1
|
Yaffe N, Rotem D, Soni A, Porath D, Shlomai J. Direct monitoring of the stepwise condensation of kinetoplast DNA networks. Sci Rep 2021; 11:1501. [PMID: 33452335 PMCID: PMC7810991 DOI: 10.1038/s41598-021-81045-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 01/04/2021] [Indexed: 11/09/2022] Open
Abstract
Condensation and remodeling of nuclear genomes play an essential role in the regulation of gene expression and replication. Yet, our understanding of these processes and their regulatory role in other DNA-containing organelles, has been limited. This study focuses on the packaging of kinetoplast DNA (kDNA), the mitochondrial genome of kinetoplastids. Severe tropical diseases, affecting large human populations and livestock, are caused by pathogenic species of this group of protists. kDNA consists of several thousand DNA minicircles and several dozen DNA maxicircles that are linked topologically into a remarkable DNA network, which is condensed into a mitochondrial nucleoid. In vitro analyses implicated the replication protein UMSBP in the decondensation of kDNA, which enables the initiation of kDNA replication. Here, we monitored the condensation of kDNA, using fluorescence and atomic force microscopy. Analysis of condensation intermediates revealed that kDNA condensation proceeds via sequential hierarchical steps, where multiple interconnected local condensation foci are generated and further assemble into higher order condensation centers, leading to complete condensation of the network. This process is also affected by the maxicircles component of kDNA. The structure of condensing kDNA intermediates sheds light on the structural organization of the condensed kDNA network within the mitochondrial nucleoid.
Collapse
Affiliation(s)
- Nurit Yaffe
- Department of Microbiology and Molecular Genetics, Institute of Medical Research Israel-Canada, The Kuvin Center for the Study of Infectious and Tropical Diseases, The Hebrew University-Hadassah Medical School, 91120, Jerusalem, Israel
| | - Dvir Rotem
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, Edmond J. Safra Campus, The Hebrew University of Jerusalem, 91904, Jerusalem, Israel
| | - Awakash Soni
- Department of Microbiology and Molecular Genetics, Institute of Medical Research Israel-Canada, The Kuvin Center for the Study of Infectious and Tropical Diseases, The Hebrew University-Hadassah Medical School, 91120, Jerusalem, Israel
| | - Danny Porath
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, Edmond J. Safra Campus, The Hebrew University of Jerusalem, 91904, Jerusalem, Israel.
| | - Joseph Shlomai
- Department of Microbiology and Molecular Genetics, Institute of Medical Research Israel-Canada, The Kuvin Center for the Study of Infectious and Tropical Diseases, The Hebrew University-Hadassah Medical School, 91120, Jerusalem, Israel.
| |
Collapse
|
2
|
Pisano S, Gilson E. Analysis of DNA-Protein Complexes by Atomic Force Microscopy Imaging: The Case of TRF2-Telomeric DNA Wrapping. Methods Mol Biol 2019; 1886:75-97. [PMID: 30374863 DOI: 10.1007/978-1-4939-8894-5_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Atomic force microscopy (AFM) is a non-optical microscopy that enables the acquisition at the nanoscale level of a 3D topographical image of the sample. For 30 years, AFM has been a valuable tool in life sciences to study biological samples in the field of tissue, cellular and molecular imaging, of mechanical properties and of force spectroscopy. Since the early beginnings of the technique, AFM has been extensively exploited as an imaging tool for structural studies of nucleic acids and nucleoprotein complexes. The morphometric analysis performed on the images can unveil specific structural and functional aspects of the sample, such as the multimerization state of proteins bound to DNA, or DNA conformational changes led by the DNA-binding proteins. Herein, a method for analyzing a complex formed by a telomeric DNA sequence wrapped around the TRF2 binding protein is presented. The described procedure could be applied to the study of any type of DNA-protein complex.
