1
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Fritsch C, Bhattacharya A, Ng MY, Li H, Nelson PC, Cooperman BS, Goldman YE. Single-Molecule Studies of Cognate and Near-Cognate Elongation in an in vitro Eukaryotic Translation System. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.29.609187. [PMID: 39257735 PMCID: PMC11383654 DOI: 10.1101/2024.08.29.609187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2024]
Abstract
The ribosome plays a central role in translation of the genetic code into amino acid sequences during synthesis of polypeptides. During each cycle of peptide elongation, the ribosome must discriminate between correct and incorrect aminoacyl-tRNAs according to the codon present in its A-site. Ribosomes rely on a complex sequence of proofreading mechanisms to minimize erroneous selection of incorrect aminoacyl-tRNAs that would lead to mistakes in translation. These mechanisms have been studied extensively in prokaryotic organisms, but eukaryotic elongation is less well understood. Here, we use single-molecule fluorescence resonance energy transfer (smFRET) with an in vitro eukaryotic translation system to investigate tRNA selection and subsequent steps during peptide elongation. We compared accommodation of a tryptophan-aminoacyl-tRNA into the ribosomal A-site containing either a cognate or near-cognate codon and unexpectedly found that, following an initial slow sampling event, subsequent near-cognate sampling events proceeded more rapidly than the initial event. Further, we found a strong negative correlation between the concentration of near-cognate aminoacyl-tRNA and the efficiency of tRNA accommodation. These novel characteristics of near-cognate interaction with the eukaryotic ribosome suggest that rejection of a near-cognate tRNAs leads to formation of an altered ribosomal conformation that assists in rejecting subsequent incorrect tRNA interactions.
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Affiliation(s)
- Clark Fritsch
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Arpan Bhattacharya
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Pharmacology and Department of Molecular and Cellular Biology, University of California, Davis, CA, 95616, USA
| | - Martin Y Ng
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Hong Li
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Philip C Nelson
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Barry S Cooperman
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Yale E Goldman
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Pennsylvania Muscle Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Pharmacology and Department of Molecular and Cellular Biology, University of California, Davis, CA, 95616, USA
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2
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Remes C, Nguyen MD, Spahr H, Ng M, Fritsch C, Bhattacharya A, Li H, Cooperman B, Rorbach J. Assembly of the Mitochondrial Translation Initiation Complex. Methods Mol Biol 2023; 2661:217-232. [PMID: 37166640 DOI: 10.1007/978-1-0716-3171-3_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Mitochondria maintain their own translational machinery that is responsible for the synthesis of essential components of the oxidative phosphorylation system. The mammalian mitochondrial translation system differs significantly from its cytosolic and bacterial counterparts. Here, we describe detailed protocols for efficient in vitro reconstitution of the mammalian mitochondrial translation initiation complex, which can be further used for mechanistic analyses of different aspects of mitochondrial translation.
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Affiliation(s)
- Cristina Remes
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA.
| | - Minh Duc Nguyen
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden
| | - Henrik Spahr
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden
| | - Martin Ng
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA
| | - Clark Fritsch
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Arpan Bhattacharya
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Hong Li
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA
| | - Barry Cooperman
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA
| | - Joanna Rorbach
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden
- Max Planck Institute Biology of Ageing, Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
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3
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Huang S, Bhattacharya A, Ghelfi MD, Li H, Fritsch C, Chenoweth DM, Goldman YE, Cooperman BS. Ataluren binds to multiple protein synthesis apparatus sites and competitively inhibits release factor-dependent termination. Nat Commun 2022; 13:2413. [PMID: 35523781 PMCID: PMC9076611 DOI: 10.1038/s41467-022-30080-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 04/12/2022] [Indexed: 12/15/2022] Open
Abstract
Genetic diseases are often caused by nonsense mutations, but only one TRID (translation readthrough inducing drug), ataluren, has been approved for clinical use. Ataluren inhibits release factor complex (RFC) termination activity, while not affecting productive binding of near-cognate ternary complex (TC, aa-tRNA.eEF1A.GTP). Here we use photoaffinity labeling to identify two sites of ataluren binding within rRNA, proximal to the decoding center (DC) and the peptidyl transfer center (PTC) of the ribosome, which are directly responsible for ataluren inhibition of termination activity. A third site, within the RFC, has as yet unclear functional consequences. Using single molecule and ensemble fluorescence assays we also demonstrate that termination proceeds via rapid RFC-dependent hydrolysis of peptidyl-tRNA followed by slow release of peptide and tRNA from the ribosome. Ataluren is an apparent competitive inhibitor of productive RFC binding, acting at or before the hydrolysis step. We propose that designing more potent TRIDs which retain ataluren's low toxicity should target areas of the RFC binding site proximal to the DC and PTC which do not overlap the TC binding site.
