1
|
Chauhan M, Arshi SA, Narayanan N, Arfin HU, Sharma A. A mechanistic insight on how Compromised Hydrolysis of Triacylglycerol 7 (CHT7) restrains the involvement of it's CXC domain from quiescence repression. Int J Biol Macromol 2024; 265:130844. [PMID: 38484809 DOI: 10.1016/j.ijbiomac.2024.130844] [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: 01/24/2024] [Revised: 03/03/2024] [Accepted: 03/11/2024] [Indexed: 03/18/2024]
Abstract
CHT7 is a regulator of quiescence repression in Chlamydomonas reinhardtii. Initially, CHT7's repression activity was thought to be managed by its DNA-binding CXC domain. Later, it was found that the CHT7-CXC domain is dispensable for CHT7's activities. Rather, CHT7's predicted protein domains were proposed to be involved in regulation activities by binding to other repressors in the cell. Yet, it remains unclear why and how CHT7 refrains its CXC domain from participating in any transcriptional activities. The question becomes more intriguing, since CXC binding regions are available in promoter regions of some of the misregulated genes in CHT7 mutant (cht7). Through biophysical experiments and molecular dynamics approaches, we studied the DNA recognition behavior of CHT7-CXC. The results indicate that this domain possesses sequence selectivity due to the differential binding abilities of its subdomains. Further, to understand if the case is that CXC loses its DNA binding capabilities in the vicinity of other repressors, we examined CHT7-CXC's DNA binding stability under the spatial constraint conditions created through fusing CHT7-CXC with AsLOV2. The results show limited ability of CHT7-CXC to withstand steric forces and provide insights to why and how algal cells may hold back CHT7-CXC's indulgence in quiescence repression. CLASSIFICATIONS: Biological Sciences, Biophysics and Computational Biology.
Collapse
Affiliation(s)
- Manisha Chauhan
- Multidisciplinary Centre for Advanced Research and Studies, Jamia Millia Islamia, New Delhi 110025, India
| | - Syeda Amna Arshi
- Multidisciplinary Centre for Advanced Research and Studies, Jamia Millia Islamia, New Delhi 110025, India
| | - Naveen Narayanan
- Regional Centre for Biotechnology, NCR-Cluster Faridabad, Haryana 121001, India
| | - Haseeb Ul Arfin
- Multidisciplinary Centre for Advanced Research and Studies, Jamia Millia Islamia, New Delhi 110025, India
| | - Amit Sharma
- Multidisciplinary Centre for Advanced Research and Studies, Jamia Millia Islamia, New Delhi 110025, India.
| |
Collapse
|
2
|
Li L, Zhang D, Cao X. EBF1, PAX5, and MYC: regulation on B cell development and association with hematologic neoplasms. Front Immunol 2024; 15:1320689. [PMID: 38318177 PMCID: PMC10839018 DOI: 10.3389/fimmu.2024.1320689] [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: 10/12/2023] [Accepted: 01/08/2024] [Indexed: 02/07/2024] Open
Abstract
During lymphocyte development, a diverse repertoire of lymphocyte antigen receptors is produced to battle against pathogens, which is the basis of adaptive immunity. The diversity of the lymphocyte antigen receptors arises primarily from recombination-activated gene (RAG) protein-mediated V(D)J rearrangement in early lymphocytes. Furthermore, transcription factors (TFs), such as early B cell factor 1 (EBF1), paired box gene 5 (PAX5), and proto-oncogene myelocytomatosis oncogene (MYC), play critical roles in regulating recombination and maintaining normal B cell development. Therefore, the aberrant expression of these TFs may lead to hematologic neoplasms.
