1
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Santoshi M, Tare P, Nagaraja V. Nucleoid-associated proteins of mycobacteria come with a distinctive flavor. Mol Microbiol 2024. [PMID: 38922783 DOI: 10.1111/mmi.15287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 05/31/2024] [Accepted: 06/05/2024] [Indexed: 06/28/2024]
Abstract
In every bacterium, nucleoid-associated proteins (NAPs) play crucial roles in chromosome organization, replication, repair, gene expression, and other DNA transactions. Their central role in controlling the chromatin dynamics and transcription has been well-appreciated in several well-studied organisms. Here, we review the diversity, distribution, structure, and function of NAPs from the genus Mycobacterium. We highlight the progress made in our understanding of the effects of these proteins on various processes and in responding to environmental stimuli and stress of mycobacteria in their free-living as well as during distinctive intracellular lifestyles. We project them as potential drug targets and discuss future studies to bridge the information gap with NAPs from well-studied systems.
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Affiliation(s)
- Meghna Santoshi
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
| | - Priyanka Tare
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
| | - Valakunja Nagaraja
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
- Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India
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2
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Sarkar D, Kang J, Wassie AT, Schroeder ME, Peng Z, Tarr TB, Tang AH, Niederst ED, Young JZ, Su H, Park D, Yin P, Tsai LH, Blanpied TA, Boyden ES. Revealing nanostructures in brain tissue via protein decrowding by iterative expansion microscopy. Nat Biomed Eng 2022; 6:1057-1073. [PMID: 36038771 PMCID: PMC9551354 DOI: 10.1038/s41551-022-00912-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Accepted: 06/22/2022] [Indexed: 12/25/2022]
Abstract
Many crowded biomolecular structures in cells and tissues are inaccessible to labelling antibodies. To understand how proteins within these structures are arranged with nanoscale precision therefore requires that these structures be decrowded before labelling. Here we show that an iterative variant of expansion microscopy (the permeation of cells and tissues by a swellable hydrogel followed by isotropic hydrogel expansion, to allow for enhanced imaging resolution with ordinary microscopes) enables the imaging of nanostructures in expanded yet otherwise intact tissues at a resolution of about 20 nm. The method, which we named 'expansion revealing' and validated with DNA-probe-based super-resolution microscopy, involves gel-anchoring reagents and the embedding, expansion and re-embedding of the sample in homogeneous swellable hydrogels. Expansion revealing enabled us to use confocal microscopy to image the alignment of pre-synaptic calcium channels with post-synaptic scaffolding proteins in intact brain circuits, and to uncover periodic amyloid nanoclusters containing ion-channel proteins in brain tissue from a mouse model of Alzheimer's disease. Expansion revealing will enable the further discovery of previously unseen nanostructures within cells and tissues.
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Affiliation(s)
- Deblina Sarkar
- Media Lab, MIT, Cambridge, MA, 02139, USA.,MIT Center for Neurobiological Engineering, MIT, Cambridge, MA, 02139, USA.,These authors contributed equally
| | - Jinyoung Kang
- MIT McGovern Institute for Brain Research, MIT, Cambridge, MA, 02139, USA.,These authors contributed equally
| | - Asmamaw T Wassie
- Department of Biological Engineering, MIT, Cambridge, MA, 02139, USA.,These authors contributed equally
| | - Margaret E. Schroeder
- MIT McGovern Institute for Brain Research, MIT, Cambridge, MA, 02139, USA.,Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, 02139, USA
| | - Zhuyu Peng
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, 02139, USA.,The Picower Institute for Learning and Memory, MIT, Cambridge, MA, 02139, USA
| | - Tyler B. Tarr
- Department of Physiology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Ai-Hui Tang
- Department of Physiology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.,CAS Key Laboratory of Brain Function and Disease, Biomedical Sciences and Health Laboratory of Anhui Province, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230031, China
| | - Emily D. Niederst
- The Picower Institute for Learning and Memory, MIT, Cambridge, MA, 02139, USA
| | - Jennie, Z. Young
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, 02139, USA.,The Picower Institute for Learning and Memory, MIT, Cambridge, MA, 02139, USA
| | - Hanquan Su
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA.,Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Demian Park
- MIT McGovern Institute for Brain Research, MIT, Cambridge, MA, 02139, USA
| | - Peng Yin
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA.,Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Li-Huei Tsai
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA. .,The Picower Institute for Learning and Memory, MIT, Cambridge, MA, USA. .,Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Thomas A. Blanpied
- Department of Physiology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.,Program in Neuroscience, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.,Correspondence and requests for materials should be addressed to Li-Huei Tsai, Thomas A. Blanpied or Edward S. Boyden. , ,
| | - Edward S. Boyden
- MIT Center for Neurobiological Engineering, MIT, Cambridge, MA, 02139, USA.,MIT McGovern Institute for Brain Research, MIT, Cambridge, MA, 02139, USA.,Department of Biological Engineering, MIT, Cambridge, MA, 02139, USA.,Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, 02139, USA.,Koch Institute, MIT, Cambridge, MA, 02139, USA.,Howard Hughes Medical Institute, Cambridge, MA, 02139, USA.,Media Arts and Sciences, MIT, Cambridge, MA, 02139, USA.,K. Lisa Yang Center for Bionics, MIT, Cambridge, MA, 02139, USA.,Correspondence and requests for materials should be addressed to Li-Huei Tsai, Thomas A. Blanpied or Edward S. Boyden. , ,
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3
