1
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Smith SS. The bisulfite reaction with cytosine and genomic DNA structure. Anal Biochem 2024; 691:115532. [PMID: 38609028 DOI: 10.1016/j.ab.2024.115532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 02/19/2024] [Accepted: 04/04/2024] [Indexed: 04/14/2024]
Abstract
The bisulfite reaction with native DNA has been extensively employed in the detection of non-B DNA structures that can form spontaneously in DNA. These sequences are dynamic in that they can adopt both normal Watson-Crick paired B-DNA or unusual structures like the Triplex, G-Quadruplex, i-motif and Cruciform or Hairpin. Considerable evidence now suggests that these dynamic sequences play roles in both epigenetics and mutagenesis. The bisulfite reaction with native DNA offers a key approach to their detection. In this application whole cells, isolated nuclei or isolated DNA are treated with bisulfite under non-denaturing conditions in order to detect bisulfite accessible regions DNA that are associated with these structures. Here I review the stereochemistry of the bisulfite reaction, the electronic structure of its DNA cytosine substrates and its application in the detection of unusual structures in native DNA.
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Affiliation(s)
- Steven S Smith
- Department of Stem Cell Biology and Regenerative Medicine, Beckman Research Institute of the City of Hope, Duarte, CA, USA.
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2
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Sigal M, Matsumoto S, Beattie A, Katoh T, Suga H. Engineering tRNAs for the Ribosomal Translation of Non-proteinogenic Monomers. Chem Rev 2024; 124:6444-6500. [PMID: 38688034 PMCID: PMC11122139 DOI: 10.1021/acs.chemrev.3c00894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/21/2024] [Accepted: 04/10/2024] [Indexed: 05/02/2024]
Abstract
Ribosome-dependent protein biosynthesis is an essential cellular process mediated by transfer RNAs (tRNAs). Generally, ribosomally synthesized proteins are limited to the 22 proteinogenic amino acids (pAAs: 20 l-α-amino acids present in the standard genetic code, selenocysteine, and pyrrolysine). However, engineering tRNAs for the ribosomal incorporation of non-proteinogenic monomers (npMs) as building blocks has led to the creation of unique polypeptides with broad applications in cellular biology, material science, spectroscopy, and pharmaceuticals. Ribosomal polymerization of these engineered polypeptides presents a variety of challenges for biochemists, as translation efficiency and fidelity is often insufficient when employing npMs. In this Review, we will focus on the methodologies for engineering tRNAs to overcome these issues and explore recent advances both in vitro and in vivo. These efforts include increasing orthogonality, recruiting essential translation factors, and creation of expanded genetic codes. After our review on the biochemical optimizations of tRNAs, we provide examples of their use in genetic code manipulation, with a focus on the in vitro discovery of bioactive macrocyclic peptides containing npMs. Finally, an analysis of the current state of tRNA engineering is presented, along with existing challenges and future perspectives for the field.
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Affiliation(s)
- Maxwell Sigal
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Satomi Matsumoto
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Adam Beattie
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takayuki Katoh
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroaki Suga
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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3
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Lahry K, Datta M, Varshney U. Genetic analysis of translation initiation in bacteria: An initiator tRNA-centric view. Mol Microbiol 2024. [PMID: 38410838 DOI: 10.1111/mmi.15243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 02/03/2024] [Accepted: 02/09/2024] [Indexed: 02/28/2024]
Abstract
Translation of messenger RNA (mRNA) in bacteria occurs in the steps of initiation, elongation, termination, and ribosome recycling. The initiation step comprises multiple stages and uses a special transfer RNA (tRNA) called initiator tRNA (i-tRNA), which is first aminoacylated and then formylated using methionine and N10 -formyl-tetrahydrofolate (N10 -fTHF), respectively. Both methionine and N10 -fTHF are produced via one-carbon metabolism, linking translation initiation with active cellular metabolism. The fidelity of i-tRNA binding to the ribosomal peptidyl-site (P-site) is attributed to the structural features in its acceptor stem, and the highly conserved three consecutive G-C base pairs (3GC pairs) in the anticodon stem. The acceptor stem region is important in formylation of the amino acid attached to i-tRNA and in its initial binding to the P-site. And, the 3GC pairs are crucial in transiting the i-tRNA through various stages of initiation. We utilized the feature of 3GC pairs to investigate the nuanced layers of scrutiny that ensure fidelity of translation initiation through i-tRNA abundance and its interactions with the components of the translation apparatus. We discuss the importance of i-tRNA in the final stages of ribosome maturation, as also the roles of the Shine-Dalgarno sequence, ribosome heterogeneity, initiation factors, ribosome recycling factor, and coevolution of the translation apparatus in orchestrating a delicate balance between the fidelity of initiation and/or its leakiness to generate proteome plasticity in cells to confer growth fitness advantages in response to the dynamic nutritional states.
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Affiliation(s)
- Kuldeep Lahry
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
| | - Madhurima Datta
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
| | - Umesh Varshney
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
- Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India
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4
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Kafri M, Patena W, Martin L, Wang L, Gomer G, Ergun SL, Sirkejyan AK, Goh A, Wilson AT, Gavrilenko SE, Breker M, Roichman A, McWhite CD, Rabinowitz JD, Cross FR, Wühr M, Jonikas MC. Systematic identification and characterization of genes in the regulation and biogenesis of photosynthetic machinery. Cell 2023; 186:5638-5655.e25. [PMID: 38065083 PMCID: PMC10760936 DOI: 10.1016/j.cell.2023.11.007] [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: 09/18/2022] [Revised: 08/03/2023] [Accepted: 11/03/2023] [Indexed: 12/18/2023]
Abstract
Photosynthesis is central to food production and the Earth's biogeochemistry, yet the molecular basis for its regulation remains poorly understood. Here, using high-throughput genetics in the model eukaryotic alga Chlamydomonas reinhardtii, we identify with high confidence (false discovery rate [FDR] < 0.11) 70 poorly characterized genes required for photosynthesis. We then enable the functional characterization of these genes by providing a resource of proteomes of mutant strains, each lacking one of these genes. The data allow assignment of 34 genes to the biogenesis or regulation of one or more specific photosynthetic complexes. Further analysis uncovers biogenesis/regulatory roles for at least seven proteins, including five photosystem I mRNA maturation factors, the chloroplast translation factor MTF1, and the master regulator PMR1, which regulates chloroplast genes via nuclear-expressed factors. Our work provides a rich resource identifying regulatory and functional genes and placing them into pathways, thereby opening the door to a system-level understanding of photosynthesis.
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Affiliation(s)
- Moshe Kafri
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Weronika Patena
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Lance Martin
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA; Lewis-Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Lianyong Wang
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Gillian Gomer
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Sabrina L Ergun
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA; Howard Hughes Medical Institute, Princeton University, Princeton, NJ 08544, USA
| | - Arthur K Sirkejyan
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Audrey Goh
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Alexandra T Wilson
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Sophia E Gavrilenko
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Michal Breker
- Laboratory of Cell Cycle Genetics, The Rockefeller University, New York, NY 10021, USA
| | - Asael Roichman
- Lewis-Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Claire D McWhite
- Lewis-Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Joshua D Rabinowitz
- Lewis-Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Frederick R Cross
- Laboratory of Cell Cycle Genetics, The Rockefeller University, New York, NY 10021, USA
| | - Martin Wühr
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA; Lewis-Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Martin C Jonikas
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA; Howard Hughes Medical Institute, Princeton University, Princeton, NJ 08544, USA.
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5
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Kim D, Seok OH, Ju S, Kim SY, Kim JM, Lee C, Hwang CS. Detection of Nα-terminally formylated native proteins by a pan-N-formyl methionine-specific antibody. J Biol Chem 2023; 299:104652. [PMID: 36990220 PMCID: PMC10164907 DOI: 10.1016/j.jbc.2023.104652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 03/03/2023] [Accepted: 03/20/2023] [Indexed: 03/29/2023] Open
Abstract
N-formyl methionine (fMet)-containing proteins are produced in bacteria, eukaryotic organelles mitochondria and plastids, and even in cytosol. However, Nα-terminally (Nt-) formylated proteins have been poorly characterized because of the lack of appropriate tools to detect fMet independently of downstream proximal sequences. Using a fMet-Gly-Ser-Gly-Cys peptide as an antigen, we generated a pan-fMet-specific rabbit polyclonal antibody called anti-fMet. The raised anti-fMet recognized universally and sequence context-independently Nt-formylated proteins in bacterial, yeast, and human cells as determined by a peptide spot array, dot blotting, and immunoblotting. We anticipate that the anti-fMet antibody will be broadly used to enable an understanding of the poorly explored functions and mechanisms of Nt-formylated proteins in various organisms.
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6
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Lescallette AR, Dunn ZD, Manning VA, Trippe KM, Li B. Biosynthetic Origin of Formylaminooxyvinylglycine and Characterization of the Formyltransferase GvgI. Biochemistry 2022; 61:2159-2164. [PMID: 36126313 DOI: 10.1021/acs.biochem.2c00374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
4-Formylaminooxyvinylglycine (FVG) is an herbicidal and antibacterial nonproteinogenic amino acid produced by several strains of the Pseudomonas fluorescens species complex. It contains a unique vinyl alkoxyamine moiety with an O-N bond, and its biosynthetic origin remains unknown. Here, we show that the gvg cluster from P. fluorescens WH6 is responsible for the biosynthesis of FVG and two additional O-N bond-containing oxyvinylglycines, guanidinooxyvinylglycine and aminooxyvinylglycine. Feeding studies in the producing bacteria indicate that these compounds originate from homoserine. We identify a formyltransferase gvgI that is required for the production of FVG and characterize the activity of this enzyme in vitro toward amino acids with a side chain amine. Sequence similarity network analysis reveals that GvgI and homologues make up a distinct group from the main classes of formyltransferases.
