1
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DNA-Binding Properties of a Novel Crenarchaeal Chromatin-Organizing Protein in Sulfolobus acidocaldarius. Biomolecules 2022; 12:biom12040524. [PMID: 35454113 PMCID: PMC9025068 DOI: 10.3390/biom12040524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/17/2022] [Accepted: 03/24/2022] [Indexed: 02/06/2023] Open
Abstract
In archaeal microorganisms, the compaction and organization of the chromosome into a dynamic but condensed structure is mediated by diverse chromatin-organizing proteins in a lineage-specific manner. While many archaea employ eukaryotic-type histones for nucleoid organization, this is not the case for the crenarchaeal model species Sulfolobus acidocaldarius and related species in Sulfolobales, in which the organization appears to be mostly reliant on the action of small basic DNA-binding proteins. There is still a lack of a full understanding of the involved proteins and their functioning. Here, a combination of in vitro and in vivo methodologies is used to study the DNA-binding properties of Sul12a, an uncharacterized small basic protein conserved in several Sulfolobales species displaying a winged helix–turn–helix structural motif and annotated as a transcription factor. Genome-wide chromatin immunoprecipitation and target-specific electrophoretic mobility shift assays demonstrate that Sul12a of S. acidocaldarius interacts with DNA in a non-sequence specific manner, while atomic force microscopy imaging of Sul12a–DNA complexes indicate that the protein induces structural effects on the DNA template. Based on these results, and a contrario to its initial annotation, it can be concluded that Sul12a is a novel chromatin-organizing protein.
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2
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Henneman B, Brouwer TB, Erkelens AM, Kuijntjes GJ, van Emmerik C, van der Valk RA, Timmer M, Kirolos NCS, van Ingen H, van Noort J, Dame RT. Mechanical and structural properties of archaeal hypernucleosomes. Nucleic Acids Res 2021; 49:4338-4349. [PMID: 33341892 PMCID: PMC8096283 DOI: 10.1093/nar/gkaa1196] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 11/13/2020] [Accepted: 11/23/2020] [Indexed: 11/21/2022] Open
Abstract
Many archaea express histones, which organize the genome and play a key role in gene regulation. The structure and function of archaeal histone–DNA complexes remain however largely unclear. Recent studies show formation of hypernucleosomes consisting of DNA wrapped around an ‘endless’ histone-protein core. However, if and how such a hypernucleosome structure assembles on a long DNA substrate and which interactions provide for its stability, remains unclear. Here, we describe micromanipulation studies of complexes of the histones HMfA and HMfB with DNA. Our experiments show hypernucleosome assembly which results from cooperative binding of histones to DNA, facilitated by weak stacking interactions between neighboring histone dimers. Furthermore, rotational force spectroscopy demonstrates that the HMfB–DNA complex has a left-handed chirality, but that torque can drive it in a right-handed conformation. The structure of the hypernucleosome thus depends on stacking interactions, torque, and force. In vivo, such modulation of the archaeal hypernucleosome structure may play an important role in transcription regulation in response to environmental changes.
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Affiliation(s)
- Bram Henneman
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333CC Leiden, The Netherlands
| | - Thomas B Brouwer
- Biological and Soft Matter Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, Niels Bohrweg 2, 2333CA Leiden, The Netherlands
| | - Amanda M Erkelens
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333CC Leiden, The Netherlands
| | - Gert-Jan Kuijntjes
- Biological and Soft Matter Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, Niels Bohrweg 2, 2333CA Leiden, The Netherlands
| | - Clara van Emmerik
- Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584CH Utrecht, The Netherlands
| | - Ramon A van der Valk
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333CC Leiden, The Netherlands
| | - Monika Timmer
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333CC Leiden, The Netherlands
| | - Nancy C S Kirolos
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333CC Leiden, The Netherlands
| | - Hugo van Ingen
- Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584CH Utrecht, The Netherlands
| | - John van Noort
- Biological and Soft Matter Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, Niels Bohrweg 2, 2333CA Leiden, The Netherlands
| | - Remus T Dame
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333CC Leiden, The Netherlands.,Centre for Microbial Cell Biology, Leiden University, Einsteinweg 55, 2333CC Leiden, The Netherlands
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3
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Yu J, Shinoda A, Kato K, Tanaka I, Yao M. A solution-free crystal-mounting platform for native SAD. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2020; 76:938-945. [PMID: 33021495 DOI: 10.1107/s2059798320011584] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 08/25/2020] [Indexed: 11/11/2022]
Abstract
The native SAD phasing method uses the anomalous scattering signals from the S atoms contained in most proteins, the P atoms in nucleic acids or other light atoms derived from the solution used for crystallization. These signals are very weak and careful data collection is required, which makes this method very difficult. One way to enhance the anomalous signal is to use long-wavelength X-rays; however, these wavelengths are more strongly absorbed by the materials in the pathway. Therefore, a crystal-mounting platform for native SAD data collection that removes solution around the crystals has been developed. This platform includes a novel solution-free mounting tool and an automatic robot, which extracts the surrounding solution, flash-cools the crystal and inserts the loop into a UniPuck cassette for use in the synchrotron. Eight protein structures (including two new structures) have been successfully solved by the native SAD method from crystals prepared using this platform.
