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González-López A, Larsson DSD, Koripella RK, Cain BN, Chavez MG, Hergenrother PJ, Sanyal S, Selmer M. Structures of the Staphylococcus aureus ribosome inhibited by fusidic acid and fusidic acid cyclopentane. Sci Rep 2024; 14:14253. [PMID: 38902339 PMCID: PMC11190147 DOI: 10.1038/s41598-024-64868-x] [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: 01/23/2024] [Accepted: 06/13/2024] [Indexed: 06/22/2024] Open
Abstract
The antibiotic fusidic acid (FA) is used to treat Staphylococcus aureus infections. It inhibits protein synthesis by binding to elongation factor G (EF-G) and preventing its release from the ribosome after translocation. While FA, due to permeability issues, is only effective against gram-positive bacteria, the available structures of FA-inhibited complexes are from gram-negative model organisms. To fill this knowledge gap, we solved cryo-EM structures of the S. aureus ribosome in complex with mRNA, tRNA, EF-G and FA to 2.5 Å resolution and the corresponding complex structures with the recently developed FA derivative FA-cyclopentane (FA-CP) to 2.0 Å resolution. With both FA variants, the majority of the ribosomal particles are observed in chimeric state and only a minor population in post-translocational state. As expected, FA binds in a pocket between domains I, II and III of EF-G and the sarcin-ricin loop of 23S rRNA. FA-CP binds in an identical position, but its cyclopentane moiety provides additional contacts to EF-G and 23S rRNA, suggesting that its improved resistance profile towards mutations in EF-G is due to higher-affinity binding. These high-resolution structures reveal new details about the S. aureus ribosome, including confirmation of many rRNA modifications, and provide an optimal starting point for future structure-based drug discovery on an important clinical drug target.
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Affiliation(s)
- Adrián González-López
- Department of Cell and Molecular Biology, Uppsala University, BMC, P.O. Box 596, 75124, Uppsala, Sweden
| | - Daniel S D Larsson
- Department of Cell and Molecular Biology, Uppsala University, BMC, P.O. Box 596, 75124, Uppsala, Sweden
| | - Ravi Kiran Koripella
- Department of Cell and Molecular Biology, Uppsala University, BMC, P.O. Box 596, 75124, Uppsala, Sweden
- Robert P. Apkarian Integrated Electron Microscopy Core, Emory University, Atlanta, USA
| | - Brett N Cain
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Martin Garcia Chavez
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Paul J Hergenrother
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Suparna Sanyal
- Department of Cell and Molecular Biology, Uppsala University, BMC, P.O. Box 596, 75124, Uppsala, Sweden
| | - Maria Selmer
- Department of Cell and Molecular Biology, Uppsala University, BMC, P.O. Box 596, 75124, Uppsala, Sweden.
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2
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Role of ribosome recycling factor in natural termination and translational coupling as a ribosome releasing factor. PLoS One 2023; 18:e0282091. [PMID: 36827443 PMCID: PMC9955659 DOI: 10.1371/journal.pone.0282091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 02/07/2023] [Indexed: 02/26/2023] Open
Abstract
The role of ribosome recycling factor (RRF) of E. coli was studied in vivo and in vitro. We used the translational coupling without the Shine-Dalgarno sequence of downstream ORF (d-ORF) as a model system of the RRF action in natural termination of protein synthesis. For the in vivo studies we used the translational coupling by the adjacent coat and lysis genes of RNA phage GA sharing the termination and initiation (UAAUG) and temperature sensitive RRF. The d-ORF translation was measured by the expression of the reporter lacZ gene connected to the 5'-terminal part of the lysis gene. The results showed that more ribosomes which finished upstream ORF (u-ORF) reading were used for downstream reading when RRF was inactivated. The in vitro translational coupling studies with 027mRNA having the junction sequence UAAUG with wild-type RRF were carried out with measuring amino acids incorporation. The results showed that ribosomes released by RRF read downstream from AUG of UAAUG. In the absence of RRF, ribosomes read downstream in frame with UAA. These in vivo and in vitro studies indicate that RRF releases ribosomes from mRNA at the termination codon of u-ORF. Furthermore, the non-dissociable ribosomes read downstream from AUG of UAAUG with RRF in vitro. This suggests that complete ribosomal splitting is not required for ribosome release by RRF in translational coupling. The data are consistent with the interpretation that RRF functions mostly as a ribosome releasing factor rather than ribosome splitting factor. Additionally, the in vivo studies showed that short (less than 5 codons) u-ORF inhibited d-ORF reading by ribosomes finishing u-ORF reading, suggesting that the termination process in short ORF is not similar to that in normal ORF. This means that all the preexisting studies on RRF with short mRNA may not represent what goes on in natural termination step.
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3
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Lang M, Krin E, Korlowski C, Sismeiro O, Varet H, Coppée JY, Mazel D, Baharoglu Z. Sleeping ribosomes: Bacterial signaling triggers RaiA mediated persistence to aminoglycosides. iScience 2021; 24:103128. [PMID: 34611612 PMCID: PMC8476650 DOI: 10.1016/j.isci.2021.103128] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 09/07/2021] [Accepted: 09/09/2021] [Indexed: 12/19/2022] Open
Abstract
Indole is a molecule proposed to be involved in bacterial signaling. We find that indole secretion is induced by sublethal tobramycin concentrations and increases persistence to aminoglycosides in V. cholerae. Indole transcriptomics showed increased expression of raiA, a ribosome associated factor. Deletion of raiA abolishes the appearance of indole dependent persisters to aminoglycosides, although its overexpression leads to 100-fold increase of persisters, and a reduction in lag phase, evocative of increased active 70S ribosome content, confirmed by sucrose gradient analysis. We propose that, under stress conditions, RaiA-bound inactive 70S ribosomes are stored as “sleeping ribosomes”, and are rapidly reactivated upon stress relief. Our results point to an active process of persister formation through ribosome protection during translational stress (e.g., aminoglycoside treatment) and reactivation upon antibiotic removal. Translation is a universal process, and these results could help elucidate a mechanism of persistence formation in a controlled, thus inducible way. Indole is produced under sub-MIC tobramycin stress in V. cholerae and upregulates raiA RaiA is involved in indole-dependent formation of aminoglycoside specific persisters RaiA overexpression allows faster growth restart and increases 70S ribosome content RaiA-bound inactive 70S ribosomes form intact and reactivable sleeping ribosome pools
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Affiliation(s)
- Manon Lang
- Département Génomes et Génétique, Institut Pasteur, UMR3525, CNRS, Unité Plasticité du Génome Bactérien, 75015 Paris, France
- Sorbonne Université, Collège Doctoral, 75005 Paris, France
| | - Evelyne Krin
- Département Génomes et Génétique, Institut Pasteur, UMR3525, CNRS, Unité Plasticité du Génome Bactérien, 75015 Paris, France
| | - Chloé Korlowski
- Département Génomes et Génétique, Institut Pasteur, UMR3525, CNRS, Unité Plasticité du Génome Bactérien, 75015 Paris, France
| | - Odile Sismeiro
- Biomics Technological Platform, Center for Technological Resources and Research, Institut Pasteur, 75015 Paris, France
| | - Hugo Varet
- Biomics Technological Platform, Center for Technological Resources and Research, Institut Pasteur, 75015 Paris, France
- Bioinformatics and Biostatistics Hub, Department of Computational Biology, USR 3756 CNRS, Institut Pasteur, 75015 Paris, France
| | - Jean-Yves Coppée
- Biomics Technological Platform, Center for Technological Resources and Research, Institut Pasteur, 75015 Paris, France
| | - Didier Mazel
- Département Génomes et Génétique, Institut Pasteur, UMR3525, CNRS, Unité Plasticité du Génome Bactérien, 75015 Paris, France
- Corresponding author
| | - Zeynep Baharoglu
- Département Génomes et Génétique, Institut Pasteur, UMR3525, CNRS, Unité Plasticité du Génome Bactérien, 75015 Paris, France
- Corresponding author
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4
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Paleskava A, Kaiumov MY, Kirillov SV, Konevega AL. Peculiarities in Activation of Hydrolytic Activity of Elongation Factors. BIOCHEMISTRY (MOSCOW) 2021; 85:1422-1433. [PMID: 33280582 DOI: 10.1134/s0006297920110103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Translational GTPases (trGTPases) belong to the family of G proteins and play key roles at all stages of protein biosynthesis on the ribosome. Unidirectional and cyclic functioning of G proteins is ensured by their ability to switch between the active and inactive states due to GTP hydrolysis accelerated by the auxiliary GTPase-activating proteins. Although trGTPases interact with the ribosomes in different conformational states, they bind to the same conserved region, which, unlike in classical GTPase-activating proteins, is represented by ribosomal RNA. The resulting catalytic sites have almost identical structure in all elongation factors suggesting a common mechanism of GTP hydrolysis. However, fine details of the activated state formation and significantly different rates of GTP hydrolysis indicate the existence of distinctive features upon GTP hydrolysis catalyzed by the different factors. Here, we present a contemporary view on the mechanism of GTPase activation and GTP hydrolysis by the elongation factors EF-Tu, EF-G, and SelB based on the analysis of structural, biochemical, and bioinformatics data.
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Affiliation(s)
- A Paleskava
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of NRC "Kurchatov Institute", Gatchina, Leningrad Region, 188300, Russia
| | - M Yu Kaiumov
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of NRC "Kurchatov Institute", Gatchina, Leningrad Region, 188300, Russia
| | - S V Kirillov
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of NRC "Kurchatov Institute", Gatchina, Leningrad Region, 188300, Russia
| | - A L Konevega
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of NRC "Kurchatov Institute", Gatchina, Leningrad Region, 188300, Russia.
