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D’Arcy BR, Silver DL. Local gene regulation in radial glia: Lessons from across the nervous system. Traffic 2020; 21:737-748. [PMID: 33058331 PMCID: PMC7723028 DOI: 10.1111/tra.12769] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 09/16/2020] [Accepted: 10/12/2020] [Indexed: 01/15/2023]
Abstract
Radial glial cells (RGCs) are progenitors of the cerebral cortex which produce both neurons and glia during development. Given their central role in development, RGC dysfunction can result in diverse neurodevelopmental disorders. RGCs have an elongated bipolar morphology that spans the entire radial width of the cortex and ends in basal endfeet connected to the pia. The basal process and endfeet are important for proper guidance of migrating neurons and are implicated in signaling. However, endfeet must function at a great distance from the cell body. This spatial separation suggests a role for local gene regulation in endfeet. Endfeet contain a local transcriptome enriched for cytoskeletal and signaling factors. These localized mRNAs are actively transported from the cell body and can be locally translated in endfeet. Yet, studies of local gene regulation in RGC endfeet are still in their infancy. Here, we draw comparisons of RGCs with foundational work in anatomically and phylogenetically related cell types, neurons and astrocytes. Our review highlights a striking overlap in the types of RNAs localized, as well as principles of local translation between these three cell types. Thus, studies in neurons, astrocytes and RGCs can mutually inform an understanding of RNA localization across the nervous system.
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Affiliation(s)
- Brooke R. D’Arcy
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina
| | - Debra L. Silver
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina
- Department of Cell Biology, Duke University Medical Center, Durham, North Carolina
- Department of Neurobiology, Duke University Medical Center, Durham, North Carolina
- Duke Institute for Brain Sciences, Duke University Medical Center, Durham, North Carolina
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Biever A, Glock C, Tushev G, Ciirdaeva E, Dalmay T, Langer JD, Schuman EM. Monosomes actively translate synaptic mRNAs in neuronal processes. Science 2020; 367:367/6477/eaay4991. [PMID: 32001627 DOI: 10.1126/science.aay4991] [Citation(s) in RCA: 132] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 10/29/2019] [Accepted: 12/18/2019] [Indexed: 12/13/2022]
Abstract
To accommodate their complex morphology, neurons localize messenger RNAs (mRNAs) and ribosomes near synapses to produce proteins locally. However, a relative paucity of polysomes (considered the active sites of translation) detected in electron micrographs of neuronal processes has suggested a limited capacity for local protein synthesis. In this study, we used polysome profiling together with ribosome footprinting of microdissected rodent synaptic regions to reveal a surprisingly high number of dendritic and/or axonal transcripts preferentially associated with monosomes (single ribosomes). Furthermore, the neuronal monosomes were in the process of active protein synthesis. Most mRNAs showed a similar translational status in the cell bodies and neurites, but some transcripts exhibited differential ribosome occupancy in the compartments. Monosome-preferring transcripts often encoded high-abundance synaptic proteins. Thus, monosome translation contributes to the local neuronal proteome.
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Affiliation(s)
- Anne Biever
- Max Planck Institute for Brain Research, Frankfurt, Germany
| | - Caspar Glock
- Max Planck Institute for Brain Research, Frankfurt, Germany
| | - Georgi Tushev
- Max Planck Institute for Brain Research, Frankfurt, Germany
| | | | - Tamas Dalmay
- Max Planck Institute for Brain Research, Frankfurt, Germany
| | - Julian D Langer
- Max Planck Institute for Brain Research, Frankfurt, Germany.,Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Erin M Schuman
- Max Planck Institute for Brain Research, Frankfurt, Germany.
