1
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Starosta AL, Lassak J, Jung K, Wilson DN. The bacterial translation stress response. FEMS Microbiol Rev 2014; 38:1172-201. [PMID: 25135187 DOI: 10.1111/1574-6976.12083] [Citation(s) in RCA: 134] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Revised: 07/18/2014] [Accepted: 08/07/2014] [Indexed: 11/30/2022] Open
Abstract
Throughout their life, bacteria need to sense and respond to environmental stress. Thus, such stress responses can require dramatic cellular reprogramming, both at the transcriptional as well as the translational level. This review focuses on the protein factors that interact with the bacterial translational apparatus to respond to and cope with different types of environmental stress. For example, the stringent factor RelA interacts with the ribosome to generate ppGpp under nutrient deprivation, whereas a variety of factors have been identified that bind to the ribosome under unfavorable growth conditions to shut-down (RelE, pY, RMF, HPF and EttA) or re-program (MazF, EF4 and BipA) translation. Additional factors have been identified that rescue ribosomes stalled due to stress-induced mRNA truncation (tmRNA, ArfA, ArfB), translation of unfavorable protein sequences (EF-P), heat shock-induced subunit dissociation (Hsp15), or antibiotic inhibition (TetM, FusB). Understanding the mechanism of how the bacterial cell responds to stress will not only provide fundamental insight into translation regulation, but will also be an important step to identifying new targets for the development of novel antimicrobial agents.
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Affiliation(s)
- Agata L Starosta
- Gene Center, Department for Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany; Center for integrated Protein Science Munich (CiPSM), Ludwig-Maximilians-Universität München, Munich, Germany
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2
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Giudice E, Macé K, Gillet R. Trans-translation exposed: understanding the structures and functions of tmRNA-SmpB. Front Microbiol 2014; 5:113. [PMID: 24711807 PMCID: PMC3968760 DOI: 10.3389/fmicb.2014.00113] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 03/05/2014] [Indexed: 11/13/2022] Open
Abstract
Ribosome stalling is a serious issue for cell survival. In bacteria, the primary rescue system is trans-translation, performed by tmRNA and its protein partner small protein B (SmpB). Since its discovery almost 20 years ago, biochemical, genetic, and structural studies have paved the way to a better understanding of how this sophisticated process takes place at the cellular and molecular levels. Here we describe the molecular details of trans-translation, with special mention of recent cryo-electron microscopy and crystal structures that have helped explain how the huge tmRNA-SmpB complex targets and delivers stalled ribosomes without interfering with canonical translation.
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Affiliation(s)
- Emmanuel Giudice
- Translation and Folding Team, Université de Rennes 1, CNRS UMR 6290 IGDR Rennes, France
| | - Kevin Macé
- Translation and Folding Team, Université de Rennes 1, CNRS UMR 6290 IGDR Rennes, France
| | - Reynald Gillet
- Translation and Folding Team, Université de Rennes 1, CNRS UMR 6290 IGDR Rennes, France ; Institut Universitaire de France France
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3
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The complex of tmRNA-SmpB and EF-G on translocating ribosomes. Nature 2012; 485:526-9. [PMID: 22622583 DOI: 10.1038/nature11006] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2011] [Accepted: 03/02/2012] [Indexed: 02/05/2023]
Abstract
Bacterial ribosomes stalled at the 3' end of malfunctioning messenger RNAs can be rescued by transfer-messenger RNA (tmRNA)-mediated trans-translation. The SmpB protein forms a complex with the tmRNA, and the transfer-RNA-like domain (TLD) of the tmRNA then enters the A site of the ribosome. Subsequently, the TLD-SmpB module is translocated to the P site, a process that is facilitated by the elongation factor EF-G, and translation is switched to the mRNA-like domain (MLD) of the tmRNA. Accurate loading of the MLD into the mRNA path is an unusual initiation mechanism. Despite various snapshots of different ribosome-tmRNA complexes at low to intermediate resolution, it is unclear how the large, highly structured tmRNA is translocated and how the MLD is loaded. Here we present a cryo-electron microscopy reconstruction of a fusidic-acid-stalled ribosomal 70S-tmRNA-SmpB-EF-G complex (carrying both of the large ligands, that is, EF-G and tmRNA) at 8.3 Å resolution. This post-translocational intermediate (TI(POST)) presents the TLD-SmpB module in an intrasubunit ap/P hybrid site and a tRNA(fMet) in an intrasubunit pe/E hybrid site. Conformational changes in the ribosome and tmRNA occur in the intersubunit space and on the solvent side. The key underlying event is a unique extra-large swivel movement of the 30S head, which is crucial for both tmRNA-SmpB translocation and MLD loading, thereby coupling translocation to MLD loading. This mechanism exemplifies the versatile, dynamic nature of the ribosome, and it shows that the conformational modes of the ribosome that normally drive canonical translation can also be used in a modified form to facilitate more complex tasks in specialized non-canonical pathways.