Collapse
Affiliation(s)
- Li Li
- Immune Mechanism and Therapy of Major Diseases of Luzhou Key Laboratory, School of Basic Medical Sciences, Southwest Medical University, Luzhou, China
| | - Daiquan Zhang
- Department of Traditional Chinese Medicine, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Xinmei Cao
- Immune Mechanism and Therapy of Major Diseases of Luzhou Key Laboratory, School of Basic Medical Sciences, Southwest Medical University, Luzhou, China
| |
Collapse
|
3
|
Jia Z, Gu Z. PAX5 alterations in B-cell acute lymphoblastic leukemia. Front Oncol 2022; 12:1023606. [PMID: 36387144 PMCID: PMC9640836 DOI: 10.3389/fonc.2022.1023606] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 10/13/2022] [Indexed: 12/01/2022] Open
Abstract
PAX5, a master regulator of B cell development and maintenance, is one of the most common targets of genetic alterations in B-cell acute lymphoblastic leukemia (B-ALL). PAX5 alterations consist of copy number variations (whole gene, partial, or intragenic), translocations, and point mutations, with distinct distribution across B-ALL subtypes. The multifaceted functional impacts such as haploinsufficiency and gain-of-function of PAX5 depending on specific variants have been described, thereby the connection between the blockage of B cell development and the malignant transformation of normal B cells has been established. In this review, we provide the recent advances in understanding the function of PAX5 in orchestrating the development of both normal and malignant B cells over the past decade, with a focus on the PAX5 alterations shown as the initiating or driver events in B-ALL. Recent large-scale genomic analyses of B-ALL have identified multiple novel subtypes driven by PAX5 genetic lesions, such as the one defined by a distinct gene expression profile and PAX5 P80R mutation, which is an exemplar leukemia entity driven by a missense mutation. Although altered PAX5 is shared as a driver in B-ALL, disparate disease phenotypes and clinical outcomes among the patients indicate further heterogeneity of the underlying mechanisms and disturbed gene regulation networks along the disease development. In-depth mechanistic studies in human B-ALL and animal models have demonstrated high penetrance of PAX5 variants alone or concomitant with other genetic lesions in driving B-cell malignancy, indicating the altered PAX5 and deregulated genes may serve as potential therapeutic targets in certain B-ALL cases.
Collapse
Affiliation(s)
- Zhilian Jia
- Department of Computational and Quantitative Medicine, Beckman Research Institute of City of Hope, Duarte, CA, United States
- Department of Systems Biology, Beckman Research Institute of City of Hope, Duarte, CA, United States
| | - Zhaohui Gu
- Department of Computational and Quantitative Medicine, Beckman Research Institute of City of Hope, Duarte, CA, United States
- Department of Systems Biology, Beckman Research Institute of City of Hope, Duarte, CA, United States
- *Correspondence: Zhaohui Gu,
| |
Collapse
|
4
|
Kozak F, Kurzbach D. How to assess the structural dynamics of transcription factors by integrating sparse NMR and EPR constraints with molecular dynamics simulations. Comput Struct Biotechnol J 2021; 19:2097-2105. [PMID: 33995905 PMCID: PMC8085671 DOI: 10.1016/j.csbj.2021.04.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 04/07/2021] [Accepted: 04/07/2021] [Indexed: 12/12/2022] Open
Abstract
We review recent advances in modeling structural ensembles of transcription factors from nuclear magnetic resonance (NMR) and electron paramagnetic resonance (EPR) spectroscopic data, integrated with molecular dynamics (MD) simulations. We focus on approaches that confirm computed conformational ensembles by sparse constraints obtained from magnetic resonance. This combination enables the deduction of functional and structural protein models even if nuclear Overhauser effects (NOEs) are too scarce for conventional structure determination. We highlight recent insights into the folding-upon-DNA binding transitions of intrinsically disordered transcription factors that could be assessed using such integrative approaches.