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Affiliation(s)
- Jian Yu
- Faculty of Advanced Life Science, Hokkaido University, North 10 West 8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan
| | - Akira Shinoda
- Faculty of Advanced Life Science, Hokkaido University, North 10 West 8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan
| | - Koji Kato
- Faculty of Advanced Life Science, Hokkaido University, North 10 West 8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan
| | - Isao Tanaka
- Faculty of Advanced Life Science, Hokkaido University, North 10 West 8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan
| | - Min Yao
- Faculty of Advanced Life Science, Hokkaido University, North 10 West 8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan
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4
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Basu S, Olieric V, Leonarski F, Matsugaki N, Kawano Y, Takashi T, Huang CY, Yamada Y, Vera L, Olieric N, Basquin J, Wojdyla JA, Bunk O, Diederichs K, Yamamoto M, Wang M. Long-wavelength native-SAD phasing: opportunities and challenges. IUCRJ 2019; 6:373-386. [PMID: 31098019 PMCID: PMC6503925 DOI: 10.1107/s2052252519002756] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 02/22/2019] [Indexed: 05/04/2023]
Abstract
Native single-wavelength anomalous dispersion (SAD) is an attractive experimental phasing technique as it exploits weak anomalous signals from intrinsic light scatterers (Z < 20). The anomalous signal of sulfur in particular, is enhanced at long wavelengths, however the absorption of diffracted X-rays owing to the crystal, the sample support and air affects the recorded intensities. Thereby, the optimal measurable anomalous signals primarily depend on the counterplay of the absorption and the anomalous scattering factor at a given X-ray wavelength. Here, the benefit of using a wavelength of 2.7 over 1.9 Å is demonstrated for native-SAD phasing on a 266 kDa multiprotein-ligand tubulin complex (T2R-TTL) and is applied in the structure determination of an 86 kDa helicase Sen1 protein at beamline BL-1A of the KEK Photon Factory, Japan. Furthermore, X-ray absorption at long wavelengths was controlled by shaping a lysozyme crystal into spheres of defined thicknesses using a deep-UV laser, and a systematic comparison between wavelengths of 2.7 and 3.3 Å is reported for native SAD. The potential of laser-shaping technology and other challenges for an optimized native-SAD experiment at wavelengths >3 Å are discussed.
