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Strassler SE, Bowles IE, Krishnamohan A, Kim H, Edgington CB, Kuiper EG, Hancock CJ, Comstock LR, Jackman JE, Conn GL. tRNA m 1G9 modification depends on substrate-specific RNA conformational changes induced by the methyltransferase Trm10. J Biol Chem 2023; 299:105443. [PMID: 37949221 PMCID: PMC10704376 DOI: 10.1016/j.jbc.2023.105443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 10/19/2023] [Accepted: 11/06/2023] [Indexed: 11/12/2023] Open
Abstract
The methyltransferase Trm10 modifies a subset of tRNAs on the base N1 position of the ninth nucleotide in the tRNA core. Trm10 is conserved throughout Eukarya and Archaea, and mutations in the human gene (TRMT10A) have been linked to neurological disorders such as microcephaly and intellectual disability, as well as defects in glucose metabolism. Of the 26 tRNAs in yeast with guanosine at position 9, only 13 are substrates for Trm10. However, no common sequence or other posttranscriptional modifications have been identified among these substrates, suggesting the presence of some other tRNA feature(s) that allow Trm10 to distinguish substrate from nonsubstrate tRNAs. Here, we show that substrate recognition by Saccharomyces cerevisiae Trm10 is dependent on both intrinsic tRNA flexibility and the ability of the enzyme to induce specific tRNA conformational changes upon binding. Using the sensitive RNA structure-probing method SHAPE, conformational changes upon binding to Trm10 in tRNA substrates, but not nonsubstrates, were identified and mapped onto a model of Trm10-bound tRNA. These changes may play an important role in substrate recognition by allowing Trm10 to gain access to the target nucleotide. Our results highlight a novel mechanism of substrate recognition by a conserved tRNA modifying enzyme. Further, these studies reveal a strategy for substrate recognition that may be broadly employed by tRNA-modifying enzymes which must distinguish between structurally similar tRNA species.
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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 and Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA; Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio, USA
| | - Aiswarya Krishnamohan
- Department of Chemistry and Biochemistry and Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA; Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio, USA
| | - Hyejeong Kim
- Department of Chemistry and Biochemistry and Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA
| | - Catherine B Edgington
- Department of Chemistry and Biochemistry and Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA
| | - Emily G Kuiper
- 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
| | - Clio J Hancock
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Lindsay R Comstock
- Department of Chemistry, Wake Forest University, Winston-Salem, North Carolina, USA
| | - Jane E Jackman
- Department of Chemistry and Biochemistry and Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA; Ohio State Biochemistry Program, The Ohio State University, 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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2
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Strassler SE, Bowles IE, Krishnamohan A, Kim H, Edgington CB, Kuiper EG, Hancock CJ, Comstock LR, Jackman JE, Conn GL. tRNA m 1G9 modification depends on substrate-specific RNA conformational changes induced by the methyltransferase Trm10. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.01.526536. [PMID: 36778341 PMCID: PMC9915607 DOI: 10.1101/2023.02.01.526536] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The methyltransferase Trm10 modifies a subset of tRNAs on the base N1 position of the 9th nucleotide in the tRNA core. Trm10 is conserved throughout Eukarya and Archaea, and mutations in the human gene (TRMT10A) have been linked to neurological disorders such as microcephaly and intellectual disability, as well as defects in glucose metabolism. Of the 26 tRNAs in yeast with guanosine at position 9, only 14 are substrates for Trm10. However, no common sequence or other posttranscriptional modifications have been identified among these substrates, suggesting the presence of some other tRNA feature(s) which allow Trm10 to distinguish substrate from nonsubstrate tRNAs. Here, we show that substrate recognition by Saccharomyces cerevisiae Trm10 is dependent on both intrinsic tRNA flexibility and the ability of the enzyme to induce specific tRNA conformational changes upon binding. Using the sensitive RNA structure-probing method SHAPE, conformational changes upon binding to Trm10 in tRNA substrates, but not nonsubstrates, were identified and mapped onto a model of Trm10-bound tRNA. These changes may play an important role in substrate recognition by allowing Trm10 to gain access to the target nucleotide. Our results highlight a novel mechanism of substrate recognition by a conserved tRNA modifying enzyme. Further, these studies reveal a strategy for substrate recognition that may be broadly employed by tRNA-modifying enzymes which must distinguish between structurally similar tRNA species.
