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Feng XL, Zhang RQ, Dong WG, Wang ZX, Xiao JJ, Wei J, Gao JM, Qi J. The Complete Genomic Sequence of Microbial Transglutaminase Producer, Streptomyces mobaraensis DSM40587. Biochem Genet 2024; 62:1087-1102. [PMID: 37532836 DOI: 10.1007/s10528-023-10463-0] [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: 05/18/2022] [Accepted: 07/18/2023] [Indexed: 08/04/2023]
Abstract
Actinomycetes are remarkable natural sources of active natural molecules and enzymes of considerable industrial value. Streptomyces mobaraensis is the first microorganism found to produce transglutaminase with broad industrial applications. Although transglutaminase in S. mobaraensis has been well studied over the past three decades, the genome of S. mobaraensis and its secondary metabolic potential were poorly reported. Here, we presented the complete genome of S. mobaraensis DSM40587 obtained from the German Collection of Microorganisms and Cell Cultures GmbH. It contains a linear chromosome of 7,633,041 bp and a circular plasmid of 23,857 bp. The chromosome with an average GC content of 73.49% was predicted to harbour 6683 protein-coding genes, seven rRNA and 69 tRNA genes. Comparative genomic analysis reveals its meaningful genomic characterisation. A comprehensive bioinformatics investigation identifies 35 putative BGCs (biosynthesis gene clusters) involved in synthesising various secondary metabolites. Of these, 13 clusters showed high similarity (> 55%) to known BGCs coding for polyketides, nonribosomal peptides, hopene, RiPP (Ribosomally synthesized and post-translationally modified peptides), and others. Furthermore, these BGCs with over 65% similarity to the known BGCs were analysed in detail. The complete genome of S. mobaraensis DSM40587 reveals its capacity to yield diverse bioactive natural products and provides additional insights into discovering novel secondary metabolites.
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Affiliation(s)
- Xi-Long Feng
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, 3 Taicheng Road, Yangling, 712100, Shaanxi, China
| | - Rui-Qi Zhang
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, 3 Taicheng Road, Yangling, 712100, Shaanxi, China
| | - Wei-Ge Dong
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, 3 Taicheng Road, Yangling, 712100, Shaanxi, China
| | - Zhen-Xin Wang
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, 3 Taicheng Road, Yangling, 712100, Shaanxi, China
| | - Jun-Jie Xiao
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, 3 Taicheng Road, Yangling, 712100, Shaanxi, China
| | - Jing Wei
- College of Biology Pharmacy & Food Engineering, Shangluo University, Shangluo, 726000, Shaanxi, China
- Qinba Mountains of Bio-Resource Collaborative Innovation Center of Southern Shaanxi Province, Hanzhong, 723000, Shaanxi, China
| | - Jin-Ming Gao
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, 3 Taicheng Road, Yangling, 712100, Shaanxi, China
| | - Jianzhao Qi
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, 3 Taicheng Road, Yangling, 712100, Shaanxi, China.
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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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Roovers M, Labar G, Wolff P, Feller A, Van Elder D, Soin R, Gueydan C, Kruys V, Droogmans L. The Bacillus subtilis open reading frame ysgA encodes the SPOUT methyltransferase RlmP forming 2'- O-methylguanosine at position 2553 in the A-loop of 23S rRNA. RNA (NEW YORK, N.Y.) 2022; 28:1185-1196. [PMID: 35710145 PMCID: PMC9380741 DOI: 10.1261/rna.079131.122] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 06/07/2022] [Indexed: 06/15/2023]
Abstract
A previous bioinformatic analysis predicted that the ysgA open reading frame of Bacillus subtilis encodes an RNA methyltransferase of the SPOUT superfamily. Here we show that YsgA is the 2'-O-methyltransferase that targets position G2553 (Escherichia coli numbering) of the A-loop of 23S rRNA. This was shown by a combination of biochemical and mass spectrometry approaches using both rRNA extracted from B. subtilis wild-type or ΔysgA cells and in vitro synthesized rRNA. When the target G2553 is mutated, YsgA is able to methylate the ribose of adenosine. However, it cannot methylate cytidine nor uridine. The enzyme modifies free 23S rRNA but not the fully assembled ribosome nor the 50S subunit, suggesting that the modification occurs early during ribosome biogenesis. Nevertheless, ribosome subunits assembly is unaffected in a B. subtilis ΔysgA mutant strain. The crystal structure of the recombinant YsgA protein, combined with mutagenesis data, outlined in this article highlights a typical SPOUT fold preceded by an L7Ae/L30 (eL8/eL30 in a new nomenclature) amino-terminal domain.
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Affiliation(s)
| | | | - Philippe Wolff
- Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, F-67084, Strasbourg, France
| | - André Feller
- Laboratoire de Chimie Biologique, Université Libre de Bruxelles (ULB), Labiris, B-1070 Bruxelles, Belgium
| | - Dany Van Elder
- Laboratoire de Chimie Biologique, Université Libre de Bruxelles (ULB), Labiris, B-1070 Bruxelles, Belgium
| | - Romuald Soin
- Laboratoire de Biologie Moléculaire du Gène, Institut de Biologie et de Médecine Moléculaires, Université Libre de Bruxelles (ULB), B-6041 Gosselies, Belgium
| | - Cyril Gueydan
- Laboratoire de Biologie Moléculaire du Gène, Institut de Biologie et de Médecine Moléculaires, Université Libre de Bruxelles (ULB), B-6041 Gosselies, Belgium
| | - Véronique Kruys
- Laboratoire de Biologie Moléculaire du Gène, Institut de Biologie et de Médecine Moléculaires, Université Libre de Bruxelles (ULB), B-6041 Gosselies, Belgium
| | - Louis Droogmans
- Laboratoire de Chimie Biologique, Université Libre de Bruxelles (ULB), Labiris, B-1070 Bruxelles, Belgium
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Structure of the mature kinetoplastids mitoribosome and insights into its large subunit biogenesis. Proc Natl Acad Sci U S A 2020; 117:29851-29861. [PMID: 33168716 PMCID: PMC7703582 DOI: 10.1073/pnas.2011301117] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Kinetoplastids is a group of flagellated unicellular eukaryotic parasites including human pathogens, such as Trypanosoma cruzi and Leishmania spp., etiologic agents of Chagas disease and leishmaniasis. They are potentially lethal, affecting more than 20 million people worldwide. Therapeutic strategies are extremely limited and highly toxic. The finding of new molecular targets represents one venue for the development of new therapeutic strategies. In this work, we present the structure of the full mitoribosomes from two kinetoplastids, Leishmania tarentolae and T. cruzi, thus far uncharacterized. We also reveal the structure of an large subunit assembly intermediate harboring 16 different factors. In addition to defining a subset of novel kinetoplastid-specific factors, our results shed light on the mitochondrial ribosomal RNA maturation process. Kinetoplastids are unicellular eukaryotic parasites responsible for such human pathologies as Chagas disease, sleeping sickness, and leishmaniasis. They have a single large mitochondrion, essential for the parasite survival. In kinetoplastid mitochondria, most of the molecular machineries and gene expression processes have significantly diverged and specialized, with an extreme example being their mitochondrial ribosomes. These large complexes are in charge of translating the few essential mRNAs encoded by mitochondrial genomes. Structural studies performed in Trypanosoma brucei already highlighted the numerous peculiarities of these mitoribosomes and the maturation of their small subunit. However, several important aspects mainly related to the large subunit (LSU) remain elusive, such as the structure and maturation of its ribosomal RNA. Here we present a cryo-electron microscopy study of the protozoans Leishmania tarentolae and Trypanosoma cruzi mitoribosomes. For both species, we obtained the structure of their mature mitoribosomes, complete rRNA of the LSU, as well as previously unidentified ribosomal proteins. In addition, we introduce the structure of an LSU assembly intermediate in the presence of 16 identified maturation factors. These maturation factors act on both the intersubunit and the solvent sides of the LSU, where they refold and chemically modify the rRNA and prevent early translation before full maturation of the LSU.