Collapse
Affiliation(s)
- Fanny Kozak
- University Vienna, Faculty of Chemistry, Institute of Biological Chemistry, Waehringer Str. 38, 1090 Vienna, Austria
| | - Dennis Kurzbach
- University Vienna, Faculty of Chemistry, Institute of Biological Chemistry, Waehringer Str. 38, 1090 Vienna, Austria
| |
Collapse
|
5
|
Perez-Borrajero C, Heinkel F, Gsponer J, McIntosh LP. Conformational Plasticity and DNA-Binding Specificity of the Eukaryotic Transcription Factor Pax5. Biochemistry 2021; 60:104-117. [PMID: 33398994 DOI: 10.1021/acs.biochem.0c00737] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The eukaryotic transcription factor Pax5 has a DNA-binding Paired domain composed of two independent helical bundle subdomains joined by a flexible linker. Previously, we showed distinct biophysical properties of the N-terminal (NTD) and C-terminal (CTD) subdomains, with implications for how these two regions cooperate to distinguish nonspecific and cognate DNA sites [Perez-Borrajero, C., et al. (2016) J. Mol. Biol. 428, 2372-2391]. In this study, we combined experimental methods and molecular dynamics (MD) simulations to dissect the mechanisms underlying the functional differences between the Pax5 subdomains. Both subdomains showed a similar dependence of DNA-binding affinity on ionic strength. However, due to a greater contribution of non-ionic interactions, the NTD bound its cognate DNA half-site with an affinity approximately 10-fold higher than that of the CTD with its half-site. These interactions involve base-mediated contacts as evidenced by nuclear magnetic resonance spectroscopy-monitored chemical shift perturbations. Isothermal titration calorimetry revealed that favorable enthalpic and compensating unfavorable entropic changes were substantially larger for DNA binding by the NTD than by the CTD. Complementary MD simulations indicated that the DNA recognition helix H3 of the NTD is particularly flexible in the absence of DNA and undergoes the largest changes in conformational dynamics upon binding. Overall, these data suggest that the differences observed for the subdomains of Pax5 are due to the coupling of DNA binding with dampening of motions in the NTD required for specific base contacts. Thus, the conformational plasticity of the Pax5 Paired domain underpins the differing roles of its subdomains in association with nonspecific versus cognate DNA sites.
Collapse
Affiliation(s)
- Cecilia Perez-Borrajero
- Genome Sciences and Technology Program, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada.,Department of Biochemistry and Molecular Biology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Florian Heinkel
- Genome Sciences and Technology Program, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada.,Department of Biochemistry and Molecular Biology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Jörg Gsponer
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada.,Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Lawrence P McIntosh
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada.,Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada.,Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| |
Collapse
|
6
|
Pal A, Levy Y. Balance between asymmetry and abundance in multi-domain DNA-binding proteins may regulate the kinetics of their binding to DNA. PLoS Comput Biol 2020; 16:e1007867. [PMID: 32453726 PMCID: PMC7274453 DOI: 10.1371/journal.pcbi.1007867] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 06/05/2020] [Accepted: 04/11/2020] [Indexed: 11/19/2022] Open
Abstract
DNA sequences are often recognized by multi-domain proteins that may have higher affinity and specificity than single-domain proteins. However, the higher affinity to DNA might be coupled with slower recognition kinetics. In this study, we address this balance between stability and kinetics for multi-domain Cys2His2- (C2H2-) type zinc-finger (ZF) proteins. These proteins are the most prevalent DNA-binding domain in eukaryotes and C2H2 type zinc-finger proteins (C2H2-ZFPs) constitute nearly one-half of all known and predicted transcription factors in human. Extensive contact with DNA via tandem ZF domains confers high stability on the sequence-specific complexes. However, this can limit target search efficiency, especially for low abundance ZFPs. Earlier, we found that asymmetrical distribution of electrostatic charge among the three ZF domains of the low abundance transcription factor Egr-1 facilitates its DNA search process. Here, on a diverse set of 273 human C2H2-ZFP comprised of 3–15 tandem ZF domains, we find that, in many cases, electrostatic charge and binding specificity are asymmetrically distributed among the ZF domains so that neighbouring domains have different DNA-binding properties. For proteins containing 3–6 ZF domains, we show that the low abundance proteins possess a higher degree of non-specific asymmetry and vice versa. Our findings suggest that where the electrostatics of tandem ZF domains are similar (i.e., symmetrical), the ZFPs are more abundant to optimize their DNA search efficiency. This study reveals new insights into the fundamental determinants of recognition by C2H2-ZFPs of their DNA binding sites in the cellular landscape. The importance of electrostatic asymmetry with respect to binding site recognition by C2H2-ZFPs suggests the possibility that it may also be important in other ZFP systems and reveals a new design feature for zinc finger engineering. Optimal recognition of proteins to DNA is governed by various factors among them the thermodynamics, kinetics and specificity of the protein-DNA complex. Multi-domain DNA-binding proteins are expected to have higher affinity and specificity due to the extensive interface they form with DNA. However, larger interface may result with higher friction when these proteins scan the DNA for the target site via the sliding mechanism. A way to overcome this drawback is to have asymmetry in the protein so that the interface with DNA is smaller. Alternatively, higher abundance can also increase the search speed. Here, using computational analysis of large data set of multi-domain zinc finger DNA-binding proteins, we report a trade-off between asymmetry and abundance.