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Affiliation(s)
- Shibom Basu
- Swiss Light Source, Paul Scherrer Institut, Villigen PSI, 5232, Switzerland
| | - Vincent Olieric
- Swiss Light Source, Paul Scherrer Institut, Villigen PSI, 5232, Switzerland
| | - Filip Leonarski
- Swiss Light Source, Paul Scherrer Institut, Villigen PSI, 5232, Switzerland
| | - Naohiro Matsugaki
- Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization, Tsukuba, 305-0801, Japan
| | - Yoshiaki Kawano
- Advanced Photon Technology Division, RIKEN SPring-8 Center, Hyogo 679-5148, Japan
| | - Tomizaki Takashi
- Swiss Light Source, Paul Scherrer Institut, Villigen PSI, 5232, Switzerland
| | - Chia-Ying Huang
- Swiss Light Source, Paul Scherrer Institut, Villigen PSI, 5232, Switzerland
| | - Yusuke Yamada
- Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization, Tsukuba, 305-0801, Japan
| | - Laura Vera
- Swiss Light Source, Paul Scherrer Institut, Villigen PSI, 5232, Switzerland
| | - Natacha Olieric
- Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institut, Villigen, PSI 5232, Switzerland
| | - Jerome Basquin
- Department of Biochemistry, Max Planck Institute of Biochemistry, Munich, Germany
| | - Justyna A. Wojdyla
- Swiss Light Source, Paul Scherrer Institut, Villigen PSI, 5232, Switzerland
| | - Oliver Bunk
- Swiss Light Source, Paul Scherrer Institut, Villigen PSI, 5232, Switzerland
| | - Kay Diederichs
- Department of Biology, University of Konstanz, Konstanz, 78457, Germany
| | - Masaki Yamamoto
- Advanced Photon Technology Division, RIKEN SPring-8 Center, Hyogo 679-5148, Japan
| | - Meitian Wang
- Swiss Light Source, Paul Scherrer Institut, Villigen PSI, 5232, Switzerland
- Correspondence e-mail:
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Vogt MS, Völpel SL, Albers SV, Essen LO, Banerjee A. Crystal structure of an Lrs14-like archaeal biofilm regulator from Sulfolobus acidocaldarius. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2018; 74:1105-1114. [PMID: 30387769 DOI: 10.1107/s2059798318014146] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 10/06/2018] [Indexed: 11/10/2022]
Abstract
The small winged helix-turn-helix (wHTH) proteins of the Lrs14 family are major transcriptional regulators and act as archaeal biofilm regulators (AbfRs) in the crenarchaeote Sulfolobus acidocaldarius. Here, the first crystal structure of an AbfR ortholog, AbfR2, the deletion of which is known to impair biofilm formation, is presented. Like most other wHTH orthologs, AbfR2 is dimeric in solution as well as in its 2.45 Å resolution crystal structure. Given the presence of three independent AbfR2 dimers in the asymmetric unit, the crystal structure shows a considerable degree of conformational variation within the dimer, the antiparallel orientations of which are stabilized by coiled-coil interaction between H4 helices. Conserved anchor interactions between helices H0 and H4 of AbfR2 further contribute to dimer stabilization. The combined structural and bioinformatic analysis reveals cluster-specific structural differences between different members of the Lrs14 protein family.
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Affiliation(s)
- Marian S Vogt
- Structural Biochemistry - Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, 35032 Marburg, Germany
| | - Simon L Völpel
- Structural Biochemistry - Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, 35032 Marburg, Germany
| | - Sonja Verena Albers
- Molecular Biology of Archaea, Institute of Biology II, University of Freiburg, 79104 Freiburg, Germany
| | - Lars Oliver Essen
- Structural Biochemistry - Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, 35032 Marburg, Germany
| | - Ankan Banerjee
- Structural Biochemistry - Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, 35032 Marburg, Germany
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6
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Olczak A, Cianci M. The signal-to-noise ratio in SAD experiments. CRYSTALLOGR REV 2017. [DOI: 10.1080/0889311x.2017.1386182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Andrzej Olczak
- Institute of General and Ecological Chemistry, Lodz University of Technology, Lodz, Poland
| | - Michele Cianci
- Department of Agricultural, Food and Environmental Sciences, Università Politecnica delle Marche, Ancona, Italy
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7
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Li L, Banerjee A, Bischof LF, Maklad HR, Hoffmann L, Henche AL, Veliz F, Bildl W, Schulte U, Orell A, Essen LO, Peeters E, Albers SV. Wing phosphorylation is a major functional determinant of the Lrs14-type biofilm and motility regulator AbfR1 in Sulfolobus acidocaldarius. Mol Microbiol 2017. [PMID: 28628237 DOI: 10.1111/mmi.13735] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
In response to a variety of environmental cues, prokaryotes can switch between a motile and a sessile, biofilm-forming mode of growth. The regulatory mechanisms and signaling pathways underlying this switch are largely unknown in archaea but involve small winged helix-turn-helix DNA-binding proteins of the archaea-specific Lrs14 family. Here, we study the Lrs14 member AbfR1 of Sulfolobus acidocaldarius. Small-angle X-ray scattering data are presented, which are consistent with a model of dimeric AbfR1 in which dimerization occurs via an antiparallel coiled coil as suggested by homology modeling. Furthermore, solution structure data of AbfR1-DNA complexes suggest that upon binding DNA, AbfR1 induces deformations in the DNA. The wing residues tyrosine 84 and serine 87, which are phosphorylated in vivo, are crucial to establish stable protein-DNA contacts and their substitution with a negatively charged glutamate or aspartate residue inhibits formation of a nucleoprotein complex. Furthermore, mutation abrogates the cellular abundance and transcription regulatory function of AbfR1 and thus affects the resulting biofilm and motility phenotype of S. acidocaldarius. This work establishes a novel wHTH DNA-binding mode for Lrs14-like proteins and hints at an important role for protein phosphorylation as a signal transduction mechanism for the control of biofilm formation and motility in archaea.
