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Ami D, Natalello A. Characterization of the Conformational Properties of Soluble and Insoluble Proteins by Fourier Transform Infrared Spectroscopy. Methods Mol Biol 2022; 2406:439-454. [PMID: 35089573 DOI: 10.1007/978-1-0716-1859-2_26] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The FTIR (micro-)spectroscopy method applied to the study of the structural properties of different soluble and insoluble proteins will be illustrated. In particular, we will discuss the procedure to analyze proteins in form of hydrated films and in solution by means of attenuated total reflection (ATR) measurements. Moreover, we will describe the procedure to characterize bacterial inclusion bodies (IBs) and amyloid deposits within human tissues by means of FTIR microspectroscopy.
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Affiliation(s)
- Diletta Ami
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy.
| | - Antonino Natalello
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy.
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2
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Marjani N, Dareini M, Asadzade-Lotfabad M, Pejhan M, Mokaberi P, Amiri-Tehranizadeh Z, Saberi MR, Chamani J. Evaluation of the binding effect and cytotoxicity assay of 2-Ethyl-5-(4-methylphenyl) pyramido pyrazole ophthalazine trione on calf thymus DNA: spectroscopic, calorimetric, and molecular dynamics approaches. LUMINESCENCE 2021; 37:310-322. [PMID: 34862709 DOI: 10.1002/bio.4173] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 10/14/2021] [Accepted: 11/17/2021] [Indexed: 01/04/2023]
Abstract
With advances in new drug therapies, it is essential to understand the interactions between drugs and target molecules. In this study, we applied multiple spectroscopic techniques including absorbance, fluorescence, circular dichroism spectroscopy, viscosity, thermal melting, calorimetric, and molecular dynamics (MD) simulation to study the interaction between 2-Ethyl-5-(4-methylphenyl) pyramido pyrazole ophthalazine trione (PPF) and calf thymus DNA (ct DNA) in the absence or presence of histone H1. PPF exhibits a high binding affinity towards ct DNA in binary and ternary systems. In addition, the result for the binding constant was observed within the range 104 M-1 achieved through fluorescence quenching data, while the values for enthalpy and entropy changes for ct DNA-PPF and (ct DNA-H1) PPF complexes were measured to be -72.54 kJ.mol-1 , -161.14 J.mol-1 K-1 , -85.34 kJ.mol-1 , and -19.023 J.mol-1 K-1 , respectively. Furthermore, in accordance with circular dichroism spectra, the inducement of ct DNA structural changes was observed during binding of PPF and H1 in binary and ternary system forms. The essential roles of hydrogen bonding and van der Waals forces throughout the interaction were suggested using thermodynamic parameters. According to the obtained data, the interaction mode of ct DNA-PPF and (ct DNA-H1) PPF complexes was intercalation binding. Suggested by the MD simulation study, the ct DNA-H1 complex caused a reduction in the stability of the DNA structure in the presence or absence of ligand, which demonstrated that PPF as an intercalating agent can further distort the structure. The information achieved from this study will be very helpful in understanding the effects of PPF on the conformational state of ct DNA in the absence or presence of the H1 molecule, which seems to be quite significant for clarifying the mechanisms of action and its pharmacokinetics.
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Affiliation(s)
- Narges Marjani
- Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | - Maryam Dareini
- Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | - Maryam Asadzade-Lotfabad
- Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | - Mahtab Pejhan
- Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | - Parisa Mokaberi
- Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | - Zeinab Amiri-Tehranizadeh
- Department of Medical Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Reza Saberi
- Department of Medical Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Jamshidkhan Chamani
- Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran
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3
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The selective adsorption performance and mechanism of multiwall magnetic carbon nanotubes for heavy metals in wastewater. Sci Rep 2021; 11:16878. [PMID: 34413419 PMCID: PMC8377063 DOI: 10.1038/s41598-021-96465-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 08/05/2021] [Indexed: 11/08/2022] Open
Abstract
The safe treatment of heavy metals in wastewater is directly related to human health and social development. In this paper, a new type of recyclable adsorbent is synthesized through the oxidation of enhancer and modification with magnetic nanoparticles. The new adsorbent not only inherits the advantages of multiwall carbon nanotubes (6O-MWCNTs), but also exhibits a new magnetic property and further improved adsorption capacity, which is conducive to the magnetic separation and recovery of heavy metals. The adsorption results indicate that multiwall magnetic carbon nanotubes (6O-MWCNTs@Fe3O4) have a good performance for Pb(II) selective adsorption, with a maximum adsorption capacity of 215.05 mg/g, much higher than the existing adsorption capacity of the same type of adsorbents. Under the action of an external magnetic field, 6O-MWCNTs@Fe3O4 that adsorbed metal ions can quickly achieve good separation from the solution. The joint characterization results of FTIR and XPS show that under the action of both coordination and electrostatic attraction, the C=O bond in the -COOH group is induced to open by the metal ions and transforms into an ionic bond, and the metal ions are stably adsorbed on the surface of 6O-MWCNTs@Fe3O4. Pb(II) has a stronger attraction than Cu(II) and Cd(II) to the lone pair of electrons in oxygen atoms to form complexes, due to the covalent index of Pb (6.41) is more larger than that of Cu (2.98) and Cd (2.71).These data provide a new type of recyclable adsorbent for the efficient treatment of heavy metal ions in wastewater and enrich relevant theoretical knowledge.
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Lipiec E, Ruggeri FS, Benadiba C, Borkowska AM, Kobierski JD, Miszczyk J, Wood BR, Deacon GB, Kulik A, Dietler G, Kwiatek WM. Infrared nanospectroscopic mapping of a single metaphase chromosome. Nucleic Acids Res 2019; 47:e108. [PMID: 31562528 PMCID: PMC6765102 DOI: 10.1093/nar/gkz630] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 07/07/2019] [Accepted: 07/13/2019] [Indexed: 01/27/2023] Open
Abstract
The integrity of the chromatin structure is essential to every process occurring within eukaryotic nuclei. However, there are no reliable tools to decipher the molecular composition of metaphase chromosomes. Here, we have applied infrared nanospectroscopy (AFM-IR) to demonstrate molecular difference between eu- and heterochromatin and generate infrared maps of single metaphase chromosomes revealing detailed information on their molecular composition, with nanometric lateral spatial resolution. AFM-IR coupled with principal component analysis has confirmed that chromosome areas containing euchromatin and heterochromatin are distinguishable based on differences in the degree of methylation. AFM-IR distribution of eu- and heterochromatin was compared to standard fluorescent staining. We demonstrate the ability of our methodology to locate spatially the presence of anticancer drug sites in metaphase chromosomes and cellular nuclei. We show that the anticancer 'rule breaker' platinum compound [Pt[N(p-HC6F4)CH2]2py2] preferentially binds to heterochromatin, forming localized discrete foci due to condensation of DNA interacting with the drug. Given the importance of DNA methylation in the development of nearly all types of cancer, there is potential for infrared nanospectroscopy to be used to detect gene expression/suppression sites in the whole genome and to become an early screening tool for malignancy.
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Affiliation(s)
- Ewelina Lipiec
- Institute of Nuclear Physics, Polish Academy of Sciences, PL-31342 Krakow, Poland
- Institute of Physics, Laboratory of Physics of Living Matter, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
- Centre for Biospectroscopy and School of Chemistry, Monash University, 3800 Victoria, Australia
| | - Francesco S Ruggeri
- Institute of Physics, Laboratory of Physics of Living Matter, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
- Department of Chemistry, University of Cambridge, CB21EW, UK
| | - Carine Benadiba
- Institute of Physics, Laboratory of Physics of Living Matter, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Anna M Borkowska
- Institute of Nuclear Physics, Polish Academy of Sciences, PL-31342 Krakow, Poland
| | - Jan D Kobierski
- Department of Pharmaceutical Biophysics, Faculty of Pharmacy Jagiellonian University Medical College, PL-31007 Cracow, Poland
| | - Justyna Miszczyk
- Institute of Nuclear Physics, Polish Academy of Sciences, PL-31342 Krakow, Poland
| | - Bayden R Wood
- Centre for Biospectroscopy and School of Chemistry, Monash University, 3800 Victoria, Australia
| | - Glen B Deacon
- School of Chemistry, Faculty of Science, Monash University, 3800 Victoria, Australia
| | - Andrzej Kulik
- Institute of Physics, Laboratory of Physics of Living Matter, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Giovanni Dietler
- Institute of Physics, Laboratory of Physics of Living Matter, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Wojciech M Kwiatek
- Institute of Nuclear Physics, Polish Academy of Sciences, PL-31342 Krakow, Poland
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Folding of poly-amino acids and intrinsically disordered proteins in overcrowded milieu induced by pH change. Int J Biol Macromol 2018; 125:244-255. [PMID: 30529354 DOI: 10.1016/j.ijbiomac.2018.12.038] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 11/27/2018] [Accepted: 12/02/2018] [Indexed: 12/24/2022]
Abstract
pH-induced structural changes of the synthetic homopolypeptides poly-E, poly-K, poly-R, and intrinsically disordered proteins (IDPs) prothymosin α (ProTα) and linker histone H1, in concentrated PEG solutions simulating macromolecular crowding conditions within the membrane-less organelles, were characterized. The conformational transitions of the studied poly-amino acids in the concentrated PEG solutions depend on the polymerization degree of these homopolypeptides, the size of their side chains, the charge distribution of the side chains, and the crowding agent concentration. The results obtained for poly-amino acids are valid for IDPs having a significant total charge. The overcrowded conditions promote a significant increase in the cooperativity of the pH-induced coil-α-helix transition of ProTα and provoke histone H1 aggregation. The most favorable conditions for the pH-induced structural transitions in concentrated PEG solutions are realized when the charged residues are grouped in blocks, and when the distance between the end of the side group carrying charge and the backbone is small. Therefore, the block-wise distribution of charged residues within the IDPs not only plays an important role in the liquid-liquid phase transitions, but may also define the expressivity of structural transitions of these proteins in the overcrowded conditions of the membrane-less organelles.
