA by direct recognition of G37 in order to monitor the global state of m(1)G37-tRNA.
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Affiliation(s)
- Reiko Sakaguchi
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, USA
| | - Anders Giessing
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
| | - Qing Dai
- Departments of Biochemistry & Molecular Biology, and Chemistry, Gordon Center for Integrative Science, University of Chicago, Chicago, Illinois 60637, USA
| | - Georges Lahoud
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, USA
| | - Zita Liutkeviciute
- Department of Biological DNA Modification, Institute of Biotechnology, Vilnius University, LT-02241 Vilnius, Lithuania
| | - Saulius Klimasauskas
- Department of Biological DNA Modification, Institute of Biotechnology, Vilnius University, LT-02241 Vilnius, Lithuania
| | - Joseph Piccirilli
- Departments of Biochemistry & Molecular Biology, and Chemistry, Gordon Center for Integrative Science, University of Chicago, Chicago, Illinois 60637, USA
| | - Finn Kirpekar
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
| | - Ya-Ming Hou
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, USA
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32
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Xu Z, Ma L, Chen H, Zhou R. In silico identification of potential drug targets in swine pathogen Haemophilus parasuis. Genes Genomics 2012. [DOI: 10.1007/s13258-011-0194-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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33
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Lahoud G, Goto-Ito S, Yoshida KI, Ito T, Yokoyama S, Hou YM. Differentiating analogous tRNA methyltransferases by fragments of the methyl donor. RNA (NEW YORK, N.Y.) 2011; 17:1236-1246. [PMID: 21602303 PMCID: PMC3138561 DOI: 10.1261/rna.2706011] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2011] [Accepted: 04/15/2011] [Indexed: 05/30/2023]
Abstract
Bacterial TrmD and eukaryotic-archaeal Trm5 form a pair of analogous tRNA methyltransferase that catalyze methyl transfer from S-adenosyl methionine (AdoMet) to N(1) of G37, using catalytic motifs that share no sequence or structural homology. Here we show that natural and synthetic analogs of AdoMet are unable to distinguish TrmD from Trm5. Instead, fragments of AdoMet, adenosine and methionine, are selectively inhibitory of TrmD rather than Trm5. Detailed structural information of the two enzymes in complex with adenosine reveals how Trm5 escapes targeting by adopting an altered structure, whereas TrmD is trapped by targeting due to its rigid structure that stably accommodates the fragment. Free energy analysis exposes energetic disparities between the two enzymes in how they approach the binding of AdoMet versus fragments and provides insights into the design of inhibitors selective for TrmD.
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Affiliation(s)
- Georges Lahoud
- Thomas Jefferson University, Department of Biochemistry and Molecular Biology, Philadelphia, Pennsylvania 19107, USA
| | - Sakurako Goto-Ito
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
- Department of Biophysics and Biochemistry, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Ken-ichi Yoshida
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
- Department of Biophysics and Biochemistry, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takuhiro Ito
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Shigeyuki Yokoyama
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
- Department of Biophysics and Biochemistry, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Ya-Ming Hou
- Thomas Jefferson University, Department of Biochemistry and Molecular Biology, Philadelphia, Pennsylvania 19107, USA
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34
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Christian T, Lahoud G, Liu C, Hou YM. Control of catalytic cycle by a pair of analogous tRNA modification enzymes. J Mol Biol 2010; 400:204-17. [PMID: 20452364 DOI: 10.1016/j.jmb.2010.05.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2009] [Revised: 04/13/2010] [Accepted: 05/03/2010] [Indexed: 10/19/2022]
Abstract
Enzymes that use distinct active site structures to perform identical reactions are known as analogous enzymes. The isolation of analogous enzymes suggests the existence of multiple enzyme structural pathways that can catalyze the same chemical reaction. A fundamental question concerning analogous enzymes is whether their distinct active-site structures would confer the same or different kinetic constraints to the chemical reaction, particularly with respect to the control of enzyme turnover. Here, we address this question with the analogous enzymes of bacterial TrmD and its eukaryotic and archaeal counterpart Trm5. TrmD and Trm5 catalyze methyl transfer to synthesize the m1G37 base at the 3' position adjacent to the tRNA anticodon, using S-adenosyl methionine (AdoMet) as the methyl donor. TrmD features a trefoil-knot active-site structure whereas Trm5 features the Rossmann fold. Pre-steady-state analysis revealed that product synthesis by TrmD proceeds linearly with time, whereas that by Trm5 exhibits a rapid burst followed by a slower and linear increase with time. The burst kinetics of Trm5 suggests that product release is the rate-limiting step of the catalytic cycle, consistent with the observation of higher enzyme affinity to the products of tRNA and AdoMet. In contrast, the lack of burst kinetics of TrmD suggests that its turnover is controlled by a step required for product synthesis. Although TrmD exists as a homodimer, it showed half-of-the-sites reactivity for tRNA binding and product synthesis. The kinetic differences between TrmD and Trm5 are parallel with those between the two classes of aminoacyl-tRNA synthetases, which use distinct active site structures to catalyze tRNA aminoacylation. This parallel suggests that the findings have a fundamental importance for enzymes that catalyze both methyl and aminoacyl transfer to tRNA in the decoding process.