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5
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Saito K, Green R, Buskirk AR. Ribosome recycling is not critical for translational coupling in Escherichia coli. eLife 2020; 9:59974. [PMID: 32965213 PMCID: PMC7538156 DOI: 10.7554/elife.59974] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Accepted: 09/22/2020] [Indexed: 12/23/2022] Open
Abstract
We used ribosome profiling to characterize the biological role of ribosome recycling factor (RRF) in Escherichia coli. As expected, RRF depletion leads to enrichment of post-termination 70S complexes in 3′-UTRs. We also observe that elongating ribosomes are unable to complete translation because they are blocked by non-recycled ribosomes at stop codons. Previous studies have suggested a role for recycling in translational coupling within operons; if a ribosome remains bound to an mRNA after termination, it may re-initiate downstream. We found, however, that RRF depletion did not significantly affect coupling efficiency in reporter assays or in ribosome density genome-wide. These findings argue that re-initiation is not a major mechanism of translational coupling in E. coli. Finally, RRF depletion has dramatic effects on the activity of ribosome rescue factors tmRNA and ArfA. Our results provide a global view of the effects of the loss of ribosome recycling on protein synthesis in E. coli.
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Affiliation(s)
- Kazuki Saito
- Department of Molecular Biology and Genetics, Baltimore, United States
| | - Rachel Green
- Department of Molecular Biology and Genetics, Baltimore, United States.,Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Allen R Buskirk
- Department of Molecular Biology and Genetics, Baltimore, United States
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6
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Rodnina MV, Peske F, Peng BZ, Belardinelli R, Wintermeyer W. Converting GTP hydrolysis into motion: versatile translational elongation factor G. Biol Chem 2020; 401:131-142. [PMID: 31600135 DOI: 10.1515/hsz-2019-0313] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 08/24/2019] [Indexed: 12/16/2022]
Abstract
Elongation factor G (EF-G) is a translational GTPase that acts at several stages of protein synthesis. Its canonical function is to catalyze tRNA movement during translation elongation, but it also acts at the last step of translation to promote ribosome recycling. Moreover, EF-G has additional functions, such as helping the ribosome to maintain the mRNA reading frame or to slide over non-coding stretches of the mRNA. EF-G has an unconventional GTPase cycle that couples the energy of GTP hydrolysis to movement. EF-G facilitates movement in the GDP-Pi form. To convert the energy of hydrolysis to movement, it requires various ligands in the A site, such as a tRNA in translocation, an mRNA secondary structure element in ribosome sliding, or ribosome recycling factor in post-termination complex disassembly. The ligand defines the direction and timing of EF-G-facilitated motion. In this review, we summarize recent advances in understanding the mechanism of EF-G action as a remarkable force-generating GTPase.
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Affiliation(s)
- Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany
| | - Frank Peske
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany
| | - Bee-Zen Peng
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany
| | - Riccardo Belardinelli
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany
| | - Wolfgang Wintermeyer
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany
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7
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Townsend GE, Han W, Schwalm ND, Hong X, Bencivenga-Barry NA, Goodman AL, Groisman EA. A Master Regulator of Bacteroides thetaiotaomicron Gut Colonization Controls Carbohydrate Utilization and an Alternative Protein Synthesis Factor. mBio 2020; 11:e03221-19. [PMID: 31992627 PMCID: PMC6989115 DOI: 10.1128/mbio.03221-19] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 12/10/2019] [Indexed: 12/24/2022] Open
Abstract
Microbial colonization of the mammalian gut is largely ascribed to the ability to utilize nutrients available in that environment. To understand how beneficial microbes establish a relationship with their hosts, it is crucial to determine what other abilities promote gut colonization. We now report that colonization of the murine gut by the beneficial microbe Bacteroides thetaiotaomicron requires activation of a putative translation factor by the major transcriptional regulator of gut colonization and carbohydrate utilization. To ascertain how this regulator-called BT4338-promotes gut colonization, we identified BT4338-regulated genes and BT4338-bound DNA sequences. Unexpectedly, the gene whose expression was most reduced upon BT4338 inactivation was fusA2, specifying a putative translation factor. We determined that fusA2 activation by BT4338 is conserved in another Bacteroides species and essential for gut colonization in B. thetaiotaomicron because a mutant lacking the BT4338 binding site in the fusA2 promoter exhibited a colonization defect similar to that of a mutant lacking the fusA2 gene. Furthermore, we demonstrated that BT4338 promotes gut colonization independently of its role in carbohydrate utilization because the fusA2 gene was dispensable for utilization of carbohydrates that depend on BT4338 Our findings suggest that microbial gut colonization requires the use of alternative protein synthesis factors.IMPORTANCE The bacteria occupying the mammalian gut have evolved unique strategies to thrive in their environment. Bacteroides organisms, which often comprise 25 to 50% of the human gut microbiota, derive nutrients from structurally diverse complex polysaccharides, commonly called dietary fibers. This ability requires an expansive genetic repertoire that is coordinately regulated to achieve expression of those genes dedicated to utilizing only those dietary fibers present in the environment. Here we identify the global regulon of a transcriptional regulator necessary for dietary fiber utilization and gut colonization. We demonstrate that this transcription factor regulates hundreds of genes putatively involved in dietary fiber utilization as well as a putative translation factor dispensable for growth on such nutrients but necessary for survival in the gut. These findings suggest that gut bacteria coordinate cellular metabolism with protein synthesis via specialized translation factors to promote survival in the mammalian gut.
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Affiliation(s)
- Guy E Townsend
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut, USA
- Yale Microbial Sciences Institute, West Haven, Connecticut, USA
- Department of Biochemistry and Molecular Biology, Penn State Health Milton S. Hershey Medical Center, Penn State Hershey College of Medicine, Hershey, Pennsylvania, USA
| | - Weiwei Han
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut, USA
- Yale Microbial Sciences Institute, West Haven, Connecticut, USA
| | - Nathan D Schwalm
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut, USA
- Yale Microbial Sciences Institute, West Haven, Connecticut, USA
| | - Xinyu Hong
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut, USA
- Yale Microbial Sciences Institute, West Haven, Connecticut, USA
| | - Natasha A Bencivenga-Barry
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut, USA
- Yale Microbial Sciences Institute, West Haven, Connecticut, USA
| | - Andrew L Goodman
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut, USA
- Yale Microbial Sciences Institute, West Haven, Connecticut, USA
| | - Eduardo A Groisman
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut, USA
- Yale Microbial Sciences Institute, West Haven, Connecticut, USA
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8
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Structural basis for ribosome recycling by RRF and tRNA. Nat Struct Mol Biol 2019; 27:25-32. [PMID: 31873307 DOI: 10.1038/s41594-019-0350-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 11/12/2019] [Indexed: 11/08/2022]
Abstract
The bacterial ribosome is recycled into subunits by two conserved proteins, elongation factor G (EF-G) and the ribosome recycling factor (RRF). The molecular basis for ribosome recycling by RRF and EF-G remains unclear. Here, we report the crystal structure of a posttermination Thermus thermophilus 70S ribosome complexed with EF-G, RRF and two transfer RNAs at a resolution of 3.5 Å. The deacylated tRNA in the peptidyl (P) site moves into a previously unsuspected state of binding (peptidyl/recycling, p/R) that is analogous to that seen during initiation. The terminal end of the p/R-tRNA forms nonfavorable contacts with the 50S subunit while RRF wedges next to central inter-subunit bridges, illuminating the active roles of tRNA and RRF in dissociation of ribosomal subunits. The structure uncovers a missing snapshot of tRNA as it transits between the P and exit (E) sites, providing insights into the mechanisms of ribosome recycling and tRNA translocation.
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9
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Ribosome structural dynamics in translocation: yet another functional role for ribosomal RNA. Q Rev Biophys 2017; 50:e12. [DOI: 10.1017/s0033583517000117] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
AbstractRibosomes are remarkable ribonucleoprotein complexes that are responsible for protein synthesis in all forms of life. They polymerize polypeptide chains programmed by nucleotide sequences in messenger RNA in a mechanism mediated by transfer RNA. One of the most challenging problems in the ribosome field is to understand the mechanism of coupled translocation of mRNA and tRNA during the elongation phase of protein synthesis. In recent years, the results of structural, biophysical and biochemical studies have provided extensive evidence that translocation is based on the structural dynamics of the ribosome itself. Detailed structural analysis has shown that ribosome dynamics, like aminoacyl-tRNA selection and catalysis of peptide bond formation, is made possible by the properties of ribosomal RNA.
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10
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A general mechanism of ribosome dimerization revealed by single-particle cryo-electron microscopy. Nat Commun 2017; 8:722. [PMID: 28959045 PMCID: PMC5620043 DOI: 10.1038/s41467-017-00718-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Accepted: 07/20/2017] [Indexed: 12/15/2022] Open
Abstract
Bacteria downregulate their ribosomal activity through dimerization of 70S ribosomes, yielding inactive 100S complexes. In Escherichia coli, dimerization is mediated by the hibernation promotion factor (HPF) and ribosome modulation factor. Here we report the cryo-electron microscopy study on 100S ribosomes from Lactococcus lactis and a dimerization mechanism involving a single protein: HPFlong. The N-terminal domain of HPFlong binds at the same site as HPF in Escherichia coli 100S ribosomes. Contrary to ribosome modulation factor, the C-terminal domain of HPFlong binds exactly at the dimer interface. Furthermore, ribosomes from Lactococcus lactis do not undergo conformational changes in the 30S head domains upon binding of HPFlong, and the Shine–Dalgarno sequence and mRNA entrance tunnel remain accessible. Ribosome activity is blocked by HPFlong due to the inhibition of mRNA recognition by the platform binding center. Phylogenetic analysis of HPF proteins suggests that HPFlong-mediated dimerization is a widespread mechanism of ribosome hibernation in bacteria. When bacteria enter the stationary growth phase, protein translation is suppressed via the dimerization of 70S ribosomes into inactive complexes. Here the authors provide a structural basis for how the dual domain hibernation promotion factor promotes ribosome dimerization and hibernation in bacteria.
