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Article ; Online: Site-Specific Fluorescent Labeling of RNA Interior Positions.

Cooperman, Barry S

2021 Volume 26, Issue 5

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 ... ...

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.
MeSH term(s)	Animals ; Fluorescent Dyes/chemistry ; Humans ; Oligonucleotide Probes/chemistry ; Protein Processing, Post-Translational ; RNA/chemistry ; Staining and Labeling
Chemical Substances	Fluorescent Dyes ; Oligonucleotide Probes ; RNA (63231-63-0)
Language	English
Publishing date	2021-03-03
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	1413402-0
ISSN	1420-3049 ; 1431-5165 ; 1420-3049
ISSN (online)	1420-3049
ISSN	1431-5165 ; 1420-3049
DOI	10.3390/molecules26051341
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Article ; Online: A High-Throughput Assay for In Vitro Determination of Release Factor-Dependent Peptide Release from a Pretermination Complex by Fluorescence Anisotropy-Application to Nonsense Suppressor Screening and Mechanistic Studies.

Ghelfi, Mikel D / Bhat, Saleem Y / Li, Hong / Cooperman, Barry S

Biomolecules

2023 Volume 13, Issue 2

Abstract: Premature termination codons (PTCs) account for ~12% of all human disease mutations. Translation readthrough-inducing drugs (TRIDs) are prominent among the several therapeutic approaches being used to overcome PTCs. Ataluren is the only TRID that has ... ...

Abstract	Premature termination codons (PTCs) account for ~12% of all human disease mutations. Translation readthrough-inducing drugs (TRIDs) are prominent among the several therapeutic approaches being used to overcome PTCs. Ataluren is the only TRID that has been approved for treating patients suffering from a PTC disease, Duchenne muscular dystrophy, but it gives variable readthrough results in cells isolated from patients suffering from other PTC diseases. We recently elucidated ataluren's mechanism of action as a competitive inhibitor of release factor complex (RFC) catalysis of premature termination and identified ataluren's binding sites on the ribosome responsible for such an inhibition. These results suggest the possibility of discovering new TRIDs, which would retain ataluren's low toxicity while displaying greater potency and generality in stimulating readthrough via the inhibition of termination. Here we present a detailed description of a new in vitro plate reader assay that we are using both to screen small compound libraries for the inhibition of RFC-dependent peptide release and to better understand the influence of termination codon identity and sequence context on RFC activity.
MeSH term(s)	Humans ; Codon, Nonsense ; Codon, Terminator ; Protein Biosynthesis ; Mutation ; Peptides/metabolism
Chemical Substances	Codon, Nonsense ; Codon, Terminator ; Peptides
Language	English
Publishing date	2023-01-27
Publishing country	Switzerland
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2701262-1
ISSN	2218-273X ; 2218-273X
ISSN (online)	2218-273X
ISSN	2218-273X
DOI	10.3390/biom13020242
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Article ; Online: Ataluren and aminoglycosides stimulate read-through of nonsense codons by orthogonal mechanisms.

Ng, Martin Y / Li, Hong / Ghelfi, Mikel D / Goldman, Yale E / Cooperman, Barry S

Proceedings of the National Academy of Sciences of the United States of America

2021 Volume 118, Issue 2

Abstract: During protein synthesis, nonsense mutations, resulting in premature stop codons (PSCs), produce truncated, inactive protein products. Such defective gene products give rise to many diseases, including cystic fibrosis, Duchenne muscular dystrophy (DMD), ... ...

