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Varassas SP, Kouvelis VN. Mitochondrial Transcription of Entomopathogenic Fungi Reveals Evolutionary Aspects of Mitogenomes. Front Microbiol 2022; 13:821638. [PMID: 35387072 PMCID: PMC8979003 DOI: 10.3389/fmicb.2022.821638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 02/22/2022] [Indexed: 11/13/2022] Open
Abstract
Entomopathogenic fungi and more specifically genera Beauveria and Metarhizium have been exploited for the biological control of pests. Genome analyses are important to understand better their mode of action and thus, improve their efficacy against their hosts. Until now, the sequences of their mitochondrial genomes were studied, but not at the level of transcription. Except of yeasts and Neurospora crassa, whose mt gene transcription is well described, in all other Ascomycota, i.e., Pezizomycotina, related information is extremely scarce. In this work, mt transcription and key enzymes of this function were studied. RT-PCR experiments and Northern hybridizations reveal the transcriptional map of the mt genomes of B. bassiana and M. brunneum species. The mt genes are transcribed in six main transcripts and undergo post-transcriptional modifications to create single gene transcripts. Promoters were determined in both mt genomes with a comparative in silico analysis, including all known information from other fungal mt genomes. The promoter consensus sequence is 5'-ATAGTTATTAT-3' which is in accordance with the definition of the polycistronic transcripts determined with the experiments described above. Moreover, 5'-RACE experiments in the case of premature polycistronic transcript nad1-nad4-atp8-atp6 revealed the 5' end of the RNA transcript immediately after the in silico determined promoter, as also found in other fungal species. Since several conserved elements were retrieved from these analyses compared to the already known data from yeasts and N. crassa, the phylogenetic analyses of mt RNA polymerase (Rpo41) and its transcriptional factor (Mtf1) were performed in order to define their evolution. As expected, it was found that fungal Rpo41 originate from the respective polymerase of T7/T3 phages, while the ancestor of Mtf1 is of alpha-proteobacterial origin. Therefore, this study presents insights about the fidelity of the mt single-subunit phage-like RNA polymerase during transcription, since the correct identification of mt promoters from Rpo41 requires an ortholog to bacterial sigma factor, i.e., Mtf1. Thus, a previously proposed hypothesis of a phage infected alpha-proteobacterium as the endosymbiotic progenitor of mitochondrion is confirmed in this study and further upgraded by the co-evolution of the bacterial (Mtf1) and viral (Rpo41) originated components in one functional unit.
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Affiliation(s)
| | - Vassili N. Kouvelis
- Department of Genetics and Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
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2
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Basu U, Bostwick AM, Das K, Dittenhafer-Reed KE, Patel SS. Structure, mechanism, and regulation of mitochondrial DNA transcription initiation. J Biol Chem 2020; 295:18406-18425. [PMID: 33127643 PMCID: PMC7939475 DOI: 10.1074/jbc.rev120.011202] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 10/29/2020] [Indexed: 12/14/2022] Open
Abstract
Mitochondria are specialized compartments that produce requisite ATP to fuel cellular functions and serve as centers of metabolite processing, cellular signaling, and apoptosis. To accomplish these roles, mitochondria rely on the genetic information in their small genome (mitochondrial DNA) and the nucleus. A growing appreciation for mitochondria's role in a myriad of human diseases, including inherited genetic disorders, degenerative diseases, inflammation, and cancer, has fueled the study of biochemical mechanisms that control mitochondrial function. The mitochondrial transcriptional machinery is different from nuclear machinery. The in vitro re-constituted transcriptional complexes of Saccharomyces cerevisiae (yeast) and humans, aided with high-resolution structures and biochemical characterizations, have provided a deeper understanding of the mechanism and regulation of mitochondrial DNA transcription. In this review, we will discuss recent advances in the structure and mechanism of mitochondrial transcription initiation. We will follow up with recent discoveries and formative findings regarding the regulatory events that control mitochondrial DNA transcription, focusing on those involved in cross-talk between the mitochondria and nucleus.
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Affiliation(s)
- Urmimala Basu
- Department of Biochemistry and Molecular Biology, Rutgers Robert Wood Johnson Medical School, Piscataway, New Jersey, USA; Graduate School of Biomedical Sciences, Rutgers Robert Wood Johnson Medical School, Piscataway, New Jersey, USA
| | | | - Kalyan Das
- Department of Microbiology, Immunology, and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | | | - Smita S Patel
- Department of Biochemistry and Molecular Biology, Rutgers Robert Wood Johnson Medical School, Piscataway, New Jersey, USA.