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11
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Soundararajan P, Manivannan A, Ko CH, Muneer S, Jeong BR. Leaf Physiological and Proteomic Analysis to Elucidate Silicon Induced Adaptive Response under Salt Stress in Rosa hybrida 'Rock Fire'. Int J Mol Sci 2017; 18:E1768. [PMID: 28805727 PMCID: PMC5578157 DOI: 10.3390/ijms18081768] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 08/05/2017] [Accepted: 08/09/2017] [Indexed: 12/13/2022] Open
Abstract
Beneficial effects of silicon (Si) on growth and development have been witnessed in several plants. Nevertheless, studies on roses are merely reported. Therefore, the present investigation was carried out to illustrate the impact of Si on photosynthesis, antioxidant defense and leaf proteome of rose under salinity stress. In vitro-grown, acclimatized Rosa hybrida 'Rock Fire' were hydroponically treated with four treatments, such as control, Si (1.8 mM), NaCl (50 mM), and Si+NaCl. After 15 days, the consequences of salinity stress and the response of Si addition were analyzed. Scorching of leaf edges and stomatal damages occurred due to salt stress was ameliorated under Si supplementation. Similarly, reduction of gas exchange, photosynthetic pigments, higher lipid peroxidation rate, and accumulation of reactive oxygen species under salinity stress were mitigated in Si treatment. Lesser oxidative stress observed was correlated with the enhanced activity and expression of antioxidant enzymes, such as superoxide dismutase, catalase, and ascorbate peroxidase in Si+NaCl treatment. Importantly, sodium transportation was synergistically restricted with the stimulated counter-uptake of potassium in Si+NaCl treatment. Furthermore, two-dimensional electrophoresis (2-DE) and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) results showed that out of 40 identified proteins, on comparison with control 34 proteins were down-accumulated and six proteins were up-accumulated due to salinity stress. Meanwhile, addition of Si with NaCl treatment enhanced the abundance of 30 proteins and downregulated five proteins. Differentially-expressed proteins were functionally classified into six groups, such as photosynthesis (22%), carbohydrate/energy metabolism (20%), transcription/translation (20%), stress/redox homeostasis (12%), ion binding (13%), and ubiquitination (8%). Hence, the findings reported in this work could facilitate a deeper understanding on potential mechanism(s) adapted by rose due to the exogenous Si supplementation during the salinity stress.
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Affiliation(s)
| | - Abinaya Manivannan
- Institute of Agriculture and Life Science, Gyeongsang National University, Jinju 660-701, Korea.
| | - Chung Ho Ko
- Division of Applied Life Science (BK21 Plus), Graduate School, Gyeongsang National University, Jinju 660-701, Korea.
| | - Sowbiya Muneer
- Division of Applied Life Science (BK21 Plus), Graduate School, Gyeongsang National University, Jinju 660-701, Korea.
| | - Byoung Ryong Jeong
- Institute of Agriculture and Life Science, Gyeongsang National University, Jinju 660-701, Korea.
- Division of Applied Life Science (BK21 Plus), Graduate School, Gyeongsang National University, Jinju 660-701, Korea.
- Institute of Life Science, Gyeongsang National University, Jinju 660-701, Korea.
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12
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Iwakura N, Yokoyama T, Quaglia F, Mitsuoka K, Mio K, Shigematsu H, Shirouzu M, Kaji A, Kaji H. Chemical and structural characterization of a model Post-Termination Complex (PoTC) for the ribosome recycling reaction: Evidence for the release of the mRNA by RRF and EF-G. PLoS One 2017; 12:e0177972. [PMID: 28542628 PMCID: PMC5443523 DOI: 10.1371/journal.pone.0177972] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 05/06/2017] [Indexed: 12/02/2022] Open
Abstract
A model Post-Termination Complex (PoTC) used for the discovery of Ribosome Recycling Factor (RRF) was purified and characterized by cryo-electron microscopic analysis and biochemical methods. We established that the model PoTC has mostly one tRNA, at the P/E or P/P position, together with one mRNA. The structural studies were supported by the biochemical measurement of bound tRNA and mRNA. Using this substrate, we establish that the release of tRNA, release of mRNA and splitting of ribosomal subunits occur during the recycling reaction. Order of these events is tRNA release first followed by mRNA release and splitting almost simultaneously. Moreover, we demonstrate that IF3 is not involved in any of the recycling reactions but simply prevents the re-association of split ribosomal subunits. Our finding demonstrates that the important function of RRF includes the release of mRNA, which is often missed by the use of a short ORF with the Shine-Dalgarno sequence near the termination site.
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Affiliation(s)
- Nobuhiro Iwakura
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Jefferson Medical College, Philadelphia, Pennsylvania, United States of America
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Takeshi Yokoyama
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, Yokohama, Japan
| | - Fabio Quaglia
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Jefferson Medical College, Philadelphia, Pennsylvania, United States of America
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- University of Camerino, School of Biosciences and Veterinary Medicine, Camerino, Italy
| | - Kaoru Mitsuoka
- Research Center for Ultra-High Voltage Electron Microscopy, Osaka University, Osaka, Japan
| | - Kazuhiro Mio
- Molecular Profiling Research Center for Drug Discovery and OPERANDO Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Hideki Shigematsu
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, Yokohama, Japan
| | - Mikako Shirouzu
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, Yokohama, Japan
| | - Akira Kaji
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- * E-mail: (HK); (AK)
| | - Hideko Kaji
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Jefferson Medical College, Philadelphia, Pennsylvania, United States of America
- * E-mail: (HK); (AK)
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13
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Borg A, Pavlov M, Ehrenberg M. Mechanism of fusidic acid inhibition of RRF- and EF-G-dependent splitting of the bacterial post-termination ribosome. Nucleic Acids Res 2016; 44:3264-75. [PMID: 27001509 PMCID: PMC4838388 DOI: 10.1093/nar/gkw178] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 03/07/2016] [Indexed: 01/13/2023] Open
Abstract
The antibiotic drug fusidic acid (FA) is commonly used in the clinic against gram-positive bacterial infections. FA targets ribosome-bound elongation factor G (EF-G), a translational GTPase that accelerates both messenger RNA (mRNA) translocation and ribosome recycling. How FA inhibits translocation was recently clarified, but FA inhibition of ribosome recycling by EF-G and ribosome recycling factor (RRF) has remained obscure. Here we use fast kinetics techniques to estimate mean times of ribosome splitting and the stoichiometry of GTP hydrolysis by EF-G at varying concentrations of FA, EF-G and RRF. These mean times together with previous data on uninhibited ribosome recycling were used to clarify the mechanism of FA inhibition of ribosome splitting. The biochemical data on FA inhibition of translocation and recycling were used to model the growth inhibitory effect of FA on bacterial populations. We conclude that FA inhibition of translocation provides the dominant cause of bacterial growth reduction, but that FA inhibition of ribosome recycling may contribute significantly to FA-induced expression of short regulatory open reading frames, like those involved in FA resistance.
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Affiliation(s)
- Anneli Borg
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Box 596, 75124 Uppsala, Sweden
| | - Michael Pavlov
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Box 596, 75124 Uppsala, Sweden
| | - Måns Ehrenberg
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Box 596, 75124 Uppsala, Sweden
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14
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Kuzmenko A, Derbikova K, Salvatori R, Tankov S, Atkinson GC, Tenson T, Ott M, Kamenski P, Hauryliuk V. Aim-less translation: loss of Saccharomyces cerevisiae mitochondrial translation initiation factor mIF3/Aim23 leads to unbalanced protein synthesis. Sci Rep 2016; 6:18749. [PMID: 26728900 PMCID: PMC4700529 DOI: 10.1038/srep18749] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 11/09/2015] [Indexed: 12/22/2022] Open
Abstract
The mitochondrial genome almost exclusively encodes a handful of transmembrane constituents of the oxidative phosphorylation (OXPHOS) system. Coordinated expression of these genes ensures the correct stoichiometry of the system’s components. Translation initiation in mitochondria is assisted by two general initiation factors mIF2 and mIF3, orthologues of which in bacteria are indispensible for protein synthesis and viability. mIF3 was thought to be absent in Saccharomyces cerevisiae until we recently identified mitochondrial protein Aim23 as the missing orthologue. Here we show that, surprisingly, loss of mIF3/Aim23 in S. cerevisiae does not indiscriminately abrogate mitochondrial translation but rather causes an imbalance in protein production: the rate of synthesis of the Atp9 subunit of F1F0 ATP synthase (complex V) is increased, while expression of Cox1, Cox2 and Cox3 subunits of cytochrome c oxidase (complex IV) is repressed. Our results provide one more example of deviation of mitochondrial translation from its bacterial origins.
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Affiliation(s)
- Anton Kuzmenko
- University of Tartu, Institute of Technology, Nooruse 1, 50411 Tartu, Estonia.,Molecular Biology Department, Faculty of Biology, M.V. Lomonosov Moscow State University, 1/12 Leninskie Gory, 119991 Moscow, Russia
| | - Ksenia Derbikova
- Molecular Biology Department, Faculty of Biology, M.V. Lomonosov Moscow State University, 1/12 Leninskie Gory, 119991 Moscow, Russia
| | - Roger Salvatori
- Department of Biochemistry and Biophysics, Center for Biomembrane Research, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Stoyan Tankov
- University of Tartu, Institute of Technology, Nooruse 1, 50411 Tartu, Estonia
| | - Gemma C Atkinson
- University of Tartu, Institute of Technology, Nooruse 1, 50411 Tartu, Estonia.,Department of Molecular Biology, Umeå University, Building 6K, 6L University Hospital Area, SE-901 87 Umeå, Sweden.,Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Building 6K and 6L, University Hospital Area, SE-901 87 Umeå, Sweden
| | - Tanel Tenson
- University of Tartu, Institute of Technology, Nooruse 1, 50411 Tartu, Estonia
| | - Martin Ott
- Department of Biochemistry and Biophysics, Center for Biomembrane Research, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Piotr Kamenski
- Molecular Biology Department, Faculty of Biology, M.V. Lomonosov Moscow State University, 1/12 Leninskie Gory, 119991 Moscow, Russia
| | - Vasili Hauryliuk
- University of Tartu, Institute of Technology, Nooruse 1, 50411 Tartu, Estonia.,Department of Molecular Biology, Umeå University, Building 6K, 6L University Hospital Area, SE-901 87 Umeå, Sweden.,Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Building 6K and 6L, University Hospital Area, SE-901 87 Umeå, Sweden
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15
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Borg A, Pavlov M, Ehrenberg M. Complete kinetic mechanism for recycling of the bacterial ribosome. RNA (NEW YORK, N.Y.) 2016; 22:10-21. [PMID: 26527791 PMCID: PMC4691825 DOI: 10.1261/rna.053157.115] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 09/03/2015] [Indexed: 05/05/2023]
Abstract
How EF-G and RRF act together to split a post-termination ribosomal complex into its subunits has remained obscure. Here, using stopped-flow experiments with Rayleigh light scattering detection and quench-flow experiments with radio-detection of GTP hydrolysis, we have clarified the kinetic mechanism of ribosome recycling and obtained precise estimates of its kinetic parameters. Ribosome splitting requires that EF-G binds to an already RRF-containing ribosome. EF-G binding to RRF-free ribosomes induces futile rounds of GTP hydrolysis and inhibits ribosome splitting, implying that while RRF is purely an activator of recycling, EF-G acts as both activator and competitive inhibitor of RRF in recycling of the post-termination ribosome. The ribosome splitting rate and the number of GTPs consumed per splitting event depend strongly on the free concentrations of EF-G and RRF. The maximal recycling rate, here estimated as 25 sec(-1), is approached at very high concentrations of EF-G and RRF with RRF in high excess over EF-G. The present in vitro results, suggesting an in vivo ribosome recycling rate of ∼5 sec(-1), are discussed in the perspective of rapidly growing bacterial cells.