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Zhang H, Ng MY, Chen Y, Cooperman BS. Kinetics of initiating polypeptide elongation in an IRES-dependent system. eLife 2016; 5. [PMID: 27253065 PMCID: PMC4963199 DOI: 10.7554/elife.13429] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 06/01/2016] [Indexed: 11/13/2022] Open
Abstract
The intergenic IRES of Cricket Paralysis Virus (CrPV-IRES) forms a tight complex with 80S ribosomes capable of initiating the cell-free synthesis of complete proteins in the absence of initiation factors. Such synthesis raises the question of what effect the necessary IRES dissociation from the tRNA binding sites, and ultimately from all of the ribosome, has on the rates of initial peptide elongation steps as nascent peptide is formed. Here we report the first results measuring rates of reaction for the initial cycles of IRES-dependent elongation. Our results demonstrate that 1) the first two cycles of elongation proceed much more slowly than subsequent cycles, 2) these reduced rates arise from slow pseudo-translocation and translocation steps, and 3) the retarding effect of ribosome-bound IRES on protein synthesis is largely overcome following translocation of tripeptidyl-tRNA. Our results also provide a straightforward approach to detailed mechanistic characterization of many aspects of eukaryotic polypeptide elongation.
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Affiliation(s)
- Haibo Zhang
- Department of Chemistry, University of Pennsylvania, Philadelphia, United States
| | - Martin Y Ng
- Department of Chemistry, University of Pennsylvania, Philadelphia, United States
| | - Yuanwei Chen
- Department of Chemistry, University of Pennsylvania, Philadelphia, United States
| | - Barry S Cooperman
- Department of Chemistry, University of Pennsylvania, Philadelphia, United States
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Yamamoto H, Qin Y, Achenbach J, Li C, Kijek J, Spahn CMT, Nierhaus KH. EF-G and EF4: translocation and back-translocation on the bacterial ribosome. Nat Rev Microbiol 2013; 12:89-100. [PMID: 24362468 DOI: 10.1038/nrmicro3176] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Ribosomes translate the codon sequence of an mRNA into the amino acid sequence of the corresponding protein. One of the most crucial events is the translocation reaction, which involves movement of both the mRNA and the attached tRNAs by one codon length and is catalysed by the GTPase elongation factor G (EF-G). Interestingly, recent studies have identified a structurally related GTPase, EF4, that catalyses movement of the tRNA2-mRNA complex in the opposite direction when the ribosome stalls, which is known as back-translocation. In this Review, we describe recent insights into the mechanistic basis of both translocation and back-translocation.
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Affiliation(s)
- Hiroshi Yamamoto
- 1] Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany. [2]
| | - Yan Qin
- 1] Laboratory of noncoding RNA, Institute of Biophysics, Chinese Academy of Science; 15 Datun Road, Beijing 100101, China. [2]
| | - John Achenbach
- 1] NOXXON Pharma AG, Max-Dohrn-Strasse 8-10, 10589 Berlin, Germany. [2]
| | - Chengmin Li
- Laboratory of noncoding RNA, Institute of Biophysics, Chinese Academy of Science; 15 Datun Road, Beijing 100101, China
| | - Jaroslaw Kijek
- Max Planck Institut für molekulare Genetik, Ihnestrasse 73, D-14195 Berlin, Germany
| | - Christian M T Spahn
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Knud H Nierhaus
- 1] Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany. [2] Max Planck Institut für molekulare Genetik, Ihnestrasse 73, D-14195 Berlin, Germany
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Abstract
In the mid-1950s, RNA was a somewhat mysterious molecule with unknown three-dimensional structure and little hard evidence of biological function. Changes began with the 1956 discoveries of the RNA double helix and the phenomenon of nucleic acid hybridization. Discovery of the DNA-RNA hybrid helix in 1960 opened the door to understanding biological information transfer. Single-crystal X-ray diffraction analysis made it possible to precisely define the RNA double helix, discover the novel L-shaped fold of transfer RNA (tRNA), and finally reveal the complete three-dimensional tRNA structure by 1974. By then, a functional understanding of protein synthesis had developed with an appreciation of the various roles of different RNA species. This was the era of RNA awakening.