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3
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De Wijngaert B, Sultana S, Singh A, Dharia C, Vanbuel H, Shen J, Vasilchuk D, Martinez SE, Kandiah E, Patel SS, Das K. Cryo-EM Structures Reveal Transcription Initiation Steps by Yeast Mitochondrial RNA Polymerase. Mol Cell 2020; 81:268-280.e5. [PMID: 33278362 DOI: 10.1016/j.molcel.2020.11.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 11/06/2020] [Accepted: 11/09/2020] [Indexed: 01/18/2023]
Abstract
Mitochondrial RNA polymerase (mtRNAP) is crucial in cellular energy production, yet understanding of mitochondrial DNA transcription initiation lags that of bacterial and nuclear DNA transcription. We report structures of two transcription initiation intermediate states of yeast mtRNAP that explain promoter melting, template alignment, DNA scrunching, abortive synthesis, and transition into elongation. In the partially melted initiation complex (PmIC), transcription factor MTF1 makes base-specific interactions with flipped non-template (NT) nucleotides "AAGT" at -4 to -1 positions of the DNA promoter. In the initiation complex (IC), the template in the expanded 7-mer bubble positions the RNA and NTP analog UTPαS, while NT scrunches into an NT loop. The scrunched NT loop is stabilized by the centrally positioned MTF1 C-tail. The IC and PmIC states coexist in solution, revealing a dynamic equilibrium between two functional states. Frequent scrunching/unscruching transitions and the imminent steric clashes of the inflating NT loop and growing RNA:DNA with the C-tail explain abortive synthesis and transition into elongation.
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Affiliation(s)
- Brent De Wijngaert
- Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000 Leuven, Belgium
| | - Shemaila Sultana
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854, USA
| | - Anupam Singh
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854, USA
| | - Chhaya Dharia
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854, USA
| | - Hans Vanbuel
- Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000 Leuven, Belgium
| | - Jiayu Shen
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854, USA
| | - Daniel Vasilchuk
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854, USA
| | - Sergio E Martinez
- Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000 Leuven, Belgium
| | - Eaazhisai Kandiah
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38043 Grenoble, France
| | - Smita S Patel
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854, USA.
| | - Kalyan Das
- Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000 Leuven, Belgium.
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4
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Sohn BK, Basu U, Lee SW, Cho H, Shen J, Deshpande A, Johnson LC, Das K, Patel SS, Kim H. The dynamic landscape of transcription initiation in yeast mitochondria. Nat Commun 2020; 11:4281. [PMID: 32855416 PMCID: PMC7452894 DOI: 10.1038/s41467-020-17793-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 07/14/2020] [Indexed: 01/24/2023] Open
Abstract
Controlling efficiency and fidelity in the early stage of mitochondrial DNA transcription is crucial for regulating cellular energy metabolism. Conformational transitions of the transcription initiation complex must be central for such control, but how the conformational dynamics progress throughout transcription initiation remains unknown. Here, we use single-molecule fluorescence resonance energy transfer techniques to examine the conformational dynamics of the transcriptional system of yeast mitochondria with single-base resolution. We show that the yeast mitochondrial transcriptional complex dynamically transitions among closed, open, and scrunched states throughout the initiation stage. Then abruptly at position +8, the dynamic states of initiation make a sharp irreversible transition to an unbent conformation with associated promoter release. Remarkably, stalled initiation complexes remain in dynamic scrunching and unscrunching states without dissociating the RNA transcript, implying the existence of backtracking transitions with possible regulatory roles. The dynamic landscape of transcription initiation suggests a kinetically driven regulation of mitochondrial transcription.
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Affiliation(s)
- Byeong-Kwon Sohn
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Urmimala Basu
- Department of Biochemistry and Molecular Biology, Rutgers University, Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA
| | - Seung-Won Lee
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Hayoon Cho
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Jiayu Shen
- Department of Biochemistry and Molecular Biology, Rutgers University, Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA
| | - Aishwarya Deshpande
- Department of Biochemistry and Molecular Biology, Rutgers University, Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA
| | - Laura C Johnson
- Department of Biochemistry and Molecular Biology, Rutgers University, Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA
| | - Kalyan Das
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000, Leuven, Belgium
| | - Smita S Patel
- Department of Biochemistry and Molecular Biology, Rutgers University, Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA.
| | - Hajin Kim
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea.
- Institute for Basic Science, Ulsan, Republic of Korea.
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5
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Sukarta OC, Townsend PD, Llewelyn A, Dixon CH, Slootweg EJ, Pålsson LO, Takken FL, Goverse A, Cann MJ. A DNA-Binding Bromodomain-Containing Protein Interacts with and Reduces Rx1-Mediated Immune Response to Potato Virus X. PLANT COMMUNICATIONS 2020; 1:100086. [PMID: 32715296 PMCID: PMC7371201 DOI: 10.1016/j.xplc.2020.100086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 06/09/2020] [Accepted: 06/11/2020] [Indexed: 06/01/2023]
Abstract
Plant NLR proteins enable the immune system to recognize and respond to pathogen attack. An early consequence of immune activation is transcriptional reprogramming. Some NLRs have been shown to act in the nucleus and interact with transcription factors. The Rx1 NLR protein of potato binds and distorts double-stranded DNA. However, the components of the chromatin-localized Rx1 complex are largely unknown. Here, we report a physical and functional interaction between Rx1 and NbDBCP, a bromodomain-containing chromatin-interacting protein. NbDBCP accumulates in the nucleoplasm and nucleolus, interacts with chromatin, and redistributes Rx1 to the nucleolus in a subpopulation of imaged cells. Rx1 overexpression reduces the interaction between NbDBCP and chromatin. NbDBCP is a negative regulator of Rx1-mediated immune responses to potato virus X (PVX), and this activity requires an intact bromodomain. Previously, Rx1 has been shown to regulate the DNA-binding activity of a Golden2-like transcription factor, NbGlk1. Rx1 and NbDBCP act synergistically to reduce NbGlk1 DNA binding, suggesting a mode of action for NbDBCP's inhibitory effect on immunity. This study provides new mechanistic insight into the mechanism by which a chromatin-localized NLR complex co-ordinates immune signaling after pathogen perception.