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Affiliation(s)
- Adam R Lescallette
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290, United States
| | - Zachary D Dunn
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290, United States
| | - Viola A Manning
- USDA-ARS Forage Seed and Cereal Research Unit, Corvallis, Oregon 97331, United States
- Department of Crop and Soil Science, Oregon State University, Corvallis, Oregon 97331, United States
| | - Kristin M Trippe
- USDA-ARS Forage Seed and Cereal Research Unit, Corvallis, Oregon 97331, United States
- Department of Crop and Soil Science, Oregon State University, Corvallis, Oregon 97331, United States
| | - Bo Li
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290, United States
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290, United States
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7
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Jew KM, Le VTB, Amaral K, Ta A, Nguyen May NM, Law M, Adelstein N, Kuhn ML. Investigation of the Importance of Protein 3D Structure for Assessing Conservation of Lysine Acetylation Sites in Protein Homologs. Front Microbiol 2022; 12:805181. [PMID: 35173693 PMCID: PMC8843374 DOI: 10.3389/fmicb.2021.805181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 12/14/2021] [Indexed: 11/16/2022] Open
Abstract
Acetylation is a protein post-translational modification (PTM) that can affect a variety of cellular processes. In bacteria, two PTM Nε-acetylation mechanisms have been identified: non-enzymatic/chemical acetylation via acetyl phosphate or acetyl coenzyme A and enzymatic acetylation via protein acetyltransferases. Prior studies have shown that extensive acetylation of Nε-lysine residues of numerous proteins from a variety of bacteria occurs via non-enzymatic acetylation. In Escherichia coli, new Nε-lysine acetyltransferases (KATs) that enzymatically acetylate other proteins have been identified, thus expanding the repertoire of protein substrates that are potentially regulated by acetylation. Therefore, we designed a study to leverage the wealth of structural data in the Protein Data Bank (PDB) to determine: (1) the 3D location of lysine residues on substrate proteins that are acetylated by E. coli KATs, and (2) investigate whether these residues are conserved on 3D structures of their homologs. Five E. coli KAT substrate proteins that were previously identified as being acetylated by YiaC and had 3D structures in the PDB were selected for further analysis: adenylate kinase (Adk), isocitrate dehydrogenase (Icd), catalase HPII (KatE), methionyl-tRNA formyltransferase (Fmt), and a peroxide stress resistance protein (YaaA). We methodically compared over 350 protein structures of these E. coli enzymes and their homologs; to accurately determine lysine residue conservation requires a strategy that incorporates both flexible structural alignments and visual inspection. Moreover, our results revealed discrepancies in conclusions about lysine residue conservation in homologs when examining linear amino acid sequences compared to 3D structures.
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Affiliation(s)
- Kristen M Jew
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA, United States
| | - Van Thi Bich Le
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA, United States
| | - Kiana Amaral
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA, United States
| | - Allysa Ta
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA, United States
| | - Nina M Nguyen May
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA, United States
| | - Melissa Law
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA, United States
| | - Nicole Adelstein
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA, United States
| | - Misty L Kuhn
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA, United States
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8
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Abstract
Putative tumor suppressor ALDH1L1, the product of natural fusion of three unrelated genes, regulates folate metabolism by catalyzing NADP+-dependent conversion of 10-formyltetrahydrofolate to tetrahydrofolate and CO2. Cryo-EM structures of tetrameric rat ALDH1L1 revealed the architecture and functional domain interactions of this complex enzyme. Highly mobile N-terminal domains, which remove formyl from 10-formyltetrahydrofolate, undergo multiple transient inter-domain interactions. The C-terminal aldehyde dehydrogenase domains, which convert formyl to CO2, form unusually large interfaces with the intermediate domains, homologs of acyl/peptidyl carrier proteins (A/PCPs), which transfer the formyl group between the catalytic domains. The 4'-phosphopantetheine arm of the intermediate domain is fully extended and reaches deep into the catalytic pocket of the C-terminal domain. Remarkably, the tetrameric state of ALDH1L1 is indispensable for catalysis because the intermediate domain transfers formyl between the catalytic domains of different protomers. These findings emphasize the versatility of A/PCPs in complex, highly dynamic enzymatic systems.
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9
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Yashiro Y, Zhang C, Sakaguchi Y, Suzuki T, Tomita K. Molecular basis of glycyl-tRNA Gly acetylation by TacT from Salmonella Typhimurium. Cell Rep 2021; 37:110130. [PMID: 34936863 DOI: 10.1016/j.celrep.2021.110130] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 10/25/2021] [Accepted: 11/23/2021] [Indexed: 10/19/2022] Open
Abstract
Bacterial toxin-antitoxin modules contribute to the stress adaptation, persistence, and dormancy of bacteria for survival under environmental stresses and are involved in bacterial pathogenesis. In Salmonella Typhimurium, the Gcn5-related N-acetyltransferase toxin TacT reportedly acetylates the α-amino groups of the aminoacyl moieties of several aminoacyl-tRNAs, inhibits protein synthesis, and promotes persister formation during the infection of macrophages. Here, we show that TacT exclusively acetylates Gly-tRNAGlyin vivo and in vitro. The crystal structure of the TacT:acetyl-Gly-tRNAGly complex and the biochemical analysis reveal that TacT specifically recognizes the discriminator U73 and G71 in tRNAGly, a combination that is only found in tRNAGly isoacceptors, and discriminates tRNAGly from other tRNA species. Thus, TacT is a Gly-tRNAGly-specific acetyltransferase toxin. The molecular basis of the specific aminoacyl-tRNA acetylation by TacT provides advanced information for the design of drugs targeting Salmonella.
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Affiliation(s)
- Yuka Yashiro
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan
| | - Chuqiao Zhang
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan
| | - Yuriko Sakaguchi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Kozo Tomita
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan.
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10
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Lee BS, Choi WJ, Lee SW, Ko BJ, Yoo TH. Towards Engineering an Orthogonal Protein Translation Initiation System. Front Chem 2021; 9:772648. [PMID: 34765589 PMCID: PMC8576571 DOI: 10.3389/fchem.2021.772648] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 10/14/2021] [Indexed: 11/24/2022] Open
Abstract
In the last two decades, methods to incorporate non-canonical amino acids (ncAAs) into specific positions of a protein have advanced significantly; these methods have become general tools for engineering proteins. However, almost all these methods depend on the translation elongation process, and strategies leveraging the initiation process have rarely been reported. The incorporation of a ncAA specifically at the translation initiation site enables the installation of reactive groups for modification at the N-termini of proteins, which are attractive positions for introducing abiological groups with minimal structural perturbations. In this study, we attempted to engineer an orthogonal protein translation initiation system. Introduction of the identity elements of Escherichia coli initiator tRNA converted an engineered Methanococcus jannaschii tRNATyr into an initiator tRNA. The engineered tRNA enabled the site-specific incorporation of O-propargyl-l-tyrosine (OpgY) into the amber (TAG) codon at the translation initiation position but was inactive toward the elongational TAG codon. Misincorporation of Gln was detected, and the engineered system was demonstrated only with OpgY. We expect further engineering of the initiator tRNA for improved activity and specificity to generate an orthogonal translation initiation system.
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Affiliation(s)
- Byeong Sung Lee
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea
| | - Woon Jong Choi
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea
| | - Sang Woo Lee
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea
| | - Byoung Joon Ko
- School of Biopharmaceutical and Medical Sciences, Sungshin Women's University, Seoul, South Korea
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea.,Department of Applied Chemistry and Biological Engineering, Ajou University, Suwon, South Korea
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11
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Bourgeois G, Seguin J, Babin M, Gondry M, Mechulam Y, Schmitt E. Structural basis of the interaction between cyclodipeptide synthases and aminoacylated tRNA substrates. RNA (NEW YORK, N.Y.) 2020; 26:1589-1602. [PMID: 32680846 PMCID: PMC7566563 DOI: 10.1261/rna.075184.120] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 07/06/2020] [Indexed: 06/11/2023]
Abstract
Cyclodipeptide synthases (CDPSs) catalyze the synthesis of various cyclodipeptides by using two aminoacyl-tRNA (aa-tRNA) substrates in a sequential mechanism. Here, we studied binding of phenylalanyl-tRNAPhe to the CDPS from Candidatus Glomeribacter gigasporarum (Cglo-CDPS) by gel filtration and electrophoretic mobility shift assay. We determined the crystal structure of the Cglo-CDPS:Phe-tRNAPhe complex to 5 Å resolution and further studied it in solution using small-angle X-ray scattering (SAXS). The data show that the major groove of the acceptor stem of the aa-tRNA interacts with the enzyme through the basic β2 and β7 strands of CDPSs belonging to the XYP subfamily. A bending of the CCA extremity enables the amino acid moiety to be positioned in the P1 pocket while the terminal A76 adenosine occupies the P2 pocket. Such a positioning indicates that the present structure illustrates the binding of the first aa-tRNA. In cells, CDPSs and the elongation factor EF-Tu share aminoacylated tRNAs as substrates. The present study shows that CDPSs and EF-Tu interact with opposite sides of tRNA. This may explain how CDPSs hijack aa-tRNAs from canonical ribosomal protein synthesis.
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Affiliation(s)
- Gabrielle Bourgeois
- Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole polytechnique, CNRS, Institut Polytechnique de Paris, 91128 Palaiseau cedex, France
| | - Jérôme Seguin
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Morgan Babin
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Muriel Gondry
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Yves Mechulam
- Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole polytechnique, CNRS, Institut Polytechnique de Paris, 91128 Palaiseau cedex, France
| | - Emmanuelle Schmitt
- Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole polytechnique, CNRS, Institut Polytechnique de Paris, 91128 Palaiseau cedex, France
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12
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Yashiro Y, Sakaguchi Y, Suzuki T, Tomita K. Mechanism of aminoacyl-tRNA acetylation by an aminoacyl-tRNA acetyltransferase AtaT from enterohemorrhagic E. coli. Nat Commun 2020; 11:5438. [PMID: 33116145 PMCID: PMC7595197 DOI: 10.1038/s41467-020-19281-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 10/07/2020] [Indexed: 11/25/2022] Open
Abstract
Toxin-antitoxin systems in bacteria contribute to stress adaptation, dormancy, and persistence. AtaT, a type-II toxin in enterohemorrhagic E. coli, reportedly acetylates the α-amino group of the aminoacyl-moiety of initiator Met-tRNAfMet, thus inhibiting translation initiation. Here, we show that AtaT has a broader specificity for aminoacyl-tRNAs than initially claimed. AtaT efficiently acetylates Gly-tRNAGly, Trp-tRNATrp, Tyr-tRNATyr and Phe-tRNAPhe isoacceptors, in addition to Met-tRNAfMet, and inhibits global translation. AtaT interacts with the acceptor stem of tRNAfMet, and the consecutive G-C pairs in the bottom-half of the acceptor stem are required for acetylation. Consistently, tRNAGly, tRNATrp, tRNATyr and tRNAPhe also possess consecutive G-C base-pairs in the bottom halves of their acceptor stems. Furthermore, misaminoacylated valyl-tRNAfMet and isoleucyl-tRNAfMet are not acetylated by AtaT. Therefore, the substrate selection by AtaT is governed by the specific acceptor stem sequence and the properties of the aminoacyl-moiety of aminoacyl-tRNAs. AtaT is a type-II toxin from enterohemorrhagic E. coli, reported to acetylate the aminoacyl-moiety of initiator Met-tRNAfMet, thus inhibiting translation initiation. Biochemical analysis suggests that AtaT has a broader specificity for aminoacyl-tRNAs and inhibits global translation. Structure of AtaT in complex with acetylated Met-tRNAfMet offers insight into the substrate selection by the enzyme.