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Chaves-Arquero B, Pantoja-Uceda D, Roque A, Ponte I, Suau P, Jiménez MA. A CON-based NMR assignment strategy for pro-rich intrinsically disordered proteins with low signal dispersion: the C-terminal domain of histone H1.0 as a case study. JOURNAL OF BIOMOLECULAR NMR 2018; 72:139-148. [PMID: 30414042 DOI: 10.1007/s10858-018-0213-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 10/24/2018] [Indexed: 05/23/2023]
Abstract
The C-terminal domain of histone H1.0 (C-H1.0) is involved in DNA binding and is a main determinant of the chromatin condensing properties of histone H1.0. Phosphorylation at the (S/T)-P-X-(K/R) motifs affects DNA binding and is crucial for regulation of C-H1.0 function. Since C-H1.0 is an intrinsically disordered domain, solution NMR is an excellent approach to characterize the effect of phosphorylation on the structural and dynamic properties of C-H1.0. However, its very repetitive, low-amino acid-diverse and Pro-rich sequence, together with the low signal dispersion observed at the 1H-15N HSQC spectra of both non- and tri-phosphorylated C-H1.0 preclude the use of standard 1H-detected assignment strategies. We have achieved an essentially complete assignment of the heavy backbone atoms (15N, 13C' and 13Cα), as well as 1HN and 13Cβ nuclei, of non- and tri-phosphorylated C-H1.0 by applying a novel 13C-detected CON-based strategy. No C-H1.0 region with a clear secondary structure tendency was detected by chemical shift analyses, confirming at residue level that C-H1.0 is disordered in aqueous solution. Phosphorylation only affected the chemical shifts of phosphorylated Thr's, and their adjacent residues. Heteronuclear {1H}-15N NOEs were also essentially equal in the non- and tri-phosphorylated states. Hence, structural tendencies and dynamic properties of C-H1.0 free in aqueous solution are unmodified by phosphorylation. We propose that the assignment strategy used for C-H1.0, which is based on the acquisition of only a few 3D spectra, is an excellent choice for short-lived intrinsically disordered proteins with repetitive sequences.
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Affiliation(s)
- Belén Chaves-Arquero
- Departamento de Química-Física Biológica, Instituto de Química Física Rocasolano (IQFR-CSIC), Serrano 119, 28006, Madrid, Spain
| | - David Pantoja-Uceda
- Departamento de Química-Física Biológica, Instituto de Química Física Rocasolano (IQFR-CSIC), Serrano 119, 28006, Madrid, Spain
| | - Alicia Roque
- Departamento de Bioquímica y Biología Molecular, Facultad de Biociencias, Universidad Autónoma de Barcelona (UAB), Bellaterra, Barcelona, Spain
| | - Inmaculada Ponte
- Departamento de Bioquímica y Biología Molecular, Facultad de Biociencias, Universidad Autónoma de Barcelona (UAB), Bellaterra, Barcelona, Spain
| | - Pedro Suau
- Departamento de Bioquímica y Biología Molecular, Facultad de Biociencias, Universidad Autónoma de Barcelona (UAB), Bellaterra, Barcelona, Spain
| | - M Angeles Jiménez
- Departamento de Química-Física Biológica, Instituto de Química Física Rocasolano (IQFR-CSIC), Serrano 119, 28006, Madrid, Spain.
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7
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Shakibapour N, Dehghani Sani F, Beigoli S, Sadeghian H, Chamani J. Multi-spectroscopic and molecular modeling studies to reveal the interaction between propyl acridone and calf thymus DNA in the presence of histone H1: binary and ternary approaches. J Biomol Struct Dyn 2018; 37:359-371. [DOI: 10.1080/07391102.2018.1427629] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Niloufar Shakibapour
- Faculty of Sciences, Department of Biology, Islamic Azad University, Mashhad Branch, Mashhad, Iran
| | - Farzad Dehghani Sani
- Faculty of Sciences, Department of Biology, Islamic Azad University, Mashhad Branch, Mashhad, Iran
| | - Sima Beigoli
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Hamid Sadeghian
- Neurogenic Inflammation Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Laboratory Sciences, School of Paramedical Sciences, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Jamshidkhan Chamani
- Faculty of Sciences, Department of Biology, Islamic Azad University, Mashhad Branch, Mashhad, Iran
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Ponte I, Romero D, Yero D, Suau P, Roque A. Complex Evolutionary History of the Mammalian Histone H1.1-H1.5 Gene Family. Mol Biol Evol 2017; 34:545-558. [PMID: 28100789 PMCID: PMC5400378 DOI: 10.1093/molbev/msw241] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
H1 is involved in chromatin higher-order structure and gene regulation. H1 has a tripartite structure. The central domain is stably folded in solution, while the N- and C-terminal domains are intrinsically disordered. The terminal domains are encoded by DNA of low sequence complexity, and are thus prone to short insertions/deletions (indels). We have examined the evolution of the H1.1-H1.5 gene family from 27 mammalian species. Multiple sequence alignment has revealed a strong preferential conservation of the number and position of basic residues among paralogs, suggesting that overall H1 basicity is under a strong purifying selection. The presence of a conserved pattern of indels, ancestral to the splitting of mammalian orders, in the N- and C-terminal domains of the paralogs, suggests that slippage may have favored the rapid divergence of the subtypes and that purifying selection has maintained this pattern because it is associated with function. Evolutionary analyses have found evidences of positive selection events in H1.1, both before and after the radiation of mammalian orders. Positive selection ancestral to mammalian radiation involved changes at specific sites that may have contributed to the low relative affinity of H1.1 for chromatin. More recent episodes of positive selection were detected at codon positions encoding amino acids of the C-terminal domain of H1.1, which may modulate the folding of the CTD. The detection of putative recombination points in H1.1-H1.5 subtypes suggests that this process may has been involved in the acquisition of the tripartite H1 structure.
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Affiliation(s)
- Inma Ponte
- Departamento de Bioquímica y Biología Molecular, Facultad de Biociencias, Universidad Autónoma de Barcelona, Barcelona, Spain
| | - Devani Romero
- Departamento de Bioquímica y Biología Molecular, Facultad de Biociencias, Universidad Autónoma de Barcelona, Barcelona, Spain
| | - Daniel Yero
- Instituto de Biotecnología y de Biomedicina (IBB) y Departamento de Genética y Microbiología, Universidad Autónoma de Barcelona, Barcelona, Spain
| | - Pedro Suau
- Departamento de Bioquímica y Biología Molecular, Facultad de Biociencias, Universidad Autónoma de Barcelona, Barcelona, Spain
| | - Alicia Roque
- Departamento de Bioquímica y Biología Molecular, Facultad de Biociencias, Universidad Autónoma de Barcelona, Barcelona, Spain
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Starkova TY, Polyanichko AM, Artamonova TO, Khodorkovskii MA, Kostyleva EI, Chikhirzhina EV, Tomilin AN. Post-translational modifications of linker histone H1 variants in mammals. Phys Biol 2017; 14:016005. [PMID: 28000612 DOI: 10.1088/1478-3975/aa551a] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The covalent modifications of the linker histone H1 and the core histones are thought to play an important role in the control of chromatin functioning. Histone H1 variants from K562 cell line (hH1), mouse (mH1) and calf (cH1) thymi were studied by matrix-activated laser desorption/ionization fourier transform ion cyclotron resonance mass-spectroscopy (MALDI-FT-ICR-MS). The proteomics analysis revealed novel post-translational modifications of the histone H1, such as meK34-mH1.4, meK35-cH1.1, meK35-mH1.1, meK75-hH1.2, meK75-hH1.3, acK26-hH1.4, acK26-hH1.3 and acK17-hH1.1. The comparison of the hH1, mH1 and cH1 proteins has demonstrated that the types and positions of the post-translational modifications of the globular domains of the H1.2-H1.4 variants are very conservative. However, the post-translational modifications of the N- and C-terminal tails of H1.2, H1.3 and H1.4 are different. The differences of post-translational modifications in the N- and C-terminal tails of H1.2, H1.3 and H1.4 likely lead to the differences in DNA-H1 and H1-protein interactions.
