1
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Arseniev A, Panfilov M, Pobegalov G, Potyseva A, Pavlinova P, Yakunina M, Lee J, Borukhov S, Severinov K, Khodorkovskii M. Single-molecule studies reveal the off-pathway early paused state intermediates as a target of streptolydigin inhibition of RNA polymerase and its dramatic enhancement by Gre factors. Nucleic Acids Res 2025; 53:gkae1135. [PMID: 39656915 PMCID: PMC11724273 DOI: 10.1093/nar/gkae1135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 10/21/2024] [Accepted: 11/08/2024] [Indexed: 12/17/2024] Open
Abstract
Antibiotic streptolydigin (Stl) inhibits bacterial transcription by blocking the trigger loop folding in the active center of RNA polymerase (RNAP), which is essential for catalysis. We use acoustic force spectroscopy to characterize the dynamics of transcription elongation in ternary elongation complexes (ECs) of RNAP in the presence of Stl at a single-molecule level. We found that Stl induces long-lived stochastic pauses while the instantaneous velocity of transcription between the pauses is unaffected. Stl enhances the short-lived pauses associated with an off-pathway early paused state intermediates of the RNAP nucleotide addition cycle. Unexpectedly, we found that transcript cleavage factors GreA and GreB, which were thought to be Stl competitors, do not alleviate the Stl-induced pausing; instead, they synergistically increase transcription inhibition by Stl. This is the first known instance of a transcriptional factor enhancing antibiotic activity. We propose a structural model of the EC-Gre-Stl complex that explains the observed Stl activities and provides insight into possible cooperative action of secondary channel factors and other antibiotics binding at the Stl pocket. These results offer a new strategy for high-throughput screening for prospective antibacterial agents.
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Affiliation(s)
- Anatolii Arseniev
- Peter the Great St. Petersburg Polytechnic University, Research Center of Nanobiotechnologies, Polytechnicheskaya, 29 B, Saint Petersburg, 195251,Russia
- Institute of Molecular Genetics, Russian Academy of Sciences, Kurchatov Sq., 2, Moscow, 123182, Russia
| | - Mikhail Panfilov
- Peter the Great St. Petersburg Polytechnic University, Research Center of Nanobiotechnologies, Polytechnicheskaya, 29 B, Saint Petersburg, 195251,Russia
| | - Georgii Pobegalov
- Department of Physics and Astronomy, University College London, Gower street, London, WC1E 6BT, UK
| | - Alina Potyseva
- Peter the Great St. Petersburg Polytechnic University, Research Center of Nanobiotechnologies, Polytechnicheskaya, 29 B, Saint Petersburg, 195251,Russia
| | - Polina Pavlinova
- Peter the Great St. Petersburg Polytechnic University, Research Center of Nanobiotechnologies, Polytechnicheskaya, 29 B, Saint Petersburg, 195251,Russia
| | - Maria Yakunina
- Peter the Great St. Petersburg Polytechnic University, Research Center of Nanobiotechnologies, Polytechnicheskaya, 29 B, Saint Petersburg, 195251,Russia
| | - Jookyung Lee
- Department of Cell Biology and Neuroscience, Rowan University School of Osteopathic Medicine, 2 Medical Center Drive, Stratford, NJ 08084-1489, USA
| | - Sergei Borukhov
- Department of Cell Biology and Neuroscience, Rowan University School of Osteopathic Medicine, 2 Medical Center Drive, Stratford, NJ 08084-1489, USA
| | - Konstantin Severinov
- Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilova Street, Moscow, 119334, Russia
| | - Mikhail Khodorkovskii
- Peter the Great St. Petersburg Polytechnic University, Research Center of Nanobiotechnologies, Polytechnicheskaya, 29 B, Saint Petersburg, 195251,Russia
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2
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Cashen BA, Naufer MN, Morse M, McCauley MJ, Rouzina I, Jones CE, Furano AV, Williams MC. L1-ORF1p nucleoprotein can rapidly assume distinct conformations and simultaneously bind more than one nucleic acid. Nucleic Acids Res 2024; 52:14013-14029. [PMID: 39565204 DOI: 10.1093/nar/gkae1141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Revised: 10/22/2024] [Accepted: 10/31/2024] [Indexed: 11/21/2024] Open
Abstract
LINE-1 (L1) is a parasitic retrotransposable DNA element, active in primates for the last 80-120 Myr. L1 has generated nearly one-third of the human genome by copying its transcripts, and those of other genetic elements (e.g. Alu and SVA), into genomic DNA by target site-primed reverse transcription (TPRT) and remains active in modern humans. L1 encodes two proteins that bind their encoding transcript (cis preference) to form an L1 ribonucleoprotein (RNP) that mediates retrotransposition. ORF2p provides reverse transcriptase and endonuclease activity. ORF1p, its major component, is a homo-trimeric phospho-protein that binds single-stranded nucleic acid (ssNA) with high affinity and exhibits nucleic acid (NA) chaperone activity. We used optical tweezers to examine ORF1p binding to individual single-stranded DNA (ssDNA) molecules and found that the arrangement of ORF1p on the ssDNA depends on their molar ratio. When the concentration of ORF1p is just sufficient to saturate the entire NA molecule, the nucleoprotein (NP) is compact and stable. However, additional ORF1p binds and destabilizes the compacted NP, allowing it to engage a second ssDNA. Our results suggest that ORF1p displaced from its RNA template during TPRT could bind and destabilize remaining downstream L1 RNP, making them susceptible to hijacking by non-L1 templates, and thereby enable retrotransposition of non-L1 transcripts.
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Affiliation(s)
- Ben A Cashen
- Northeastern University, Department of Physics, 360 Huntington Avenue, Boston, MA 02115, USA
| | - M Nabuan Naufer
- Northeastern University, Department of Physics, 360 Huntington Avenue, Boston, MA 02115, USA
| | - Michael Morse
- Northeastern University, Department of Physics, 360 Huntington Avenue, Boston, MA 02115, USA
| | - Micah J McCauley
- Northeastern University, Department of Physics, 360 Huntington Avenue, Boston, MA 02115, USA
| | - Ioulia Rouzina
- Ohio State University, Department of Chemistry and Biochemistry, Center for Retroviral Research and Center for RNA Biology, 281 W Lane Avenue, Columbus, OH 43210, USA
| | - Charles E Jones
- The Laboratory of Molecular and Cellular Biology, NIDDK, NIH, 8 Center Drive, Bethesda, MD 20892, USA
| | - Anthony V Furano
- The Laboratory of Molecular and Cellular Biology, NIDDK, NIH, 8 Center Drive, Bethesda, MD 20892, USA
| | - Mark C Williams
- Northeastern University, Department of Physics, 360 Huntington Avenue, Boston, MA 02115, USA
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3
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Walbrun A, Wang T, Matthies M, Šulc P, Simmel FC, Rief M. Single-molecule force spectroscopy of toehold-mediated strand displacement. Nat Commun 2024; 15:7564. [PMID: 39217165 PMCID: PMC11365964 DOI: 10.1038/s41467-024-51813-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 08/16/2024] [Indexed: 09/04/2024] Open
Abstract
Toehold-mediated strand displacement (TMSD) is extensively utilized in dynamic DNA nanotechnology and for a wide range of DNA or RNA-based reaction circuits. Investigation of TMSD kinetics typically relies on bulk fluorescence measurements providing effective, bulk-averaged reaction rates. Information on individual molecules or even base pairs is scarce. In this work, we explore the dynamics of strand displacement processes at the single-molecule level using single-molecule force spectroscopy with a microfluidics-enhanced optical trap supported by state-of-the-art coarse-grained simulations. By applying force, we can trigger and observe TMSD in real-time with microsecond and nanometer resolution. We find TMSD proceeds very rapidly under load with single step times of 1 µs. Tuning invasion efficiency by introducing mismatches allows studying thousands of forward/backward invasion events on a single molecule and analyze the kinetics of the invasion process. Extrapolation to zero force reveals single step times for DNA invading DNA four times faster than for RNA invading RNA. We also study the kinetics of DNA invading RNA, a process that in the absence of force would rarely occur. Our results reveal the importance of sequence effects for the TMSD process and have relevance for a wide range of applications in nucleic acid nanotechnology and synthetic biology.
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Affiliation(s)
- Andreas Walbrun
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Center for Functional Protein Assemblies (CPA), Garching, Germany
| | - Tianhe Wang
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Garching, Germany
| | - Michael Matthies
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Garching, Germany
| | - Petr Šulc
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Garching, Germany
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Friedrich C Simmel
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Garching, Germany.
| | - Matthias Rief
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Center for Functional Protein Assemblies (CPA), Garching, Germany.
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4
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Qian J, Wang B, Artsimovitch I, Dunlap D, Finzi L. Force and the α-C-terminal domains bias RNA polymerase recycling. Nat Commun 2024; 15:7520. [PMID: 39214958 PMCID: PMC11364550 DOI: 10.1038/s41467-024-51603-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Accepted: 08/13/2024] [Indexed: 09/04/2024] Open
Abstract
After an RNA polymerase reaches a terminator, instead of dissociating from the template, it may diffuse along the DNA and recommence RNA synthesis from the previous or a different promoter. Magnetic tweezers were used to monitor such secondary transcription and determine the effects of low forces assisting or opposing translocation, protein roadblocks, and transcription factors. Remarkably, up to 50% of Escherichia coli (E. coli) RNA polymerases diffused along the DNA after termination. Force biased the direction of diffusion (sliding) and the velocity increased rapidly with force up to 0.7 pN and much more slowly thereafter. Sigma factor 70 (σ70) likely remained associated with the DNA promoting sliding and enabling re-initiation from promoters in either orientation. However, deletions of the α-C-terminal domains severely limited the ability of RNAP to turn around between successive rounds of transcription. The addition of elongation factor NusG, which competes with σ70 for binding to RNAP, limited additional rounds of transcription. Surprisingly, sliding RNA polymerases blocked by a DNA-bound lac repressor could slowly re-initiate transcription and were not affected by NusG, suggesting a σ-independent pathway. Low forces effectively biased promoter selection suggesting a prominent role for topological entanglements that affect RNA polymerase translocation.
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Affiliation(s)
- Jin Qian
- Physics Department, Emory University, Atlanta, GA, USA
| | - Bing Wang
- The Center for RNA Biology and Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | - Irina Artsimovitch
- The Center for RNA Biology and Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | - David Dunlap
- Department of Physics & Astronomy, Clemson University, Clemson, SC, USA
| | - Laura Finzi
- Department of Physics & Astronomy, Clemson University, Clemson, SC, USA.