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Affiliation(s)
- Yuka Yashiro
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8562, Japan
| | - Yuriko Sakaguchi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Kozo Tomita
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8562, Japan.
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13
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Webster MW, Takacs M, Zhu C, Vidmar V, Eduljee A, Abdelkareem M, Weixlbaumer A. Structural basis of transcription-translation coupling and collision in bacteria. Science 2020; 369:1355-1359. [DOI: 10.1126/science.abb5036] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 07/17/2020] [Indexed: 01/01/2023]
Abstract
Prokaryotic messenger RNAs (mRNAs) are translated as they are transcribed. The lead ribosome potentially contacts RNA polymerase (RNAP) and forms a supramolecular complex known as the expressome. The basis of expressome assembly and its consequences for transcription and translation are poorly understood. Here, we present a series of structures representing uncoupled, coupled, and collided expressome states determined by cryo–electron microscopy. A bridge between the ribosome and RNAP can be formed by the transcription factor NusG, which stabilizes an otherwise-variable interaction interface. Shortening of the intervening mRNA causes a substantial rearrangement that aligns the ribosome entrance channel to the RNAP exit channel. In this collided complex, NusG linkage is no longer possible. These structures reveal mechanisms of coordination between transcription and translation and provide a framework for future study.
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Affiliation(s)
- Michael William Webster
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67404 Illkirch, France
- Université de Strasbourg, 67404 Illkirch, France
- CNRS UMR7104, 67404 Illkirch, France
- INSERM U1258, 67404 Illkirch, France
| | - Maria Takacs
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67404 Illkirch, France
- Université de Strasbourg, 67404 Illkirch, France
- CNRS UMR7104, 67404 Illkirch, France
- INSERM U1258, 67404 Illkirch, France
| | - Chengjin Zhu
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67404 Illkirch, France
- Université de Strasbourg, 67404 Illkirch, France
- CNRS UMR7104, 67404 Illkirch, France
- INSERM U1258, 67404 Illkirch, France
| | - Vita Vidmar
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67404 Illkirch, France
- Université de Strasbourg, 67404 Illkirch, France
- CNRS UMR7104, 67404 Illkirch, France
- INSERM U1258, 67404 Illkirch, France
| | - Ayesha Eduljee
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67404 Illkirch, France
- Université de Strasbourg, 67404 Illkirch, France
- CNRS UMR7104, 67404 Illkirch, France
- INSERM U1258, 67404 Illkirch, France
| | - Mo’men Abdelkareem
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67404 Illkirch, France
- Université de Strasbourg, 67404 Illkirch, France
- CNRS UMR7104, 67404 Illkirch, France
- INSERM U1258, 67404 Illkirch, France
| | - Albert Weixlbaumer
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67404 Illkirch, France
- Université de Strasbourg, 67404 Illkirch, France
- CNRS UMR7104, 67404 Illkirch, France
- INSERM U1258, 67404 Illkirch, France
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14
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Tsiamantas C, Rogers JM, Suga H. Initiating ribosomal peptide synthesis with exotic building blocks. Chem Commun (Camb) 2020; 56:4265-4272. [PMID: 32267262 DOI: 10.1039/d0cc01291b] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ribosomal peptide synthesis begins almost exclusively with the amino acid methionine, across all domains of life. The ubiquity of methionine initiation raises the question; to what extent could polypeptide synthesis be realized with other amino acids, proteinogenic or otherwise? This highlight describes the breadth of building blocks now known to be accepted by the ribosome initiation machinery, from subtle methionine analogues to large exotic non-proteinogenic structures. We outline the key methodological developments that have enabled these discoveries, including the exploitation of methionyl-tRNA synthetase promiscuity, synthetase and tRNA engineering, and the utilization of artificial tRNA-loading ribozymes, flexizymes. Using these methods, the number and diversity of validated initiation building blocks is rapidly expanding permitting the use of the ribosome to synthesize ever more artificial polymers in search of new functional molecules.
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Affiliation(s)
- Christos Tsiamantas
- Department of Chemistry, School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-0033, Japan.
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15
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Liu Y, Martinez A, Yamashita S, Tomita K. Crystal structure of human cytoplasmic tRNAHis-specific 5'-monomethylphosphate capping enzyme. Nucleic Acids Res 2020; 48:1572-1582. [PMID: 31919512 PMCID: PMC7026607 DOI: 10.1093/nar/gkz1216] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 12/15/2019] [Accepted: 12/17/2019] [Indexed: 12/31/2022] Open
Abstract
BCDIN3 domain containing RNA methyltransferase, BCDIN3D, monomethylates the 5′-monophosphate of cytoplasmic tRNAHis with a G−1:A73 mispair at the top of an eight-nucleotide-long acceptor helix, using S-adenosyl-l-methionine (SAM) as a methyl group donor. In humans, BCDIN3D overexpression is associated with the tumorigenic phenotype and poor prognosis in breast cancer. Here, we present the crystal structure of human BCDIN3D complexed with S-adenosyl-l-homocysteine. BCDIN3D adopts a classical Rossmann-fold methyltransferase structure. A comparison of the structure with that of the closely related methylphosphate capping enzyme, MePCE, which monomethylates the 5′-γ-phosphate of 7SK RNA, revealed the important residues for monomethyl transfer from SAM onto the 5′-monophosphate of tRNAHis and for tRNAHis recognition by BCDIN3D. A structural model of tRNAHis docking onto BCDIN3D suggested the molecular mechanism underlying the different activities between BCDIN3D and MePCE. A loop in BCDIN3D is shorter, as compared to the corresponding region that forms an α-helix to recognize the 5′-end of RNA in MePCE, and the G−1:A73 mispair in tRNAHis allows the N-terminal α-helix of BCDIN3D to wedge the G−1:A73 mispair of tRNAHis. As a result, the 5′-monophosphate of G−1 of tRNAHis is deep in the catalytic pocket for 5′-phosphate methylation. Thus, BCDIN3D is a tRNAHis-specific 5′-monomethylphosphate capping enzyme that discriminates tRNAHis from other tRNA species, and the structural information presented in this study also provides the molecular basis for the development of drugs against breast cancers.
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Affiliation(s)
- Yining Liu
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan
| | - Anna Martinez
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan
| | - Seisuke Yamashita
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan
| | - Kozo Tomita
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan
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16
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Muraki N, Ishii K, Uchiyama S, Itoh SG, Okumura H, Aono S. Structural characterization of HypX responsible for CO biosynthesis in the maturation of NiFe-hydrogenase. Commun Biol 2019; 2:385. [PMID: 31646188 PMCID: PMC6802093 DOI: 10.1038/s42003-019-0631-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 09/20/2019] [Indexed: 12/20/2022] Open
Abstract
Several accessory proteins are required for the assembly of the metal centers in hydrogenases. In NiFe-hydrogenases, CO and CN- are coordinated to the Fe in the NiFe dinuclear cluster of the active center. Though these diatomic ligands are biosynthesized enzymatically, detail mechanisms of their biosynthesis remain unclear. Here, we report the structural characterization of HypX responsible for CO biosynthesis to assemble the active site of NiFe hydrogenase. CoA is constitutionally bound in HypX. Structural characterization of HypX suggests that the formyl-group transfer will take place from N10-formyl-THF to CoA to form formyl-CoA in the N-terminal domain of HypX, followed by decarbonylation of formyl-CoA to produce CO in the C-terminal domain though the direct experimental results are not available yet. The conformation of CoA accommodated in the continuous cavity connecting the N- and C-terminal domains will interconvert between the extended and the folded conformations for HypX catalysis.
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Affiliation(s)
- Norifumi Muraki
- Department of Creative Research, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki 444-8787 Japan
- Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki 444-8787 Japan
- Department of Structural Molecular Science, The Graduate University for Advanced Studies, 38 Nishogo-naka, Myodaiji-cho, Okazaki 444-8585 Japan
| | - Kentaro Ishii
- Department of Creative Research, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki 444-8787 Japan
| | - Susumu Uchiyama
- Department of Creative Research, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki 444-8787 Japan
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871 Japan
| | - Satoru G. Itoh
- Department of Creative Research, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki 444-8787 Japan
- Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki 444-8787 Japan
- Department of Structural Molecular Science, The Graduate University for Advanced Studies, 38 Nishogo-naka, Myodaiji-cho, Okazaki 444-8585 Japan
| | - Hisashi Okumura
- Department of Creative Research, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki 444-8787 Japan
- Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki 444-8787 Japan
- Department of Structural Molecular Science, The Graduate University for Advanced Studies, 38 Nishogo-naka, Myodaiji-cho, Okazaki 444-8585 Japan
| | - Shigetoshi Aono
- Department of Creative Research, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki 444-8787 Japan
- Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki 444-8787 Japan
- Department of Structural Molecular Science, The Graduate University for Advanced Studies, 38 Nishogo-naka, Myodaiji-cho, Okazaki 444-8585 Japan
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17
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Rae CD, Gordiyenko Y, Ramakrishnan V. How a circularized tmRNA moves through the ribosome. Science 2019; 363:740-744. [PMID: 30765567 DOI: 10.1126/science.aav9370] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 01/22/2019] [Indexed: 01/05/2023]
Abstract
During trans-translation, transfer-messenger RNA (tmRNA) and small protein B (SmpB) together rescue ribosomes stalled on a truncated mRNA and tag the nascent polypeptide for degradation. We used cryo-electron microscopy to determine the structures of three key states of the tmRNA-SmpB-ribosome complex during trans translation at resolutions of 3.7 to 4.4 angstroms. The results show how tmRNA and SmpB act specifically on stalled ribosomes and how the circularized complex moves through the ribosome, enabling translation to switch from the old defective message to the reading frame on tmRNA.
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Affiliation(s)
- Christopher D Rae
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, England, UK
| | - Yuliya Gordiyenko
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, England, UK
| | - V Ramakrishnan
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, England, UK.
