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Biomolecules
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RNA Polymerase and Transcription Mechanism: Forefront of Physicochemical Study
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RNA Polymerase and Transcription Mechanism: Forefront of Physicochemical Study

A special issue of Biomolecules (ISSN 2218-273X). This special issue belongs to the section "Enzymology".

Deadline for manuscript submissions: closed (31 August 2021) | Viewed by 20247

Special Issue Editors

Prof. Dr. Nobuo Shimamoto

E-Mail Website
Guest Editor
National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
Interests: nanobiology; protein sliding along DNA; one-dimensional diffusion; chemical ratchet; detailed balance; physiological conformation
Dr. Masahiko Imashimizu

E-Mail Website
Guest Editor
Cellular and Molecular Biotechnology Research, National Institute of Advanced Industrial Science and Technology, Koto-ku, Tokyo 135-0064, Japan
Interests: terabiology; fidelity of enzyme; hydrogen–bond network; biomolecule–water-coupled motions

Special Issue Information

Dear Colleagues,

For a half century, the study on the mechanism of RNA polymerase has been one of the top runners in terms of using newly developed methods. The obtained results on transcriptional regulation have stimulated biomedical applications such as drug discovery targeting RNA polymerases, and thus, physicochemical and genetic analyses of RNA polymerases and their accessary molecules have acquired a biomedical significance. However, recently, such a multidisciplinary method development appears to become slow or is perhaps saturated. We tend to believe that our image on biological macromolecules has been perfectly established, but it has not well been recognized that methodological saturation is partly caused by a lack of understanding of physicochemical properties of biological macromolecules, including the surrounding water molecules. For example, conventional time-averaging does not always provide the correct data and can lead to misunderstanding. It is also useful to clarify the limitation of tools that were originally developed for simpler polymers and small molecules and later applied for biomolecules.

The main goal of this Special Issue of Biomolecules is to clarify the ignored properties of macromolecules by rethinking the basis of chemical reaction in transcriptional regulations.

The topics includes (i) experimental and analytical tools for inhomogeneity of protein conformations and (ii) the contribution of thermal processes in transcriptional regulation, such as Brownian ratchet and one-dimensional diffusion.

Prof. Nobuo Shimamoto
Dr. Masahiko Imashimizu
Guest Editors

Manuscript Submission Information

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Keywords

  • RNA polymerase
  • transcriptional regulation
  • thermal process
  • Brownian ratchet
  • one-dimensional diffusion
  • active conformation

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Published Papers (6 papers)

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Research

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21 pages, 2906 KiB  
Article
Control of Transcription Initiation by Biased Thermal Fluctuations on Repetitive Genomic Sequences
by Masahiko Imashimizu, Yuji Tokunaga, Ariel Afek, Hiroki Takahashi, Nobuo Shimamoto and David B. Lukatsky
Biomolecules 2020, 10(9), 1299; https://doi.org/10.3390/biom10091299 - 9 Sep 2020
Cited by 5 | Viewed by 4033
Abstract
In the process of transcription initiation by RNA polymerase, promoter DNA sequences affect multiple reaction pathways determining the productivity of transcription. However, the question of how the molecular mechanism of transcription initiation depends on the sequence properties of promoter DNA remains poorly understood. [...] Read more.
In the process of transcription initiation by RNA polymerase, promoter DNA sequences affect multiple reaction pathways determining the productivity of transcription. However, the question of how the molecular mechanism of transcription initiation depends on the sequence properties of promoter DNA remains poorly understood. Here, combining the statistical mechanical approach with high-throughput sequencing results, we characterize abortive transcription and pausing during transcription initiation by Escherichia coli RNA polymerase at a genome-wide level. Our results suggest that initially transcribed sequences, when enriched with thymine bases, contain the signal for inducing abortive transcription, whereas certain repetitive sequence elements embedded in promoter regions constitute the signal for inducing pausing. Both signals decrease the productivity of transcription initiation. Based on solution NMR and in vitro transcription measurements, we suggest that repetitive sequence elements within the promoter DNA modulate the nonlocal base pair stability of its double-stranded form. This stability profoundly influences the reaction coordinates of the productive initiation via pausing. Full article
(This article belongs to the Special Issue RNA Polymerase and Transcription Mechanism: Forefront of Physicochemical Study)
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29 pages, 7478 KiB  
Article
Nucleotide Loading Modes of Human RNA Polymerase II as Deciphered by Molecular Simulations
by Nicolas E. J. Génin and Robert O. J. Weinzierl
Biomolecules 2020, 10(9), 1289; https://doi.org/10.3390/biom10091289 - 7 Sep 2020
Cited by 2 | Viewed by 3493
Abstract
Mapping the route of nucleoside triphosphate (NTP) entry into the sequestered active site of RNA polymerase (RNAP) has major implications for elucidating the complete nucleotide addition cycle. Constituting a dichotomy that remains to be resolved, two alternatives, direct NTP delivery via the secondary [...] Read more.
Mapping the route of nucleoside triphosphate (NTP) entry into the sequestered active site of RNA polymerase (RNAP) has major implications for elucidating the complete nucleotide addition cycle. Constituting a dichotomy that remains to be resolved, two alternatives, direct NTP delivery via the secondary channel (CH2) or selection to downstream sites in the main channel (CH1) prior to catalysis, have been proposed. In this study, accelerated molecular dynamics simulations of freely diffusing NTPs about RNAPII were applied to refine the CH2 model and uncover atomic details on the CH1 model that previously lacked a persuasive structural framework to illustrate its mechanism of action. Diffusion and binding of NTPs to downstream DNA, and the transfer of a preselected NTP to the active site, are simulated for the first time. All-atom simulations further support that CH1 loading is transcription factor IIF (TFIIF) dependent and impacts catalytic isomerization. Altogether, the alternative nucleotide loading systems may allow distinct transcriptional landscapes to be expressed. Full article
(This article belongs to the Special Issue RNA Polymerase and Transcription Mechanism: Forefront of Physicochemical Study)
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Review