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Tierrafría VH, Rioualen C, Salgado H, Lara P, Gama-Castro S, Lally P, Gómez-Romero L, Peña-Loredo P, López-Almazo AG, Alarcón-Carranza G, Betancourt-Figueroa F, Alquicira-Hernández S, Polanco-Morelos JE, García-Sotelo J, Gaytan-Nuñez E, Méndez-Cruz CF, Muñiz LJ, Bonavides-Martínez C, Moreno-Hagelsieb G, Galagan JE, Wade JT, Collado-Vides J. RegulonDB 11.0: Comprehensive high-throughput datasets on transcriptional regulation in Escherichia coli K-12. Microb Genom 2022; 8. [PMID: 35584008 PMCID: PMC9465075 DOI: 10.1099/mgen.0.000833] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Genomics has set the basis for a variety of methodologies that produce high-throughput datasets identifying the different players that define gene regulation, particularly regulation of transcription initiation and operon organization. These datasets are available in public repositories, such as the Gene Expression Omnibus, or ArrayExpress. However, accessing and navigating such a wealth of data is not straightforward. No resource currently exists that offers all available high and low-throughput data on transcriptional regulation in Escherichia coli K-12 to easily use both as whole datasets, or as individual interactions and regulatory elements. RegulonDB (https://regulondb.ccg.unam.mx) began gathering high-throughput dataset collections in 2009, starting with transcription start sites, then adding ChIP-seq and gSELEX in 2012, with up to 99 different experimental high-throughput datasets available in 2019. In this paper we present a radical upgrade to more than 2000 high-throughput datasets, processed to facilitate their comparison, introducing up-to-date collections of transcription termination sites, transcription units, as well as transcription factor binding interactions derived from ChIP-seq, ChIP-exo, gSELEX and DAP-seq experiments, besides expression profiles derived from RNA-seq experiments. For ChIP-seq experiments we offer both the data as presented by the authors, as well as data uniformly processed in-house, enhancing their comparability, as well as the traceability of the methods and reproducibility of the results. Furthermore, we have expanded the tools available for browsing and visualization across and within datasets. We include comparisons against previously existing knowledge in RegulonDB from classic experiments, a nucleotide-resolution genome viewer, and an interface that enables users to browse datasets by querying their metadata. A particular effort was made to automatically extract detailed experimental growth conditions by implementing an assisted curation strategy applying Natural language processing and machine learning. We provide summaries with the total number of interactions found in each experiment, as well as tools to identify common results among different experiments. This is a long-awaited resource to make use of such wealth of knowledge and advance our understanding of the biology of the model bacterium E. coli K-12.
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Affiliation(s)
- Víctor H Tierrafría
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Cuernavaca 62210, Morelos, Mexico.,Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, MA 02215, USA
| | - Claire Rioualen
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Cuernavaca 62210, Morelos, Mexico
| | - Heladia Salgado
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Cuernavaca 62210, Morelos, Mexico
| | - Paloma Lara
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Cuernavaca 62210, Morelos, Mexico
| | - Socorro Gama-Castro
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Cuernavaca 62210, Morelos, Mexico
| | - Patrick Lally
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, MA 02215, USA
| | - Laura Gómez-Romero
- Instituto Nacional de Medicina Genómica, INMEGEN, Periférico Sur 4809, Arenal Tepepan, Tlalpan 14610, CDMX, Mexico
| | - Pablo Peña-Loredo
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Cuernavaca 62210, Morelos, Mexico
| | - Andrés G López-Almazo
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Cuernavaca 62210, Morelos, Mexico
| | - Gabriel Alarcón-Carranza
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Cuernavaca 62210, Morelos, Mexico
| | - Felipe Betancourt-Figueroa
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Cuernavaca 62210, Morelos, Mexico
| | - Shirley Alquicira-Hernández
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Cuernavaca 62210, Morelos, Mexico
| | - J Enrique Polanco-Morelos
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Cuernavaca 62210, Morelos, Mexico
| | - Jair García-Sotelo
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Querétaro 76230, Querétaro, Mexico
| | - Estefani Gaytan-Nuñez
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Cuernavaca 62210, Morelos, Mexico
| | - Carlos-Francisco Méndez-Cruz
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Cuernavaca 62210, Morelos, Mexico
| | - Luis J Muñiz
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Cuernavaca 62210, Morelos, Mexico
| | - César Bonavides-Martínez
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Cuernavaca 62210, Morelos, Mexico
| | - Gabriel Moreno-Hagelsieb
- Department of Biology, Wilfrid Laurier University, 75 University Ave W, Waterloo, ON N2L 3C5, Canada
| | - James E Galagan
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, MA 02215, USA
| | - Joseph T Wade
- Wadsworth Center, New York State Department of Health, Albany, NY, USA.,Department of Biomedical Sciences, University at Albany, SUNY, Albany, NY, USA
| | - Julio Collado-Vides
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Cuernavaca 62210, Morelos, Mexico.,Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, MA 02215, USA.,Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Universitat Pompeu Fabra(UPF), Barcelona, Spain
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4
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Pietrzyk-Brzezinska AJ, Cociurovscaia A. Structures of the TetR-like transcription regulator RcdA alone and in complexes with ligands. Proteins 2021; 90:33-44. [PMID: 34288132 DOI: 10.1002/prot.26183] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 05/20/2021] [Accepted: 07/11/2021] [Indexed: 01/25/2023]
Abstract
RcdA is a helix-turn-helix (HTH) transcriptional regulator belonging to the TetR family. The protein regulates the transcription of curlin subunit gene D, the master regulator of biofilm formation. Moreover, it was predicted that it might be involved in the regulation of up to 27 different genes. However, an effector of RcdA and the environmental conditions which trigger RcdA action remain unknown. Herein, we report the first crystal structures of RcdA in complexes with ligands, trimethylamine N-oxide (TMAO) and tris(hydroxymethyl)aminomethane (Tris), which might serve as RcdA effectors. Based on these structures, the ligand-binding pocket of RcdA was characterized in detail. The conservation of the amino acid residues forming the ligand-binding cavity was analyzed and the comprehensive search for RcdA structural homologs was performed. This analysis indicated that RcdA is structurally similar to multidrug-binding TetR family members, however, its ligand-binding cavity differs significantly from the pockets of its structural homologs. The interaction of RcdA with TMAO and Tris indicates that the protein might be involved in alkaline stress response.