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5
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Cashen BA, Morse M, Rouzina I, Karpel RL, Williams MC. C-terminal Domain of T4 gene 32 Protein Enables Rapid Filament Reorganization and Dissociation. J Mol Biol 2024; 436:168544. [PMID: 38508303 DOI: 10.1016/j.jmb.2024.168544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 02/27/2024] [Accepted: 03/14/2024] [Indexed: 03/22/2024]
Abstract
Bacteriophage T4 gene 32 protein (gp32) is a single-stranded DNA (ssDNA) binding protein essential for DNA replication. gp32 forms stable protein filaments on ssDNA through cooperative interactions between its core and N-terminal domain. gp32's C-terminal domain (CTD) is believed to primarily help coordinate DNA replication via direct interactions with constituents of the replisome. However, the exact mechanisms of these interactions are not known, and it is unclear how tightly-bound gp32 filaments are readily displaced from ssDNA as required for genomic processing. Here, we utilized truncated gp32 variants to demonstrate a key role of the CTD in regulating gp32 dissociation. Using optical tweezers, we probed the binding and dissociation dynamics of CTD-truncated gp32, *I, to an 8.1 knt ssDNA molecule and compared these measurements with those for full-length gp32. The *I-ssDNA helical filament becomes progressively unwound with increased protein concentration but remains significantly more stable than that of full-length, wild-type gp32. Protein oversaturation, concomitant with filament unwinding, facilitates rapid dissociation of full-length gp32 from across the entire ssDNA segment. In contrast, *I primarily unbinds slowly from only the ends of the cooperative clusters, regardless of the protein density and degree of DNA unwinding. Our results suggest that the CTD may constrain the relative twist angle of proteins within the ssDNA filament such that upon critical unwinding the cooperative interprotein interactions largely vanish, facilitating prompt removal of gp32. We propose a model of CTD-mediated gp32 displacement via internal restructuring of its filament, providing a mechanism for rapid ssDNA clearing during genomic processing.
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Affiliation(s)
- Ben A Cashen
- Department of Physics, Northeastern University, 360 Huntington Avenue, Boston, MA 02115, USA
| | - Michael Morse
- Department of Physics, Northeastern University, 360 Huntington Avenue, Boston, MA 02115, USA
| | - Ioulia Rouzina
- Department of Chemistry and Biochemistry, Center for Retroviral Research and Center for RNA Biology, Ohio State University, 281 W Lane Avenue, Columbus, OH 43210, USA
| | - Richard L Karpel
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA
| | - Mark C Williams
- Department of Physics, Northeastern University, 360 Huntington Avenue, Boston, MA 02115, USA.
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6
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Malinowska AM, van Mameren J, Peterman EJG, Wuite GJL, Heller I. Introduction to Optical Tweezers: Background, System Designs, and Applications. Methods Mol Biol 2024; 2694:3-28. [PMID: 37823997 DOI: 10.1007/978-1-0716-3377-9_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
Optical tweezers are a means to manipulate objects with light. With the technique, microscopically small objects can be held and steered, allowing for accurate measurement of the forces applied to these objects. Optical tweezers can typically obtain a nanometer spatial resolution, a picoNewton force resolution, and a millisecond time resolution, which makes the technique well suited for the study of biological processes from the single-cell down to the single-molecule level. In this chapter, we aim to provide an introduction to the use of optical tweezers for single-molecule analyses. We start from the basic principles and methodology involved in optical trapping, force calibration, and force measurements. Next, we describe the components of an optical tweezers setup and their experimental relevance. Finally, we will provide an overview of the broad applications in context of biological research, with the emphasis on the measurement modes, experimental assays, and possible combinations with fluorescence microscopy techniques.
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Affiliation(s)
- Agata M Malinowska
- LaserLaB Amsterdam and Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Joost van Mameren
- Institute of Physics, University of Amsterdam, Amsterdam, The Netherlands
| | - Erwin J G Peterman
- LaserLaB Amsterdam and Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Gijs J L Wuite
- LaserLaB Amsterdam and Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Iddo Heller
- LaserLaB Amsterdam and Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
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7
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Tare P, Bhowmick T, Katagi G, China A, Nagaraja V. Comparison of Transcription Elongation Rates of Three RNA Polymerases in Real Time. ACS OMEGA 2023; 8:47510-47519. [PMID: 38144119 PMCID: PMC10733919 DOI: 10.1021/acsomega.3c04754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 09/11/2023] [Indexed: 12/26/2023]
Abstract
RNA polymerases (RNAPs) across the bacterial kingdom have retained a conserved structure and function. In spite of the remarkable similarity of the enzyme in different bacteria, a wide variation is found in the promoter-polymerase interaction, transcription initiation, and termination. However, the transcription elongation was considered to be a monotonic process, although the rate of elongation could vary in different bacteria. Such variations in RNAP elongation rates could be important to fine-tune the transcription, which in turn would influence cellular metabolism and growth rates. Here, we describe a quantitative study to measure the transcription rates for the RNAPs from three bacteria, namely, Mycobacterium tuberculosis, Mycobacterium smegmatis, and Escherichia coli, which exhibit different growth kinetics. The RNA synthesis rates of the RNAPs were calculated from the real-time elongation kinetic profile using surface plasmon resonance through a computational flux flow model. The computational model revealed the modular process of elongation, with different rate profiles for the three RNAPs. Notably, the transcription elongation rates of these RNAPs followed the trend in the growth rates of these bacteria.
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Affiliation(s)
- Priyanka Tare
- Department
of Microbiology and Cell Biology, Indian
Institute of Science, Bangalore 560012, India
| | - Tuhin Bhowmick
- Department
of Physics, Indian Institute of Science, Bangalore 560012, India
- Centre
for Cellular and Molecular Platforms, NCBS-TIFR, Pandorum Technologies Pvt. Ltd., Bangalore 560065, India
| | - Gurunath Katagi
- Centre
for Cellular and Molecular Platforms, NCBS-TIFR, Pandorum Technologies Pvt. Ltd., Bangalore 560065, India
| | - Arnab China
- Department
of Microbiology and Cell Biology, Indian
Institute of Science, Bangalore 560012, India
| | - Valakunja Nagaraja
- Department
of Microbiology and Cell Biology, Indian
Institute of Science, Bangalore 560012, India
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8
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Arseniev A, Panfilov M, Pobegalov G, Potyseva A, Pavlinova P, Yakunina M, Lee J, Borukhov S, Severinov K, Khodorkovskii M. Single-molecule studies reveal the off-pathway elemental pause state as a target of streptolydigin inhibition of RNA polymerase and its dramatic enhancement by Gre factors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.05.542125. [PMID: 37333075 PMCID: PMC10274647 DOI: 10.1101/2023.06.05.542125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Antibiotic streptolydigin (Stl) inhibits bacterial transcription by blocking the trigger loop folding in the active center of RNA polymerase (RNAP), which is essential for catalysis. We use acoustic force spectroscopy to characterize the dynamics of transcription elongation in ternary elongation complexes of RNAP (ECs) in the presence of Stl at a single-molecule level. We found that Stl induces long-lived stochastic pauses while the instantaneous velocity of transcription between the pauses is unaffected. Stl enhances the short-lived pauses associated with an off-pathway elemental paused state of the RNAP nucleotide addition cycle. Unexpectedly, we found that transcript cleavage factors GreA and GreB, which were thought to be Stl competitors, do not alleviate the streptolydigin-induced pausing; instead, they synergistically increase transcription inhibition by Stl. This is the first known instance of a transcriptional factor enhancing antibiotic activity. We propose a structural model of the EC-Gre-Stl complex that explains the observed Stl activities and provides insight into possible cooperative action of secondary channel factors and other antibiotics binding at the Stl-pocket. These results offer a new strategy for high-throughput screening for prospective antibacterial agents.
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Affiliation(s)
- Anatolii Arseniev
- Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, Russia
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russian Federation
| | - Mikhail Panfilov
- Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, Russia
| | - Georgii Pobegalov
- Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, Russia
| | - Alina Potyseva
- Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, Russia
| | - Polina Pavlinova
- Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, Russia
| | - Maria Yakunina
- Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, Russia
| | - Jookyung Lee
- Department of Cell Biology and Neuroscience, Rowan University School of Osteopathic Medicine, Stratford, NJ 08084-1489, USA
| | - Sergei Borukhov
- Department of Cell Biology and Neuroscience, Rowan University School of Osteopathic Medicine, Stratford, NJ 08084-1489, USA
| | - Konstantin Severinov
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
- Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ, United States
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9
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Huang D, Johnson AE, Sim BS, Lo TW, Merrikh H, Wiggins PA. The in vivo measurement of replication fork velocity and pausing by lag-time analysis. Nat Commun 2023; 14:1762. [PMID: 36997519 PMCID: PMC10063678 DOI: 10.1038/s41467-023-37456-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 03/17/2023] [Indexed: 03/31/2023] Open
Abstract
AbstractAn important step towards understanding the mechanistic basis of the central dogma is the quantitative characterization of the dynamics of nucleic-acid-bound molecular motors in the context of the living cell. To capture these dynamics, we develop lag-time analysis, a method for measuring in vivo dynamics. Using this approach, we provide quantitative locus-specific measurements of fork velocity, in units of kilobases per second, as well as replisome pause durations, some with the precision of seconds. The measured fork velocity is observed to be both locus and time dependent, even in wild-type cells. In this work, we quantitatively characterize known phenomena, detect brief, locus-specific pauses at ribosomal DNA loci in wild-type cells, and observe temporal fork velocity oscillations in three highly-divergent bacterial species.
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10
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Wee LM, Tong AB, Florez Ariza AJ, Cañari-Chumpitaz C, Grob P, Nogales E, Bustamante CJ. A trailing ribosome speeds up RNA polymerase at the expense of transcript fidelity via force and allostery. Cell 2023; 186:1244-1262.e34. [PMID: 36931247 PMCID: PMC10135430 DOI: 10.1016/j.cell.2023.02.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 11/14/2022] [Accepted: 02/06/2023] [Indexed: 03/18/2023]
Abstract
In prokaryotes, translation can occur on mRNA that is being transcribed in a process called coupling. How the ribosome affects the RNA polymerase (RNAP) during coupling is not well understood. Here, we reconstituted the E. coli coupling system and demonstrated that the ribosome can prevent pausing and termination of RNAP and double the overall transcription rate at the expense of fidelity. Moreover, we monitored single RNAPs coupled to ribosomes and show that coupling increases the pause-free velocity of the polymerase and that a mechanical assisting force is sufficient to explain the majority of the effects of coupling. Also, by cryo-EM, we observed that RNAPs with a terminal mismatch adopt a backtracked conformation, while a coupled ribosome allosterically induces these polymerases toward a catalytically active anti-swiveled state. Finally, we demonstrate that prolonged RNAP pausing is detrimental to cell viability, which could be prevented by polymerase reactivation through a coupled ribosome.
