1
|
Choi SR, Lee J, Seo YJ, Jin HS, Ahn HB, Go Y, Kim NK, Ryu KS, Lee JH. Molecular basis of facilitated target search and sequence discrimination of TALE homeodomain transcription factor Meis1. Nat Commun 2024; 15:6984. [PMID: 39143123 PMCID: PMC11325038 DOI: 10.1038/s41467-024-51297-7] [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: 02/22/2023] [Accepted: 08/05/2024] [Indexed: 08/16/2024] Open
Abstract
Transcription factors specifically bind to their consensus sequence motifs and regulate transcription efficiency. Transcription factors are also able to non-specifically contact the phosphate backbone of DNA through electrostatic interaction. The homeodomain of Meis1 TALE human transcription factor (Meis1-HD) recognizes its target DNA sequences via two DNA contact regions, the L1-α1 region and the α3 helix (specific binding mode). This study demonstrates that the non-specific binding mode of Meis1-HD is the energetically favored process during DNA binding, achieved by the interaction of the L1-α1 region with the phosphate backbone. An NMR dynamics study suggests that non-specific binding might set up an intermediate structure which can then rapidly and easily find the consensus region on a long section of genomic DNA in a facilitated binding process. Structural analysis using NMR and molecular dynamics shows that key structural distortions in the Meis1-HD-DNA complex are induced by various single nucleotide mutations in the consensus sequence, resulting in decreased DNA binding affinity. Collectively, our results elucidate the detailed molecular mechanism of how Meis1-HD recognizes single nucleotide mutations within its consensus sequence: (i) through the conformational features of the α3 helix; and (ii) by the dynamic features (rigid or flexible) of the L1 loop and the α3 helix. These findings enhance our understanding of how single nucleotide mutations in transcription factor consensus sequences lead to dysfunctional transcription and, ultimately, human disease.
Collapse
Affiliation(s)
- Seo-Ree Choi
- Department of Chemistry and RINS, Gyeongsang National University, Jinju, Gyeongsangnam-do, 52828, Republic of Korea
- Advanced Analysis Data Center, Korea Institute of Science and Technology, Seoul, 02456, Republic of Korea
| | - Juyong Lee
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, and College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea.
- Research Institute of Pharmaceutical Science, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea.
- Arontier Co., Seoul, 06735, Republic of Korea.
| | - Yeo-Jin Seo
- Department of Chemistry and RINS, Gyeongsang National University, Jinju, Gyeongsangnam-do, 52828, Republic of Korea
| | - Ho-Seong Jin
- Department of Chemistry and RINS, Gyeongsang National University, Jinju, Gyeongsangnam-do, 52828, Republic of Korea
| | - Hye-Bin Ahn
- Department of Chemistry and RINS, Gyeongsang National University, Jinju, Gyeongsangnam-do, 52828, Republic of Korea
| | - Youyeon Go
- Department of Chemistry and RINS, Gyeongsang National University, Jinju, Gyeongsangnam-do, 52828, Republic of Korea
| | - Nak-Kyoon Kim
- Advanced Analysis Data Center, Korea Institute of Science and Technology, Seoul, 02456, Republic of Korea
| | - Kyoung-Seok Ryu
- Protein Structure Research Team, Korea Basic Science Institute, Cheongju, Chungcheongbuk-do, 28119, Republic of Korea
| | - Joon-Hwa Lee
- Department of Chemistry and RINS, Gyeongsang National University, Jinju, Gyeongsangnam-do, 52828, Republic of Korea
| |
Collapse
|
2
|
Gupta S, Friedman LJ, Gelles J, Bell SP. A helicase-tethered ORC flip enables bidirectional helicase loading. eLife 2021; 10:74282. [PMID: 34882090 PMCID: PMC8828053 DOI: 10.7554/elife.74282] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 12/08/2021] [Indexed: 11/13/2022] Open
Abstract
Replication origins are licensed by loading two Mcm2‑7 helicases around DNA in a head-to-head conformation poised to initiate bidirectional replication. This process requires ORC, Cdc6, and Cdt1. Although different Cdc6 and Cdt1 molecules load each helicase, whether two ORC proteins are required is unclear. Using colocalization single-molecule spectroscopy combined with FRET, we investigated interactions between ORC and Mcm2‑7 during helicase loading. In the large majority of events, we observed a single ORC molecule recruiting both Mcm2‑7/Cdt1 complexes via similar interactions that end upon Cdt1 release. Between first and second helicase recruitment, a rapid change in interactions between ORC and the first Mcm2-7 occurs. Within seconds, ORC breaks the interactions mediating first Mcm2-7 recruitment, releases from its initial DNA-binding site, and forms a new interaction with the opposite face of the first Mcm2-7. This rearrangement requires release of the first Cdt1 and tethers ORC as it flips over the first Mcm2-7 to form an inverted Mcm2‑7-ORC-DNA complex required for second-helicase recruitment. To ensure correct licensing, this complex is maintained until head-to-head interactions between the two helicases are formed. Our findings reconcile previous observations and reveal a highly-coordinated series of events through which a single ORC molecule can load two oppositely-oriented helicases.