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Affiliation(s)
- Agnieszka J Pietrzyk-Brzezinska
- Institute of Molecular and Industrial Biotechnology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Lodz, Poland
| | - Anna Cociurovscaia
- Institute of Molecular and Industrial Biotechnology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Lodz, Poland
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5
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Zhang Y, Guo X, Wang G, Liu J, Liang P, Wang H, Zhu C, Wu Q. Effects of rhodioloside on the neurological functions of rats with total cerebral ischemia/reperfusion and cone neuron injury in the hippocampal CA1 region. PeerJ 2020; 8:e10056. [PMID: 33240590 PMCID: PMC7659626 DOI: 10.7717/peerj.10056] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 09/07/2020] [Indexed: 01/12/2023] Open
Abstract
Rhodioloside, the main effective constituent of Rhodiola rosea, demonstrates antiaging and antioxidative stress functions and inhibits calcium overloading in cells. These functions imply that rhodioloside may exert protective effects on hippocampal neurons after total cerebral ischemia/reperfusion injury. In this study, male Wistar rat models of total cerebral ischemia were constructed and randomly divided into four groups: sham-operation, ischemia/reperfusion, low-dosage, and high-dosage groups. The result showed that rhodioloside treatment reduced the apoptosis rates of hippocampal neurons and the histological grades of cone cells in the hippocampal CA1 region, but neuronal density was significantly increased. Besides, the protein expressions of Bcl-2/Bax and p53 were measured and found Bcl-2/Bax was increased and p53 protein level was reduced. Therefore, rhodioloside might have protective effects on rats with ischemia/reperfusion brain injury.
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Affiliation(s)
- Yue Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xinqing Guo
- Department of Basic Medicine, Heze Medical College, Heze, China
| | - Guohua Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Jidan Liu
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Peiyu Liang
- Medical College, Qinghai University, Xining, China
| | - Huan Wang
- Medical College, Qinghai University, Xining, China
| | - Chunyan Zhu
- Pharmaceutical Section of Municipal hospital of Heze, Shandong, China
| | - Qiong Wu
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
- Medical College, Qinghai University, Xining, China
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6
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Ogasawara H, Ishizuka T, Hotta S, Aoki M, Shimada T, Ishihama A. Novel regulators of the csgD gene encoding the master regulator of biofilm formation in Escherichia coli K-12. Microbiology (Reading) 2020; 166:880-890. [DOI: 10.1099/mic.0.000947] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Under stressful conditions,
Escherichia coli
forms biofilm for survival by sensing a variety of environmental conditions. CsgD, the master regulator of biofilm formation, controls cell aggregation by directly regulating the synthesis of Curli fimbriae. In agreement of its regulatory role, as many as 14 transcription factors (TFs) have so far been identified to participate in regulation of the csgD promoter, each monitoring a specific environmental condition or factor. In order to identify the whole set of TFs involved in this typical multi-factor promoter, we performed in this study ‘promoter-specific transcription-factor’ (PS-TF) screening in vitro using a set of 198 purified TFs (145 TFs with known functions and 53 hitherto uncharacterized TFs). A total of 48 TFs with strong binding to the csgD promoter probe were identified, including 35 known TFs and 13 uncharacterized TFs, referred to as Y-TFs. As an attempt to search for novel regulators, in this study we first analysed a total of seven Y-TFs, including YbiH, YdcI, YhjC, YiaJ, YiaU, YjgJ and YjiR. After analysis of curli fimbriae formation, LacZ-reporter assay, Northern-blot analysis and biofilm formation assay, we identified at least two novel regulators, repressor YiaJ (renamed PlaR) and activator YhjC (renamed RcdB), of the csgD promoter.
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Affiliation(s)
- Hiroshi Ogasawara
- Academic Assembly School of Humanities and Social Sciences Institute of Humanities, Shinshu University, Asahi 3-1-1, Matsumoto, 390–8621, Japan
- Research Center for Supports to Advanced Science, Division of Gene Research, Shinshu University, Ueda, Nagano 386-8567, Japan
| | - Toshiyuki Ishizuka
- Research Center for Supports to Advanced Science, Division of Gene Research, Shinshu University, Ueda, Nagano 386-8567, Japan
| | - Shuhei Hotta
- Research Center for Supports to Advanced Science, Division of Gene Research, Shinshu University, Ueda, Nagano 386-8567, Japan
| | - Michiko Aoki
- Research Center for Supports to Advanced Science, Division of Gene Research, Shinshu University, Ueda, Nagano 386-8567, Japan
| | - Tomohiro Shimada
- School of Agriculture, Meiji University, 1-1-1 Higashi Mita, Tama-ku, Kawasaki, Kanagawa 214–8571, Japan
| | - Akira Ishihama
- Research Center for Micro-Nano Technology, Hosei University, Koganei, Tokyo 184-8584, Japan
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7
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Tan X, Ravasio A, Ong HT, Wu J, Hew CL. White spot syndrome viral protein VP9 alters the cellular higher-order chromatin structure. FASEB Bioadv 2020; 2:264-279. [PMID: 32259052 PMCID: PMC7133739 DOI: 10.1096/fba.2019-00086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Revised: 10/26/2019] [Accepted: 02/05/2020] [Indexed: 12/21/2022] Open
Abstract
Viral protein 9 (VP9) is a non-structural protein of white spot syndrome virus (WSSV) highly expressed during the early stage of infection. The crystal structure of VP9 suggests that the polymers of VP9 dimers resemble a DNA mimic, but its function remains elusive. In this study, we demonstrated that VP9 impedes histones binding to DNA via single-molecule manipulation. We established VP9 expression in HeLa cells due to the lack of a WSSV-susceptible cell line, and observed abundant VP9 in the nucleus, which mirrors its distribution in the hemocytes of WSSV-infected shrimp. VP9 expression increased the dynamics and rotational mobility of histones in stable H3-GFP HeLa cells as revealed by fluorescent recovery after photobleaching and fluorescence anisotropy imaging, which suggested a loosened compaction of chromatin structure. Successive salt fractionation showed that a prominent population of histones was solubilized in high salt concentrations, which implies alterations of bulk chromatin structure. Southern blotting identified that VP9 alters juxtacentromeric chromatin structures to be more accessible to micrococcal nuclease digestion. RNA microarray revealed that VP9 expression also leads to significant changes of cellular gene expression. Our findings provide evidence that VP9 alters the cellular higher-order chromatin structure, uncovering a potential strategy adopted by WSSV to facilitate its replication.