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Affiliation(s)
- T Yu Starkova
- Institute of Cytology of the Russian Academy of Sciences, St Petersburg, Russia. Saint Petersburg State University, Saint Petersburg, Russia. Author to whom any correspondence should be addressed. The authors made equal contribution to preparation of the manuscript
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Kowalski A, Pałyga J. Modulation of chromatin function through linker histone H1 variants. Biol Cell 2016; 108:339-356. [PMID: 27412812 DOI: 10.1111/boc.201600007] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Revised: 07/08/2016] [Accepted: 07/08/2016] [Indexed: 12/30/2022]
Abstract
In this review, the structural aspects of linker H1 histones are presented as a background for characterization of the factors influencing their function in animal and human chromatin. The action of H1 histone variants is largely determined by dynamic alterations of their intrinsically disordered tail domains, posttranslational modifications and allelic diversification. The interdependent effects of these factors can establish dynamic histone H1 states that may affect the organization and function of chromatin regions.
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Affiliation(s)
- Andrzej Kowalski
- Department of Biochemistry and Genetics, Institute of Biology, Jan Kochanowski University, 25-406 Kielce, Poland
| | - Jan Pałyga
- Department of Biochemistry and Genetics, Institute of Biology, Jan Kochanowski University, 25-406 Kielce, Poland
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SETD7 Regulates the Differentiation of Human Embryonic Stem Cells. PLoS One 2016; 11:e0149502. [PMID: 26890252 PMCID: PMC4758617 DOI: 10.1371/journal.pone.0149502] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 02/01/2016] [Indexed: 01/01/2023] Open
Abstract
The successful use of specialized cells in regenerative medicine requires an optimization in the differentiation protocols that are currently used. Understanding the molecular events that take place during the differentiation of human pluripotent cells is essential for the improvement of these protocols and the generation of high quality differentiated cells. In an effort to understand the molecular mechanisms that govern differentiation we identify the methyltransferase SETD7 as highly induced during the differentiation of human embryonic stem cells and differentially expressed between induced pluripotent cells and somatic cells. Knock-down of SETD7 causes differentiation defects in human embryonic stem cell including delay in both the silencing of pluripotency-related genes and the induction of differentiation genes. We show that SETD7 methylates linker histone H1 in vitro causing conformational changes in H1. These effects correlate with a decrease in the recruitment of H1 to the pluripotency genes OCT4 and NANOG during differentiation in the SETD7 knock down that might affect the proper silencing of these genes during differentiation.
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12
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Liao R, Mizzen CA. Interphase H1 phosphorylation: Regulation and functions in chromatin. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1859:476-85. [PMID: 26657617 DOI: 10.1016/j.bbagrm.2015.11.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Revised: 11/24/2015] [Accepted: 11/25/2015] [Indexed: 12/25/2022]
Abstract
Many metazoan cell types differentially express multiple non-allelic amino acid sequence variants of histone H1. Although early work revealed that H1 variants, collectively, are phosphorylated during interphase and mitosis, differences between individual H1 variants in the sites they possess for mitotic and interphase phosphorylation have been elucidated only relatively recently. Here, we review current knowledge on the regulation and function of interphase H1 phosphorylation, with a particular emphasis on how differences in interphase phosphorylation among the H1 variants of mammalian cells may enable them to have differential effects on transcription and other chromatin processes.
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Affiliation(s)
- Ruiqi Liao
- Department of Cell and Developmental Biology, University of Illinois at Urbana Champaign, USA
| | - Craig A Mizzen
- Department of Cell and Developmental Biology, University of Illinois at Urbana Champaign, USA; Institute for Genomic Biology, University of Illinois at Urbana Champaign, USA.
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Parseghian MH. What is the role of histone H1 heterogeneity? A functional model emerges from a 50 year mystery. AIMS BIOPHYSICS 2015; 2:724-772. [PMID: 31289748 PMCID: PMC6615755 DOI: 10.3934/biophy.2015.4.724] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
For the past 50 years, understanding the function of histone H1 heterogeneity has been mired in confusion and contradiction. Part of the reason for this is the lack of a working model that tries to explain the large body of data that has been collected about the H1 subtypes so far. In this review, a global model is described largely based on published data from the author and other researchers over the past 20 years. The intrinsic disorder built into H1 protein structure is discussed to help the reader understand that these histones are multi-conformational and adaptable to interactions with different targets. We discuss the role of each structural section of H1 (as we currently understand it), but we focus on the H1's C-terminal domain and its effect on each subtype's affinity, mobility and compaction of chromatin. We review the multiple ways these characteristics have been measured from circular dichroism to FRAP analysis, which has added to the sometimes contradictory assumptions made about each subtype. Based on a tabulation of these measurements, we then organize the H1 variants according to their ability to condense chromatin and produce nucleosome repeat lengths amenable to that compaction. This subtype variation generates a continuum of different chromatin states allowing for fine regulatory control and some overlap in the event one or two subtypes are lost to mutation. We also review the myriad of disparate observations made about each subtype, both somatic and germline specific ones, that lend support to the proposed model. Finally, to demonstrate its adaptability as new data further refines our understanding of H1 subtypes, we show how the model can be applied to experimental observations of telomeric heterochromatin in aging cells.
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Roque A, Ponte I, Suau P. Interplay between histone H1 structure and function. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1859:444-54. [PMID: 26415976 DOI: 10.1016/j.bbagrm.2015.09.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 09/21/2015] [Accepted: 09/22/2015] [Indexed: 01/10/2023]
Abstract
H1 linker histones are involved both in the maintenance of higher-order chromatin structure and in gene regulation. Histone H1 exists in multiple isoforms, is evolutionarily variable and undergoes a large variety of post-translational modifications. We review recent progress in the understanding of the folding and structure of histone H1 domains with an emphasis on the interactions with DNA. The importance of intrinsic disorder and hydrophobic interactions in the folding and function of the carboxy-terminal domain (CTD) is discussed. The induction of a molten globule-state in the CTD by macromolecular crowding is also considered. The effects of phosphorylation by cyclin-dependent kinases on the structure of the CTD, as well as on chromatin condensation and oligomerization, are described. We also address the extranuclear functions of histone H1, including the interaction with the β-amyloid peptide.
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Affiliation(s)
- Alicia Roque
- Departamento de Bioquímica y Biología Molecular, Facultad de Biociencias, Universidad Autónoma de Barcelona, Spain
| | - Inma Ponte
- Departamento de Bioquímica y Biología Molecular, Facultad de Biociencias, Universidad Autónoma de Barcelona, Spain
| | - Pedro Suau
- Departamento de Bioquímica y Biología Molecular, Facultad de Biociencias, Universidad Autónoma de Barcelona, Spain.
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Cutter AR, Hayes JJ. A brief review of nucleosome structure. FEBS Lett 2015; 589:2914-22. [PMID: 25980611 DOI: 10.1016/j.febslet.2015.05.016] [Citation(s) in RCA: 215] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 04/29/2015] [Accepted: 05/05/2015] [Indexed: 12/23/2022]
Abstract
The nucleosomal subunit organization of chromatin provides a multitude of functions. Nucleosomes elicit an initial ∼7-fold linear compaction of genomic DNA. They provide a critical mechanism for stable repression of genes and other DNA-dependent activities by restricting binding of trans-acting factors to cognate DNA sequences. Conversely they are engineered to be nearly meta-stable and disassembled (and reassembled) in a facile manner to allow rapid access to the underlying DNA during processes such as transcription, replication and DNA repair. Nucleosomes protect the genome from DNA damaging agents and provide a lattice onto which a myriad of epigenetic signals are deposited. Moreover, vast strings of nucleosomes provide a framework for assembly of the chromatin fiber and higher-order chromatin structures. Thus, in order to provide a foundation for understanding these functions, we present a review of the basic elements of nucleosome structure and stability, including the association of linker histones.
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Affiliation(s)
- Amber R Cutter
- Department of Biochemistry & Biophysics, University of Rochester Medical Center, Rochester, NY 14642, United States
| | - Jeffrey J Hayes
- Department of Biochemistry & Biophysics, University of Rochester Medical Center, Rochester, NY 14642, United States.
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16
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Natalello A, Doglia SM. Insoluble protein assemblies characterized by fourier transform infrared spectroscopy. Methods Mol Biol 2015; 1258:347-69. [PMID: 25447875 DOI: 10.1007/978-1-4939-2205-5_20] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Fourier transform infrared (FTIR) spectroscopy is a useful tool for the structural characterization of insoluble protein assemblies, as it allows to obtain information on the protein secondary structures and on their intermolecular interactions. The protocols for FTIR spectroscopy and microspectroscopy measurements in transmission and attenuated total reflection modes will be presented and illustrated in the following examples: bacterial inclusion bodies, self-assembling peptides, thermal aggregates, and amyloid fibrils.
