Miller, O. L., Hamkalo, B. A. & Thomas, C. A. Visualization of bacterial genes in action. Science 169, 392–395 (1970).
Blaha, G. M. & Wade, J. T. Transcription–translation coupling in bacteria. Annu. Rev. Genet. 56, 187–205 (2022).
McGary, K. & Nudler, E. RNA polymerase and the ribosome: the close relationship. Curr. Opin. Microbiol. 16, 112–117 (2013).
Irastortza-Olaziregi, M. & Amster-Choder, O. Coupled transcription–translation in prokaryotes: an old couple with new surprises. Front. Microbiol. 11, 624830 (2020).
Burmann, B. M. et al. A NusE:NusG complex links transcription and translation. Science 328, 501–504 (2010).
Webster, M. W. et al. Structural basis of transcription-translation coupling and collision in bacteria. Science 369, 1355–1359 (2020).
Wang, C. et al. Structural basis of transcription-translation coupling. Science 369, 1359–1365 (2020).
O’Reilly, F. J. et al. In-cell architecture of an actively transcribing–translating expressome. Science 369, 554–557 (2020).
Kohler, R., Mooney, R. A., Mills, D. J., Landick, R. & Cramer, P. Architecture of a transcribing–translating expressome. Science 356, 194–197 (2017).
Wee, L. M. et al. A trailing ribosome speeds up RNA polymerase at the expense of transcript fidelity via force and allostery. Cell 186, 1244–1262.e1234 (2023).
Stevenson-Jones, F., Woodgate, J., Castro-Roa, D. & Zenkin, N. Ribosome reactivates transcription by physically pushing RNA polymerase out of transcription arrest. Proc. Natl Acad. Sci. USA 117, 8462–8467 (2020).
Proshkin, S., Rahmouni, A. R., Mironov, A. & Nudler, E. Cooperation between translating ribosomes and RNA polymerase in transcription elongation. Science 328, 504–508 (2010).
Zhu, M., Mori, M., Hwa, T. & Dai, X. Disruption of transcription–translation coordination in Escherichia coli leads to premature transcriptional termination. Nat. Microbiol. 4, 2347–2356 (2019).
Woodgate, J., Mosaei, H., Brazda, P., Stevenson-Jones, F. & Zenkin, N. Translation selectively destroys non-functional transcription complexes. Nature 626, 891–896 (2024).
Duss, O. et al. Real-time assembly of ribonucleoprotein complexes on nascent RNA transcripts. Nat. Commun. 9, 5087 (2018).
Dorywalska, M. et al. Site-specific labeling of the ribosome for single-molecule spectroscopy. Nucleic Acids Res. 33, 182–189 (2005).
Marshall, R. A., Dorywalska, M. & Puglisi, J. D. Irreversible chemical steps control intersubunit dynamics during translation. Proc. Natl Acad. Sci. USA 105, 15364–15369 (2008).
Chen, J., Tsai, A., O’Leary, S. E., Petrov, A. & Puglisi, J. D. Unraveling the dynamics of ribosome translocation. Curr. Opin. Struct. Biol. 22, 804–814 (2012).
Chen, J., Petrov, A., Tsai, A., O’Leary, S. E. & Puglisi, J. D. Coordinated conformational and compositional dynamics drive ribosome translocation. Nat. Struct. Mol. Biol. 20, 718–727 (2013).
Tsai, A. et al. Heterogeneous pathways and timing of factor departure during translation initiation. Nature 487, 390–393 (2012).
Prabhakar, A., Puglisi, E. V. & Puglisi, J. D. Single-molecule fluorescence applied to translation. Cold Spring Harb. Perspect. Biol. 11, a032714 (2019).
Das, A., Bao, C. & Ermolenko, D. N. Comparing FRET pairs that report on intersubunit rotation in bacterial ribosomes. J. Mol. Biol. 435, 168185 (2023).
Farewell, A. & Neidhardt, F. C. Effect of temperature on in vivo protein synthetic capacity in Escherichia coli. J. Bacteriol. 180, 4704–4710 (1998).
Zhu, M., Dai, X. & Wang, Y. P. Real time determination of bacterial in vivo ribosome translation elongation speed based on LacZα complementation system. Nucleic Acids Res. 44, e155 (2016).
Capece, M. C., Kornberg, G. L., Petrov, A. & Puglisi, J. D. A simple real-time assay for in vitro translation. RNA 21, 296–305 (2015).
Dangkulwanich, M., Ishibashi, T., Bintu, L. & Bustamante, C. Molecular mechanisms of transcription through single-molecule experiments. Chem. Rev. 114, 3203–3223 (2014).
Ryals, J., Little, R. & Bremer, H. Temperature dependence of RNA synthesis parameters in Escherichia coli. J. Bacteriol. 151, 879–887 (1982).
Aitken, C. E. & Puglisi, J. D. Following the intersubunit conformation of the ribosome during translation in real time. Nat. Struct. Mol. Biol. 17, 793–800 (2010).