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Affiliation(s)
- Xi Tan
- Mechanobiology InstituteNational University of SingaporeSingaporeSingapore
- Present address:
School of Basic Medical SciencesGuizhou University of Traditional Chinese MedicineGuiyangGuizhou ProvinceChina
| | - Andrea Ravasio
- Institute for Biological and Medical EngineeringSchools of Engineering, Medicine and Biological SciencesPontificia Universidad Católica de ChileSantiago de ChileChile
| | - Hui T. Ong
- Mechanobiology InstituteNational University of SingaporeSingaporeSingapore
| | - Jinlu Wu
- Department of Biological SciencesNational University of SingaporeSingaporeSingapore
| | - Choy L. Hew
- Mechanobiology InstituteNational University of SingaporeSingaporeSingapore
- Department of Biological SciencesNational University of SingaporeSingaporeSingapore
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8
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Tan W, van Twest S, Leis A, Bythell-Douglas R, Murphy VJ, Sharp M, Parker MW, Crismani W, Deans AJ. Monoubiquitination by the human Fanconi anemia core complex clamps FANCI:FANCD2 on DNA in filamentous arrays. eLife 2020; 9:e54128. [PMID: 32167469 PMCID: PMC7156235 DOI: 10.7554/elife.54128] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 03/12/2020] [Indexed: 12/24/2022] Open
Abstract
FANCI:FANCD2 monoubiquitination is a critical event for replication fork stabilization by the Fanconi anemia (FA) DNA repair pathway. It has been proposed that at stalled replication forks, monoubiquitinated-FANCD2 serves to recruit DNA repair proteins that contain ubiquitin-binding motifs. Here, we have reconstituted the FA pathway in vitro to study functional consequences of FANCI:FANCD2 monoubiquitination. We report that monoubiquitination does not promote any specific exogenous protein:protein interactions, but instead stabilizes FANCI:FANCD2 heterodimers on dsDNA. This clamping requires monoubiquitination of only the FANCD2 subunit. We further show using electron microscopy that purified monoubiquitinated FANCI:FANCD2 forms filament-like arrays on long dsDNA. Our results reveal how monoubiquitinated FANCI:FANCD2, defective in many cancer types and all cases of FA, is activated upon DNA binding.
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Affiliation(s)
- Winnie Tan
- Genome Stability Unit, St. Vincent’s Institute of Medical ResearchFitzroyAustralia
- Department of Medicine (St. Vincent’s Health), The University of MelbourneMelbourneAustralia
| | - Sylvie van Twest
- Genome Stability Unit, St. Vincent’s Institute of Medical ResearchFitzroyAustralia
| | - Andrew Leis
- Bio21 Institute, University of MelbourneParkvilleAustralia
| | | | - Vincent J Murphy
- Genome Stability Unit, St. Vincent’s Institute of Medical ResearchFitzroyAustralia
| | - Michael Sharp
- Genome Stability Unit, St. Vincent’s Institute of Medical ResearchFitzroyAustralia
| | - Michael W Parker
- Bio21 Institute, University of MelbourneParkvilleAustralia
- Structural Biology Unit, St. Vincent’s Institute of Medical ResearchFitzroyAustralia
| | - Wayne Crismani
- Genome Stability Unit, St. Vincent’s Institute of Medical ResearchFitzroyAustralia
- Department of Medicine (St. Vincent’s Health), The University of MelbourneMelbourneAustralia
| | - Andrew J Deans
- Genome Stability Unit, St. Vincent’s Institute of Medical ResearchFitzroyAustralia
- Department of Medicine (St. Vincent’s Health), The University of MelbourneMelbourneAustralia
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9
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Dahlke K, Sing CE. Influence of Nucleoid-Associated Proteins on DNA Supercoiling. J Phys Chem B 2019; 123:10152-10162. [PMID: 31710235 DOI: 10.1021/acs.jpcb.9b07436] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
DNA supercoiling, where the DNA strand forms a writhe to relieve torsional stress, plays a vital role in packaging the genetic material in cells. Experiment, simulation, and theory have all demonstrated how supercoiling emerges due to the over- or underwinding of the DNA strand. Nucleoid-associated proteins (NAPs) help structure DNA in prokaryotes, yet the role that they play in the supercoiling process has not been as thoroughly investigated. We develop a coarse-grained simulation to model DNA supercoiling in the presence of proteins, providing a rigorous physical understanding of how NAPs affect supercoiling behavior. Specifically, we demonstrate how the force and torque necessary to form supercoils are affected by the presence of NAPs. NAPs that bend DNA stabilize the supercoil, thus shifting the transition between extended and supercoiled DNAs. We develop a theory to explain how NAP binding affects DNA supercoiling. This provides insight into how NAPs modulate DNA compaction via a combination of supercoiling and local protein-dependent deformations.
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Affiliation(s)
- Katelyn Dahlke
- Department of Chemical and Biomolecular Engineering , University of Illinois Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Charles E Sing
- Department of Chemical and Biomolecular Engineering , University of Illinois Urbana-Champaign , Urbana , Illinois 61801 , United States
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10
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Shimada T, Yamamoto K, Nakano M, Watanabe H, Schleheck D, Ishihama A. Regulatory role of CsqR (YihW) in transcription of the genes for catabolism of the anionic sugar sulfoquinovose (SQ) in Escherichia coli K-12. MICROBIOLOGY-SGM 2018; 165:78-89. [PMID: 30372406 DOI: 10.1099/mic.0.000740] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The binding sites of YihW, an uncharacterized DeoR-family transcription factor (TF) of Escherichia coli K-12, were identified using Genomic SELEX screening at two closely located sites, one inside the spacer between the bidirectional transcription units comprising the yihUTS operon and the yihV gene, and another one upstream of the yihW gene itself. Recently the YihUTS and YihV proteins were identified as catalysing the catabolism of sulfoquinovose (SQ), a hydrolysis product of sulfoquinovosyl diacylglycerol (SQDG) derived from plants and other photosynthetic organisms. Gel shift assay in vitro and reporter assay in vivo indicated that YihW functions as a repressor for all three transcription units. De-repression of the yih operons was found to be under the control of SQ as inducer, but not of lactose, glucose or galactose. Furthermore, a mode of its cooperative DNA binding was suggested for YihW by atomic force microscopy. Hence, as a regulator of the catabolism of SQ, we renamed YihW as CsqR.