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Affiliation(s)
- Liang Meng Wee
- QB3-Berkeley, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California Berkeley, Berkeley, CA, USA
| | - Alexander B Tong
- QB3-Berkeley, Berkeley, CA, USA; Department of Chemistry, University of California Berkeley, Berkeley, CA, USA
| | - Alfredo Jose Florez Ariza
- QB3-Berkeley, Berkeley, CA, USA; Biophysics Graduate Group, University of California Berkeley, Berkeley, CA, USA
| | - Cristhian Cañari-Chumpitaz
- QB3-Berkeley, Berkeley, CA, USA; Department of Chemistry, University of California Berkeley, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California Berkeley, Berkeley, CA, USA
| | - Patricia Grob
- QB3-Berkeley, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California Berkeley, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
| | - Eva Nogales
- QB3-Berkeley, Berkeley, CA, USA; Biophysics Graduate Group, University of California Berkeley, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California Berkeley, Berkeley, CA, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Carlos J Bustamante
- QB3-Berkeley, Berkeley, CA, USA; Biophysics Graduate Group, University of California Berkeley, Berkeley, CA, USA; Department of Chemistry, University of California Berkeley, Berkeley, CA, USA; Department of Physics, University of California Berkeley, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA; Kavli Energy Nanoscience Institute, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California Berkeley, Berkeley, CA, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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11
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Li X, Chou T. Stochastic dynamics and ribosome-RNAP interactions in transcription-translation coupling. Biophys J 2023; 122:254-266. [PMID: 36199250 PMCID: PMC9822797 DOI: 10.1016/j.bpj.2022.09.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 09/22/2022] [Accepted: 09/27/2022] [Indexed: 01/11/2023] Open
Abstract
Under certain cellular conditions, transcription and mRNA translation in prokaryotes appear to be "coupled," in which the formation of mRNA transcript and production of its associated protein are temporally correlated. Such transcription-translation coupling (TTC) has been evoked as a mechanism that speeds up the overall process, provides protection against premature termination, and/or regulates the timing of transcript and protein formation. What molecular mechanisms underlie ribosome-RNAP coupling and how they can perform these functions have not been explicitly modeled. We develop and analyze a continuous-time stochastic model that incorporates ribosome and RNAP elongation rates, initiation and termination rates, RNAP pausing, and direct ribosome and RNAP interactions (exclusion and binding). Our model predicts how distributions of delay times depend on these molecular features of transcription and translation. We also propose additional measures for TTC: a direct ribosome-RNAP binding probability and the fraction of time the translation-transcription process is "protected" from attack by transcription-terminating proteins. These metrics quantify different aspects of TTC and differentially depend on parameters of known molecular processes. We use our metrics to reveal how and when our model can exhibit either acceleration or deceleration of transcription, as well as protection from termination. Our detailed mechanistic model provides a basis for designing new experimental assays that can better elucidate the mechanisms of TTC.
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Affiliation(s)
- Xiangting Li
- Department of Computational Medicine, University of California, Los Angeles, Los Angeles, California
| | - Tom Chou
- Department of Computational Medicine, University of California, Los Angeles, Los Angeles, California; Department of Mathematics, University of California, Los Angeles, Los Angeles, California.
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12
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Pekarek L, Zimmer MM, Gribling-Burrer AS, Buck S, Smyth R, Caliskan N. Cis-mediated interactions of the SARS-CoV-2 frameshift RNA alter its conformations and affect function. Nucleic Acids Res 2022; 51:728-743. [PMID: 36537211 PMCID: PMC9881162 DOI: 10.1093/nar/gkac1184] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 11/11/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022] Open
Abstract
The RNA genome of SARS-CoV-2 contains a frameshift stimulatory element (FSE) that allows access to an alternative reading frame through -1 programmed ribosomal frameshifting (PRF). -1PRF in the 1a/1b gene is essential for efficient viral replication and transcription of the viral genome. -1PRF efficiency relies on the presence of conserved RNA elements within the FSE. One of these elements is a three-stemmed pseudoknot, although alternative folds of the frameshift site might have functional roles as well. Here, by complementing ensemble and single-molecule structural analysis of SARS-CoV-2 frameshift RNA variants with functional data, we reveal a conformational interplay of the 5' and 3' immediate regions with the FSE and show that the extended FSE exists in multiple conformations. Furthermore, limiting the base pairing of the FSE with neighboring nucleotides can favor or impair the formation of the alternative folds, including the pseudoknot. Our results demonstrate that co-existing RNA structures can function together to fine-tune SARS-CoV-2 gene expression, which will aid efforts to design specific inhibitors of viral frameshifting.
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Affiliation(s)
- Lukas Pekarek
- Helmholtz Institute for RNA-based Infection Research (HIRI-HZI), Würzburg, Germany
| | | | | | | | - Redmond Smyth
- Correspondence may also be addressed to Redmond Smyth.
| | - Neva Caliskan
- To whom correspondence should be addressed. Tel: +49 931 318 5298;
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13
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Kor R, Mohammad-Rafiee F. Theoretical study of RNA-polymerase behavior considering the backtracking state. SOFT MATTER 2022; 18:5979-5988. [PMID: 35920142 DOI: 10.1039/d2sm00232a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The dynamical behavior of the RNA polymerase in the transcription process is vital to gene expression. During the transcription process, the 3' end of the transcribed RNA can be dislocated from the active site of the enzyme and as a result, the RNA polymerase goes to the backtracked state. Here, we develop a theoretical model to study the transcription process considering the backtracking state. We aim at describing the behavior of the enzyme in the backtracking state in the presence of an external force, which leads to two possibilities: (i) rescuing from the backtracking state and, (ii) the arresting of the enzyme. We study the probability and the rate of the mentioned processes. In addition, we find that entering the backtracking state behaves like the Brownian ratchet mechanism. This model could shed some light on the modeling of the transcription process and further studies on the energy landscape of the backtracking channel and the gene regulation.
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Affiliation(s)
- Razieh Kor
- Department of Physics, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan 45137-66731, Iran.
| | - Farshid Mohammad-Rafiee
- Department of Physics, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan 45137-66731, Iran.
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14
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The Development of Single Molecule Force Spectroscopy: From Polymer Biophysics to Molecular Machines. Q Rev Biophys 2022; 55:e9. [PMID: 35916314 DOI: 10.1017/s0033583522000087] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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15
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Landgraf T, Völklein AE, Fürtig B, Schwalbe H. The cotranscriptional folding landscape for two cyclic di-nucleotide-sensing riboswitches with highly homologous aptamer domains acting either as ON- or OFF-switches. Nucleic Acids Res 2022; 50:6639-6655. [PMID: 35736222 PMCID: PMC9262584 DOI: 10.1093/nar/gkac514] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 05/03/2022] [Accepted: 06/07/2022] [Indexed: 12/24/2022] Open
Abstract
Riboswitches are gene regulatory elements located in untranslated mRNA regions. They bind inducer molecules with high affinity and specificity. Cyclic-di-nucleotide-sensing riboswitches are major regulators of genes for the environment, membranes and motility (GEMM) of bacteria. Up to now, structural probing assays or crystal structures have provided insight into the interaction between cyclic-di-nucleotides and their corresponding riboswitches. ITC analysis, NMR analysis and computational modeling allowed us to gain a detailed understanding of the gene regulation mechanisms for the Cd1 (Clostridium difficile) and for the pilM (Geobacter metallireducens) riboswitches and their respective di-nucleotides c-di-GMP and c-GAMP. Binding capability showed a 25 nucleotide (nt) long window for pilM and a 61 nt window for Cd1. Within this window, binding affinities ranged from 35 μM to 0.25 μM spanning two orders of magnitude for Cd1 and pilM showing a strong dependence on competing riboswitch folds. Experimental results were incorporated into a Markov simulation to further our understanding of the transcriptional folding pathways of riboswitches. Our model showed the ability to predict riboswitch gene regulation and its dependence on transcription speed, pausing and ligand concentration.
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Affiliation(s)
| | | | - Boris Fürtig
- Correspondence may also be addressed to Boris Fürtig.
| | - Harald Schwalbe
- To whom correspondence should be addressed. Tel: +49 69 798 29737; Fax: +49 69 798 29515;
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16
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Janissen R, Eslami-Mossallam B, Artsimovitch I, Depken M, Dekker NH. High-throughput single-molecule experiments reveal heterogeneity, state switching, and three interconnected pause states in transcription. Cell Rep 2022; 39:110749. [PMID: 35476989 DOI: 10.1016/j.celrep.2022.110749] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 02/17/2022] [Accepted: 04/07/2022] [Indexed: 11/19/2022] Open
Abstract
Pausing by bacterial RNA polymerase (RNAp) is vital in the recruitment of regulatory factors, RNA folding, and coupled translation. While backtracking and intra-structural isomerization have been proposed to trigger pausing, our mechanistic understanding of backtrack-associated pauses and catalytic recovery remains incomplete. Using high-throughput magnetic tweezers, we examine the Escherichia coli RNAp transcription dynamics over a wide range of forces and NTP concentrations. Dwell-time analysis and stochastic modeling identify, in addition to a short-lived elemental pause, two distinct long-lived backtrack pause states differing in recovery rates. We identify two stochastic sources of transcription heterogeneity: alterations in short-pause frequency that underlies elongation-rate switching, and variations in RNA cleavage rates in long-lived backtrack states. Together with effects of force and Gre factors, we demonstrate that recovery from deep backtracks is governed by intrinsic RNA cleavage rather than diffusional Brownian dynamics. We introduce a consensus mechanistic model that unifies our findings with prior models.
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Affiliation(s)
- Richard Janissen
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Behrouz Eslami-Mossallam
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Irina Artsimovitch
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA.
| | - Martin Depken
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, The Netherlands.
| | - Nynke H Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, The Netherlands.
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17
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Xu W, Yan Y, Artsimovitch I, Dunlap D, Finzi L. Positive supercoiling favors transcription elongation through lac repressor-mediated DNA loops. Nucleic Acids Res 2022; 50:2826-2835. [PMID: 35188572 PMCID: PMC8934669 DOI: 10.1093/nar/gkac093] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 12/22/2021] [Accepted: 02/20/2022] [Indexed: 11/30/2022] Open
Abstract
Some proteins, like the lac repressor (LacI), mediate long-range loops that alter DNA topology and create torsional barriers. During transcription, RNA polymerase generates supercoiling that may facilitate passage through such barriers. We monitored E. coli RNA polymerase progress along templates in conditions that prevented, or favored, 400 bp LacI-mediated DNA looping. Tethered particle motion measurements revealed that RNA polymerase paused longer at unlooped LacI obstacles or those barring entry to a loop than those barring exit from the loop. Enhanced dissociation of a LacI roadblock by the positive supercoiling generated ahead of a transcribing RNA polymerase within a torsion-constrained DNA loop may be responsible for this reduction in pause time. In support of this idea, RNA polymerase transcribed 6-fold more slowly through looped DNA and paused at LacI obstacles for 66% less time on positively supercoiled compared to relaxed templates, especially under increased tension (torque). Positive supercoiling propagating ahead of polymerase facilitated elongation along topologically complex, protein-coated templates.
