1
|
Usachev KS, Yusupov MM, Validov SZ. Hibernation as a Stage of Ribosome Functioning. BIOCHEMISTRY (MOSCOW) 2021; 85:1434-1442. [PMID: 33280583 DOI: 10.1134/s0006297920110115] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
In response to stress, eubacteria reduce the level of protein synthesis and either disassemble ribosomes into the 30S and 50S subunits or turn them into translationally inactive 70S and 100S complexes. This helps the cell to solve two principal tasks: (i) to reduce the cost of protein biosynthesis under unfavorable conditions, and (ii) to preserve functional ribosomes for rapid recovery of protein synthesis until favorable conditions are restored. All known genes for ribosome silencing factors and hibernation proteins are located in the operons associated with the response to starvation as one of the stress factors, which helps the cells to coordinate the slowdown of protein synthesis with the overall stress response. It is possible that hibernation systems work as regulators that coordinate the intensity of protein synthesis with the energy state of bacterial cell. Taking into account the limited amount of nutrients in natural conditions and constant pressure of other stress factors, bacterial ribosome should remain most of time in a complex with the silencing/hibernation proteins. Therefore, hibernation is an additional stage between the ribosome recycling and translation initiation, at which the ribosome is maintained in a "preserved" state in the form of separate subunits, non-translating 70S particles, or 100S dimers. The evolution of the ribosome hibernation has occurred within a very long period of time; ribosome hibernation is a conserved mechanism that is essential for maintaining the energy- and resource-consuming process of protein biosynthesis in organisms living in changing environment under stress conditions.
Collapse
Affiliation(s)
- K S Usachev
- Kazan Federal University, Kazan, 420008, Russia
| | - M M Yusupov
- Kazan Federal University, Kazan, 420008, Russia. .,Institute of Genetics and Molecular and Cellular Biology, Illkirch-Graffenstaden, 67400, France
| | | |
Collapse
|
2
|
Sharma IM, Woodson SA. RbfA and IF3 couple ribosome biogenesis and translation initiation to increase stress tolerance. Nucleic Acids Res 2020; 48:359-372. [PMID: 31728529 PMCID: PMC7145577 DOI: 10.1093/nar/gkz1065] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 10/09/2019] [Accepted: 11/04/2019] [Indexed: 12/12/2022] Open
Abstract
Bacterial ribosome biogenesis and translation occur in the same cellular compartment. Therefore, a biochemical gate-keeping step is required to prevent error-prone immature ribosomes from engaging in protein synthesis. Here, we provide evidence for a previously unknown quality control mechanism in which the abundant ribosome assembly factor, RbfA, suppresses protein synthesis by immature Escherichia coli 30S subunits. After 30S maturation, RbfA is displaced by initiation factor 3 (IF3), which promotes translation initiation. Genetic interactions between RbfA and IF3 show that RbfA release by IF3 is important during logarithmic growth as well as during stress encountered during stationary phase, low nutrition, low temperature, and antibiotics. By gating the transition from 30S biogenesis to translation initiation, RbfA and IF3 maintain the fidelity of bacterial protein synthesis.