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Affiliation(s)
- Anneli Borg
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, 751 24 Uppsala, Sweden
| | - Michael Pavlov
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, 751 24 Uppsala, Sweden
| | - Måns Ehrenberg
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, 751 24 Uppsala, Sweden
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16
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Lata M, Sharma D, Deo N, Tiwari PK, Bisht D, Venkatesan K. Proteomic analysis of ofloxacin-mono resistant Mycobacterium tuberculosis isolates. J Proteomics 2015; 127:114-21. [PMID: 26238929 DOI: 10.1016/j.jprot.2015.07.031] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Revised: 07/21/2015] [Accepted: 07/27/2015] [Indexed: 01/22/2023]
Abstract
Drug resistance particularly, multi drug resistance tuberculosis (MDR-TB) has emerged as a major problem in the chemotherapy of tuberculosis. Ofloxacin (OFX) has been used as second-line drug against MDR-TB. The principal target of the OFX is DNA gyrase encoded by gyrA and gyrB genes. Many explanations have been proposed for drug resistance to OFX but still some mechanisms are unknown. As proteins manifest most of the biological processes, these are attractive targets for developing drugs and diagnostics/therapeutics. We examined the OFX resistant Mycobacterium tuberculosis isolates by proteomic approach (2DE-MALDI-TOF-MS) and bioinformatic tools under OFX induced conditions. Our study showed fourteen proteins (Rv0685, Rv0363c, Rv2744c, Rv3803c, Rv2534c, Rv2140c, Rv1475c, Rv0440, Rv2245, Rv1436, Rv3551, Rv0148, Rv2882c and Rv0733) with increased intensities in OFX resistant and OFX induced as compared to susceptible isolates. Bioinformatic analysis of hypothetical proteins (Rv2744c, Rv2140c, Rv3551 and Rv0148) revealed the presence of conserved motifs and domains. Molecular docking showed proper interaction of OFX with residues of conserved motifs. These proteins might be involved in the OFX modulation/neutralization and act as novel resistance mechanisms as well as potential for diagnostics and drug targets against OFX resistance. This article is part of a Special Issue entitled: Proteomics in India.
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Affiliation(s)
- Manju Lata
- Department of Biochemistry, National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Tajganj, Agra 282004, India..
| | - Divakar Sharma
- Department of Biochemistry, National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Tajganj, Agra 282004, India..
| | - Nirmala Deo
- Department of Biochemistry, National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Tajganj, Agra 282004, India..
| | | | - Deepa Bisht
- Department of Biochemistry, National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Tajganj, Agra 282004, India..
| | - Krishnamurthy Venkatesan
- Department of Biochemistry, National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Tajganj, Agra 282004, India..
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17
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Pelchovich G, Nadejda S, Dana A, Tuller T, Bravo IG, Gophna U. Ribosomal mutations affecting the translation of genes that use non-optimal codons. FEBS J 2014; 281:3701-18. [PMID: 24966114 DOI: 10.1111/febs.12892] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Revised: 06/10/2014] [Accepted: 06/23/2014] [Indexed: 01/26/2023]
Abstract
Genes that are laterally acquired by a new host species often contain codons that are non-optimal to the tRNA repertoire of the new host, which may lead to insufficient translational levels. Inefficient translation can be overcome by different mechanisms, such as incremental amelioration of the coding sequence, compensatory mutations in the regulatory sequences leading to increased transcription or increase in gene copy number. However, there is also a possibility that ribosomal mutations can improve the expression of such genes. To test this hypothesis, we examined the effects of point mutations in the endogenous ribosomal proteins S12 and S5 in Escherichia coli, which are known to be involved in the decoding of the mRNA, on the efficiency of translation of exogenous genes that use non-optimal codons, in vivo. We show that an S12 mutant in E. coli is able to express exogenous genes, with non-optimal codons, to higher levels than the wild-type, and explore the mechanisms underlying this phenomenon in this mutant. Our results suggest that the transient emergence of mutants that allow efficient expression of exogenous genes with non-optimal codons could also increase the chances of fixation of laterally transferred genes.
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Affiliation(s)
- Gidi Pelchovich
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Israel
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18
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Shang G, Feng D, Lu F, Zhang H, Cang H, Gao W, Bi R. Purification, crystallization and preliminary crystallographic analysis of a ribosome-recycling factor from Thermoanaerobacter tengcongensis (TteRRF). ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2014; 70:588-91. [PMID: 24817715 DOI: 10.1107/s2053230x1400507x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2013] [Accepted: 03/05/2014] [Indexed: 11/10/2022]
Abstract
Ribosome-recycling factor (RRF) plays an essential role in the fourth step of protein synthesis in prokaryotes. RRF combined with elongation factor G (EF-G) disassembles the post-termination ribosome complex and recycles the protein synthesis machine for the next round of translation. A reductive-methylation-modified RRF from Thermoanaerobacter tengcongensis (TteRRF) has been crystallized using the vapour-diffusion method. The crystal grew in a condition consisting of 0.1 M citric acid pH 3.5, 3.0 M NaCl and 50 mg ml(-1) methylated protein solution at 289 K. A complete data set was collected from a crystal to 2.80 Å resolution using synchrotron radiation at 100 K. The crystal belonged to space group P6122/P6522 with unit-cell parameters a = b = 103.26, c = 89.17 Å. The asymmetric unit was estimated to contain one molecule of TteRRF.
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Affiliation(s)
- Guijun Shang
- College of Science, Beijing Forestry University, 35 Qinghuadong Road, Haidian District, Beijing 100083, People's Republic of China
| | - Duo Feng
- College of Science, Beijing Forestry University, 35 Qinghuadong Road, Haidian District, Beijing 100083, People's Republic of China
| | - Fang Lu
- College of Science, Beijing Forestry University, 35 Qinghuadong Road, Haidian District, Beijing 100083, People's Republic of China
| | - Hongjie Zhang
- Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, People's Republic of China
| | - Huaixing Cang
- College of Science, Beijing Forestry University, 35 Qinghuadong Road, Haidian District, Beijing 100083, People's Republic of China
| | - Wei Gao
- College of Science, Beijing Forestry University, 35 Qinghuadong Road, Haidian District, Beijing 100083, People's Republic of China
| | - Ruchang Bi
- Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, People's Republic of China
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19
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Uchiyama S, Ohshima A, Yoshida T, Ohkubo T, Kobayashi Y. Thermodynamic assessment of domain-domain interactions and in vitro activities of mesophilic and thermophilic ribosome recycling factors. Biopolymers 2013; 100:366-79. [DOI: 10.1002/bip.22233] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Revised: 02/20/2013] [Accepted: 02/28/2013] [Indexed: 11/07/2022]
Affiliation(s)
- Susumu Uchiyama
- Department of Biotechnology, Graduate School of Engineering; Osaka University; Suita; 565-0871; Japan
| | - Atsushi Ohshima
- Department of Pharmaceutical Sciences, Graduate School of Pharmaceutical Sciences; Osaka University; Suita; 565-0871; Japan
| | - Takuya Yoshida
- Department of Pharmaceutical Sciences, Graduate School of Pharmaceutical Sciences; Osaka University; Suita; 565-0871; Japan
| | - Tadayasu Ohkubo
- Department of Pharmaceutical Sciences, Graduate School of Pharmaceutical Sciences; Osaka University; Suita; 565-0871; Japan
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20
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Affiliation(s)
- Peter B. Moore
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107;
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21
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Polikanov YS, Blaha GM, Steitz TA. How hibernation factors RMF, HPF, and YfiA turn off protein synthesis. Science 2012; 336:915-8. [PMID: 22605777 DOI: 10.1126/science.1218538] [Citation(s) in RCA: 151] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Eubacteria inactivate their ribosomes as 100S dimers or 70S monomers upon entry into stationary phase. In Escherichia coli, 100S dimer formation is mediated by ribosome modulation factor (RMF) and hibernation promoting factor (HPF), or alternatively, the YfiA protein inactivates ribosomes as 70S monomers. Here, we present high-resolution crystal structures of the Thermus thermophilus 70S ribosome in complex with each of these stationary-phase factors. The binding site of RMF overlaps with that of the messenger RNA (mRNA) Shine-Dalgarno sequence, which prevents the interaction between the mRNA and the 16S ribosomal RNA. The nearly identical binding sites of HPF and YfiA overlap with those of the mRNA, transfer RNA, and initiation factors, which prevents translation initiation. The binding of RMF and HPF, but not YfiA, to the ribosome induces a conformational change of the 30S head domain that promotes 100S dimer formation.