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Affiliation(s)
- Lingling Li
- Molecular Biology of Archaea, Institute of Biology II, University of Freiburg, Freiburg, Germany
| | - Ankan Banerjee
- Structural Biochemistry, Department of Chemistry, Philipps University of Marburg, Marburg, Germany
| | - Lisa Franziska Bischof
- Molecular Biology of Archaea, Institute of Biology II, University of Freiburg, Freiburg, Germany.,Spemann Graduate School of Biology and Medicine, Freiburg, Germany
| | - Hassan Ramadan Maklad
- Research Group of Microbiology, Department of Bio-engineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Lena Hoffmann
- Molecular Biology of Archaea, Institute of Biology II, University of Freiburg, Freiburg, Germany
| | - Anna-Lena Henche
- Molecular Biology of Archaea, Institute of Biology II, University of Freiburg, Freiburg, Germany
| | - Fabian Veliz
- Molecular Microbiology of Extremophiles Group, Centre for Genomics and Bioinformatics, Faculty of Sciences, University Mayor, Santiago, Chile
| | - Wolfgang Bildl
- Institute of Physiology, University of Freiburg, Freiburg, Germany
| | - Uwe Schulte
- Institute of Physiology, University of Freiburg, Freiburg, Germany.,Center for Biological Signaling Studies (BIOSS), Freiburg, Germany
| | - Alvaro Orell
- Molecular Biology of Archaea, Institute of Biology II, University of Freiburg, Freiburg, Germany.,Molecular Microbiology of Extremophiles Group, Centre for Genomics and Bioinformatics, Faculty of Sciences, University Mayor, Santiago, Chile.,Max Planck Institute of Terrestrial Microbiology, Marburg, Germany
| | - Lars-Oliver Essen
- Structural Biochemistry, Department of Chemistry, Philipps University of Marburg, Marburg, Germany.,LOEWE Center for Synthetic Microbiology, Marburg, Germany
| | - Eveline Peeters
- Research Group of Microbiology, Department of Bio-engineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Institute of Biology II, University of Freiburg, Freiburg, Germany
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8
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Transcription Factor-Mediated Gene Regulation in Archaea. RNA METABOLISM AND GENE EXPRESSION IN ARCHAEA 2017. [DOI: 10.1007/978-3-319-65795-0_2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
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9
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Driessen RPC, Lin SN, Waterreus WJ, van der Meulen ALH, van der Valk RA, Laurens N, Moolenaar GF, Pannu NS, Wuite GJL, Goosen N, Dame RT. Diverse architectural properties of Sso10a proteins: Evidence for a role in chromatin compaction and organization. Sci Rep 2016; 6:29422. [PMID: 27403582 PMCID: PMC4941522 DOI: 10.1038/srep29422] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 06/17/2016] [Indexed: 11/19/2022] Open
Abstract
Sso10a proteins are small DNA-binding proteins expressed by the crenarchaeal model organism Sulfolobus solfataricus. Based on the structure of Sso10a1, which contains a winged helix-turn-helix motif, it is believed that Sso10a proteins function as sequence-specific transcription factors. Here we show that Sso10a1 and Sso10a2 exhibit different distinct DNA-binding modes. While the ability to bend DNA is shared between the two proteins, DNA bridging is observed only for Sso10a1 and only Sso10a2 exhibits filament formation along DNA. The architectural properties of Sso10a proteins suggest that these proteins fulfil generic roles in chromatin organization and compaction. As these proteins exhibit different binding behaviour depending on their DNA binding stoichiometry, altered levels of expression in the cell can be exploited to drive changes in local genome folding, which may operate to modulate transcription.