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Affiliation(s)
- Tomohiro Shimada
- 1Meiji University, School of Agriculture, Kawasaki, Kanagawa, Japan
| | - Kaneyoshi Yamamoto
- 2Department of Frontier Bioscience, Hosei University, Koganei, Tokyo, Japan.,3Hosei University, Micro-Nano Technology Research Center, Koganei, Tokyo, Japan
| | - Masahiro Nakano
- 4Kyoto University, Institute for Frontier Life and Medical Sciences, Sakyo-ku, Kyoto, Japan
| | - Hiroki Watanabe
- 2Department of Frontier Bioscience, Hosei University, Koganei, Tokyo, Japan
| | - David Schleheck
- 5Department of Biology and Konstanz Research School Chemical Biology, University of Konstanz, D-78457 Konstanz, Germany
| | - Akira Ishihama
- 3Hosei University, Micro-Nano Technology Research Center, Koganei, Tokyo, Japan
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11
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Efremov AK, Yan J. Transfer-matrix calculations of the effects of tension and torque constraints on DNA-protein interactions. Nucleic Acids Res 2018; 46:6504-6527. [PMID: 29878241 PMCID: PMC6061897 DOI: 10.1093/nar/gky478] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Accepted: 05/17/2018] [Indexed: 12/12/2022] Open
Abstract
Organization and maintenance of the chromosomal DNA in living cells strongly depends on the DNA interactions with a plethora of DNA-binding proteins. Single-molecule studies show that formation of nucleoprotein complexes on DNA by such proteins is frequently subject to force and torque constraints applied to the DNA. Although the existing experimental techniques allow to exert these type of mechanical constraints on individual DNA biopolymers, their exact effects in regulation of DNA-protein interactions are still not completely understood due to the lack of systematic theoretical methods able to efficiently interpret complex experimental observations. To fill this gap, we have developed a general theoretical framework based on the transfer-matrix calculations that can be used to accurately describe behaviour of DNA-protein interactions under force and torque constraints. Potential applications of the constructed theoretical approach are demonstrated by predicting how these constraints affect the DNA-binding properties of different types of architectural proteins. Obtained results provide important insights into potential physiological functions of mechanical forces in the chromosomal DNA organization by architectural proteins as well as into single-DNA manipulation studies of DNA-protein interactions.
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Affiliation(s)
- Artem K Efremov
- Mechanobiology Institute, National University of Singapore, 117411, Singapore
- Centre for Bioimaging Sciences, National University of Singapore, 117557, Singapore
| | - Jie Yan
- Mechanobiology Institute, National University of Singapore, 117411, Singapore
- Centre for Bioimaging Sciences, National University of Singapore, 117557, Singapore
- Department of Physics, National University of Singapore, 117551, Singapore
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12
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Abstract
Nucleoid-associated proteins (NAPs) are important factors in shaping bacterial nucleoid and regulating global gene expression. A great deal of insights into NAPs can be obtained through studies using single DNA molecule, which has been made possible owing to recent rapid development of single-DNA manipulation techniques. These studies provide information on modes of binding to DNA, which shed light on the mechanism underlying the regulatory function of NAPs. In addition, how NAPs organize DNA and thus their contribution to chromosomal DNA packaging can be determined. In this chapter, we introduce transverse magnetic tweezers that allows for convenient manipulation of long DNA molecules, and its applications in studies of NAPs as exemplified by the E. coli H-NS protein. We describe how transverse magnetic tweezers is a powerful tool that can be used to characterize the DNA binding and organization modes of NAPs and how such information leads to better understanding of its roles in DNA packaging of bacterial nucleoid and transcription regulation.
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13
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Joyeux M. Role of Salt Valency in the Switch of H-NS Proteins between DNA-Bridging and DNA-Stiffening Modes. Biophys J 2018; 114:2317-2325. [PMID: 29576193 DOI: 10.1016/j.bpj.2018.02.030] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 02/05/2018] [Accepted: 02/28/2018] [Indexed: 11/17/2022] Open
Abstract
This work investigates the interactions of H-NS proteins and bacterial genomic DNA through computer simulations performed with a coarse-grained model. The model was developed specifically to study the switch of H-NS proteins from the DNA-stiffening to the DNA-bridging mode, which has been observed repeatedly upon addition of multivalent cations to the buffer but is still not understood. Unraveling the corresponding mechanism is all the more crucial, as the regulation properties of H-NS proteins, as well as other nucleoid proteins, are linked to their DNA-binding properties. The simulations reported here support a mechanism, according to which the primary role of multivalent cations consists in decreasing the strength of H-NS/DNA interactions compared to H-NS/H-NS interactions, with the latter ones becoming energetically favored with respect to the former ones above a certain threshold of the effective valency of the cations of the buffer. Below the threshold, H-NS dimers form filaments, which stretch along the DNA molecule but are quite inefficient in bridging genomically distant DNA sites (DNA-stiffening mode). In contrast, just above the threshold, H-NS dimers form three-dimensional clusters, which are able to connect DNA sites that are distant from the genomic point of view (DNA-bridging mode). The model provides clear rationales for the experimental observations that the switch between the two modes is a threshold effect and that the ability of H-NS dimers to form higher order oligomers is crucial for their bridging capabilities.
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Affiliation(s)
- Marc Joyeux
- Laboratoire Interdisciplinaire de Physique, CNRS and Université Grenoble Alpes, Grenoble, France.