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Shine-Dalgarno interaction prevents incorporation of noncognate amino acids at the codon following the AUG. Proc Natl Acad Sci U S A 2008; 105:10715-20. [PMID: 18667704 DOI: 10.1073/pnas.0801974105] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
During translation, usually only one in approximately 400 misincorporations affects the function of a nascent protein, because only chemically similar near-cognate amino acids are misincorporated in place of the cognate one. The deleterious misincorporation of a chemically dissimilar noncognate amino acid during the selection process is precluded by the presence of a tRNA at the ribosomal E-site. However, the selection of first aminoacyl-tRNA, directly after initiation, occurs without an occupied E-site, i.e., when only the P-site is filled with the initiator tRNA and thus should be highly error-prone. Here, we show how bacterial ribosomes have solved this accuracy problem: In the absence of a Shine-Dalgarno (SD) sequence, the first decoding step at the A-site after initiation is extremely error-prone, even resulting in the significant incorporation of noncognate amino acids. In contrast, when a SD sequence is present, the incorporation of noncognate amino acids is not observed. This is precisely the effect that the presence of a cognate tRNA at the E-site has during the elongation phase. These findings suggest that during the initiation phase, the SD interaction functionally compensates for the lack of codon-anticodon interaction at the E-site by reducing the misincorporation of near-cognate amino acids and prevents noncognate misincorporation.
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Sergiev PV, Lesnyak DV, Kiparisov SV, Burakovsky DE, Leonov AA, Bogdanov AA, Brimacombe R, Dontsova OA. Function of the ribosomal E-site: a mutagenesis study. Nucleic Acids Res 2005; 33:6048-56. [PMID: 16243787 PMCID: PMC1266066 DOI: 10.1093/nar/gki910] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Ribosomes synthesize proteins according to the information encoded in mRNA. During this process, both the incoming amino acid and the nascent peptide are bound to tRNA molecules. Three binding sites for tRNA in the ribosome are known: the A-site for aminoacyl-tRNA, the P-site for peptidyl-tRNA and the E-site for the deacylated tRNA leaving the ribosome. Here, we present a study of Escherichia coli ribosomes with the E-site binding destabilized by mutation C2394G of the 23S rRNA. Expression of the mutant 23S rRNA in vivo caused increased frameshifting and stop codon readthrough. The progression of these ribosomes through the ribosomal elongation cycle in vitro reveals ejection of deacylated tRNA during the translocation step or shortly after. E-site compromised ribosomes can undergo translocation, although in some cases it is less efficient and results in a frameshift. The mutation affects formation of the P/E hybrid site and leads to a loss of stimulation of the multiple turnover GTPase activity of EF-G by deacylated tRNA bound to the ribosome.
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Affiliation(s)
| | - Dmitry V. Lesnyak
- Department of Bioinformatics and Bioengineering, Moscow State UniversityMoscow, 119899, Russia
| | | | | | | | | | | | - Olga A. Dontsova
- To whom correspondence should be addressed. Tel: +7 095 9328824; Fax: +7 095 9393181;
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Abstract
I had the good luck to start research at the dawn of molecular biology when it was possible to ask fundamental questions about the nature of the nucleic acids and how information is transferred in living systems. The search for answers led me into many different areas, often with the question of how molecular structure leads to biological function. Early work in this period provided some of the roots supporting the current explosive developments in life sciences. Here I give a brief account of my development, describe some contributions, and provide a hint of the exhilaration in discovering new things. Most of all, I had the good fortune to have inspiring teachers, stimulating colleagues, and excellent students.
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Affiliation(s)
- Alexander Rich
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-430, USA
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Affiliation(s)
- Jonathan R Warner
- Dept of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
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BEKHOR IJ, BAVETTA LA. ACTINOMYCIN D INHIBITION OF MICROSOMAL-BOUND HYDROXYPROLINE FORMATION IN RABBIT EMBRYO SKIN IN VITRO. Proc Natl Acad Sci U S A 1996; 53:613-9. [PMID: 14338241 PMCID: PMC336985 DOI: 10.1073/pnas.53.3.613] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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ARLINGHAUS R, SHAEFER J, SCHWEET R. MECHANISM OF PEPTIDE BOND FORMATION IN POLYPEPTIDE SYNTHESIS. Proc Natl Acad Sci U S A 1996; 51:1291-9. [PMID: 14215654 PMCID: PMC300251 DOI: 10.1073/pnas.51.6.1291] [Citation(s) in RCA: 145] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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KAJI H, KAJI A. SPECIFIC BINDING OF SRNA WITH THE TEMPLATE-RIBOSOME COMPLEX. Proc Natl Acad Sci U S A 1996; 52:1541-7. [PMID: 14243530 PMCID: PMC300483 DOI: 10.1073/pnas.52.6.1541] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Affiliation(s)
- A Rich
- Biology Department, Massachusetts Institute of Technology, Cambridge 02139, USA
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Remme J, Margus T, Villems R, Nierhaus KH. The third ribosomal tRNA-binding site, the E site, is occupied in native polysomes. EUROPEAN JOURNAL OF BIOCHEMISTRY 1989; 183:281-4. [PMID: 2667995 DOI: 10.1111/j.1432-1033.1989.tb14925.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The nucleic acids of Escherichia coli cells were uniformly labelled with 32P by growing the cells in [32P]orthophosphoric acid for about four generations. The cells were harvested in the logarithmic phase, resuspended in a buffer containing 6 mM Mg2+, 150 mM NH4+ and polyamines and incubated for 3 min at 37 degrees C in the presence of 3H-labelled amino acids. This procedure preferentially labels growing peptidyl chains. Polysomes were isolated, the fraction in the post-translocational state was assessed by a puromycin reaction and the tRNA content/70S ribosome was quantified in comparison to the amount of 5S rRNA determined after separation by gel electrophoresis. The data revealed that at least 75% of post-translocational ribosomes in isolated native polysomes carry a tRNA in their E site. The results are consistent with the allosteric three-site model for the elongation cycle but disagree with the two-site model.