Collapse
Affiliation(s)
- Sabrina Pisano
- Université Côte d'Azur, CNRS UMR 7284/INSERM U108, Institute for Research on Cancer and Aging, Nice (IRCAN), Medical School, Nice, France.
| | - Eric Gilson
- Université Côte d'Azur, CNRS UMR 7284/INSERM U108, Institute for Research on Cancer and Aging, Nice (IRCAN), Medical School, Nice, France
- International Laboratory in Hematology and Cancer, Pôle Sino-Français de Recherche en Sciences du Vivant et Génomique, Shanghai Ruijin Hospital, Shanghai Jiao Tong University School of Medicine/Ruijin Hospital/CNRS/INSERM/Nice University, Shanghai, China
- Department of Genetics, CHU Nice, Université Côte d'Azur, Nice, France
| |
Collapse
|
3
|
Oncofetal HMGA2 effectively curbs unconstrained (+) and (-) DNA supercoiling. Sci Rep 2017; 7:8440. [PMID: 28814752 PMCID: PMC5559611 DOI: 10.1038/s41598-017-09104-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 07/20/2017] [Indexed: 02/06/2023] Open
Abstract
HMGA2 belongs to the family of the high mobility group (HMG) proteins. It binds DNA via three AT-hook domains to the minor groove of adenine-thymine (AT) rich DNA. Recently, a new function of HMGA2 as a replication fork chaperone that protects stem and cancer cells from replication fork collapse induced by chemotherapeutic agents was uncovered, suggesting a previously uncharacterized binding at replication forks. In this study, we examined HMGA2 binding to four DNA structures relevant to replication forks, namely ds DNA, ss DNA, forked DNA and supercoiled DNA plectonemes. We detected HMGA2 binding to supercoiled DNA at the lowest concentration and this binding mode transiently stabilizes the supercoiled plectonemes against relaxation by type I topoisomerase. Together, these findings suggest a plausible mechanism how fork regression and collapse are attenuated by HMGA2 during replication stress, i.e. through transient stabilization of positively supercoiled plectonemes in the parental duplex.
Collapse
|
4
|
Efremov AK, Qu Y, Maruyama H, Lim CJ, Takeyasu K, Yan J. Transcriptional Repressor TrmBL2 from Thermococcus kodakarensis Forms Filamentous Nucleoprotein Structures and Competes with Histones for DNA Binding in a Salt- and DNA Supercoiling-dependent Manner. J Biol Chem 2015; 290:15770-15784. [PMID: 25931116 DOI: 10.1074/jbc.m114.626705] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Indexed: 11/06/2022] Open
Abstract
Architectural DNA proteins play important roles in the chromosomal DNA organization and global gene regulation in living cells. However, physiological functions of some DNA-binding proteins from archaea remain unclear. Recently, several abundant DNA-architectural proteins including histones, Alba, and TrmBL2 have been identified in model euryarchaeon Thermococcus kodakarensis. Although histones and Alba proteins have been previously characterized, the DNA binding properties of TrmBL2 and its interplay with the other major architectural proteins in the chromosomal DNA organization and gene transcription regulation remain largely unexplored. Here, we report single-DNA studies showing that at low ionic strength (<300 mM KCl), TrmBL2 binds to DNA largely in non-sequence-specific manner with positive cooperativity, resulting in formation of stiff nucleoprotein filamentous patches, whereas at high ionic strength (>300 mM KCl) TrmBL2 switches to more sequence-specific interaction, suggesting the presence of high affinity TrmBL2-filament nucleation sites. Furthermore, in vitro assays indicate the existence of DNA binding competition between TrmBL2 and archaeal histones B from T. kodakarensis, which can be strongly modulated by DNA supercoiling and ionic strength of surrounding solution. Overall, these results advance our understanding of TrmBL2 DNA binding properties and provide important insights into potential functions of architectural proteins in nucleoid organization and gene regulation in T. kodakarensis.