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Lai YP, Ioerger TR. Exploiting Homoplasy in Genome-Wide Association Studies to Enhance Identification of Antibiotic-Resistance Mutations in Bacterial Genomes. Evol Bioinform Online 2020; 16:1176934320944932. [PMID: 32782426 PMCID: PMC7385850 DOI: 10.1177/1176934320944932] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 06/30/2020] [Indexed: 12/23/2022] Open
Abstract
Many antibacterial drugs have multiple mechanisms of resistance, which are often represented simultaneously by a mixture of resistance mutations (some more frequent than others) in a clinical population. This presents a challenge for Genome-Wide Association Studies (GWAS) methods, making it difficult to detect less prevalent resistance mechanisms purely through (weak) statistical associations. Homoplasy, or the occurrence of multiple independent mutations at the same site, is often observed with drug resistance mutations and can be a strong indicator of positive selection. However, traditional GWAS methods, such as those based on allele counting or linear regression, are not designed to take homoplasy into account. In this article, we present a new method, called ECAT (for Evolutionary Cluster-based Association Test), that extends traditional regression-based GWAS methods with the ability to take advantage of homoplasy. This is achieved through a preprocessing step which identifies hypervariable regions in the genome exhibiting statistically significant clusters of distinct evolutionary changes, to which association testing by a linear mixed model (LMM) is applied using GEMMA (a well-established LMM-based GWAS tool). Thus, the approach can be viewed as extending GEMMA from the usual site- or gene-level analysis to focusing on clustered regions of mutations. This approach was evaluated on a large collection of more than 600 clinical isolates of multidrug-resistant (MDR) Mycobacterium tuberculosis from Lima, Peru. We show that ECAT does a better job of detecting known resistance mutations for several antitubercular drugs (including less prevalent mutations with weaker associations), compared with (site- or gene-based) GEMMA, as representative of existing GWAS methods. The power of the multiphase approach in ECAT comes from focusing association testing on the hypervariable regions of the genome, which reduces complexity in the model and increases statistical power.
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Affiliation(s)
- Yi-Pin Lai
- Department of Computer Science and Engineering, Texas A&M University, College Station, TX, USA
| | - Thomas R Ioerger
- Department of Computer Science and Engineering, Texas A&M University, College Station, TX, USA
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Xu Y, Li S, Yan Z, Ge B, Huang F, Yue T. Revealing Cooperation between Knotted Conformation and Dimerization in Protein Stabilization by Molecular Dynamics Simulations. J Phys Chem Lett 2019; 10:5815-5822. [PMID: 31525988 DOI: 10.1021/acs.jpclett.9b02209] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The topological knot is thought to play a stabilizing role in maintaining the global fold and nature of proteins with the underlying mechanism yet to be elucidated. Given that most proteins containing trefoil knots exist and function as homodimers with a large part of the dimer interface occupied by the knotted region, we reason that the knotted conformation cooperates with dimerization in protein stabilization. Here, we take YbeA from Escherichia coli as the knotted protein model, using molecular dynamics (MD) simulations to compare the stability of two pairs of dimeric proteins having the same sequence and secondary structures but differing in the presence or absence of a trefoil knot in each subunit. The dimer interface of YbeA is identified to involve favorable contacts among three α-helices (α1, α3, and α5), one of which (α5) is threaded through a loop connected with α3 to form the knot. Upon removal of the knot by appropriate change of the knot-making crossing of the polypeptide chain, relevant domains are less constrained and exhibit enhanced fluctuations to decrease contacts at the interface. Unknotted subunits are less compact and undergo structural changes to ease the dimer separation. Such a stabilizing effect is evidenced by steered MD simulations, showing that the mechanical force required for dimer separation is significantly reduced by removing the knot. In addition to the knotted conformation, dimerization further improves the protein stability by restricting the α1-α5 separation, which is defined as a leading step for protein unfolding. These results provide important insights into the structure-function relationship of dimerization in knotted proteins.
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Affiliation(s)
- Yan Xu
- State Key Laboratory of Heavy Oil Processing, Center for Bioengineering and Biotechnology, College of Chemical Engineering , China University of Petroleum (East China) , Qingdao 266580 , China
- College of Electronic Engineering and Automation , Shandong University of Science and Technology , Qingdao 266590 , China
| | - Shixin Li
- State Key Laboratory of Heavy Oil Processing, Center for Bioengineering and Biotechnology, College of Chemical Engineering , China University of Petroleum (East China) , Qingdao 266580 , China
| | - Zengshuai Yan
- State Key Laboratory of Heavy Oil Processing, Center for Bioengineering and Biotechnology, College of Chemical Engineering , China University of Petroleum (East China) , Qingdao 266580 , China
| | - Baosheng Ge
- State Key Laboratory of Heavy Oil Processing, Center for Bioengineering and Biotechnology, College of Chemical Engineering , China University of Petroleum (East China) , Qingdao 266580 , China
| | - Fang Huang
- State Key Laboratory of Heavy Oil Processing, Center for Bioengineering and Biotechnology, College of Chemical Engineering , China University of Petroleum (East China) , Qingdao 266580 , China
| | - Tongtao Yue
- State Key Laboratory of Heavy Oil Processing, Center for Bioengineering and Biotechnology, College of Chemical Engineering , China University of Petroleum (East China) , Qingdao 266580 , China
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7
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Avilamycin and evernimicin induce structural changes in rProteins uL16 and CTC that enhance the inhibition of A-site tRNA binding. Proc Natl Acad Sci U S A 2016; 113:E6796-E6805. [PMID: 27791159 DOI: 10.1073/pnas.1614297113] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Two structurally unique ribosomal antibiotics belonging to the orthosomycin family, avilamycin and evernimicin, possess activity against Enterococci, Staphylococci, and Streptococci, and other Gram-positive bacteria. Here, we describe the high-resolution crystal structures of the eubacterial large ribosomal subunit in complex with them. Their extended binding sites span the A-tRNA entrance corridor, thus inhibiting protein biosynthesis by blocking the binding site of the A-tRNA elbow, a mechanism not shared with other known antibiotics. Along with using the ribosomal components that bind and discriminate the A-tRNA-namely, ribosomal RNA (rRNA) helices H89, H91, and ribosomal proteins (rProtein) uL16-these structures revealed novel interactions with domain 2 of the CTC protein, a feature typical to various Gram-positive bacteria. Furthermore, analysis of these structures explained how single nucleotide mutations and methylations in helices H89 and H91 confer resistance to orthosomycins and revealed the sequence variations in 23S rRNA nucleotides alongside the difference in the lengths of the eukaryotic and prokaryotic α1 helix of protein uL16 that play a key role in the selectivity of those drugs. The accurate interpretation of the crystal structures that could be performed beyond that recently reported in cryo-EM models provide structural insights that may be useful for the design of novel pathogen-specific antibiotics, and for improving the potency of orthosomycins. Because both drugs are extensively metabolized in vivo, their environmental toxicity is very low, thus placing them at the frontline of drugs with reduced ecological hazards.
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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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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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Ochi A, Makabe K, Yamagami R, Hirata A, Sakaguchi R, Hou YM, Watanabe K, Nureki O, Kuwajima K, Hori H. The catalytic domain of topological knot tRNA methyltransferase (TrmH) discriminates between substrate tRNA and nonsubstrate tRNA via an induced-fit process. J Biol Chem 2013; 288:25562-25574. [PMID: 23867454 DOI: 10.1074/jbc.m113.485128] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
A conserved guanosine at position 18 (G18) in the D-loop of tRNAs is often modified to 2'-O-methylguanosine (Gm). Formation of Gm18 in eubacterial tRNA is catalyzed by tRNA (Gm18) methyltransferase (TrmH). TrmH enzymes can be divided into two types based on their substrate tRNA specificity. Type I TrmH, including Thermus thermophilus TrmH, can modify all tRNA species, whereas type II TrmH, for example Escherichia coli TrmH, modifies only a subset of tRNA species. Our previous crystal study showed that T. thermophilus TrmH is a class IV S-adenosyl-l-methionine-dependent methyltransferase, which maintains a topological knot structure in the catalytic domain. Because TrmH enzymes have short stretches at the N and C termini instead of a clear RNA binding domain, these stretches are believed to be involved in tRNA recognition. In this study, we demonstrate by site-directed mutagenesis that both N- and C-terminal regions function in tRNA binding. However, in vitro and in vivo chimera protein studies, in which four chimeric proteins of type I and II TrmHs were used, demonstrated that the catalytic domain discriminates substrate tRNAs from nonsubstrate tRNAs. Thus, the N- and C-terminal regions do not function in the substrate tRNA discrimination process. Pre-steady state analysis of complex formation between mutant TrmH proteins and tRNA by stopped-flow fluorescence measurement revealed that the C-terminal region works in the initial binding process, in which nonsubstrate tRNA is not excluded, and that structural movement of the motif 2 region of the catalytic domain in an induced-fit process is involved in substrate tRNA discrimination.
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Affiliation(s)
- Anna Ochi
- From the Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, 3 Bunkyo, Matsuyama, Ehime 790-8577, Japan
| | - Koki Makabe
- the Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan
| | - Ryota Yamagami
- From the Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, 3 Bunkyo, Matsuyama, Ehime 790-8577, Japan
| | - Akira Hirata
- From the Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, 3 Bunkyo, Matsuyama, Ehime 790-8577, Japan
| | - Reiko Sakaguchi
- the Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107
| | - Ya-Ming Hou
- the Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107
| | - Kazunori Watanabe
- From the Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, 3 Bunkyo, Matsuyama, Ehime 790-8577, Japan
| | - Osamu Nureki
- the Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan, and
| | - Kunihiro Kuwajima
- the Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan
| | - Hiroyuki Hori
- From the Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, 3 Bunkyo, Matsuyama, Ehime 790-8577, Japan,; the Venture Business Laboratory, Ehime University, 3 Bunkyo, Matsuyama, Ehime 790-8577, Japan.