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Affiliation(s)
- Wenxuan Xu
- Physics Department, Emory University, Atlanta, GA, USA
| | - Yan Yan
- Physics Department, Emory University, Atlanta, GA, USA
| | | | - David Dunlap
- Physics Department, Emory University, Atlanta, GA, USA
| | - Laura Finzi
- Physics Department, Emory University, Atlanta, GA, USA
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18
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Nemashkalo A, Phipps ME, Hennelly SP, Goodwin PM. Real-time, single-molecule observation of biomolecular interactions inside nanophotonic zero mode waveguides. NANOTECHNOLOGY 2022; 33:165101. [PMID: 34959227 DOI: 10.1088/1361-6528/ac467c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 12/26/2021] [Indexed: 06/14/2023]
Abstract
Living cells rely on numerous protein-protein, RNA-protein and DNA-protein interactions for processes such as gene expression, biomolecular assembly, protein and RNA degradation. Single-molecule microscopy and spectroscopy are ideal tools for real-time observation and quantification of nucleic acids-protein and protein-protein interactions. One of the major drawbacks of conventional single-molecule imaging methods is low throughput. Methods such as sequencing by synthesis utilizing nanofabrication and single-molecule spectroscopy have brought high throughput into the realm of single-molecule biology. The Pacific Biosciences RS2 sequencer utilizes sequencing by synthesis within nanophotonic zero mode waveguides. A number of years ago this instrument was unlocked by Pacific Biosciences for custom use by researchers allowing them to monitor biological interactions at the single-molecule level with high throughput. In this capability letter we demonstrate the use of the RS2 sequencer for real-time observation of DNA-to-RNA transcription and RNA-protein interactions. We use a relatively complex model-transcription of structured ribosomal RNA fromE. coliand interactions of ribosomal RNA with ribosomal proteins. We also show evidence of observation of transcriptional pausing without the application of an external force (as is required for single-molecule pausing studies using optical traps). Overall, in the unlocked, custom mode, the RS2 sequencer can be used to address a wide variety of biological assembly and interaction questions at the single-molecule level with high throughput. This instrument is available for use at the Center for Integrated Nanotechnologies Gateway located at Los Alamos National Laboratory.
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Affiliation(s)
- A Nemashkalo
- MPA-CINT (Materials Physics and Applications, Center for Integrated Nanotechnologies, Los Alamos National Laboratory), United States of America
| | - M E Phipps
- MPA-CINT (Materials Physics and Applications, Center for Integrated Nanotechnologies, Los Alamos National Laboratory), United States of America
| | - S P Hennelly
- B-11 (Bioenergy and Biome Sciences, Los Alamos National Laboratory), United States of America
| | - P M Goodwin
- MPA-CINT (Materials Physics and Applications, Center for Integrated Nanotechnologies, Los Alamos National Laboratory), United States of America
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19
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Zhu M, Mu H, Han F, Wang Q, Dai X. Quantitative analysis of asynchronous transcription-translation and transcription processivity in Bacillus subtilis under various growth conditions. iScience 2021; 24:103333. [PMID: 34805793 PMCID: PMC8586808 DOI: 10.1016/j.isci.2021.103333] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 08/31/2021] [Accepted: 10/20/2021] [Indexed: 10/25/2022] Open
Abstract
Tight coordination between transcription and translation has long been recognized as the hallmark of gene expression in bacteria. In Escherichia coli cells, disruption of the transcription-translation coordination leads to the loss of transcription processivity via triggering Rho-mediated premature transcription termination. Here we quantitatively characterize the transcription and translation kinetics in Gram-positive model bacterium Bacillus subtilis. We found that the speed of transcription elongation is much faster than that of translation elongation in B. subtilis under various growth conditions. Moreover, a Rho-independent loss of transcription processivity occurs constitutively in several genes/operons but is not subject to translational control. When the transcription elongation is decelerated under poor nutrients, low temperature, or nucleotide depletion, the loss of transcription processivity is strongly enhanced, suggesting that its degree is modulated by the speed of transcription elongation. Our study reveals distinct design principles of gene expression in E. coli and B. subtilis.
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Affiliation(s)
- Manlu Zhu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei Province, China
| | - Haoyan Mu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei Province, China
| | - Fei Han
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei Province, China
| | - Qian Wang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei Province, China
| | - Xiongfeng Dai
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei Province, China
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20
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Lee CY, Myong S. Probing steps in DNA transcription using single-molecule methods. J Biol Chem 2021; 297:101086. [PMID: 34403697 PMCID: PMC8441165 DOI: 10.1016/j.jbc.2021.101086] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 08/12/2021] [Accepted: 08/13/2021] [Indexed: 11/22/2022] Open
Abstract
Transcriptional regulation is one of the key steps in determining gene expression. Diverse single-molecule techniques have been applied to characterize the stepwise progression of transcription, yielding complementary results. These techniques include, but are not limited to, fluorescence-based microscopy with single or multiple colors, force measuring and manipulating microscopy using magnetic field or light, and atomic force microscopy. Here, we summarize and evaluate these current methodologies in studying and resolving individual steps in the transcription reaction, which encompasses RNA polymerase binding, initiation, elongation, mRNA production, and termination. We also describe the advantages and disadvantages of each method for studying transcription.
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Affiliation(s)
- Chun-Ying Lee
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, USA
| | - Sua Myong
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, USA; Physics Frontier Center (Center for Physics of Living Cells), University of Illinois, Urbana, Illinois, USA.
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21
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Li Q, Apostolidou D, Marszalek PE. Reconstruction of mechanical unfolding and refolding pathways of proteins with atomic force spectroscopy and computer simulations. Methods 2021; 197:39-53. [PMID: 34020035 DOI: 10.1016/j.ymeth.2021.05.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 05/14/2021] [Accepted: 05/15/2021] [Indexed: 12/29/2022] Open
Abstract
Most proteins in proteomes are large, typically consist of more than one domain and are structurally complex. This often makes studying their mechanical unfolding pathways challenging. Proteins composed of tandem repeat domains are a subgroup of multi-domain proteins that, when stretched, display a saw-tooth pattern in their mechanical unfolding force extension profiles due to their repetitive structure. However, the assignment of force peaks to specific repeats undergoing mechanical unraveling is complicated because all repeats are similar and they interact with their neighbors and form a contiguous tertiary structure. Here, we describe in detail a combination of experimental and computational single-molecule force spectroscopy methods that proved useful for examining the mechanical unfolding and refolding pathways of ankyrin repeat proteins. Specifically, we explain and delineate the use of atomic force microscope-based single molecule force spectroscopy (SMFS) to record the mechanical unfolding behavior of ankyrin repeat proteins and capture their unusually strong refolding propensity that is responsible for generating impressive refolding force peaks. We also describe Coarse Grain Steered Molecular Dynamic (CG-SMD) simulations which complement the experimental observations and provide insights in understanding the unfolding and refolding of these proteins. In addition, we advocate the use of novel coiled-coils-based mechanical polypeptide probes which we developed to demonstrate the vectorial character of folding and refolding of these repeat proteins. The combination of AFM-based SMFS on native and CC-equipped proteins with CG-SMD simulations is powerful not only for ankyrin repeat polypeptides, but also for other repeat proteins and more generally to various multidomain, non-repetitive proteins with complex topologies.
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Affiliation(s)
- Qing Li
- Department of Mechanical Engineering and Materials Science, Duke University, 27708 Durham, NC, United States
| | - Dimitra Apostolidou
- Department of Mechanical Engineering and Materials Science, Duke University, 27708 Durham, NC, United States
| | - Piotr E Marszalek
- Department of Mechanical Engineering and Materials Science, Duke University, 27708 Durham, NC, United States.
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22
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Yang J, Han YH, Im J, Seo SW. Synthetic protein quality control to enhance full-length translation in bacteria. Nat Chem Biol 2021; 17:421-427. [PMID: 33542534 DOI: 10.1038/s41589-021-00736-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 01/08/2021] [Indexed: 01/30/2023]
Abstract
Coupled transcription and translation processes in bacteria cause indiscriminate translation of intact and truncated messenger RNAs, inevitably generating nonfunctional polypeptides. Here, we devised a synthetic protein quality control (ProQC) system that enables translation only when both ends of mRNAs are present and followed by circularization based on sequence-specific RNA-RNA hybridization. We demonstrate that the ProQC system dramatically improved the fraction of full-length proteins among all synthesized polypeptides by selectively translating intact mRNA and reducing abortive translation. As a result, full-length protein synthesis increased up to 2.5-fold without changing the transcription or translation efficiency. Furthermore, we applied the ProQC system for 3-hydroxypropionic acid, violacein and lycopene production by ensuring full-length expression of enzymes in biosynthetic pathways, resulting in 1.6- to 2.3-fold greater biochemical production. We believe that our ProQC system can be universally applied to improve not only the quality of recombinant protein production but also efficiencies of metabolic pathways.
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Affiliation(s)
- Jina Yang
- School of Chemical and Biological Engineering, Seoul National University, Seoul, Korea.,Institute of Chemical Processes, Seoul National University, Seoul, Korea
| | - Yong Hee Han
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, Korea
| | - Jongwon Im
- School of Chemical and Biological Engineering, Seoul National University, Seoul, Korea
| | - Sang Woo Seo
- School of Chemical and Biological Engineering, Seoul National University, Seoul, Korea. .,Institute of Chemical Processes, Seoul National University, Seoul, Korea. .,Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, Korea. .,Bio-MAX Institute, Seoul National University, Seoul, Korea. .,Institute of Engineering Research, Seoul National University, Seoul, Korea.