Collapse
Affiliation(s)
- Artem K Efremov
- Mechanobiology Institute, National University of Singapore, Singapore 117411, Singapore; Centre for Bioimaging Sciences, National University of Singapore, Singapore 117546, Singapore
| | - Yuanyuan Qu
- Centre for Bioimaging Sciences, National University of Singapore, Singapore 117546, Singapore; Department of Physics, National University of Singapore, Singapore 117542, Singapore; School of Physics, Shandong University, Jinan 250100, China
| | - Hugo Maruyama
- Department of Bacteriology, Osaka Dental University, Hirakata 573-1121, Japan
| | - Ci J Lim
- Mechanobiology Institute, National University of Singapore, Singapore 117411, Singapore; Centre for Bioimaging Sciences, National University of Singapore, Singapore 117546, Singapore; National University of Singapore Graduate School for Integrative Sciences and Engineering, Singapore 119077
| | - Kunio Takeyasu
- Laboratory of Plasma Membrane and Nuclear Signaling, Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan.
| | - Jie Yan
- Mechanobiology Institute, National University of Singapore, Singapore 117411, Singapore; Centre for Bioimaging Sciences, National University of Singapore, Singapore 117546, Singapore; Department of Physics, National University of Singapore, Singapore 117542, Singapore; National University of Singapore Graduate School for Integrative Sciences and Engineering, Singapore 119077.
| |
Collapse
|
5
|
Mechanochemical regulations of RPA's binding to ssDNA. Sci Rep 2015; 5:9296. [PMID: 25787788 PMCID: PMC4365408 DOI: 10.1038/srep09296] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 02/24/2015] [Indexed: 11/10/2022] Open
Abstract
Replication protein A (RPA) is a ubiquitous eukaryotic single-stranded DNA (ssDNA) binding protein that serves to protect ssDNA from degradation and annealing, and as a template for recruitment of many downstream factors in virtually all DNA transactions in cell. During many of these transactions, DNA is tethered and is likely subject to force. Previous studies of RPA's binding behavior on ssDNA were conducted in the absence of force; therefore the RPA-ssDNA conformations regulated by force remain unclear. Here, using a combination of atomic force microscopy imaging and mechanical manipulation of single ssDNA tethers, we show that force mediates a switch of the RPA bound ssDNA from amorphous aggregation to a much more regular extended conformation. Further, we found an interesting non-monotonic dependence of the binding affinity on monovalent salt concentration in the presence of force. In addition, we discovered that zinc in micromolar concentrations drives ssDNA to a unique, highly stiff and more compact state. These results provide new mechanochemical insights into the influences and the mechanisms of action of RPA on large single ssDNA.
Collapse
|
6
|
Winardhi RS, Gulvady R, Mellies JL, Yan J. Locus of enterocyte effacement-encoded regulator (Ler) of pathogenic Escherichia coli competes off histone-like nucleoid-structuring protein (H-NS) through noncooperative DNA binding. J Biol Chem 2014; 289:13739-50. [PMID: 24668810 DOI: 10.1074/jbc.m113.545954] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The locus of enterocyte effacement-encoded regulator (Ler) of enteropathogenic and enterohemorrhagic Escherichia coli (EPEC and EHEC) functions to activate transcription of virulence genes silenced by the histone-like nucleoid-structuring protein (H-NS). Despite its important role in the bacterial gene regulation, the binding mode of Ler to DNA and its mechanism in alleviating genes repressed by H-NS are largely unknown. In this study, we use magnetic tweezers to demonstrate that Ler binds extended DNA through a largely noncooperative process, which results in DNA stiffening and DNA folding depending on protein concentration. We also show that Ler can replace prebound H-NS on DNA over a range of potassium and magnesium concentrations. Our findings reveal the DNA binding properties of Ler and shed light to further understand the anti-silencing activity of Ler.