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Affiliation(s)
- J Remme
- Institute of Chemical Physics and Biophysics, Academy of Sciences, Estonian SSR, Tartu
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Abstract
The ribosomal elongation cycle represents a series of reactions during which the polypeptide is prolonged by one amino acid and after which the prolonged polypeptidyl residue is again ready to accept the next aminoacyl residue. It is generally believed that the ribosome carries two tRNA binding sites, the A site for aminoacyl-tRNA and the P site for peptidyl-tRNA, leading to the classical two-site model of the ribosome as a description for the elongation cycle. However, evidence is accumulating which is in conflict with the classical two-site model. These conflicts are resolved in a new three-site model which is discussed in detail in this paper.
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Rheinberger HJ, Nierhaus KH. Testing an alternative model for the ribosomal peptide elongation cycle. Proc Natl Acad Sci U S A 1983; 80:4213-7. [PMID: 6348767 PMCID: PMC384007 DOI: 10.1073/pnas.80.14.4213] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
A kinetic analysis of poly(U)-dependent poly(Phe) synthesis with [14C]tRNAPhe and [3H]phenylalanine demonstrated that, in the course of efficient poly(Phe) synthesis, two tRNAs are present per 70S ribosome at all times, although at least 70% of the poly(Phe)-tRNAPhe is found at the peptidyl-tRNA (P) site. Together with our recent observation of a third tRNA-binding site on Escherichia coli ribosomes, these findings suggest a model for the peptide elongation cycle in which two tRNA molecules are present on the ribosome at both the pre- and the post-translocational state. This model predicts that deacylated tRNA is not released from the P site but translocated to the exit (E) site before release occurs. A series of translocation experiments with deacylated [14C]tRNAPhe at the P site and oligo [( 3H]Phe)-tRNA at the aminoacyl-tRNA (A) site proved that efficient elongation factor G-dependent translocation is not accompanied by a corresponding [14C]tRNAPhe release. However, significant [14C]tRNAPhe release was observed after translocation when an aminoacyl-tRNA was bound to the A site. Thus, deacylated tRNA is not released from the P site but is translocated to the E site, which therefore must be located "upstream" adjacent to the P site. Furthermore, the trigger for the release of deacylated tRNA from the E site is the binding of aminoacyl-tRNA to the A site.