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11
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Zhang H, Wan H, Gao ZQ, Wei Y, Wang WJ, Liu GF, Shtykova EV, Xu JH, Dong YH. Insights into the catalytic mechanism of 16S rRNA methyltransferase RsmE (m³U1498) from crystal and solution structures. J Mol Biol 2012; 423:576-89. [PMID: 22925577 DOI: 10.1016/j.jmb.2012.08.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2012] [Revised: 08/07/2012] [Accepted: 08/20/2012] [Indexed: 12/29/2022]
Abstract
RsmE is the founding member of a new RNA methyltransferase (MTase) family responsible for methylation of U1498 in 16S ribosomal RNA in Escherichia coli. It is well conserved across bacteria and plants and may play an important role in ribosomal intersubunit communication. The crystal structure in monomer showed that it consists of two distinct but structurally related domains: the PUA (pseudouridine synthases and archaeosine-specific transglycosylases)-like RNA recognition and binding domain and the conserved MTase domain with a deep trefoil knot. Analysis of small-angle X-ray scattering data revealed that RsmE forms a flexible dimeric conformation that may be essential for substrate binding. The S-adenosyl-l-methionine (AdoMet)-binding characteristic determined by isothermal titration calorimetry suggested that there is only one AdoMet molecule bound in the subunit of the homodimer. In vitro methylation assay of the mutants based on the RsmE-AdoMet-uridylic acid complex model showed key residues involved in substrate binding and catalysis. Comprehensive comparisons of RsmE with closely related MTases, combined with the biochemical experiments, indicated that the MTase domain of one subunit in dimeric RsmE is responsible for binding of one AdoMet molecule and catalytic process while the PUA-like domain in the other subunit is mainly responsible for recognition of one substrate molecule (the ribosomal RNA fragment and ribosomal protein complex). The methylation process is required by collaboration of both subunits, and dimerization is functionally critical for catalysis. In general, our study provides new information on the structure-function relationship of RsmE and thereby suggests a novel catalytic mechanism.
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Affiliation(s)
- Heng Zhang
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, 19B, Yuquan Road, Beijing 100049, China
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12
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Deng Y, Lei M, Zhang W, Li W, Zhou E, Liu Z, Qi C. Monoclonal antibodies directed against Fpr3 protein as molecular chaperones. Hybridoma (Larchmt) 2012; 30:491-3. [PMID: 22008079 DOI: 10.1089/hyb.2011.0053] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Fpr3 is the third member of the FKBP (FK506 binding protein) family in yeast. In this study, the fpr3 gene from Saccharomyces cerevisiae was overexpressed and the protein product was purified using different methods. The recombinant Fpr3 fusion protein (rFpr3) was then used as antigen to immunize BALB/c mice for the production of monoclonal antibodies (MAb). Western blot and ELISA results indicated that rFpr3 had specific binding ability to the MAbs, and isotyping results classified the MAb as the subclass IgG1 by antibody. The MAbs obtained in this study will be used as a molecular chaperone to obtain Fpr3 crystals.
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Affiliation(s)
- Yan Deng
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, College of Life Science, Huazhong Normal University, Wuhan, People's Republic of China
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13
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Yang H, Wang Z, Shen Y, Wang P, Jia X, Zhao L, Zhou P, Gong R, Li Z, Yang Y, Chen D, Murchie AIH, Xu Y. Crystal Structure of the Nosiheptide-Resistance Methyltransferase of Streptomyces actuosus. Biochemistry 2010; 49:6440-50. [DOI: 10.1021/bi1005915] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Huirong Yang
- Cancer Institute, Shanghai Cancer Center, Fudan University, and Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
- Institutes of Biomedical Sciences, Fudan University, 130 Dong-An Road, Shanghai 200032, China
- School of Life Sciences, Fudan University, 220 Han-Dan Road, Shanghai 200433, China
| | - Zhe Wang
- Institutes of Biomedical Sciences, Fudan University, 130 Dong-An Road, Shanghai 200032, China
- Department of Pharmacy, Fudan University, Shanghai 201203, China
| | - Yan Shen
- Institutes of Biomedical Sciences, Fudan University, 130 Dong-An Road, Shanghai 200032, China
- Department of Pharmacy, Fudan University, Shanghai 201203, China
| | - Ping Wang
- Institutes of Biomedical Sciences, Fudan University, 130 Dong-An Road, Shanghai 200032, China
- School of Life Sciences, Fudan University, 220 Han-Dan Road, Shanghai 200433, China
| | - Xu Jia
- Institutes of Biomedical Sciences, Fudan University, 130 Dong-An Road, Shanghai 200032, China
- Department of Pharmacy, Fudan University, Shanghai 201203, China
| | - Liang Zhao
- Institutes of Biomedical Sciences, Fudan University, 130 Dong-An Road, Shanghai 200032, China
- Department of Chemistry, Fudan University, Han-Dan Road, Shanghai 200433, China
| | - Pei Zhou
- Department of Pharmacy, Fudan University, Shanghai 201203, China
| | - Rui Gong
- Institutes of Biomedical Sciences, Fudan University, 130 Dong-An Road, Shanghai 200032, China
- School of Life Sciences, Fudan University, 220 Han-Dan Road, Shanghai 200433, China
| | - Ze Li
- Institutes of Biomedical Sciences, Fudan University, 130 Dong-An Road, Shanghai 200032, China
- School of Life Sciences, Fudan University, 220 Han-Dan Road, Shanghai 200433, China
| | - Ying Yang
- Institutes of Biomedical Sciences, Fudan University, 130 Dong-An Road, Shanghai 200032, China
- School of Life Sciences, Fudan University, 220 Han-Dan Road, Shanghai 200433, China
| | - Dongrong Chen
- Institutes of Biomedical Sciences, Fudan University, 130 Dong-An Road, Shanghai 200032, China
- Department of Pharmacy, Fudan University, Shanghai 201203, China
| | - Alastair I. H. Murchie
- Institutes of Biomedical Sciences, Fudan University, 130 Dong-An Road, Shanghai 200032, China
- Department of Pharmacy, Fudan University, Shanghai 201203, China
| | - Yanhui Xu
- Cancer Institute, Shanghai Cancer Center, Fudan University, and Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
- Institutes of Biomedical Sciences, Fudan University, 130 Dong-An Road, Shanghai 200032, China
- School of Life Sciences, Fudan University, 220 Han-Dan Road, Shanghai 200433, China
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14
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Yang H, Wang P, Dong Z, Li X, Gong R, Yang Y, Li Z, Xu Y, Xu Y. Crystallization and preliminary crystallographic analysis of nosiheptide-resistance methyltransferase from Streptomyces actuosus in complex with SAM. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:579-82. [PMID: 20445264 DOI: 10.1107/s1744309110011395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2010] [Accepted: 03/25/2010] [Indexed: 11/10/2022]
Abstract
Nosiheptide-resistance methyltransferase (NSR) methylates 23S rRNA at the nucleotide adenosine 1067 in Escherichia coli and thus contributes to resistance against nosiheptide, a sulfur-containing peptide antibiotic. Here, the expression, purification and crystallization of NSR from Streptomyces actuosus are reported. Diffracting crystals were grown by the hanging-drop vapour-diffusion method in reservoir solution consisting of 0.35 M ammonium chloride, 24%(w/v) PEG 3350, 0.1 M MES pH 5.7 at 293 K. Native data have been collected from the apo enzyme and a SAM complex, as well as apo SeMet SAD data. The diffraction patterns of the apo form of NSR, of NSR complexed with SAM and of SeMet-labelled NSR crystals extended to 1.90, 1.95 and 2.25 A resolution, respectively, using synchrotron radiation. All crystals belonged to space group P2(1), with approximate unit-cell parameters a = 64.6, b = 69.6, c = 64.9 A, beta = 117.8 degrees .