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4
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Janssen BD, Hayes CS. The tmRNA ribosome-rescue system. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2012; 86:151-91. [PMID: 22243584 DOI: 10.1016/b978-0-12-386497-0.00005-0] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The bacterial tmRNA quality control system monitors protein synthesis and recycles stalled translation complexes in a process termed "ribosome rescue." During rescue, tmRNA acts first as a transfer RNA to bind stalled ribosomes, then as a messenger RNA to add the ssrA peptide tag to the C-terminus of the nascent polypeptide chain. The ssrA peptide targets tagged peptides for proteolysis, ensuring rapid degradation of potentially deleterious truncated polypeptides. Ribosome rescue also facilitates turnover of the damaged messages responsible for translational arrest. Thus, tmRNA increases the fidelity of gene expression by promoting the synthesis of full-length proteins. In addition to serving as a global quality control system, tmRNA also plays important roles in bacterial development, pathogenesis, and environmental stress responses. This review focuses on the mechanism of tmRNA-mediated ribosome rescue and the role of tmRNA in bacterial physiology.
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Affiliation(s)
- Brian D Janssen
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, California, USA
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5
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Keiler KC, Ramadoss NS. Bifunctional transfer-messenger RNA. Biochimie 2011; 93:1993-7. [PMID: 21664408 DOI: 10.1016/j.biochi.2011.05.029] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2011] [Accepted: 05/25/2011] [Indexed: 01/14/2023]
Abstract
Transfer-messenger RNA (tmRNA) is a bifunctional RNA that has properties of a tRNA and an mRNA. tmRNA uses these two functions to release ribosomes stalled during translation and target the nascent polypeptides for degradation. This concerted reaction, known as trans-translation, contributes to translational quality control and regulation of gene expression in bacteria. tmRNA is conserved throughout bacteria, and is one of the most abundant RNAs in the cell, suggesting that trans-translation is of fundamental importance for bacterial fitness. Mutants lacking tmRNA activity typically have severe phenotypes, including defects in viability, virulence, and responses to environmental stresses.
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Affiliation(s)
- Kenneth C Keiler
- Pennsylvania State University, Department of Biochemistry & Molecular Biology, 401 Althouse Lab, University Park, PA 16802, USA.
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6
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Chadani Y, Ono K, Kutsukake K, Abo T. Escherichia coli YaeJ protein mediates a novel ribosome-rescue pathway distinct from SsrA- and ArfA-mediated pathways. Mol Microbiol 2011; 80:772-85. [DOI: 10.1111/j.1365-2958.2011.07607.x] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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7
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Kurita D, Muto A, Himeno H. tRNA/mRNA Mimicry by tmRNA and SmpB in Trans-Translation. J Nucleic Acids 2011; 2011:130581. [PMID: 21253384 PMCID: PMC3022190 DOI: 10.4061/2011/130581] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2010] [Accepted: 12/15/2010] [Indexed: 11/20/2022] Open
Abstract
Since accurate translation from mRNA to protein is critical to survival, cells have developed translational quality control systems. Bacterial ribosomes stalled on truncated mRNA are rescued by a system involving tmRNA and SmpB referred to as trans-translation. Here, we review current understanding of the mechanism of trans-translation. Based on results obtained by using directed hydroxyl radical probing, we propose a new type of molecular mimicry during trans-translation. Besides such chemical approaches, biochemical and cryo-EM studies have revealed the structural and functional aspects of multiple stages of trans-translation. These intensive works provide a basis for studying the dynamics of tmRNA/SmpB in the ribosome.