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Affiliation(s)
- Octavina C.A. Sukarta
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Philip D. Townsend
- Department of Biosciences, Durham University, South Road, Durham DH1 3LE, UK
- Biophysical Sciences Institute, Durham University, South Road, Durham DH1 3LE, UK
| | - Alexander Llewelyn
- Department of Biosciences, Durham University, South Road, Durham DH1 3LE, UK
- Biophysical Sciences Institute, Durham University, South Road, Durham DH1 3LE, UK
| | - Christopher H. Dixon
- Department of Biosciences, Durham University, South Road, Durham DH1 3LE, UK
- Biophysical Sciences Institute, Durham University, South Road, Durham DH1 3LE, UK
| | - Erik J. Slootweg
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Lars-Olof Pålsson
- Biophysical Sciences Institute, Durham University, South Road, Durham DH1 3LE, UK
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, UK
| | - Frank L.W. Takken
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Aska Goverse
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Martin J. Cann
- Department of Biosciences, Durham University, South Road, Durham DH1 3LE, UK
- Biophysical Sciences Institute, Durham University, South Road, Durham DH1 3LE, UK
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6
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Basu U, Lee SW, Deshpande A, Shen J, Sohn BK, Cho H, Kim H, Patel SS. The C-terminal tail of the yeast mitochondrial transcription factor Mtf1 coordinates template strand alignment, DNA scrunching and timely transition into elongation. Nucleic Acids Res 2020; 48:2604-2620. [PMID: 31980825 PMCID: PMC7049685 DOI: 10.1093/nar/gkaa040] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 12/20/2019] [Accepted: 01/13/2020] [Indexed: 11/16/2022] Open
Abstract
Mitochondrial RNA polymerases depend on initiation factors, such as TFB2M in humans and Mtf1 in yeast Saccharomyces cerevisiae, for promoter-specific transcription. These factors drive the melting of promoter DNA, but how they support RNA priming and growth was not understood. We show that the flexible C-terminal tails of Mtf1 and TFB2M play a crucial role in RNA priming by aiding template strand alignment in the active site for high-affinity binding of the initiating nucleotides. Using single-molecule fluorescence approaches, we show that the Mtf1 C-tail promotes RNA growth during initiation by stabilizing the scrunched DNA conformation. Additionally, due to its location in the path of the nascent RNA, the C-tail of Mtf1 serves as a sensor of the RNA-DNA hybrid length. Initially, steric clashes of the Mtf1 C-tail with short RNA-DNA hybrids cause abortive synthesis but clashes with longer RNA-DNA trigger conformational changes for the timely release of the promoter DNA to commence the transition into elongation. The remarkable similarities in the functions of the C-tail and σ3.2 finger of the bacterial factor suggest mechanistic convergence of a flexible element in the transcription initiation factor that engages the DNA template for RNA priming and growth and disengages when needed to generate the elongation complex.
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Affiliation(s)
- Urmimala Basu
- Department of Biochemistry and Molecular Biology, Rutgers University, Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA
- Graduate School of Biomedical Sciences at Robert Wood Johnson Medical School of the Rutgers University, USA
| | - Seung-Won Lee
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Aishwarya Deshpande
- Department of Biochemistry and Molecular Biology, Rutgers University, Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA
| | - Jiayu Shen
- Department of Biochemistry and Molecular Biology, Rutgers University, Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA
- Graduate School of Biomedical Sciences at Robert Wood Johnson Medical School of the Rutgers University, USA
| | - Byeong-Kwon Sohn
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Hayoon Cho
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Hajin Kim
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Republic of Korea
| | - Smita S Patel
- Department of Biochemistry and Molecular Biology, Rutgers University, Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA
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7
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Duchi D, Gryte K, Robb NC, Morichaud Z, Sheppard C, Brodolin K, Wigneshweraraj S, Kapanidis AN. Conformational heterogeneity and bubble dynamics in single bacterial transcription initiation complexes. Nucleic Acids Res 2019; 46:677-688. [PMID: 29177430 PMCID: PMC5778504 DOI: 10.1093/nar/gkx1146] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 10/31/2017] [Indexed: 12/16/2022] Open
Abstract
Transcription initiation is a major step in gene regulation for all organisms. In bacteria, the promoter DNA is first recognized by RNA polymerase (RNAP) to yield an initial closed complex. This complex subsequently undergoes conformational changes resulting in DNA strand separation to form a transcription bubble and an RNAP-promoter open complex; however, the series and sequence of conformational changes, and the factors that influence them are unclear. To address the conformational landscape and transitions in transcription initiation, we applied single-molecule Förster resonance energy transfer (smFRET) on immobilized Escherichia coli transcription open complexes. Our results revealed the existence of two stable states within RNAP–DNA complexes in which the promoter DNA appears to adopt closed and partially open conformations, and we observed large-scale transitions in which the transcription bubble fluctuated between open and closed states; these transitions, which occur roughly on the 0.1 s timescale, are distinct from the millisecond-timescale dynamics previously observed within diffusing open complexes. Mutational studies indicated that the σ70 region 3.2 of the RNAP significantly affected the bubble dynamics. Our results have implications for many steps of transcription initiation, and support a bend-load-open model for the sequence of transitions leading to bubble opening during open complex formation.