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Affiliation(s)
- Huirong Yang
- Department of Pathology, Cancer Hospital, Fudan University, Shanghai 200032, People's Republic of China
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15
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Ochi A, Makabe K, Kuwajima K, Hori H. Flexible recognition of the tRNA G18 methylation target site by TrmH methyltransferase through first binding and induced fit processes. J Biol Chem 2010; 285:9018-29. [PMID: 20053984 DOI: 10.1074/jbc.m109.065698] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Transfer RNA (Gm18) methyltransferase (TrmH) catalyzes methyl transfer from S-adenosyl-l-methionine to a conserved G18 in tRNA. We investigated the recognition mechanism of Thermus thermophilus TrmH for its guanosine target. Thirteen yeast tRNA(Phe) mutant transcripts were prepared in which the modification site and/or other nucleotides in the D-loop were substituted by dG, inosine, or other nucleotides. We then conducted methyl transfer kinetic studies, gel shift assays, and inhibition experiments using these tRNA variants. Sites of methylation were confirmed with RNA sequencing or primer extension. Although the G18G19 sequence is not essential for methylation by TrmH, disruption of G18G19 severely reduces the efficiency of methyl transfer. There is strict recognition of guanosine by TrmH, in that methylation occurs at the adjacent G19 when the G18 is replaced by dG or adenosine. The fact that TrmH methylates guanosine in D-loops from 4 to 12 nucleotides in length suggests that selection of the position of guanosine within the D-loop is relatively flexible. Our studies also demonstrate that the oxygen 6 atom of the guanine base is a positive determinant for TrmH recognition. The recognition process of TrmH for substrate is inducible and product-inhibited, in that tRNAs containing Gm18 are excluded by TrmH. In contrast, substitution of G18 with dG18 results in the formation of a more stable TrmH-tRNA complex. To address the mechanism, we performed the stopped-flow pre-steady state kinetic analysis. The result clearly showed that the binding of TrmH to tRNA is composed of at least three steps, the first bi-molecular binding and the subsequent two uni-molecular induced-fit processes.
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Affiliation(s)
- Anna Ochi
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577
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16
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Wurm JP, Meyer B, Bahr U, Held M, Frolow O, Kötter P, Engels JW, Heckel A, Karas M, Entian KD, Wöhnert J. The ribosome assembly factor Nep1 responsible for Bowen-Conradi syndrome is a pseudouridine-N1-specific methyltransferase. Nucleic Acids Res 2010; 38:2387-98. [PMID: 20047967 PMCID: PMC2853112 DOI: 10.1093/nar/gkp1189] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Nep1 (Emg1) is a highly conserved nucleolar protein with an essential function in ribosome biogenesis. A mutation in the human Nep1 homolog causes Bowen-Conradi syndrome-a severe developmental disorder. Structures of Nep1 revealed a dimer with a fold similar to the SPOUT-class of RNA-methyltransferases suggesting that Nep1 acts as a methyltransferase in ribosome biogenesis. The target for this putative methyltransferase activity has not been identified yet. We characterized the RNA-binding specificity of Methanocaldococcus jannaschii Nep1 by fluorescence- and NMR-spectroscopy as well as by yeast three-hybrid screening. Nep1 binds with high affinity to short RNA oligonucleotides corresponding to nt 910-921 of M. jannaschii 16S rRNA through a highly conserved basic surface cleft along the dimer interface. Nep1 only methylates RNAs containing a pseudouridine at a position corresponding to a previously identified hypermodified N1-methyl-N3-(3-amino-3-carboxypropyl) pseudouridine (m1acp3-Psi) in eukaryotic 18S rRNAs. Analysis of the methylated nucleoside by MALDI-mass spectrometry, HPLC and NMR shows that the methyl group is transferred to the N1 of the pseudouridine. Thus, Nep1 is the first identified example of an N1-specific pseudouridine methyltransferase. This enzymatic activity is also conserved in human Nep1 suggesting that Nep1 is the methyltransferase in the biosynthesis of m1acp3-Psi in eukaryotic 18S rRNAs.
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Affiliation(s)
- Jan Philip Wurm
- Institut für Molekulare Biowissenschaften, Johann-Wolfgang-Goethe-Universität, 60438 Frankfurt/M., Germany
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17
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Dunstan MS, Hang PC, Zelinskaya NV, Honek JF, Conn GL. Structure of the thiostrepton resistance methyltransferase.S-adenosyl-L-methionine complex and its interaction with ribosomal RNA. J Biol Chem 2009; 284:17013-17020. [PMID: 19369248 PMCID: PMC2719339 DOI: 10.1074/jbc.m901618200] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2009] [Revised: 03/31/2009] [Indexed: 12/03/2022] Open
Abstract
The x-ray crystal structure of the thiostrepton resistance RNA methyltransferase (Tsr).S-adenosyl-L-methionine (AdoMet) complex was determined at 2.45-A resolution. Tsr is definitively confirmed as a Class IV methyltransferase of the SpoU family with an N-terminal "L30-like" putative target recognition domain. The structure and our in vitro analysis of the interaction of Tsr with its target domain from 23 S ribosomal RNA (rRNA) demonstrate that the active biological unit is a Tsr homodimer. In vitro methylation assays show that Tsr activity is optimal against a 29-nucleotide hairpin rRNA though the full 58-nucleotide L11-binding domain and intact 23 S rRNA are also effective substrates. Molecular docking experiments predict that Tsr.rRNA binding is dictated entirely by the sequence and structure of the rRNA hairpin containing the A1067 target nucleotide and is most likely driven primarily by large complementary electrostatic surfaces. One L30-like domain is predicted to bind the target loop and the other is near an internal loop more distant from the target site where a nucleotide change (U1061 to A) also decreases methylation by Tsr. Furthermore, a predicted interaction with this internal loop by Tsr amino acid Phe-88 was confirmed by mutagenesis and RNA binding experiments. We therefore propose that Tsr achieves its absolute target specificity using the N-terminal domains of each monomer in combination to recognize the two distinct structural elements of the target rRNA hairpin such that both Tsr subunits contribute directly to the positioning of the target nucleotide on the enzyme.
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MESH Headings
- Base Sequence
- Catalytic Domain
- Crystallography, X-Ray
- Dimerization
- Drug Resistance, Bacterial
- Macromolecular Substances
- Methyltransferases/chemistry
- Methyltransferases/genetics
- Methyltransferases/metabolism
- Models, Molecular
- Nucleic Acid Conformation
- Protein Structure, Quaternary
- Protein Structure, Secondary
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Ribosomal, 23S/chemistry
- RNA, Ribosomal, 23S/genetics
- RNA, Ribosomal, 23S/metabolism
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
- S-Adenosylmethionine/chemistry
- S-Adenosylmethionine/metabolism
- Staphylococcus aureus/drug effects
- Staphylococcus aureus/enzymology
- Staphylococcus aureus/genetics
- Static Electricity
- Thiostrepton/pharmacology
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Affiliation(s)
- Mark S Dunstan
- From the Manchester Interdisciplinary Biocentre, Faculty of Life Sciences, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Pei C Hang
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Natalia V Zelinskaya
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322
| | - John F Honek
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Graeme L Conn
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322.
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18
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Kim DJ, Kim HS, Lee SJ, Suh SW. Crystal structure ofThermotoga maritimaSPOUT superfamily RNA methyltransferase Tm1570 in complex with S-adenosyl-L-methionine. Proteins 2009; 74:245-9. [DOI: 10.1002/prot.22249] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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19
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Abstract
The issue of how a newly synthesized polypeptide chain folds to form a protein with a unique three-dimensional structure, otherwise known as the 'protein-folding problem', remains a fundamental question in the life sciences. Over the last few decades, much information has been gathered about the mechanisms by which proteins fold. However, despite the vast topological diversity observed in biological structures, it was thought improbable, if not impossible, that a polypeptide chain could 'knot' itself to form a functional protein. Nevertheless, such knotted structures have since been identified, raising questions about how such complex topologies can arise during folding. Their formation does not fit any current folding models or mechanisms, and therefore represents an important piece of the protein-folding puzzle. This article reviews the progress made towards discovering how nature codes for, and contends with, knots during protein folding, and examines the insights gained from both experimental and computational studies. Mechanisms to account for the formation of knotted structures that were previously thought unfeasible, and their implications for protein folding, are also discussed.
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Affiliation(s)
- Anna L Mallam
- St John's College and University Chemical Laboratory, Cambridge, UK.
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20
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Abstract
One of the most striking topological features to be found in a protein is that of a distinct knot formed by the path of the polypeptide backbone. Such knotted structures represent some of the smallest "self-tying" knots observed in Nature. Proteins containing a knot deep within their structure add an extra complication to the already challenging protein-folding problem; it is not obvious how, during the process of folding, a substantial length of polypeptide chain manages to spontaneously thread itself through a loop. Here, we probe the folding mechanism of YibK, a homodimeric alpha/beta-knot protein containing a deep trefoil knot at its carboxy terminus. By analyzing the effect of mutations made in the knotted region of the protein we show that the native structure in this area remains undeveloped until very late in the folding reaction. Single-site destabilizing mutations made in the knot structure significantly affect only the folding kinetics of a late-forming intermediate and the slow dimerization step. Furthermore, we find evidence to suggest that the heterogeneity observed in the denatured state is not caused by isomerization of the single cis proline bond as previously thought, but instead could be a result of the knotting mechanism. These results allow us to propose a folding model for YibK where the threading of the polypeptide chain and the formation of native structure in the knotted region of the protein occur independently as successive events.