Abstract	During protein synthesis, nonsense mutations, resulting in premature stop codons (PSCs), produce truncated, inactive protein products. Such defective gene products give rise to many diseases, including cystic fibrosis, Duchenne muscular dystrophy (DMD), and some cancers. Small molecule nonsense suppressors, known as TRIDs (translational read-through-inducing drugs), stimulate stop codon read-through. The best characterized TRIDs are ataluren, which has been approved by the European Medicines Agency for the treatment of DMD, and G418, a structurally dissimilar aminoglycoside. Previously [1], we applied a highly purified in vitro eukaryotic translation system to demonstrate that both aminoglycosides like G418 and more hydrophobic molecules like ataluren stimulate read-through by direct interaction with the cell's protein synthesis machinery. Our results suggested that they might do so by different mechanisms. Here, we pursue this suggestion through a more-detailed investigation of ataluren and G418 effects on read-through. We find that ataluren stimulation of read-through derives exclusively from its ability to inhibit release factor activity. In contrast, G418 increases functional near-cognate tRNA mispairing with a PSC, resulting from binding to its tight site on the ribosome, with little if any effect on release factor activity. The low toxicity of ataluren suggests that development of new TRIDs exclusively directed toward inhibiting termination should be a priority in combatting PSC diseases. Our results also provide rate measurements of some of the elementary steps during the eukaryotic translation elongation cycle, allowing us to determine how these rates are modified when cognate tRNA is replaced by near-cognate tRNA ± TRIDs.
MeSH term(s)	Aminoglycosides/metabolism ; Aminoglycosides/pharmacology ; Animals ; Artemia/genetics ; Codon, Nonsense/drug effects ; Codon, Nonsense/metabolism ; Codon, Terminator/drug effects ; Codon, Terminator/metabolism ; Cystic Fibrosis/genetics ; Muscular Dystrophy, Duchenne/genetics ; Oxadiazoles/metabolism ; Oxadiazoles/pharmacology ; Peptide Chain Elongation, Translational/drug effects ; Protein Biosynthesis/drug effects ; Protein Synthesis Inhibitors ; RNA, Transfer/drug effects ; RNA, Transfer/genetics ; RNA, Transfer/metabolism ; Ribosomes/drug effects ; Saccharomyces/genetics
Chemical Substances	Aminoglycosides ; Codon, Nonsense ; Codon, Terminator ; Oxadiazoles ; Protein Synthesis Inhibitors ; RNA, Transfer (9014-25-9) ; ataluren (K16AME9I3V)
Language	English
Publishing date	2021-01-07
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.2020599118
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Article ; Online: Ataluren binds to multiple protein synthesis apparatus sites and competitively inhibits release factor-dependent termination.

Huang, Shijie / Bhattacharya, Arpan / Ghelfi, Mikel D / Li, Hong / Fritsch, Clark / Chenoweth, David M / Goldman, Yale E / Cooperman, Barry S

Nature communications

2022 Volume 13, Issue 1, Page(s) 2413

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 ... ...

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.
MeSH term(s)	Oxadiazoles/pharmacology ; Peptide Termination Factors/metabolism ; Protein Biosynthesis ; RNA, Transfer/metabolism ; Ribosomes/metabolism
Chemical Substances	Oxadiazoles ; Peptide Termination Factors ; RNA, Transfer (9014-25-9) ; ataluren (K16AME9I3V)
Language	English
Publishing date	2022-05-06
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-022-30080-6
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Article ; Online: Human mitochondria require mtRF1 for translation termination at non-canonical stop codons.

Krüger, Annika / Remes, Cristina / Shiriaev, Dmitrii Igorevich / Liu, Yong / Spåhr, Henrik / Wibom, Rolf / Atanassov, Ilian / Nguyen, Minh Duc / Cooperman, Barry S / Rorbach, Joanna

Nature communications

2023 Volume 14, Issue 1, Page(s) 30

Abstract: The mitochondrial translation machinery highly diverged from its bacterial counterpart. This includes deviation from the universal genetic code, with AGA and AGG codons lacking cognate tRNAs in human mitochondria. The locations of these codons at the end ...