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Affiliation(s)
- Sarah E. Strassler
- Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road NE, Atlanta GA, 30322, USA
- Graduate Program in Biochemistry, Cell and Developmental Biology, Graduate Division of Biological and Biomedical Sciences, Emory University
| | - Isobel E. Bowles
- Department of Chemistry and Biochemistry, Center for RNA Biology and Ohio State Biochemistry Program, 484 W. 12 Avenue, Columbus, OH, 43210, USA
- Ohio State Biochemistry Program, The Ohio State University, 484 W. 12 Avenue, Columbus, OH, 43210, USA
| | - Aiswarya Krishnamohan
- Department of Chemistry and Biochemistry, Center for RNA Biology and Ohio State Biochemistry Program, 484 W. 12 Avenue, Columbus, OH, 43210, USA
- Ohio State Biochemistry Program, The Ohio State University, 484 W. 12 Avenue, Columbus, OH, 43210, USA
| | - Hyejeong Kim
- Department of Chemistry and Biochemistry, Center for RNA Biology and Ohio State Biochemistry Program, 484 W. 12 Avenue, Columbus, OH, 43210, USA
| | - Catherine B. Edgington
- Department of Chemistry and Biochemistry, Center for RNA Biology and Ohio State Biochemistry Program, 484 W. 12 Avenue, Columbus, OH, 43210, USA
| | - Emily G. Kuiper
- Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road NE, Atlanta GA, 30322, USA
- Graduate Program in Biochemistry, Cell and Developmental Biology, Graduate Division of Biological and Biomedical Sciences, Emory University
| | - Clio J. Hancock
- Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road NE, Atlanta GA, 30322, USA
| | - Lindsay R. Comstock
- Department of Chemistry, Wake Forest University, 1834 Wake Forest Road, Winston-Salem, NC 27106, USA
| | - Jane E. Jackman
- Department of Chemistry and Biochemistry, Center for RNA Biology and Ohio State Biochemistry Program, 484 W. 12 Avenue, Columbus, OH, 43210, USA
- Ohio State Biochemistry Program, The Ohio State University, 484 W. 12 Avenue, Columbus, OH, 43210, USA
| | - Graeme L. Conn
- Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road NE, Atlanta GA, 30322, USA
- Graduate Program in Biochemistry, Cell and Developmental Biology, Graduate Division of Biological and Biomedical Sciences, Emory University
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3
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Jeremia L, Deprez BE, Dey D, Conn GL, Wuest WM. Ribosome-targeting antibiotics and resistance via ribosomal RNA methylation. RSC Med Chem 2023; 14:624-643. [PMID: 37122541 PMCID: PMC10131624 DOI: 10.1039/d2md00459c] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 02/17/2023] [Indexed: 03/05/2023] Open
Abstract
The rise of multidrug-resistant bacterial infections is a cause of global concern. There is an urgent need to both revitalize antibacterial agents that are ineffective due to resistance while concurrently developing new antibiotics with novel targets and mechanisms of action. Pathogen associated resistance-conferring ribosomal RNA (rRNA) methyltransferases are a growing threat that, as a group, collectively render a total of seven clinically-relevant ribosome-targeting antibiotic classes ineffective. Increasing frequency of identification and their growing prevalence relative to other resistance mechanisms suggests that these resistance determinants are rapidly spreading among human pathogens and could contribute significantly to the increased likelihood of a post-antibiotic era. Herein, with a view toward stimulating future studies to counter the effects of these rRNA methyltransferases, we summarize their prevalence, the fitness cost(s) to bacteria of their acquisition and expression, and current efforts toward targeting clinically relevant enzymes of this class.