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21
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Wu H, Min J, Zeng H, Plotnikov AN. Crystal structure of the methyltransferase domain of human TARBP1. Proteins 2008; 72:519-25. [PMID: 18412263 DOI: 10.1002/prot.22065] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Hong Wu
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada M5G 1L6.
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22
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Mallam AL, Onuoha SC, Grossmann JG, Jackson SE. Knotted fusion proteins reveal unexpected possibilities in protein folding. Mol Cell 2008; 30:642-8. [PMID: 18538662 DOI: 10.1016/j.molcel.2008.03.019] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2007] [Revised: 02/22/2008] [Accepted: 03/28/2008] [Indexed: 11/28/2022]
Abstract
Proteins that contain a distinct knot in their native structure are impressive examples of biological self-organization. Although this topological complexity does not appear to cause a folding problem, the mechanisms by which such knotted proteins form are unknown. We found that the fusion of an additional protein domain to either the amino terminus, the carboxy terminus, or to both termini of two small knotted proteins did not affect their ability to knot. The multidomain constructs remained able to fold to structures previously thought unfeasible, some representing the deepest protein knots known. By examining the folding kinetics of these fusion proteins, we found evidence to suggest that knotting is not rate limiting during folding, but instead occurs in a denatured-like state. These studies offer experimental insights into when knot formation occurs in natural proteins and demonstrate that early folding events can lead to diverse and sometimes unexpected protein topologies.
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Affiliation(s)
- Anna L Mallam
- Chemistry Department, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
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23
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Subcellular localization and RNA interference of an RNA methyltransferase gene from silkworm, Bombyx mori. Comp Funct Genomics 2008:571023. [PMID: 18509492 PMCID: PMC2396236 DOI: 10.1155/2008/571023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2007] [Accepted: 03/17/2008] [Indexed: 11/24/2022] Open
Abstract
RNA methylation, which is a form of posttranscriptional modification, is catalyzed by S-adenosyl-L-methionone-dependent RNA methyltransterases (RNA MTases). We have identified a novel silkworm gene, BmRNAMTase, containing a 369-bp open reading frame that encodes a putative protein containing 122 amino acid residues and having a molecular weight of 13.88 kd. We expressed a recombinant His-tagged BmRNAMTase in E. coli BL21 (DE3), purified the fusion protein by metal-chelation affinity chromatography, and injected a New Zealand rabbit with the purified protein to generate anti-BmRNAMTase polyclonal antibodies. Immunohistochemistry revealed that BmRNAMTase is abundant in the cytoplasm of Bm5 cells. In addition, using RNA interference to reduce the intracellular activity and content of BmRNAMTase, we determined that this cytoplasmic RNA methyltransferase may be involved in preventing cell death in the silkworm.
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24
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Taylor AB, Meyer B, Leal BZ, Kötter P, Schirf V, Demeler B, Hart PJ, Entian KD, Wöhnert J. The crystal structure of Nep1 reveals an extended SPOUT-class methyltransferase fold and a pre-organized SAM-binding site. Nucleic Acids Res 2008; 36:1542-54. [PMID: 18208838 PMCID: PMC2275143 DOI: 10.1093/nar/gkm1172] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2007] [Revised: 12/18/2007] [Accepted: 12/20/2007] [Indexed: 11/13/2022] Open
Abstract
Ribosome biogenesis in eukaryotes requires the participation of a large number of ribosome assembly factors. The highly conserved eukaryotic nucleolar protein Nep1 has an essential but unknown function in 18S rRNA processing and ribosome biogenesis. In Saccharomyces cerevisiae the malfunction of a temperature-sensitive Nep1 protein (nep1-1(ts)) was suppressed by the addition of S-adenosylmethionine (SAM). This suggests the participation of Nep1 in a methyltransferase reaction during ribosome biogenesis. In addition, yeast Nep1 binds to a 6-nt RNA-binding motif also found in 18S rRNA and facilitates the incorporation of ribosomal protein Rps19 during the formation of pre-ribosomes. Here, we present the X-ray structure of the Nep1 homolog from the archaebacterium Methanocaldococcus jannaschii in its free form (2.2 A resolution) and bound to the S-adenosylmethionine analog S-adenosylhomocysteine (SAH, 2.15 A resolution) and the antibiotic and general methyltransferase inhibitor sinefungin (2.25 A resolution). The structure reveals a fold which is very similar to the conserved core fold of the SPOUT-class methyltransferases but contains a novel extension of this common core fold. SAH and sinefungin bind to Nep1 at a preformed binding site that is topologically equivalent to the cofactor-binding site in other SPOUT-class methyltransferases. Therefore, our structures together with previous genetic data suggest that Nep1 is a genuine rRNA methyltransferase.
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Affiliation(s)
- Alexander B. Taylor
- Department of Biochemistry, X-ray Crystallography Core Laboratory, The University of Texas Health Science Center San Antonio, San Antonio, TX-78229, USA, Excellence Center: Macromolecular Complexes and Institut für Molekulare Biowissenschaften, Johann-Wolfgang-Goethe-Universität, 60438 Frankfurt/M., Germany, Center for Analytical Ultracentrifugation of Macromolecular Assemblies, The University of Texas Health Science Center San Antonio and Geriatric Research, Education, and Clinical Center, Department of Veterans Affairs, South Texas Veterans Health Care System, San Antonio, Texas 78229, USA
| | - Britta Meyer
- Department of Biochemistry, X-ray Crystallography Core Laboratory, The University of Texas Health Science Center San Antonio, San Antonio, TX-78229, USA, Excellence Center: Macromolecular Complexes and Institut für Molekulare Biowissenschaften, Johann-Wolfgang-Goethe-Universität, 60438 Frankfurt/M., Germany, Center for Analytical Ultracentrifugation of Macromolecular Assemblies, The University of Texas Health Science Center San Antonio and Geriatric Research, Education, and Clinical Center, Department of Veterans Affairs, South Texas Veterans Health Care System, San Antonio, Texas 78229, USA
| | - Belinda Z. Leal
- Department of Biochemistry, X-ray Crystallography Core Laboratory, The University of Texas Health Science Center San Antonio, San Antonio, TX-78229, USA, Excellence Center: Macromolecular Complexes and Institut für Molekulare Biowissenschaften, Johann-Wolfgang-Goethe-Universität, 60438 Frankfurt/M., Germany, Center for Analytical Ultracentrifugation of Macromolecular Assemblies, The University of Texas Health Science Center San Antonio and Geriatric Research, Education, and Clinical Center, Department of Veterans Affairs, South Texas Veterans Health Care System, San Antonio, Texas 78229, USA
| | - Peter Kötter
- Department of Biochemistry, X-ray Crystallography Core Laboratory, The University of Texas Health Science Center San Antonio, San Antonio, TX-78229, USA, Excellence Center: Macromolecular Complexes and Institut für Molekulare Biowissenschaften, Johann-Wolfgang-Goethe-Universität, 60438 Frankfurt/M., Germany, Center for Analytical Ultracentrifugation of Macromolecular Assemblies, The University of Texas Health Science Center San Antonio and Geriatric Research, Education, and Clinical Center, Department of Veterans Affairs, South Texas Veterans Health Care System, San Antonio, Texas 78229, USA
| | - Virgil Schirf
- Department of Biochemistry, X-ray Crystallography Core Laboratory, The University of Texas Health Science Center San Antonio, San Antonio, TX-78229, USA, Excellence Center: Macromolecular Complexes and Institut für Molekulare Biowissenschaften, Johann-Wolfgang-Goethe-Universität, 60438 Frankfurt/M., Germany, Center for Analytical Ultracentrifugation of Macromolecular Assemblies, The University of Texas Health Science Center San Antonio and Geriatric Research, Education, and Clinical Center, Department of Veterans Affairs, South Texas Veterans Health Care System, San Antonio, Texas 78229, USA
| | - Borries Demeler
- Department of Biochemistry, X-ray Crystallography Core Laboratory, The University of Texas Health Science Center San Antonio, San Antonio, TX-78229, USA, Excellence Center: Macromolecular Complexes and Institut für Molekulare Biowissenschaften, Johann-Wolfgang-Goethe-Universität, 60438 Frankfurt/M., Germany, Center for Analytical Ultracentrifugation of Macromolecular Assemblies, The University of Texas Health Science Center San Antonio and Geriatric Research, Education, and Clinical Center, Department of Veterans Affairs, South Texas Veterans Health Care System, San Antonio, Texas 78229, USA
| | - P. John Hart
- Department of Biochemistry, X-ray Crystallography Core Laboratory, The University of Texas Health Science Center San Antonio, San Antonio, TX-78229, USA, Excellence Center: Macromolecular Complexes and Institut für Molekulare Biowissenschaften, Johann-Wolfgang-Goethe-Universität, 60438 Frankfurt/M., Germany, Center for Analytical Ultracentrifugation of Macromolecular Assemblies, The University of Texas Health Science Center San Antonio and Geriatric Research, Education, and Clinical Center, Department of Veterans Affairs, South Texas Veterans Health Care System, San Antonio, Texas 78229, USA
| | - Karl-Dieter Entian
- Department of Biochemistry, X-ray Crystallography Core Laboratory, The University of Texas Health Science Center San Antonio, San Antonio, TX-78229, USA, Excellence Center: Macromolecular Complexes and Institut für Molekulare Biowissenschaften, Johann-Wolfgang-Goethe-Universität, 60438 Frankfurt/M., Germany, Center for Analytical Ultracentrifugation of Macromolecular Assemblies, The University of Texas Health Science Center San Antonio and Geriatric Research, Education, and Clinical Center, Department of Veterans Affairs, South Texas Veterans Health Care System, San Antonio, Texas 78229, USA