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23
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Abraham Punnoose J, Hayden A, Zhou L, Halvorsen K. Wi-Fi Live-Streaming Centrifuge Force Microscope for Benchtop Single-Molecule Experiments. Biophys J 2020; 119:2231-2239. [PMID: 33121943 PMCID: PMC7732769 DOI: 10.1016/j.bpj.2020.10.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 10/02/2020] [Accepted: 10/08/2020] [Indexed: 11/21/2022] Open
Abstract
The ability to apply controlled forces to individual molecules has been revolutionary in shaping our understanding of biophysics in areas as diverse as dynamic bond strength, biological motor operation, and DNA replication. However, the methodology to perform single-molecule experiments remains relatively inaccessible because of cost and complexity. In 2010, we introduced the centrifuge force microscope (CFM) as a platform for accessible and high-throughput single-molecule experimentation. The CFM consists of a rotating microscope with which prescribed centrifugal forces can be applied to microsphere-tethered biomolecules. In this work, we develop and demonstrate a next-generation Wi-Fi CFM that offers unprecedented ease of use and flexibility in design. The modular CFM unit fits within a standard benchtop centrifuge and connects by Wi-Fi to an external computer for live control and streaming at near gigabit speeds. The use of commercial wireless hardware allows for flexibility in programming and provides a streamlined upgrade path as Wi-Fi technology advances. To facilitate ease of use, detailed build and setup instructions, as well as LabVIEW-based control software and MATLAB-based analysis software, are provided. We demonstrate the instrument’s performance by analysis of force-dependent dissociation of short DNA duplexes of 7, 8, and 9 bp. We showcase the sensitivity of the approach by resolving distinct dissociation kinetic rates for a 7 bp duplex in which one G-C basepair is mutated to an A-T basepair.
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Affiliation(s)
| | | | - Lifeng Zhou
- RNA Institute, SUNY at Albany, Albany, New York
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24
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The Impact of Leadered and Leaderless Gene Structures on Translation Efficiency, Transcript Stability, and Predicted Transcription Rates in Mycobacterium smegmatis. J Bacteriol 2020; 202:JB.00746-19. [PMID: 32094162 PMCID: PMC7148126 DOI: 10.1128/jb.00746-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 02/19/2020] [Indexed: 12/31/2022] Open
Abstract
Regulation of gene expression is critical for Mycobacterium tuberculosis to tolerate stressors encountered during infection and for nonpathogenic mycobacteria such as Mycobacterium smegmatis to survive environmental stressors. Unlike better-studied models, mycobacteria express ∼14% of their genes as leaderless transcripts. However, the impacts of leaderless transcript structures on mRNA half-life and translation efficiency in mycobacteria have not been directly tested. For leadered transcripts, the contributions of 5' untranslated regions (UTRs) to mRNA half-life and translation efficiency are similarly unknown. In M. tuberculosis and M. smegmatis, the essential sigma factor, SigA, is encoded by a transcript with a relatively short half-life. We hypothesized that the long 5' UTR of sigA causes this instability. To test this, we constructed fluorescence reporters and measured protein abundance, mRNA abundance, and mRNA half-life and calculated relative transcript production rates. The sigA 5' UTR conferred an increased transcript production rate, shorter mRNA half-life, and decreased apparent translation rate compared to a synthetic 5' UTR commonly used in mycobacterial expression plasmids. Leaderless transcripts appeared to be translated with similar efficiency as those with the sigA 5' UTR but had lower predicted transcript production rates. A global comparison of M. tuberculosis mRNA and protein abundances failed to reveal systematic differences in protein/mRNA ratios for leadered and leaderless transcripts, suggesting that variability in translation efficiency is largely driven by factors other than leader status. Our data are also discussed in light of an alternative model that leads to different conclusions and suggests leaderless transcripts may indeed be translated less efficiently.IMPORTANCE Tuberculosis, caused by Mycobacterium tuberculosis, is a major public health problem killing 1.5 million people globally each year. During infection, M. tuberculosis must alter its gene expression patterns to adapt to the stress conditions it encounters. Understanding how M. tuberculosis regulates gene expression may provide clues for ways to interfere with the bacterium's survival. Gene expression encompasses transcription, mRNA degradation, and translation. Here, we used Mycobacterium smegmatis as a model organism to study how 5' untranslated regions affect these three facets of gene expression in multiple ways. We furthermore provide insight into the expression of leaderless mRNAs, which lack 5' untranslated regions and are unusually prevalent in mycobacteria.
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25
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Douglas J, Kingston R, Drummond AJ. Bayesian inference and comparison of stochastic transcription elongation models. PLoS Comput Biol 2020; 16:e1006717. [PMID: 32059006 PMCID: PMC7046298 DOI: 10.1371/journal.pcbi.1006717] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 02/27/2020] [Accepted: 12/13/2019] [Indexed: 02/06/2023] Open
Abstract
Transcription elongation can be modelled as a three step process, involving polymerase translocation, NTP binding, and nucleotide incorporation into the nascent mRNA. This cycle of events can be simulated at the single-molecule level as a continuous-time Markov process using parameters derived from single-molecule experiments. Previously developed models differ in the way they are parameterised, and in their incorporation of partial equilibrium approximations. We have formulated a hierarchical network comprised of 12 sequence-dependent transcription elongation models. The simplest model has two parameters and assumes that both translocation and NTP binding can be modelled as equilibrium processes. The most complex model has six parameters makes no partial equilibrium assumptions. We systematically compared the ability of these models to explain published force-velocity data, using approximate Bayesian computation. This analysis was performed using data for the RNA polymerase complexes of E. coli, S. cerevisiae and Bacteriophage T7. Our analysis indicates that the polymerases differ significantly in their translocation rates, with the rates in T7 pol being fast compared to E. coli RNAP and S. cerevisiae pol II. Different models are applicable in different cases. We also show that all three RNA polymerases have an energetic preference for the posttranslocated state over the pretranslocated state. A Bayesian inference and model selection framework, like the one presented in this publication, should be routinely applicable to the interrogation of single-molecule datasets. Transcription is a critical biological process which occurs in all living organisms. It involves copying the organism’s genetic material into messenger RNA (mRNA) which directs protein synthesis on the ribosome. Transcription is performed by RNA polymerases which have been extensively studied using both ensemble and single-molecule techniques. Single-molecule data provides unique insights into the molecular behaviour of RNA polymerases. Transcription at the single-molecule level can be computationally simulated as a continuous-time Markov process and the model outputs compared with experimental data. In this study we use Bayesian techniques to perform a systematic comparison of 12 stochastic models of transcriptional elongation. We demonstrate how equilibrium approximations can strengthen or weaken the model, and show how Bayesian techniques can identify necessary or unnecessary model parameters. We describe a framework to a) simulate, b) perform inference on, and c) compare models of transcription elongation.
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Affiliation(s)
- Jordan Douglas
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
- Centre for Computational Evolution, School of Computer Science, University of Auckland, Auckland, New Zealand
- * E-mail:
| | - Richard Kingston
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Alexei J. Drummond
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
- Centre for Computational Evolution, School of Computer Science, University of Auckland, Auckland, New Zealand
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26
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Singh AK, Jaiswal A, Kodgire P. AID preferentially targets the top strand in nucleosome sequences. Mol Immunol 2019; 112:198-205. [DOI: 10.1016/j.molimm.2019.05.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Revised: 04/29/2019] [Accepted: 05/31/2019] [Indexed: 02/06/2023]
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27
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Kang JY, Mishanina TV, Landick R, Darst SA. Mechanisms of Transcriptional Pausing in Bacteria. J Mol Biol 2019; 431:4007-4029. [PMID: 31310765 DOI: 10.1016/j.jmb.2019.07.017] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 07/08/2019] [Accepted: 07/08/2019] [Indexed: 12/21/2022]
Abstract
Pausing by RNA polymerase (RNAP) during transcription regulates gene expression in all domains of life. In this review, we recap the history of transcriptional pausing discovery, summarize advances in our understanding of the underlying causes of pausing since then, and describe new insights into the pausing mechanisms and pause modulation by transcription factors gained from structural and biochemical experiments. The accumulated evidence to date suggests that upon encountering a pause signal in the nucleic-acid sequence being transcribed, RNAP rearranges into an elemental, catalytically inactive conformer unable to load NTP substrate. The conformation, and as a consequence lifetime, of an elemental paused RNAP is modulated by backtracking, nascent RNA structure, binding of transcription regulators, or a combination of these mechanisms. We conclude the review by outlining open questions and directions for future research in the field of transcriptional pausing.
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Affiliation(s)
- Jin Young Kang
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejon 34141, Republic of Korea.
| | - Tatiana V Mishanina
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA.
| | - Robert Landick
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Seth A Darst
- The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
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Kim S, Jacobs-Wagner C. Effects of mRNA Degradation and Site-Specific Transcriptional Pausing on Protein Expression Noise. Biophys J 2019; 114:1718-1729. [PMID: 29642040 DOI: 10.1016/j.bpj.2018.02.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 01/30/2018] [Accepted: 02/07/2018] [Indexed: 12/20/2022] Open
Abstract
Genetically identical cells exhibit diverse phenotypes even when experiencing the same environment. This phenomenon in part originates from cell-to-cell variability (noise) in protein expression. Although various kinetic schemes of stochastic transcription initiation are known to affect gene expression noise, how posttranscription initiation events contribute to noise at the protein level remains incompletely understood. To address this question, we developed a stochastic simulation-based model of bacterial gene expression that integrates well-known dependencies between transcription initiation, transcription elongation dynamics, mRNA degradation, and translation. We identified realistic conditions under which mRNA lifetime and transcriptional pauses modulate the protein expression noise initially introduced by the promoter architecture. For instance, we found that the short lifetime of bacterial mRNAs facilitates the production of protein bursts. Conversely, RNA polymerase (RNAP) pausing at specific sites during transcription elongation can attenuate protein bursts by fluidizing the RNAP traffic to the point of erasing the effect of a bursty promoter. Pause-prone sites, if located close to the promoter, can also affect noise indirectly by reducing both transcription and translation initiation due to RNAP and ribosome congestion. Our findings highlight how the interplay between transcription initiation, transcription elongation, translation, and mRNA degradation shapes the distribution in protein numbers. They also have implications for our understanding of gene evolution and suggest combinatorial strategies for modulating phenotypic variability by genetic engineering.
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Affiliation(s)
- Sangjin Kim
- Microbial Sciences Institute, West Haven, Connecticut; Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut; Howard Hughes Medical Institute, New Haven, Connecticut
| | - Christine Jacobs-Wagner
- Microbial Sciences Institute, West Haven, Connecticut; Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut; Howard Hughes Medical Institute, New Haven, Connecticut; Department of Microbial Pathogenesis, Yale School of Medicine, Yale University, New Haven, Connecticut.