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Affiliation(s)
- Yury S Polikanov
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA
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22
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Rowland JG, Simon WJ, Prakash JSS, Slabas AR. Proteomics Reveals a Role for the RNA Helicase crhR in the Modulation of Multiple Metabolic Pathways during Cold Acclimation of Synechocystis sp. PCC6803. J Proteome Res 2011; 10:3674-89. [DOI: 10.1021/pr200299t] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- John G. Rowland
- School of Biological and Biomedical Sciences, Durham University, Durham DH1 3LE, United Kingdom
| | - William J. Simon
- School of Biological and Biomedical Sciences, Durham University, Durham DH1 3LE, United Kingdom
| | - Jogadhenu S. S. Prakash
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad 500 046, India
| | - Antoni R. Slabas
- School of Biological and Biomedical Sciences, Durham University, Durham DH1 3LE, United Kingdom
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23
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Nakamura Y, Ito K. tRNA mimicry in translation termination and beyond. WILEY INTERDISCIPLINARY REVIEWS-RNA 2011; 2:647-68. [DOI: 10.1002/wrna.81] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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24
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Activation of initiation factor 2 by ligands and mutations for rapid docking of ribosomal subunits. EMBO J 2010; 30:289-301. [PMID: 21151095 DOI: 10.1038/emboj.2010.328] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2010] [Accepted: 11/17/2010] [Indexed: 11/08/2022] Open
Abstract
We previously identified mutations in the GTPase initiation factor 2 (IF2), located outside its tRNA-binding domain, compensating strongly (A-type) or weakly (B-type) for initiator tRNA formylation deficiency. We show here that rapid docking of 30S with 50S subunits in initiation of translation depends on switching 30S subunit-bound IF2 from its inactive to active form. Activation of wild-type IF2 requires GTP and formylated initiator tRNA (fMet-tRNA(i)). In contrast, extensive activation of A-type IF2 occurs with only GTP or with GDP and fMet-tRNA(i), implying a passive role for initiator tRNA as activator of IF2 in subunit docking. The theory of conditional switching of GTPases quantitatively accounts for all our experimental data. We find that GTP, GDP, fMet-tRNA(i) and A-type mutations multiplicatively increase the equilibrium ratio, K, between active and inactive forms of IF2 from a value of 4 × 10(-4) for wild-type apo-IF2 by factors of 300, 8, 80 and 20, respectively. Functional characterization of the A-type mutations provides keys to structural interpretation of conditional switching of IF2 and other multidomain GTPases.
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25
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Seshadri A, Dubey B, Weber MHW, Varshney U. Impact of rRNA methylations on ribosome recycling and fidelity of initiation inEscherichia coli. Mol Microbiol 2009; 72:795-808. [DOI: 10.1111/j.1365-2958.2009.06685.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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26
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Complementary roles of initiation factor 1 and ribosome recycling factor in 70S ribosome splitting. EMBO J 2008; 27:1706-17. [PMID: 18497739 DOI: 10.1038/emboj.2008.99] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2008] [Accepted: 04/28/2008] [Indexed: 11/09/2022] Open
Abstract
We demonstrate that ribosomes containing a messenger RNA (mRNA) with a strong Shine-Dalgarno sequence are rapidly split into subunits by initiation factors 1 (IF1) and 3 (IF3), but slowly split by ribosome recycling factor (RRF) and elongation factor G (EF-G). Post-termination-like (PTL) ribosomes containing mRNA and a P-site-bound deacylated transfer RNA (tRNA) are split very rapidly by RRF and EF-G, but extremely slowly by IF1 and IF3. Vacant ribosomes are split by RRF/EF-G much more slowly than PTL ribosomes and by IF1/IF3 much more slowly than mRNA-containing ribosomes. These observations reveal complementary splitting of different ribosomal complexes by IF1/IF3 and RRF/EF-G, and suggest the existence of two major pathways for ribosome splitting into subunits in the living cell. We show that the identity of the deacylated tRNA in the PTL ribosome strongly affects the rate by which it is split by RRF/EF-G and that IF3 is involved in the mechanism of ribosome splitting by IF1/IF3 but not by RRF/EF-G. With support from our experimental data, we discuss the principally different mechanisms of ribosome splitting by IF1/IF3 and by RRF/EF-G.
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27
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Pai RD, Zhang W, Schuwirth BS, Hirokawa G, Kaji H, Kaji A, Cate JHD. Structural Insights into ribosome recycling factor interactions with the 70S ribosome. J Mol Biol 2008; 376:1334-47. [PMID: 18234219 PMCID: PMC2712656 DOI: 10.1016/j.jmb.2007.12.048] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2007] [Revised: 12/11/2007] [Accepted: 12/19/2007] [Indexed: 11/25/2022]
Abstract
At the end of translation in bacteria, ribosome recycling factor (RRF) is used together with elongation factor G to recycle the 30S and 50S ribosomal subunits for the next round of translation. In x-ray crystal structures of RRF with the Escherichia coli 70S ribosome, RRF binds to the large ribosomal subunit in the cleft that contains the peptidyl transferase center. Upon binding of either E. coli or Thermus thermophilus RRF to the E. coli ribosome, the tip of ribosomal RNA helix 69 in the large subunit moves away from the small subunit toward RRF by 8 A, thereby disrupting a key contact between the small and large ribosomal subunits termed bridge B2a. In the ribosome crystals, the ability of RRF to destabilize bridge B2a is influenced by crystal packing forces. Movement of helix 69 involves an ordered-to-disordered transition upon binding of RRF to the ribosome. The disruption of bridge B2a upon RRF binding to the ribosome seen in the present structures reveals one of the key roles that RRF plays in ribosome recycling, the dissociation of 70S ribosomes into subunits. The structures also reveal contacts between domain II of RRF and protein S12 in the 30S subunit that may also play a role in ribosome recycling.
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Affiliation(s)
- Raj D Pai
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
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28
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Yoo JH, RajBhandary UL. Requirements for translation re-initiation in Escherichia coli: roles of initiator tRNA and initiation factors IF2 and IF3. Mol Microbiol 2008; 67:1012-26. [PMID: 18221266 PMCID: PMC2268962 DOI: 10.1111/j.1365-2958.2008.06104.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Despite its importance in post-transcriptional regulation of polycistronic operons in Escherichia coli, little is known about the mechanism of translation re-initiation, which occurs when the same ribosome used to translate an upstream open reading frame (ORF) also translates a downstream ORF. To investigate translation re-initiation in Escherichia coli, we constructed a di-cistronic reporter in which a firefly luciferase gene was linked to a chloramphenicol acetyltransferase gene using a segment of the translationally coupled geneV–geneVII intercistronic region from M13 phage. With this reporter and mutant initiator tRNAs, we show that two of the unique properties of E. coli initiator tRNA – formylation of the amino acid attached to the tRNA and binding of the tRNA to the ribosomal P-site – are as important for re-initiation as for de novo initiation. Overexpression of IF2 or increasing the affinity of mutant initiator tRNA for IF2 enhanced re-initiation efficiency, suggesting that IF2 is required for efficient re-initiation. In contrast, overexpression of IF3 led to a marked decrease in re-initiation efficiency, suggesting that a 30S ribosome and not a 70S ribosome is used for translation re-initiation. Strikingly, overexpression of IF3 also blocked E. coli from acting as a host for propagation of M13 phage.
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Affiliation(s)
- Jae-Ho Yoo
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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29
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Zhang LQ, Zhang HJ, Guo P, Xue P, Xie ZS, Chen Z, Jing GZ. C-terminal effect of Thermoanaerobacter tengcongensis ribosome recycling factor on its activity and conformation changes. Arch Biochem Biophys 2007; 466:211-20. [PMID: 17697668 DOI: 10.1016/j.abb.2007.06.030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2007] [Revised: 06/22/2007] [Accepted: 06/27/2007] [Indexed: 11/24/2022]
Abstract
The in vivo activities and conformational changes of ribosome recycling factor from Thermoanaerobacter tengcongensis (TteRRF) with 12 successive C-terminal deletions were compared. The results showed that TteRRF mutants lacking one to four amino acid residues are inactive, those lacking five to nine are reactivated to a similar or a little higher level than wild-type TteRRF, and those lacking ten to twelve are inactivated again gradually. Conformational studies indicated that only the ANS binding fluorescence change is correlated well with the RRF in vivo activity change, while the secondary structure and local structure at the aromatic residues are not changed significantly. Trypsin cleavage site identification and protein stability measurement suggested that mutation only induced subtle conformation change and increased flexibility of the protein. Our results indicated that the ANS-detected local conformation changes of TteRRF and mutants are one verified direct reason of the in vivo inactivation and reactivation in Escherichia coli.
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Affiliation(s)
- Li-Qiang Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
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30
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Santos MDO, Castro NDS, Pereira M, Soares CMDA. Genes involved in translation of Mycoplasma hyopneumoniae and Mycoplasma synoviae. Genet Mol Biol 2007. [DOI: 10.1590/s1415-47572007000200010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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31
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Lo RYC, Sathiamoorthy S, Shewen PE. Analysis of in vivo expressed genes in Mannheimia haemolytica A1. FEMS Microbiol Lett 2006; 265:18-25. [PMID: 16984402 DOI: 10.1111/j.1574-6968.2006.00460.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The expression of Mannheimia haemolytica A1 genes during in vivo growth was examined by reverse transcriptase-polymerase chain reaction (RT-PCR) using total RNA extracted directly from M. haemolytica A1 recovered from pneumonic lungs of cattle. Primers specific for three groups of genes were used. Group 1 includes virulence-related genes: lktC, tbpB, ahs, nmaA, gs60 and gcp. Group 2 includes genes that code for putative two-component regulatory systems: narP, narQ, ttrR, ttrS, phoB and phoR. Group 3 includes genes involved in regular cellular functions such as plp4, thiL and rrf. The RT-PCR data were examined in conjunction with the percent pneumonic lesion in each lung scored during necropsy. The analysis showed that lungs with a higher percent pneumonic score exhibit expression of more M. haemolytica A1 genes. For group 1 genes, lktC was expressed in the majority of samples, whereas the other genes were only expressed in some samples. This was not unexpected as the leukotoxin is a major virulence factor of the bacterium. The genes encoding the response regulators for the putative two-component regulatory systems were found to be expressed in more samples than the genes encoding the sensor proteins. The regulator proteins may be required in higher levels to regulate expression of target genes.
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Affiliation(s)
- Reggie Y C Lo
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada.