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27 pages, 3695 KiB  
Review
Composition of Transcription Machinery and Its Crosstalk with Nucleoid-Associated Proteins and Global Transcription Factors
by Georgi Muskhelishvili, Patrick Sobetzko, Sanja Mehandziska and Andrew Travers
Biomolecules 2021, 11(7), 924; https://doi.org/10.3390/biom11070924 - 22 Jun 2021
Cited by 10 | Viewed by 3334
Abstract
The coordination of bacterial genomic transcription involves an intricate network of interdependent genes encoding nucleoid-associated proteins (NAPs), DNA topoisomerases, RNA polymerase subunits and modulators of transcription machinery. The central element of this homeostatic regulatory system, integrating the information on cellular physiological state and [...] Read more.
The coordination of bacterial genomic transcription involves an intricate network of interdependent genes encoding nucleoid-associated proteins (NAPs), DNA topoisomerases, RNA polymerase subunits and modulators of transcription machinery. The central element of this homeostatic regulatory system, integrating the information on cellular physiological state and producing a corresponding transcriptional response, is the multi-subunit RNA polymerase (RNAP) holoenzyme. In this review article, we argue that recent observations revealing DNA topoisomerases and metabolic enzymes associated with RNAP supramolecular complex support the notion of structural coupling between transcription machinery, DNA topology and cellular metabolism as a fundamental device coordinating the spatiotemporal genomic transcription. We analyse the impacts of various combinations of RNAP holoenzymes and global transcriptional regulators such as abundant NAPs, on genomic transcription from this viewpoint, monitoring the spatiotemporal patterns of couplons—overlapping subsets of the regulons of NAPs and RNAP sigma factors. We show that the temporal expression of regulons is by and large, correlated with that of cognate regulatory genes, whereas both the spatial organization and temporal expression of couplons is distinctly impacted by the regulons of NAPs and sigma factors. We propose that the coordination of the growth phase-dependent concentration gradients of global regulators with chromosome configurational dynamics determines the spatiotemporal patterns of genomic expression. Full article
(This article belongs to the Special Issue RNA Polymerase and Transcription Mechanism: Forefront of Physicochemical Study)
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12 pages, 1501 KiB  
Review
RNA Polymerase and Transcription Mechanisms: The Forefront of Physicochemical Studies of Chemical Reactions
by Nobuo Shimamoto and Masahiko Imashimizu
Biomolecules 2021, 11(1), 32; https://doi.org/10.3390/biom11010032 - 29 Dec 2020
Cited by 3 | Viewed by 2761
Abstract
The study of transcription and its regulation is an interdisciplinary field that is closely connected with genetics, structural biology, and reaction theory. Among these, although less attention has been paid to reaction theory, it is becoming increasingly useful for research on transcription. Rate [...] Read more.
The study of transcription and its regulation is an interdisciplinary field that is closely connected with genetics, structural biology, and reaction theory. Among these, although less attention has been paid to reaction theory, it is becoming increasingly useful for research on transcription. Rate equations are commonly used to describe reactions involved in transcription, but they tend to be used unaware of the timescales of relevant physical processes. In this review, we discuss the limitation of rate equation for describing three-dimensional diffusion and one-dimensional diffusion along DNA. We then introduce the chemical ratchet mechanism recently proposed for explaining the antenna effect, an enhancement of the binding affinity to a specific site on longer DNA, which deviates from a thermodynamic rule. We show that chemical ratchet cannot be described with a single set of rate equations but alternative sets of rate equations that temporally switch no faster than the binding reaction. Full article
(This article belongs to the Special Issue RNA Polymerase and Transcription Mechanism: Forefront of Physicochemical Study)