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Affiliation(s)
- Daisuke Kurita
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki 036-8561, Japan
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8
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Bugaeva EY, Surkov S, Golovin AV, Ofverstedt LG, Skoglund U, Isaksson LA, Bogdanov AA, Shpanchenko OV, Dontsova OA. Structural features of the tmRNA-ribosome interaction. RNA (NEW YORK, N.Y.) 2009; 15:2312-2320. [PMID: 19861420 PMCID: PMC2779675 DOI: 10.1261/rna.1584209] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2009] [Accepted: 09/08/2009] [Indexed: 05/28/2023]
Abstract
Trans-translation is a process which switches the synthesis of a polypeptide chain encoded by a nonstop messenger RNA to the mRNA-like domain of a transfer-messenger RNA (tmRNA). It is used in bacterial cells for rescuing the ribosomes arrested during translation of damaged mRNA and directing this mRNA and the product polypeptide for degradation. The molecular basis of this process is not well understood. Earlier, we developed an approach that allowed isolation of tmRNA-ribosomal complexes arrested at a desired step of tmRNA passage through the ribosome. We have here exploited it to examine the tmRNA structure using chemical probing and cryo-electron microscopy tomography. Computer modeling has been used to develop a model for spatial organization of the tmRNA inside the ribosome at different stages of trans-translation.
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MESH Headings
- Base Sequence
- Cryoelectron Microscopy
- Escherichia coli/chemistry
- Escherichia coli/metabolism
- Models, Molecular
- Molecular Sequence Data
- Nucleic Acid Conformation
- Protein Biosynthesis
- RNA, Bacterial/chemistry
- RNA, Bacterial/metabolism
- RNA, Bacterial/ultrastructure
- RNA, Messenger/chemistry
- RNA, Messenger/metabolism
- RNA, Messenger/ultrastructure
- RNA, Transfer/chemistry
- RNA, Transfer/metabolism
- RNA, Transfer/ultrastructure
- Ribosomes/chemistry
- Ribosomes/metabolism
- Ribosomes/ultrastructure
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Affiliation(s)
- Elizaveta Y Bugaeva
- Belozersky Institute, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia
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9
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Shcherbakova DM, Sokolov KA, Zvereva MI, Dontsova OA. Telomerase from yeast Saccharomyces cerevisiae is active in vitro as a monomer. BIOCHEMISTRY (MOSCOW) 2009; 74:749-55. [PMID: 19747095 DOI: 10.1134/s0006297909070074] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
A system for isolation of yeast telomerase via RNA affinity tag in TLC1 RNA was developed. Streptavidin aptamer was inserted at two different positions in TLC1 RNA. Telomerase with TLC1 RNA with one of these inserts is functional in vivo and can be isolated by affinity chromatography in vitro. A telomerase preparation isolated using this technique from a strain producing two distinguishable TLC1 RNA molecules (with and without aptameric insertion) resulted in isolation of active telomerase containing only TLC1 RNA with the aptamer. Our results indicate that yeast telomerase is active in vitro as a monomer.
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Affiliation(s)
- D M Shcherbakova
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119992, Russia
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10
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Bugaeva EY, Shpanchenko OV, Felden B, Isaksson LA, Dontsova OA. One SmpB molecule accompanies tmRNA during its passage through the ribosomes. FEBS Lett 2008; 582:1532-6. [PMID: 18396159 DOI: 10.1016/j.febslet.2008.03.049] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2008] [Revised: 03/19/2008] [Accepted: 03/21/2008] [Indexed: 11/17/2022]
Abstract
tmRNA and SmpB are the main participants of trans-translation, a process which rescues the ribosome blocked during translation of non-stop mRNA. While a one-to-one stoichiometry of tmRNA to the ribosome is generally accepted, the number of SmpB molecules in the complex is still under question. We have isolated tmRNA-ribosome complexes blocked at different steps of the tmRNA path through the ribosome and analyzed the stoichiometry of the complexes. Ribosome, tmRNA and SmpB were found in equimolar amount in the tmRNA-ribosome complexes stopped at the position of the 2nd, 4th, 5th or the 11th codons of the coding part of the tmRNA.