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18
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Kenjić N, Hoag MR, Moraski GC, Caperelli CA, Moran GR, Lamb AL. PvdF of pyoverdin biosynthesis is a structurally unique N 10-formyltetrahydrofolate-dependent formyltransferase. Arch Biochem Biophys 2019; 664:40-50. [PMID: 30689984 DOI: 10.1016/j.abb.2019.01.028] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 01/21/2019] [Accepted: 01/23/2019] [Indexed: 11/17/2022]
Abstract
The hydroxyornithine transformylase from Pseudomonas aeruginosa is known by the gene name pvdF, and has been hypothesized to use N10-formyltetrahydrofolate (N10-fTHF) as a co-substrate formyl donor to convert N5-hydroxyornithine (OHOrn) to N5-formyl- N5-hydroxyornithine (fOHOrn). PvdF is in the biosynthetic pathway for pyoverdin biosynthesis, a siderophore generated under iron-limiting conditions that has been linked to virulence, quorum sensing and biofilm formation. The structure of PvdF was determined by X-ray crystallography to 2.3 Å, revealing a formyltransferase fold consistent with N10-formyltetrahydrofolate dependent enzymes, such as the glycinamide ribonucleotide transformylases, N-sugar transformylases and methionyl-tRNA transformylases. Whereas the core structure, including the catalytic triad, is conserved, PvdF has three insertions of 18 or more amino acids, which we hypothesize are key to binding the OHOrn substrate. Steady state kinetics revealed a non-hyperbolic rate curve, promoting the hypothesis that PvdF uses a random-sequential mechanism, and favors folate binding over OHOrn.
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Affiliation(s)
- Nikola Kenjić
- Department of Molecular Biosciences, 1200 Sunnyside Ave, University of Kansas, Lawrence, KS, 66045, USA
| | - Matthew R Hoag
- Department of Chemistry and Biochemistry, 3210 N Cramer St, University of Wisconsin-Milwaukee, Milwaukee, WI, 53211, USA
| | - Garrett C Moraski
- Department of Chemistry and Biochemistry, 103 Chemistry and Biochemistry Building, Montana State University, Bozeman, MT, 59717, USA
| | - Carol A Caperelli
- Winkle College of Pharmacy, University of Cincinnati, ML 0514, 231 Albert Sabin Way, MSB 3109B, Cincinnati, OH, 45267, USA
| | - Graham R Moran
- Department of Chemistry and Biochemistry, 1068 W Sheridan Rd, Loyola University Chicago, Chicago, IL, 60660, USA
| | - Audrey L Lamb
- Department of Molecular Biosciences, 1200 Sunnyside Ave, University of Kansas, Lawrence, KS, 66045, USA.
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19
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Zou X, Sun Z, Zhao H, Zhang CY. Mechanistic insight into photocrosslinking reaction between triplet state 4-thiopyrimidine and thymine. Phys Chem Chem Phys 2019; 21:21305-21316. [DOI: 10.1039/c9cp04089g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Multiple nonadiabatic pathways greatly facilitate the proceeding of photocrosslinking reactions between 4-thiopyrimidine and thymine.
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Affiliation(s)
- Xiaoran Zou
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
| | - Zhonghua Sun
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
| | - Hongmei Zhao
- Beijing National Laboratory for Molecular Science, Institute of Chemistry, Chinese Academy of Science
- Beijing
- P. R. China
| | - Chun-yang Zhang
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
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20
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Reimer JM, Harb I, Ovchinnikova OG, Jiang J, Whitfield C, Schmeing TM. Structural Insight into a Novel Formyltransferase and Evolution to a Nonribosomal Peptide Synthetase Tailoring Domain. ACS Chem Biol 2018; 13:3161-3172. [PMID: 30346688 DOI: 10.1021/acschembio.8b00739] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Nonribosomal peptide synthetases (NRPSs) increase the chemical diversity of their products by acquiring tailoring domains. Linear gramicidin synthetase starts with a tailoring formylation (F) domain, which likely originated from a sugar formyltransferase (FT) gene. Here, we present studies on an Anoxybacillus kamchatkensis sugar FT representative of the prehorizontal gene transfer FT. Gene cluster analysis reveals that this FT acts on a UDP-sugar in a novel pathway for synthesis of a 7-formamido derivative of CMP-pseudaminic acid. We recapitulate the pathway up to and including the formylation step in vitro, experimentally demonstrating the role of the FT. We also present X-ray crystal structures of the FT alone and with ligands, which unveil contrasts with other structurally characterized sugar FTs and show close structural similarity with the F domain. The structures reveal insights into the adaptations that were needed to co-opt and evolve a sugar FT into a functional and useful NRPS domain.
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Affiliation(s)
- Janice M. Reimer
- Department of Biochemistry, McGill University, Montréal, Québec H3G 0B1, Canada
| | - Ingrid Harb
- Department of Biochemistry, McGill University, Montréal, Québec H3G 0B1, Canada
| | - Olga G. Ovchinnikova
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Jessie Jiang
- Department of Biochemistry, McGill University, Montréal, Québec H3G 0B1, Canada
| | - Chris Whitfield
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - T. Martin Schmeing
- Department of Biochemistry, McGill University, Montréal, Québec H3G 0B1, Canada
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21
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Yang L, Zhong Z, Tong C, Jia H, Liu Y, Chen G. Single-Molecule Mechanical Folding and Unfolding of RNA Hairpins: Effects of Single A-U to A·C Pair Substitutions and Single Proton Binding and Implications for mRNA Structure-Induced -1 Ribosomal Frameshifting. J Am Chem Soc 2018; 140:8172-8184. [PMID: 29884019 DOI: 10.1021/jacs.8b02970] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
A wobble A·C pair can be protonated at near physiological pH to form a more stable wobble A+·C pair. Here, we constructed an RNA hairpin (rHP) and three mutants with one A-U base pair substituted with an A·C mismatch on the top (near the loop, U22C), middle (U25C), and bottom (U29C) positions of the stem, respectively. Our results on single-molecule mechanical (un)folding using optical tweezers reveal the destabilization effect of A-U to A·C pair substitution and protonation-dependent enhancement of mechanical stability facilitated through an increased folding rate, or decreased unfolding rate, or both. Our data show that protonation may occur rapidly upon the formation of an apparent mechanical folding transition state. Furthermore, we measured the bulk -1 ribosomal frameshifting efficiencies of the hairpins by a cell-free translation assay. For the mRNA hairpins studied, -1 frameshifting efficiency correlates with mechanical unfolding force at equilibrium and folding rate at around 15 pN. U29C has a frameshifting efficiency similar to that of rHP (∼2%). Accordingly, the bottom 2-4 base pairs of U29C may not form under a stretching force at pH 7.3, which is consistent with the fact that the bottom base pairs of the hairpins may be disrupted by ribosome at the slippery site. U22C and U25C have a similar frameshifting efficiency (∼1%), indicating that both unfolding and folding rates of an mRNA hairpin in a crowded environment may affect frameshifting. Our data indicate that mechanical (un)folding of RNA hairpins may mimic how mRNAs unfold and fold in the presence of translating ribosomes.
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Affiliation(s)
- Lixia Yang
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371
| | - Zhensheng Zhong
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371.,School of Physics, and State Key Laboratory of Optoelectronic Materials and Technologies , Sun Yat-sen University , Guangzhou 510275 , People's Republic of China
| | - Cailing Tong
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371
| | - Huan Jia
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371
| | - Yiran Liu
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371
| | - Gang Chen
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371
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22
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Wang J, Forster AC. Translational roles of the C75 2'OH in an in vitro tRNA transcript at the ribosomal A, P and E sites. Sci Rep 2017; 7:6709. [PMID: 28751745 PMCID: PMC5532260 DOI: 10.1038/s41598-017-06991-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 06/21/2017] [Indexed: 11/26/2022] Open
Abstract
Aminoacyl-tRNAs containing a deoxy substitution in the penultimate nucleotide (C75 2′OH → 2′H) have been widely used in translation for incorporation of unnatural amino acids (AAs). However, this supposedly innocuous modification surprisingly increased peptidyl-tRNAAlaugc drop off in biochemical assays of successive incorporations. Here we predict the function of this tRNA 2′OH in the ribosomal A, P and E sites using recent co-crystal structures of ribosomes and tRNA substrates and test these structure-function models by systematic kinetics analyses. Unexpectedly, the C75 2′H did not affect A- to P-site translocation nor peptidyl donor activity of tRNAAlaugc. Rather, the peptidyl acceptor activity of the A-site Ala-tRNAAlaugc and the translocation of the P-site deacylated tRNAAlaugc to the E site were impeded. Delivery by EF-Tu was not significantly affected. This broadens our view of the roles of 2′OH groups in tRNAs in translation.
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Affiliation(s)
- Jinfan Wang
- Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, Uppsala, 75124, Sweden
| | - Anthony C Forster
- Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, Uppsala, 75124, Sweden.
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23
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Monestier A, Aleksandrov A, Coureux PD, Panvert M, Mechulam Y, Schmitt E. The structure of an E. coli tRNA fMet A 1-U 72 variant shows an unusual conformation of the A 1-U 72 base pair. RNA (NEW YORK, N.Y.) 2017; 23:673-682. [PMID: 28143889 PMCID: PMC5393177 DOI: 10.1261/rna.057877.116] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 01/26/2017] [Indexed: 06/06/2023]
Abstract
Translation initiation in eukaryotes and archaea involves a methionylated initiator tRNA delivered to the ribosome in a ternary complex with e/aIF2 and GTP. Eukaryotic and archaeal initiator tRNAs contain a highly conserved A1-U72 base pair at the top of the acceptor stem. The importance of this base pair to discriminate initiator tRNAs from elongator tRNAs has been established previously using genetics and biochemistry. However, no structural data illustrating how the A1-U72 base pair participates in the accurate selection of the initiator tRNAs by the translation initiation systems are available. Here, we describe the crystal structure of a mutant E. coli initiator tRNAfMetA1-U72, aminoacylated with methionine, in which the C1:A72 mismatch at the end of the tRNA acceptor stem has been changed to an A1-U72 base pair. Sequence alignments show that the mutant E. coli tRNA is a good mimic of archaeal initiator tRNAs. The crystal structure, determined at 2.8 Å resolution, shows that the A1-U72 pair adopts an unusual arrangement. A1 is in a syn conformation and forms a single H-bond interaction with U72 This interaction requires protonation of the N1 atom of A1 Moreover, the 5' phosphoryl group folds back into the major groove of the acceptor stem and interacts with the N7 atom of G2 A possible role of this unusual geometry of the A1-U72 pair in the recognition of the initiator tRNA by its partners during eukaryotic and archaeal translation initiation is discussed.