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Affiliation(s)
- Antonino Natalello
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, Milan, 20126, Italy,
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17
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Terme JM, Millán-Ariño L, Mayor R, Luque N, Izquierdo-Bouldstridge A, Bustillos A, Sampaio C, Canes J, Font I, Sima N, Sancho M, Torrente L, Forcales S, Roque A, Suau P, Jordan A. Dynamics and dispensability of variant-specific histone H1 Lys-26/Ser-27 and Thr-165 post-translational modifications. FEBS Lett 2014; 588:2353-62. [PMID: 24873882 DOI: 10.1016/j.febslet.2014.05.035] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Revised: 05/14/2014] [Accepted: 05/15/2014] [Indexed: 12/31/2022]
Abstract
In mammals, the linker histone H1, involved in DNA packaging into chromatin, is represented by a family of variants. H1 tails undergo post-translational modifications (PTMs) that can be detected by mass spectrometry. We developed antibodies to analyze several of these as yet unexplored PTMs including the combination of H1.4 K26 acetylation or trimethylation and S27 phosphorylation. H1.2-T165 phosphorylation was detected at S and G2/M phases of the cell cycle and was dispensable for chromatin binding and cell proliferation; while the H1.4-K26 residue was essential for proper cell cycle progression. We conclude that histone H1 PTMs are dynamic over the cell cycle and that the recognition of modified lysines may be affected by phosphorylation of adjacent residues.
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Affiliation(s)
- Jean-Michel Terme
- Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Parc Científic de Barcelona, Barcelona, Catalonia, Spain
| | - Lluís Millán-Ariño
- Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Parc Científic de Barcelona, Barcelona, Catalonia, Spain
| | - Regina Mayor
- Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Parc Científic de Barcelona, Barcelona, Catalonia, Spain
| | - Neus Luque
- Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Parc Científic de Barcelona, Barcelona, Catalonia, Spain
| | | | - Alberto Bustillos
- Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Parc Científic de Barcelona, Barcelona, Catalonia, Spain
| | - Cristina Sampaio
- Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Parc Científic de Barcelona, Barcelona, Catalonia, Spain
| | - Jordi Canes
- Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Parc Científic de Barcelona, Barcelona, Catalonia, Spain
| | - Isaura Font
- Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Parc Científic de Barcelona, Barcelona, Catalonia, Spain
| | - Núria Sima
- Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Parc Científic de Barcelona, Barcelona, Catalonia, Spain
| | - Mónica Sancho
- Centro de Investigación Príncipe Felipe, Valencia, Spain
| | - Laura Torrente
- Institut de Medecina Predictiva i Personalitzada del Cancer, Badalona, Catalonia, Spain
| | - Sonia Forcales
- Institut de Medecina Predictiva i Personalitzada del Cancer, Badalona, Catalonia, Spain
| | - Alicia Roque
- Universitat Autònoma de Barcelona, Bellaterra, Catalonia, Spain
| | - Pere Suau
- Universitat Autònoma de Barcelona, Bellaterra, Catalonia, Spain
| | - Albert Jordan
- Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Parc Científic de Barcelona, Barcelona, Catalonia, Spain.
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18
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González-Romero R, Ausio J. dBigH1, a second histone H1 in Drosophila, and the consequences for histone fold nomenclature. Epigenetics 2014; 9:791-7. [PMID: 24622397 DOI: 10.4161/epi.28427] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Recently, Pérez-Montero and colleagues (Developmental cell, 26: 578-590, 2013) described the occurrence of a new histone H1 variant (dBigH1) in Drosophila. The presence of unusual acidic amino acid patches at the N-terminal end of dBigH1 is in contrast to the arginine patches that exist at the N- and C-terminal domains of other histone H1-related proteins found in the sperm of some organisms. This departure from the strictly lysine-rich composition of the somatic histone H1 raises a question about the true definition of its protein members. Their minimal essential requirements appear to be the presence of a lysine- and alanine-rich, intrinsically disordered C-terminal domain, with a highly helicogenic potential upon binding to the linker DNA regions of chromatin. In metazoans, specific targeting of these regions is further achieved by a linker histone fold domain (LHFD), distinctively different from the characteristic core histone fold domain (CHFD) of the nucleosome core histones.
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Affiliation(s)
| | - Juan Ausio
- Department of Biochemistry and Microbiology; University of Victoria; Victoria, BC, Canada
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Over RS, Michaels SD. Open and closed: the roles of linker histones in plants and animals. MOLECULAR PLANT 2014; 7:481-91. [PMID: 24270504 PMCID: PMC3941478 DOI: 10.1093/mp/sst164] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Accepted: 11/11/2013] [Indexed: 05/19/2023]
Abstract
Histones package DNA in all eukaryotes and play key roles in regulating gene expression. Approximately 150 base pairs of DNA wraps around an octamer of core histones to form the nucleosome, the basic unit of chromatin. Linker histones compact chromatin further by binding to and neutralizing the charge of the DNA between nucleosomes. It is well established that chromatin packing is regulated by a complex pattern of posttranslational modifications (PTMs) to core histones, but linker histone function is less well understood. In this review, we describe the current understanding of the many roles that linker histones play in cellular processes, including gene regulation, cell division, and development, while putting the linker histone in the context of other nuclear proteins. Although intriguing roles for plant linker histones are beginning to emerge, much of our current understanding comes from work in animal systems. Many unanswered questions remain and additional work is required to fully elucidate the complex processes mediated by linker histones in plants.
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Affiliation(s)
| | - Scott D. Michaels
- To whom correspondence should be addressed. E-mail , fax 812-855-6082, tel. 812-856-0302
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20
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Muñoz F, Palomares-Jerez MF, Daleo G, Villalaín J, Guevara MG. Possible mechanism of structural transformations induced by StAsp-PSI in lipid membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1838:339-47. [DOI: 10.1016/j.bbamem.2013.08.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Revised: 08/02/2013] [Accepted: 08/06/2013] [Indexed: 01/19/2023]
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Abstract
Members of histone H1 family bind to nucleosomal and linker DNA to assist in stabilization of higher-order chromatin structures. Moreover, histone H1 is involved in regulation of a variety of cellular processes by interactions with cytosolic and nuclear proteins. Histone H1, composed of a series of subtypes encoded by distinct genes, is usually differentially expressed in specialized cells and frequently non-randomly distributed in different chromatin regions. Moreover, a role of specific histone H1 subtype might be also modulated by post-translational modifications and/or presence of polymorphic isoforms. While the significance of covalently modified histone H1 subtypes has been partially recognized, much less is known about the importance of histone H1 polymorphic variants identified in various plant and animal species, and human cells as well. Recent progress in elucidating amino acid composition-dependent functioning and interactions of the histone H1 with a variety of molecular partners indicates a potential role of histone H1 polymorphic variation in adopting specific protein conformations essential for chromatin function. The histone H1 allelic variants might affect chromatin in order to modulate gene expression underlying some physiological traits and, therefore could modify the course of diverse histone H1-dependent biological processes. This review focuses on the histone H1 allelic variability, and biochemical and genetic aspects of linker histone allelic isoforms to emphasize their likely biological relevance.
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Fioretti FM, Febbraio F, Carbone A, Branno M, Carratore V, Fucci L, Ausió J, Piscopo M. A sperm nuclear basic protein from the sperm of the marine worm Chaetopterus variopedatus with sequence similarity to the arginine-rich C-termini of chordate protamine-likes. DNA Cell Biol 2012; 31:1392-402. [PMID: 22536787 DOI: 10.1089/dna.2011.1547] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The sperm nuclear basic proteins (SNBPs) of the marine annelid worm Chaetopterus variopedatus have been shown previously to consist of a mixture of two SNBPs: histone H1-like (CvH1) and C.variopedatus protamine-like (CvPL). Here, we report the structural characterization of CvPL. The protein has a molecular weight of 8370.5 Da, a K/R ratio of 0.34, and a secondary structure, which are intermediate between those of protamine (P) and protamine-like (PL) SNBPs. The N-terminal sequence of CvPL shows a high extent of similarity with the arginine-rich C-terminal domain of chordate PL-type SNBPs. Furthermore, the protein binds to DNA in a similar fashion as vertebrate PLs and their own CvH1, but in a way that is different from that of the lysine-rich somatic H1 histones. We have experimentally determined the molar ratio CvH1:CvPL to be ∼1:6 in C. variopedatus sperm. Based on all of these, a model is proposed for the organization of the sperm chromatin by CvH1 and CvPL.