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Dong Z, Zhang JT. Initiation factor eIF3 and regulation of mRNA translation, cell growth, and cancer. Crit Rev Oncol Hematol 2006; 59:169-80. [PMID: 16829125 DOI: 10.1016/j.critrevonc.2006.03.005] [Citation(s) in RCA: 115] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2005] [Revised: 03/30/2006] [Accepted: 03/30/2006] [Indexed: 11/20/2022] Open
Abstract
One important regulation of gene expression in eukaryotes occurs at the level of mRNA translation, specifically at the step of translational initiation. Deregulation at this step will cause abnormal gene expression, leading to altered cell growth and possibly cancer. Translational initiation is controlled by multiple eIFs and one of these, eIF3, is the most complex and important factor for regulation of translation. Various subunits of eIF3 have recently been implicated to play important roles in regulating translation of specific mRNAs encoding proteins important for cell growth control. The expression of these eIF3 subunits has also been found altered in various human tumors and their altered expression may cause cancer and/or affect prognosis. Although the importance of translational regulation in cell growth control and oncogenesis is being slowly recognized, more vigorous studies on the role of eIFs in oncogenesis and cancer will likely benefit diagnosis, prognosis, and treatment of human cancers.
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Affiliation(s)
- Zizheng Dong
- Department of Pharmacology and Toxicology, Indiana University Cancer Center, Indianapolis, IN 46202, USA
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Antoun A, Pavlov MY, Lovmar M, Ehrenberg M. How initiation factors tune the rate of initiation of protein synthesis in bacteria. EMBO J 2006; 25:2539-50. [PMID: 16724118 PMCID: PMC1478179 DOI: 10.1038/sj.emboj.7601140] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2006] [Accepted: 04/20/2006] [Indexed: 11/09/2022] Open
Abstract
The kinetics of initiator transfer RNA (tRNA) interaction with the messenger RNA (mRNA)-programmed 30S subunit and the rate of 50S subunit docking to the 30S preinitiation complex were measured for different combinations of initiation factors in a cell-free Escherichia coli system for protein synthesis with components of high purity. The major results are summarized by a Michaelis-Menten scheme for initiation. All three initiation factors are required for maximal efficiency (kcat/KM) of initiation and for maximal in vivo rate of initiation at normal concentration of initiator tRNA. Spontaneous release of IF3 from the 30S preinitiation complex is required for subunit docking. The presence of initiator tRNA on the 30S subunit greatly increases the rate of 70S ribosome formation by increasing the rate of IF3 dissociation from the 30S subunit and the rate of 50S subunit docking to the IF3-free 30S preinitiation complex. The reasons why IF1 and IF3 are essential in E. coli are discussed in the light of the present observations.
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Affiliation(s)
| | | | | | - Måns Ehrenberg
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Box 596, Husargatan 3, Uppsala 751 24, Sweden. Tel.: +46 18 471 4213; Fax: +46 18 471 4262; E-mail:
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Zhang L, Guo P, Zhang H, Jing G. Cooperative unfolding of Escherichia coli ribosome recycling factor originating from its domain-domain interaction and its implication for function. Arch Biochem Biophys 2006; 450:191-202. [PMID: 16684502 DOI: 10.1016/j.abb.2006.03.029] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2006] [Revised: 03/24/2006] [Accepted: 03/27/2006] [Indexed: 11/27/2022]
Abstract
Cooperative unfolding of Escherichia coli ribosome recycling factor (RRF) and its implication for function were investigated by comparing the in vitro unfolding and the in vivo activity of wild-type E. coli RRF and its temperature-sensitive mutant RRF(V117D). The experiments show that mutation V117D at domain I could perturb the domain II structure as evidenced in the near-UV CD and tyrosine fluorescence spectra though no significant globular conformation change occurred. Both equilibrium unfolding induced by heat or denaturant and kinetic unfolding induced by denaturant obey the two-state transition model, indicating V117D mutation does not perturb the efficient interdomain interaction, which results in cooperative unfolding of the RRF protein. However, the mutation significantly destabilizes the E. coli RRF protein, moving the thermal unfolding transition temperature range from 50-65 to 35-50 degrees C, which spans the non-permissive temperature for the growth of E. coli LJ14 strain (frr(ts)). The in vivo activity assays showed that although V117D mutation results in a temperature sensitive phenotype of E. coli LJ14 strain (frr(ts)), over-expression of mutant RRF(V117D) can eliminate the temperature sensitive phenotype at the non-permissive temperature (42 degrees C). Taking all the results into consideration, it can be suggested that the mechanism of the temperature sensitive phenotype of the E. coli LJ14 cells is due to inactivation of mutant RRF(V117D) caused by unfolding at the non-permissive temperatures.
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Affiliation(s)
- Liqiang Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, China
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Guo P, Zhang L, Zhang H, Feng Y, Jing G. Domain II plays a crucial role in the function of ribosome recycling factor. Biochem J 2006; 393:767-77. [PMID: 16262604 PMCID: PMC1360730 DOI: 10.1042/bj20050780] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
RRF (ribosome recycling factor) consists of two domains, and in concert with EF-G (elongation factor-G), triggers dissociation of the post-termination ribosomal complex. However, the function of the individual domains of RRF remains unclear. To clarify this, two RRF chimaeras, EcoDI/TteDII and TteDI/EcoDII, were created by domain swaps between the proteins from Escherichia coli and Thermoanaerobacter tengcongensis. The ribosome recycling activity of the RRF chimaeras was compared with their wild-type RRFs by using in vivo and in vitro activity assays. Like wild-type TteRRF (T. tengcongensis RRF), the EcoDI/TteDII chimaera is non-functional in E. coli, but both wild-type TteRRF, and EcoDI/TteDII can be activated by coexpression of T. tengcongensis EF-G in E. coli. By contrast, like wild-type E. coli RRF (EcoRRF), TteDI/EcoDII is fully functional in E. coli. These findings suggest that domain II of RRF plays a crucial role in the concerted action of RRF and EF-G for the post-termination complex disassembly, and the specific interaction between RRF and EF-G on ribosomes mainly depends on the interaction between domain II of RRF and EF-G. This study provides direct genetic and biochemical evidence for the function of the individual domains of RRF.
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Affiliation(s)
- Peng Guo
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Rd., Chaoyang District, Beijing 100101, China
| | - Liqiang Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Rd., Chaoyang District, Beijing 100101, China
| | - Hongjie Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Rd., Chaoyang District, Beijing 100101, China
| | - Yanming Feng
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Rd., Chaoyang District, Beijing 100101, China
| | - Guozhong Jing
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Rd., Chaoyang District, Beijing 100101, China
- To whom correspondence should be addressed (email )
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36
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Unique features of selenocysteine incorporation function within the context of general eukaryotic translational processes. Biochem Soc Trans 2005; 33:1493-7. [PMID: 16246153 DOI: 10.1042/bst0331493] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Unlike other essential dietary trace elements, selenium exerts its biological actions through its direct incorporation into selenoproteins, as a part of the 21st amino acid, selenocysteine. Fundamental studies have elucidated the unique structures and putative functions of multiple co-translational factors required for the incorporation of selenocysteine into selenoproteins. The current challenge is to understand how these selenocysteine incorporation factors function within the framework of translation. In eukaryotes, co-ordinating nuclear transcription with cytoplasmic translation of genes is a challenge involving complex spatial and temporal regulation. Selenoproteins utilize the common cellular machinery required for synthesis of non-selenoproteins. This machinery includes the elements involved in transcription, mRNA splicing and transport, and translational processes. Many investigators have emphasized the differences between the expression of selenoproteins and other eukaryotic proteins, whereas this review will attempt to highlight common themes and point out where additional interactions may be discovered.
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Asano K, Kurita D, Takada K, Konno T, Muto A, Himeno H. Competition between trans-translation and termination or elongation of translation. Nucleic Acids Res 2005; 33:5544-52. [PMID: 16204455 PMCID: PMC1243801 DOI: 10.1093/nar/gki871] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The effects of tRNA, RF1 and RRF on trans-translation by tmRNA were examined using a stalled complex of ribosome prepared using a synthetic mRNA and pure Escherichia coli translation factors. No endoribonucleolytic cleavage of mRNA around the A site was found in the stalled ribosome and was required for the tmRNA action. When the A site was occupied by a stop codon, alanyl-tmRNA competed with RF1 with the efficiency of peptidyl-transfer to alanyl-tmRNA for trans-translation inversely correlated to the efficiency of translation termination. The competition was not affected by RF3. A sense codon also serves as a target for alanyl-tmRNA with competition of aminoacyl-tRNA. The extent of inhibition was decreased with the length of the 3′-extension of mRNA. RRF, only at a high concentration, slightly affected peptidyl-transfer for trans-translation, although it did not affect the canonical elongation. These results indicate that alanyl-tmRNA does not absolutely require the truncation of mRNA around the A site but prefers an mRNA of a short 3′-extension from the A site and that it can operate on either a sense or termination codon at the A site, at which alanyl-tmRNA competes with aminoacyl-tRNA, RF and RRF.
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Affiliation(s)
- Krisana Asano
- Department of Biochemistry and Biotechnology, Faculty of Agriculture and Life Science, Hirosaki UniversityHirosaki 036-8561
| | - Daisuke Kurita
- Department of Biochemistry and Biotechnology, Faculty of Agriculture and Life Science, Hirosaki UniversityHirosaki 036-8561
| | - Kazuma Takada
- The United Graduate School of Agricultural Sciences, Iwate UniversityMorioka 020-8550
| | - Takayuki Konno
- The United Graduate School of Agricultural Sciences, Iwate UniversityMorioka 020-8550
- Department of Microbiology, AKITA Prefectural Institute of Public HealthAkita 010-0874, Japan
| | - Akira Muto
- Department of Biochemistry and Biotechnology, Faculty of Agriculture and Life Science, Hirosaki UniversityHirosaki 036-8561
- The United Graduate School of Agricultural Sciences, Iwate UniversityMorioka 020-8550
| | - Hyouta Himeno
- Department of Biochemistry and Biotechnology, Faculty of Agriculture and Life Science, Hirosaki UniversityHirosaki 036-8561
- The United Graduate School of Agricultural Sciences, Iwate UniversityMorioka 020-8550
- To whom correspondence should be addressed. Tel: +81 172 39 3592; Fax: +81 172 39 3593;
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Ivanova N, Pavlov MY, Ehrenberg M. tmRNA-induced release of messenger RNA from stalled ribosomes. J Mol Biol 2005; 350:897-905. [PMID: 15967466 DOI: 10.1016/j.jmb.2005.05.033] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2005] [Revised: 05/16/2005] [Accepted: 05/17/2005] [Indexed: 11/20/2022]
Abstract
A ribosome stalled on a truncated mRNA in the eubacterial cell can be rescued by tmRNA via a process called trans-translation. We demonstrate here that release of truncated mRNAs from stalled ribosomes accelerates significantly already after trans-peptidation following tmRNA binding to the ribosome. However, rapid release of truncated mRNA requires EF-G-dependent translocation of peptidyl-tmRNA from the A to the P site of the ribosome. We show also that the rate of mRNA release before and after peptidyl-tmRNA translocation correlates well with the rate of dissociation of deacylated tRNA, indicating that mRNA is retained on the ribosome mainly through codon:anticodon interaction with tRNA. The rate of mRNA release is reduced for mRNAs with strong Shine-Dalgarno (SD)-like sequences in the vicinity of the truncation site as well as for mRNAs with long 3' extensions downstream from the P-site codon. The reduced rate of release in the former case was due to a persisting SD-anti SD interaction between mRNA and the ribosome.