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14
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Uncharacterized Bacterial Structures Revealed by Electron Cryotomography. J Bacteriol 2017; 199:JB.00100-17. [PMID: 28607161 DOI: 10.1128/jb.00100-17] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 05/27/2017] [Indexed: 01/06/2023] Open
Abstract
Electron cryotomography (ECT) can reveal the native structure and arrangement of macromolecular complexes inside intact cells. This technique has greatly advanced our understanding of the ultrastructure of bacterial cells. We now view bacteria as structurally complex assemblies of macromolecular machines rather than as undifferentiated bags of enzymes. To date, our group has applied ECT to nearly 90 different bacterial species, collecting more than 15,000 cryotomograms. In addition to known structures, we have observed, to our knowledge, several uncharacterized features in these tomograms. Some are completely novel structures; others expand the features or species range of known structure types. Here, we present a survey of these uncharacterized bacterial structures in the hopes of accelerating their identification and study, and furthering our understanding of the structural complexity of bacterial cells.IMPORTANCE Bacteria are more structurally complex than is commonly appreciated. Here we present a survey of previously uncharacterized structures that we observed in bacterial cells by electron cryotomography, structures that will initiate new lines of research investigating their identities and roles.
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15
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Briegel A, Oikonomou CM, Chang YW, Kjær A, Huang AN, Kim KW, Ghosal D, Nguyen HH, Kenny D, Ogorzalek Loo RR, Gunsalus RP, Jensen GJ. Morphology of the archaellar motor and associated cytoplasmic cone in Thermococcus kodakaraensis. EMBO Rep 2017; 18:1660-1670. [PMID: 28729461 DOI: 10.15252/embr.201744070] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 06/29/2017] [Accepted: 07/04/2017] [Indexed: 11/09/2022] Open
Abstract
Archaeal swimming motility is driven by archaella: rotary motors attached to long extracellular filaments. The structure of these motors, and particularly how they are anchored in the absence of a peptidoglycan cell wall, is unknown. Here, we use electron cryotomography to visualize the archaellar basal body in vivo in Thermococcus kodakaraensis KOD1. Compared to the homologous bacterial type IV pilus (T4P), we observe structural similarities as well as several unique features. While the position of the cytoplasmic ATPase appears conserved, it is not braced by linkages that extend upward through the cell envelope as in the T4P, but rather by cytoplasmic components that attach it to a large conical frustum up to 500 nm in diameter at its base. In addition to anchoring the lophotrichous bundle of archaella, the conical frustum associates with chemosensory arrays and ribosome-excluding material and may function as a polar organizing center for the coccoid cells.
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Affiliation(s)
- Ariane Briegel
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Catherine M Oikonomou
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Yi-Wei Chang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Andreas Kjær
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Audrey N Huang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Ki Woo Kim
- School of Ecology and Environmental System, Kyungpook National University, Sangju, South Korea
| | - Debnath Ghosal
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Hong H Nguyen
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
| | - Dorothy Kenny
- Department of Microbiology, Immunology and Molecular Genetics, The UCLA DOE Institute, University of California, Los Angeles, CA, USA
| | - Rachel R Ogorzalek Loo
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
| | - Robert P Gunsalus
- Department of Microbiology, Immunology and Molecular Genetics, The UCLA DOE Institute, University of California, Los Angeles, CA, USA
| | - Grant J Jensen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA .,Howard Hughes Medical Institute, Pasadena, CA, USA
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16
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Sugino H, Usui T, Shimada T, Nakano M, Ogasawara H, Ishihama A, Hirata A. A structural sketch of RcdA, a transcription factor controlling the master regulator of biofilm formation. FEBS Lett 2017; 591:2019-2031. [PMID: 28608551 DOI: 10.1002/1873-3468.12713] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 05/30/2017] [Accepted: 06/01/2017] [Indexed: 12/23/2022]
Abstract
RcdA is a regulator of curlin subunit gene D, the master regulator of biofilm formation in Escherichia coli. Here, we determined the X-ray structure of RcdA at 2.55 Å resolution. RcdA consists of an N-terminal DNA-binding domain (DBD) containing a helix-turn-helix (HTH) motif and a C-terminal dimerization domain, and forms a homodimer in crystals. A computational docking model of the RcdA-DNA complex allowed prediction of the candidate residues responsible for DNA binding. Our structure-guided mutagenesis, in combination with gel shift assay, atomic force microscopic observation, and reporter assay, indicate that R32 in α2 of the HTH motif plays an essential role in the recognition and binding of target DNA while T46 in α3 influences the mode of oligomerization. These results provide insights into the DNA-binding mode of RcdA.
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Affiliation(s)
- Hirotaka Sugino
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Matsuyama, Japan
| | - Takanori Usui
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Matsuyama, Japan
| | - Tomohiro Shimada
- School of Agriculture, Meiji University, Tama-ku, Kawasaki-shi, Kanagawa, Japan
| | - Masahiro Nakano
- Department of Virus Research, Institute for Frontier Life and Medical Science, Kyoto University, Japan
| | - Hiroshi Ogasawara
- Research Center for Supports to Advanced Science, Division of Gene Research, Shinshu University, Ueda, Nagano, Japan.,Research Center for Fungal and Microbial Dynamism, Shinshu University, Nagano, Japan
| | - Akira Ishihama
- Micro-Nano Technology Research Center and Department of Frontier Bioscience, Hosei University, Koganei, Tokyo, Japan
| | - Akira Hirata
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Matsuyama, Japan
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17
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Jarillo J, Morín JA, Beltrán-Heredia E, Villaluenga JPG, Ibarra B, Cao FJ. Mechanics, thermodynamics, and kinetics of ligand binding to biopolymers. PLoS One 2017; 12:e0174830. [PMID: 28380044 PMCID: PMC5381885 DOI: 10.1371/journal.pone.0174830] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2017] [Accepted: 03/15/2017] [Indexed: 01/20/2023] Open
Abstract
Ligands binding to polymers regulate polymer functions by changing their physical and chemical properties. This ligand regulation plays a key role in many biological processes. We propose here a model to explain the mechanical, thermodynamic, and kinetic properties of the process of binding of small ligands to long biopolymers. These properties can now be measured at the single molecule level using force spectroscopy techniques. Our model performs an effective decomposition of the ligand-polymer system on its covered and uncovered regions, showing that the elastic properties of the ligand-polymer depend explicitly on the ligand coverage of the polymer (i.e., the fraction of the polymer covered by the ligand). The equilibrium coverage that minimizes the free energy of the ligand-polymer system is computed as a function of the applied force. We show how ligands tune the mechanical properties of a polymer, in particular its length and stiffness, in a force dependent manner. In addition, it is shown how ligand binding can be regulated applying mechanical tension on the polymer. Moreover, the binding kinetics study shows that, in the case where the ligand binds and organizes the polymer in different modes, the binding process can present transient shortening or lengthening of the polymer, caused by changes in the relative coverage by the different ligand modes. Our model will be useful to understand ligand-binding regulation of biological processes, such as the metabolism of nucleic acid. In particular, this model allows estimating the coverage fraction and the ligand mode characteristics from the force extension curves of a ligand-polymer system.