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Affiliation(s)
- Diego Duchi
- Gene Machines Group, Biological Physics Research Unit, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
| | - Kristofer Gryte
- Gene Machines Group, Biological Physics Research Unit, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
| | - Nicole C Robb
- Gene Machines Group, Biological Physics Research Unit, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
| | - Zakia Morichaud
- CNRS UMR 9004, Institut de Recherche en Infectiologie de Montpellier, Université de Montpellier, 1919 route de Mende, 34293 Montpellier, France
| | - Carol Sheppard
- MRC Centre for Molecular Microbiology and Infection, Imperial College London, London SW7 2AZ, UK
| | - Konstantin Brodolin
- CNRS UMR 9004, Institut de Recherche en Infectiologie de Montpellier, Université de Montpellier, 1919 route de Mende, 34293 Montpellier, France
| | | | - Achillefs N Kapanidis
- Gene Machines Group, Biological Physics Research Unit, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
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8
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Regulation of PCNA cycling on replicating DNA by RFC and RFC-like complexes. Nat Commun 2019; 10:2420. [PMID: 31160570 PMCID: PMC6546911 DOI: 10.1038/s41467-019-10376-w] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 05/07/2019] [Indexed: 02/03/2023] Open
Abstract
Replication-Factor-C (RFC) and RFC-like complexes (RLCs) mediate chromatin engagement of the proliferating cell nuclear antigen (PCNA). It remains controversial how RFC and RLCs cooperate to regulate PCNA loading and unloading. Here, we show the distinct PCNA loading or unloading activity of each clamp loader. ATAD5-RLC possesses the potent PCNA unloading activity. ATPase motif and collar domain of ATAD5 are crucial for the unloading activity. DNA structures did not affect PCNA unloading activity of ATAD5-RLC. ATAD5-RLC could unload ubiquitinated PCNA. Through single molecule measurements, we reveal that ATAD5-RLC unloaded PCNA through one intermediate state before ATP hydrolysis. RFC loaded PCNA through two intermediate states on DNA, separated by ATP hydrolysis. Replication proteins such as Fen1 could inhibit the PCNA unloading activity of Elg1-RLC, a yeast homolog of ATAD5-RLC in vitro. Our findings provide molecular insights into how PCNA is released from chromatin to finalize DNA replication/repair.
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9
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Townsend PD, Dixon CH, Slootweg EJ, Sukarta OCA, Yang AWH, Hughes TR, Sharples GJ, Pålsson LO, Takken FLW, Goverse A, Cann MJ. The intracellular immune receptor Rx1 regulates the DNA-binding activity of a Golden2-like transcription factor. J Biol Chem 2018; 293:3218-3233. [PMID: 29217772 PMCID: PMC5836133 DOI: 10.1074/jbc.ra117.000485] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 11/14/2017] [Indexed: 12/22/2022] Open
Abstract
Plant nucleotide-binding leucine-rich repeat (NLR) proteins enable the immune system to recognize and respond to pathogen attack. An early consequence of immune activation is transcriptional reprogramming, and some NLRs have been shown to act in the nucleus and interact with transcription factors. The Rx1 NLR protein of potato is further able to bind and distort double-stranded DNA. However, Rx1 host targets that support a role for Rx1 in transcriptional reprogramming at DNA are unknown. Here, we report a functional interaction between Rx1 and NbGlk1, a Golden2-like transcription factor. Rx1 binds to NbGlk1 in vitro and in planta. NbGlk1 binds to known Golden2-like consensus DNA sequences. Rx1 reduces the binding affinity of NbGlk1 for DNA in vitro. NbGlk1 activates cellular responses to potato virus X, whereas Rx1 associates with NbGlk1 and prevents its assembly on DNA in planta unless activated by PVX. This study provides new mechanistic insight into how an NLR can coordinate an immune signaling response at DNA following pathogen perceptions.
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Affiliation(s)
- Philip D Townsend
- From the Department of Biosciences
- Biophysical Sciences Institute, and
| | | | - Erik J Slootweg
- the Laboratory of Nematology, Department of Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Octavina C A Sukarta
- the Laboratory of Nematology, Department of Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Ally W H Yang
- the Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada, and
| | - Timothy R Hughes
- the Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada, and
| | - Gary J Sharples
- From the Department of Biosciences
- Biophysical Sciences Institute, and
| | - Lars-Olof Pålsson
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, United Kingdom
| | - Frank L W Takken
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Aska Goverse
- the Laboratory of Nematology, Department of Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Martin J Cann
- From the Department of Biosciences,
- Biophysical Sciences Institute, and
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10
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Ramachandran A, Basu U, Sultana S, Nandakumar D, Patel SS. Human mitochondrial transcription factors TFAM and TFB2M work synergistically in promoter melting during transcription initiation. Nucleic Acids Res 2016; 45:861-874. [PMID: 27903899 PMCID: PMC5314767 DOI: 10.1093/nar/gkw1157] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 11/02/2016] [Accepted: 11/04/2016] [Indexed: 12/26/2022] Open
Abstract
Human mitochondrial DNA is transcribed by POLRMT with the help of two initiation factors, TFAM and TFB2M. The current model postulates that the role of TFAM is to recruit POLRMT and TFB2M to melt the promoter. However, we show that TFAM has ‘post-recruitment’ roles in promoter melting and RNA synthesis, which were revealed by studying the pre-initiation steps of promoter binding, bending and melting, and abortive RNA synthesis. Our 2-aminopurine mapping studies show that the LSP (Light Strand Promoter) is melted from −4 to +1 in the open complex with all three proteins and from −4 to +3 with addition of ATP. Our equilibrium binding studies show that POLRMT forms stable complexes with TFB2M or TFAM on LSP with low-nanomolar Kd values, but these two-component complexes lack the mechanism to efficiently melt the promoter. This indicates that POLRMT needs both TFB2M and TFAM to melt the promoter. Additionally, POLRMT+TFB2M makes 2-mer abortives on LSP, but longer RNAs are observed only with TFAM. These results are explained by TFAM playing a role in promoter melting and/or stabilization of the open complex on LSP. Based on our results, we propose a refined model of transcription initiation by the human mitochondrial transcription machinery.