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Affiliation(s)
- Natalia Ivanova
- Department of Cell and Molecular Biology, BMC, Uppsala University, Box 596, S-75 124 Uppsala, Sweden
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Yamami T, Ito K, Fujiwara T, Nakamura Y. Heterologous expression of Aquifex aeolicus ribosome recycling factor in Escherichia coli is dominant lethal by forming a complex that lacks functional co-ordination for ribosome disassembly. Mol Microbiol 2005; 55:150-61. [PMID: 15612924 DOI: 10.1111/j.1365-2958.2004.04387.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Recycling the post-termination ribosomal complex requires the co-ordinated effort of the ribosome, ribosome recycling factor (RRF) and elongation factor EF-G. Although Aquifex aeolicus RRF (aaRRF) binds Escherichia coli ribosomes as efficiently as E. coli RRF, the resulting complex is non-functional and dominant lethal in E. coli, even in the presence of homologous A. aeolicus EF-G. These findings suggest that the E. coli post-termination ribosomal complex with aaRRF lacks functional co-ordination with EF-G required for ribosome recycling. A chimeric EF-G (E. coli domains I-III, A. aeolicus domains IV-V) or an A. aeolicus EF-G with distinct mutations in the domain I-II interface could activate aaRRF. Furthermore, novel mutations that localize to one surface of the L-shape structure of aaRRF restored activity in E. coli. These aaRRF mutations are spatially distinct from mutations previously described and suggest a novel active centre for coupling EF-G's G domain motor action to ribosome disassembly.
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Affiliation(s)
- Tohru Yamami
- Department of Basic Medical Sciences, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
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Abstract
As part of an international effort and a national programme, structural analysis of mycobacterial proteins involved in recombination and repair, stringent response and protein synthesis has been undertaken, and work on proteins in a couple of metabolic pathways has been initiated. Already X-ray analysed are Mycobacterium tuberculosis and Mycobacterium smegmatis RecA and their nucleotide complexes, and different crystal forms of M. tuberculosis single-stranded DNA binding protein, M. smegmatis DNA binding protein from stationary phase cells and M. tuberculosis ribosome recycling factor. A comparative study involving these structures and those of similar proteins from other sources brings out the special features of the mycobacterial proteins, which are likely to be useful in selective inhibitor design. The structures provide insights into the plasticity of the molecules and its biological implications, and yield valuable information on their assembly and quaternary structure. They also provide leads for further structural investigations.
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Affiliation(s)
- M Vijayan
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India.
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Hirokawa G, Nijman RM, Raj VS, Kaji H, Igarashi K, Kaji A. The role of ribosome recycling factor in dissociation of 70S ribosomes into subunits. RNA (NEW YORK, N.Y.) 2005; 11:1317-28. [PMID: 16043510 PMCID: PMC1370814 DOI: 10.1261/rna.2520405] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Protein synthesis is initiated on ribosomal subunits. However, it is not known how 70S ribosomes are dissociated into small and large subunits. Here we show that 70S ribosomes, as well as the model post-termination complexes, are dissociated into stable subunits by cooperative action of three translation factors: ribosome recycling factor (RRF), elongation factor G (EF-G), and initiation factor 3 (IF3). The subunit dissociation is stable enough to be detected by conventional sucrose density gradient centrifugation (SDGC). GTP, but not nonhydrolyzable GTP analog, is essential in this process. We found that RRF and EF-G alone transiently dissociate 70S ribosomes. However, the transient dissociation cannot be detected by SDGC. IF3 stabilizes the dissociation by binding to the transiently formed 30S subunits, preventing re-association back to 70S ribosomes. The three-factor-dependent stable dissociation of ribosomes into subunits completes the ribosome cycle and the resulting subunits are ready for the next round of translation.
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Affiliation(s)
- Go Hirokawa
- Department of Microbiology, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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Stagg SM, Harvey SC. Exploring the flexibility of ribosome recycling factor using molecular dynamics. Biophys J 2005; 89:2659-66. [PMID: 16055531 PMCID: PMC1366766 DOI: 10.1529/biophysj.104.052373] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Ribosome recycling factor is proposed to be flexible, and that flexibility is believed to be important to its function. Here we use molecular dynamics to test the flexibility of Escherichia coli RRF (ecRRF) with and without decanoic acid bound to a hydrophobic pocket between domains 1 and 2, and Thermus thermophilus RRF (ttRRF) with and without a mutation in the hinge between domains 1 and 2. Our simulations show that the structure of ecRRF rapidly goes from having an interdomain angle of 124 degrees to an angle of 98 degrees independently of the presence of decanoic acid. The simulations also show that the presence or absence of decanoic acid leads to changes in ecRRF flexibility. Simulations of wild-type and mutant ttRRF (R32G) show that mutating Arg-32 to glycine decreases RRF flexibility. This was unexpected because the range of dihedral angles for arginine is limited relative to glycine. Furthermore, the interdomain angle of wild-type T. thermophilus goes from 81 degrees to 118 degrees whereas the R32G mutant remains very close to the crystallographic angle of 78 degrees . We propose that this difference accounts for the fact that mutant ttRRF complements an RRF deficient strain of E. coli whereas wild-type ttRRF does not. When the ensemble of RRF structures is modeled into the ribosomal crystal structure, a series of overlaps is found that corresponds with regions where conformational changes have been found in the cryoelectron microscopic structure of the RRF/ribosome complex, and in the crystal structure of a cocomplex of RRF with the 50S subunit. There are also overlaps with the P-site, suggesting that RRF flexibility plays a role in removing the deacylated P-site tRNA during termination of translation.
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Affiliation(s)
- Scott M Stagg
- Department of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA.
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Guo P, Zhang L, Qi Z, Chen R, Jing G. Expression in Escherichia coli, Purification and Characterization of Thermoanaerobacter tengcongensis Ribosome Recycling Factor. ACTA ACUST UNITED AC 2005; 138:89-94. [PMID: 16046452 DOI: 10.1093/jb/mvi102] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
A very promising approach to understanding the mechanism of protein thermostability is to investigate the structure-function relationship of homologous proteins with different thermostabilities. Ribosome recycling factor (RRF), which is an essential factor for protein synthesis in bacteria, may be a good candidate for such study. In this report, a ribosome recycling factor from Thermoanaerobacter tengcongensis was expressed and characterized. This protein contains 184 residues, shows 51.4% identity to that of Escherichia coli RRF, and has very strong antigenic cross-reactivity with antibody to E. coli RRF. In vivo activity assay shows that weak residual activity may remain in TteRRF in E. coli cells. Circular dichroism spectral analysis shows that TteRRF has a very similar secondary structure to that of E. coli RRF, implying that they have similar tertiary structures. However, their thermostabilities are significantly different. To find which domain of RRF is mainly responsible for maintaining stability, TteDI/EcoDII and EcoDI/TteDII RRF chimeras were created. Their domain I and domain II are from E. coli and T. tengcongensis RRFs, respectively. The results of GdnHCl and heat induced denaturation of the chimeric RRFs suggest that the domain I plays a major role in maintaining the stability of the RRF molecule.
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Affiliation(s)
- Peng Guo
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, PR China
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Gao N, Zavialov AV, Li W, Sengupta J, Valle M, Gursky RP, Ehrenberg M, Frank J. Mechanism for the Disassembly of the Posttermination Complex Inferred from Cryo-EM Studies. Mol Cell 2005; 18:663-74. [PMID: 15949441 DOI: 10.1016/j.molcel.2005.05.005] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2004] [Revised: 04/13/2005] [Accepted: 05/09/2005] [Indexed: 11/22/2022]
Abstract
Ribosome recycling, the disassembly of the posttermination complex after each round of protein synthesis, is an essential step in mRNA translation, but its mechanism has remained obscure. In eubacteria, recycling is catalyzed by RRF (ribosome recycling factor) and EF-G (elongation factor G). By using cryo-electron microscopy, we have obtained two density maps, one of the RRF bound posttermination complex and one of the 50S subunit bound with both EF-G and RRF. Comparing the two maps, we found domain I of RRF to be in the same orientation, while domain II in the EF-G-containing 50S subunit is extensively rotated (approximately 60 degrees) compared to its orientation in the 70S complex. Mapping the 50S conformation of RRF onto the 70S posttermination complex suggests that it can disrupt the intersubunit bridges B2a and B3, and thus effect a separation of the two subunits. These observations provide the structural basis for the mechanism by which the posttermination complex is split into subunits by the joint action of RRF and EF-G.