Collapse
Affiliation(s)
- Ricksen S Winardhi
- From the NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore 117456, Singapore, the Mechanobiology Institute, Singapore 117411, Singapore, the Centre for BioImaging Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Ranjit Gulvady
- the Mechanobiology Institute, Singapore 117411, Singapore, the Centre for BioImaging Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Jay L Mellies
- the Biology Department, Reed College, Portland, Oregon 97202, and
| | - Jie Yan
- the Mechanobiology Institute, Singapore 117411, Singapore, the Centre for BioImaging Sciences, National University of Singapore, Singapore 117543, Singapore, the Department of Physics, National University of Singapore, Singapore 117542, Singapore
| |
Collapse
|
7
|
Qu Y, Lim CJ, Whang YR, Liu J, Yan J. Mechanism of DNA organization by Mycobacterium tuberculosis protein Lsr2. Nucleic Acids Res 2013; 41:5263-72. [PMID: 23580555 PMCID: PMC3664827 DOI: 10.1093/nar/gkt249] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Bacterial nucleoid-associated proteins, such as H-NS-like proteins in Enterobacteriaceae, are abundant DNA-binding proteins that function in chromosomal DNA organization and gene transcription regulation. The Mycobacterium tuberculosis Lsr2 protein has been proposed to be the first identified H-NS analogue in Gram-positive bacteria based on its capability to complement numerous in vivo functions of H-NS. Here, we report that Lsr2 cooperatively binds to DNA forming a rigid Lsr2 nucleoprotein complex that restricts DNA accessibility, similar to H-NS. On large DNA, the rigid Lsr2 nucleoprotein complexes can mediate DNA condensation into highly compact DNA conformations. In addition, the responses of Lsr2 nucleoprotein complex to environmental factors (salt concentration, temperature and pH) were studied over physiological ranges. These results provide mechanistic insights into how Lsr2 may mediate its gene silencing, genomic DNA protection and organization functions in vivo. Finally, our results strongly support that Lsr2 is an H-NS-like protein in Gram-positive bacteria from a structural perspective.
Collapse
Affiliation(s)
- Yuanyuan Qu
- Department of Physics, National University of Singapore, Singapore 117542, Singapore
| | | | | | | | | |
Collapse
|
8
|
Lim CJ, Lee SY, Teramoto J, Ishihama A, Yan J. The nucleoid-associated protein Dan organizes chromosomal DNA through rigid nucleoprotein filament formation in E. coli during anoxia. Nucleic Acids Res 2012. [PMID: 23180762 PMCID: PMC3553945 DOI: 10.1093/nar/gks1126] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Dan is a transcription factor that regulates the ttd operon encoding tartrate dehydratase. During anaerobic conditions, its copy number increases by 100-fold, making Dan an abundant nucleoid-associated protein. However, little is known about the mode of Dan–DNA interaction. To understand its cellular functions, we used single-molecule manipulation and imaging techniques to show that Dan binds cooperatively along DNA, resulting in formation of a rigid periodic nucleoprotein filament that strongly restricts accessibility to DNA. Furthermore, in the presence of physiologic levels of magnesium, these filaments interact with each other to cause global DNA condensation. Overall, these results shed light on the architectural role of Dan in the compaction of Escherichia coli chromosomal DNA under anaerobic conditions. Formation of the nucleoprotein filament provides a basis in understanding how Dan may play roles in both chromosomal DNA protection and gene regulation.