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Affiliation(s)
- Shijie Huang
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, 19104, USA
- GSK, 14200 Shady Grove Rd, Rockville, MD, 20850, USA
| | - Arpan Bhattacharya
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Mikel D Ghelfi
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Hong Li
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Clark Fritsch
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - David M Chenoweth
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Yale E Goldman
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Barry S Cooperman
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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4
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Site-Specific Fluorescent Labeling of RNA Interior Positions. Molecules 2021; 26:molecules26051341. [PMID: 33802273 PMCID: PMC7959133 DOI: 10.3390/molecules26051341] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/26/2021] [Accepted: 03/01/2021] [Indexed: 02/08/2023] Open
Abstract
The introduction of fluorophores into RNA for both in vitro and in cellulo studies of RNA function and cellular distribution is a subject of great current interest. Here I briefly review methods, some well-established and others newly developed, which have been successfully exploited to site-specifically fluorescently label interior positions of RNAs, as a guide to investigators seeking to apply this approach to their studies. Most of these methods can be applied directly to intact RNAs, including (1) the exploitation of natural posttranslational modifications, (2) the repurposing of enzymatic transferase reactions, and (3) the nucleic acid-assisted labeling of intact RNAs. In addition, several methods are described in which specifically labeled RNAs are prepared de novo.
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5
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Dellac S, Ben-Dov H, Raanan A, Saleem H, Zamostiano R, Semyatich R, Lavi S, Witz IP, Bacharach E, Ehrlich M. Constitutive low expression of antiviral effectors sensitizes melanoma cells to a novel oncolytic virus. Int J Cancer 2020; 148:2321-2334. [PMID: 33197301 DOI: 10.1002/ijc.33401] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Revised: 10/30/2020] [Accepted: 11/03/2020] [Indexed: 12/15/2022]
Abstract
STAT1 is a critical effector and a target gene of interferon (IFN) signaling, and thus a central mediator of antiviral responses. As both a mediator and a target of IFN signals, STAT1 expression reports on, and determines IFN activity. Gene expression analyses of melanoma patient samples revealed varied levels of STAT1 expression, which highly correlated with expression of >700 genes. The ability of oncolytic viruses to exploit tumor-induced defects to antiviral responses suggests that oncolytic viruses may efficiently target a subset of melanomas, yet these should be defined. We modeled this scenario with murine B16F10 melanomas, immortalized skin fibroblasts as controls and a novel oncolytic virus, EHDV-TAU. In B16F10 cells, constitutive low expression of STAT1 and its target genes, which included intracellular pattern recognition receptors (PRRs), correlated with their inability to mount IFN-based antiviral responses upon EHDV-TAU challenge, and with potency of EHDV-TAU-induced oncolysis. This underexpression of interferon stimulated genes (ISGs) and PRRs, and the inability of EHDV-TAU to induce their expression, were reversed by epigenetic modifiers, suggesting epigenetic silencing as a basis for their underexpression. Despite their inability to mount IFN/STAT-based responses upon viral infection, EHDV-TAU infected B16F10 cells secreted immune-stimulatory chemokines. Accordingly, in vivo, EHDV-TAU enhanced intratumoral infiltration of cytotoxic T-cells and reduced growth of local and distant tumors. We propose that "STAT1 signatures" should guide melanoma virotherapy treatments, and that oncolytic viruses such as EHDV-TAU have the potential to exploit the cellular context of low-STAT1 tumors.