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23
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Dynamic Fuzziness During Linker Histone Action. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 725:15-26. [DOI: 10.1007/978-1-4614-0659-4_2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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24
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Natalello A, Ami D, Doglia SM. Fourier transform infrared spectroscopy of intrinsically disordered proteins: measurement procedures and data analyses. Methods Mol Biol 2012; 895:229-44. [PMID: 22760323 DOI: 10.1007/978-1-61779-927-3_16] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
A peculiar property of intrinsically disordered proteins (IDPs), or of intrinsically disordered domains, is the absence of a well-defined three dimensional structure under native conditions. Moreover, IDPs usually acquire a specific structure in the presence of different interactors. In this framework, Fourier transform infrared (FTIR) spectroscopy is a powerful tool to assess the disordered character of a protein and to study its induced folding. In this chapter, we will show the detailed experimental procedures to measure the FTIR spectra of protein samples and the spectral analyses required to obtain information on the protein secondary structures and aggregation.
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Affiliation(s)
- Antonino Natalello
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy.
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25
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Sieber T, Scholz R, Spoerner M, Schumann F, Kalbitzer HR, Dobner T. Intrinsic disorder in the common N-terminus of human adenovirus 5 E1B-55K and its related E1BN proteins indicated by studies on E1B-93R. Virology 2011; 418:133-43. [DOI: 10.1016/j.virol.2011.07.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2011] [Revised: 07/13/2011] [Accepted: 07/18/2011] [Indexed: 10/17/2022]
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26
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Brocca S, Testa L, Sobott F, Samalikova M, Natalello A, Papaleo E, Lotti M, De Gioia L, Doglia SM, Alberghina L, Grandori R. Compaction properties of an intrinsically disordered protein: Sic1 and its kinase-inhibitor domain. Biophys J 2011; 100:2243-52. [PMID: 21539793 DOI: 10.1016/j.bpj.2011.02.055] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2010] [Revised: 02/04/2011] [Accepted: 02/22/2011] [Indexed: 01/02/2023] Open
Abstract
IDPs in their unbound state can transiently acquire secondary and tertiary structure. Describing such intrinsic structure is important to understand the transition between free and bound state, leading to supramolecular complexes with physiological interactors. IDP structure is highly dynamic and, therefore, difficult to study by conventional techniques. This work focuses on conformational analysis of the KID fragment of the Sic1 protein, an IDP with a key regulatory role in the cell-cycle of Saccharomyces cerevisiae. FT-IR spectroscopy, ESI-MS, and IM measurements are used to capture dynamic and short-lived conformational states, probing both secondary and tertiary protein structure. The results indicate that the isolated Sic1 KID retains dynamic helical structure and populates collapsed states of different compactness. A metastable, highly compact species is detected. Comparison between the fragment and the full-length protein suggests that chain length is crucial to the stabilization of compact states of this IDP. The two proteins are compared by a length-independent compaction index.
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Affiliation(s)
- Stefania Brocca
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
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27
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Raimondi S, Guglielmi F, Giorgetti S, Gaetano SD, Arciello A, Monti DM, Relini A, Nichino D, Doglia SM, Natalello A, Pucci P, Mangione P, Obici L, Merlini G, Stoppini M, Robustelli P, Tartaglia GG, Vendruscolo M, Dobson CM, Piccoli R, Bellotti V. Effects of the Known Pathogenic Mutations on the Aggregation Pathway of the Amyloidogenic Peptide of Apolipoprotein A-I. J Mol Biol 2011; 407:465-76. [DOI: 10.1016/j.jmb.2011.01.044] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2010] [Revised: 12/22/2010] [Accepted: 01/23/2011] [Indexed: 11/30/2022]
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Roque A, Ponte I, Suau P. Secondary structure of protamine in sperm nuclei: an infrared spectroscopy study. BMC STRUCTURAL BIOLOGY 2011; 11:14. [PMID: 21435240 PMCID: PMC3073880 DOI: 10.1186/1472-6807-11-14] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2010] [Accepted: 03/24/2011] [Indexed: 11/23/2022]
Abstract
Background Protamines are small basic proteins that condense the DNA in mature spermatozoa. Typical protamines are of simple composition and very arginine-rich, usually in the range of 60-80%. Arginine residues are distributed in a number of stretches separated by neutral amino acids. We have used Fourier transform infrared spectroscopy (FTIR) to gain access for the first time to the secondary structure of protamines in sperm nuclei. This technique is particularly well suited to the study of DNA-bound protamine in whole nuclei since it is not affected by turbidity. Results We show that DNA -bound salmon (salmine) and squid protamines contain α-helix, β-turns and a proportion of other structures not stabilized by intramolecular hydrogen bonding. No β-sheet was observed. In salmine, the α-helix amounted to ~20%, while in squid protamine it reached ~40%. In contrast, the structure not stabilized by intermolecular hydrogen bonding was more abundant in salmine (~40%) than in squid protamine (~20%). Both protamines contained ~40% β-turns. The different helical potential of salmine and squid protamine was confirmed by structure predictions and CD in the presence of trifluoroethanol. Conclusion DNA-bound protamine in sperm nuclei contains large amounts of defined secondary structure stabilized by intramolecular hydrogen bonding. Both salmine and squid protamine contain similar amounts of β-turns, but differ in the proportions of α-helix and non-hydrogen bonded conformations. In spite of the large differences in the proportions of secondary structure motifs between salmon and squid protamines, they appear to be equally efficient in promoting tight hexagonal packing of the DNA molecules in sperm nuclei.
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Affiliation(s)
- Alicia Roque
- Departamento de Bioquímica y Biología Molecular, Facultad de Biociencias, Universidad Autónoma de Barcelona, 08193 Bellaterra (Cerdanyola del Vallès), Barcelona, Spain
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29
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Two polymorphic linker histone loci in Guinea fowl erythrocytes. C R Biol 2011; 334:6-12. [DOI: 10.1016/j.crvi.2010.10.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2009] [Revised: 10/29/2010] [Accepted: 10/29/2010] [Indexed: 11/30/2022]
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30
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Piscopo M, Conte M, Di Paola F, Conforti S, Rana G, De Petrocellis L, Fucci L, Geraci G. Relevance of arginines in the mode of binding of H1 histones to DNA. DNA Cell Biol 2010; 29:339-47. [PMID: 20438368 DOI: 10.1089/dna.2009.0993] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The mode of binding of sperm and somatic H1 histones to DNA has been investigated by analyzing the effect of their addition on the electrophoretic mobility of linear and circular plasmid molecules. Low concentrations of sperm histones do not appear to alter the electrophoretic mobility of DNA, whereas at increasing concentrations, an additional DNA band is observed near the migration origin. This band then becomes the only component at higher values. In contrast, somatic histones cause a gradual retardation in the mobility of the DNA band at low concentrations and aggregated structures are observed only at higher values. Experiments on the H1 globular domain obtained by limited proteolysis indicate that the mode of binding to DNA depends on the H1 globular domain. The arginine residues appear to be relevant for the different effects as indicated by experiments on sperm histone and on protamine with arginines deguanidinated to ornithines. The modified molecules influence DNA mobility like somatic H1s, indicating that the positive guanidino groups of arginines cannot be substituted by the positive amino groups of ornithines. Modifications of the amino groups of lysines show that these residues are necessary for the binding of H1 histones to DNA but they have no influence on the binding mode.
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Affiliation(s)
- Marina Piscopo
- Department of Structural and Functional Biology, University of Naples Federico II, Italy.
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31
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Zheng Y, John S, Pesavento JJ, Schultz-Norton JR, Schiltz RL, Baek S, Nardulli AM, Hager GL, Kelleher NL, Mizzen CA. Histone H1 phosphorylation is associated with transcription by RNA polymerases I and II. ACTA ACUST UNITED AC 2010; 189:407-15. [PMID: 20439994 PMCID: PMC2867294 DOI: 10.1083/jcb.201001148] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Histone H1 phosphorylation affects chromatin condensation and function, but little is known about how specific phosphorylations impact the function of H1 variants in higher eukaryotes. In this study, we show that specific sites in H1.2 and H1.4 of human cells are phosphorylated only during mitosis or during both mitosis and interphase. Antisera generated to individual H1.2/H1.4 interphase phosphorylations reveal that they are distributed throughout nuclei and enriched in nucleoli. Moreover, interphase phosphorylated H1.4 is enriched at active 45S preribosomal RNA gene promoters and is rapidly induced at steroid hormone response elements by hormone treatment. Our results imply that site-specific interphase H1 phosphorylation facilitates transcription by RNA polymerases I and II and has an unanticipated function in ribosome biogenesis and control of cell growth. Differences in the numbers, structure, and locations of interphase phosphorylation sites may contribute to the functional diversity of H1 variants.
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Affiliation(s)
- Yupeng Zheng
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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32
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Multifunctionality of the linker histones: an emerging role for protein-protein interactions. Cell Res 2010; 20:519-28. [PMID: 20309017 DOI: 10.1038/cr.2010.35] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Linker histones, e.g., H1, are best known for their ability to bind to nucleosomes and stabilize both nucleosome structure and condensed higher-order chromatin structures. However, over the years many investigators have reported specific interactions between linker histones and proteins involved in important cellular processes. The purpose of this review is to highlight evidence indicating an important alternative mode of action for H1, namely protein-protein interactions. We first review key aspects of the traditional view of linker histone action, including the importance of the H1 C-terminal domain. We then discuss the current state of knowledge of linker histone interactions with other proteins, and, where possible, highlight the mechanism of linker histone-mediated protein-protein interactions. Taken together, the data suggest a combinatorial role for the linker histones, functioning both as primary chromatin architectural proteins and simultaneously as recruitment hubs for proteins involved in accessing and modifying the chromatin fiber.