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Affiliation(s)
- Aparna Ramachandran
- Department of Biochemistry and Molecular Biology, Rutgers, Robert Wood Johnson Medical school, Piscataway, NJ 08854, USA
| | - Urmimala Basu
- Department of Biochemistry and Molecular Biology, Rutgers, Robert Wood Johnson Medical school, Piscataway, NJ 08854, USA.,Graduate School of Biomedical Sciences, Rutgers University, Piscataway, NJ 08854, USA
| | - Shemaila Sultana
- Department of Biochemistry and Molecular Biology, Rutgers, Robert Wood Johnson Medical school, Piscataway, NJ 08854, USA
| | - Divya Nandakumar
- Department of Biochemistry and Molecular Biology, Rutgers, Robert Wood Johnson Medical school, Piscataway, NJ 08854, USA
| | - Smita S Patel
- Department of Biochemistry and Molecular Biology, Rutgers, Robert Wood Johnson Medical school, Piscataway, NJ 08854, USA
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11
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Yoo J, Kim H, Aksimentiev A, Ha T. Direct evidence for sequence-dependent attraction between double-stranded DNA controlled by methylation. Nat Commun 2016; 7:11045. [PMID: 27001929 PMCID: PMC4804163 DOI: 10.1038/ncomms11045] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 02/16/2016] [Indexed: 02/06/2023] Open
Abstract
Although proteins mediate highly ordered DNA organization in vivo, theoretical studies suggest that homologous DNA duplexes can preferentially associate with one another even in the absence of proteins. Here we combine molecular dynamics simulations with single-molecule fluorescence resonance energy transfer experiments to examine the interactions between duplex DNA in the presence of spermine, a biological polycation. We find that AT-rich DNA duplexes associate more strongly than GC-rich duplexes, regardless of the sequence homology. Methyl groups of thymine acts as a steric block, relocating spermine from major grooves to interhelical regions, thereby increasing DNA–DNA attraction. Indeed, methylation of cytosines makes attraction between GC-rich DNA as strong as that between AT-rich DNA. Recent genome-wide chromosome organization studies showed that remote contact frequencies are higher for AT-rich and methylated DNA, suggesting that direct DNA–DNA interactions that we report here may play a role in the chromosome organization and gene regulation. Theoretical studies suggest that homologous DNA duplexes can preferentially associate with one another in the absence of proteins. Here, the authors show that GC-rich DNA with methylated cytosine and AT-rich DNA duplexes associate more strongly than GC-rich duplexes regardless of the sequence homology.
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Affiliation(s)
- Jejoong Yoo
- Department of Physics and the Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Hajin Kim
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Korea.,Center for Soft and Living Matter, Institute for Basic Science, Ulsan, Korea
| | - Aleksei Aksimentiev
- Department of Physics and the Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Taekjip Ha
- Department of Physics and the Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.,Howard Hughes Medical Institute, Baltimore, Maryland 21205, USA.,Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, Maryland 21205, USA.,Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21205, USA.,Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21205, USA
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12
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Fenyk S, Townsend PD, Dixon CH, Spies GB, de San Eustaquio Campillo A, Slootweg EJ, Westerhof LB, Gawehns FKK, Knight MR, Sharples GJ, Goverse A, Pålsson LO, Takken FLW, Cann MJ. The Potato Nucleotide-binding Leucine-rich Repeat (NLR) Immune Receptor Rx1 Is a Pathogen-dependent DNA-deforming Protein. J Biol Chem 2015; 290:24945-60. [PMID: 26306038 PMCID: PMC4599002 DOI: 10.1074/jbc.m115.672121] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 08/14/2015] [Indexed: 11/06/2022] Open
Abstract
Plant nucleotide-binding leucine-rich repeat (NLR) proteins enable cells to respond to pathogen attack. Several NLRs act in the nucleus; however, conserved nuclear targets that support their role in immunity are unknown. Previously, we noted a structural homology between the nucleotide-binding domain of NLRs and DNA replication origin-binding Cdc6/Orc1 proteins. Here we show that the NB-ARC (nucleotide-binding, Apaf-1, R-proteins, and CED-4) domain of the Rx1 NLR of potato binds nucleic acids. Rx1 induces ATP-dependent bending and melting of DNA in vitro, dependent upon a functional P-loop. In situ full-length Rx1 binds nuclear DNA following activation by its cognate pathogen-derived effector protein, the coat protein of potato virus X. In line with its obligatory nucleocytoplasmic distribution, DNA binding was only observed when Rx1 was allowed to freely translocate between both compartments and was activated in the cytoplasm. Immune activation induced by an unrelated NLR-effector pair did not trigger an Rx1-DNA interaction. DNA binding is therefore not merely a consequence of immune activation. These data establish a role for DNA distortion in Rx1 immune signaling and define DNA as a molecular target of an activated NLR.