Collapse
Affiliation(s)
- Arumay Pal
- Department of Structural Biology, Weizmann Institute of Science Rehovot, Israel
| | - Yaakov Levy
- Department of Structural Biology, Weizmann Institute of Science Rehovot, Israel
- * E-mail:
| |
Collapse
|
7
|
Jin X, Hapsari ND, Lee S, Jo K. DNA binding fluorescent proteins as single-molecule probes. Analyst 2020; 145:4079-4095. [DOI: 10.1039/d0an00218f] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
DNA binding fluorescent proteins are useful probes for a broad range of biological applications.
Collapse
Affiliation(s)
- Xuelin Jin
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology
- Sogang University
- Seoul
- Republic of Korea
| | - Natalia Diyah Hapsari
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology
- Sogang University
- Seoul
- Republic of Korea
- Chemistry Education Program
| | - Seonghyun Lee
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology
- Sogang University
- Seoul
- Republic of Korea
| | - Kyubong Jo
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology
- Sogang University
- Seoul
- Republic of Korea
| |
Collapse
|
8
|
PAX5 biallelic genomic alterations define a novel subgroup of B-cell precursor acute lymphoblastic leukemia. Leukemia 2019; 33:1895-1909. [PMID: 30842609 DOI: 10.1038/s41375-019-0430-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 01/29/2019] [Accepted: 02/04/2019] [Indexed: 11/08/2022]
Abstract
Chromosomal rearrangements and specific aneuploidy patterns are initiating events and define subgroups in B-cell precursor acute lymphoblastic leukemia (BCP-ALL). Here we analyzed 250 BCP-ALL cases and identified a novel subgroup ('PAX5-plus', n = 19) by distinct DNA methylation and gene expression profiles. All patients in this subgroup harbored mutations in the B-lineage transcription factor PAX5, with p.P80R as hotspot. Mutations either affected two independent codons, consistent with compound heterozygosity, or suffered LOH predominantly through chromosome 9p aberrations. These biallelic events resulted in disruption of PAX5 transcriptional programs regulating B-cell differentiation and tumor suppressor functions. Homozygous CDKN2A/B deletions and RAS-activating hotspot mutations were highly enriched as cooperating events in the genomic profile of PAX5-plus ALL. Together, this defined a specific pattern of triple alterations, exclusive to the novel subgroup. PAX5-plus ALL was observed in pediatric and adult patients. Although restricted by the limited sample size, a tendency for more favorable clinical outcome was observed, with 10 of 12 adult PAX5-plus patients achieving long-term survival. PAX5-plus represents the first BCP-ALL subgroup defined by sequence alterations in contrast to gross chromosomal events and exemplifies how deregulated differentiation (PAX5), impaired cell cycle control (CDKN2A/B) and sustained proliferative signaling (RAS) cooperatively drive leukemogenesis.
Collapse
|
9
|
Krepel D, Levy Y. Intersegmental transfer of proteins between DNA regions in the presence of crowding. Phys Chem Chem Phys 2018; 19:30562-30569. [PMID: 29115315 DOI: 10.1039/c7cp05251k] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Intersegmental transfer that involves direct relocation of a DNA-binding protein from one nonspecific DNA site to another was previously shown to contribute to speeding up the identification of the DNA target site. This mechanism is promoted when the protein is composed of at least two domains that have different DNA binding affinities and thus show a degree of mobility. In this study, we investigate the effect of particle crowding on the ability of a multi-domain protein to perform intersegmental transfer. We show that although crowding conditions often favor 1D diffusion of proteins along DNA over 3D diffusion, relocation of one of the tethered domains to initiate intersegmental transfer is possible even under crowding conditions. The tendency to perform intersegmental transfer by a multi-domain protein under crowding conditions is much higher for larger crowding particles than smaller ones and can be even greater than under no-crowding conditions. We report that the asymmetry of the two domains is even magnified by the crowders. The observations that crowding supports intersegmental transfer serve as another example that in vivo complexity does not necessarily slow down DNA search kinetics by proteins.