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Affiliation(s)
- Auriane Monestier
- Laboratoire de Biochimie, Ecole polytechnique, CNRS, Université Paris-Saclay, 91128 Palaiseau cedex, France
| | - Alexey Aleksandrov
- Laboratoire de Biochimie, Ecole polytechnique, CNRS, Université Paris-Saclay, 91128 Palaiseau cedex, France
| | - Pierre-Damien Coureux
- Laboratoire de Biochimie, Ecole polytechnique, CNRS, Université Paris-Saclay, 91128 Palaiseau cedex, France
| | - Michel Panvert
- Laboratoire de Biochimie, Ecole polytechnique, CNRS, Université Paris-Saclay, 91128 Palaiseau cedex, France
| | - Yves Mechulam
- Laboratoire de Biochimie, Ecole polytechnique, CNRS, Université Paris-Saclay, 91128 Palaiseau cedex, France
| | - Emmanuelle Schmitt
- Laboratoire de Biochimie, Ecole polytechnique, CNRS, Université Paris-Saclay, 91128 Palaiseau cedex, France
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24
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Modeling of interactions between functional domains of ALDH1L1. Chem Biol Interact 2017; 276:23-30. [PMID: 28414156 DOI: 10.1016/j.cbi.2017.04.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 03/23/2017] [Accepted: 04/13/2017] [Indexed: 11/20/2022]
Abstract
ALDH1L1, a member of the aldehyde dehydrogenase superfamily of enzymes, catalyzes the conversion of 10-formyltetrahydrofolate to tetrahydrofolate and CO2. The enzyme is a tetramer of identical subunits, with each subunit consisting of three functional domains that originated from unrelated genes. The N- and C-terminal domains are catalytic, while the intermediate domain transfers the reaction intermediate from the N- to the C-terminal domain. The intermediate domain is an acyl carrier protein, possessing the covalently attached 4'-phosphopantetheine (4-PP) prosthetic group. This prosthetic group is known to function as a swinging arm transferring intermediates between enzymes in complex biosynthetic reactions. Here we have applied computer modeling using available structures of the three functional domains of ALDH1L1 to evaluate the extent of flexibility within the full-length protein. This approach allowed us to define positions of the 4-PP arm within the two catalytic domains and to predict N-terminal:intermediate and intermediate:C-terminal domain interfaces. Our models further suggested high degree of flexibility within the full-length enzyme.
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25
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Hussain T, Llácer JL, Wimberly BT, Kieft JS, Ramakrishnan V. Large-Scale Movements of IF3 and tRNA during Bacterial Translation Initiation. Cell 2016; 167:133-144.e13. [PMID: 27662086 PMCID: PMC5037330 DOI: 10.1016/j.cell.2016.08.074] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 08/04/2016] [Accepted: 08/23/2016] [Indexed: 11/19/2022]
Abstract
In bacterial translational initiation, three initiation factors (IFs 1–3) enable the selection of initiator tRNA and the start codon in the P site of the 30S ribosomal subunit. Here, we report 11 single-particle cryo-electron microscopy (cryoEM) reconstructions of the complex of bacterial 30S subunit with initiator tRNA, mRNA, and IFs 1–3, representing different steps along the initiation pathway. IF1 provides key anchoring points for IF2 and IF3, thereby enhancing their activities. IF2 positions a domain in an extended conformation appropriate for capturing the formylmethionyl moiety charged on tRNA. IF3 and tRNA undergo large conformational changes to facilitate the accommodation of the formylmethionyl-tRNA (fMet-tRNAfMet) into the P site for start codon recognition. Structures of the 30S ribosomal subunit with initiation factors, tRNA and mRNA IF3 helps to position the correct start codon in the P site before binding of tRNA Large-scale conformational changes of IF3 and tRNA are observed IF3 movements facilitate the accommodation of initiator tRNA in P site
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Affiliation(s)
| | - Jose L Llácer
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Brian T Wimberly
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK; Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, CO 80045, USA
| | - Jeffrey S Kieft
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, CO 80045, USA; RNA BioScience Initiative, University of Colorado Denver School of Medicine, Aurora, CO 80045, USA
| | - V Ramakrishnan
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK.
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26
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Structural effects of modified ribonucleotides and magnesium in transfer RNAs. Bioorg Med Chem 2016; 24:4826-4834. [PMID: 27364608 DOI: 10.1016/j.bmc.2016.06.037] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Revised: 06/16/2016] [Accepted: 06/17/2016] [Indexed: 11/20/2022]
Abstract
Modified nucleotides are ubiquitous and important to tRNA structure and function. To understand their effect on tRNA conformation, we performed a series of molecular dynamics simulations on yeast tRNAPhe and tRNAinit, Escherichia coli tRNAinit and HIV tRNALys. Simulations were performed with the wild type modified nucleotides, using the recently developed CHARMM compatible force field parameter set for modified nucleotides (J. Comput. Chem.2016, 37, 896), or with the corresponding unmodified nucleotides, and in the presence or absence of Mg2+. Results showed a stabilizing effect associated with the presence of the modifications and Mg2+ for some important positions, such as modified guanosine in position 37 and dihydrouridines in 16/17 including both structural properties and base interactions. Some other modifications were also found to make subtle contributions to the structural properties of local domains. While we were not able to investigate the effect of adenosine 37 in tRNAinit and limitations were observed in the conformation of E. coli tRNAinit, the presence of the modified nucleotides and of Mg2+ better maintained the structural features and base interactions of the tRNA systems than in their absence indicating the utility of incorporating the modified nucleotides in simulations of tRNA and other RNAs.
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Genetic and Functional Analysis of the Biosynthesis of a Non-Ribosomal Peptide Siderophore in Burkholderia xenovorans LB400. PLoS One 2016; 11:e0151273. [PMID: 26963250 PMCID: PMC4786211 DOI: 10.1371/journal.pone.0151273] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 02/25/2016] [Indexed: 11/26/2022] Open
Abstract
B. xenovorans LB400 is a model bacterium for the study of the metabolism of aromatic compounds. The aim of this study was the genomic and functional characterization of a non-ribosomal peptide synthetase containing gene cluster that encodes a siderophore in B. xenovorans LB400. The mba gene cluster from strain LB400 encodes proteins involved in the biosynthesis and transport of a hydroxamate-type siderophore. Strain LB400 has a unique mba gene organization, although mba gene clusters have been observed in diverse Burkholderiales. Bioinformatic analysis revealed the presence of promoters in the mba gene cluster that strongly suggest regulation by the ferric uptake regulator protein (Fur) and by the alternative RNA polymerase extracytoplasmic function sigma factor MbaF. Reverse transcriptase PCR analyses showed the expression of iron-regulated transcriptional units mbaFGHIJKL, mbaN, mbaABCE, mbaO, mbaP and mbaD genes under iron limitation. Chrome azurol S (CAS) assay strongly suggests that strain LB400 synthesized a siderophore under iron limitation. Mass spectrometry ESI-MS and MALDI-TOF-MS analyses revealed that the siderophore is a non-ribosomal peptide, and forms an iron complex with a molecular mass of 676 Da. Based on bioinformatic prediction, CAS assay and MS analyses, we propose that the siderophore is L-Nδ-hydroxy-Nδ-formylOrn-D-β-hydroxyAsp-L-Ser-L-Nδ-hydroxy-Nδ-formylOrn-1,4-diaminobutane that is closely related to malleobactin-type siderophores reported in B. thailandensis.
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28
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Transfer RNA: From pioneering crystallographic studies to contemporary tRNA biology. Arch Biochem Biophys 2016; 602:95-105. [PMID: 26968773 DOI: 10.1016/j.abb.2016.03.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 02/29/2016] [Accepted: 03/03/2016] [Indexed: 12/17/2022]
Abstract
Transfer RNAs (tRNAs) play a key role in protein synthesis as adaptor molecules between messenger RNA and protein sequences on the ribosome. Their discovery in the early sixties provoked a worldwide infatuation with the study of their architecture and their function in the decoding of genetic information. tRNAs are also emblematic molecules in crystallography: the determination of the first tRNA crystal structures represented a milestone in structural biology and tRNAs were for a long period the sole source of information on RNA folding, architecture, and post-transcriptional modifications. Crystallographic data on tRNAs in complex with aminoacyl-tRNA synthetases (aaRSs) also provided the first insight into protein:RNA interactions. Beyond the translation process and the history of structural investigations on tRNA, this review also illustrates the renewal of tRNA biology with the discovery of a growing number of tRNA partners in the cell, the involvement of tRNAs in a variety of regulatory and metabolic pathways, and emerging applications in biotechnology and synthetic biology.
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29
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Sprink T, Ramrath DJF, Yamamoto H, Yamamoto K, Loerke J, Ismer J, Hildebrand PW, Scheerer P, Bürger J, Mielke T, Spahn CMT. Structures of ribosome-bound initiation factor 2 reveal the mechanism of subunit association. SCIENCE ADVANCES 2016; 2:e1501502. [PMID: 26973877 PMCID: PMC4783127 DOI: 10.1126/sciadv.1501502] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 01/12/2016] [Indexed: 05/30/2023]
Abstract
Throughout the four phases of protein biosynthesis-initiation, elongation, termination, and recycling-the ribosome is controlled and regulated by at least one specified translational guanosine triphosphatase (trGTPase). Although the structural basis for trGTPase interaction with the ribosome has been solved for the last three steps of translation, the high-resolution structure for the key initiation trGTPase, initiation factor 2 (IF2), complexed with the ribosome, remains elusive. We determine the structure of IF2 complexed with a nonhydrolyzable guanosine triphosphate analog and initiator fMet-tRNAi (Met) in the context of the Escherichia coli ribosome to 3.7-Å resolution using cryo-electron microscopy. The structural analysis reveals previously unseen intrinsic conformational modes of the 70S initiation complex, establishing the mutual interplay of IF2 and initator transfer RNA (tRNA) with the ribsosome and providing the structural foundation for a mechanistic understanding of the final steps of translation initiation.