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Affiliation(s)
- Stepan Fenyk
- From the School of Biological and Biomedical Sciences, Biophysical Sciences Institute
| | - Philip D Townsend
- From the School of Biological and Biomedical Sciences, Biophysical Sciences Institute
| | - Christopher H Dixon
- From the School of Biological and Biomedical Sciences, Biophysical Sciences Institute
| | - Gerhard B Spies
- From the School of Biological and Biomedical Sciences, Biophysical Sciences Institute
| | | | - Erik J Slootweg
- the Laboratory of Nematology, Department of Plant Sciences, Wageningen University, 6708 PB, Wageningen, The Netherlands, and
| | - Lotte B Westerhof
- the Laboratory of Nematology, Department of Plant Sciences, Wageningen University, 6708 PB, Wageningen, The Netherlands, and
| | - Fleur K K Gawehns
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Marc R Knight
- From the School of Biological and Biomedical Sciences, Biophysical Sciences Institute
| | - Gary J Sharples
- From the School of Biological and Biomedical Sciences, Biophysical Sciences Institute
| | - Aska Goverse
- the Laboratory of Nematology, Department of Plant Sciences, Wageningen University, 6708 PB, Wageningen, The Netherlands, and
| | - Lars-Olof Pålsson
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, United Kingdom
| | - Frank L W Takken
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Martin J Cann
- From the School of Biological and Biomedical Sciences, Biophysical Sciences Institute,
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13
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Traverso JJ, Manoranjan VS, Bishop AR, Rasmussen KØ, Voulgarakis NK. Allostery through protein-induced DNA bubbles. Sci Rep 2015; 5:9037. [PMID: 25762409 PMCID: PMC4356955 DOI: 10.1038/srep09037] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 02/13/2015] [Indexed: 01/03/2023] Open
Abstract
Allostery through DNA is increasingly recognized as an important modulator of DNA functions. Here, we show that the coalescence of protein-induced DNA bubbles can mediate allosteric interactions that drive protein aggregation. We propose that such allostery may regulate DNA's flexibility and the assembly of the transcription machinery. Mitochondrial transcription factor A (TFAM), a dual-function protein involved in mitochondrial DNA (mtDNA) packaging and transcription initiation, is an ideal candidate to test such a hypothesis owing to its ability to locally unwind the double helix. Numerical simulations demonstrate that the coalescence of TFAM-induced bubbles can explain experimentally observed TFAM oligomerization. The resulting melted DNA segment, approximately 10 base pairs long, around the joints of the oligomers act as flexible hinges, which explains the efficiency of TFAM in compacting DNA. Since mitochondrial polymerase (mitoRNAP) is involved in melting the transcription bubble, TFAM may use the same allosteric interaction to both recruit mitoRNAP and initiate transcription.
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Affiliation(s)
- Joseph J Traverso
- 1] Department of Mathematics, Washington State University, Richland, WA 99354, USA [2] Department of Mechanical Engineering, Washington State University, Richland, WA 99354, USA
| | | | - A R Bishop
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Kim Ø Rasmussen
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
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14
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Deshpande AP, Patel SS. Interactions of the yeast mitochondrial RNA polymerase with the +1 and +2 promoter bases dictate transcription initiation efficiency. Nucleic Acids Res 2014; 42:11721-32. [PMID: 25249624 PMCID: PMC4191429 DOI: 10.1093/nar/gku868] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Mitochondrial promoters of Saccharomyces cerevisiae share a conserved -8 to +1 sequence with +1+2 AA, AG or AT initiation sequence, which dictates the efficiency of transcription initiation by the mitochondrial RNA polymerase Rpo41 and its initiation factor Mtf1. We used 2-aminopurine fluorescence to monitor promoter melting and measured the kcat/Km of 2-mer synthesis to quantify initiation efficiency with systematic changes of the +1+2 base pairs to matched and mismatched pairs. We show that AA promoters are most efficient, followed by AG and then AT promoters, and the differences in their efficiencies stem specifically from differential melting of +1+2 region without affecting melting of the upstream -4 to -1 region. Inefficient +1+2 melting increases the initial NTPs Kms of the AG and AT promoters relative to AA or singly mispaired promoters. The 16-100-fold higher catalytic efficiency of AA initiation sequence relative to AG and AT, respectively, is partly due to Rpo41-Mtf1 interactions with the +1+2 non-template adenines that generate a stable pre-transcribing complex. We propose a model where the +2 base pair regulates the efficiency of initial transcription by controlling multiple steps including downstream promoter opening, +1+2 NTPs binding, and the rate of 2-mer synthesis.