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Affiliation(s)
- Sarah Dellac
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Hamutal Ben-Dov
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Ayala Raanan
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Hanna Saleem
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Rachel Zamostiano
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Rinat Semyatich
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Sara Lavi
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Isaac P Witz
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Eran Bacharach
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Marcelo Ehrlich
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
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6
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Dhakal R, Tong C, Anderson S, Kashina A, Cooperman B, Bau H. Dynamics of intracellular stress-induced tRNA trafficking. Nucleic Acids Res 2019; 47:2002-2010. [PMID: 30496477 PMCID: PMC6393242 DOI: 10.1093/nar/gky1208] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 11/09/2018] [Accepted: 11/20/2018] [Indexed: 01/15/2023] Open
Abstract
Stress is known to induce retrograde tRNA translocation from the cytoplasm to the nucleus but translocation kinetics and tRNA-spatial distribution have not been characterized previously. We microinject fluorescently-labeled tRNA into living cells and use confocal microscopy to image tRNA spatial distribution in single cells at various levels of starvation and to determine translocation rate constants. Retrograde tRNA translocation occurs reversibly, within minutes after nutrition depletion of the extracellular medium. Such nutritional starvation leads to down-regulation of tRNA nuclear import and nearly complete curtailment of its nuclear export. Nuclear tRNA accumulation is suppressed in cells treated with the translation inhibitor puromycin, but is enhanced in cells treated with the microtubule inhibitor nocodazole. tRNA in the cytoplasm exhibits distinct spatial distribution inconsistent with diffusion, implying that such distribution is actively maintained. We propose that tRNA biological complexes and/or cytoplasmic electric fields are the likely regulators of cytoplasmic tRNA spatial distribution.
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Affiliation(s)
- Rabin Dhakal
- Department of Mechanical Engineering and Applied mechanics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Chunyi Tong
- Department of Mechanical Engineering and Applied mechanics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sean Anderson
- Department of Mechanical Engineering and Applied mechanics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Anna S Kashina
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Barry Cooperman
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19014, USA
| | - Haim H Bau
- Department of Mechanical Engineering and Applied mechanics, University of Pennsylvania, Philadelphia, PA 19104, USA
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7
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A heterogeneous tRNA granule structure exhibiting rapid, bi-directional neuritic transport. Eur J Cell Biol 2018; 97:168-179. [PMID: 29482850 DOI: 10.1016/j.ejcb.2018.02.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 02/09/2018] [Accepted: 02/12/2018] [Indexed: 11/23/2022] Open
Abstract
mRNA translation is regulated by diverse mechanisms that converge at the initiation and elongation steps to determine the rate, profile, and localization of proteins synthesized. A consistently relevant feature of these mechanisms is the spatial re-distribution of translation machinery, a process of particular importance in neural cells. This process has, however, been largely overlooked with respect to its potential role in regulating the local concentration of cytoplasmic tRNAs, even as a multitude of data suggest that spatial regulation of the tRNA pool may help explain the remarkably high rates of peptide elongation. Here, we report that Cy3/Cy5-labeled bulk tRNAs transfected into neural cells distribute into granule-like structures - "tRNA granules" - that exhibit dynamic mixing of tRNAs between granules and rapid, bi-directional vectorial movement within neurites. Imaging of endogenous tRNAgly and tRNAlys by fluorescent in situ hybridization revealed a similar granular distribution of tRNAs in somata and neurites; this distribution was highly overlapping with granules imaged by introduction of exogenous Cy5-tRNAthr and Cy3-tRNAval. A subset of tRNA granules located in the cell body, neurite branch points and growth cones displayed fluorescence resonance energy transfer (FRET) between Cy3 and Cy5-labeled tRNAs indicative of translation, and co-localization with elongation machinery. A population of smaller, rapidly trafficked granules in neurites lacked FRET and showed poor colocalization with translation initiation and elongation factors, suggesting that they are a translationally inactive tRNA transport particle. Our data suggest that tRNAs are packaged into granules that are rapidly transported to loci where translation is needed, where they may greatly increase the local concentration of tRNAs in support of efficient elongation. The potential implications of this newly described structure for channeling of elongation, local translation, and diseases associated with altered tRNA levels or function are discussed.