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Rheinberger HJ, Sternbach H, Nierhaus KH. Three tRNA binding sites on Escherichia coli ribosomes. Proc Natl Acad Sci U S A 1981; 78:5310-4. [PMID: 7029532 PMCID: PMC348734 DOI: 10.1073/pnas.78.9.5310] [Citation(s) in RCA: 152] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The binding of N-acetyl-Phe-tRNAPhe (an analogue of peptidyl-tRNA), Phe-tRNAPhe, and deacylated tRNAPhe to poly(U)-programmed tightly coupled 70S ribosomes was studied. The N-acetyl-Phe-tRNAPhe binding is governed by an exclusion principle: not more than one N-acetyl-Phe-tRNAPhe can be bound per ribosome, although this peptidyl-tRNA analogue can be present either at the aminoacyl-tRNA (A) site or the peptidyl-tRNA (P) site. Two Phe-tRNAPhe molecules are accepted by one ribosome in the presence of poly(U). This aminoacyl-tRNA binds enzymatically (in the presence of elongation factor Tu and GTP) and nonenzymatically to the A site and is then transferred to the P site, if that site is free. If this elongation factor G-independent movement is hampered, either by using an incubation temperature of 0 degrees C or by the addition of the translocation inhibitor viomycin, only one Phe-tRNAPhe per ribosome can be bound. The effect of the peptidyltransferase inhibitor chloramphenicol on the binding is similar to that of viomycin. In the absence of poly(U), Phe-tRNAPhe cannot bind to the ribosome. Deacylated [14C]tRNAPhe can bind in three copies to one ribosome. The new third tRNA binding site is called the "E" site. The sequence of filling the sites is P, E, and A. The apparent binding constants for the P and the E sites are both approximately 9 X 10(6) M-1 and that for the A site is 1.3 X 10(6) M-1. In the absence of poly(U), only one deacylated tRNAPhe can be bound per ribosome. This tRNAPhe most likely occupies the P site.
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Garrick LM, Garrick MD. Testing with puromycin and amino acyl tRNAs that limit the rate of peptide chain extension. Mol Cell Biochem 1978; 19:49-59. [PMID: 246496 DOI: 10.1007/bf00231234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
With puromycin one can recognize when the synthesis of a given protein is dependent on amino acyl tRNA that is present in rate limiting amount. We demonstrate this use of puromycin by its interaction with another inhibitor, L-o-methylthreonine. L-o-methylthreonine lowers the Ile-tRNA concentration in the cell, thereby inhibiting synthesis of proteins containing isoleucine. In certain rabbits, the alpha hemoglobin chain has three isoleucyl residues and the beta chain none. L-o-methylthreonine thus inhibits alpha globin synthesis in intact reticulocytes from these rabbits. When puromycin and L-o-methylthreonine are used together, the two inhibitors synergize in inhibiting alpha globin synthesis. Hence, puromycin is a more effective inhibitor when the Ile-tRNA concentration is lowered. Cycloheximide and sodium fluoride have different modes of action from puromycin. Neither synergizes with L-o-methylthreonine; instead, the interaction is less than additive. We have found that beta chain synthesis in rabbit reticulocytes is more sensitive than alpha to inhibition by puromycin. This difference could reflect either differences in amino acid sequence or tRNA dependent limitations of beta chain elongation. The switch from fetal to adult hemoglobin in humans does not involve changes in limiting amino acyl tRNA because, for cord blood from infants of different developmental ages, the puromycin sensitivity of incorporation into gamma and beta chains remains constant.
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Garrick LM, Dembure PP, Garrick MD. Interaction between the synthesis of alpha and beta globin. EUROPEAN JOURNAL OF BIOCHEMISTRY 1975; 58:339-50. [PMID: 1183442 DOI: 10.1111/j.1432-1033.1975.tb02380.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
We have examined the relationship between alpha and beta globin chain syntheses by utilizing the distribution of isoleucyl residues in rabbit hemoglobin. The alpha globin chain contains three isoleucyl residues while the beta chain of certain rabbits contains no isoleucine. O-Methyl-L-threonine, an isoleucine isostere, inhibits incorporation of radiolabeled amino acids into alpha chains in rabbit reticulocytes. When alpha chain synthesis is inhibited by 50-85%, beta synthesis is stimulated by 15-50%. The excess labeled beta chains are not distinguishable from authentic beta chains by any of the following criteria: (a) carboxymethyl cellulose chromatography in sodium phosphate-urea buffers, (b) electrophoresis on polyacrylamide gels containing sodium dodecyl sulfate, and (c) electrophoresis of methionine-containing tryptic peptides. The stimulation of beta synthesis continues after the pool of excess alpha chains has been exhausted by preincubation with O-methyl-L-threonine. The stimulation does not occur, however, when 1 mM 2-mercaptoethanol is added to the incubation medium or when the cells are excessively diluted in the incubation mixture. The rates of beta chain initiation and elongation during stimulation have been compared to the rates during normal synthesis. Although both rates are increased, the rate of elongation increases more than initiation, suggesting that initiation is the rate-limiting step in increased beta chain production. The stimulation of beta synthesis when alpha synthesis is inhibited is interpreted as resulting from relief of competition between alpha and beta mRNAs for limiting components of the protein synthetic apparatus.