Abstract	The mitochondrial translation machinery highly diverged from its bacterial counterpart. This includes deviation from the universal genetic code, with AGA and AGG codons lacking cognate tRNAs in human mitochondria. The locations of these codons at the end of COX1 and ND6 open reading frames, respectively, suggest they might function as stop codons. However, while the canonical stop codons UAA and UAG are known to be recognized by mtRF1a, the release mechanism at AGA and AGG codons remains a debated issue. Here, we show that upon the loss of another member of the mitochondrial release factor family, mtRF1, mitoribosomes accumulate specifically at AGA and AGG codons. Stalling of mitoribosomes alters COX1 transcript and protein levels, but not ND6 synthesis. In addition, using an in vitro reconstituted mitochondrial translation system, we demonstrate the specific peptide release activity of mtRF1 at the AGA and AGG codons. Together, our results reveal the role of mtRF1 in translation termination at non-canonical stop codons in mitochondria.
MeSH term(s)	Humans ; Codon, Terminator/metabolism ; Mitochondria/metabolism ; Peptide Termination Factors/metabolism ; Protein Biosynthesis ; Ribosomes/metabolism
Chemical Substances	Codon, Terminator ; Peptide Termination Factors ; MTRF1L protein, human
Language	English
Publishing date	2023-01-03
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-022-35684-6
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Article ; Online: Engine out of the chassis: cell-free protein synthesis and its uses.

Rosenblum, Gabriel / Cooperman, Barry S

FEBS letters

2013 Volume 588, Issue 2, Page(s) 261–268

Abstract: The translation machinery is the engine of life. Extracting the cytoplasmic milieu from a cell affords a lysate capable of producing proteins in concentrations reaching to tens of micromolar. Such lysates, derivable from a variety of cells, allow the ... ...

Abstract	The translation machinery is the engine of life. Extracting the cytoplasmic milieu from a cell affords a lysate capable of producing proteins in concentrations reaching to tens of micromolar. Such lysates, derivable from a variety of cells, allow the facile addition and subtraction of components that are directly or indirectly related to the translation machinery and/or the over-expressed protein. The flexible nature of such cell-free expression systems, when coupled with high throughput monitoring, can be especially suitable for protein engineering studies, allowing one to bypass multiple steps typically required using conventional in vivo protein expression.
MeSH term(s)	Animals ; Cell-Free System/metabolism ; Genetic Engineering/methods ; Humans ; Protein Biosynthesis
Language	English
Publishing date	2013-10-22
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	212746-5
ISSN	1873-3468 ; 0014-5793
ISSN (online)	1873-3468
ISSN	0014-5793
DOI	10.1016/j.febslet.2013.10.016
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Article ; Online: The kinetic mechanism of bacterial ribosome recycling.

Chen, Yuanwei / Kaji, Akira / Kaji, Hideko / Cooperman, Barry S

Nucleic acids research

2017 Volume 45, Issue 17, Page(s) 10168–10177

Abstract: Bacterial ribosome recycling requires breakdown of the post-termination complex (PoTC), comprising a messenger RNA (mRNA) and an uncharged transfer RNA (tRNA) cognate to the terminal mRNA codon bound to the 70S ribosome. The translation factors, ... ...

Abstract	Bacterial ribosome recycling requires breakdown of the post-termination complex (PoTC), comprising a messenger RNA (mRNA) and an uncharged transfer RNA (tRNA) cognate to the terminal mRNA codon bound to the 70S ribosome. The translation factors, elongation factor G and ribosome recycling factor, are known to be required for recycling, but there is controversy concerning whether these factors act primarily to effect the release of mRNA and tRNA from the ribosome, with the splitting of the ribosome into subunits being somewhat dispensable, or whether their main function is to catalyze the splitting reaction, which necessarily precedes mRNA and tRNA release. Here, we utilize three assays directly measuring the rates of mRNA and tRNA release and of ribosome splitting in several model PoTCs. Our results largely reconcile these previously held views. We demonstrate that, in the absence of an upstream Shine-Dalgarno (SD) sequence, PoTC breakdown proceeds in the order: mRNA release followed by tRNA release and then by 70S splitting. By contrast, in the presence of an SD sequence all three processes proceed with identical apparent rates, with the splitting step likely being rate-determining. Our results are consistent with ribosome profiling results demonstrating the influence of upstream SD-like sequences on ribosome occupancy at or just before the mRNA stop codon.
Language	English
Publishing date	2017-09-29
Publishing country	England
Document type	Journal Article
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkx694
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Article ; Online: Cytosolic and mitochondrial translation elongation are coordinated through the molecular chaperone TRAP1 for the synthesis and import of mitochondrial proteins.