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29
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Kienle DF, Falatach RM, Kaar JL, Schwartz DK. Correlating Structural and Functional Heterogeneity of Immobilized Enzymes. ACS NANO 2018; 12:8091-8103. [PMID: 30067333 DOI: 10.1021/acsnano.8b02956] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Many nanobiotechnology applications rely on stable and efficient integration of functional biomacromolecules with synthetic nanomaterials. Unfortunately, the reasons for the ubiquitous loss of activity of immobilized enzymes remain poorly understood due to the difficulty in distinguishing between distinct molecular-level mechanisms. Here, we employ complementary single-molecule fluorescence methods that independently measure the impact of immobilization on the structure and function ( i. e., substrate binding kinetics) of nitroreductase (NfsB). Stochastic statistical modeling methods were used to unambiguously quantify the effects of immobilized NfsB structural dynamics on function, allowing us to explicitly separate effects due to conformation and accessibility. Interestingly, we found that nonspecifically tethered NfsB exhibited enhanced stability compared to site-specifically tethered NfsB; however, the folded state of site-specifically tethered NfsB had faster substrate binding rates, suggesting improved active site accessibility. This demonstrated an unexpected intrinsic trade-off associated with competing bioconjugation methods, suggesting that it may be necessary to balance conformational stability versus active site accessibility. This nuanced view of the impact of immobilization will facilitate a rational approach to the integration of enzymes with synthetic nanomaterials.
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Affiliation(s)
- Daniel F Kienle
- Department of Chemical and Biological Engineering , University of Colorado , Boulder , Colorado 80309 , United States
| | - Rebecca M Falatach
- Department of Chemical and Biological Engineering , University of Colorado , Boulder , Colorado 80309 , United States
| | - Joel L Kaar
- Department of Chemical and Biological Engineering , University of Colorado , Boulder , Colorado 80309 , United States
| | - Daniel K Schwartz
- Department of Chemical and Biological Engineering , University of Colorado , Boulder , Colorado 80309 , United States
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30
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van Mameren J, Wuite GJL, Heller I. Introduction to Optical Tweezers: Background, System Designs, and Commercial Solutions. Methods Mol Biol 2018; 1665:3-23. [PMID: 28940061 DOI: 10.1007/978-1-4939-7271-5_1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Optical tweezers are a means to manipulate objects with light. With the technique, microscopically small objects can be held and steered, while forces on the trapped objects can be accurately measured and exerted. Optical tweezers can typically obtain a nanometer spatial resolution, a picoNewton force resolution, and a millisecond time resolution, which makes them excellently suited to study biological processes from the single-cell down to the single-molecule level. In this chapter, we will provide an introduction on the use of optical tweezers in single-molecule approaches. We will introduce the basic principles and methodology involved in optical trapping, force calibration, and force measurements. Next we describe the components of an optical tweezers setup and their experimental relevance in single-molecule approaches. Finally, we provide a concise overview of commercial optical tweezers systems. Commercial systems are becoming increasingly available and provide access to single-molecule optical tweezers experiments without the need for a thorough background in physics.
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Affiliation(s)
- Joost van Mameren
- Institute of Physics, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Gijs J L Wuite
- LaserLaB and Department of Physics and Astronomy, Vrije Universiteit, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands.
| | - Iddo Heller
- LaserLaB and Department of Physics and Astronomy, Vrije Universiteit, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
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31
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Steinert H, Sochor F, Wacker A, Buck J, Helmling C, Hiller F, Keyhani S, Noeske J, Grimm S, Rudolph MM, Keller H, Mooney RA, Landick R, Suess B, Fürtig B, Wöhnert J, Schwalbe H. Pausing guides RNA folding to populate transiently stable RNA structures for riboswitch-based transcription regulation. eLife 2017; 6. [PMID: 28541183 PMCID: PMC5459577 DOI: 10.7554/elife.21297] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 05/24/2017] [Indexed: 01/18/2023] Open
Abstract
In bacteria, the regulation of gene expression by cis-acting transcriptional riboswitches located in the 5'-untranslated regions of messenger RNA requires the temporal synchronization of RNA synthesis and ligand binding-dependent conformational refolding. Ligand binding to the aptamer domain of the riboswitch induces premature termination of the mRNA synthesis of ligand-associated genes due to the coupled formation of 3'-structural elements acting as terminators. To date, there has been no high resolution structural description of the concerted process of synthesis and ligand-induced restructuring of the regulatory RNA element. Here, we show that for the guanine-sensing xpt-pbuX riboswitch from Bacillus subtilis, the conformation of the full-length transcripts is static: it exclusively populates the functional off-state but cannot switch to the on-state, regardless of the presence or absence of ligand. We show that only the combined matching of transcription rates and ligand binding enables transcription intermediates to undergo ligand-dependent conformational refolding. DOI:http://dx.doi.org/10.7554/eLife.21297.001
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Affiliation(s)
- Hannah Steinert
- Center for Biomolecular Magnetic Resonance, Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt am Main, Frankfurt am Main, Germany
| | - Florian Sochor
- Center for Biomolecular Magnetic Resonance, Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt am Main, Frankfurt am Main, Germany
| | - Anna Wacker
- Center for Biomolecular Magnetic Resonance, Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt am Main, Frankfurt am Main, Germany
| | - Janina Buck
- Center for Biomolecular Magnetic Resonance, Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt am Main, Frankfurt am Main, Germany
| | - Christina Helmling
- Center for Biomolecular Magnetic Resonance, Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt am Main, Frankfurt am Main, Germany
| | - Fabian Hiller
- Center for Biomolecular Magnetic Resonance, Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt am Main, Frankfurt am Main, Germany
| | - Sara Keyhani
- Center for Biomolecular Magnetic Resonance, Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt am Main, Frankfurt am Main, Germany
| | - Jonas Noeske
- Center for Biomolecular Magnetic Resonance, Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt am Main, Frankfurt am Main, Germany
| | - Steffen Grimm
- Center for Biomolecular Magnetic Resonance, Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt am Main, Frankfurt am Main, Germany
| | - Martin M Rudolph
- Department of Biology, Technical University Darmstadt, Darmstadt, Germany
| | - Heiko Keller
- Center for Biomolecular Magnetic Resonance, Institute of Molecular Biosciences, Johann Wolfgang Goethe-University Frankfurt am Main, Frankfurt am Main, Germany
| | - Rachel Anne Mooney
- Department of Biochemistry, University of Wisconsin-Madison, Madison, United States
| | - Robert Landick
- Department of Biochemistry, University of Wisconsin-Madison, Madison, United States
| | - Beatrix Suess
- Department of Biology, Technical University Darmstadt, Darmstadt, Germany
| | - Boris Fürtig
- Center for Biomolecular Magnetic Resonance, Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt am Main, Frankfurt am Main, Germany
| | - Jens Wöhnert
- Center for Biomolecular Magnetic Resonance, Institute of Molecular Biosciences, Johann Wolfgang Goethe-University Frankfurt am Main, Frankfurt am Main, Germany
| | - Harald Schwalbe
- Center for Biomolecular Magnetic Resonance, Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt am Main, Frankfurt am Main, Germany
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32
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Malkusch N, Dörfler T, Nagy J, Eilert T, Michaelis J. smFRET experiments of the RNA polymerase II transcription initiation complex. Methods 2017; 120:115-124. [PMID: 28434999 DOI: 10.1016/j.ymeth.2017.04.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 03/21/2017] [Accepted: 04/14/2017] [Indexed: 01/23/2023] Open
Abstract
Single-molecule fluorescence and in particular single-molecule Förster Resonance Energy Transfer (smFRET) is a powerful tool to provide real-time information on the dynamic architecture of large macromolecular structures such as eukaryotic transcription initiation complexes. In contrast to other structural biology methods, not only structural details, but dynamics transitions are revealed thus closing in on the underlying molecular mechanisms. Here, we describe a comprehensive quantitative biophysical toolbox which can be used for rigorous analysis of dynamic protein-nucleic acid complexes and is applied to the study of eukaryotic transcription initiation. We present detailed protocols for the purification of all essential protein components of the minimal eukaryotic transcription initiation complex. Moreover, we demonstrate how elaborate strategies for site-specific protein labeling can be used to produce complexes with dye molecules attached to arbitrary desired positions. These complexes are then used for smFRET measurements. Moreover, we describe the Nano-Positioning System (NPS) which allows us to quantitatively use the results from a network of smFRET measurements to obtain structural information. With this we provide a toolbox to answer open questions which could not be addressed using methods like X-ray crystallography or cryo-electron microscopy.
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Affiliation(s)
- Nicole Malkusch
- Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Thilo Dörfler
- Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Julia Nagy
- Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Tobias Eilert
- Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Jens Michaelis
- Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany.
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33
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Vörös Z, Yan Y, Kovari DT, Finzi L, Dunlap D. Proteins mediating DNA loops effectively block transcription. Protein Sci 2017; 26:1427-1438. [PMID: 28295806 PMCID: PMC5477534 DOI: 10.1002/pro.3156] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Revised: 03/07/2017] [Accepted: 03/08/2017] [Indexed: 12/17/2022]
Abstract
Loops are ubiquitous topological elements formed when proteins simultaneously bind to two noncontiguous DNA sites. While a loop‐mediating protein may regulate initiation at a promoter, the presence of the protein at the other site may be an obstacle for RNA polymerases (RNAP) transcribing a different gene. To test whether a DNA loop alters the extent to which a protein blocks transcription, the lac repressor (LacI) was used. The outcome of in vitro transcription along templates containing two LacI operators separated by 400 bp in the presence of LacI concentrations that produced both looped and unlooped molecules was visualized with scanning force microscopy (SFM). An analysis of transcription elongation complexes, moving for 60 s at an average of 10 nt/s on unlooped DNA templates, revealed that they more often surpassed LacI bound to the lower affinity O2 operator than to the highest affinity Os operator. However, this difference was abrogated in looped DNA molecules where LacI became a strong roadblock independently of the affinity of the operator. Recordings of transcription elongation complexes, using magnetic tweezers, confirmed that they halted for several minutes upon encountering a LacI bound to a single operator. The average pause lifetime is compatible with RNAP waiting for LacI dissociation, however, the LacI open conformation visualized in the SFM images also suggests that LacI could straddle RNAP to let it pass. Independently of the mechanism by which RNAP bypasses the LacI roadblock, the data indicate that an obstacle with looped topology more effectively interferes with transcription.