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Nwagwu M. Preparation of polyribosome aminoacyl-transfer ribonucleic acid from the muscle of chick embryos. Biochem J 1975; 147:473-7. [PMID: 241328 PMCID: PMC1165474 DOI: 10.1042/bj1470473] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A procedure for preparing polyribosome aminoacyl-tRNA free from contamination by supernatant aminoacyl-tRNA and free amino acids is described. Important features of the procedure are the use of acidic buffers to help protect the amino acid-tRNA linkage and the inclusion of sodium dodecyl sulphate, to inhibit ribonuclease activity. The specific radioactivity of polyribosome aminoacyl-tRNA is high within 30s and reaches a maximum in 2 1/2 min, well ahead of polyribosome peptides which, as described by Herrmann et al. (1971), attain maximum specific radioactivity in about 10 min.
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Smith DW, McNamara AL. The Distribution of Transfer Ribonucleic Acid in Rabbit Reticulocytes. J Biol Chem 1974. [DOI: 10.1016/s0021-9258(19)42885-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Garrick MD, Bricker J, Garrick LM. An electrophoretically silent polymorphism for the beta chains of rabbit hemoglobin and associated polyribosome patterns. Genetics 1974; 76:99-108. [PMID: 4818267 PMCID: PMC1213058 DOI: 10.1093/genetics/76.1.99] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The beta chain of rabbit (Oryctolagus caniculus) hemoglobin has previously been reported to contain a single residue of isoleucine at beta(112). We have detected other rabbits with either zero isoleucyl residues or half a residue per beta chain. This character is polymorphic and inherited as a simple mendelian autosomal codominant.-Normally the modal number of ribosomes per polyribosome is 4 to 6 in reticulocyte lysates; but incubation of rabbit reticulocytes prior to lysis with L-o-methylthreonine (OMT), an isostere of isoleucine, leads to a bimodal distribution in lysates with 2-3 and 8-12 ribosomes as modes. This alteration has been attributed to ribosomal traffic jams caused by starvation for ile-tRNA at mRNA codons corresponding to the locations of isoleucyl residues at positions alpha(10), alpha(17), alpha(55) and beta(112). We have confirmed this interpretation by incubating OMT with reticulocytes from rabbits with integral, half integral and nil values for isoleucyl residues per beta chain to show that formation of the larger clusters of polyribosomes requires that beta(112) = ile.
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Gaskill P, Kabat D. Unexpectedly large size of globin messenger ribonucleic acid. Proc Natl Acad Sci U S A 1971; 68:72-5. [PMID: 5276303 PMCID: PMC391105 DOI: 10.1073/pnas.68.1.72] [Citation(s) in RCA: 78] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
The globin messenger RNA of rabbit reticulocytes is identified on the basis of its presence in polysomes, absence from single ribosomes, and sedimentation coefficient of 9 S. Analysis of this RNA by electrophoresis in polyacrylamide gels provides evidence that its size is unexpectedly large (approximately 650 nucleotides) for a messenger coding for the 141 and 146 amino acids of a globin polypeptide. Reticulocyte RNA molecules were labeled in vivo with [(32)P]orthophosphate. Globin messenger RNA and transfer RNA appear to be synthesized late in erythropoiesis, whereas ribosomal RNA and 5S RNA are synthesized at the beginning stages of cytodifferentiation. At least one fragment of ribosomal RNA accumulates in erythrocytes in the terminal stages of maturation.
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Udem SA, Kaufman K, Warner JR. Small ribosomal ribonucleic acid species of Saccharomyces cerevisiae. J Bacteriol 1971; 105:101-6. [PMID: 5540996 PMCID: PMC248327 DOI: 10.1128/jb.105.1.101-106.1971] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Yeast ribosomes contain two small molecular-weight species of ribonucleic acid (RNA), in addition to transiently associated transfer RNA. The 5S RNA species is part of the large ribosomal subunit and appears to be exactly the same size as 5S RNA from other organisms. There is another RNA molecule, approximately 5.8S or 150 nucleotides in size, which is noncovalently attached to the 25S ribosomal RNA and can be freed by gentle heating or urea treatment. Neither 5 nor 5.8S RNA are methylated. The 5.8S RNA is probably derived from a part of the 35S precursor RNA, whereas the 5S RNA is made de novo. These results substantiate the notion that ribosome biosynthesis in yeast is analogous to that of the higher eukaryotes.