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Affiliation(s)
- Learnmore Jeremia
- Department of Chemistry, Emory University 1515 Dickey Dr. Atlanta GA 30322 USA
| | - Benjamin E Deprez
- Department of Chemistry, Emory University 1515 Dickey Dr. Atlanta GA 30322 USA
| | - Debayan Dey
- Department of Biochemistry, Emory University School of Medicine 1510 Clifton Rd. Atlanta GA 30322 USA
| | - Graeme L Conn
- Department of Biochemistry, Emory University School of Medicine 1510 Clifton Rd. Atlanta GA 30322 USA
- Emory Antibiotic Resistance Center, Emory University School of Medicine 1510 Clifton Rd. Atlanta GA 30322 USA
| | - William M Wuest
- Department of Chemistry, Emory University 1515 Dickey Dr. Atlanta GA 30322 USA
- Emory Antibiotic Resistance Center, Emory University School of Medicine 1510 Clifton Rd. Atlanta GA 30322 USA
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4
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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] [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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5
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Bailly C. The bacterial thiopeptide thiostrepton. An update of its mode of action, pharmacological properties and applications. Eur J Pharmacol 2022; 914:174661. [PMID: 34863996 DOI: 10.1016/j.ejphar.2021.174661] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 11/29/2021] [Indexed: 12/20/2022]
Abstract
The bacterial thiopeptide thiostrepton (TS) is used as a veterinary medicine to treat bacterial infections. TS is a protein translation inhibitor, essentially active against Gram-positive bacteria and some Gram-negative bacteria. In procaryotes, TS abrogates binding of GTPase elongation factors to the 70S ribosome, by altering the structure of rRNA-L11 protein complexes. TS exerts also antimalarial effects by disrupting protein synthesis in the apicoplast genome of Plasmodium falciparum. Interestingly, the drug targets both the infectious pathogen (bacteria or parasite) and host cell, by inducing endoplasmic reticulum stress-mediated autophagy which contributes to enhance the host cell defense. In addition, TS has been characterized as a potent chemical inhibitor of the oncogenic transcription factor FoxM1, frequently overexpressed in cancers or other diseases. The capacity of TS to crosslink FoxM1, and a few other proteins such as peroxiredoxin 3 (PRX3) and the 19S proteasome, contributes to the anticancer effects of the thiopeptide. The anticancer activities of TS evidenced using diverse tumor cell lines, in vivo models and drug combinations are reviewed here, together with the implicated targets and mechanisms. The difficulty to formulate TS is a drag on the pharmaceutical development of the natural product. However, the design of hemisynthetic analogues and the use of micellar drug delivery systems should facilitate a broader utilization of the compound in human and veterinary medicines. This review shed light on the many pharmacological properties of TS, with the objective to promote its use as a pharmacological tool and medicinal product.
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Affiliation(s)
- Christian Bailly
- OncoWitan, Scientific Consulting Office, Lille, Wasquehal, 59290, France.
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6
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Sagar A, Xue B. Recent Advances in Machine Learning Based Prediction of RNA-protein Interactions. Protein Pept Lett 2019; 26:601-619. [PMID: 31215361 DOI: 10.2174/0929866526666190619103853] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 04/04/2019] [Accepted: 06/01/2019] [Indexed: 12/18/2022]
Abstract
The interactions between RNAs and proteins play critical roles in many biological processes. Therefore, characterizing these interactions becomes critical for mechanistic, biomedical, and clinical studies. Many experimental methods can be used to determine RNA-protein interactions in multiple aspects. However, due to the facts that RNA-protein interactions are tissuespecific and condition-specific, as well as these interactions are weak and frequently compete with each other, those experimental techniques can not be made full use of to discover the complete spectrum of RNA-protein interactions. To moderate these issues, continuous efforts have been devoted to developing high quality computational techniques to study the interactions between RNAs and proteins. Many important progresses have been achieved with the application of novel techniques and strategies, such as machine learning techniques. Especially, with the development and application of CLIP techniques, more and more experimental data on RNA-protein interaction under specific biological conditions are available. These CLIP data altogether provide a rich source for developing advanced machine learning predictors. In this review, recent progresses on computational predictors for RNA-protein interaction were summarized in the following aspects: dataset, prediction strategies, and input features. Possible future developments were also discussed at the end of the review.
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Affiliation(s)
- Amit Sagar
- Department of Cell Biology, Microbiology and Molecular Biology, School of Natural Sciences and Mathematics, College of Arts and Sciences, University of South Florida, Tampa, Florida 33620, United States
| | - Bin Xue
- Department of Cell Biology, Microbiology and Molecular Biology, School of Natural Sciences and Mathematics, College of Arts and Sciences, University of South Florida, Tampa, Florida 33620, United States
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7
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Bhandare VV, Ramaswamy A. The proteinopathy of D169G and K263E mutants at the RNA Recognition Motif (RRM) domain of tar DNA-binding protein (tdp43) causing neurological disorders: A computational study. J Biomol Struct Dyn 2017; 36:1075-1093. [DOI: 10.1080/07391102.2017.1310670] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
| | - Amutha Ramaswamy
- Centre for Bioinformatics, Pondicherry University, Pondicherry 605014, India
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8
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Mugweru J, Makafe G, Cao Y, Zhang Y, Wang B, Huang S, Njire M, Chhotaray C, Tan Y, Li X, Liu J, Tan S, Deng J, Zhang T. A Cassette Containing Thiostrepton, Gentamicin Resistance Genes, and dif sequences Is Effective in Construction of Recombinant Mycobacteria. Front Microbiol 2017; 8:468. [PMID: 28392781 PMCID: PMC5364183 DOI: 10.3389/fmicb.2017.00468] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 03/07/2017] [Indexed: 11/24/2022] Open
Abstract
The genetic manipulation of Mycobacterium tuberculosis genome is limited by the availability of selection markers. Spontaneous resistance mutation rate of M. tuberculosis to the widely used kanamycin is relatively high which often leads to some false positive transformants. Due to the few available markers, we have created a cassette containing thiostrepton resistance gene (tsr) for selection in M. tuberculosis and M. bovis BCG, and gentamicin resistance gene (aacC1) for Escherichia coli and M. smegmatis mc2155, flanked with dif sequences recognized by the Xer system of mycobacteria. This cassette adds to the limited available selection markers for mycobacteria.