Chen, J. et al. Coupling of mRNA structure rearrangement to ribosome movement during bypassing of non-coding regions. Cell 163, 1267–1280 (2015).
Wang, J. et al. Rapid 40S scanning and its regulation by mRNA structure during eukaryotic translation initiation. Cell 185, 1–14 (2022).
Yin, J. et al. Genetically encoded short peptide tag for versatile protein labeling by Sfp phosphopantetheinyl transferase. Proc. Natl Acad. Sci. USA 102, 15815–15820 (2005).
Kapanidis, A. N. et al. Alternating-laser excitation of single molecules. Acc. Chem. Res. 38, 523–533 (2005).
Wang, C., Molodtsov, V., Kaelber, J. T., Blaha, G. & Ebright, R. H. Structural basis of long-range transcription–translation coupling. Preprint at bioRxiv https://doi.org/10.1101/2024.07.20.604413 (2024).
Bailey, E. J., Gottesman, M. E. & Gonzalez, R. L. Jr NusG-mediated coupling of transcription and translation enhances gene expression by suppressing RNA polymerase backtracking. J. Mol. Biol. 434, 167330 (2022).
Kang, J. Y. et al. Structural basis for transcript elongation control by NusG family universal regulators. Cell 173, 1650–1662.e1614 (2018).
Washburn, R. S. et al. Escherichia coli NusG links the lead ribosome with the transcription elongation complex. iScience 23, 101352 (2020).
Webster, M. W. & Weixlbaumer, A. Macromolecular assemblies supporting transcription-translation coupling. Transcription 12, 103–125 (2021).
Burmann, B. M., Scheckenhofer, U., Schweimer, K. & Rosch, P. Domain interactions of the transcription–translation coupling factor Escherichia coli NusG are intermolecular and transient. Biochem. J 435, 783–789 (2011).
Weixlbaumer, A., Grunberger, F., Werner, F. & Grohmann, D. Coupling of transcription and translation in archaea: cues from the bacterial world. Front. Microbiol. 12, 661827 (2021).
Zhu, C. et al. Transcription factors modulate RNA polymerase conformational equilibrium. Nat. Commun. 13, 1546 (2022).
Ha, K. S., Toulokhonov, I., Vassylyev, D. G. & Landick, R. The NusA N-terminal domain is necessary and sufficient for enhancement of transcriptional pausing via interaction with the RNA exit channel of RNA polymerase. J. Mol. Biol. 401, 708–725 (2010).
Mooney, R. A., Schweimer, K., Rösch, P., Gottesman, M. & Landick, R. Two structurally independent domains of E. coli NusG create regulatory plasticity via distinct interactions with RNA polymerase and regulators. J. Mol. Biol. 391, 341–358 (2009).
Landick, R. Transcriptional pausing as a mediator of bacterial gene regulation. Annu. Rev. Microbiol. 75, 291–314 (2021).
Guo, X. et al. Structural basis for NusA stabilized transcriptional pausing. Mol. Cell 69, 816–827.e814 (2018).
Fan, H. et al. Transcription–translation coupling: direct interactions of RNA polymerase with ribosomes and ribosomal subunits. Nucleic Acids Res. 45, 11043–11055 (2017).
Chen, M. & Fredrick, K. Measures of single- versus multiple-round translation argue against a mechanism to ensure coupling of transcription and translation. Proc. Natl Acad. Sci. USA 115, 10774–10779 (2018).
Chen, M. & Fredrick, K. RNA polymerase’s relationship with the ribosome: not so physical, most of the time. J. Mol. Biol. 432, 3981–3986 (2020).
Johnson, G. E., Lalanne, J. B., Peters, M. L. & Li, G. W. Functionally uncoupled transcription-translation in Bacillus subtilis. Nature 585, 124–128 (2020).
Ochman, H. & Jones, I. B. Evolutionary dynamics of full genome content in Escherichia coli. EMBO J. 19, 6637–6643 (2000).
Molodtsov, V., Wang, C., Firlar, E., Kaelber, J. T. & Ebright, R. H. Structural basis of Rho-dependent transcription termination. Nature 614, 367–374 (2023).
Said, N. et al. Steps toward translocation-independent RNA polymerase inactivation by terminator ATPase ρ. Science 371, eabd1673 (2021).
Koslover, D. J., Fazal, F. M., Mooney, R. A., Landick, R. & Block, S. M. Binding and translocation of termination factor rho studied at the single-molecule level. J. Mol. Biol. 423, 664–676 (2012).
Qureshi, N. S. & Duss, O. Co-transcriptional assembly mechanisms of protein-RNA complexes. FEBS Lett. 597, 2599–2600 (2023).
Huang, Y. H. et al. Structure-based mechanisms of a molecular RNA polymerase/chaperone machine required for ribosome biosynthesis. Mol. Cell 79, 1024–1036.e1025 (2020).