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Affiliation(s)
- Aishwarya P Deshpande
- Department of Biochemistry and Molecular Biology, RUTGERS-Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA
| | - Smita S Patel
- Department of Biochemistry and Molecular Biology, RUTGERS-Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA
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15
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Protein-guided RNA dynamics during early ribosome assembly. Nature 2014; 506:334-8. [PMID: 24522531 PMCID: PMC3968076 DOI: 10.1038/nature13039] [Citation(s) in RCA: 124] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Accepted: 01/20/2014] [Indexed: 01/30/2023]
Abstract
The assembly of 30S ribosomes requires the precise addition of 20 proteins to the 16S ribosomal RNA. How early binding proteins change the rRNA structure so that later proteins may join the complex is poorly understood. Here we use single molecule fluorescence resonance energy transfer (smFRET) to observe real-time encounters between ribosomal protein S4 and the 16S 5′ domain RNA at an early stage of 30S assembly. Dynamic initial S4-RNA complexes pass through a stable non-native intermediate before converting to the native complex, showing that non-native structures can offer a low free energy path to protein-RNA recognition. Three-color FRET and molecular dynamics (MD) simulations reveal how S4 changes the frequency and direction of RNA helix motions, guiding a conformational switch that enforces the hierarchy of protein addition. This protein-guided dynamics offers an alternative explanation for induced fit in RNA-protein complexes.
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16
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Fluorescent methods to study transcription initiation and transition into elongation. EXPERIENTIA SUPPLEMENTUM (2012) 2014; 105:105-30. [PMID: 25095993 PMCID: PMC4430081 DOI: 10.1007/978-3-0348-0856-9_6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
The DNA-dependent RNA polymerases induce specific conformational changes in the promoter DNA during transcription initiation. Fluorescence spectroscopy sensitively monitors these DNA conformational changes in real time and at equilibrium providing powerful ways to estimate interactions in transcriptional complexes and to assess how transcription is regulated by the promoter DNA sequence, transcription factors, and small ligands. Ensemble fluorescence methods described here probe the individual steps of promoter binding, bending, opening, and transition into the elongation using T7 phage and mitochondrial transcriptional systems as examples.
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17
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Single-molecule and single-particle imaging of molecular motors in vitro and in vivo. EXPERIENTIA SUPPLEMENTUM (2012) 2014; 105:131-59. [PMID: 25095994 DOI: 10.1007/978-3-0348-0856-9_7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Motor proteins are multi-potent molecular machines, whose localisation, function and regulation are achieved through tightly controlled processes involving conformational changes and interactions with their tracks, cargos and binding partners. Understanding how these complex machines work requires dissection of these processes both in space and time. Complementing the traditional ensemble measurements, single-molecule assays enable the detection of rare or short-lived intermediates and molecular heterogeneities, and the measurements of subpopulation dynamics. This chapter is focusing on the fluorescence imaging of single motors and their cargo. It discusses what is required in order to achieve single-molecule imaging with high temporal and spatial resolution and how these requirements are met both in vitro and in vivo. It also presents a general overview and applied examples of the major single-molecule imaging techniques and experimental assays which have been used to study motor proteins.
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18
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Deshayes S, Divita G. Fluorescence technologies for monitoring interactions between biological molecules in vitro. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2013; 113:109-43. [PMID: 23244790 DOI: 10.1016/b978-0-12-386932-6.00004-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Over the last two centuries, the discovery and understanding of the principle of fluorescence have provided new means of characterizing physical/biological/chemical processes in a noninvasive manner. Fluorescence spectroscopy has become one of the most powerful and widely applied methods in the life sciences, from fundamental research to clinical applications. In vitro, fluorescence approaches offer the potential to sense in real-time extra and intracellular molecular interactions and enzymatic reactions, which constitutes a major advantage over other approaches to the study of biomolecular interactions. This technology has been used for the characterization of protein/protein, protein/nucleic acid, protein/substrate, and biomembrane/biomolecule interactions, which play crucial roles in the regulation of cellular pathways. This chapter reviews the different fluorescence strategies that have been developed for sensing molecular interactions in vitro at both steady- and pre-steady-state levels.
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Affiliation(s)
- Sebastien Deshayes
- Centre de Recherches de Biochimie Macromoléculaire, Department of Chemical Biology and Nanotechnology for Therapeutics, CRBM-CNRS, UMR-5237, UM1-UM2, University of Montpellier, 1919 Route de Mende, Montpellier, France
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19
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Kim H, Ha T. Single-molecule nanometry for biological physics. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2013; 76:016601. [PMID: 23249673 PMCID: PMC3549428 DOI: 10.1088/0034-4885/76/1/016601] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Precision measurement is a hallmark of physics but the small length scale (∼nanometer) of elementary biological components and thermal fluctuations surrounding them challenge our ability to visualize their action. Here, we highlight the recent developments in single-molecule nanometry where the position of a single fluorescent molecule can be determined with nanometer precision, reaching the limit imposed by the shot noise, and the relative motion between two molecules can be determined with ∼0.3 nm precision at ∼1 ms time resolution, as well as how these new tools are providing fundamental insights into how motor proteins move on cellular highways. We will also discuss how interactions between three and four fluorescent molecules can be used to measure three and six coordinates, respectively, allowing us to correlate the movements of multiple components. Finally, we will discuss recent progress in combining angstrom-precision optical tweezers with single-molecule fluorescent detection, opening new windows for multi-dimensional single-molecule nanometry for biological physics.