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Affiliation(s)
- Julius Mugweru
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of SciencesGuangzhou, China
- University of Chinese Academy of SciencesBeijing, China
| | - Gaelle Makafe
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of SciencesGuangzhou, China
- University of Chinese Academy of SciencesBeijing, China
| | - Yuanyuan Cao
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of SciencesGuangzhou, China
| | - Yang Zhang
- Key Laboratory of Biotechnology of Antibiotics, Ministry of Health, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing, China
| | - Bangxing Wang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of SciencesGuangzhou, China
| | - Shaobo Huang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of SciencesGuangzhou, China
| | - Moses Njire
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of SciencesGuangzhou, China
- University of Chinese Academy of SciencesBeijing, China
| | - Chiranjibi Chhotaray
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of SciencesGuangzhou, China
- University of Chinese Academy of SciencesBeijing, China
| | - Yaoju Tan
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, Guangzhou Chest HospitalGuangzhou, China
| | - Xinjie Li
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, Guangzhou Chest HospitalGuangzhou, China
| | - Jianxiong Liu
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, Guangzhou Chest HospitalGuangzhou, China
| | - Shouyong Tan
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, Guangzhou Chest HospitalGuangzhou, China
| | - Jiaoyu Deng
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of SciencesWuhan, China
| | - Tianyu Zhang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of SciencesGuangzhou, China
- University of Chinese Academy of SciencesBeijing, China
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9
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Burkhart BJ, Schwalen CJ, Mann G, Naismith JH, Mitchell DA. YcaO-Dependent Posttranslational Amide Activation: Biosynthesis, Structure, and Function. Chem Rev 2017; 117:5389-5456. [PMID: 28256131 DOI: 10.1021/acs.chemrev.6b00623] [Citation(s) in RCA: 134] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
With advances in sequencing technology, uncharacterized proteins and domains of unknown function (DUFs) are rapidly accumulating in sequence databases and offer an opportunity to discover new protein chemistry and reaction mechanisms. The focus of this review, the formerly enigmatic YcaO superfamily (DUF181), has been found to catalyze a unique phosphorylation of a ribosomal peptide backbone amide upon attack by different nucleophiles. Established nucleophiles are the side chains of Cys, Ser, and Thr which gives rise to azoline/azole biosynthesis in ribosomally synthesized and posttranslationally modified peptide (RiPP) natural products. However, much remains unknown about the potential for YcaO proteins to collaborate with other nucleophiles. Recent work suggests potential in forming thioamides, macroamidines, and possibly additional post-translational modifications. This review covers all knowledge through mid-2016 regarding the biosynthetic gene clusters (BGCs), natural products, functions, mechanisms, and applications of YcaO proteins and outlines likely future research directions for this protein superfamily.
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Affiliation(s)
| | | | - Greg Mann
- Biomedical Science Research Complex, University of St Andrews , BSRC North Haugh, St Andrews KY16 9ST, United Kingdom
| | - James H Naismith
- Biomedical Science Research Complex, University of St Andrews , BSRC North Haugh, St Andrews KY16 9ST, United Kingdom.,State Key Laboratory of Biotherapy, Sichuan University , Sichuan, China
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10
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Myers CL, Kuiper EG, Grant PC, Hernandez J, Conn GL, Honek JF. Functional roles in S-adenosyl-L-methionine binding and catalysis for active site residues of the thiostrepton resistance methyltransferase. FEBS Lett 2015; 589:3263-70. [PMID: 26450779 DOI: 10.1016/j.febslet.2015.09.028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Revised: 09/28/2015] [Accepted: 09/28/2015] [Indexed: 11/17/2022]
Abstract
Resistance to the antibiotic thiostrepton, in producing Streptomycetes, is conferred by the S-adenosyl-L-methionine (SAM)-dependent SPOUT methyltransferase Tsr. For this and related enzymes, the roles of active site amino acids have been inadequately described. Herein, we have probed SAM interactions in the Tsr active site by investigating the catalytic activity and the thermodynamics of SAM binding by site-directed Tsr mutants. Two arginine residues were demonstrated to be critical for binding, one of which appears to participate in the catalytic reaction. Additionally, evidence consistent with the involvement of an asparagine in the structural organization of the SAM binding site is presented.