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Affiliation(s)
- Thomas Christian
- Thomas Jefferson University, Department of Biochemistry and Molecular Biology, 233 South 10th Street, BLSB 220, Philadelphia, PA 19107, USA
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35
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Hou YM, Perona JJ. Stereochemical mechanisms of tRNA methyltransferases. FEBS Lett 2009; 584:278-86. [PMID: 19944101 DOI: 10.1016/j.febslet.2009.11.075] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2009] [Revised: 11/18/2009] [Accepted: 11/19/2009] [Indexed: 12/31/2022]
Abstract
Methylation of tRNA on the four canonical bases adds structural complexity to the molecule, and improves decoding specificity and efficiency. While many tRNA methylases are known, detailed insight into the catalytic mechanism is only available in a few cases. Of interest among all tRNA methylases is the structural basis for nucleotide selection, by which the specificity is limited to a single site, or broadened to multiple sites. General themes in catalysis include the basis for rate acceleration at highly diverse nucleophilic centers for methyl transfer, using S-adenosylmethionine as a cofactor. Studies of tRNA methylases have also yielded insights into molecular evolution, particularly in the case of enzymes that recognize distinct structures to perform identical reactions at the same target nucleotide.
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Affiliation(s)
- Ya-Ming Hou
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 233 South 10th St., Philadelphia, PA 19107, USA.
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36
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Goto-Ito S, Ito T, Ishii R, Muto Y, Bessho Y, Yokoyama S. Crystal structure of archaeal tRNA(m(1)G37)methyltransferase aTrm5. Proteins 2009; 72:1274-89. [PMID: 18384044 DOI: 10.1002/prot.22019] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Methylation of the N1 atom of guanosine at position 37 in tRNA, the position 3'-adjacent to the anticodon, generates the modified nucleoside m(1)G37. In archaea and eukaryotes, m(1)G37 synthesis is catalyzed by tRNA(m(1)G37)methyltransferase (archaeal or eukaryotic Trm5, a/eTrm5). Here we report the crystal structure of archaeal Trm5 (aTrm5) from Methanocaldococcus jannaschii (formerly known as Methanococcus jannaschii) in complex with the methyl donor analogue at 2.2 A resolution. The crystal structure revealed that the entire protein is composed of three structural domains, D1, D2, and D3. In the a/eTrm5 primary structures, D2 and D3 are highly conserved, while D1 is not conserved. The D3 structure is the Rossmann fold, which is the hallmark of the canonical class-I methyltransferases. The a/eTrm5-defining domain, D2, exhibits structural similarity to some class-I methyltransferases. In contrast, a DALI search with the D1 structure yielded no structural homologues. In the crystal structure, D3 contacts both D1 and D2. The residues involved in the D1:D3 interactions are not conserved, while those participating in the D2:D3 interactions are well conserved. D1 and D2 do not contact each other, and the linker between them is disordered. aTrm5 fragments corresponding to the D1 and D2-D3 regions were prepared in a soluble form. The NMR analysis of the D1 fragment revealed that D1 is well folded by itself, and it did not interact with either the D2-D3 fragment or the tRNA. The NMR analysis of the D2-D3 fragment revealed that it is well folded, independently of D1, and that it interacts with tRNA. Furthermore, the D2-D3 fragment was as active as the full-length enzyme for tRNA methylation. The positive charges on the surface of D2-D3 may be involved in tRNA binding. Therefore, these findings suggest that the interaction between D1 and D3 is not persistent, and that the D2-D3 region plays the major role in tRNA methylation.