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Affiliation(s)
- Elizaveta Y Bugaeva
- Belozersky Institute, Build. A, Moscow State University, Moscow 119992, Russia
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11
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Abstract
Small protein B (SmpB) is a requisite component of the transfer messenger RNA (tmRNA)-mediated bacterial translational quality control system known as trans-translation. The initial binding of tmRNA and its subsequent accommodation into the ribosomal A-site are activities intimately linked to SmpB protein function. From a mechanistic perspective, two key unanswered questions that require further investigation are: 1) what constitutes a stalled ribosome recognition complex and 2) does SmpB pre-bind ribosomes to recruit tmRNA. We have assessed, both in vivo and in vitro, the nature and stability of free SmpB interactions with stalled ribosomes and examined whether these interactions are functionally relevant. We present evidence to demonstrate that interaction of free SmpB with ribosomes is salt sensitive and significantly more labile than interaction of the SmpB.tmRNA complex with ribosomes. Upon dissociation of 70 S ribosomes SmpB partitions primarily with tmRNA rather than ribosomal subunits. This finding is consistent with biochemical and structural data demonstrating that tmRNA is the high-affinity binding partner of SmpB. Moreover, we show that under normal physiological conditions roughly similar numbers of SmpB and tmRNA molecules are present in cells. Our investigations also reveal that upon induction of a nonstop mRNA, SmpB is enriched in stalled ribosome fractions only in the presence of tmRNA. Based on these findings, we conclude that SmpB does not pre-bind stalled ribosome and that functional SmpB-stalled ribosome interactions require tmRNA. We propose that a 1:1:1 complex of SmpB.tmRNA.EF-Tu(GTP) recognizes and binds a stalled ribosome to initiate trans-translation.
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Affiliation(s)
| | - A. Wali Karzai
- Department of Biochemistry and Cell Biology
- Center for Infectious Diseases of Stony Brook University Stony Brook, NY 11794 USA
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12
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Abstract
The tmRNA system performs translational surveillance and ribosome rescue in all eubacteria and some eukaryotic organelles. This system intervenes when ribosomes read to the 3' end of an mRNA or pause at internal codons with subsequent mRNA cleavage. A complex of alanyl-tmRNA (which functions as a tRNA and mRNA), SmpB protein, and EF-TucGTP binds stalled ribosomes, the nascent polypeptide is transferred to the alanine on tmRNA, and translation switches from the original message to a short tmRNA open reading frame (ORF) that encodes a degradation tag. Translation of the ORF and normal termination releases the tagged polypeptide for degradation and permits disassembly and recycling of ribosomal subunits for new rounds of protein synthesis. Structural and biochemical studies suggest mechanisms that keep tmRNA from interrupting normal translation and target ribosomes stalled with very short 3' mRNA extensions. Additional biological roles of tmRNA include stress management and the regulation of transcriptional circuits.