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Affiliation(s)
- Thiemo Sprink
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - David J F Ramrath
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Hiroshi Yamamoto
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Kaori Yamamoto
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Justus Loerke
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Jochen Ismer
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Peter W Hildebrand
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Patrick Scheerer
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Jörg Bürger
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany.; UltraStrukturNetzwerk, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany
| | - Thorsten Mielke
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany.; UltraStrukturNetzwerk, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany
| | - Christian M T Spahn
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
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30
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Piatkov KI, Vu TTM, Hwang CS, Varshavsky A. Formyl-methionine as a degradation signal at the N-termini of bacterial proteins. MICROBIAL CELL (GRAZ, AUSTRIA) 2016; 2:376-393. [PMID: 26866044 PMCID: PMC4745127 DOI: 10.15698/mic2015.10.231] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 08/17/2015] [Indexed: 02/04/2023]
Abstract
In bacteria, all nascent proteins bear the pretranslationally formed N-terminal formyl-methionine (fMet) residue. The fMet residue is cotranslationally deformylated by a ribosome-associated deformylase. The formylation of N-terminal Met in bacterial proteins is not strictly essential for either translation or cell viability. Moreover, protein synthesis by the cytosolic ribosomes of eukaryotes does not involve the formylation of N-terminal Met. What, then, is the main biological function of this metabolically costly, transient, and not strictly essential modification of N-terminal Met, and why has Met formylation not been eliminated during bacterial evolution? One possibility is that the similarity of the formyl and acetyl groups, their identical locations in N-terminally formylated (Nt-formylated) and Nt-acetylated proteins, and the recently discovered proteolytic function of Nt-acetylation in eukaryotes might also signify a proteolytic role of Nt-formylation in bacteria. We addressed this hypothesis about fMet-based degradation signals, termed fMet/N-degrons, using specific E. coli mutants, pulse-chase degradation assays, and protein reporters whose deformylation was altered, through site-directed mutagenesis, to be either rapid or relatively slow. Our findings strongly suggest that the formylated N-terminal fMet can act as a degradation signal, largely a cotranslational one. One likely function of fMet/N-degrons is the control of protein quality. In bacteria, the rate of polypeptide chain elongation is nearly an order of magnitude higher than in eukaryotes. We suggest that the faster emergence of nascent proteins from bacterial ribosomes is one mechanistic and evolutionary reason for the pretranslational design of bacterial fMet/N-degrons, in contrast to the cotranslational design of analogous Ac/N-degrons in eukaryotes.
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Affiliation(s)
- Konstantin I. Piatkov
- Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
- Center for Biotechnology and Biomedicine, Skolkovo Institute of Science and Technology, Moscow, 143026, Russia
| | - Tri T. M. Vu
- Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
| | - Cheol-Sang Hwang
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, 790-784, South Korea
| | - Alexander Varshavsky
- Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
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31
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Reimer JM, Aloise MN, Harrison PM, Schmeing TM. Synthetic cycle of the initiation module of a formylating nonribosomal peptide synthetase. Nature 2016; 529:239-42. [PMID: 26762462 DOI: 10.1038/nature16503] [Citation(s) in RCA: 113] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Accepted: 12/02/2015] [Indexed: 12/22/2022]
Abstract
Nonribosomal peptide synthetases (NRPSs) are very large proteins that produce small peptide molecules with wide-ranging biological activities, including environmentally friendly chemicals and many widely used therapeutics. NRPSs are macromolecular machines, with modular assembly-line logic, a complex catalytic cycle, moving parts and many active sites. In addition to the core domains required to link the substrates, they often include specialized tailoring domains, which introduce chemical modifications and allow the product to access a large expanse of chemical space. It is still unknown how the NRPS tailoring domains are structurally accommodated into megaenzymes or how they have adapted to function in nonribosomal peptide synthesis. Here we present a series of crystal structures of the initiation module of an antibiotic-producing NRPS, linear gramicidin synthetase. This module includes the specialized tailoring formylation domain, and states are captured that represent every major step of the assembly-line synthesis in the initiation module. The transitions between conformations are large in scale, with both the peptidyl carrier protein domain and the adenylation subdomain undergoing huge movements to transport substrate between distal active sites. The structures highlight the great versatility of NRPSs, as small domains repurpose and recycle their limited interfaces to interact with their various binding partners. Understanding tailoring domains is important if NRPSs are to be utilized in the production of novel therapeutics.
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Affiliation(s)
- Janice M Reimer
- Department of Biochemistry, McGill University, 3649 Promenade Sir-William-Osler, Montréal, Québec H3G 0B1, Canada
| | - Martin N Aloise
- Department of Biochemistry, McGill University, 3649 Promenade Sir-William-Osler, Montréal, Québec H3G 0B1, Canada
| | - Paul M Harrison
- Department of Biology, McGill University, 1205 Dr Penfield Avenue, Montréal, Québec H3A 1B1, Canada
| | - T Martin Schmeing
- Department of Biochemistry, McGill University, 3649 Promenade Sir-William-Osler, Montréal, Québec H3G 0B1, Canada
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32
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Functional Importance of Mobile Ribosomal Proteins. BIOMED RESEARCH INTERNATIONAL 2015; 2015:539238. [PMID: 26457300 PMCID: PMC4592705 DOI: 10.1155/2015/539238] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 08/12/2015] [Indexed: 01/07/2023]
Abstract
Although the dynamic motions and peptidyl transferase activity seem to be embedded in the rRNAs, the ribosome contains more than 50 ribosomal proteins (r-proteins), whose functions remain largely elusive. Also, the precise forms of some of these r-proteins, as being part of the ribosome, are not structurally solved due to their high flexibility, which hinders the efforts in their functional elucidation. Owing to recent advances in cryo-electron microscopy, single-molecule techniques, and theoretical modeling, much has been learned about the dynamics of these r-proteins. Surprisingly, allosteric regulations have been found in between spatially separated components as distant as those in the opposite sides of the ribosome. Here, we focus on the functional roles and intricate regulations of the mobile L1 and L12 stalks and L9 and S1 proteins. Conformational flexibility also enables versatile functions for r-proteins beyond translation. The arrangement of r-proteins may be under evolutionary pressure that fine-tunes mass distributions for optimal structural dynamics and catalytic activity of the ribosome.
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33
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Gualerzi CO, Pon CL. Initiation of mRNA translation in bacteria: structural and dynamic aspects. Cell Mol Life Sci 2015; 72:4341-67. [PMID: 26259514 PMCID: PMC4611024 DOI: 10.1007/s00018-015-2010-3] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 07/28/2015] [Accepted: 07/30/2015] [Indexed: 01/12/2023]
Abstract
Initiation of mRNA translation is a major checkpoint for regulating level and fidelity of protein synthesis. Being rate limiting in protein synthesis, translation initiation also represents the target of many post-transcriptional mechanisms regulating gene expression. The process begins with the formation of an unstable 30S pre-initiation complex (30S pre-IC) containing initiation factors (IFs) IF1, IF2 and IF3, the translation initiation region of an mRNA and initiator fMet-tRNA whose codon and anticodon pair in the P-site following a first-order rearrangement of the 30S pre-IC produces a locked 30S initiation complex (30SIC); this is docked by the 50S subunit to form a 70S complex that, following several conformational changes, positional readjustments of its ligands and ejection of the IFs, becomes a 70S initiation complex productive in initiation dipeptide formation. The first EF-G-dependent translocation marks the beginning of the elongation phase of translation. Here, we review structural, mechanistic and dynamical aspects of this process.
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MESH Headings
- Bacteria/genetics
- Bacteria/metabolism
- Binding Sites/genetics
- Codon, Initiator/genetics
- Codon, Initiator/metabolism
- Models, Genetic
- Nucleic Acid Conformation
- Peptide Initiation Factors/genetics
- Peptide Initiation Factors/metabolism
- Protein Biosynthesis
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Transfer, Met/chemistry
- RNA, Transfer, Met/genetics
- RNA, Transfer, Met/metabolism
- Ribosomes/metabolism
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Affiliation(s)
| | - Cynthia L Pon
- Laboratory of Genetics, University of Camerino, 62032, Camerino, Italy.
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34
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Sinha A, Köhrer C, Weber MHW, Masuda I, Mootha VK, Hou YM, RajBhandary UL. Biochemical characterization of pathogenic mutations in human mitochondrial methionyl-tRNA formyltransferase. J Biol Chem 2014; 289:32729-41. [PMID: 25288793 DOI: 10.1074/jbc.m114.610626] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
N-Formylation of initiator methionyl-tRNA (Met-tRNA(Met)) by methionyl-tRNA formyltransferase (MTF) is important for translation initiation in bacteria, mitochondria, and chloroplasts. Unlike all other translation systems, the metazoan mitochondrial system is unique in using a single methionine tRNA (tRNA(Met)) for both initiation and elongation. A portion of Met-tRNA(Met) is formylated for initiation, whereas the remainder is used for elongation. Recently, we showed that compound heterozygous mutations within the nuclear gene encoding human mitochondrial MTF (mt-MTF) significantly reduced mitochondrial translation efficiency, leading to combined oxidative phosphorylation deficiency and Leigh syndrome in two unrelated patients. Patient P1 has a stop codon mutation in one of the MTF genes and an S209L mutation in the other MTF gene. P2 has a S125L mutation in one of the MTF genes and the same S209L mutation as P1 in the other MTF gene. Here, we have investigated the effect of mutations at Ser-125 and Ser-209 on activities of human mt-MTF and of the corresponding mutations, Ala-89 or Ala-172, respectively, on activities of Escherichia coli MTF. The S125L mutant has 653-fold lower activity, whereas the S209L mutant has 36-fold lower activity. Thus, both patients depend upon residual activity of the S209L mutant to support low levels of mitochondrial protein synthesis. We discuss the implications of these and other results for whether the effect of the S209L mutation on mitochondrial translational efficiency is due to reduced activity of the mutant mt-MTF and/or reduced levels of the mutant mt-MTF.
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Affiliation(s)
- Akesh Sinha
- From the Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Caroline Köhrer
- From the Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Michael H W Weber
- From the Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Isao Masuda
- the Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, and
| | - Vamsi K Mootha
- the Howard Hughes Medical Institute, Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114
| | - Ya-Ming Hou
- the Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, and
| | - Uttam L RajBhandary
- From the Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139,
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35
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Pon CL, Fabbretti A, Brandi L. Antibiotics Targeting Translation Initiation in Prokaryotes. Antibiotics (Basel) 2013. [DOI: 10.1002/9783527659685.ch17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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36
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Sivasakthi V, Anbarasu A, Ramaiah S. π–π Interactions in Structural Stability: Role in RNA Binding Proteins. Cell Biochem Biophys 2013; 67:853-63. [DOI: 10.1007/s12013-013-9573-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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37
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Stolboushkina E, Nikonov S, Zelinskaya N, Arkhipova V, Nikulin A, Garber M, Nikonov O. Crystal structure of the archaeal translation initiation factor 2 in complex with a GTP analogue and Met-tRNAf(Met.). J Mol Biol 2013; 425:989-98. [PMID: 23291527 DOI: 10.1016/j.jmb.2012.12.023] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2012] [Revised: 10/24/2012] [Accepted: 12/26/2012] [Indexed: 11/29/2022]
Abstract
Heterotrimeric aIF2αβγ (archaeal homologue of the eukaryotic translation initiation factor 2) in its GTP-bound form delivers Met-tRNAi(Met) to the small ribosomal subunit. It is known that the heterodimer containing the GTP-bound γ subunit and domain 3 of the α subunit of aIF2 is required for the formation of a stable complex with Met-tRNAi. Here, the crystal structure of an incomplete ternary complex including aIF2αD3γ⋅GDPNP⋅Met-tRNAf(Met) has been solved at 3.2Å resolution. This structure is in good agreement with biochemical and hydroxyl radical probing data. The analysis of the complex shows that despite the structural similarity of aIF2γ and the bacterial translation elongation factor EF-Tu, their modes of tRNA binding are very different. Remarkably, the recently published 5.0-Å-resolution structure of almost the same ternary initiation complex differs dramatically from the structure presented. Reasons for this discrepancy are discussed.