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Affiliation(s)
- Rosalie P C Driessen
- Leiden Institute of Chemistry, Cell Observatory and Centre for Microbial Cell Biology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Szu-Ning Lin
- Leiden Institute of Chemistry, Cell Observatory and Centre for Microbial Cell Biology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands.,Department of Physics and Astronomy, VU University, Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - Willem-Jan Waterreus
- Leiden Institute of Chemistry, Cell Observatory and Centre for Microbial Cell Biology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Alson L H van der Meulen
- Leiden Institute of Chemistry, Cell Observatory and Centre for Microbial Cell Biology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Ramon A van der Valk
- Leiden Institute of Chemistry, Cell Observatory and Centre for Microbial Cell Biology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Niels Laurens
- Department of Physics and Astronomy, VU University, Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - Geri F Moolenaar
- Leiden Institute of Chemistry, Cell Observatory and Centre for Microbial Cell Biology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Navraj S Pannu
- Leiden Institute of Chemistry, Cell Observatory and Centre for Microbial Cell Biology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Gijs J L Wuite
- Department of Physics and Astronomy, VU University, Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - Nora Goosen
- Leiden Institute of Chemistry, Cell Observatory and Centre for Microbial Cell Biology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Remus T Dame
- Leiden Institute of Chemistry, Cell Observatory and Centre for Microbial Cell Biology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
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10
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Ahmad MUD, Waege I, Hausner W, Thomm M, Boos W, Diederichs K, Welte W. Structural Insights into Nonspecific Binding of DNA by TrmBL2, an Archaeal Chromatin Protein. J Mol Biol 2015; 427:3216-3229. [PMID: 26299937 DOI: 10.1016/j.jmb.2015.08.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Revised: 08/04/2015] [Accepted: 08/10/2015] [Indexed: 10/23/2022]
Abstract
The crystal structure of TrmBL2 from the archaeon Pyrococcus furiosus shows an association of two pseudosymmetric dimers. The dimers follow the prototypical design of known bacterial repressors with two helix-turn-helix (HTH) domains binding to successive major grooves of the DNA. However, in TrmBL2, the two dimers are arranged at a mutual displacement of approximately 2bp so that they associate with the DNA along the double-helical axis at an angle of approximately 80°. While the deoxyribose phosphate groups of the double-stranded DNA (dsDNA) used for co-crystallization are clearly seen in the electron density map, most of the nucleobases are averaged out. Refinement required to assume a superposition of at least three mutually displaced dsDNAs. The HTH domains interact primarily with the deoxyribose phosphate groups and polar interactions with the nucleobases are almost absent. This hitherto unseen mode of DNA binding by TrmBL2 seems to arise from nonoptimal protein-DNA contacts made by its four HTH domains resulting in a low-affinity, nonspecific binding to DNA.
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Affiliation(s)
- Misbha Ud Din Ahmad
- University of Konstanz Department of Biology, Universitätsstrasse 10, 78456 Konstanz, Germany
| | - Ingrid Waege
- University Regensburg Lehrstuhl für Mikrobiologie, Universitätsstrasse 31, 93053 Regensburg, Germany
| | - Winfried Hausner
- University Regensburg Lehrstuhl für Mikrobiologie, Universitätsstrasse 31, 93053 Regensburg, Germany
| | - Michael Thomm
- University Regensburg Lehrstuhl für Mikrobiologie, Universitätsstrasse 31, 93053 Regensburg, Germany
| | - Winfried Boos
- University of Konstanz Department of Biology, Universitätsstrasse 10, 78456 Konstanz, Germany
| | - Kay Diederichs
- University of Konstanz Department of Biology, Universitätsstrasse 10, 78456 Konstanz, Germany
| | - Wolfram Welte
- University of Konstanz Department of Biology, Universitätsstrasse 10, 78456 Konstanz, Germany.