Avolio, Rosario / Agliarulo, Ilenia / Criscuolo, Daniela / Sarnataro, Daniela / Auriemma, Margherita / De Lella, Sabrina / Pennacchio, Sara / Calice, Giovanni / Ng, Martin Y / Giorgi, Carlotta / Pinton, Paolo / Cooperman, Barry S / Landriscina, Matteo / Esposito, Franca / Matassa, Danilo Swann

Genome research

2023 Volume 33, Issue 8, Page(s) 1242–1257

Abstract: A complex interplay between mRNA translation and cellular respiration has been recently unveiled, but its regulation in humans is poorly characterized in either health or disease. Cancer cells radically reshape both biosynthetic and bioenergetic pathways ...

Abstract	A complex interplay between mRNA translation and cellular respiration has been recently unveiled, but its regulation in humans is poorly characterized in either health or disease. Cancer cells radically reshape both biosynthetic and bioenergetic pathways to sustain their aberrant growth rates. In this regard, we have shown that the molecular chaperone TRAP1 not only regulates the activity of respiratory complexes, behaving alternatively as an oncogene or a tumor suppressor, but also plays a concomitant moonlighting function in mRNA translation regulation. Herein, we identify the molecular mechanisms involved, showing that TRAP1 (1) binds both mitochondrial and cytosolic ribosomes, as well as translation elongation factors; (2) slows down translation elongation rate; and (3) favors localized translation in the proximity of mitochondria. We also provide evidence that TRAP1 is coexpressed in human tissues with the mitochondrial translational machinery, which is responsible for the synthesis of respiratory complex proteins. Altogether, our results show an unprecedented level of complexity in the regulation of cancer cell metabolism, strongly suggesting the existence of a tight feedback loop between protein synthesis and energy metabolism, based on the demonstration that a single molecular chaperone plays a role in both mitochondrial and cytosolic translation, as well as in mitochondrial respiration.
MeSH term(s)	Humans ; HSP90 Heat-Shock Proteins/genetics ; HSP90 Heat-Shock Proteins/metabolism ; Mitochondrial Proteins/genetics ; Mitochondrial Proteins/metabolism ; Molecular Chaperones/genetics ; Molecular Chaperones/metabolism ; Neoplasms/genetics ; Neoplasms/metabolism ; Neoplasms/pathology ; Protein Biosynthesis/genetics ; Protein Biosynthesis/physiology ; Ribosomes/genetics ; Ribosomes/metabolism ; Peptide Chain Elongation, Translational/genetics ; Peptide Chain Elongation, Translational/physiology ; Mitochondria/genetics ; Mitochondria/metabolism
Chemical Substances	HSP90 Heat-Shock Proteins ; Mitochondrial Proteins ; Molecular Chaperones ; TRAP1 protein, human
Language	English
Publishing date	2023-07-24
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1284872-4
ISSN	1549-5469 ; 1088-9051 ; 1054-9803
ISSN (online)	1549-5469
ISSN	1088-9051 ; 1054-9803
DOI	10.1101/gr.277755.123
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Zs.A 3729: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
Zs.MG 8: Show issues

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Article ; Online: tRNA Fluctuations Observed on Stalled Ribosomes Are Suppressed during Ongoing Protein Synthesis.

Jamiolkowski, Ryan M / Chen, Chunlai / Cooperman, Barry S / Goldman, Yale E

Biophysical journal

2017 Volume 113, Issue 11, Page(s) 2326–2335

Abstract: The pretranslocation complex of the ribosome can undergo spontaneous fluctuations of messenger RNA and transfer RNAs (tRNAs) between classical and hybrid states, and occupation of the hybrid tRNA positions has been proposed to precede translocation. The ... ...