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Affiliation(s)
- Elena Stolboushkina
- Institute of Protein Research, Russian Academy of Sciences, 142290, Pushchino, Moscow Region, Russian Federation
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38
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In silico method for modelling metabolism and gene product expression at genome scale. Nat Commun 2012; 3:929. [PMID: 22760628 DOI: 10.1038/ncomms1928] [Citation(s) in RCA: 186] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Accepted: 05/28/2012] [Indexed: 11/09/2022] Open
Abstract
Transcription and translation use raw materials and energy generated metabolically to create the macromolecular machinery responsible for all cellular functions, including metabolism. A biochemically accurate model of molecular biology and metabolism will facilitate comprehensive and quantitative computations of an organism's molecular constitution as a function of genetic and environmental parameters. Here we formulate a model of metabolism and macromolecular expression. Prototyping it using the simple microorganism Thermotoga maritima, we show our model accurately simulates variations in cellular composition and gene expression. Moreover, through in silico comparative transcriptomics, the model allows the discovery of new regulons and improving the genome and transcription unit annotations. Our method presents a framework for investigating molecular biology and cellular physiology in silico and may allow quantitative interpretation of multi-omics data sets in the context of an integrated biochemical description of an organism.
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39
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Liu B, Chen M, Perepelov AV, Liu J, Ovchinnikova OG, Zhou D, Feng L, Rozalski A, Knirel YA, Wang L. Genetic analysis of the O-antigen of Providencia alcalifaciens O30 and biochemical characterization of a formyltransferase involved in the synthesis of a Qui4N derivative. Glycobiology 2012; 22:1236-44. [PMID: 22661447 DOI: 10.1093/glycob/cws089] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
O-Antigen is a component of the outer membrane of Gram-negative bacteria and one of the most variable cell surface constituents, giving rise to major antigenic variability. The diversity of O-antigen is almost entirely attributed to genetic variations in O-antigen gene clusters. Bacteria of the genus Providencia are facultative pathogens, which can cause urinary tract infections, wound infections and enteric diseases. Recently, the O-antigen gene cluster of Providencia was localized between the cpxA and yibK genes in the genome. However, few genes involved in the synthesis of Providencia O-antigens have been functionally identified. In this study, the putative O-antigen gene cluster of Providencia alcalifaciens O30 was sequenced and analyzed. Almost all putative genes for the O-antigen synthesis were found, including a novel formyltransferase gene vioF that was proposed to be responsible for the conversion of dTDP-4-amino-4,6- dideoxy-D-glucose (dTDP-D-Qui4N) to dTDP-4,6-dideoxy-4-formamido-D-glucose (dTDP-D-Qui4NFo). vioF was cloned, and the enzyme product was expressed as a His-tagged fusion protein, purified and assayed for its activity. High-performance liquid chromatography was used to monitor the enzyme-substrate reaction, and the structure of the product dTDP-D-Qui4NFo was established by electrospray ionization tandem mass spectrometry and nuclear magnetic resonance spectroscopy. Kinetic parameters of VioF were determined, and effects of temperature and cations on its activity were also examined. Together, the functional analyses support the identification of the O-antigen gene cluster of P. alcalifaciens O30.
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Affiliation(s)
- Bin Liu
- TEDA School of Biological Sciences and Biotechnology, Tianjin, PR China
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40
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Neubauer C, Gillet R, Kelley AC, Ramakrishnan V. Decoding in the absence of a codon by tmRNA and SmpB in the ribosome. Science 2012; 335:1366-9. [PMID: 22422985 DOI: 10.1126/science.1217039] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
In bacteria, ribosomes stalled at the end of truncated messages are rescued by transfer-messenger RNA (tmRNA), a bifunctional molecule that acts as both a transfer RNA (tRNA) and a messenger RNA (mRNA), and SmpB, a small protein that works in concert with tmRNA. Here, we present the crystal structure of a tmRNA fragment, SmpB and elongation factor Tu bound to the ribosome at 3.2 angstroms resolution. The structure shows how SmpB plays the role of both the anticodon loop of tRNA and portions of mRNA to facilitate decoding in the absence of an mRNA codon in the A site of the ribosome and explains why the tmRNA-SmpB system does not interfere with normal translation.
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Affiliation(s)
- Cajetan Neubauer
- Medical Research Council (MRC) Laboratory of Molecular Biology, Cambridge, UK
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41
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Bosello M, Mielcarek A, Giessen TW, Marahiel MA. An enzymatic pathway for the biosynthesis of the formylhydroxyornithine required for rhodochelin iron coordination. Biochemistry 2012; 51:3059-66. [PMID: 22439765 DOI: 10.1021/bi201837f] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Rhodochelin, a mixed catecholate-hydroxamate type siderophore isolated from Rhodococcus jostii RHA1, holds two L-δ-N-formyl-δ-N-hydroxyornithine (L-fhOrn) moieties essential for proper iron coordination. Previously, bioinformatic and genetic analysis proposed rmo and rft as the genes required for the tailoring of the L-ornithine (L-Orn) precursor [Bosello, M. (2011) J. Am. Chem. Soc.133, 4587-4595]. In order to investigate if both Rmo and Rft constitute a pathway for L-fhOrn biosynthesis, the enzymes were heterologously produced and assayed in vitro. In the presence of molecular oxygen, NADPH and FAD, Rmo monooxygenase was able to convert L-Orn into L-δ-N-hydroxyornithine (L-hOrn). As confirmed in a coupled reaction assay, this hydroxylated intermediate serves as a substrate for the subsequent N(10)-formyl-tetrahydrofolate-dependent (N(10)-fH(4)F) Rtf-catalyzed formylation reaction, establishing a route for the L-fhOrn biosynthesis, prior to its incorporation by the NRPS assembly line. It is of particular interest that a major improvement to this study has been reached with the use of an alternative approach to the chemoenzymatic FolD-dependent N(10)-fH(4)F conversion, also rescuing the previously inactive CchA, the Rft-homologue in coelichelin assembly line [Buchenau, B. (2004) Arch. Microbiol.182, 313-325; Pohlmann, V. (2008) Org. Biomol. Chem.6, 1843-1848].
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Affiliation(s)
- Mattia Bosello
- Biochemistry, Department of Chemistry, Philipps-University Marburg, Hans-Meerwein-Strasse, D-35043 Marburg, Germany
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42
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Wang PPS, Ruvinsky I. Family size and turnover rates among several classes of small non-protein-coding RNA genes in Caenorhabditis nematodes. Genome Biol Evol 2012; 4:565-74. [PMID: 22467905 PMCID: PMC3342880 DOI: 10.1093/gbe/evs034] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
It is important to understand the forces that shape the size and evolutionary histories of gene families. Here, we investigated the evolution of non–protein-coding RNA genes in the genomes of Caenorhabditis nematodes. We specifically focused on nested arrangements, that is, cases in which an RNA gene is entirely contained in an intron of another gene. Comparing these arrangements between species simplifies the inference of orthology and, therefore, of evolutionary fates of nested genes. Two distinct patterns are evident in the data. Genes encoding small nuclear RNAs (snRNAs) and transfer RNAs form large families, which have persisted since before the common ancestor of Metazoa. Yet, individual genes die relatively rapidly, with few orthologs having survived since the divergence of Caenorhabditis elegans and Caenorhabditis briggsae. In contrast, genes encoding small nucleolar RNAs (snoRNAs) are either single-copy or form small families. Individual snoRNAs turn over at a relatively slow rate—most C. elegans genes have clearly identifiable orthologs in C. briggsae. We also found that in Drosophila, genes from larger snRNA families die at a faster rate than their counterparts from single-gene families. These results suggest that a relationship between family size and the rate of gene turnover may be a general feature of genome evolution.
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Affiliation(s)
- Paul Po-Shen Wang
- Department of Ecology and Evolution, Institute for Genomics and Systems Biology, The University of Chicago, IL, USA
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Schmitt E, Panvert M, Lazennec-Schurdevin C, Coureux PD, Perez J, Thompson A, Mechulam Y. Structure of the ternary initiation complex aIF2-GDPNP-methionylated initiator tRNA. Nat Struct Mol Biol 2012; 19:450-4. [PMID: 22447243 DOI: 10.1038/nsmb.2259] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Accepted: 02/07/2012] [Indexed: 01/09/2023]
Abstract
Eukaryotic and archaeal translation initiation factor 2 (e/aIF2) is a heterotrimeric GTPase that has a crucial role in the selection of the correct start codon on messenger RNA. We report the 5-Å resolution crystal structure of the ternary complex formed by archaeal aIF2 from Sulfolobus solfataricus, the GTP analog GDPNP and methionylated initiator tRNA. The 3D model is further supported by solution studies using small-angle X-ray scattering. The tRNA is bound by the α and γ subunits of aIF2. Contacts involve the elbow of the tRNA and the minor groove of the acceptor stem, but not the T-stem minor groove. We conclude that despite considerable structural homology between the core γ subunit of aIF2 and the elongation factor EF1A, these two G proteins of the translation apparatus use very different tRNA-binding strategies.
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Affiliation(s)
- Emmanuelle Schmitt
- Laboratoire de Biochimie, Unité mixte de Recherche 7654, Ecole Polytechnique, Centre National de la Recherche Scientifique, Palaiseau, France.
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Abstract
Selection of correct start codons on messenger RNAs is a key step required for faithful translation of the genetic message. Such a selection occurs in a complex process, during which a translation-competent ribosome assembles, eventually having in its P site a specialized methionyl-tRNAMet base-paired with the start codon on the mRNA. This chapter summarizes recent advances describing at the molecular level the successive steps involved in the process. Special emphasis is put on the roles of the three initiation factors and of the initiator tRNA, which are crucial for the efficiency and the specificity of the process. In particular, structural analyses concerning complexes containing ribosomal subunits, as well as detailed kinetic studies, have shed new light on the sequence of events leading to faithful initiation of protein synthesis in Bacteria.