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33
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Roque A, Ponte I, Suau P. Role of Charge Neutralization in the Folding of the Carboxy-Terminal Domain of Histone H1. J Phys Chem B 2009; 113:12061-6. [DOI: 10.1021/jp9022579] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Alicia Roque
- Departamento de Bioquímica y Biología Molecular, Facultad de Biociencias, Universidad Autónoma de Barcelona, 08193 Bellaterra (Cerdanyola del Vallès), Barcelona, Spain
| | - Inma Ponte
- Departamento de Bioquímica y Biología Molecular, Facultad de Biociencias, Universidad Autónoma de Barcelona, 08193 Bellaterra (Cerdanyola del Vallès), Barcelona, Spain
| | - Pedro Suau
- Departamento de Bioquímica y Biología Molecular, Facultad de Biociencias, Universidad Autónoma de Barcelona, 08193 Bellaterra (Cerdanyola del Vallès), Barcelona, Spain
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Wetzler DE, Gallo M, Melis R, Eliseo T, Nadra AD, Ferreiro DU, Paci M, Sánchez IE, Cicero DO, de Prat Gay G. A strained DNA binding helix is conserved for site recognition, folding nucleation, and conformational modulation. Biopolymers 2009; 91:432-43. [PMID: 19156829 DOI: 10.1002/bip.21146] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Nucleic acid recognition is often mediated by alpha-helices or disordered regions that fold into alpha-helix on binding. A peptide bearing the DNA recognition helix of HPV16 E2 displays type II polyproline (PII) structure as judged by pH, temperature, and solvent effects on the CD spectra. NMR experiments indicate that the canonical alpha-helix is stabilized at the N-terminus, while the PII forms at the C-terminus half of the peptide. Re-examination of the dihedral angles of the DNA binding helix in the crystal structure and analysis of the NMR chemical shift indexes confirm that the N-terminus half is a canonical alpha-helix, while the C-terminal half adopts a 3(10) helix structure. These regions precisely match two locally driven folding nucleii, which partake in the native hydrophobic core and modulate a conformational switch in the DNA binding helix. The peptide shows only weak and unspecific residual DNA binding, 10(4)-fold lower affinity, and 500-fold lower discrimination capacity compared with the domain. Thus, the precise side chain conformation required for modulated and tight physiological binding by HPV E2 is largely determined by the noncanonical strained alpha-helix conformation, "presented" by this unique architecture. (c) 2009 Wiley Periodicals, Inc. Biopolymers 91: 432-443, 2009.
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Affiliation(s)
- Diana E Wetzler
- Fundación Instituto Leloir and IIBBA-CONICET, Patricias Argentinas 435 (C1405BWE), Buenos Aires, Argentina
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Raghuram N, Carrero G, Th’ng J, Hendzel MJ. Molecular dynamics of histone H1This paper is one of a selection of papers published in this Special Issue, entitled CSBMCB’s 51st Annual Meeting – Epigenetics and Chromatin Dynamics, and has undergone the Journal’s usual peer review process. Biochem Cell Biol 2009; 87:189-206. [DOI: 10.1139/o08-127] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The histone H1 family of nucleoproteins represents an important class of structural and architectural proteins that are responsible for maintaining and stabilizing higher-order chromatin structure. Essential for mammalian cell viability, they are responsible for gene-specific regulation of transcription and other DNA-dependent processes. In this review, we focus on the wealth of information gathered on the molecular kinetics of histone H1 molecules using novel imaging techniques, such as fluorescence recovery after photobleaching. These experiments have shed light on the effects of H1 phosphorylation and core histone acetylation in influencing chromatin structure and dynamics. We also delineate important concepts surrounding the C-terminal domain of H1, such as the intrinsic disorder hypothesis, and how it affects H1 function. Finally, we address the biochemical mechanisms behind low-affinity H1 binding.
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Affiliation(s)
- Nikhil Raghuram
- Department of Oncology, University of Alberta, University Avenue NW, Edmonton, AB T6G 1Z2, Canada
- Mathematics, Center for Science, Athabasca University, Edmonton, AB T5J 3S8, Canada
- Regional Cancer Centre, Medical Science Division, Northern Ontario School of Medicine, Thunder Bay Regional Health Sciences Centre, Thunder Bay, ON P7B 6V4, Canada
| | - Gustavo Carrero
- Department of Oncology, University of Alberta, University Avenue NW, Edmonton, AB T6G 1Z2, Canada
- Mathematics, Center for Science, Athabasca University, Edmonton, AB T5J 3S8, Canada
- Regional Cancer Centre, Medical Science Division, Northern Ontario School of Medicine, Thunder Bay Regional Health Sciences Centre, Thunder Bay, ON P7B 6V4, Canada
| | - John Th’ng
- Department of Oncology, University of Alberta, University Avenue NW, Edmonton, AB T6G 1Z2, Canada
- Mathematics, Center for Science, Athabasca University, Edmonton, AB T5J 3S8, Canada
- Regional Cancer Centre, Medical Science Division, Northern Ontario School of Medicine, Thunder Bay Regional Health Sciences Centre, Thunder Bay, ON P7B 6V4, Canada
| | - Michael J. Hendzel
- Department of Oncology, University of Alberta, University Avenue NW, Edmonton, AB T6G 1Z2, Canada
- Mathematics, Center for Science, Athabasca University, Edmonton, AB T5J 3S8, Canada
- Regional Cancer Centre, Medical Science Division, Northern Ontario School of Medicine, Thunder Bay Regional Health Sciences Centre, Thunder Bay, ON P7B 6V4, Canada
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Lu X, Hamkalo B, Parseghian MH, Hansen JC. Chromatin condensing functions of the linker histone C-terminal domain are mediated by specific amino acid composition and intrinsic protein disorder. Biochemistry 2009; 48:164-72. [PMID: 19072710 DOI: 10.1021/bi801636y] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Linker histones bind to the nucleosomes and linker DNA of chromatin fibers, causing changes in linker DNA structure and stabilization of higher order folded and oligomeric chromatin structures. Linker histones affect chromatin structure acting primarily through their approximately 100-residue C-terminal domain (CTD). We have previously shown that the ability of the linker histone H1 degrees to alter chromatin structure was localized to two discontinuous 24-/25-residue CTD regions (Lu, X., and Hansen, J. C. (2004) J. Biol. Chem. 279, 8701-8707). To determine the biochemical basis for these results, we have characterized chromatin model systems assembled with endogenous mouse somatic H1 isoforms or recombinant H1 degrees CTD mutants in which the primary sequence has been scrambled, the amino acid composition mutated, or the location of various CTD regions swapped. Our results indicate that specific amino acid composition plays a fundamental role in molecular recognition and function by the H1 CTD. Additionally, these experiments support a new molecular model for CTD function and provide a biochemical basis for the redundancy observed in H1 isoform knockout experiments in vivo.
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Affiliation(s)
- Xu Lu
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523-1870, USA
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37
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Rose KL, Li A, Zalenskaya I, Zhang Y, Unni E, Hodgson KC, Yu Y, Shabanowitz J, Meistrich ML, Hunt DF, Ausió J. C-terminal phosphorylation of murine testis-specific histone H1t in elongating spermatids. J Proteome Res 2008; 7:4070-8. [PMID: 18698803 DOI: 10.1021/pr8003908] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Previous studies gave differing results as to whether the testis-specific histone H1t was phosphorylated during rodent spermatogenesis. We show here that histones extracted from germ cell populations enriched with spermatids at different stages of development in rat testes reveal an electrophoretic shift in the position of H1t to slower mobilities in elongating spermatids as compared to that from preceding stages. Alkaline phosphatase treatment and radioactive labeling with (32)P demonstrated that the electrophoretic shift is due to phosphorylation. Mass spectrometric analysis of histone H1t purified from sexually mature mice and rat testes confirmed the occurrence of singly, doubly, and triply phosphorylated species, with phosphorylation sites predominantly found at the C-terminal end of the molecule. Furthermore, using collision-activated dissociation (CAD) and electron transfer dissociation (ETD), we have been able to identify the major phosphorylation sites. These include a new, previously unidentified putative H1t-specific cdc2 phosphorylation site in linker histones. The presence of phosphorylation at the C-terminal end of H1t and the timing of its appearance suggest that this post-translational modification is involved in the reduction of H1t binding strength to DNA. It is proposed that this could participate in the opening of the chromatin fiber in preparation for histone displacement by transition proteins in the next phase of spermiogenesis.