Collapse
Affiliation(s)
- Shalini Gupta
- Department of Biology, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, United States
| | - Larry J Friedman
- Department of Biochemistry, Brandeis University, Waltham, United States
| | - Jeff Gelles
- Department of Biochemistry, Brandeis University, Waltham, United States
| | - Stephen P Bell
- Department of Biology, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, United States
| |
Collapse
|
3
|
Lee AR, Hwang J, Hur JH, Ryu KS, Kim KK, Choi BS, Kim NK, Lee JH. NMR Dynamics Study Reveals the Zα Domain of Human ADAR1 Associates with and Dissociates from Z-RNA More Slowly than Z-DNA. ACS Chem Biol 2019; 14:245-255. [PMID: 30592616 DOI: 10.1021/acschembio.8b00914] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Human RNA editing enzyme ADAR1 deaminates adenosine in pre-mRNA to yield inosine. The Zα domain of human ADAR1 (hZαADAR1) binds specifically to left-handed Z-RNA as well as Z-DNA and stabilizes the Z-conformation. To answer the question of how hZαADAR1 can induce both the B-Z transition of DNA and the A-Z transition of RNA, we investigated the structure and dynamics of hZαADAR1 in complex with 6-base-pair Z-DNA or Z-RNA. We performed chemical shift perturbation and relaxation dispersion experiments on hZαADAR1 upon binding to Z-DNA as well as Z-RNA. Our study demonstrates the unique dynamics of hZαADAR1 during the A-Z transition of RNA, in which the hZαADAR1 protein forms a thermodynamically stable complex with Z-RNA, similar to Z-DNA, but kinetically converts RNA to the Z-form more slowly than DNA. We also discovered some distinct structural features of hZαADAR1 in the Z-RNA binding conformation. Our results suggest that the A-Z transition of RNA facilitated by hZαADAR1 displays unique structural and dynamic features that may be involved in targeting ADAR1 for a role in recognition of RNA substrates.
Collapse
Affiliation(s)
- Ae-Ree Lee
- Department of Chemistry and RINS, Gyeongsang National University, Gyeongnam 52828, South Korea
| | - Jihyun Hwang
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea
| | - Jeong Hwan Hur
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Gyeonggi 16419, South Korea
| | - Kyoung-Seok Ryu
- Protein Structure Research Team, Korea Basic Science Institute, Chungbuk 28119, South Korea
| | - Kyeong Kyu Kim
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Gyeonggi 16419, South Korea
| | - Byong-Seok Choi
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea
| | - Nak-Kyoon Kim
- Advanced Analysis Center, Korea Institute of Science and Technology, Seoul 02792, South Korea
| | - Joon-Hwa Lee
- Department of Chemistry and RINS, Gyeongsang National University, Gyeongnam 52828, South Korea
| |
Collapse
|
4
|
Iwahara J, Zandarashvili L, Kemme CA, Esadze A. NMR-based investigations into target DNA search processes of proteins. Methods 2018; 148:57-66. [PMID: 29753002 DOI: 10.1016/j.ymeth.2018.05.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 05/04/2018] [Indexed: 10/16/2022] Open
Abstract
To perform their function, transcription factors and DNA-repair/modifying enzymes must first locate their targets in the vast presence of nonspecific, but structurally similar sites on genomic DNA. Before reaching their targets, these proteins stochastically scan DNA and dynamically move from one site to another on DNA. Solution NMR spectroscopy provides unique atomic-level insights into the dynamic DNA-scanning processes, which are difficult to gain by any other experimental means. In this review, we provide an introductory overview on the NMR methods for the structural, dynamic, and kinetic investigations of target DNA search by proteins. We also discuss advantages and disadvantages of these NMR methods over other methods such as single-molecule techniques and biochemical approaches.