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MESH Headings
- Amino Acid Sequence
- Base Sequence
- Macromolecular Substances
- Models, Molecular
- Molecular Sequence Data
- Nucleic Acid Conformation
- Open Reading Frames
- Peptide Elongation Factor Tu/metabolism
- Protein Biosynthesis
- Protein Conformation
- RNA Stability
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Transfer/chemistry
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
- RNA-Binding Proteins/metabolism
- Ribosomes/metabolism
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Affiliation(s)
- Sean D Moore
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
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13
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Tsuda N, Chang DZ, Mine T, Efferson C, García-Sastre A, Wang X, Ferrone S, Ioannides CG. Taxol Increases the Amount and T Cell–Activating Ability of Self-Immune Stimulatory Multimolecular Complexes Found in Ovarian Cancer Cells. Cancer Res 2007; 67:8378-87. [PMID: 17804754 DOI: 10.1158/0008-5472.can-07-0327] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
It has been proposed that chemotherapy enhances tumor antigen (TA)-specific immunity. The molecular form of TA from ovarian tumor that activates cellular immunity is unknown. We report here identification of a novel molecular form of immunogenic TA for CD8(+) cells named self-immune stimulatory multimolecular complexes (ISMMC). ISMMC consist of a molecular complex of polyosome/ribosome-bound ubiquitinated nascent HER-2 polypeptides. This complex is chaperoned by heat shock protein Gp96, which mediates ISMMC uptake by antigen-presenting cells through the scavenger receptor CD91. RNAs in ISMMC stimulate immature dendritic cells to secrete interleukin 12 and induce IFN-gamma in peripheral blood mononuclear cells. ISMMC dissociate, retrotranslocate from the lysosome to cytoplasm, and are processed to peptides by the proteasome. At subpharmacologic doses, Taxol increased the amount of ISMMC by three to four times and modified their composition by inducing the attachment of cochaperones of HSP70, such as the mitotic-phase phosphoprotein 11J. On a total protein basis, Taxol induced ISMMC, expanded more CD8(+) cells, activated more CD56(+) NKG2D(+) cells to produce IFN-gamma, and were more potent inducers of high T-cell receptor density Perforin(+) cells than native ISMMC and peptide E75. Elucidation of the composition of ISMMC and identification of adducts formed by Taxol should be important for developing molecular cancer vaccines.
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Affiliation(s)
- Naotake Tsuda
- Department of Gynecologic Oncology, The University of Texas M D Anderson Cancer Center, Houston, TX 77030, USA
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14
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Wilson DN, Nierhaus KH. The weird and wonderful world of bacterial ribosome regulation. Crit Rev Biochem Mol Biol 2007; 42:187-219. [PMID: 17562451 DOI: 10.1080/10409230701360843] [Citation(s) in RCA: 169] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
In every organism, translation of the genetic information into functional proteins is performed on the ribosome. In Escherichia coli up to 40% of the cell's total energy turnover is channelled toward the ribosome and protein synthesis. Thus, elaborate networks of translation regulation pathways have evolved to modulate gene expression in response to growth rate and external factors, ranging from nutrient deprivation, to chemical (pH, ionic strength) and physical (temperature) fluctuations. Since the fundamental players involved in regulation of the different phases of translation have already been extensively reviewed elsewhere, this review focuses on lesser known and characterized factors that regulate the ribosome, ranging from processing, modification and assembly factors, unusual initiation and elongation factors, to a variety of stress response proteins.
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Affiliation(s)
- Daniel N Wilson
- Gene Center and Department of Chemistry and Biochemistry, University of Munich, Munich, Germany.
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15
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Bessho Y, Shibata R, Sekine SI, Murayama K, Higashijima K, Hori-Takemoto C, Shirouzu M, Kuramitsu S, Yokoyama S. Structural basis for functional mimicry of long-variable-arm tRNA by transfer-messenger RNA. Proc Natl Acad Sci U S A 2007; 104:8293-8. [PMID: 17488812 PMCID: PMC1895943 DOI: 10.1073/pnas.0700402104] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
tmRNA and small protein B (SmpB) are essential trans-translation system components. In the present study, we determined the crystal structure of SmpB in complex with the entire tRNA domain of the tmRNA from Thermus thermophilus. Overall, the ribonucleoprotein complex (tRNP) mimics a long-variable-arm tRNA (class II tRNA) in the canonical L-shaped tertiary structure. The tmRNA terminus corresponds to the acceptor and T arms, or the upper part, of tRNA. On the other hand, the SmpB protein simulates the lower part, the anticodon and D stems, of tRNA. Intriguingly, several amino acid residues collaborate with tmRNA bases to reproduce the canonical tRNA core layers. The linker helix of tmRNA had been considered to correspond to the anticodon stem, but the complex structure unambiguously shows that it corresponds to the tRNA variable arm. The tmRNA linker helix, as well as the long variable arm of class II tRNA, may occupy the gap between the large and small ribosomal subunits. This suggested how the tRNA domain is connected to the mRNA domain entering the mRNA channel. A loop of SmpB in the tRNP is likely to participate in the interaction with alanyl-tRNA synthetase, which may be the mechanism for the promotion of tmRNA alanylation by the SmpB protein. Therefore, the tRNP may simulate a tRNA, both structurally and functionally, with respect to aminoacylation and ribosome entry.