Collapse
Affiliation(s)
- Ci Ji Lim
- National University of Singapore, Graduate School for Integrative Sciences and Engineering, Singapore
| | | | | | | | | |
Collapse
|
9
|
Lin J, Chen H, Dröge P, Yan J. Physical organization of DNA by multiple non-specific DNA-binding modes of integration host factor (IHF). PLoS One 2012; 7:e49885. [PMID: 23166787 PMCID: PMC3498176 DOI: 10.1371/journal.pone.0049885] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Accepted: 10/15/2012] [Indexed: 11/18/2022] Open
Abstract
The integration host factor (IHF) is an abundant nucleoid-associated protein and an essential co-factor for phage λ site-specific recombination and gene regulation in E. coli. Introduction of a sharp DNA kink at specific cognate sites is critical for these functions. Interestingly, the intracellular concentration of IHF is much higher than the concentration needed for site-specific interactions, suggesting that non-specific binding of IHF to DNA plays a role in the physical organization of bacterial chromatin. However, it is unclear how non-specific DNA association contributes to DNA organization. By using a combination of single DNA manipulation and atomic force microscopy imaging methods, we show here that distinct modes of non-specific DNA binding of IHF result in complex global DNA conformations. Changes in KCl and IHF concentrations, as well as tension applied to DNA, dramatically influence the degree of DNA-bending. In addition, IHF can crosslink DNA into a highly compact DNA meshwork that is observed in the presence of magnesium at low concentration of monovalent ions and high IHF-DNA stoichiometries. Our findings provide important insights into how IHF contributes to bacterial chromatin organization, gene regulation, and biofilm formation.
Collapse
Affiliation(s)
- Jie Lin
- Department of Physics, National University of Singapore, Singapore, Singapore
- Mechanobiology Institute, National University of Singapore, Singapore, Singapore
- Centre for Bioimaging Sciences, National University of Singapore, Singapore, Singapore
| | - Hu Chen
- Mechanobiology Institute, National University of Singapore, Singapore, Singapore
| | - Peter Dröge
- Division of Molecular Genetics and Cell Biology, School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- * E-mail: (PD); (JY)
| | - Jie Yan
- Department of Physics, National University of Singapore, Singapore, Singapore
- Mechanobiology Institute, National University of Singapore, Singapore, Singapore
- Centre for Bioimaging Sciences, National University of Singapore, Singapore, Singapore
- * E-mail: (PD); (JY)
| |
Collapse
|
10
|
Xiao B, Freedman BS, Miller KE, Heald R, Marko JF. Histone H1 compacts DNA under force and during chromatin assembly. Mol Biol Cell 2012; 23:4864-71. [PMID: 23097493 PMCID: PMC3521692 DOI: 10.1091/mbc.e12-07-0518] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Histone H1 binds to linker DNA between nucleosomes, but the dynamics and biological ramifications of this interaction remain poorly understood. We performed single-molecule experiments using magnetic tweezers to determine the effects of H1 on naked DNA in buffer or during chromatin assembly in Xenopus egg extracts. In buffer, nanomolar concentrations of H1 induce bending and looping of naked DNA at stretching forces below 0.6 pN, effects that can be reversed with 2.7-pN force or in 200 mM monovalent salt concentrations. Consecutive tens-of-nanometer bending events suggest that H1 binds to naked DNA in buffer at high stoichiometries. In egg extracts, single DNA molecules assemble into nucleosomes and undergo rapid compaction. Histone H1 at endogenous physiological concentrations increases the DNA compaction rate during chromatin assembly under 2-pN force and decreases it during disassembly under 5-pN force. In egg cytoplasm, histone H1 protects sperm nuclei undergoing genome-wide decondensation and chromatin assembly from becoming abnormally stretched or fragmented due to astral microtubule pulling forces. These results reveal functional ramifications of H1 binding to DNA at the single-molecule level and suggest an important physiological role for H1 in compacting DNA under force and during chromatin assembly.
Collapse
Affiliation(s)
- Botao Xiao
- Department of Physics and Astronomy, Northwestern University, Evanston, IL 60208, USA.