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Affiliation(s)
- Sakurako Goto-Ito
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
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37
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Baker MR, Zarubica T, Wright HT, Rife JP. Scintillation proximity assay for measurement of RNA methylation. Nucleic Acids Res 2009; 37:e32. [PMID: 19181706 PMCID: PMC2651799 DOI: 10.1093/nar/gkn1038] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Methylation of RNA by methyltransferases is a phylogenetically ubiquitous post-transcriptional modification that occurs most extensively in transfer RNA (tRNA) and ribosomal RNA (rRNA). Biochemical characterization of RNA methyltransferase enzymes and their methylated product RNA or RNA–protein complexes is usually done by measuring the incorporation of radiolabeled methyl groups into the product over time. This has traditionally required the separation of radiolabeled product from radiolabeled methyl donor through a filter binding assay. We have adapted and optimized a scintillation proximity assay (SPA) to replace the more costly, wasteful and cumbersome filter binding assay and demonstrate its utility in studies of three distinct methyltransferases, RmtA, KsgA and ErmC’. In vitro, RmtA and KsgA methylate different bases in 16S rRNA in 30S ribosomal particles, while ErmC’ most efficiently methylates protein-depleted or protein-free 23S rRNA. This assay does not utilize engineered affinity tags that are often required in SPA, and is capable of detecting either radiolabeled RNA or RNA–protein complex. We show that this method is suitable for quantitating extent of RNA methylation or active RNA methyltransferase, and for testing RNA-methyltransferase inhibitors. This assay can be carried out with techniques routinely used in a typical biochemistry laboratory or could be easily adapted for a high throughput screening format.
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Affiliation(s)
- Matthew R Baker
- Department of Medicinal Chemistry, Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, VA 23298-0133, USA
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38
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Toyooka T, Awai T, Kanai T, Imanaka T, Hori H. Stabilization of tRNA (mG37) methyltransferase [TrmD] from Aquifex aeolicus by an intersubunit disulfide bond formation. Genes Cells 2008; 13:807-16. [PMID: 18651851 DOI: 10.1111/j.1365-2443.2008.01207.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Recombinant Aquifex aeolicus TrmD protein has a Cys20-Cys20 disulfide bond between its two subunits. This was demonstrated by SDS-polyacrylamide gel analysis of wild-type enzyme and C20S mutant protein (in which the Cys20 residue is substituted by serine), in the absence or presence of various concentrations of dithiothreitol. Analytical gel-filtration chromatography revealed that the C20S mutant protein forms a dimer structure even though it is missing the disulfide bond. Western blotting analysis suggests that the Cys20-Cys20 disulfide bond is formed in native TrmD protein in living A. aeolicus cells. Incubation at 85 degrees C for 20 min caused the precipitation of more than half of the C20S protein, while more than 70% of the wild-type enzyme was soluble at that temperature. This assay clearly demonstrates that the disulfide bond enhances the protein stability at 85 degrees C. A kinetic assay showed that the methyl-transfer activity of the C20S mutant protein was slightly less than that of the wild-type enzyme at 70 degrees C. Comparison of the CD-spectra of wild-type and C20S proteins reveals that some of the alpha-helices in the C20S mutant protein are less tightly packed than those of the wild-type enzyme at 70 degrees C.
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Affiliation(s)
- Takashi Toyooka
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Matsuyama, Ehime, Japan
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Christian T, Hou YM. Distinct determinants of tRNA recognition by the TrmD and Trm5 methyl transferases. J Mol Biol 2007; 373:623-32. [PMID: 17868690 PMCID: PMC2064070 DOI: 10.1016/j.jmb.2007.08.010] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2007] [Accepted: 08/03/2007] [Indexed: 11/24/2022]
Abstract
TrmD and Trm5 are, respectively, the bacterial and eukarya/archaea methyl transferases that catalyze transfer of the methyl group from S-adenosyl methionine (AdoMet) to the N1 position of G37 in tRNA to synthesize m1G37-tRNA. The m1G37 modification prevents tRNA frameshifts on the ribosome by assuring correct codon-anticodon pairings, and thus is essential for the fidelity of protein synthesis. Although TrmD and Trm5 are derived from unrelated AdoMet families and recognize the cofactor using distinct motifs, the question of whether they select G37 on tRNA by the same, or different, mechanism has not been answered. Here we address this question by kinetic analysis of tRNA truncation mutants that lack domains typically present in the canonical L shaped structure, and by evaluation of the site of modification on tRNA variants with an expanded or contracted anticodon loop. With both experimental approaches, we show that TrmD and Trm5 exhibit separate and distinct mode of tRNA recognition, suggesting that they evolved by independent and non-overlapping pathways from their unrelated AdoMet families. Our results also shed new light onto the significance of the m1G37 modification in the controversial quadruplet-pairing model of tRNA frameshift suppressors.