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36
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Roufa DJ, Skogerson LE, Leder P. Translation of phage Qbeta mRNA: a test of the two-site model for ribosomal function. Nature 1970; 227:567-70. [PMID: 5429287 DOI: 10.1038/227567a0] [Citation(s) in RCA: 39] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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37
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38
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Kaji H. Intraribosomal environment of the nascent peptide chain. INTERNATIONAL REVIEW OF CYTOLOGY 1970; 29:169-211. [PMID: 4928380 DOI: 10.1016/s0074-7696(08)60035-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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39
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Abstract
To study the mechanism by which chloramphenicol inhibits bacterial protein synthesis, we examined the kinetics of the puromycin-induced release of peptides from transfer ribonucleic acid (tRNA) in the presence and in the absence of chloramphenicol. Washed Escherichia coli ribosomes with nascent peptides which had been radioactively labeled in vivo were used for this study. When such ribosomes were incubated in the presence of 10 mug of puromycin per ml, approximately one-fourth of the radioactive peptide material was rapidly released from tRNA. This rapid, puromycin-dependent reaction is assumed to be equivalent to the peptidyl transferase reaction. Chloramphenicol inhibited the extent of the puromycin-induced release of peptides by only 50%, demonstrating that some of the peptide chains which are present on active ribosomes react with puromycin, even in the presence of chloramphenicol. The addition of the supernatant fraction and guanosine triphosphate (GTP) increased the extent of the puromycin-induced release; this additional release was completely inhibited by chloramphenicol. Peptidyl chains on washed ribosomes prepared from chloramphenicol-inhibited cells were not released by puromycin in the presence of chloramphenicol and reacted slowly with puromycin in the absence of chloramphenicol. The release of peptidyl groups from these ribosomes became largely insensitive to chloramphenicol after preincubation of the ribosomes with GTP and the supernatant fraction. We conclude that chloramphenicol does not inhibit the peptidyl transferase reaction as measured by the puromycin-induced release of peptides from tRNA, but rather inhibits some step in the peptide synthesis cycle prior to this reaction.
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40
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Sarkar S, Thach RE. Inhibition of formylmethionyl-transfer RNA binding to ribosomes by tetracycline. Proc Natl Acad Sci U S A 1968; 60:1479-86. [PMID: 5244755 PMCID: PMC224944 DOI: 10.1073/pnas.60.4.1479] [Citation(s) in RCA: 59] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
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41
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Matthaei H, Sander G, Swan D, Kreuzer T, Caffier H, Parmeggiani A. [Reaction steps of polypeptide synthesis on ribosomes. Mechanisms of protein synthesis, X]. THE SCIENCE OF NATURE - NATURWISSENSCHAFTEN 1968; 55:281-94. [PMID: 4878450 DOI: 10.1007/bf00591706] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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42
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Evidence for the Enzymatic Binding of Aminoacyl Transfer Ribonucleic Acid to Rat Liver Ribosomes. J Biol Chem 1968. [DOI: 10.1016/s0021-9258(19)81735-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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43
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The Genetic Code After The Excitement. ADVANCES IN GENETICS 1968. [DOI: 10.1016/s0065-2660(08)60429-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register]
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44
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Die Orthologie und Pathologie der Zelle im elektronenmikroskopischen Bild. STOFFWECHSEL UND FEINSTRUKTUR DER ZELLE I 1968. [DOI: 10.1007/978-3-642-88276-0_2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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45
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Bekhor I, Bavetta LA. Evidence for a low-molecular-weight collagen precursor. Proc Natl Acad Sci U S A 1967; 58:2351-8. [PMID: 5242211 PMCID: PMC223842 DOI: 10.1073/pnas.58.6.2351] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
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46