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Affiliation(s)
- Kristie L Rose
- Department of Chemistry, University of Virginia, Charlottesville, Virginia, USA
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38
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Roque A, Ponte I, Arrondo JLR, Suau P. Phosphorylation of the carboxy-terminal domain of histone H1: effects on secondary structure and DNA condensation. Nucleic Acids Res 2008; 36:4719-26. [PMID: 18632762 PMCID: PMC2504289 DOI: 10.1093/nar/gkn440] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Linker histone H1 plays an important role in chromatin folding. Phosphorylation by cyclin-dependent kinases is the main post-translational modification of histone H1. We studied the effects of phosphorylation on the secondary structure of the DNA-bound H1 carboxy-terminal domain (CTD), which contains most of the phosphorylation sites of the molecule. The effects of phosphorylation on the secondary structure of the DNA-bound CTD were site-specific and depended on the number of phosphate groups. Full phosphorylation significantly increased the proportion of beta-structure and decreased that of alpha-helix. Partial phosphorylation increased the amount of undefined structure and decreased that of alpha-helix without a significant increase in beta-structure. Phosphorylation had a moderate effect on the affinity of the CTD for the DNA, which was proportional to the number of phosphate groups. Partial phosphorylation drastically reduced the aggregation of DNA fragments by the CTD, but full phosphorylation restored to a large extent the aggregation capacity of the unphosphorylated domain. These results support the involvement of H1 hyperphosphorylation in metaphase chromatin condensation and of H1 partial phosphorylation in interphase chromatin relaxation. More generally, our results suggest that the effects of phosphorylation are mediated by specific structural changes and are not simply a consequence of the net charge.
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Affiliation(s)
- Alicia Roque
- Departamento de Bioquímica y Biología Molecular, Facultad de Biociencias, Universidad Autónoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
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39
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Subach FV, Liquier J, Gromova ES. Investigation of restriction endonuclease EcoRII complex with DNA in solution by FTIR spectroscopy. RUSS J GEN CHEM+ 2008. [DOI: 10.1134/s1070363208050435] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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40
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sNASP, a histone H1-specific eukaryotic chaperone dimer that facilitates chromatin assembly. Biophys J 2008; 95:1314-25. [PMID: 18456819 DOI: 10.1529/biophysj.108.130021] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
NASP has been described as a histone H1 chaperone in mammals. However, the molecular mechanisms involved have not yet been characterized. Here, we show that this protein is not only present in mammals but is widely distributed throughout eukaryotes both in its somatic and testicular forms. The secondary structure of the human somatic version consists mainly of clusters of alpha-helices and exists as a homodimer in solution. The protein binds nonspecifically to core histone H2A-H2B dimers and H3-H4 tetramers but only forms specific complexes with histone H1. The formation of the NASP-H1 complexes is mediated by the N- and C-terminal domains of histone H1 and does not involve the winged helix domain that is characteristic of linker histones. In vitro chromatin reconstitution experiments show that this protein facilitates the incorporation of linker histones onto nucleosome arrays and hence is a bona fide linker histone chaperone.
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41
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Galius V, Leontiou C, Richmond T, Wider G. Projected [(1)H, (15)N]-HMQC-[ (1)H, (1)H]-NOESY for large molecular systems: application to a 121 kDa protein-DNA complex. JOURNAL OF BIOMOLECULAR NMR 2008; 40:175-181. [PMID: 18231863 DOI: 10.1007/s10858-008-9219-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2007] [Accepted: 01/08/2008] [Indexed: 05/25/2023]
Abstract
We present a projected [(1)H,(15)N]-HMQC-[(1)H,(1)H]-NOESY experiment for observation of NOE interactions between amide protons with degenerate (15)N chemical shifts in large molecular systems. The projection is achieved by simultaneous evolution of the multiple quantum coherence of the nitrogen spin and the attached proton spin. In this way NOE signals can be separated from direct-correlation peaks also in spectra with low resolution by fully exploiting both (1)H and (15)N frequency differences, such that sensitivity can be increased by using short maximum evolution times. The sensitivity of the experiment is not dependent on the projection angle for projections up to 45 degrees and no additional pulses or delays are required as compared to the conventional 2D [(1)H,(15)N]-HMQC-NOESY. The experiment provides two distinct 2D spectra corresponding to the positive and negative angle projections, respectively. With a linear combination of 1D cross-sections from the two projections the unavoidable sensitivity loss in projection spectra can be compensated for each particular NOE interaction. We demonstrate the application of the novel projection experiment for the observation of an NOE interaction between two sequential glycines with degenerate (15)N chemical shifts in a 121.3 kDa complex of the linker H1 histone protein with a 152 bp linear DNA.
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Affiliation(s)
- Veniamin Galius
- Institute of Molecular Biology and Biophysics, ETH Zurich, 8093, Zurich, Switzerland
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42
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Roque A, Ponte I, Suau P. Macromolecular crowding induces a molten globule state in the C-terminal domain of histone H1. Biophys J 2007; 93:2170-7. [PMID: 17513371 PMCID: PMC1959549 DOI: 10.1529/biophysj.107.104513] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We studied the secondary structure of the C-terminal domains of the histone H1 subtypes H1 degrees (C-H1 degrees ) and H1t (C-H1t) in the presence of macromolecular crowding agents (Ficoll 70 and PEG 6000) by IR spectroscopy. The carboxyl-terminal domain has little structure in aqueous solution but became extensively folded in the presence of crowding agents. In 30% PEG, C-H1 degrees contained 19% alpha-helix, 28% beta-sheet, 16% turns, and 31% open loops. Similar proportions were observed in 30% Ficoll 70 and for C-H1t in both crowding agents. The proportions of secondary structure motifs were comparable to those of the DNA-bound domain. Kratky plots of the small-angle x-ray scattering showed that in crowding agents the C-terminus had the compaction of a globular state. Progressive dissipation of the secondary structure and a linear increase in partial heat capacity with temperature together with increased binding of ANS indicated that the C-terminus is not cooperatively folded in crowded conditions. Native-like secondary structure and compactness in absence of folding cooperativity indicate that the C-terminus in crowding agents is in a molten globule state. Folding of the C-terminus in crowded conditions may increase the rate of the transition toward the DNA-bound state and facilitate H1 diffusion inside cell nuclei.
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Affiliation(s)
- Alicia Roque
- Departamento de Bioquímica y Biología Molecular, Facultad de Biociencias, Universidad Autónoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
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43
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Heit R, Underhill DA, Chan G, Hendzel MJ. Epigenetic regulation of centromere formation and kinetochore functionThis paper is one of a selection of papers published in this Special Issue, entitled 27th International West Coast Chromatin and Chromosome Conference, and has undergone the Journal's usual peer review process. Biochem Cell Biol 2006; 84:605-18. [PMID: 16936832 DOI: 10.1139/o06-080] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
In the midst of an increasingly detailed understanding of the molecular basis of genome regulation, we still only vaguely understand the relationship between molecular biochemistry and the structure of the chromatin inside of cells. The centromere is a structurally and functionally unique region of each chromosome and provides an example in which the molecular understanding far exceeds the understanding of the structure and function relationships that emerge on the chromosomal scale. The centromere is located at the primary constriction of the chromosome. During entry into mitosis, the centromere specifies the assembly site of the kinetochore, the structure that binds to microtubules to enable transport of the chromosomes into daughter cells. The epigenetic contributions to the molecular organization and function of the centromere are reviewed in the context of structural mechanisms of chromatin function.
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Affiliation(s)
- Ryan Heit
- Department of Oncology, University of Alberta, Edmonton, AB T6G 1Z2, Canada
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44
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Abstract
Two allelic isoforms (H1.a1 and H1.a2) of histone H1.a were identified within two conservative flocks (R11 and R55) of Rhode Island Red chickens. These proteins form three phenotypes: a1, a2 and a1a2. Birds with phenotype a1 were most common (frequency 0.825-0.980) while the a1a2 chickens appeared relatively rarely (0.017-0.175). The third phenotype a2, not detected in the tested populations, has only been revealed in progeny of the purpose-mated a1a2 birds. The polymorphism of histone H1.a was observed in all examined chicken tissues, so that the H1 preparations isolated from the lung, spleen, kidney and testis from the same individual exhibited identical phenotypes (a1, a2, or a1a2). This finding, together with inheritance data, supports the genetic nature of the H1.a polymorphism. As indicated by cleavages with alpha-chymotrypsin and protease V8, the H1.a1 and H1.a2 are two highly related proteins which differ within N-terminal part of their C-terminal tails. Only a single nonconservative amino acid substitution between both H1.a allelic isoforms was detected by Edman degradation: glutamic acid present at position 117 in histone H1.a1 was replaced by lysine in histone H1.a2. Furthermore, using microsequencing techniques we have found a sequence homology between the N- and C-terminal parts of an unknown minor protein H1.y, present in the phenotype a2, and similar regions of histone H1.b.