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Affiliation(s)
- Yoshitaka Bessho
- *Genomic Sciences Center, Yokohama Institute, RIKEN 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
- RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Rie Shibata
- *Genomic Sciences Center, Yokohama Institute, RIKEN 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Shun-ichi Sekine
- *Genomic Sciences Center, Yokohama Institute, RIKEN 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; and
| | - Kazutaka Murayama
- *Genomic Sciences Center, Yokohama Institute, RIKEN 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Kyoko Higashijima
- *Genomic Sciences Center, Yokohama Institute, RIKEN 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Chie Hori-Takemoto
- *Genomic Sciences Center, Yokohama Institute, RIKEN 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Mikako Shirouzu
- *Genomic Sciences Center, Yokohama Institute, RIKEN 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
- RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Seiki Kuramitsu
- RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
- Department of Biology, Graduate School of Science, Osaka University, Osaka 560-0043, Japan
| | - Shigeyuki Yokoyama
- *Genomic Sciences Center, Yokohama Institute, RIKEN 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
- RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; and
- To whom correspondence should be addressed. E-mail:
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16
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Kaur S, Gillet R, Li W, Gursky R, Frank J. Cryo-EM visualization of transfer messenger RNA with two SmpBs in a stalled ribosome. Proc Natl Acad Sci U S A 2006; 103:16484-9. [PMID: 17056712 PMCID: PMC1618813 DOI: 10.1073/pnas.0607438103] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In eubacterial translation, lack of a stop codon on the mRNA results in a defective, potentially toxic polypeptide stalled on the ribosome. Bacteria possess a specialized mRNA, called transfer messenger RNA (tmRNA), to rescue such a stalled system. tmRNA contains a transfer RNA (tRNA)-like domain (TLD), which enters the ribosome as a tRNA and places an ORF into the mRNA channel. This ORF codes for a signal marking the polypeptide for degradation and ends in a stop codon, leading to release of the faulty polypeptide and recycling of the ribosome. The binding of tmRNA to the stalled ribosome is mediated by small protein B (SmpB). By means of cryo-EM, we obtained a density map for the preaccommodated state of the tmRNA.SmpB.EF-Tu.70S ribosome complex with much improved definition for the tmRNA-SmpB complex, showing two SmpB molecules bound per ribosome, one toward the A site on the 30S subunit side and the other bound to the 50S subunit near the GTPase-associated center. tmRNA is strongly attached to the 30S subunit head by multiple contact sites, involving most of its pseudoknots and helices. The map clarifies that the TLD is located near helix 34 and protein S19 of the 30S subunit, rather than in the A site as tRNA for normal translation, so that the TLD is oriented toward the ORF.