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11
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Gorgel M, Bøggild A, Ulstrup JJ, Weiss MS, Müller U, Nissen P, Boesen T. Against the odds? De novo structure determination of a pilin with two cysteine residues by sulfur SAD. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:1095-101. [PMID: 25945575 DOI: 10.1107/s1399004715003272] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 02/16/2015] [Indexed: 11/11/2022]
Abstract
Exploiting the anomalous signal of the intrinsic S atoms to phase a protein structure is advantageous, as ideally only a single well diffracting native crystal is required. However, sulfur is a weak anomalous scatterer at the typical wavelengths used for X-ray diffraction experiments, and therefore sulfur SAD data sets need to be recorded with a high multiplicity. In this study, the structure of a small pilin protein was determined by sulfur SAD despite several obstacles such as a low anomalous signal (a theoretical Bijvoet ratio of 0.9% at a wavelength of 1.8 Å), radiation damage-induced reduction of the cysteines and a multiplicity of only 5.5. The anomalous signal was improved by merging three data sets from different volumes of a single crystal, yielding a multiplicity of 17.5, and a sodium ion was added to the substructure of anomalous scatterers. In general, all data sets were balanced around the threshold values for a successful phasing strategy. In addition, a collection of statistics on structures from the PDB that were solved by sulfur SAD are presented and compared with the data. Looking at the quality indicator R(anom)/R(p.i.m.), an inconsistency in the documentation of the anomalous R factor is noted and reported.
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Affiliation(s)
- Manuela Gorgel
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10C, DK-8000 Aarhus C, Denmark
| | - Andreas Bøggild
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10C, DK-8000 Aarhus C, Denmark
| | - Jakob Jensen Ulstrup
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10C, DK-8000 Aarhus C, Denmark
| | - Manfred S Weiss
- Macromolecular Crystallography (HZB-MX), Helmholtz Zentrum Berlin für Materialien und Energie, Albert-Einstein-Strasse 15, D-12489 Berlin, Germany
| | - Uwe Müller
- Macromolecular Crystallography (HZB-MX), Helmholtz Zentrum Berlin für Materialien und Energie, Albert-Einstein-Strasse 15, D-12489 Berlin, Germany
| | - Poul Nissen
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10C, DK-8000 Aarhus C, Denmark
| | - Thomas Boesen
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10C, DK-8000 Aarhus C, Denmark
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12
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Peeters E, Driessen RPC, Werner F, Dame RT. The interplay between nucleoid organization and transcription in archaeal genomes. Nat Rev Microbiol 2015; 13:333-41. [PMID: 25944489 DOI: 10.1038/nrmicro3467] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The archaeal genome is organized by either eukaryotic-like histone proteins or bacterial-like nucleoid-associated proteins. Recent studies have revealed novel insights into chromatin dynamics and their effect on gene expression in archaeal model organisms. In this Progress article, we discuss the interplay between chromatin proteins, such as histones and Alba, and components of the basal transcription machinery, as well as between chromatin structure and gene-specific transcription factors in archaea. Such an interplay suggests that chromatin might have a role in regulating gene expression on both a global and a gene-specific level. Moreover, several archaeal transcription factors combine a global gene regulatory role with an architectural role, thus contributing to chromatin organization and compaction, as well as gene expression. We describe the emerging principles underlying how these factors cooperate in nucleoid structuring and gene regulation.
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Affiliation(s)
- Eveline Peeters
- 1] Research Group of Microbiology, Department of Bio-engineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium. [2]
| | - Rosalie P C Driessen
- 1] Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands. [2]
| | - Finn Werner
- Institute for Structural and Molecular Biology, Division of Biosciences, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
| | - Remus T Dame
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
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Chromatin structure and dynamics in hot environments: architectural proteins and DNA topoisomerases of thermophilic archaea. Int J Mol Sci 2014; 15:17162-87. [PMID: 25257534 PMCID: PMC4200833 DOI: 10.3390/ijms150917162] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 08/19/2014] [Accepted: 09/09/2014] [Indexed: 01/20/2023] Open
Abstract
In all organisms of the three living domains (Bacteria, Archaea, Eucarya) chromosome-associated proteins play a key role in genome functional organization. They not only compact and shape the genome structure, but also regulate its dynamics, which is essential to allow complex genome functions. Elucidation of chromatin composition and regulation is a critical issue in biology, because of the intimate connection of chromatin with all the essential information processes (transcription, replication, recombination, and repair). Chromatin proteins include architectural proteins and DNA topoisomerases, which regulate genome structure and remodelling at two hierarchical levels. This review is focussed on architectural proteins and topoisomerases from hyperthermophilic Archaea. In these organisms, which live at high environmental temperature (>80 °C <113 °C), chromatin proteins and modulation of the DNA secondary structure are concerned with the problem of DNA stabilization against heat denaturation while maintaining its metabolic activity.