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45
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Hsu CH, Chen C, Jou ML, Lee AYL, Lin YC, Yu YP, Huang WT, Wu SH. Structural and DNA-binding studies on the bovine antimicrobial peptide, indolicidin: evidence for multiple conformations involved in binding to membranes and DNA. Nucleic Acids Res 2005; 33:4053-64. [PMID: 16034027 PMCID: PMC1179735 DOI: 10.1093/nar/gki725] [Citation(s) in RCA: 210] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Indolicidin, a l3-residue antimicrobial peptide-amide, which is unusually rich in tryptophan and proline, is isolated from the cytoplasmic granules of bovine neutrophils. In this study, the structures of indolicidin in 50% D3-trifluoroethanol and in the absence and presence of SDS and D38-dodecylphosphocholine were determined using NMR spectroscopy. Multiple conformations were found and were shown to be due to different combinations of contact between the two WPW motifs. Although indolicidin is bactericidal and able to permeabilize bacterial membranes, it does not lead to cell wall lysis, showing that there is more than one mechanism of antimicrobial action. The structure of indolicidin in aqueous solution was a globular and amphipathic conformation, differing from the wedge shape adopted in lipid micelles, and these two structures were predicted to have different functions. Indolicidin, which is known to inhibit DNA synthesis and induce filamentation of bacteria, was shown to bind DNA in gel retardation and fluorescence quenching experiments. Further investigations using surface plasmon resonance confirmed the DNA-binding ability and showed the sequence preference of indolicidin. Based on our biophysical studies and previous results, we present a diagram illustrating the DNA-binding mechanism of the antimicrobial action of indolicidin and explaining the roles of the peptide when interacting with lipid bilayers at different concentrations.
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Affiliation(s)
- Chun-Hua Hsu
- Institute of Biological Chemistry, Academia SinicaTaipei, Taiwan
| | - Chinpan Chen
- Institute of Biomedical Sciences, Academia SinicaTaipei, Taiwan
| | - Maou-Lin Jou
- Institute of Biochemical Sciences, National Taiwan UniversityTaipei, Taiwan
| | | | - Yu-Ching Lin
- Institute of Biological Chemistry, Academia SinicaTaipei, Taiwan
| | - Yi-Ping Yu
- Institute of Biological Chemistry, Academia SinicaTaipei, Taiwan
| | - Wei-Ting Huang
- Institute of Biological Chemistry, Academia SinicaTaipei, Taiwan
| | - Shih-Hsiung Wu
- Institute of Biological Chemistry, Academia SinicaTaipei, Taiwan
- Institute of Biochemical Sciences, National Taiwan UniversityTaipei, Taiwan
- To whom correspondence should be addressed. Tel: +886 2 2785 5696, ext. 7101; Fax: +886 2 2653 9142;
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46
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Roque A, Iloro I, Ponte I, Arrondo JLR, Suau P. DNA-induced secondary structure of the carboxyl-terminal domain of histone H1. J Biol Chem 2005; 280:32141-7. [PMID: 16006555 DOI: 10.1074/jbc.m505636200] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We have studied the secondary structure of the carboxyl-terminal domains of linker histone H1 subtypes H1(0) (C-H1(0)) and H1t (C-H1t), free in solution and bound to DNA, by IR spectroscopy. The carboxyl-terminal domain has little structure in aqueous solution but becomes extensively folded upon interaction with DNA. The secondary structure elements present in the bound carboxyl-terminal domain include the alpha-helix, beta-structure, turns, and open loops. The structure of the bound domain shows a significant dependence on salt concentration. In low salt (10 mm NaCl), there is a residual amount of random coil, 7% in C-H1(0) and 12% in C-H1t. In physiological salt concentrations (140 mm NaCl), the carboxyl termini become fully structured. Under these conditions, C-H1(0) contained 24% alpha-helix, 25% beta-structure, 17% open loops, and 33% turns. The latter component could include a substantial proportion of the 3(10) helix. Despite their low sequence identity (approximately 30%), the representation of the different structural motifs in C-H1t was similar to that in C-H1(0). Examination of the changes in the amide I components in the 20-80 degrees C temperature interval showed that the secondary structure of the DNA-bound C-H1t is for the most part extremely stable. The H1 carboxyl-terminal domain appears to belong to the so-called disordered proteins, undergoing coupled binding and folding.
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Affiliation(s)
- Alicia Roque
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias, Universidad Autónoma de Barcelona, Bellaterra, Spain
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47
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Roque A, Orrego M, Ponte I, Suau P. The preferential binding of histone H1 to DNA scaffold-associated regions is determined by its C-terminal domain. Nucleic Acids Res 2004; 32:6111-9. [PMID: 15562002 PMCID: PMC534626 DOI: 10.1093/nar/gkh945] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2004] [Revised: 10/29/2004] [Accepted: 10/29/2004] [Indexed: 01/11/2023] Open
Abstract
Histone H1 preferentially binds and aggregates scaffold-associated regions (SARs) via the numerous homopolymeric oligo(dA).oligo(dT) tracts present within these sequences. Here we show that the mammalian somatic subtypes H1a,b,c,d,e and H1 degrees and the male germline-specific subtype H1t, all preferentially bind to the Drosophila histone SAR. Experiments with the isolated domains show that whilst the C-terminal domain maintains strong and preferential binding, the N-terminal and globular domains show weak binding and poor specificity for the SAR. The preferential binding of SAR by the H1 molecule thus appears to be determined by its highly basic C-terminal domain. Salmine, a typical fish protamine, which could have its evolutionary origin in histone H1, also shows preferential binding to the SAR. The interaction of distamycin, a minor groove binder with high affinity for homopolymeric oligo(dA).oligo(dT) tracts, abolishes preferential binding of the C-terminal domain of histone H1 and protamine to the SAR, suggesting the involvement of the DNA minor groove in the interaction.
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Affiliation(s)
- Alicia Roque
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias, Universidad Autónoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
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48
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Hendzel MJ, Lever MA, Crawford E, Th'ng JPH. The C-terminal domain is the primary determinant of histone H1 binding to chromatin in vivo. J Biol Chem 2004; 279:20028-34. [PMID: 14985337 DOI: 10.1074/jbc.m400070200] [Citation(s) in RCA: 168] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We have used a combination of kinetic measurements and targeted mutations to show that the C-terminal domain is required for high-affinity binding of histone H1 to chromatin, and phosphorylations can disrupt binding by affecting the secondary structure of the C terminus. By measuring the fluorescence recovery after photo-bleaching profiles of green fluorescent protein-histone H1 proteins in living cells, we find that the deletion of the N terminus only modestly reduces binding affinity. Deletion of the C terminus, however, almost completely eliminates histone H1.1 binding. Specific mutations of the C-terminal domain identified Thr-152 and Ser-183 as novel regulatory switches that control the binding of histone H1.1 in vivo. It is remarkable that the single amino acid substitution of Thr-152 with glutamic acid was almost as effective as the truncation of the C terminus to amino acid 151 in destabilizing histone H1.1 binding in vivo. We found that modifications to the C terminus can affect histone H1 binding dramatically but have little or no influence on the charge distribution or the overall net charge of this domain. A comparison of individual point mutations and deletion mutants, when reviewed collectively, cannot be reconciled with simple charge-dependent mechanisms of C-terminal domain function of linker histones.
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Affiliation(s)
- Michael J Hendzel
- Cross Cancer Institute and Department of Oncology, University of Alberta, Edmonton, Alberta T6G 1Z2, Canada
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49
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Kostova NN, Srebreva L, Markov DV, Rundquist I. Histone H1 and chromatin interactions in human fibroblast nuclei after H1 depletion and reconstitution with H1 subfractions. ACTA ACUST UNITED AC 2004; 58:132-9. [PMID: 15057966 DOI: 10.1002/cyto.a.10119] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
BACKGROUND Linker histones constitute a family of lysine-rich proteins associated with nucleosome core particles and linker DNA in eukaryotic chromatin. In permeabilized cells, they can be extracted from nuclei by using salt concentration in the range of 0.3 to 0.7 M. Although other nuclear proteins are also extracted at 0.7 M salt, the remaining nucleus represents a template that is relatively intact. METHODS A cytochemical method was used to study the affinity of reconstituted linker histones for chromatin in situ in cultured human fibroblasts. We also investigated their ability to condense chromatin by using DNA-specific osmium ammine staining for electron microscopy. RESULTS Permeabilized and H1-depleted fibroblast nuclei were suitable for the study of linker histone-chromatin interactions after reconstitution with purified linker histone subfractions. Our results showed that exogenous linker histones bind to chromatin with lower affinity than the native ones. We detected no significant differences between the main H1 and H1 degrees histone fractions with respect to their affinity for chromatin or in their ability to condense chromatin. CONCLUSIONS Linker histone interactions with chromatin are controlled also by mechanisms independent of linker histone subtype composition.
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Affiliation(s)
- Nora N Kostova
- Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia, Bulgaria
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50
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Ausió J, Abbott D. The role of histone variability in chromatin stability and folding. ACTA ACUST UNITED AC 2004. [DOI: 10.1016/s0167-7306(03)39010-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2023]
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