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Affiliation(s)
- Sukhjit Kaur
- *Wadsworth Center, New York State Department of Health, Empire State Plaza, Albany, NY 12201-0509
| | - Reynald Gillet
- Institut Fédératif de Recherche 140, Unité Propre de Recherche de l' Enseignement Jeune Equipe 2311, Institut National de la Santé et de la Recherche Médicale Biochimie Pharmaceutique, Université de Rennes I, 2 Avenue du Prof. Léon Bernard, 35043 Rennes, France; and
| | - Wen Li
- *Wadsworth Center, New York State Department of Health, Empire State Plaza, Albany, NY 12201-0509
| | - Richard Gursky
- Howard Hughes Medical Institute
- Health Research Inc., and
| | - Joachim Frank
- Howard Hughes Medical Institute
- Health Research Inc., and
- *Wadsworth Center, New York State Department of Health, Empire State Plaza, Albany, NY 12201-0509
- Department of Biomedical Sciences, State University of New York, Empire State Plaza, Albany, NY 12201-0509
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17
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Hallier M, Desreac J, Felden B. Small protein B interacts with the large and the small subunits of a stalled ribosome during trans-translation. Nucleic Acids Res 2006; 34:1935-43. [PMID: 16611927 PMCID: PMC1435831 DOI: 10.1093/nar/gkl097] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
During trans-translation, stalled bacterial ribosomes are rescued by small protein B (SmpB) and by transfer-messenger RNA (tmRNA). Stalled ribosomes switch translation from the defective messages to a short internal reading frame on tmRNA that tags the nascent peptide chain for degradation and recycles the ribosomes. We present evidences that SmpB binds the large and small ribosomal subunits in vivo and in vitro. The binding between SmpB and the ribosomal subunits is very tight, with a dissociation constant of 1.7 × 10−10 M, similar to its KD for the 70S ribosome or for tmRNA. tmRNA displaces SmpB from its 50S binding but not from the 30S. In vivo, SmpB is detected on the 50S when trans-translation is impaired by lacking tmRNA or a functional SmpB. SmpB contacts the large subunit transiently and early during the trans-translational process. The affinity of SmpB for the two ribosomal subunits is modulated by tmRNA in the course of trans-translation. It is the first example of two copies of the same protein interacting with two different functional sites of the ribosomes.
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Affiliation(s)
| | | | - Brice Felden
- To whom correspondence should be addressed. Tel: +332 2323 4851; Fax: +332 2323 4456;
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Nonin-Lecomte S, Felden B, Dardel F. NMR structure of the Aquifex aeolicus tmRNA pseudoknot PK1: new insights into the recoding event of the ribosomal trans-translation. Nucleic Acids Res 2006; 34:1847-53. [PMID: 16595798 PMCID: PMC1428798 DOI: 10.1093/nar/gkl111] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The transfer-messenger RNA (tmRNA) pseudoknot PK1 is essential for bacterial trans-translation, a ribosomal rescue mechanism. We report the solution structure of PK1 from Aquifex aeolicus, which despite an unprecedented small number of nucleotides and thus an unprecented compact size, displays a very high thermal stability. Several unusual structural features account for these properties and indicate that PK1 belongs to the class of ribosomal frameshift pseudoknots. This suggests a similarity between the mechanism of programmed ribosomal frameshifting and trans-translation.
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Affiliation(s)
- Sylvie Nonin-Lecomte
- Université Descartes Paris V-Faculté de Pharmacie, Laboratoire de Cristallographie et RMN Biologiques, CNRS UMR 8015, 4, av. de l'Observatoire-75006 Paris, France.
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19
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Aleksei Alekseevich Bogdanov. Mol Biol 2005. [DOI: 10.1007/s11008-005-0078-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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20
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Ivanova N, Pavlov MY, Bouakaz E, Ehrenberg M, Schiavone LH. Mapping the interaction of SmpB with ribosomes by footprinting of ribosomal RNA. Nucleic Acids Res 2005; 33:3529-39. [PMID: 15972795 PMCID: PMC1156966 DOI: 10.1093/nar/gki666] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2005] [Revised: 06/06/2005] [Accepted: 06/06/2005] [Indexed: 12/01/2022] Open
Abstract
In trans-translation transfer messenger RNA (tmRNA) and small protein B (SmpB) rescue ribosomes stalled on truncated or in other ways problematic mRNAs. SmpB promotes the binding of tmRNA to the ribosome but there is uncertainty about the number of participating SmpB molecules as well as their ribosomal location. Here, the interaction of SmpB with ribosomal subunits and ribosomes was studied by isolation of SmpB containing complexes followed by chemical modification of ribosomal RNA with dimethyl sulfate, kethoxal and hydroxyl radicals. The results show that SmpB binds 30S and 50S subunits with 1:1 molar ratios and the 70S ribosome with 2:1 molar ratio. SmpB-footprints are similar on subunits and the ribosome. In the 30S subunit, SmpB footprints nucleotides that are in the vicinity of the P-site facing the E-site, and in the 50S subunit SmpB footprints nucleotides that are located below the L7/L12 stalk in the 3D structure of the ribosome. Based on these results, we suggest a mechanism where two molecules of SmpB interact with tmRNA and the ribosome during trans-translation. The first SmpB molecule binds near the factor-binding site on the 50S subunit helping tmRNA accommodation on the ribosome, whereas the second SmpB molecule may functionally substitute for a missing anticodon stem-loop in tmRNA during later steps of trans-translation.