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Affiliation(s)
- Ning Gao
- Wadsworth Center, State University of New York at Albany, Empire State Plaza, Albany, New York 12201, USA
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Peske F, Rodnina MV, Wintermeyer W. Sequence of Steps in Ribosome Recycling as Defined by Kinetic Analysis. Mol Cell 2005; 18:403-12. [PMID: 15893724 DOI: 10.1016/j.molcel.2005.04.009] [Citation(s) in RCA: 118] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2005] [Revised: 03/27/2005] [Accepted: 04/07/2005] [Indexed: 11/23/2022]
Abstract
After termination of protein synthesis in bacteria, ribosomes are recycled from posttermination complexes by the combined action of elongation factor G (EF-G), ribosome recycling factor (RRF), and initiation factor 3 (IF3). The functions of the factors and the sequence in which ribosomal subunits, tRNA, and mRNA are released from posttermination complexes are unclear and, in part, controversial. Here, we study the reaction by rapid kinetics monitoring fluorescence. We show that RRF and EF-G with GTP, but not with GDPNP, promote the dissociation of 50S subunits from the posttermination complex without involving translocation or a translocation-like event. IF3 does not affect subunit dissociation but prevents reassociation, thereby masking the dissociating effect of EF-G-RRF under certain experimental conditions. IF3 is required for the subsequent ejection of tRNA and mRNA from the small subunit. The latter step is slower than subunit dissociation and constitutes the rate-limiting step of ribosome recycling.
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Affiliation(s)
- Frank Peske
- Institute of Molecular Biology, University of Witten/Herdecke, 58448 Witten, Germany
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46
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Kolupaeva VG, Unbehaun A, Lomakin IB, Hellen CUT, Pestova TV. Binding of eukaryotic initiation factor 3 to ribosomal 40S subunits and its role in ribosomal dissociation and anti-association. RNA (NEW YORK, N.Y.) 2005; 11:470-86. [PMID: 15703437 PMCID: PMC1370736 DOI: 10.1261/rna.7215305] [Citation(s) in RCA: 93] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2004] [Accepted: 12/22/2004] [Indexed: 05/19/2023]
Abstract
The multisubunit eukaryotic initiation factor (eIF) 3 plays various roles in translation initiation that all involve interaction with 40S ribosomal subunits. eIF3 can be purified in two forms: with or without the loosely associated eIF3j subunit (eIF3j+ and eIF3j-, respectively). Although unlike eIF3j+, eIF3j- does not bind 40S subunits stably enough to withstand sucrose density gradient centrifugation, we found that in addition to the known stabilization of the eIF3/40S subunit interaction by the eIF2*GTP*Met-tRNA(i)Met ternary complex, eIF3j-/40S subunit complexes were also stabilized by single-stranded RNA or DNA cofactors that were at least 25 nt long and could be flanked by stable hairpins. Of all homopolymers, oligo(rU), oligo(dT), and oligo(dC) stimulated the eIF3/40S subunit interaction, whereas oligo(rA), oligo(rG), oligo(rC), oligo(dA), and oligo(dG) did not. Oligo(U) or oligo(dT) sequences interspersed by other bases also promoted this interaction. The ability of oligonucleotides to stimulate eIF3/40S subunit association correlated with their ability to bind to the 40S subunit, most likely to its mRNA-binding cleft. Although eIF3j+ could bind directly to 40S subunits, neither eIF3j- nor eIF3j+ alone was able to dissociate 80S ribosomes or protect 40S and 60S subunits from reassociation. Significantly, the dissociation/anti-association activities of both forms of eIF3 became apparent in the presence of either eIF2-ternary complexes or any oligonucleotide cofactor that promoted eIF3/40S subunit interaction. Ribosomal dissociation and anti-association activities of eIF3 were strongly enhanced by eIF1. The potential biological role of stimulation of eIF3/40S subunit interaction by an RNA cofactor in the absence of eIF2-ternary complex is discussed.
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Affiliation(s)
- Victoria G Kolupaeva
- Department of Microbiology and Immunology, SUNY Downstate Medical Center, 450 Clarkson Ave., Box 44, Brooklyn, NY 11203, USA
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Raj VS, Kaji H, Kaji A. Interaction of RRF and EF-G from E. coli and T. thermophilus with ribosomes from both origins--insight into the mechanism of the ribosome recycling step. RNA (NEW YORK, N.Y.) 2005; 11:275-84. [PMID: 15661844 PMCID: PMC1370717 DOI: 10.1261/rna.7201805] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2004] [Accepted: 11/30/2004] [Indexed: 05/20/2023]
Abstract
Ribosome recycling factor (RRF), elongation factor-G (EF-G), and ribosomes from Thermus thermophilus (tt-) and Escherichia coli (ec-) were used to study the disassembly mechanism of post-termination ribosomal complexes by these factors. With tt-RRF, ec-EF-G can release bound-tRNA from ec-model post-termination complexes. However, tt-RRF is not released by ec-EF-G from ec-ribosomes. This complex with tt-RRF and ec-ribosomes after the tRNA release by ec-EF-G is regarded as an intermediate of the disassembly reaction. Not only tt-RRF, but also mRNA, cannot be released from ec-ribosomes by tt-RRF and ec-EF-G. These data suggest that the release of RRF from ribosomes is coupled or closely related to the release of mRNA during disassembly of post-termination complexes. With tt-ribosomes, ec-EF-G cannot release ribosome-bound ec-RRF even though they are from the same species, showing that proper interaction of ec-RRF and ec-EF-G does not occur on tt-ribosomes. On the other hand, in contrast to a published report, tt-EF-G functions with ec-RRF to disassemble ec-post-termination complexes. In support of this finding, tt-EF-G translocates peptidyl tRNA on ec-ribosomes and catalyzes ec-ribosome-dependent GTPase, showing that tt-EF-G has in vitro translocation activity with ec-ribosomes. Since tt-EF-G with ec-RRF can release tRNA from ec-post-termination complexes, the data are consistent with the hypothesis that the release of tRNA by RRF and EF-G from post-termination complexes is a result of a translocation-like activity of EF-G on RRF.
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Affiliation(s)
- V Samuel Raj
- Department of Microbiology, School of Medicine, University of Pennsylvania, Room 203B, Johnson Pavilion, 3610 Hamilton Walk, Philadelphia, PA 19104, USA
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Saikrishnan K, Kalapala SK, Varshney U, Vijayan M. X-ray structural studies of Mycobacterium tuberculosis RRF and a comparative study of RRFs of known structure. Molecular plasticity and biological implications. J Mol Biol 2005; 345:29-38. [PMID: 15567408 DOI: 10.1016/j.jmb.2004.10.034] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2004] [Revised: 10/10/2004] [Accepted: 10/13/2004] [Indexed: 10/26/2022]
Abstract
The crystal structure of Mycobacterium tuberculosis ribosome recycling factor has been determined and refined against three X-ray diffraction data sets, two collected at room temperature and the other at 100K. The two room-temperature data sets differ in the radiation damage suffered by the crystals before the data used for processing were collected. A comparison between the structures refined against the two data sets indicates the possibility of radiation-induced conformational change. The L-shaped molecule is composed of a long three-helix bundle domain (domain I) and a globular domain (domain II) connected by a linker region. The main difference between the room-temperature structure and the low temperature structure is in the rotation of domain II about an axis close to its libration axis. This observation and a detailed comparative study of ribosome recycling factors (RRFs) of known structures led to an elaboration of the present understanding of the structural variability of RRF. The variability involves a change in the angle between the two arms of the molecule, a rotation of domain II in a plane nearly perpendicular to the axis of the helix bundle and an internal rotation of domain II. Furthermore, the domains and the linker could be delineated into fixed and variable regions in a physically meaningful manner. The relative mobility of the domains of the molecule in the crystal structure appears to be similar to that in the ribosome--RRF complex. That permits a meaningful discussion of the structural features of RRF in terms of ribosome--RRF interactions. The structure also provides insights into the results of inter-species complementation studies.
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Affiliation(s)
- K Saikrishnan
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
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Fujiwara T, Ito K, Yamami T, Nakamura Y. Ribosome recycling factor disassembles the post-termination ribosomal complex independent of the ribosomal translocase activity of elongation factor G. Mol Microbiol 2005; 53:517-28. [PMID: 15228531 DOI: 10.1111/j.1365-2958.2004.04156.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Ribosome recycling factor (RRF) disassembles post-termination ribosomal complexes in concert with elongation factor EF-G freeing the ribosome for a new round of polypeptide synthesis. How RRF interacts with EF-G and disassembles post-termination ribosomes is unknown. RRF is structurally similar to tRNA and is therefore thought to bind to the ribosomal A site and be translocated by EF-G during ribosome disassembly as a mimic of tRNA. However, EF-G variants that remain active in GTP hydrolysis but are defective in tRNA translocation fully activate RRF function in vivo and in vitro. Furthermore, RRF and the GTP form of EF-G do not co-occupy the terminating ribosome in vitro; RRF is ejected by EF-G from the preformed complex. These findings suggest that RRF is not a functional mimic of tRNA and disassembles the post-termination ribosomal complex independently of the translocation activity of EF-G.
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Affiliation(s)
- Toshinobu Fujiwara
- Department of Basic Medical Sciences, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
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Moll I, Hirokawa G, Kiel MC, Kaji A, Bläsi U. Translation initiation with 70S ribosomes: an alternative pathway for leaderless mRNAs. Nucleic Acids Res 2004; 32:3354-63. [PMID: 15215335 PMCID: PMC443539 DOI: 10.1093/nar/gkh663] [Citation(s) in RCA: 138] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2004] [Revised: 05/28/2004] [Accepted: 06/04/2004] [Indexed: 11/13/2022] Open
Abstract
It is generally accepted that translation in bacteria is initiated by 30S ribosomal subunits. In contrast, several lines of rather indirect in vitro evidence suggest that 70S monosomes are capable of initiating translation of leaderless mRNAs, starting with the A of the initiation codon. In this study, we demonstrate the proficiency of dedicated 70S ribosomes in in vitro translation of leaderless mRNAs. In support, we show that a natural leaderless mRNA can be translated with crosslinked 70S wild-type ribosomes. Moreover, we report that leaderless mRNA translation continues under conditions where the prevalence of 70S ribosomes is created in vivo, and where translation of bulk mRNA ceases. These studies provide in vivo as well as direct in vitro evidence for a 70S initiation pathway of a naturally occurring leaderless mRNA, and are discussed in light of their significance for bacterial growth under adverse conditions and their evolutionary implications for translation.
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Affiliation(s)
- Isabella Moll
- Max F. Perutz Laboratories, Department of Microbiology and Genetics, University Department at the Vienna Biocenter, Dr Bohrgasse 9/4, 1030 Vienna, Austria
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