Collapse
Affiliation(s)
- Indra Mani Sharma
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
| | - Sarah A Woodson
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
| |
Collapse
|
3
|
Avila-Bonilla RG, Yocupicio-Monroy M, Marchat LA, De Nova-Ocampo MA, Del Ángel RM, Salas-Benito JS. Analysis of the miRNA profile in C6/36 cells persistently infected with dengue virus type 2. Virus Res 2017; 232:139-151. [PMID: 28267608 DOI: 10.1016/j.virusres.2017.03.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 02/27/2017] [Accepted: 03/01/2017] [Indexed: 12/28/2022]
Abstract
Dengue virus (DENV) is the most important arbovirus in the world; DENV is transmitted by the Aedes genus of mosquitoes and can establish a life-long persistent infection in mosquitoes. However, the exact mechanism by which persistent infection is established remains unknown. In this study the differential expression of miRNAs was analysed by deep sequencing and RT-qPCR using a previously established C6/36-HT cell line persistently infected with DENV 2 (C6-L) as a model. miR-927, miR-87, miR-210, miR-2a-3p, miR-190 and miR-970 were up-regulated, whereas miR-252, miR-263a-3p, miR-92b, miR-10-5p miR-9a-5p, miR-9a-1, miR-124, miR-286a and miR-286b were down-regulated in C6-L cells compared with C6/36 cells acutely infected with the same virus or mock-infected cells. Deep sequencing results were validated by RT-qPCR for the highly differentially expressed miR-927 and miR-9a-5p, which were up- and down-regulated, respectively, compared with both acutely and mock-infected C6/36 cells. The putative targets of these miRNAs include components of the ubiquitin conjugation pathway, vesicle-mediated transport, autophagy, and the JAK-STAT cascade as well as proteins with endopeptidase activity. Other putative targets include members of the Toll signalling pathway and proteins with kinase, ATPase, protease, scavenger receptor or Lectin C-type activity or that participate in fatty acid biosynthesis or oxidative stress. Our results suggest that several specific miRNAs help regulate the cellular functions that maintain equilibrium between viral replication and the antiviral response during persistent infection of mosquito cells. This study is the first report of a global miRNA profile in a mosquito cell line persistently infected with DENV.
Collapse
Affiliation(s)
- Rodolfo Gamaliel Avila-Bonilla
- Programa Institucional de Biomedicina Molecular, Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional, Guillermo Massieu Helguera 249, La Escalera-Ticomán, Mexico City, CP 07320, Mexico; Programa de Doctorado en Ciencias en Biotecnología, Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional, Guillermo Massieu Helguera 249, La Escalera-Ticomán, Mexico City, CP 07320, Mexico.
| | - Martha Yocupicio-Monroy
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, San Lorenzo 290, Del Valle Sur, Mexico City, CP 03100, Mexico.
| | - Laurence A Marchat
- Programa Institucional de Biomedicina Molecular, Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional, Guillermo Massieu Helguera 249, La Escalera-Ticomán, Mexico City, CP 07320, Mexico; Programa de Doctorado en Ciencias en Biotecnología, Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional, Guillermo Massieu Helguera 249, La Escalera-Ticomán, Mexico City, CP 07320, Mexico.
| | - Mónica A De Nova-Ocampo
- Programa Institucional de Biomedicina Molecular, Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional, Guillermo Massieu Helguera 249, La Escalera-Ticomán, Mexico City, CP 07320, Mexico; Programa de Doctorado en Ciencias en Biotecnología, Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional, Guillermo Massieu Helguera 249, La Escalera-Ticomán, Mexico City, CP 07320, Mexico.
| | - Rosa María Del Ángel
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados-IPN. Av, Instituto Politécnico Nacional 2508, San Pedro Zacatenco, Mexico City, CP 07360, Mexico.
| | - Juan Santiago Salas-Benito
- Programa Institucional de Biomedicina Molecular, Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional, Guillermo Massieu Helguera 249, La Escalera-Ticomán, Mexico City, CP 07320, Mexico; Programa de Doctorado en Ciencias en Biotecnología, Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional, Guillermo Massieu Helguera 249, La Escalera-Ticomán, Mexico City, CP 07320, Mexico.
| |
Collapse
|
4
|
Ostojić J, Panozzo C, Bourand-Plantefol A, Herbert CJ, Dujardin G, Bonnefoy N. Ribosome recycling defects modify the balance between the synthesis and assembly of specific subunits of the oxidative phosphorylation complexes in yeast mitochondria. Nucleic Acids Res 2016; 44:5785-97. [PMID: 27257059 PMCID: PMC4937339 DOI: 10.1093/nar/gkw490] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 05/20/2016] [Indexed: 01/07/2023] Open
Abstract
Mitochondria have their own translation machinery that produces key subunits of the OXPHOS complexes. This machinery relies on the coordinated action of nuclear-encoded factors of bacterial origin that are well conserved between humans and yeast. In humans, mutations in these factors can cause diseases; in yeast, mutations abolishing mitochondrial translation destabilize the mitochondrial DNA. We show that when the mitochondrial genome contains no introns, the loss of the yeast factors Mif3 and Rrf1 involved in ribosome recycling neither blocks translation nor destabilizes mitochondrial DNA. Rather, the absence of these factors increases the synthesis of the mitochondrially-encoded subunits Cox1, Cytb and Atp9, while strongly impairing the assembly of OXPHOS complexes IV and V. We further show that in the absence of Rrf1, the COX1 specific translation activator Mss51 accumulates in low molecular weight forms, thought to be the source of the translationally-active form, explaining the increased synthesis of Cox1. We propose that Rrf1 takes part in the coordination between translation and OXPHOS assembly in yeast mitochondria. These interactions between general and specific translation factors might reveal an evolutionary adaptation of the bacterial translation machinery to the set of integral membrane proteins that are translated within mitochondria.