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Affiliation(s)
- Hajin Kim
- Howard Hughes Medical Institute, Urbana, IL 61801, USA
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20
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Treutlein B, Muschielok A, Andrecka J, Jawhari A, Buchen C, Kostrewa D, Hög F, Cramer P, Michaelis J. Dynamic architecture of a minimal RNA polymerase II open promoter complex. Mol Cell 2012; 46:136-46. [PMID: 22424775 DOI: 10.1016/j.molcel.2012.02.008] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2011] [Revised: 11/04/2011] [Accepted: 02/10/2012] [Indexed: 01/22/2023]
Abstract
The open promoter complex (OC) is a central intermediate during transcription initiation that contains a DNA bubble. Here, we employ single-molecule Förster resonance energy transfer experiments and Nano-Positioning System analysis to determine the three-dimensional architecture of a minimal OC consisting of promoter DNA, including a TATA box and an 11-nucleotide mismatched region around the transcription start site, TATA box-binding protein (TBP), RNA polymerase (Pol) II, and general transcription factor (TF)IIB and TFIIF. In this minimal OC, TATA-DNA and TBP reside above the Pol II cleft between clamp and protrusion domains. Downstream DNA is dynamically loaded into and unloaded from the Pol II cleft at a timescale of seconds. The TFIIB core domain is displaced from the Pol II wall, where it is located in the closed promoter complex. These results reveal large overall structural changes during the initiation-elongation transition, which are apparently accommodated by the intrinsic flexibility of TFIIB.
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Affiliation(s)
- Barbara Treutlein
- Department of Chemistry and Center for Integrated Protein Science München, Ludwig-Maximilians-Universität München, Butenandtstr.11, 81377 Munich, Germany
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21
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Mechanism of transcription initiation by the yeast mitochondrial RNA polymerase. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2012; 1819:930-8. [PMID: 22353467 DOI: 10.1016/j.bbagrm.2012.02.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2011] [Revised: 02/03/2012] [Accepted: 02/04/2012] [Indexed: 02/03/2023]
Abstract
Mitochondria are the major supplier of cellular energy in the form of ATP. Defects in normal ATP production due to dysfunctions in mitochondrial gene expression are responsible for many mitochondrial and aging related disorders. Mitochondria carry their own DNA genome which is transcribed by relatively simple transcriptional machinery consisting of the mitochondrial RNAP (mtRNAP) and one or more transcription factors. The mtRNAPs are remarkably similar in sequence and structure to single-subunit bacteriophage T7 RNAP but they require accessory transcription factors for promoter-specific initiation. Comparison of the mechanisms of T7 RNAP and mtRNAP provides a framework to better understand how mtRNAP and the transcription factors work together to facilitate promoter selection, DNA melting, initiating nucleotide binding, and promoter clearance. This review focuses primarily on the mechanistic characterization of transcription initiation by the yeast Saccharomyces cerevisiae mtRNAP (Rpo41) and its transcription factor (Mtf1) drawing insights from the homologous T7 and the human mitochondrial transcription systems. We discuss regulatory mechanisms of mitochondrial transcription and the idea that the mtRNAP acts as the in vivo ATP "sensor" to regulate gene expression. This article is part of a Special Issue entitled: Mitochondrial Gene Expression.
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22
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Tang GQ, Deshpande AP, Patel SS. Transcription factor-dependent DNA bending governs promoter recognition by the mitochondrial RNA polymerase. J Biol Chem 2011; 286:38805-38813. [PMID: 21911502 DOI: 10.1074/jbc.m111.261966] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Promoter recognition is the first and the most important step during gene expression. Our studies of the yeast (Saccharomyces cerevisiae) mitochondrial (mt) transcription machinery provide mechanistic understandings on the basic problem of how the mt RNA polymerase (RNAP) with the help of the initiation factor discriminates between promoter and non-promoter sequences. We have used fluorescence-based approaches to quantify DNA binding, bending, and opening steps by the core mtRNAP subunit (Rpo41) and the transcription factor (Mtf1). Our results show that promoter recognition is not achieved by tight and selective binding to the promoter sequence. Instead, promoter recognition is achieved by an induced-fit mechanism of transcription factor-dependent differential conformational changes in the promoter and non-promoter DNAs. While Rpo41 induces a slight bend upon binding both the DNAs, addition of the Mtf1 results in severe bending of the promoter and unbending of the non-promoter DNA. Only the sharply bent DNA results in the catalytically active open complex. Such an induced-fit mechanism serves three purposes: 1) assures catalysis at promoter sites, 2) prevents RNA synthesis at non-promoter sites, and 3) provides a conformational state at the non-promoter sites that would aid in facile translocation to scan for specific sites.
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Affiliation(s)
- Guo-Qing Tang
- Department of Biochemistry, Robert Wood Johnson Medical School, University of Medicine & Dentistry of New Jersey (UMDNJ), Piscataway, New Jersey 08854
| | - Aishwarya P Deshpande
- Department of Biochemistry, Robert Wood Johnson Medical School, University of Medicine & Dentistry of New Jersey (UMDNJ), Piscataway, New Jersey 08854
| | - Smita S Patel
- Department of Biochemistry, Robert Wood Johnson Medical School, University of Medicine & Dentistry of New Jersey (UMDNJ), Piscataway, New Jersey 08854.
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