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MESH Headings
- Base Sequence
- Binding Sites
- Models, Molecular
- Molecular Sequence Data
- Protein Biosynthesis
- Protein Footprinting
- RNA, Ribosomal/chemistry
- RNA, Ribosomal/metabolism
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/metabolism
- RNA, Ribosomal, 23S/chemistry
- RNA, Ribosomal, 23S/metabolism
- RNA-Binding Proteins/metabolism
- Ribosomes/chemistry
- Ribosomes/metabolism
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Affiliation(s)
- Natalia Ivanova
- Department of Cell and Molecular Biology, BMC, Uppsala UniversityBox 596, S-75 124 Uppsala, Sweden
- Cell Biology Unit, Department of Life SciencesSödertörns Högskola, S-141 89 Huddinge, Sweden
| | - Michael Y. Pavlov
- Department of Cell and Molecular Biology, BMC, Uppsala UniversityBox 596, S-75 124 Uppsala, Sweden
- Cell Biology Unit, Department of Life SciencesSödertörns Högskola, S-141 89 Huddinge, Sweden
| | - Elli Bouakaz
- Department of Cell and Molecular Biology, BMC, Uppsala UniversityBox 596, S-75 124 Uppsala, Sweden
- Cell Biology Unit, Department of Life SciencesSödertörns Högskola, S-141 89 Huddinge, Sweden
| | - Måns Ehrenberg
- Department of Cell and Molecular Biology, BMC, Uppsala UniversityBox 596, S-75 124 Uppsala, Sweden
- Cell Biology Unit, Department of Life SciencesSödertörns Högskola, S-141 89 Huddinge, Sweden
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Saguy M, Gillet R, Metzinger L, Felden B. tmRNA and associated ligands: a puzzling relationship. Biochimie 2005; 87:897-903. [PMID: 16164997 DOI: 10.1016/j.biochi.2005.03.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2005] [Revised: 02/10/2005] [Accepted: 03/18/2005] [Indexed: 11/23/2022]
Abstract
Translation is an efficient and accurate mechanism, needing thorough systems of control-quality to ensure the correspondence between the information carried by the messenger RNA (mRNA) and the newly synthesized protein. Among them, trans-translation ensures delivering of stalled ribosomes when translation occurs on truncated mRNAs in bacteria, followed by the degradation of the incomplete nascent proteins. This process requires transfer-messenger RNA (tmRNA), an original molecule acting as both a tRNA and an mRNA. tmRNA first enters the decoding site of stuck ribosomes and, despite the lack of any codon-anticodon interaction, acts as a tRNA by transferring its alanine to the incomplete protein. Translation then switches to a small internal coding sequence (mRNA domain), which encodes a tag directing the incomplete protein towards degradation. Although playing a central role during trans-translation, tmRNA function depends on associated proteins. Genetic, biochemical and recent structural data are starting to unravel how the process takes place, by involving three main protein partners. Small protein B (SmpB) interacts with the tRNA-like domain (TLD) of tmRNA and is indispensable and specific to the process. Elongation factor Tu (EF-Tu) binds simultaneously the TLD and brings aminoacylated tmRNA to the ribosome, as for canonical tRNAs. Ribosomal protein S1 forms complexes with tmRNA, facilitating its recruitment by the stalled ribosomes. The chronology of events, however, is poorly understood and recent data shed light on the functions attributed to the proteins involved in trans-translation. This review focuses on the puzzling relationship that tmRNA has with these three protein ligands, putting forward trans-translation as a highly dynamical process.
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Affiliation(s)
- Matthieu Saguy
- Université de Rennes I, UPRES JE 2311, Inserm ESPRI, Biochimie Pharmaceutique, 2, avenue du Prof. Léon Bernard, 35043 Rennes, France
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