| | - Jens Wöhnert
- Department of Biochemistry, X-ray Crystallography Core Laboratory, The University of Texas Health Science Center San Antonio, San Antonio, TX-78229, USA, Excellence Center: Macromolecular Complexes and Institut für Molekulare Biowissenschaften, Johann-Wolfgang-Goethe-Universität, 60438 Frankfurt/M., Germany, Center for Analytical Ultracentrifugation of Macromolecular Assemblies, The University of Texas Health Science Center San Antonio and Geriatric Research, Education, and Clinical Center, Department of Veterans Affairs, South Texas Veterans Health Care System, San Antonio, Texas 78229, USA
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25
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Kuratani M, Bessho Y, Nishimoto M, Grosjean H, Yokoyama S. Crystal structure and mutational study of a unique SpoU family archaeal methylase that forms 2'-O-methylcytidine at position 56 of tRNA. J Mol Biol 2007; 375:1064-75. [PMID: 18068186 DOI: 10.1016/j.jmb.2007.11.023] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2007] [Revised: 10/30/2007] [Accepted: 11/09/2007] [Indexed: 11/15/2022]
Abstract
The conserved cytidine residue at position 56 of tRNA contributes to the maintenance of the L-shaped tertiary structure. aTrm56 catalyzes the 2'-O-methylation of the cytidine residue in archaeal tRNA, using S-adenosyl-L-methionine. Based on the amino acid sequence, aTrm56 is the most distant member of the SpoU family. Here, we determined the crystal structure of Pyrococcus horikoshii aTrm56 complexed with S-adenosyl-L-methionine at 2.48 A resolution. aTrm56 consists of the SPOUT domain, which contains the characteristic deep trefoil knot, and a unique C-terminal beta-hairpin. aTrm56 forms a dimer. The S-adenosyl-L-methionine binding and dimerization of aTrm56 were similar to those of the other SpoU members. A structure-based sequence alignment revealed that aTrm56 conserves only motif II, among the four signature motifs. However, an essential Arg16 residue is located at a novel position within motif I. Biochemical assays showed that aTrm56 prefers the L-shaped tRNA to the lambda form as its substrate.
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MESH Headings
- Amino Acid Motifs
- Amino Acid Sequence
- Binding Sites
- Crystallography, X-Ray
- Cytidine/analogs & derivatives
- Cytidine/chemistry
- Dimerization
- Hydrogen Bonding
- Hydrophobic and Hydrophilic Interactions
- Methylation
- Models, Chemical
- Models, Molecular
- Molecular Sequence Data
- Mutation
- Protein Binding
- Protein Conformation
- Protein Structure, Secondary
- Protein Structure, Tertiary
- Pyrococcus horikoshii/enzymology
- RNA, Archaeal/chemistry
- RNA, Archaeal/genetics
- RNA, Archaeal/metabolism
- RNA, Transfer/chemistry
- RNA, Transfer/metabolism
- Recombinant Proteins/chemistry
- Recombinant Proteins/metabolism
- S-Adenosylmethionine/metabolism
- Sequence Homology, Amino Acid
- tRNA Methyltransferases/chemistry
- tRNA Methyltransferases/genetics
- tRNA Methyltransferases/metabolism
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Affiliation(s)
- Mitsuo Kuratani
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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26
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Schubert HL, Blumenthal RM, Cheng X. 1 Protein Methyltransferases: Their Distribution Among the Five Structural Classes of AdoMet-Dependent Methyltransferases. Enzymes 2007; 24:3-28. [PMID: 26718035 DOI: 10.1016/s1874-6047(06)80003-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
S-adenosyl-l-methionine (AdoMet) dependent methyltransferases (MTases) are involved in biosynthesis, signal transduction, protein repair, chromatin regulation, and gene silencing. Five different structural folds (designated I through V) have been described that bind AdoMet and catalyze methyltransfer to diverse substrates, although the great majority of known MTases have the Class I fold. Even within a particular MTase class the amino-acid sequence similarity can be as low as 10%. Thus, the structural and catalytic requirements for methyltransfer from AdoMet appear to be remarkably flexible. MTases that act on protein substrates have been found to date among three of the five structural classes (I, the classical fold; III, the corrin MTase fold; and V, the SET fold). "There are many paths to the top of the mountain, but the view is always the same."-Chinese proverb The Columbia World of Quotations, New York, Columbia University Press, 1996.
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Affiliation(s)
- Heidi L Schubert
- Department of Biochemistry University of Utah 15 North Medical DriveEast Salt Lake City, UT 84112, USA
| | - Robert M Blumenthal
- Department of Medical Microbiology and Immunology and Program in Bioinformatics and Proteomics/Genomics Medical University of Ohio 3000 Arlington Avenue Toledo, OH 43614, USA
| | - Xiaodong Cheng
- Department of Biochemistry Emory University School of Medicine 1510 Clifton Road Northeast Atlanta, GA 30322, USA
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27
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Abstract
Knotted proteins are more commonly observed in recent years due to the enormously growing number of structures in the Protein Data Bank (PDB). Studies show that the knot regions contribute to both ligand binding and enzyme activity in proteins such as the chromophore-binding domain of phytochrome, ketol–acid reductoisomerase or SpoU methyltransferase. However, there are still many misidentified knots published in the literature due to the absence of a convenient web tool available to the general biologists. Here, we present the first web server to detect the knots in proteins as well as provide information on knotted proteins in PDB—the protein KNOT (pKNOT) web server. In pKNOT, users can either input PDB ID or upload protein coordinates in the PDB format. The pKNOT web server will detect the knots in the protein using the Taylor's smoothing algorithm. All the detected knots can be visually inspected using a Java-based 3D graphics viewer. We believe that the pKNOT web server will be useful to both biologists in general and structural biologists in particular.
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Affiliation(s)
- Yan-Long Lai
- Institute of Bioinformatics, National Chiao Tung University, Hsinchu 30050, Taiwan and Core Facility for Structural Bioinformatics, National Chiao Tung University, Hsinchu 30050, Taiwan
| | - Shih-Chung Yen
- Institute of Bioinformatics, National Chiao Tung University, Hsinchu 30050, Taiwan and Core Facility for Structural Bioinformatics, National Chiao Tung University, Hsinchu 30050, Taiwan
| | - Sung-Huan Yu
- Institute of Bioinformatics, National Chiao Tung University, Hsinchu 30050, Taiwan and Core Facility for Structural Bioinformatics, National Chiao Tung University, Hsinchu 30050, Taiwan
| | - Jenn-Kang Hwang
- Institute of Bioinformatics, National Chiao Tung University, Hsinchu 30050, Taiwan and Core Facility for Structural Bioinformatics, National Chiao Tung University, Hsinchu 30050, Taiwan
- *To whom correspondence should be addressed. +886-3-513-1337+886-3-572-9288
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28
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Structural and evolutionary bioinformatics of the SPOUT superfamily of methyltransferases. BMC Bioinformatics 2007; 8:73. [PMID: 17338813 PMCID: PMC1829167 DOI: 10.1186/1471-2105-8-73] [Citation(s) in RCA: 130] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2006] [Accepted: 03/05/2007] [Indexed: 11/29/2022] Open
Abstract
Background SPOUT methyltransferases (MTases) are a large class of S-adenosyl-L-methionine-dependent enzymes that exhibit an unusual alpha/beta fold with a very deep topological knot. In 2001, when no crystal structures were available for any of these proteins, Anantharaman, Koonin, and Aravind identified homology between SpoU and TrmD MTases and defined the SPOUT superfamily. Since then, multiple crystal structures of knotted MTases have been solved and numerous new homologous sequences appeared in the databases. However, no comprehensive comparative analysis of these proteins has been carried out to classify them based on structural and evolutionary criteria and to guide functional predictions. Results We carried out extensive searches of databases of protein structures and sequences to collect all members of previously identified SPOUT MTases, and to identify previously unknown homologs. Based on sequence clustering, characterization of domain architecture, structure predictions and sequence/structure comparisons, we re-defined families within the SPOUT superfamily and predicted putative active sites and biochemical functions for the so far uncharacterized members. We have also delineated the common core of SPOUT MTases and inferred a multiple sequence alignment for the conserved knot region, from which we calculated the phylogenetic tree of the superfamily. We have also studied phylogenetic distribution of different families, and used this information to infer the evolutionary history of the SPOUT superfamily. Conclusion We present the first phylogenetic tree of the SPOUT superfamily since it was defined, together with a new scheme for its classification, and discussion about conservation of sequence and structure in different families, and their functional implications. We identified four protein families as new members of the SPOUT superfamily. Three of these families are functionally uncharacterized (COG1772, COG1901, and COG4080), and one (COG1756 represented by Nep1p) has been already implicated in RNA metabolism, but its biochemical function has been unknown. Based on the inference of orthologous and paralogous relationships between all SPOUT families we propose that the Last Universal Common Ancestor (LUCA) of all extant organisms contained at least three SPOUT members, ancestors of contemporary RNA MTases that carry out m1G, m3U, and 2'O-ribose methylation, respectively. In this work we also speculate on the origin of the knot and propose possible 'unknotted' ancestors. The results of our analysis provide a comprehensive 'roadmap' for experimental characterization of SPOUT MTases and interpretation of functional studies in the light of sequence-structure relationships.