Collapse
Affiliation(s)
- Jelena Ostojić
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, UEVE, 91198, Gif-sur-Yvette cedex, France
| | - Cristina Panozzo
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, UEVE, 91198, Gif-sur-Yvette cedex, France
| | - Alexa Bourand-Plantefol
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, UEVE, 91198, Gif-sur-Yvette cedex, France
| | - Christopher J Herbert
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, UEVE, 91198, Gif-sur-Yvette cedex, France
| | - Geneviève Dujardin
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, UEVE, 91198, Gif-sur-Yvette cedex, France
| | - Nathalie Bonnefoy
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, UEVE, 91198, Gif-sur-Yvette cedex, France
| |
Collapse
|
5
|
Selvaraj M, Govindan A, Seshadri A, Dubey B, Varshney U, Vijayan M. Molecular flexibility of Mycobacterium tuberculosis ribosome recycling factor and its functional consequences: an exploration involving mutants. J Biosci 2014; 38:845-55. [PMID: 24296887 DOI: 10.1007/s12038-013-9381-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Internal mobility of the two domain molecule of ribosome recycling factor (RRF) is known to be important for its action. Mycobacterium tuberculosis RRF does not complement E. coli for its deficiency of RRF (in the presence of E. coli EF-G alone). Crystal structure had revealed higher rigidity of the M. tuberculosis RRF due to the presence of additional salt bridges between domains. Two inter-domain salt bridges and one between the linker region and the domain containing C-terminal residues were disrupted by appropriate mutations. Except for a C-terminal deletion mutant, all mutants showed RRF activity in E. coli when M. tuberculosis EF-G was also co-expressed. The crystal structures of the point mutants, that of the C-terminal deletion mutant and that of the protein grown in the presence of a detergent, were determined. The increased mobility resulting from the disruption of the salt bridge involving the hinge region allows the appropriate mutant to weakly complement E. coli for its deficiency of RRF even in the absence of simultaneous expression of the mycobacterial EF-G. The loss of activity of the C-terminal deletion mutant appears to be partly due to the rigidification of the molecule consequent to changes in the hinge region.
Collapse
Affiliation(s)
- M Selvaraj
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | | | | | | | | | | |
Collapse
|
6
|
Structural insights into initial and intermediate steps of the ribosome-recycling process. EMBO J 2012; 31:1836-46. [PMID: 22388519 DOI: 10.1038/emboj.2012.22] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2011] [Accepted: 01/17/2012] [Indexed: 11/08/2022] Open
Abstract
The ribosome-recycling factor (RRF) and elongation factor-G (EF-G) disassemble the 70S post-termination complex (PoTC) into mRNA, tRNA, and two ribosomal subunits. We have determined cryo-electron microscopic structures of the PoTC·RRF complex, with and without EF-G. We find that domain II of RRF initially interacts with universally conserved residues of the 23S rRNA helices 43 and 95, and protein L11 within the 50S ribosomal subunit. Upon EF-G binding, both RRF and tRNA are driven towards the tRNA-exit (E) site, with a large rotational movement of domain II of RRF towards the 30S ribosomal subunit. During this intermediate step of the recycling process, domain II of RRF and domain IV of EF-G adopt hitherto unknown conformations. Furthermore, binding of EF-G to the PoTC·RRF complex reverts the ribosome from ratcheted to unratcheted state. These results suggest that (i) the ribosomal intersubunit reorganizations upon RRF binding and subsequent EF-G binding could be instrumental in destabilizing the PoTC and (ii) the modes of action of EF-G during tRNA translocation and ribosome-recycling steps are markedly different.