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Affiliation(s)
| | - Ya-Ming Hou
- *Corresponding author. Telephone: 215-503-4480; Fax: 215-503-4954;
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Christian T, Evilia C, Hou YM. Catalysis by the second class of tRNA(m1G37) methyl transferase requires a conserved proline. Biochemistry 2006; 45:7463-73. [PMID: 16768442 PMCID: PMC2517134 DOI: 10.1021/bi0602314] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The enzyme tRNA(m1G37) methyl transferase catalyzes the transfer of a methyl group from S-adenosyl methionine (AdoMet) to the N1 position of G37, which is 3' to the anticodon sequence and whose modification is important for maintaining the reading frame fidelity. While the enzyme in bacteria is highly conserved and is encoded by the trmD gene, recent studies show that the counterpart of this enzyme in archaea and eukarya, encoded by the trm5 gene, is unrelated to trmD both in sequence and in structure. To further test this prediction, we seek to identify residues in the second class of tRNA(m1G37) methyl transferase that are required for catalysis. Such residues should provide mechanistic insights into the distinct structural origins of the two classes. Using the Trm5 enzyme of the archaeon Methanocaldococcus jannaschii (previously MJ0883) as an example, we have created mutants to test many conserved residues for their catalytic potential and substrate-binding capabilities with respect to both AdoMet and tRNA. We identified that the proline at position 267 (P267) is a critical residue for catalysis, because substitution of this residue severely decreases the kcat of the methylation reaction in steady-state kinetic analysis, and the k(chem) in single turnover kinetic analysis. However, substitution of P267 has milder effect on the Km and little effect on the Kd of either substrate. Because P267 has no functional side chain that can directly participate in the chemistry of methyl transfer, we suggest that its role in catalysis is to stabilize conformations of enzyme and substrates for proper alignment of reactive groups at the enzyme active site. Sequence analysis shows that P267 is embedded in a peptide motif that is conserved among the Trm5 family, but absent from the TrmD family, supporting the notion that the two families are descendants of unrelated protein structures.
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Affiliation(s)
- Thomas Christian
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 233 South 10th Street, Philadelphia, Pennsylvania 19107, USA
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Watts JM, Gabruzsk J, Holmes WM. Ligand-Mediated Anticodon Conformational Changes Occur during tRNA Methylation by a TrmD Methyltransferase. Biochemistry 2005; 44:6629-39. [PMID: 15850396 DOI: 10.1021/bi0481038] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Orthologs of TrmD, G37 tRNA methyltransferases, have been analyzed with regard to post-tRNA binding events required to move the residue G37 in proximity to bound AdoMet for catalysis. This was approached initially by probing tRNA with T2 nuclease or Pb acetate in the presence, then absence, of Escherichia coli TrmD protein. Cleavage patterns clearly show that portions of the anticodon loop phosphodiester backbone are protected from cleavage only in the presence of sinefungin, a potent AdoMet analogue. This demonstrates that there must be considerable movement of the loop region and/or protein as the AdoMet site is occupied. Florescence energy transfer experiments were employed to better assess the movement of the G37 and G36 base residues in response to occupancy of the AdoMet site. When the Streptococcus pneumoniae TrmD protein was bound to synthetic tRNA(1)(Leu) substituted with 2-aminopurine at positions 36 and 37, fluorescence energy transfer analysis showed that a decrease in 2-aminopurine fluorescence occurs only when AdoMet is present. Taken together, these results suggest that the base to be methylated by the TrmD protein is mobilized into the active center after tRNA binding only when the AdoMet site is occupied.
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Affiliation(s)
- Joseph M Watts
- Department of Biochemistry, Medical College of Virginia campus of Virginia Commonwealth University, Institute for Structural Biology and Drug Discovery, 800 East Leigh Street, Suite 212, Richmond, Virginia 23219, USA
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