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8
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Masuda I, Igarashi T, Sakaguchi R, Nitharwal RG, Takase R, Han KY, Leslie BJ, Liu C, Gamper H, Ha T, Sanyal S, Hou YM. A genetically encoded fluorescent tRNA is active in live-cell protein synthesis. Nucleic Acids Res 2017; 45:4081-4093. [PMID: 27956502 PMCID: PMC5397188 DOI: 10.1093/nar/gkw1229] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 12/06/2016] [Indexed: 11/14/2022] Open
Abstract
Transfer RNAs (tRNAs) perform essential tasks for all living cells. They are major components of the ribosomal machinery for protein synthesis and they also serve in non-ribosomal pathways for regulation and signaling metabolism. We describe the development of a genetically encoded fluorescent tRNA fusion with the potential for imaging in live Escherichia coli cells. This tRNA fusion carries a Spinach aptamer that becomes fluorescent upon binding of a cell-permeable and non-toxic fluorophore. We show that, despite having a structural framework significantly larger than any natural tRNA species, this fusion is a viable probe for monitoring tRNA stability in a cellular quality control mechanism that degrades structurally damaged tRNA. Importantly, this fusion is active in E. coli live-cell protein synthesis allowing peptidyl transfer at a rate sufficient to support cell growth, indicating that it is accommodated by translating ribosomes. Imaging analysis shows that this fusion and ribosomes are both excluded from the nucleoid, indicating that the fusion and ribosomes are in the cytosol together possibly engaged in protein synthesis. This fusion methodology has the potential for developing new tools for live-cell imaging of tRNA with the unique advantage of both stoichiometric labeling and broader application to all cells amenable to genetic engineering.
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Affiliation(s)
- Isao Masuda
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 233 South 10th Street, Philadelphia, PA 19107, USA
| | - Takao Igarashi
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 233 South 10th Street, Philadelphia, PA 19107, USA
| | - Reiko Sakaguchi
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 233 South 10th Street, Philadelphia, PA 19107, USA
| | - Ram G Nitharwal
- Department of Cell and Molecular Biology, Uppsala University, Box-596, BMC 75124, Uppsala, Sweden
| | - Ryuichi Takase
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 233 South 10th Street, Philadelphia, PA 19107, USA
| | - Kyu Young Han
- Department of Physics and Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.,CREOL, College of Optics & Photonics, University of Central Florida, 4304 Scorpius St., Orlando, FL 32816, USA
| | - Benjamin J Leslie
- Department of Physics and Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.,Howard Hughes Medical Institute, Baltimore, MD 21205, USA
| | - Cuiping Liu
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 233 South 10th Street, Philadelphia, PA 19107, USA
| | - Howard Gamper
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 233 South 10th Street, Philadelphia, PA 19107, USA
| | - Taekjip Ha
- Department of Physics and Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.,Howard Hughes Medical Institute, Baltimore, MD 21205, USA.,Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA.,Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA.,Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Suparna Sanyal
- Department of Cell and Molecular Biology, Uppsala University, Box-596, BMC 75124, Uppsala, Sweden
| | - Ya-Ming Hou
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 233 South 10th Street, Philadelphia, PA 19107, USA
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9
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Plochowietz A, Farrell I, Smilansky Z, Cooperman BS, Kapanidis AN. In vivo single-RNA tracking shows that most tRNA diffuses freely in live bacteria. Nucleic Acids Res 2016; 45:926-937. [PMID: 27625389 PMCID: PMC5314786 DOI: 10.1093/nar/gkw787] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 07/29/2016] [Accepted: 08/20/2016] [Indexed: 11/21/2022] Open
Abstract
Transfer RNA (tRNA) links messenger RNA nucleotide sequence with amino acid sequence during protein synthesis. Despite the importance of tRNA for translation, its subcellular distribution and diffusion properties in live cells are poorly understood. Here, we provide the first direct report on tRNA diffusion localization in live bacteria. We internalized tRNA labeled with organic fluorophores into live bacteria, applied single-molecule fluorescence imaging with single-particle tracking and localized and tracked single tRNA molecules over seconds. We observed two diffusive species: fast (with a diffusion coefficient of ∼8 μm2/s, consistent with free tRNA) and slow (consistent with tRNA bound to larger complexes). Our data indicate that a large fraction of internalized fluorescent tRNA (>70%) appears to diffuse freely in the bacterial cell. We also obtained the subcellular distribution of fast and slow diffusing tRNA molecules in multiple cells by normalizing for cell morphology. While fast diffusing tRNA is not excluded from the bacterial nucleoid, slow diffusing tRNA is localized to the cell periphery (showing a 30% enrichment versus a uniform distribution), similar to non-uniform localizations previously observed for mRNA and ribosomes.