Abstract	The pretranslocation complex of the ribosome can undergo spontaneous fluctuations of messenger RNA and transfer RNAs (tRNAs) between classical and hybrid states, and occupation of the hybrid tRNA positions has been proposed to precede translocation. The classical and hybrid state tRNA positions have been extensively characterized when the ribosome is stalled along the messenger RNA by either the absence or delayed addition of elongation factor G (EF-G), or by the presence of antibiotics or GTP analogs that block translocation. However, during multiple ongoing elongation cycles when both EF-G and ternary complexes are present, EF-G can bind to the pretranslocation complex much faster than the timescale of the classic-hybrid transitions. Using single-molecule fluorescence resonance energy transfer between adjacent tRNAs and between A-site tRNA and ribosomal protein L11, we found that the tRNAs do not fluctuate between the hybrid and classical states, but instead adopt a position with fluorescence resonance energy transfer efficiencies between those of the stalled classical and hybrid states.
MeSH term(s)	Fluorescence Resonance Energy Transfer ; Peptide Elongation Factor G/metabolism ; Protein Biosynthesis ; RNA, Transfer/genetics ; Ribosomal Proteins/metabolism ; Ribosomes/genetics ; Ribosomes/metabolism
Chemical Substances	Peptide Elongation Factor G ; Ribosomal Proteins ; ribosomal protein L11 ; RNA, Transfer (9014-25-9)
Language	English
Publishing date	2017-12-05
Publishing country	United States
Document type	Journal Article
ZDB-ID	218078-9
ISSN	1542-0086 ; 0006-3495
ISSN (online)	1542-0086
ISSN	0006-3495
DOI	10.1016/j.bpj.2017.08.052
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Zs.A 235: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
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Article ; Online: Structural dynamics of translation elongation factor Tu during aa-tRNA delivery to the ribosome.

Kavaliauskas, Darius / Chen, Chunlai / Liu, Wei / Cooperman, Barry S / Goldman, Yale E / Knudsen, Charlotte R

Nucleic acids research

2018 Volume 46, Issue 16, Page(s) 8651–8661

Abstract: The GTPase elongation factor EF-Tu delivers aminoacyl-tRNAs to the mRNA-programmed ribosome during translation. Cognate codon-anticodon interaction stimulates GTP hydrolysis within EF-Tu. It has been proposed that EF-Tu undergoes a large conformational ... ...

Abstract	The GTPase elongation factor EF-Tu delivers aminoacyl-tRNAs to the mRNA-programmed ribosome during translation. Cognate codon-anticodon interaction stimulates GTP hydrolysis within EF-Tu. It has been proposed that EF-Tu undergoes a large conformational change subsequent to GTP hydrolysis, which results in the accommodation of aminoacyl-tRNA into the ribosomal A-site. However, this proposal has never been tested directly. Here, we apply single-molecule total internal reflection fluorescence microscopy to study the conformational dynamics of EF-Tu when bound to the ribosome. Our studies show that GTP hydrolysis initiates a partial, comparatively small conformational change of EF-Tu on the ribosome, not directly along the path from the solution 'GTP' to the 'GDP' structure. The final motion is completed either concomitant with or following dissociation of EF-Tu from the ribosome. The structural transition of EF-Tu on the ribosome is slower when aa-tRNA binds to a cognate versus a near-cognate codon. The resulting longer residence time of EF-Tu on the ribosome may be important for promoting accommodation of the cognate aminoacyl-tRNA into the A-site.
MeSH term(s)	Anticodon/genetics ; Codon/genetics ; Escherichia coli/genetics ; GTP Phosphohydrolases/chemistry ; GTP Phosphohydrolases/genetics ; Guanosine Diphosphate/chemistry ; Guanosine Triphosphate/chemistry ; Hydrolysis ; Kinetics ; Peptide Elongation Factor Tu/chemistry ; Peptide Elongation Factor Tu/genetics ; Protein Biosynthesis/genetics ; Protein Conformation ; RNA, Messenger/chemistry ; RNA, Messenger/genetics ; RNA, Transfer, Amino Acyl/chemistry ; RNA, Transfer, Amino Acyl/genetics ; Ribosomes/chemistry ; Ribosomes/genetics
Chemical Substances	Anticodon ; Codon ; RNA, Messenger ; RNA, Transfer, Amino Acyl ; Guanosine Diphosphate (146-91-8) ; Guanosine Triphosphate (86-01-1) ; GTP Phosphohydrolases (EC 3.6.1.-) ; Peptide Elongation Factor Tu (EC 3.6.1.-)
Language	English
Publishing date	2018-08-11
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gky651
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