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Affiliation(s)
- Zsuzsanna Vörös
- Department of Physics, Emory University, Atlanta, Georgia, 30322
| | - Yan Yan
- Department of Physics, Emory University, Atlanta, Georgia, 30322
| | - Daniel T Kovari
- Department of Physics, Emory University, Atlanta, Georgia, 30322
| | - Laura Finzi
- Department of Physics, Emory University, Atlanta, Georgia, 30322
| | - David Dunlap
- Department of Physics, Emory University, Atlanta, Georgia, 30322
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34
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Herrera-Asmat O, Lubkowska L, Kashlev M, Bustamante CJ, Guerra DG, Kireeva ML. Production and characterization of a highly pure RNA polymerase holoenzyme from Mycobacterium tuberculosis. Protein Expr Purif 2017; 134:1-10. [PMID: 28323168 DOI: 10.1016/j.pep.2017.03.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 03/15/2017] [Accepted: 03/16/2017] [Indexed: 10/19/2022]
Abstract
Recent publications have shown that active RNA polymerase (RNAP) from Mycobacterium tuberculosis (MtbRNAP) can be produced by expressing all four subunits in a single recombinant Escherichia coli strain [1-3]. By reducing the number of plasmids and changing the codon usage of the Mtb genes in the co-expression system published by Banerjee et al. [1], we present a simplified, detailed and reproducible protocol for the purification of recombinant MtbRNAP containing the ω subunit. Moreover, we describe the formation of ternary elongation complexes (TECs) with a short fluorescence-labeled RNA primer and DNA oligonucleotides, suitable for transcription elongation studies. The purification of milligram quantities of the pure and highly active holoenzyme omits ammonium sulfate or polyethylene imine precipitation steps [4] and requires only 5 g of wet cells. Our results indicate that subunit assemblies other than α2ββ'ω·σA can be separated by ion-exchange chromatography on Mono Q column and that assemblies with the wrong RNAP subunit stoichiometry lack transcriptional activity. We show that MtbRNAP TECs can be stalled by NTP substrate deprivation and chased upon the addition of missing NTP(s) without the need of any accessory proteins. Finally, we demonstrate the ability of the purified MtbRNAP to initiate transcription from a promoter and establish that its open promoter complexes are stabilized by the M. tuberculosis protein CarD.
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Affiliation(s)
- Omar Herrera-Asmat
- Jason Choy Laboratory of Single Molecule Biophysics, Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA; Laboratorio de Moléculas Individuales, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Av. Honorio Delgado 430, San Martin de Porras, Lima-31, Peru
| | | | | | - Carlos J Bustamante
- Jason Choy Laboratory of Single Molecule Biophysics, Department of Molecular and Cell Biology, Department of Physics and Department of Chemistry, Kavli Energy Nanoscience Institute, Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA.
| | - Daniel G Guerra
- Laboratorio de Moléculas Individuales, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Av. Honorio Delgado 430, San Martin de Porras, Lima-31, Peru.
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35
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Abstract
The reversible Michaelis-Menten equation is shown to follow from a very broad class of steady-state kinetic models involving enzymes that adopt a unique free (i.e., not complexed to substrate/product) state in solution. In the case of enzymes with multiple free states/conformations (e.g., fluctuating, hysteretic, or co-operative monomeric enzymes), Michaelian behavior is still assured if the relative steady-state populations of free enzyme states are independent of substrate and product concentration. Prior models for Michaelian behavior in multiple conformer enzymes are shown to be special cases of this single condition.
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Affiliation(s)
- Itay Barel
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, USA and Department of Physics, University of California, Santa Barbara, California 93106, USA
| | - Frank L H Brown
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, USA and Department of Physics, University of California, Santa Barbara, California 93106, USA
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36
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Abstract
Thirty years after their invention by Arthur Ashkin and colleagues at Bell Labs in 1986 [1], optical tweezers (or traps) have become a versatile tool to address numerous biological problems. Put simply, an optical trap is a highly focused laser beam that is capable of holding and applying forces to micron-sized dielectric objects. However, their development over the last few decades has converted these tools from boutique instruments into highly versatile instruments of molecular biophysics. This introductory chapter intends to give a brief overview of the field, highlight some important scientific achievements, and demonstrate why optical traps have become a powerful tool in the biological sciences. We introduce a typical optical setup, describe the basic theoretical concepts of how trapping forces arise, and present the quantitative position and force measurement techniques that are most widely used today.
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37
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Landuzzi F, Palla PL, Cleri F. Stability of radiation-damaged DNA after multiple strand breaks. Phys Chem Chem Phys 2017; 19:14641-14651. [DOI: 10.1039/c7cp02266b] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Radiation induced double-strand breaks in DNA are more stable against thermal and mechanical stress than usually thought.
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Affiliation(s)
- Fabio Landuzzi
- Institut d'Electronique
- Microelectronique et Nanotechnologie (IEMN Cnrs UMR 8520)
- Université de Lille I
- 59652 Villeneuve d'Ascq
- France
| | - Pier Luca Palla
- Institut d'Electronique
- Microelectronique et Nanotechnologie (IEMN Cnrs UMR 8520)
- Université de Lille I
- 59652 Villeneuve d'Ascq
- France
| | - Fabrizio Cleri
- Institut d'Electronique
- Microelectronique et Nanotechnologie (IEMN Cnrs UMR 8520)
- Université de Lille I
- 59652 Villeneuve d'Ascq
- France
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38
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Transcriptional bursting is intrinsically caused by interplay between RNA polymerases on DNA. Nat Commun 2016; 7:13788. [PMID: 27924870 PMCID: PMC5151093 DOI: 10.1038/ncomms13788] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 11/01/2016] [Indexed: 11/18/2022] Open
Abstract
Cell-to-cell variability plays a critical role in cellular responses and decision-making in a population, and transcriptional bursting has been broadly studied by experimental and theoretical approaches as the potential source of cell-to-cell variability. Although molecular mechanisms of transcriptional bursting have been proposed, there is little consensus. An unsolved key question is whether transcriptional bursting is intertwined with many transcriptional regulatory factors or is an intrinsic characteristic of RNA polymerase on DNA. Here we design an in vitro single-molecule measurement system to analyse the kinetics of transcriptional bursting. The results indicate that transcriptional bursting is caused by interplay between RNA polymerases on DNA. The kinetics of in vitro transcriptional bursting is quantitatively consistent with the gene-nonspecific kinetics previously observed in noisy gene expression in vivo. Our kinetic analysis based on a cellular automaton model confirms that arrest and rescue by trailing RNA polymerase intrinsically causes transcriptional bursting.
Transcriptional bursting is a potential source of cell-to-cell variability but the molecular mechanisms are unclear. Here the authors use single molecule imaging to analyse the kinetics of bursting on DNA and observe that bursting is an intrinsic property of RNA polymerases on DNA.
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39
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Abstract
The production of a single mRNA is the result of many sequential steps, from docking of transcription factors to polymerase initiation, elongation, splicing, and, finally, termination. Much of our knowledge about the fundamentals of RNA synthesis and processing come from ensemble in vitro biochemical measurements. Single-molecule approaches are very much in this same reductionist tradition but offer exquisite sensitivity in space and time along with the ability to observe heterogeneous behavior and actually manipulate macromolecules. These techniques can also be applied in vivo, allowing one to address questions in living cells that were previously restricted to reconstituted systems. In this review, we examine the unique insights that single-molecule techniques have yielded on the mechanisms of gene expression.
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Affiliation(s)
- Huimin Chen
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Daniel R Larson
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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40
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Heberling T, Davis L, Gedeon J, Morgan C, Gedeon T. A Mechanistic Model for Cooperative Behavior of Co-transcribing RNA Polymerases. PLoS Comput Biol 2016; 12:e1005069. [PMID: 27517607 PMCID: PMC4982667 DOI: 10.1371/journal.pcbi.1005069] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 07/20/2016] [Indexed: 11/19/2022] Open
Abstract
In fast-transcribing prokaryotic genes, such as an rrn gene in Escherichia coli, many RNA polymerases (RNAPs) transcribe the DNA simultaneously. Active elongation of RNAPs is often interrupted by pauses, which has been observed to cause RNAP traffic jams; yet some studies indicate that elongation seems to be faster in the presence of multiple RNAPs than elongation by a single RNAP. We propose that an interaction between RNAPs via the torque produced by RNAP motion on helically twisted DNA can explain this apparent paradox. We have incorporated the torque mechanism into a stochastic model and simulated transcription both with and without torque. Simulation results illustrate that the torque causes shorter pause durations and fewer collisions between polymerases. Our results suggest that the torsional interaction of RNAPs is an important mechanism in maintaining fast transcription times, and that transcription should be viewed as a cooperative group effort by multiple polymerases.
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Affiliation(s)
- Tamra Heberling
- Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Lisa Davis
- Department of Mathematical Sciences, Montana State University, Bozeman, Montana, United States of America
| | - Jakub Gedeon
- Computer Science Department, Montana State University, Bozeman, Montana, United States of America
| | - Charles Morgan
- Department of Mathematical Sciences, Montana State University, Bozeman, Montana, United States of America
| | - Tomáš Gedeon
- Department of Mathematical Sciences, Montana State University, Bozeman, Montana, United States of America
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41
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Abstract
During DNA transcription, RNA polymerases often adopt inactive backtracked states. Recovery from backtracks can occur by 1D diffusion or cleavage of backtracked RNA, but how polymerases make this choice is unknown. Here, we use single-molecule optical tweezers experiments and stochastic theory to show that the choice of a backtrack recovery mechanism is determined by a kinetic competition between 1D diffusion and RNA cleavage. Notably, RNA polymerase I (Pol I) and Pol II recover from shallow backtracks by 1D diffusion, use RNA cleavage to recover from intermediary depths, and are unable to recover from extensive backtracks. Furthermore, Pol I and Pol II use distinct mechanisms to avoid nonrecoverable backtracking. Pol I is protected by its subunit A12.2, which decreases the rate of 1D diffusion and enables transcript cleavage up to 20 nt. In contrast, Pol II is fully protected through association with the cleavage stimulatory factor TFIIS, which enables rapid recovery from any depth by RNA cleavage. Taken together, we identify distinct backtrack recovery strategies of Pol I and Pol II, shedding light on the evolution of cellular functions of these key enzymes.
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42
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Uchihashi T, Watanabe H, Fukuda S, Shibata M, Ando T. Functional extension of high-speed AFM for wider biological applications. Ultramicroscopy 2016; 160:182-196. [DOI: 10.1016/j.ultramic.2015.10.017] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Revised: 09/25/2015] [Accepted: 10/12/2015] [Indexed: 11/24/2022]
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43
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Hassanzadeh A, Azami D. Graphene based resonance structure to enhance the optical pressure between two planar surfaces. OPTICS EXPRESS 2015; 23:33681-33690. [PMID: 26832031 DOI: 10.1364/oe.23.033681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
To enhance the optical pressure on a thin dielectric sample, a resonance structure using graphene layers coated over a metal film on a high index prism sputtered with MgF2 was theoretically analyzed. The number of graphene layers and the thicknesses of metal and MgF2 films were optimized to achieve the highest optical pressure on the sample. Effects of three different types of metals on the optical pressure were investigated numerically. In addition, simulations were carried out for samples with various thicknesses. Our numerical results show that the optical pressure increased by more than five orders of magnitude compared to the conventional metal-film-base resonance structure. The highest optical pressure was obtained for 10 layers of graphene deposited on 29-nm thick Au film and 650 nm thickness of MgF2 at 633nm wavelength, The proposed graphene based resonance structure can open new possibilities for optical tweezers, nanomechnical devices and surface plasmon based sensing and imaging techniques.