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Julián P, Milon P, Agirrezabala X, Lasso G, Gil D, Rodnina MV, Valle M. The Cryo-EM structure of a complete 30S translation initiation complex from Escherichia coli. PLoS Biol 2011; 9:e1001095. [PMID: 21750663 PMCID: PMC3130014 DOI: 10.1371/journal.pbio.1001095] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2010] [Accepted: 05/24/2011] [Indexed: 12/04/2022] Open
Abstract
Formation of the 30S initiation complex (30S IC) is an important checkpoint in regulation of gene expression. The selection of mRNA, correct start codon, and the initiator fMet-tRNAfMet requires the presence of three initiation factors (IF1, IF2, IF3) of which IF3 and IF1 control the fidelity of the process, while IF2 recruits fMet-tRNAfMet. Here we present a cryo-EM reconstruction of the complete 30S IC, containing mRNA, fMet-tRNAfMet, IF1, IF2, and IF3. In the 30S IC, IF2 contacts IF1, the 30S subunit shoulder, and the CCA end of fMet-tRNAfMet, which occupies a novel P/I position (P/I1). The N-terminal domain of IF3 contacts the tRNA, whereas the C-terminal domain is bound to the platform of the 30S subunit. Binding of initiation factors and fMet-tRNAfMet induces a rotation of the head relative to the body of the 30S subunit, which is likely to prevail through 50S subunit joining until GTP hydrolysis and dissociation of IF2 take place. The structure provides insights into the mechanism of mRNA selection during translation initiation. Translation is the process by which a ribosome converts the sequence of a messenger RNA (mRNA)—produced from a gene—into the sequence of amino acids that comprise a protein. Bacterial ribosomes each have one large and one small subunit: the 50S and 30S subunits. Initiation of translation entails selection of an mRNA, identification of the correct starting point from which to read its code, and engagement of the initial amino acid carrier (tRNA). These events take place in the 30S subunit and require the presence of three initiation factors (IF1, IF2, IF3). Formation of this 30S initiation complex precedes joining with the 50S subunit to assemble the functional ribosome. By using a cryo-electron microscopy approach to visualize the structures without fixation or staining, we have determined the structure of a complete 30S initiation complex and identified the positions and orientations of the tRNA and all three initiation factors. We found that the presence of the initiation factors and tRNA induces rotation of the head relative to the body of the 30S subunit, which may be essential for rapid binding to the 50S subunit and for regulating selection of the mRNA. IF3 had not been seen previously in the context of the 30S structure and its visualization gives insight into a potential role in preventing association of the two ribosomal subunits. These findings are important for understanding how the interplay of elements during the early stages of translation selects the mRNA and regulates formation of functional ribosomes.
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Affiliation(s)
- Patricia Julián
- Structural Biology Unit, Center for Cooperative Research in Biosciences (CIC bioGUNE), Parque Tecnológico de Bizkaia, Derio, Spain
| | - Pohl Milon
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Xabier Agirrezabala
- Structural Biology Unit, Center for Cooperative Research in Biosciences (CIC bioGUNE), Parque Tecnológico de Bizkaia, Derio, Spain
| | - Gorka Lasso
- Structural Biology Unit, Center for Cooperative Research in Biosciences (CIC bioGUNE), Parque Tecnológico de Bizkaia, Derio, Spain
| | - David Gil
- Structural Biology Unit, Center for Cooperative Research in Biosciences (CIC bioGUNE), Parque Tecnológico de Bizkaia, Derio, Spain
| | - Marina V. Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Mikel Valle
- Structural Biology Unit, Center for Cooperative Research in Biosciences (CIC bioGUNE), Parque Tecnológico de Bizkaia, Derio, Spain
- Department of Biochemistry and Molecular Biology. Faculty of Science and Technology, University of the Basque Country, Bilbao, Spain
- * E-mail:
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The role of L1 stalk-tRNA interaction in the ribosome elongation cycle. J Mol Biol 2010; 402:741-60. [PMID: 20691699 DOI: 10.1016/j.jmb.2010.07.056] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2010] [Revised: 07/23/2010] [Accepted: 07/27/2010] [Indexed: 01/08/2023]
Abstract
The ribosomal L1 stalk is a mobile structure implicated in directing tRNA movement during translocation through the ribosome. This article investigates three aspects of L1 stalk-tRNA interaction. First, by combining data from cryo electron microscopy, X-ray crystallography, and molecular dynamics simulations through the molecular dynamics flexible fitting method, we obtained atomic models of different tRNAs occupying the hybrid P/E state interacting with the L1 stalk. These models confirm the assignment of fluorescence resonance energy transfer states from previous single-molecule investigations of L1 stalk dynamics. Second, the models reconcile how initiator tRNA(fMet) interacts less strongly with the L1 stalk compared to elongator tRNA(Phe), as seen in previous single-molecule experiments. Third, results from a simulation of the entire ribosome in which the L1 stalk is moved from a half-closed conformation to its open conformation are found to support the hypothesis that L1 stalk opening is involved in tRNA release from the ribosome.
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Tsuboi M, Morita H, Nozaki Y, Akama K, Ueda T, Ito K, Nierhaus KH, Takeuchi N. EF-G2mt is an exclusive recycling factor in mammalian mitochondrial protein synthesis. Mol Cell 2009; 35:502-10. [PMID: 19716793 DOI: 10.1016/j.molcel.2009.06.028] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2009] [Revised: 05/04/2009] [Accepted: 06/18/2009] [Indexed: 11/30/2022]
Abstract
Bacterial translation elongation factor G (EF-G) catalyzes translocation during peptide elongation and mediates ribosomal disassembly during ribosome recycling in concert with the ribosomal recycling factor (RRF). Two homologs of EF-G have been identified in mitochondria from yeast to man, EF-G1mt and EF-G2mt. Here, we demonstrate that the dual function of bacterial EF-G is divided between EF-G1mt and EF-G2mt in human mitochondria (RRFmt). EF-G1mt specifically catalyzes translocation, whereas EF-G2mt mediates ribosome recycling with human mitochondrial RRF but lacks translocation activity. Domain swapping experiments suggest that the functional specificity for EF-G2mt resides in domains III and IV. Furthermore, GTP hydrolysis by EF-G2mt is not necessary for ribosomal splitting, in contrast to the bacterial-recycling mode. Because EF-G2mt represents a class of translational GTPase that is involved in ribosome recycling, we propose to rename this factor mitochondrial ribosome recycling factor 2 (RRF2mt).
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Affiliation(s)
- Masafumi Tsuboi
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, 5-1-5, Kashiwanoha, Kashiwa-shi, Chiba 277-8562, Japan
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Krupenko SA. FDH: an aldehyde dehydrogenase fusion enzyme in folate metabolism. Chem Biol Interact 2008; 178:84-93. [PMID: 18848533 DOI: 10.1016/j.cbi.2008.09.007] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2008] [Accepted: 09/02/2008] [Indexed: 10/21/2022]
Abstract
FDH (10-formyltetrahydrofolate dehydrogenase, Aldh1L1, EC 1.5.1.6) converts 10-formyltetrahydrofolate (10-formyl-THF) to tetrahydrofolate and CO(2) in a NADP(+)-dependent reaction. It is a tetramer of four identical 902 amino acid residue subunits. The protein subunit is a product of a natural fusion of three unrelated genes and consists of three distinct domains. The N-terminal domain of FDH (residues 1-310) carries the folate binding site and shares sequence homology and structural topology with other enzymes utilizing 10-formyl-THF as a substrate. In vitro it functions as 10-formyl-THF hydrolase, and evidence indicate that this activity is a part of the overall FDH mechanism. The C-terminal domain of FDH (residues 400-902) originated from an aldehyde dehydrogenase-related gene and is capable of oxidation of short-chain aldehydes to corresponding acids. Similar to classes 1 and 2 aldehyde dehydrogenases, this domain exists as a tetramer and defines the oligomeric structure of the full-length enzyme. The two catalytic domains are connected by an intermediate linker (residues 311-399), which is a structural and functional homolog of carrier proteins possessing a 4'-phosphopantetheine prosthetic group. In the FDH mechanism, the intermediate linker domain transfers a formyl, covalently attached to the sulfhydryl group of the phosphopantetheine arm, from the N-terminal domain to the C-terminal domain. The overall FDH mechanism is a coupling of two sequential reactions, a hydrolase and a formyl dehydrogenase, bridged by a substrate transfer step. In this mechanism, one domain provides the folate binding site and a hydrolase catalytic center to remove the formyl group from the folate substrate, another provides a transfer vehicle between catalytic centers and the third one contributes the dehydrogenase machinery further oxidizing formyl to CO(2).
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Affiliation(s)
- Sergey A Krupenko
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, United States.
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Barraud P, Schmitt E, Mechulam Y, Dardel F, Tisné C. A unique conformation of the anticodon stem-loop is associated with the capacity of tRNAfMet to initiate protein synthesis. Nucleic Acids Res 2008; 36:4894-901. [PMID: 18653533 PMCID: PMC2528185 DOI: 10.1093/nar/gkn462] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
In all organisms, translational initiation takes place on the small ribosomal subunit and two classes of methionine tRNA are present. The initiator is used exclusively for initiation of protein synthesis while the elongator is used for inserting methionine internally in the nascent polypeptide chain. The crystal structure of Escherichia coli initiator tRNAfMet has been solved at 3.1 Å resolution. The anticodon region is well-defined and reveals a unique structure, which has not been described in any other tRNA. It encompasses a Cm32•A38 base pair with a peculiar geometry extending the anticodon helix, a base triple between A37 and the G29-C41 pair in the major groove of the anticodon stem and a modified stacking organization of the anticodon loop. This conformation is associated with the three GC basepairs in the anticodon stem, characteristic of initiator tRNAs and suggests a mechanism by which the translation initiation machinery could discriminate the initiator tRNA from all other tRNAs.
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Affiliation(s)
- Pierre Barraud
- Laboratoire de Cristallographie et RMN Biologiques, Université Paris Descartes, CNRS, 4 avenue de l'Observatoire, 75006 Paris, France
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Brandi L, Fabbretti A, Pon CL, Dahlberg AE, Gualerzi CO. Initiation of protein synthesis: a target for antimicrobials. Expert Opin Ther Targets 2008; 12:519-34. [PMID: 18410237 DOI: 10.1517/14728222.12.5.519] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
BACKGROUND Translation initiation is a basic and universal biological process that employs significantly different components and displays substantially different mechanisms in bacterial, archaeal and eukaryotic cells. A large amount of detailed mechanistic and structural information on the bacterial translation initiation apparatus has been uncovered in recent years. OBJECTIVE to understand which translation initiation steps could represent a novel or underexploited target for the discovery of new and specific antibacterial drugs. METHODS Brief descriptions of the properties and mechanism of action of the major antibiotics that have a documented direct inhibitory effect on bacterial translation initiation are presented. RESULTS/CONCLUSIONS Considerations and predictions concerning a future scenario for research and identification of bacterial translation initiation inhibitors are presented.
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