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Affiliation(s)
- Cullen L Myers
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Emily G Kuiper
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Pei C Grant
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Jennifer Hernandez
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Graeme L Conn
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - John F Honek
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada.
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11
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Yin S, Jiang H, Chen D, Murchie AIH. Substrate recognition and modification by the nosiheptide resistance methyltransferase. PLoS One 2015; 10:e0122972. [PMID: 25910005 PMCID: PMC4409310 DOI: 10.1371/journal.pone.0122972] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 02/11/2015] [Indexed: 11/29/2022] Open
Abstract
Background The proliferation of antibiotic resistant pathogens is an increasing threat to the general public. Resistance may be conferred by a number of mechanisms including covalent or mutational modification of the antibiotic binding site, covalent modification of the drug, or the over-expression of efflux pumps. The nosiheptide resistance methyltransferase (NHR) confers resistance to the thiazole antibiotic nosiheptide in the nosiheptide producer organism Streptomyces actuosus through 2ʹO-methylation of 23S rRNA at the nucleotide A1067. Although the crystal structures of NHR and the closely related thiostrepton-resistance methyltransferase (TSR) in complex with the cofactor S-Adenosyl-L-methionine (SAM) are available, the principles behind NHR substrate recognition and catalysis remain unclear. Methodology/Principal Findings We have analyzed the binding interactions between NHR and model 58 and 29 nucleotide substrate RNAs by gel electrophoresis mobility shift assays (EMSA) and fluorescence anisotropy. We show that the enzyme binds to RNA as a dimer. By constructing a hetero-dimer complex composed of one wild-type subunit and one inactive mutant NHR-R135A subunit, we show that only one functional subunit of the NHR homodimer is required for its enzymatic activity. Mutational analysis suggests that the interactions between neighbouring bases (G1068 and U1066) and A1067 have an important role in methyltransfer activity, such that the substitution of a deoxy sugar spacer (5ʹ) to the target nucleotide achieved near wild-type levels of methylation. A series of atomic substitutions at specific positions on the substrate adenine show that local base-base interactions between neighbouring bases are important for methylation. Conclusion/Significance Taken together these data suggest that local base-base interactions play an important role in aligning the substrate 2’ hydroxyl group of A1067 for methyl group transfer. Methylation of nucleic acids is playing an increasingly important role in fundamental biological processes and we anticipate that the approach outlined in this manuscript may be useful for investigating other classes of nucleic acid methyltransferases.
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Affiliation(s)
- Sitao Yin
- Key Laboratory of Molecular Medicine, the Ministry of Education, Department of Biochemistry and Molecular Biology, Fudan University Shanghai Medical College, Shanghai 200032, PR China
- Institutes of Biomedical Sciences, Fudan University Shanghai Medical College, Shanghai 200032, PR China
| | - Hengyi Jiang
- Key Laboratory of Molecular Medicine, the Ministry of Education, Department of Biochemistry and Molecular Biology, Fudan University Shanghai Medical College, Shanghai 200032, PR China
- Institutes of Biomedical Sciences, Fudan University Shanghai Medical College, Shanghai 200032, PR China
| | - Dongrong Chen
- Key Laboratory of Molecular Medicine, the Ministry of Education, Department of Biochemistry and Molecular Biology, Fudan University Shanghai Medical College, Shanghai 200032, PR China
- Institutes of Biomedical Sciences, Fudan University Shanghai Medical College, Shanghai 200032, PR China
- * E-mail: (AM); (DC)
| | - Alastair I. H. Murchie
- Key Laboratory of Molecular Medicine, the Ministry of Education, Department of Biochemistry and Molecular Biology, Fudan University Shanghai Medical College, Shanghai 200032, PR China
- Institutes of Biomedical Sciences, Fudan University Shanghai Medical College, Shanghai 200032, PR China
- * E-mail: (AM); (DC)
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