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Affiliation(s)
- Anne Plochowietz
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, OX1 3PU, Oxford, UK
| | - Ian Farrell
- Anima Inc, 75 Claremont Road, Suite 102, Bernardsville, NJ 07924-2270, USA.,Department of Chemistry, University of Pennsylvania, 231 S. 34 Street, Philadelphia, PA 19104-6323, USA
| | - Zeev Smilansky
- Anima Inc, 75 Claremont Road, Suite 102, Bernardsville, NJ 07924-2270, USA
| | - Barry S Cooperman
- Department of Chemistry, University of Pennsylvania, 231 S. 34 Street, Philadelphia, PA 19104-6323, USA
| | - Achillefs N Kapanidis
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, OX1 3PU, Oxford, UK
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10
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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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11
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Tu C, Santo L, Mishima Y, Raje N, Smilansky Z, Zoldan J. Monitoring protein synthesis in single live cancer cells. Integr Biol (Camb) 2016; 8:645-53. [PMID: 26956582 DOI: 10.1039/c5ib00279f] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Protein synthesis is generally under sophisticated and dynamic regulation to meet the ever-changing demands of a cell. Global up or down-regulation of protein synthesis and the shift of protein synthesis location (as shown, for example, during cellular stress or viral infection) are recognized as cellular responses to environmental changes such as nutrient/oxygen deprivation or to alterations such as pathological mutations in cancer cells. Monitoring protein synthesis in single live cells can be a powerful tool for cancer research. Here we employed a microfluidic platform to perform high throughput delivery of fluorescent labeled tRNAs into multiple myeloma cells with high transfection efficiency (∼45%) and high viability (>80%). We show that the delivered tRNAs were actively recruited to the ER for protein synthesis and that treatment with puromycin effectively disrupted this process. Interestingly, we observed the scattered distribution of tRNAs in cells undergoing mitosis, which has not been previously reported. Fluorescence lifetime analysis detected extensive FRET signals generated from tRNAs labeled as FRET pairs, further confirming that the delivered tRNAs were used by active ribosomes for protein translation. Our work demonstrates that the microfluidic delivery of FRET labeled tRNAs into living cancer cells can provide new insights into basic cancer metabolism and has the potential to serve as a platform for drug screening, diagnostics, or personalized medication.
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Affiliation(s)
- Chengyi Tu
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, USA.
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12
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Direct visualization of newly synthesized target proteins in situ. Nat Methods 2015; 12:411-4. [PMID: 25775042 DOI: 10.1038/nmeth.3319] [Citation(s) in RCA: 200] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 01/29/2015] [Indexed: 12/15/2022]
Abstract
Protein synthesis is a dynamic process that tunes the cellular proteome in response to internal and external demands. Metabolic labeling approaches identify the general proteomic response but cannot visualize specific newly synthesized proteins within cells. Here we describe a technique that couples noncanonical amino acid tagging or puromycylation with the proximity ligation assay to visualize specific newly synthesized proteins and monitor their origin, redistribution and turnover in situ.
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13
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Liu J, Pampillo M, Guo F, Liu S, Cooperman BS, Farrell I, Dahary D, Gan BS, O'Gorman DB, Smilansky Z, Babwah AV, Leask A. Monitoring collagen synthesis in fibroblasts using fluorescently labeled tRNA pairs. J Cell Physiol 2014; 229:1121-9. [PMID: 24676899 DOI: 10.1002/jcp.24630] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Accepted: 03/24/2014] [Indexed: 12/13/2022]
Abstract
There is a critical need for techniques that directly monitor protein synthesis within cells isolated from normal and diseased tissue. Fibrotic disease, for which there is no drug treatment, is characterized by the overexpression of collagens. Here, we use a bioinformatics approach to identify a pair of glycine and proline isoacceptor tRNAs as being specific for the decoding of collagen mRNAs, leading to development of a FRET-based approach, dicodon monitoring of protein synthesis (DiCoMPS), that directly monitors the synthesis of collagen. DiCoMPS aimed at detecting collagen synthesis will be helpful in identifying novel anti-fibrotic compounds in cells derived from patients with fibrosis of any etiology, and, suitably adapted, should be widely applicable in monitoring the synthesis of other proteins in cells.
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Affiliation(s)
- Jiaqi Liu
- Department of Physiology and Pharmacology, University of Western Ontario, London, Ontario, Canada; Department of Burns and Cutaneous Surgery, Xijing Hospital, The Fourth Military Medical University, Xi'an, Shaanxi, China
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