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Affiliation(s)
- Javier Jarillo
- Departamento de Física Atómica, Molecular y Nuclear. Facultad de Ciencias Físicas. Universidad Complutense de Madrid. Pza. de las Ciencias, 1. Madrid. Spain
| | - José A. Morín
- Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA Nanociencia) & CNB-CSIC-IMDEA Nanociencia Associated Unit ‘Unidad de Nanobiotecnología’, Madrid, Spain
| | - Elena Beltrán-Heredia
- Departamento de Física Atómica, Molecular y Nuclear. Facultad de Ciencias Físicas. Universidad Complutense de Madrid. Pza. de las Ciencias, 1. Madrid. Spain
| | - Juan P. G. Villaluenga
- Departamento de Física Aplicada I. Facultad de Ciencias Físicas. Universidad Complutense de Madrid. Pza. de las Ciencias, 1. Madrid. Spain
| | - Borja Ibarra
- Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA Nanociencia) & CNB-CSIC-IMDEA Nanociencia Associated Unit ‘Unidad de Nanobiotecnología’, Madrid, Spain
| | - Francisco J. Cao
- Departamento de Física Atómica, Molecular y Nuclear. Facultad de Ciencias Físicas. Universidad Complutense de Madrid. Pza. de las Ciencias, 1. Madrid. Spain
- * E-mail:
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18
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Strategies for manipulation of oxygen utilization by the electron transfer chain in microbes for metabolic engineering purposes. J Ind Microbiol Biotechnol 2016; 44:647-658. [PMID: 27800562 DOI: 10.1007/s10295-016-1851-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 10/06/2016] [Indexed: 12/14/2022]
Abstract
Microaerobic growth is of importance in ecological niches, pathogenic infections and industrial production of chemicals. The use of low levels of oxygen enables the cell to gain energy and grow more robustly in the presence of a carbon source that can be oxidized and provide electrons to the respiratory chain in the membrane. A considerable amount of information is available on the genes and proteins involved in respiratory growth and the regulation of genes involved in aerobic and anaerobic metabolism. The dependence of regulation on sensing systems that respond to reduced quinones (e.g. ArcB) or oxygen levels that affect labile redox components of transcription regulators (Fnr) are key in understanding the regulation. Manipulation of the amount of respiration can be difficult to control in dense cultures or inadequately mixed reactors leading to inhomogeneous cultures that may have lower than optimal performance. Efforts to control respiration through genetic means have been reported and address mutations affecting components of the electron transport chain. In a recent report completion for intermediates of the ubiquinone biosynthetic pathway was used to dial the level of respiration vs lactate formation in an aerobically grown E. coli culture.
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19
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Regulation of Bacterial DNA Packaging in Early Stationary Phase by Competitive DNA Binding of Dps and IHF. Sci Rep 2015; 5:18146. [PMID: 26657062 PMCID: PMC4677351 DOI: 10.1038/srep18146] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 11/12/2015] [Indexed: 02/01/2023] Open
Abstract
The bacterial nucleoid, a bacterial genome packed by nucleoid binding proteins, forms the physical basis for cellular processes such as gene transcription and DNA replication. Bacteria need to dynamically modulate their nucleoid structures at different growth phases and in response to environmental changes. At the nutrients deficient stationary phase, DNA-binding proteins from starved cells (Dps) and Integration host factors (IHF) are the two most abundant nucleoid associated proteins in E. coli. Yet, it remains unclear how the nucleoid architecture is controlled by the interplay between these two proteins, as well as the nucleoid's response to environmental changes. This question is addressed here using single DNA manipulation approach. Our results reveal that the two proteins are differentially selected for DNA binding, which can be tuned by changing environmental factors over physiological ranges including KCl (50-300 mM), MgCl2 (0-10 mM), pH (6.5-8.5) and temperature (23-37 °C). Increasing pH and MgCl2 concentrations switch from Dps-binding to IHF-binding. Stable Dps-DNA and IHF-DNA complexes are insensitive to temperature changes for the range tested. The environment dependent selection between IHF and Dps results in different physical organizations of DNA. Overall, our findings provide important insights into E. coli nucleoid architecture.
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20
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Abstract
It is now well established that prokaryotic cells assemble diverse proteins into dynamic cytoskeletal filaments that perform essential cellular functions. Although most of the filaments assemble on their own to form higher order structures, growing evidence suggests that there are a number of prokaryotic proteins that polymerise only in the presence of a matrix such as DNA, lipid membrane or even another filament. Matrix-assisted filament systems are frequently nucleotide dependent and cytomotive but rarely considered as part of the bacterial cytoskeleton. Here, we categorise this family of filament-forming systems as collaborative filaments and introduce a simple nomenclature. Collaborative filaments are frequent in both eukaryotes and prokaryotes and are involved in vital cellular processes including chromosome segregation, DNA repair and maintenance, gene silencing and cytokinesis to mention a few. In this review, we highlight common principles underlying collaborative filaments and correlate these with known functions.