Collapse
|
7
|
Lazarev VN, Borisenko GG, Shkarupeta MM, Demina IA, Serebryakova MV, Galyamina MA, Levitskiy SA, Govorun VM. The role of intracellular glutathione in the progression of Chlamydia trachomatis infection. Free Radic Biol Med 2010; 49:1947-55. [PMID: 20888409 DOI: 10.1016/j.freeradbiomed.2010.09.024] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2010] [Revised: 08/17/2010] [Accepted: 09/23/2010] [Indexed: 12/17/2022]
Abstract
The productive internalization in the host cell of Chlamydia trachomatis elementary bodies and their infectivity depends on the degree of reduction of disulfide bonds in the outer envelope of the elementary body. We have hypothesized that the reducing agent may be intracellular glutathione (GSH). Three approaches were used to modulate the intracellular GSH concentration: (1) treatment of cells with buthionine sulfoximine, which causes irreversible inhibition of GSH biosynthesis; (2) hydrogen peroxide-induced oxidation of GSH by intracellular glutathione peroxidases; and (3) treatment of cells with N-acetyl-l-cysteine (NAC), a precursor of glutathione. In the first two cases, we observed a four- to sixfold inhibition of C. trachomatis infection, whereas in NAC-treated cells we detected an increase in the size of chlamydial inclusions. Using a proteomics approach, we showed that the inhibition of chlamydial infection does not combine with alterations in protein expression patterns after cell treatment. These results suggest that GSH plays a key role in the reduction of disulfide bonds in the C. trachomatis outer envelope at an initial stage of the infection.
Collapse
|
8
|
Suematsu T, Yokobori SI, Morita H, Yoshinari S, Ueda T, Kita K, Takeuchi N, Watanabe YI. A bacterial elongation factor G homologue exclusively functions in ribosome recycling in the spirochaete Borrelia burgdorferi. Mol Microbiol 2010; 75:1445-54. [PMID: 20132446 DOI: 10.1111/j.1365-2958.2010.07067.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Translation elongation factor G (EF-G) in bacteria plays two distinct roles in different phases of the translation system. EF-G catalyses the translocation of tRNAs on the ribosome in the elongation step, as well as the dissociation of the post-termination state ribosome into two subunits in the recycling step. In contrast to this conventional view, it has very recently been demonstrated that the dual functions of bacterial EF-G are distributed over two different EF-G paralogues in human mitochondria. In the present study, we show that the same division of roles of EF-G is also found in bacteria. Two EF-G paralogues are found in the spirochaete Borrelia burgdorferi, EF-G1 and EF-G2. We demonstrate that EF-G1 is a translocase, while EF-G2 is an exclusive recycling factor. We further demonstrate that B. burgdorferi EF-G2 does not require GTP hydrolysis for ribosome disassembly, provided that translation initiation factor 3 (IF-3) is present in the reaction. These results indicate that two B. burgdorferi EF-G paralogues are close relatives to mitochondrial EF-G paralogues rather than the conventional bacterial EF-G, in both their phylogenetic and biochemical features.
Collapse
Affiliation(s)
- Takuma Suematsu
- Department of Biomedical Chemistry, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan
| | | | | | | | | | | | | | | |
Collapse
|
9
|
Fei J, Wang J, Sternberg SH, MacDougall DD, Elvekrog MM, Pulukkunat DK, Englander MT, Gonzalez RL. A highly purified, fluorescently labeled in vitro translation system for single-molecule studies of protein synthesis. Methods Enzymol 2010; 472:221-59. [PMID: 20580967 PMCID: PMC4748369 DOI: 10.1016/s0076-6879(10)72008-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Single-molecule fluorescence resonance energy transfer (smFRET) has emerged as a powerful tool for mechanistic investigations of increasingly complex biochemical systems. Recently, we and others have successfully used smFRET to directly investigate the role of structural dynamics in the function and regulation of the cellular protein synthesis machinery. A significant challenge to these experiments, and to analogous experiments in similarly complex cellular machineries, is the need for specific and efficient fluorescent labeling of the biochemical system at locations that are both mechanistically informative and minimally perturbative to the biological activity. Here, we describe the development of a highly purified, fluorescently labeled in vitro translation system that we have successfully designed for smFRET studies of protein synthesis. The general approaches we outline should be amenable to single-molecule fluorescence studies of other complex biochemical systems.