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11 pages, 1358 KiB  
Review
Validation of Omega Subunit of RNA Polymerase as a Functional Entity
by Unnatiben Rajeshbhai Patel, Sudhanshu Gautam and Dipankar Chatterji
Biomolecules 2020, 10(11), 1588; https://doi.org/10.3390/biom10111588 - 23 Nov 2020
Cited by 8 | Viewed by 3334
Abstract
The bacterial RNA polymerase (RNAP) is a multi-subunit protein complex (α2ββ’ω σ) containing the smallest subunit, ω. Although identified early in RNAP research, its function remained ambiguous and shrouded with controversy for a considerable period. It was shown before that the protein has [...] Read more.
The bacterial RNA polymerase (RNAP) is a multi-subunit protein complex (α2ββ’ω σ) containing the smallest subunit, ω. Although identified early in RNAP research, its function remained ambiguous and shrouded with controversy for a considerable period. It was shown before that the protein has a structural role in maintaining the conformation of the largest subunit, β’, and its recruitment in the enzyme assembly. Despite evolutionary conservation of ω and its role in the assembly of RNAP, E. coli mutants lacking rpoZ (codes for ω) are viable due to the association of the global chaperone protein GroEL with RNAP. To get a better insight into the structure and functional role of ω during transcription, several dominant lethal mutants of ω were isolated. The mutants showed higher binding affinity compared to that of native ω to the α2ββ’ subassembly. We observed that the interaction between α2ββ’ and these lethal mutants is driven by mostly favorable enthalpy and a small but unfavorable negative entropy term. However, during the isolation of these mutants we isolated a silent mutant serendipitously, which showed a lethal phenotype. Silent mutant of a given protein is defined as a protein having the same sequence of amino acids as that of wild type but having mutation in the gene with alteration in base sequence from more frequent code to less frequent one due to codon degeneracy. Eventually, many silent mutants were generated to understand the role of rare codons at various positions in rpoZ. We observed that the dominant lethal mutants of ω having either point mutation or silent in nature are more structured in comparison to the native ω. However, the silent code’s position in the reading frame of rpoZ plays a role in the structural alteration of the translated protein. This structural alteration in ω makes it more rigid, which affects the plasticity of the interacting domain formed by ω and α2ββ’. Here, we attempted to describe how the conformational flexibility of the ω helps in maintaining the plasticity of the active site of RNA polymerase. The dominant lethal mutant of ω has a suppressor mapped near the catalytic center of the β’ subunit, and it is the same for both types of mutants. Full article
(This article belongs to the Special Issue RNA Polymerase and Transcription Mechanism: Forefront of Physicochemical Study)
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Other

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3 pages, 181 KiB  
Commentary
The Limitation of the Combination of Transition State Theory and Thermodynamics for the Reactions of Proteins and Nucleic Acids
by Nobuo Shimamoto
Biomolecules 2022, 12(1), 28; https://doi.org/10.3390/biom12010028 - 25 Dec 2021
Cited by 1 | Viewed by 2120
Abstract
When a reaction is accompanied by a change with the speed close to or slower than the reaction rate, a circulating reaction flow can exist among the reaction states in the macroscopic stationary state. If the accompanying change were at equilibrium in the [...] Read more.
When a reaction is accompanied by a change with the speed close to or slower than the reaction rate, a circulating reaction flow can exist among the reaction states in the macroscopic stationary state. If the accompanying change were at equilibrium in the timescale of the relevant reaction, the transition-state theory would hold to eliminate the flow. Full article
(This article belongs to the Special Issue RNA Polymerase and Transcription Mechanism: Forefront of Physicochemical Study)
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