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29
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Mallam AL, Jackson SE. The Dimerization of an α/β-Knotted Protein Is Essential for Structure and Function. Structure 2007; 15:111-22. [PMID: 17223537 DOI: 10.1016/j.str.2006.11.007] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2006] [Revised: 11/24/2006] [Accepted: 11/29/2006] [Indexed: 11/29/2022]
Abstract
alpha/beta-Knotted proteins are an extraordinary example of biological self-assembly; they contain a deep topological trefoil knot formed by the backbone polypeptide chain. Evidence suggests that all are dimeric and function as methyltransferases, and the deep knot forms part of the active site. We investigated the significance of the dimeric structure of the alpha/beta-knot protein, YibK, from Haemophilus influenzae by the design and engineering of monomeric versions of the protein, followed by examination of their structural, functional, stability, and kinetic folding properties. Monomeric forms of YibK display similar characteristics to an intermediate species populated during the formation of the wild-type dimer. However, a notable loss in structure involving disruption to the active site, rendering it incapable of cofactor binding, is observed in monomeric YibK. Thus, dimerization is vital for preservation of the native structure and, therefore, activity of the protein.
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Affiliation(s)
- Anna L Mallam
- Chemistry Department, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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30
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Zhu CH, Lu FP, He YN, Han ZL, Du LX. Regulation of avilamycin biosynthesis in Streptomyces viridochromogenes: effects of glucose, ammonium ion, and inorganic phosphate. Appl Microbiol Biotechnol 2007; 73:1031-8. [PMID: 16941176 DOI: 10.1007/s00253-006-0572-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2006] [Revised: 06/19/2006] [Accepted: 07/09/2006] [Indexed: 11/30/2022]
Abstract
Effects of glucose, ammonium ions and phosphate on avilamycin biosynthesis in Streptomyces viridochromogenes AS4.126 were investigated. Twenty grams per liter of glucose, 10 mmol/L ammonium ions, and 10 mmol/L phosphate in the basal medium stimulated avilamycin biosynthesis. When the concentrations of glucose, ammonium ions, and phosphate in the basal medium exceeded 20 g/L, 10 mmol/L, and 10 mmol/L, respectively, avilamycin biosynthesis greatly decreased. When 20 g/L glucose was added at 32 h, avilamycin yield decreased by 70.2%. Avilamycin biosynthesis hardly continued when 2-deoxy-glucose was added into the basal medium at 32 h. There was little influence on avilamycin biosynthesis with the addition of the 3-methyl-glucose (20 g/L) at 32 h. In the presence of excess (NH4)2SO4 (20 mmol/L), the activities of valine dehydrogenase and glucose-6-phosphate dehydrogenase were depressed 47.7 and 58.3%, respectively, of that of the control at 48 h. The activity of succinate dehydrogenase increased 49.5% compared to the control at 48 h. The intracellular adenosine triphosphate level and 6-phosphate glucose content of S. viridochromogenes were 128 and 129%, respectively, of that of the control at 48 h, with the addition of the 40 mmol/L of KH2PO4. As a result, high concentrations of glucose, ammonium ions, and inorganic phosphate all led to the absence of the precursors for avilamycin biosynthesis and affected antibiotic synthesis.
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Affiliation(s)
- Chuan-he Zhu
- Tianjin Key Lab of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, 30022, Tianjin, People's Republic of China
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31
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Mallam AL, Jackson SE. A comparison of the folding of two knotted proteins: YbeA and YibK. J Mol Biol 2006; 366:650-65. [PMID: 17169371 DOI: 10.1016/j.jmb.2006.11.014] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2006] [Revised: 10/19/2006] [Accepted: 11/03/2006] [Indexed: 10/23/2022]
Abstract
The extraordinary topology of proteins belonging to the alpha/beta-knot superfamily of proteins is unexpected, due to the apparent complexities involved in the formation of a deep trefoil knot in a polypeptide backbone. Despite this, an increasing number of knotted structures are being identified; how such proteins fold remains a mystery. Studies on the dimeric protein YibK from Haemophilus influenzae have led to the characterisation of its folding pathway in some detail. To complement research into the folding of YibK, and to address whether folding pathways are conserved for members of the alpha/beta-knot superfamily, the structurally similar knotted protein YbeA from Escherichia coli has been studied. A comprehensive thermodynamic and kinetic analysis of the folding of YbeA is presented here, and compared to that of YibK. Both fold via an intermediate state populated under equilibrium conditions that is monomeric and considerably structured. The unfolding/refolding kinetics of YbeA are simpler than those found for YibK and involve two phases attributed to the formation of a monomeric intermediate state and a dimerisation step. In contrast to YibK, a change in the rate-determining step on the unfolding pathway for YbeA is observed with a changing concentration of urea. Despite this difference, both proteins fold by a mechanism involving at least one sequential monomeric intermediate that has properties similar to that observed during the equilibrium unfolding. The rate of dimerisation observed for YbeA and YibK is very similar, as is the rate constant for formation of the kinetic monomeric intermediate that precedes dimerisation. The findings suggest that relatively slow folding and dimerisation may be common attributes of knotted proteins.
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Affiliation(s)
- Anna L Mallam
- University Chemical Laboratory, Lensfield Road, Cambridge, CB2 1EW, UK
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32
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Watanabe K, Nureki O, Fukai S, Endo Y, Hori H. Functional Categorization of the Conserved Basic Amino Acid Residues in TrmH (tRNA (Gm18) Methyltansferase) Enzymes. J Biol Chem 2006; 281:34630-9. [PMID: 16963456 DOI: 10.1074/jbc.m606141200] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Transfer RNA (Gm18) methyltransferase (TrmH) catalyzes the methyl transfer from S-adenosyl-L-methionine (AdoMet) to the 2'-OH group of the G18 ribose in tRNA. To identify amino acid residues responsible for the tRNA recognition, we have carried out the alanine substitution mutagenesis of the basic amino acid residues that are conserved only in TrmH enzymes and not in the other SpoU proteins. We analyzed the mutant proteins by S-adenosyl-L-homocysteine affinity column chromatography, gel mobility shift assay, and kinetic assay of the methyl transfer reaction. Based on these biochemical studies and the crystal structure of TrmH, we found that the conserved residues can be categorized according to their role (i) in the catalytic center (Arg-41), (ii) in the initial site of tRNA binding (Lys-90, Arg-166, Arg-168, and Arg-176), (iii) in the tRNA binding site required for continuation the catalytic cycle (Arg-8, Arg-19, and Lys-32), (iv) in the structural element involved in release of S-adenosyl-L-homocysteine (Arg-11-His-71-Met-147 interaction), (v) in the assisted phosphate binding site (His-34), or (vi) in an unknown function (Arg-109). Furthermore, the difference between the Kd and Km values for tRNA suggests that the affinity for tRNA is enhanced in the presence of AdoMet. To confirm this idea, we carried out the kinetic studies, a gel mobility shift assay with a mutant protein disrupted in the catalytic center, and the analytical gel-filtration chromatography. Our experimental results clearly show that the enzyme has a semi-ordered sequential mechanism in which AdoMet both enhances the affinity for tRNA and induces formation of the tetramer structure.