| | | | | | | | | |
Collapse
|
11
|
Usukura J, Yoshimura A, Minakata S, Youn D, Ahn J, Cho SJ. Use of the unroofing technique for atomic force microscopic imaging of the intra-cellular cytoskeleton under aqueous conditions. JOURNAL OF ELECTRON MICROSCOPY 2012; 61:321-326. [PMID: 22872282 DOI: 10.1093/jmicro/dfs055] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Atomic force microscopy (AFM) combined with unroofing techniques enabled clear imaging of the intracellular cytoskeleton and the cytoplasmic surface of the cell membrane under aqueous condition. Many actin filaments were found to form a complex meshwork on the cytoplasmic surface of the membrane, as observed in freeze-etching electron microscopy. Characteristic periodic striations of about 5 nm formed by the assembly of G-actin were detected along actin filaments at higher magnification. Actin filaments aggregated and dispersed at several points, thereby dividing the cytoplasmic surface of the membrane into several large domains. Microtubules were also easily detected and were often tethered to the membrane surface by fine filaments. Furthermore, clathrin coats on the membrane were clearly visualized for the first time in water by AFM. Although the resolution of these images is lower than electron micrographs of freeze-etched samples processed similarly, the measurement capabilities of the AFM in a more biologically relevant conditions demonstrate that it is an important tool for imaging intracellular structures and cell surfaces in the native, aqueous state.
Collapse
Affiliation(s)
- Jiro Usukura
- EcoTopia Science Institute, Nagoya University, Nagoya, Japan.
| | | | | | | | | | | |
Collapse
|
12
|
Kalle W, Strappe P. Atomic force microscopy on chromosomes, chromatin and DNA: a review. Micron 2012; 43:1224-31. [PMID: 22633852 DOI: 10.1016/j.micron.2012.04.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2012] [Revised: 04/06/2012] [Accepted: 04/08/2012] [Indexed: 01/19/2023]
Abstract
The purpose of this review is to discuss the achievements and progress that has been made in the use of atomic force microscopy in DNA related research in the last 25 years. For this review DNA related research is split up in chromosomal-, chromatin- and DNA focused research to achieve a logical flow from large- to smaller structures. The focus of this review is not only on the AFM as imaging tool but also on the AFM as measuring tool using force spectroscopy, as therein lays its greatest advantage and future. The amazing technological and experimental progress that has been made during the last 25 years is too extensive to fully cover in this review but some key developments and experiments have been described to give an overview of the evolution of AFM use from 'imaging tool' to 'measurement tool' on chromosomes, chromatin and DNA.
Collapse
Affiliation(s)
- Wouter Kalle
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, Australia.
| | | |
Collapse
|
13
|
Lim CJ, Whang YR, Kenney LJ, Yan J. Gene silencing H-NS paralogue StpA forms a rigid protein filament along DNA that blocks DNA accessibility. Nucleic Acids Res 2011; 40:3316-28. [PMID: 22187157 PMCID: PMC3333869 DOI: 10.1093/nar/gkr1247] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Nucleoid-associated proteins are bacterial proteins that are responsible for chromosomal DNA compaction and global gene regulation. One such protein is Escherichia coli Histone-like nucleoid structuring protein (H-NS) which functions as a global gene silencer. Whereas the DNA-binding mechanism of H-NS is well-characterized, its paralogue, StpA which is also able to silence genes is less understood. Here we show that StpA is similar to H-NS in that it is able to form a rigid filament along DNA. In contrast to H-NS, the StpA filament interacts with a naked DNA segment to cause DNA bridging which results in simultaneous stiffening and bridging of DNA. DNA accessibility is effectively blocked after the formation of StpA filament on DNA, suggesting rigid filament formation is the important step in promoting gene silencing. We also show that >1 mM magnesium promotes higher order DNA condensation, suggesting StpA may also play a role in chromosomal DNA packaging.
Collapse
Affiliation(s)
- Ci Ji Lim
- NUS Graduate school for Integrative Sciences and Engineering, National University of Singapore, 28 Medical Drive, Singapore, 119077, Singapore
| | | | | | | |
Collapse
|
14
|
Flors C, Earnshaw WC. Super-resolution fluorescence microscopy as a tool to study the nanoscale organization of chromosomes. Curr Opin Chem Biol 2011; 15:838-44. [DOI: 10.1016/j.cbpa.2011.10.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2011] [Revised: 09/27/2011] [Accepted: 10/17/2011] [Indexed: 01/26/2023]
|