Collapse
Affiliation(s)
- Jingyi Fei
- Department of Chemistry, Columbia University, New York, NY 10027 Tel.: (212) 854-0162 FAX: (212) 932-1289 J.F. J.W. D.D.M M.M.E. D.K.P. M.T.E.
| | - Jiangning Wang
- Department of Chemistry, Columbia University, New York, NY 10027 Tel.: (212) 854-0162 FAX: (212) 932-1289 J.F. J.W. D.D.M M.M.E. D.K.P. M.T.E.
| | - Samuel H. Sternberg
- Department of Chemistry, Columbia University, New York, NY 10027 Tel.: (212) 854-0162 FAX: (212) 932-1289 J.F. J.W. D.D.M M.M.E. D.K.P. M.T.E.
| | - Daniel D. MacDougall
- Department of Chemistry, Columbia University, New York, NY 10027 Tel.: (212) 854-0162 FAX: (212) 932-1289 J.F. J.W. D.D.M M.M.E. D.K.P. M.T.E.
| | - Margaret M. Elvekrog
- Department of Chemistry, Columbia University, New York, NY 10027 Tel.: (212) 854-0162 FAX: (212) 932-1289 J.F. J.W. D.D.M M.M.E. D.K.P. M.T.E.
| | - Dileep K. Pulukkunat
- Department of Chemistry, Columbia University, New York, NY 10027 Tel.: (212) 854-0162 FAX: (212) 932-1289 J.F. J.W. D.D.M M.M.E. D.K.P. M.T.E.
| | - Michael T. Englander
- Department of Chemistry, Columbia University, New York, NY 10027 Tel.: (212) 854-0162 FAX: (212) 932-1289 J.F. J.W. D.D.M M.M.E. D.K.P. M.T.E.
- Integrated Program in Cellular, Molecular, and Biomedical Sciences
| | - Ruben L. Gonzalez
- Department of Chemistry, Columbia University, New York, NY 10027 Tel.: (212) 854-1096 FAX: (212) 932-1289
| |
Collapse
|
10
|
Hirokawa G, Iwakura N, Kaji A, Kaji H. The role of GTP in transient splitting of 70S ribosomes by RRF (ribosome recycling factor) and EF-G (elongation factor G). Nucleic Acids Res 2008; 36:6676-87. [PMID: 18948280 PMCID: PMC2588517 DOI: 10.1093/nar/gkn647] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Ribosome recycling factor (RRF), elongation factor G (EF-G) and GTP split 70S ribosomes into subunits. Here, we demonstrated that the splitting was transient and the exhaustion of GTP resulted in re-association of the split subunits into 70S ribosomes unless IF3 (initiation factor 3) was present. However, the splitting was observed with sucrose density gradient centrifugation (SDGC) without IF3 if RRF, EF-G and GTP were present in the SDGC buffer. The splitting of 70S ribosomes causes the decrease of light scattering by ribosomes. Kinetic constants obtained from the light scattering studies are sufficient to account for the splitting of 70S ribosomes by RRF and EF-G/GTP during the lag phase for activation of ribosomes for the log phase. As the amount of 70S ribosomes increased, more RRF, EF-G and GTP were necessary to split 70S ribosomes. In the presence of a physiological amount of polyamines, GTP and factors, even 0.6 microM 70S ribosomes (12 times higher than the 70S ribosomes for routine assay) were split. Spermidine (2 mM) completely inhibited anti-association activity of IF3, and the RRF/EF-G/GTP-dependent splitting of 70S ribosomes.