Collapse
Affiliation(s)
- Junji Iwahara
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, United States.
| | - Levani Zandarashvili
- Department of Biochemistry and Biophysics, University of Pennsylvania, United States
| | - Catherine A Kemme
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, United States
| | - Alexandre Esadze
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University, United States
| |
Collapse
|
5
|
Wieczór M, Czub J. How proteins bind to DNA: target discrimination and dynamic sequence search by the telomeric protein TRF1. Nucleic Acids Res 2017. [PMID: 28633355 PMCID: PMC5737604 DOI: 10.1093/nar/gkx534] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Target search as performed by DNA-binding proteins is a complex process, in which multiple factors contribute to both thermodynamic discrimination of the target sequence from overwhelmingly abundant off-target sites and kinetic acceleration of dynamic sequence interrogation. TRF1, the protein that binds to telomeric tandem repeats, faces an intriguing variant of the search problem where target sites are clustered within short fragments of chromosomal DNA. In this study, we use extensive (>0.5 ms in total) MD simulations to study the dynamical aspects of sequence-specific binding of TRF1 at both telomeric and non-cognate DNA. For the first time, we describe the spontaneous formation of a sequence-specific native protein-DNA complex in atomistic detail, and study the mechanism by which proteins avoid off-target binding while retaining high affinity for target sites. Our calculated free energy landscapes reproduce the thermodynamics of sequence-specific binding, while statistical approaches allow for a comprehensive description of intermediate stages of complex formation.
Collapse
Affiliation(s)
- Milosz Wieczór
- Department of Physical Chemistry, Gdansk University of Technology, ul. Narutowicza 11/12, 80-233 Gdansk, Poland
| | - Jacek Czub
- Department of Physical Chemistry, Gdansk University of Technology, ul. Narutowicza 11/12, 80-233 Gdansk, Poland
| |
Collapse
|
6
|
Ganji M, Docter M, Le Grice SFJ, Abbondanzieri EA. DNA binding proteins explore multiple local configurations during docking via rapid rebinding. Nucleic Acids Res 2016; 44:8376-84. [PMID: 27471033 PMCID: PMC5041478 DOI: 10.1093/nar/gkw666] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 07/12/2016] [Indexed: 12/15/2022] Open
Abstract
Finding the target site and associating in a specific orientation are essential tasks for DNA-binding proteins. In order to make the target search process as efficient as possible, proteins should not only rapidly diffuse to the target site but also dynamically explore multiple local configurations before diffusing away. Protein flipping is an example of this second process that has been observed previously, but the underlying mechanism of flipping remains unclear. Here, we probed the mechanism of protein flipping at the single molecule level, using HIV-1 reverse transcriptase (RT) as a model system. In order to test the effects of long-range attractive forces on flipping efficiency, we varied the salt concentration and macromolecular crowding conditions. As expected, increased salt concentrations weaken the binding of RT to DNA while increased crowding strengthens the binding. Moreover, when we analyzed the flipping kinetics, i.e. the rate and probability of flipping, at each condition we found that flipping was more efficient when RT bound more strongly. Our data are consistent with a view that DNA bound proteins undergo multiple rapid re-binding events, or short hops, that allow the protein to explore other configurations without completely dissociating from the DNA.
Collapse
Affiliation(s)
- Mahipal Ganji
- Kavli Institute of Nanoscience, Department of Bionanoscience, TU Delft, 2629HZ, Delft, The Netherlands
| | - Margreet Docter
- Kavli Institute of Nanoscience, Department of Bionanoscience, TU Delft, 2629HZ, Delft, The Netherlands
| | - Stuart F J Le Grice
- Basic Research Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Elio A Abbondanzieri
- Kavli Institute of Nanoscience, Department of Bionanoscience, TU Delft, 2629HZ, Delft, The Netherlands
| |
Collapse
|
7
|
Mahmutovic A, Berg OG, Elf J. What matters for lac repressor search in vivo--sliding, hopping, intersegment transfer, crowding on DNA or recognition? Nucleic Acids Res 2015; 43:3454-64. [PMID: 25779051 PMCID: PMC4402528 DOI: 10.1093/nar/gkv207] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 02/28/2015] [Indexed: 01/04/2023] Open
Abstract
We have investigated which aspects of transcription factor DNA interactions are most important to account for the recent in vivo search time measurements for the dimeric lac repressor. We find the best agreement for a sliding model where non-specific binding to DNA is improbable at first contact and the sliding LacI protein binds at high probability when reaching the specific Osym operator. We also find that the contribution of hopping to the overall search speed is negligible although physically unavoidable. The parameters that give the best fit reveal sliding distances, including hopping, close to what has been proposed in the past, i.e. ∼40 bp, but with an unexpectedly high 1D diffusion constant on non-specific DNA sequences. Including a mechanism of inter-segment transfer between distant DNA segments does not bring down the 1D diffusion to the expected fraction of the in vitro value. This suggests a mechanism where transcription factors can slide less hindered in vivo than what is given by a simple viscosity scaling argument or that a modification of the model is needed. For example, the estimated diffusion rate constant would be consistent with the expectation if parts of the chromosome, away from the operator site, were inaccessible for searching.
Collapse
Affiliation(s)
- Anel Mahmutovic
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75124 Uppsala, Sweden
| | - Otto G Berg
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75124 Uppsala, Sweden
| | - Johan Elf
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75124 Uppsala, Sweden
| |
Collapse
|