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Liu J, Hanne J, Britton BM, Shoffner M, Albers AE, Bennett J, Zatezalo R, Barfield R, Rabuka D, Lee JB, Fishel R. An Efficient Site-Specific Method for Irreversible Covalent Labeling of Proteins with a Fluorophore. Sci Rep 2015; 5:16883. [PMID: 26582263 PMCID: PMC4652282 DOI: 10.1038/srep16883] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 09/07/2015] [Indexed: 11/09/2022] Open
Abstract
Fluorophore labeling of proteins while preserving native functions is essential for bulk Förster resonance energy transfer (FRET) interaction and single molecule imaging analysis. Here we describe a versatile, efficient, specific, irreversible, gentle and low-cost method for labeling proteins with fluorophores that appears substantially more robust than a similar but chemically distinct procedure. The method employs the controlled enzymatic conversion of a central Cys to a reactive formylglycine (fGly) aldehyde within a six amino acid Formylglycine Generating Enzyme (FGE) recognition sequence in vitro. The fluorophore is then irreversibly linked to the fGly residue using a Hydrazinyl-Iso-Pictet-Spengler (HIPS) ligation reaction. We demonstrate the robust large-scale fluorophore labeling and purification of E.coli (Ec) mismatch repair (MMR) components. Fluorophore labeling did not alter the native functions of these MMR proteins in vitro or in singulo. Because the FGE recognition sequence is easily portable, FGE-HIPS fluorophore-labeling may be easily extended to other proteins.
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Affiliation(s)
- Jiaquan Liu
- Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University Medical Center, Columbus, OH 43210
| | - Jeungphill Hanne
- Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University Medical Center, Columbus, OH 43210
| | - Brooke M Britton
- Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University Medical Center, Columbus, OH 43210
| | - Matthew Shoffner
- Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University Medical Center, Columbus, OH 43210
| | | | - Jared Bennett
- Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University Medical Center, Columbus, OH 43210
| | - Rachel Zatezalo
- Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University Medical Center, Columbus, OH 43210
| | | | | | - Jong-Bong Lee
- Department of Physics, Pohang University of Science and Technology (POSTECH), Pohang, Korea.,School of Interdisciplinary Bioscience and Bioengineering, POSTECH, Pohang, Korea
| | - Richard Fishel
- Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University Medical Center, Columbus, OH 43210.,Physics Department, The Ohio State University, Columbus, OH 43210
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Vance KW, Woodcock DJ, Reid JE, Bretschneider T, Ott S, Koentges G. Conserved Cis-Regulatory Modules Control Robustness in Msx1 Expression at Single-Cell Resolution. Genome Biol Evol 2015; 7:2762-78. [PMID: 26342140 PMCID: PMC4607535 DOI: 10.1093/gbe/evv179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The process of transcription is highly stochastic leading to cell-to-cell variations and noise in gene expression levels. However, key essential genes have to be precisely expressed at the correct amount and time to ensure proper cellular development and function. Studies in yeast and bacterial systems have shown that gene expression noise decreases as mean expression levels increase, a relationship that is controlled by promoter DNA sequence. However, the function of distal cis-regulatory modules (CRMs), an evolutionary novelty of metazoans, in controlling transcriptional robustness and variability is poorly understood. In this study, we used live cell imaging of transfected reporters combined with a mathematical modelling and statistical inference scheme to quantify the function of conserved Msx1 CRMs and promoters in modulating single-cell real-time transcription rates in C2C12 mouse myoblasts. The results show that the mean expression–noise relationship is solely promoter controlled for this key pluripotency regulator. In addition, we demonstrate that CRMs modulate single-cell basal promoter rate distributions in a graded manner across a population of cells. This extends the rheostatic model of CRM action to provide a more detailed understanding of CRM function at single-cell resolution. We also identify a novel CRM transcriptional filter function that acts to reduce intracellular variability in transcription rates and show that this can be phylogenetically separable from rate modulating CRM activities. These results are important for understanding how the expression of key vertebrate developmental transcription factors is precisely controlled both within and between individual cells.
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Affiliation(s)
- Keith W Vance
- Department of Biology and Biochemistry, University of Bath, United Kingdom Warwick Systems Biology Centre, University of Warwick, Coventry, United Kingdom School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Dan J Woodcock
- Warwick Systems Biology Centre, University of Warwick, Coventry, United Kingdom
| | - John E Reid
- MRC Biostatistics Unit, Robinson Way, Cambridge, United Kingdom
| | - Till Bretschneider
- Warwick Systems Biology Centre, University of Warwick, Coventry, United Kingdom
| | - Sascha Ott
- Warwick Systems Biology Centre, University of Warwick, Coventry, United Kingdom
| | - Georgy Koentges
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
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Kim K, Guo J, Xu X, Fan DL. Recent Progress on Man-Made Inorganic Nanomachines. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2015; 11:4037-4057. [PMID: 26114572 DOI: 10.1002/smll.201500407] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 04/17/2015] [Indexed: 06/04/2023]
Abstract
The successful development of nanoscale machinery, which can operate with high controllability, high precision, long lifetimes, and tunable driving powers, is pivotal for the realization of future intelligent nanorobots, nanofactories, and advanced biomedical devices. However, the development of nanomachines remains one of the most difficult research areas, largely due to the grand challenges in fabrication of devices with complex components and actuation with desired efficiency, precision, lifetime, and/or environmental friendliness. In this work, the cutting-edge efforts toward fabricating and actuating various types of nanomachines and their applications are reviewed, with a special focus on nanomotors made from inorganic nanoscale building blocks, which are introduced according to the employed actuation mechanism. The unique characteristics and obstacles for each type of nanomachine are discussed, and perspectives and challenges of this exciting field are presented.
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Affiliation(s)
- Kwanoh Kim
- Department of Mechanical Engineering, the University of Texas at Austin, Austin, TX, 78712, USA
| | - Jianhe Guo
- Materials Science and Engineering Program, the University of Texas at Austin, Austin, TX, 78712, USA
| | - Xiaobin Xu
- Materials Science and Engineering Program, the University of Texas at Austin, Austin, TX, 78712, USA
| | - D L Fan
- Department of Mechanical Engineering, the University of Texas at Austin, Austin, TX, 78712, USA
- Materials Science and Engineering Program, the University of Texas at Austin, Austin, TX, 78712, USA
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Enhanced immunoassay for porcine circovirus type 2 antibody using enzyme-loaded and quantum dots-embedded shell–core silica nanospheres based on enzyme-linked immunosorbent assay. Anal Chim Acta 2015; 887:192-200. [DOI: 10.1016/j.aca.2015.06.024] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Revised: 05/21/2015] [Accepted: 06/11/2015] [Indexed: 11/21/2022]
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Mejia YX, Nudler E, Bustamante C. Trigger loop folding determines transcription rate of Escherichia coli's RNA polymerase. Proc Natl Acad Sci U S A 2015; 112:743-8. [PMID: 25552559 PMCID: PMC4311812 DOI: 10.1073/pnas.1421067112] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Two components of the RNA polymerase (RNAP) catalytic center, the bridge helix and the trigger loop (TL), have been linked with changes in elongation rate and pausing. Here, single molecule experiments with the WT and two TL-tip mutants of the Escherichia coli enzyme reveal that tip mutations modulate RNAP's pause-free velocity, identifying TL conformational changes as one of two rate-determining steps in elongation. Consistent with this observation, we find a direct correlation between helix propensity of the modified amino acid and pause-free velocity. Moreover, nucleotide analogs affect transcription rate, suggesting that their binding energy also influences TL folding. A kinetic model in which elongation occurs in two steps, TL folding on nucleoside triphosphate (NTP) binding followed by NTP incorporation/pyrophosphate release, quantitatively accounts for these results. The TL plays no role in pause recovery remaining unfolded during a pause. This model suggests a finely tuned mechanism that balances transcription speed and fidelity.
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Affiliation(s)
- Yara X Mejia
- Jason L. Choy Laboratory of Single-Molecule Biophysics, the California Institute of Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720
| | - Evgeny Nudler
- Department of Biochemistry and Molecular Pharmacology and Howard Hughes Medical Institute, New York University School of Medicine, New York, NY 10016
| | - Carlos Bustamante
- Jason L. Choy Laboratory of Single-Molecule Biophysics, the California Institute of Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720; Department of Molecular and Cell Biology, Department of Physics, Department of Chemistry, Biophysics Graduate Group and Howard Hughes Medical Institute, University of California, Berkeley, CA 94720; and Kavli Energy Nanosciences Institute at Berkeley, Berkeley, CA 94720
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Wang J, Pfeuty B, Thommen Q, Romano MC, Lefranc M. Minimal model of transcriptional elongation processes with pauses. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2014; 90:050701. [PMID: 25493724 DOI: 10.1103/physreve.90.050701] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2014] [Indexed: 06/04/2023]
Abstract
Fundamental biological processes such as transcription and translation, where a genetic sequence is sequentially read by a macromolecule, have been well described by a classical model of nonequilibrium statistical physics, the totally asymmetric exclusion principle (TASEP). This model describes particles hopping between sites of a one-dimensional lattice, with the particle current determining the transcription or translation rate. An open problem is how to analyze a TASEP where particles can pause randomly, as has been observed during transcription. In this work, we report that surprisingly, a simple mean-field model predicts well the particle current for all values of the average pause duration, using a simple description of blocking behind paused particles.
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Affiliation(s)
- Jingkui Wang
- Laboratoire de Physique des Lasers, Atomes, et Molécules, Université Lille 1, CNRS UMR 8523, F-59655 Villeneuve d'Ascq, France
| | - Benjamin Pfeuty
- Laboratoire de Physique des Lasers, Atomes, et Molécules, Université Lille 1, CNRS UMR 8523, F-59655 Villeneuve d'Ascq, France
| | - Quentin Thommen
- Laboratoire de Physique des Lasers, Atomes, et Molécules, Université Lille 1, CNRS UMR 8523, F-59655 Villeneuve d'Ascq, France
| | - M Carmen Romano
- SUPA, Institute for Complex Systems and Mathematical Biology, University of Aberdeen, Aberdeen AB24 3UE, United Kingdom and Institute of Medical Sciences, Foresterhill, University of Aberdeen, Aberdeen AB25 2ZD, United Kingdom
| | - Marc Lefranc
- Laboratoire de Physique des Lasers, Atomes, et Molécules, Université Lille 1, CNRS UMR 8523, F-59655 Villeneuve d'Ascq, France
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