Collapse
Affiliation(s)
- Go Hirokawa
- Department of Biochemistry and Molecular Biology, Kimmel Cancer Center, Jefferson Medical College, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | | | | | | |
Collapse
|
11
|
Singh NS, Ahmad R, Sangeetha R, Varshney U. Recycling of Ribosomal Complexes Stalled at the Step of Elongation in Escherichia coli. J Mol Biol 2008; 380:451-64. [DOI: 10.1016/j.jmb.2008.05.033] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2008] [Revised: 05/11/2008] [Accepted: 05/15/2008] [Indexed: 10/22/2022]
|
12
|
Gong M, Cruz-Vera LR, Yanofsky C. Ribosome recycling factor and release factor 3 action promotes TnaC-peptidyl-tRNA Dropoff and relieves ribosome stalling during tryptophan induction of tna operon expression in Escherichia coli. J Bacteriol 2007; 189:3147-55. [PMID: 17293419 PMCID: PMC1855834 DOI: 10.1128/jb.01868-06] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Upon tryptophan induction of tna operon expression in Escherichia coli, the leader peptidyl-tRNA, TnaC-tRNA(2)(Pro), resists cleavage, resulting in ribosome stalling at the tnaC stop codon. This stalled ribosome blocks Rho factor binding and action, preventing transcription termination in the tna operon's leader region. Plasmid-mediated overexpression of tnaC was previously shown to inhibit cell growth by reducing uncharged tRNA(2)(Pro) availability. Which factors relieve ribosome stalling, facilitate TnaC-tRNA(2)(Pro) cleavage, and relieve growth inhibition were addressed in the current study. In strains containing the chromosomal tna operon and lacking a tnaC plasmid, the overproduction of ribosome recycling factor (RRF) and release factor 3 (RF3) reduced tna operon expression. Their overproduction in vivo also increased the rate of cleavage of TnaC-tRNA(2)(Pro), relieving the growth inhibition associated with plasmid-mediated tnaC overexpression. The overproduction of elongation factor G or initiation factor 3 did not have comparable effects, and tmRNA was incapable of attacking TnaC-tRNA(2)(Pro) in stalled ribosome complexes. The stability of TnaC-tRNA(2)(Pro) was increased appreciably in strains deficient in RRF and RF3 or deficient in peptidyl-tRNA hydrolase. These findings reveal the existence of a natural mechanism whereby an amino acid, tryptophan, binds to ribosomes that have just completed the synthesis of TnaC-tRNA(2)(Pro). Bound tryptophan inhibits RF2-mediated cleavage of TnaC-tRNA(2)(Pro), resulting in the stalling of the ribosome translating tnaC mRNA. This stalling results in increased transcription of the structural genes of the tna operon. RRF and RF3 then bind to this stalled ribosome complex and slowly release TnaC-tRNA(2)(Pro). This release allows ribosome recycling and permits the cleavage of TnaC-tRNA(2)(Pro) by peptidyl-tRNA hydrolase.
Collapse
Affiliation(s)
- Ming Gong
- Department of Biological Sciences, Stanford University, Stanford, CA 94305, USA
| | | | | |
Collapse
|
13
|
Allen GS, Frank J. Structural insights on the translation initiation complex: ghosts of a universal initiation complex. Mol Microbiol 2006; 63:941-50. [PMID: 17238926 DOI: 10.1111/j.1365-2958.2006.05574.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
All living organisms utilize ribosomes to translate messenger RNA into proteins. Initiation of translation, the process of bringing together mRNA, initiator transfer RNA, and the ribosome, is therefore of critical importance to all living things. Two protein factors, IF1 (a/eIF1A) and IF2 (a/eIF5B), are conserved among all three kingdoms of life and have been called universal initiation factors (Roll-Mecak et al., 2001). Recent X-ray, NMR and cryo-EM structures of the universal factors, alone and in complex with eubacterial ribosomes, point to the structural homology among the initiation factors and initiation complexes. Taken together with genomic and functional evidence, the structural studies allow us to predict some features of eukaryotic and archaeal initiation complexes. Although initiation of translation in eukaryotes and archaea requires more initiation factors than in eubacteria we propose the existence of a common denominator initiation complex with structural and functional homology across all kingdoms of life.
Collapse
Affiliation(s)
- Gregory S Allen
- Howard Hughes Medical Institute, Health Research, Inc., Wadsworth Center, Empire State Plaza, Albany, NY 12201, USA
| | | |
Collapse
|