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Ghosh HP, Khorana HG. Studies on polynucleotides, LXXXIV. On the role of ribosomal subunits in protein synthesis. Proc Natl Acad Sci U S A 1967; 58:2455-61. [PMID: 4873591 PMCID: PMC223857 DOI: 10.1073/pnas.58.6.2455] [Citation(s) in RCA: 51] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
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47
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Mangiarotti G, Schlessinger D. Polyribosome Metabolism in Escherichia coli II. Formation and Lifetime of Messenger RNA Molecules, Ribosomal Subunit Couples and Polyribosomes. J Mol Biol 1967; 29:395-418. [PMID: 31031418 PMCID: PMC6481303 DOI: 10.1016/0022-2836(67)90107-6] [Citation(s) in RCA: 93] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
During a continuous label with [3H]uracil of fragile Escherichia coli cells in exponential growth, all or very nearly all the hybridizable mRNA of the cells can be observed in polyribosomes during zonal sedimentation in sucrose gradients. In contrast, all the newly formed rRNA appears to be free of polyribosomes until it is part of complete ribosomal subunits. The separation of the two major classes of newly formed RNA permits the direct observation of the growth with time of mRNA molecules, of ribosomal subunits and of polyribosomes. A complete chain of ribosomal RNA forms in one to two minutes; completion of either a 30 s or 50 s ribosome requires a minimum of about five minutes more. The specific activities of free ribosomal subunits and those that are present in polyribosomes increase at identical rates, consistent with very rapid exchange of the two classes. Before any new subunits are finished, the 3H-labeled RNA in polyribosomes is the cellular mRNA, which can therefore be extracted and observed separated from ribosomal RNA. Assuming that their sedimentation rates in sucrose gradients are related to molecular weights as are those of ribosomal rRNA and that no degradation occurs dining extraction, most of the molecules of mRNA are large enough to code for only one or two protein chains of 30,000 molecular weight. The kinetics of entry of all the new mRNA into polyribosomes is in agreement with the view that a polyribosome forms as the corresponding messenger RNA is synthesized, over a period of at least a minute. 3% of the total cellular RNA in these cultures (doubling time 120 minutes) is mRNA, with an average chemical lifetime of 11 to 12·5 minutes.
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Affiliation(s)
- Giorgio Mangiarotti
- Department of Microbiology, Washington University School of Medicine St. Louis, Mo. 63110, U.S.A
| | - David Schlessinger
- Department of Microbiology, Washington University School of Medicine St. Louis, Mo. 63110, U.S.A
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Economou AE, Nakamoto T. Further studies on the initiation of protein synthesis with N-formylmethionine in E. coli extracts. Proc Natl Acad Sci U S A 1967; 58:1033-9. [PMID: 4861303 PMCID: PMC335743 DOI: 10.1073/pnas.58.3.1033] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
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49
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Abstract
The properties of a site, on Escherichia coli ribosomes, which binds peptidyl-s-RNA (where s-RNA refers to ;soluble' or transfer RNA) have been investigated. The binding is stable both in low Mg(2+) concentration (0.1mm), and in high Mg(2+) concentration (10mm) in the absence or presence of potassium chloride (86mm). Puromycin has been used to break the bond between the s-RNA and the polypeptide, and in the absence of further protein synthesis this technique exposes free s-RNA molecules on the ribosomes. The s-RNA exposed remains bound in high Mg(2+) concentration, but the binding is unstable in high Mg(2+) concentration with potassium chloride and the s-RNA can be freed completely from the ribosomes by lowering the Mg(2+) concentration. It can also be displaced by s-RNA in the medium. It is suggested that this ribosomal binding site for peptidyl-s-RNA is the site for peptide bond formation. Further, it is proposed that it is the same site that can be demonstrated on ribosomes not engaged in protein synthesis and that, in high Mg(2+) concentration, will bind s-RNA molecules charged or uncharged with amino acids.
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50
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Leder P, Nau MM. Initiation of protein synthesis. 3. Factor-GTP-codon-dependent binding of F-met-tRNA to ribosomes. Proc Natl Acad Sci U S A 1967; 58:774-81. [PMID: 4860758 PMCID: PMC335700 DOI: 10.1073/pnas.58.2.774] [Citation(s) in RCA: 50] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
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