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Affiliation(s)
| | - Jan Löwe
- MRC Laboratory of Molecular Biology, Cambridge, UK
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21
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Li W, Wong WJ, Lim CJ, Ju HP, Li M, Yan J, Wang PY. Complex kinetics of DNA condensation revealed through DNA twist tracing. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 92:022707. [PMID: 26382432 DOI: 10.1103/physreve.92.022707] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2015] [Indexed: 06/05/2023]
Abstract
Toroid formation is an important mechanism for DNA condensation in cells. The length change during DNA condensation was investigated in previous single-molecule experiments. However, DNA twist is key to understanding the topological kinetics of DNA condensation. In this study, DNA twist as well as DNA length was traced during the DNA condensation by the freely orbiting magnetic tweezers and the tilted magnetic tweezers combined with Brownian dynamics simulations. The experimental results disclose the complex relationship between DNA extension and backbone rotation. Brownian dynamics simulations show that the toroid formation follows a wiggling pathway which leads to the complex DNA backbone rotation as revealed in our experiments. These findings provide the complete description of multivalent cation-dependent DNA toroid formation under tension.
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Affiliation(s)
- Wei Li
- Beijing National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Wei Juan Wong
- Department of Physics, National University of Singapore, Singapore 117542
- Mechanobiology Institute, National University of Singapore, Singapore 117411
| | - Ci Ji Lim
- Department of Physics, National University of Singapore, Singapore 117542
- Mechanobiology Institute, National University of Singapore, Singapore 117411
| | - Hai-Peng Ju
- Beijing National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Ming Li
- Beijing National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Jie Yan
- Department of Physics, National University of Singapore, Singapore 117542
- Mechanobiology Institute, National University of Singapore, Singapore 117411
| | - Peng-Ye Wang
- Beijing National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
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22
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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.
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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.
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23
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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.
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24
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Yamamoto K, Watanabe H, Ishihama A. Expression levels of transcription factors in Escherichia coli: growth phase- and growth condition-dependent variation of 90 regulators from six families. Microbiology (Reading) 2014; 160:1903-1913. [DOI: 10.1099/mic.0.079889-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The expression pattern of the genome in Escherichia coli is controlled by regulating the utilization of a limited number of RNA polymerases between a total of 4600 genes on its genome. The distribution pattern of RNA polymerase on the genome changes after two steps of protein–protein interaction with seven sigma subunits and about 300 transcription factors (TFs). Based on a systematic search for the regulation target promoters recognized by each TF, we propose two novel concepts: each TF regulates a number of target promoters; and each promoter is regulated by many TFs. In parallel, attempts have been made to determine the intracellular concentrations of all TFs using two systems: quantitative immunoblot analysis using TF-specific antibodies; and reporter assay of TF promoter activities. The direct measurement of TF protein level has so far been published for a set of 60 regulators with known functions. This study describes the determination of growth phase-dependent expression levels of 90 TFs using the reporter assay system. The translational fusion vector was constructed from the TF promoter sequence including an N-terminal proximal TF segment and the reporter GFP. At the beginning of cell growth, high-level expression was observed only for a small number of TFs. In the exponential phase, approximately 80 % TFs are expressed, but the expressed TF species change upon transfer to the stationary phase. Significant changes in the pattern of TF expression were observed between aerobic and anaerobic conditions. The list of intracellular levels of TFs provides further understanding to the transcription regulation of the E. coli genome under various stressful conditions.
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Affiliation(s)
- Kaneyoshi Yamamoto
- Research Institute of Micro-Nano Technology, Hosei University, Koganei, Tokyo 185-8584, Japan
- Department of Frontier Bioscience, Hosei University, Koganei, Tokyo 185-8584, Japan
| | - Hiroki Watanabe
- Department of Frontier Bioscience, Hosei University, Koganei, Tokyo 185-8584, Japan
| | - Akira Ishihama
- Research Institute of Micro-Nano Technology, Hosei University, Koganei, Tokyo 185-8584, Japan
- Department of Frontier Bioscience, Hosei University, Koganei, Tokyo 185-8584, Japan
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25
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Lim CJ, Kenney LJ, Yan J. Single-molecule studies on the mechanical interplay between DNA supercoiling and H-NS DNA architectural properties. Nucleic Acids Res 2014; 42:8369-78. [PMID: 24990375 PMCID: PMC4117784 DOI: 10.1093/nar/gku566] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The Escherichia coli H-NS protein is a major nucleoid-associated protein that is involved in chromosomal DNA packaging and gene regulatory functions. These biological processes are intimately related to the DNA supercoiling state and thus suggest a direct relationship between H-NS binding and DNA supercoiling. Here, we show that H-NS, which has two distinct DNA-binding modes, is able to differentially regulate DNA supercoiling. H-NS DNA-stiffening mode caused by nucleoprotein filament formation is able to suppress DNA plectoneme formation during DNA supercoiling. In contrast, when H-NS is in its DNA-bridging mode, it is able to promote DNA plectoneme formation during DNA supercoiling. In addition, the DNA-bridging mode is able to block twists diffusion thus trapping DNA in supercoiled domains. Overall, this work reveals the mechanical interplay between H-NS and DNA supercoiling which provides insights to H-NS organization of chromosomal DNA based on its two distinct DNA architectural properties.
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Affiliation(s)
- Ci Ji Lim
- Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore Centre for Bioimaging Sciences, National University of Singapore, Singapore Mechanobiology Institute, Singapore Department of Physics, National University of Singapore, Singapore
| | - Linda J Kenney
- Mechanobiology Institute, Singapore Jesse Brown Veterans Affairs Medical Center, Chicago, IL, USA Department of Microbiology & Immunology, University of Illinois-Chicago, Chicago, IL, USA Department of Biological Sciences, National University of Singapore, Singapore
| | - Jie Yan
- Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore Centre for Bioimaging Sciences, National University of Singapore, Singapore Mechanobiology Institute, Singapore Department of Physics, National University of Singapore, Singapore
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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.
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Affiliation(s)
- Yuanyuan Qu
- Department of Physics, National University of Singapore, Singapore 117542, Singapore
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