Collapse
Affiliation(s)
- Dana Krepel
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel.
| | | |
Collapse
|
10
|
Konnova TA, Singer CM, Nesmelova IV. NMR solution structure of the RED subdomain of the Sleeping Beauty transposase. Protein Sci 2017; 26:1171-1181. [PMID: 28345263 DOI: 10.1002/pro.3167] [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: 01/31/2017] [Accepted: 03/22/2017] [Indexed: 12/22/2022]
Abstract
DNA transposons can be employed for stable gene transfer in vertebrates. The Sleeping Beauty (SB) DNA transposon has been recently adapted for human application and is being evaluated in clinical trials, however its molecular mechanism is not clear. SB transposition is catalyzed by the transposase enzyme, which is a multi-domain protein containing the catalytic and the DNA-binding domains. The DNA-binding domain of the SB transposase contains two structurally independent subdomains, PAI and RED. Recently, the structures of the catalytic domain and the PAI subdomain have been determined, however no structural information on the RED subdomain and its interactions with DNA has been available. Here, we used NMR spectroscopy to determine the solution structure of the RED subdomain and characterize its interactions with the transposon DNA.
Collapse
Affiliation(s)
- Tatiana A Konnova
- Department of Physics and Optical Science, University of North Carolina, Charlotte, North Carolina, 28223
| | - Christopher M Singer
- Department of Physics and Optical Science, University of North Carolina, Charlotte, North Carolina, 28223
| | - Irina V Nesmelova
- Department of Physics and Optical Science, University of North Carolina, Charlotte, North Carolina, 28223.,Center for Biomedical Engineering and Science, University of North Carolina, Charlotte, North Carolina, 28223
| |
Collapse
|
11
|
Desjardins G, Okon M, Graves BJ, McIntosh LP. Conformational Dynamics and the Binding of Specific and Nonspecific DNA by the Autoinhibited Transcription Factor Ets-1. Biochemistry 2016; 55:4105-18. [PMID: 27362745 PMCID: PMC5568661 DOI: 10.1021/acs.biochem.6b00460] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The affinity of the Ets-1 transcription factor for DNA is autoinhibited by an intrinsically disordered serine-rich region (SRR) and a helical inhibitory module (IM) appended to its winged helix-turn-helix ETS domain. Using NMR spectroscopy, we investigated how Ets-1 recognizes specific versus nonspecific DNA, with a focus on the roles of protein dynamics and autoinhibition in these processes. Upon binding either DNA, the two marginally stable N-terminal helices of the IM predominantly unfold, but still sample partially ordered conformations. Also, on the basis of amide chemical shift perturbation mapping, Ets-1 associates with both specific and nonspecific DNA through the same canonical ETS domain interface. These interactions are structurally independent of the SRR, and thus autoinhibition does not impart DNA-binding specificity. However, relative to the pronounced NMR spectroscopic changes in Ets-1 resulting from specific DNA binding, the spectra of the nonspecific DNA complexes showed conformational exchange broadening and lacked several diagnostic amide and indole signals attributable to hydrogen bonding interactions seen in reported X-ray crystallographic structures of this transcription factor with its cognate DNA sequences. Such differences are highlighted by the chemical shift and relaxation properties of several interfacial lysine and arginine side chains. Collectively, these data support a general model in which Ets-1 interacts with nonspecific DNA via dynamic electrostatic interactions, whereas hydrogen bonding drives the formation of well-ordered complexes with specific DNA.
Collapse
Affiliation(s)
- Geneviève Desjardins
- Department of Biochemistry and Molecular Biology, Department of Chemistry, and Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Mark Okon
- Department of Biochemistry and Molecular Biology, Department of Chemistry, and Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Barbara J. Graves
- Department of Oncological Sciences, University of Utah School of Medicine, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112-5550, United States
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, United States
| | - Lawrence P. McIntosh
- Department of Biochemistry and Molecular Biology, Department of Chemistry, and Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| |
Collapse
|