Zhang, S. et al. Structure of a transcribing RNA polymerase II–U1 snRNP complex. Science 371, 305–309 (2021).
Meinnel, T. & Blanquet, S. Maturation of pre-tRNAfMet by Escherichia coli RNase P is specified by a guanosine of the 5′-flanking sequence. J. Biol. Chem. 270, 15908–15914 (1995).
Svetlov, V. & Artsimovitch, I. Purification of bacterial RNA polymerase: tools and protocols. Methods Mol. Biol. 1276, 13–29 (2015).
Yin, J., Lin, A. J., Golan, D. E. & Walsh, C. T. Site-specific protein labeling by Sfp phosphopantetheinyl transferase. Nat. Protoc. 1, 280–285 (2006).
Zhou, Z. et al. Genetically encoded short peptide tags for orthogonal protein labeling by Sfp and AcpS phosphopantetheinyl transferases. ACS Chem. Biol. 2, 337–346 (2007).
Mellot, P., Mechulam, Y., Le Corre, D., Blanquet, S. & Fayat, G. Identification of an amino acid region supporting specific methionyl-tRNA synthetase: tRNA recognition. J. Mol. Biol. 208, 429–443 (1989).
Kitagawa, M. et al. Complete set of ORF clones of Escherichia coli ASKA library (a complete set of E. coli K-12 ORF archive): unique resources for biological research. DNA Res. 12, 291–299 (2005).
Mechulam, Y., Guillon, L., Yatime, L., Blanquet, S. & Schmitt, E. Protection-based assays to measure aminoacyl-tRNA binding to translation initiation factors. Methods Enzymol. 430, 265–281 (2007).
Schmitt, E., Blanquet, S. & Mechulam, Y. Crystallization and preliminary X-ray analysis of Escherichia coli methionyl-tRNAMetf formyltransferase complexed with formyl-methionyl-tRNAMetf. Acta Crystallogr. D 55, 332–334 (1999).
Walker, S. E. & Fredrick, K. Preparation and evaluation of acylated tRNAs. Methods 44, 81–86 (2008).
Fritz, B. R. & Jewett, M. C. The impact of transcriptional tuning on in vitro integrated rRNA transcription and ribosome construction. Nucleic Acids Res. 42, 6774–6785 (2014).
Wang, J. et al. eIF5B gates the transition from translation initiation to elongation. Nature 573, 605–608 (2019).
Duss, O., Stepanyuk, G. A., Puglisi, J. D. & Williamson, J. R. Transient protein–RNA interactions guide nascent ribosomal RNA folding. Cell 179, 1357–1369 (2019).
Landick, R., Wang, D. & Chan, C. L. Quantitative analysis of transcriptional pausing by Escherichia coli RNA polymerase: his leader pause site as paradigm. Methods Enzymol. 274, 334–353 (1996).
Chandradoss, S. D. et al. Surface passivation for single-molecule protein studies. J. Vis. Exp. https://doi.org/10.3791/50549 (2014).
Blanchard, S. C., Kim, H. D., Gonzalez, R. L. Jr, Puglisi, J. D. & Chu, S. tRNA dynamics on the ribosome during translation. Proc. Natl Acad. Sci. USA 101, 12893–12898 (2004). a.
Blanchard, S. C., Gonzalez, R. L., Kim, H. D., Chu, S. & Puglisi, J. D. tRNA selection and kinetic proofreading in translation. Nat. Struct. Mol. Biol. 11, 1008–1014 (2004). b.
Juette, M. F. et al. Single-molecule imaging of non-equilibrium molecular ensembles on the millisecond timescale. Nat. Methods 13, 341–344 (2016).
Verma, A. R., Ray, K. K., Bodick, M., Kinz-Thompson, C. D. & Gonzalez, R. L. Jr Increasing the accuracy of single-molecule data analysis using tMAVEN. Biophys. J. 123, 2765–2780 (2024).
Lapointe, C. P. et al. eIF5B and eIF1A reorient initiator tRNA to allow ribosomal subunit joining. Nature 607, 185–190 (2022).
Duss, O., & Qureshi, N. Tracking transcription–translation coupling in real-time. Zenodo https://doi.org/10.5281/zenodo.13271669 (2024).
Demo, G. et al. Structure of RNA polymerase bound to ribosomal 30S subunit. eLife 6, e28560 (2017).
Greek Live Channels Όλα τα Ελληνικά κανάλια:
Βρίσκεστε μακριά από το σπίτι ή δεν έχετε πρόσβαση σε τηλεόραση;
Το IPTV σας επιτρέπει να παρακολουθείτε όλα τα Ελληνικά κανάλια και άλλο περιεχόμενο από οποιαδήποτε συσκευή συνδεδεμένη στο διαδίκτυο.
Αν θες πρόσβαση σε όλα τα Ελληνικά κανάλια
Πατήστε Εδώ
Ακολουθήστε το TechFreak.GR στο Google News για να μάθετε πρώτοι όλες τις ειδήσεις τεχνολογίας.