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Affiliation(s)
- Kazunori Watanabe
- Department of Applied Chemistry, Faculty of Engineering, Ehime University, Bunkyo 3, Matsuyama 790-8577, Japan
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33
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Purta E, van Vliet F, Tkaczuk KL, Dunin-Horkawicz S, Mori H, Droogmans L, Bujnicki JM. The yfhQ gene of Escherichia coli encodes a tRNA:Cm32/Um32 methyltransferase. BMC Mol Biol 2006; 7:23. [PMID: 16848900 PMCID: PMC1569432 DOI: 10.1186/1471-2199-7-23] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2006] [Accepted: 07/18/2006] [Indexed: 11/10/2022] Open
Abstract
Background Naturally occurring tRNAs contain numerous modified nucleosides. They are formed by enzymatic modification of the primary transcripts during the complex RNA maturation process. In model organisms Escherichia coli and Saccharomyces cerevisiae most enzymes involved in this process have been identified. Interestingly, it was found that tRNA methylation, one of the most common modifications, can be introduced by S-adenosyl-L-methionine (AdoMet)-dependent methyltransferases (MTases) that belong to two structurally and phylogenetically unrelated protein superfamilies: RFM and SPOUT. Results As a part of a large-scale project aiming at characterization of a complete set of RNA modification enzymes of model organisms, we have studied the Escherichia coli proteins YibK, LasT, YfhQ, and YbeA for their ability to introduce the last unassigned methylations of ribose at positions 32 and 34 of the tRNA anticodon loop. We found that YfhQ catalyzes the AdoMet-dependent formation of Cm32 or Um32 in tRNASer1 and tRNAGln2 and that an E. coli strain with a disrupted yfhQ gene lacks the tRNA:Cm32/Um32 methyltransferase activity. Thus, we propose to rename YfhQ as TrMet(Xm32) according to the recently proposed, uniform nomenclature for all RNA modification enzymes, or TrmJ, according to the traditional nomenclature for bacterial tRNA MTases. Conclusion Our results reveal that methylation at position 32 is carried out by completely unrelated TrMet(Xm32) enzymes in eukaryota and prokaryota (RFM superfamily member Trm7 and SPOUT superfamily member TrmJ, respectively), mirroring the scenario observed in the case of the m1G37 modification (introduced by the RFM member Trm5 in eukaryota and archaea, and by the SPOUT member TrmD in bacteria).
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Affiliation(s)
- Elzbieta Purta
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, ul. ks. Trojdena 4, 02-109 Warsaw, Poland
- Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Françoise van Vliet
- Institut de Recherches Microbiologiques Wiame, avenue E. Gryson 1, B-1070 Bruxelles, Belgium
| | - Karolina L Tkaczuk
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, ul. ks. Trojdena 4, 02-109 Warsaw, Poland
- Institute of Technical Biochemistry, Technical University of Lodz, B. Stefanowskiego 4/10, 90-924 Lodz, Poland
| | - Stanislaw Dunin-Horkawicz
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, ul. ks. Trojdena 4, 02-109 Warsaw, Poland
| | - Hirotada Mori
- Institute of Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0035, Japan
| | - Louis Droogmans
- Laboratoire de Microbiologie, Université Libre de Bruxelles, Institut de Recherches Microbiologiques Wiame, avenue E. Gryson 1, B-1070 Bruxelles, Belgium
| | - Janusz M Bujnicki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, ul. ks. Trojdena 4, 02-109 Warsaw, Poland
- Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
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34
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Mallam AL, Jackson SE. Probing Nature’s Knots: The Folding Pathway of a Knotted Homodimeric Protein. J Mol Biol 2006; 359:1420-36. [PMID: 16787779 DOI: 10.1016/j.jmb.2006.04.032] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2006] [Revised: 04/11/2006] [Accepted: 04/13/2006] [Indexed: 11/24/2022]
Abstract
The homodimeric protein YibK from Haemophilus influenzae belongs to a recently discovered superfamily of knotted proteins that has brought about a new protein-folding conundrum. Members of the alpha/beta-knot clan form deep trefoil knots in their native backbone structure, a topological feature that is currently unexplained in the protein-folding field. To help solve the puzzle of how a polypeptide chain can efficiently knot itself, the folding kinetics of YibK have been studied extensively and the results are reported here. Folding was monitored using probes for changes in both secondary and tertiary structure, and the monomer-dimer equilibrium was perturbed with a variety of solution conditions to allow characterisation of otherwise inaccessible states. Multiphasic kinetics were observed in the unfolding and refolding reactions of YibK, and under conditions where the dimer is favoured, dissociation and association were rate-limiting, respectively. A folding model consistent with all kinetic data is proposed: YibK appears to fold via two parallel pathways, partitioned by proline isomerisation events, to two distinct monomeric intermediates. These form a common third intermediate that is able to fold to native dimer. Kinetic simulations suggest that all intermediates are on-pathway. These results provide the valuable groundwork required to further understand how Nature codes for knot formation.
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35
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Tkaczuk KL, Obarska A, Bujnicki JM. Molecular phylogenetics and comparative modeling of HEN1, a methyltransferase involved in plant microRNA biogenesis. BMC Evol Biol 2006; 6:6. [PMID: 16433904 PMCID: PMC1397878 DOI: 10.1186/1471-2148-6-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2005] [Accepted: 01/24/2006] [Indexed: 11/17/2022] Open
Abstract
Background Recently, HEN1 protein from Arabidopsis thaliana was discovered as an essential enzyme in plant microRNA (miRNA) biogenesis. HEN1 transfers a methyl group from S-adenosylmethionine to the 2'-OH or 3'-OH group of the last nucleotide of miRNA/miRNA* duplexes produced by the nuclease Dicer. Previously it was found that HEN1 possesses a Rossmann-fold methyltransferase (RFM) domain and a long N-terminal extension including a putative double-stranded RNA-binding motif (DSRM). However, little is known about the details of the structure and the mechanism of action of this enzyme, and about its phylogenetic origin. Results Extensive database searches were carried out to identify orthologs and close paralogs of HEN1. Based on the multiple sequence alignment a phylogenetic tree of the HEN1 family was constructed. The fold-recognition approach was used to identify related methyltransferases with experimentally solved structures and to guide the homology modeling of the HEN1 catalytic domain. Additionally, we identified a La-like predicted RNA binding domain located C-terminally to the DSRM domain and a domain with a peptide prolyl cis/trans isomerase (PPIase) fold, but without the conserved PPIase active site, located N-terminally to the catalytic domain. Conclusion The bioinformatics analysis revealed that the catalytic domain of HEN1 is not closely related to any known RNA:2'-OH methyltransferases (e.g. to the RrmJ/fibrillarin superfamily), but rather to small-molecule methyltransferases. The structural model was used as a platform to identify the putative active site and substrate-binding residues of HEN and to propose its mechanism of action.
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Affiliation(s)
- Karolina L Tkaczuk
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland
- Institute of Technical Biochemistry, Technical University of Lodz, Stefanowskiego 4/10, 90-924 Lodz, Poland
| | - Agnieszka Obarska
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland
| | - Janusz M Bujnicki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland
- Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
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36
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Pleshe E, Truesdell J, Batey RT. Structure of a class II TrmH tRNA-modifying enzyme from Aquifex aeolicus. Acta Crystallogr Sect F Struct Biol Cryst Commun 2005; 61:722-8. [PMID: 16511140 PMCID: PMC1952360 DOI: 10.1107/s1744309105022980] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2005] [Accepted: 07/19/2005] [Indexed: 11/10/2022]
Abstract
Biological RNAs contain a variety of post-transcriptional modifications that facilitate their efficient function in the cellular environment. One of the two most common forms of modification is methylation of the 2'-hydroxyl group of the ribose sugar, which is performed by a number of S-adenosylmethionine (SAM) dependent methyltransferases. In bacteria, many of these modifications in tRNA and rRNA are carried out by the alpha/beta-knot superfamily of enzymes, whose SAM-binding pocket is created by a characteristic deep trefoil knot. TrmH, an enzyme found throughout all three kingdoms of life, modifies the universally conserved guanosine 18 position of tRNA. The crystal structure of TrmH from the thermophilic bacterium Aquifex aeolicus has been determined at 1.85 A resolution using data collected from a synchrotron-radiation source. The protein reveals a fold typical of members of the SpoU clan of proteins, a subfamily of the alpha/beta-knot superfamily, with alpha-helical extensions at the N- and C-termini that are likely to be involved in tRNA binding.
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Affiliation(s)
- Elizabeth Pleshe
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, Campus Box 215, Boulder, CO 80309-0215, USA
| | - John Truesdell
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, Campus Box 215, Boulder, CO 80309-0215, USA
| | - Robert T. Batey
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, Campus Box 215, Boulder, CO 80309-0215, USA
- Correspondence e-mail:
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