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15
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16
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Abstract
Crenarchaeal genomes are organized into a compact nucleoid by a set of small chromatin proteins. Although there is little knowledge of chromatin structure in Archaea, similarities between crenarchaeal and bacterial chromatin proteins suggest that organization and regulation could be achieved by similar mechanisms. In the present review, we describe the molecular properties of crenarchaeal chromatin proteins and discuss the possible role of these architectural proteins in organizing the crenarchaeal chromatin and in gene regulation.
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Krug M, Lee SJ, Boos W, Diederichs K, Welte W. The three-dimensional structure of TrmB, a transcriptional regulator of dual function in the hyperthermophilic archaeon Pyrococcus furiosus in complex with sucrose. Protein Sci 2013; 22:800-8. [PMID: 23576322 DOI: 10.1002/pro.2263] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Revised: 03/06/2013] [Accepted: 03/06/2013] [Indexed: 01/02/2023]
Abstract
TrmB is a repressor that binds maltose, maltotriose, and sucrose, as well as other α-glucosides. It recognizes two different operator sequences controlling the TM (Trehalose/Maltose) and the MD (Maltodextrin) operon encoding the respective ABC transporters and sugar-degrading enzymes. Binding of maltose to TrmB abrogates repression of the TM operon but maintains the repression of the MD operon. On the other hand, binding of sucrose abrogates repression of the MD operon but maintains repression of the TM operon. The three-dimensional structure of TrmB in complex with sucrose was solved and refined to a resolution of 3.0 Å. The structure shows the N-terminal DNA binding domain containing a winged-helix-turn-helix (wHTH) domain followed by an amphipathic helix with a coiled-coil motif. The latter promotes dimerization and places the symmetry mates of the putative recognition helix in the wHTH motif about 30 Å apart suggesting a canonical binding to two successive major grooves of duplex palindromic DNA. This suggests that the structure resembles the conformation of TrmB recognizing the pseudopalindromic TM promoter but not the conformation recognizing the nonpalindromic MD promoter.
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Affiliation(s)
- Michael Krug
- Department of Biology, University of Konstanz, Konstanz, Germany
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Doyle CM, Rumfeldt JA, Broom HR, Broom A, Stathopulos PB, Vassall KA, Almey JJ, Meiering EM. Energetics of oligomeric protein folding and association. Arch Biochem Biophys 2012; 531:44-64. [PMID: 23246784 DOI: 10.1016/j.abb.2012.12.005] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Revised: 11/29/2012] [Accepted: 12/05/2012] [Indexed: 12/11/2022]
Abstract
In nature, proteins most often exist as complexes, with many of these consisting of identical subunits. Understanding of the energetics governing the folding and misfolding of such homooligomeric proteins is central to understanding their function and misfunction, in disease or biotechnology. Much progress has been made in defining the mechanisms and thermodynamics of homooligomeric protein folding. In this review, we outline models as well as calorimetric and spectroscopic methods for characterizing oligomer folding, and describe extensive results obtained for diverse proteins, ranging from dimers to octamers and higher order aggregates. To our knowledge, this area has not been reviewed comprehensively in years, and the collective progress is impressive. The results provide evolutionary insights into the development of subunit interfaces, mechanisms of oligomer folding, and contributions of oligomerization to protein stability, function and regulation. Thermodynamic analyses have also proven valuable for understanding protein misfolding and aggregation mechanisms, suggesting new therapeutic avenues. Successful recent designs of novel, functional proteins demonstrate increased understanding of oligomer folding. Further rigorous analyses using multiple experimental and computational approaches are still required, however, to achieve consistent and accurate prediction of oligomer folding energetics. Modeling the energetics remains challenging but is a promising avenue for future advances.
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Affiliation(s)
- Colleen M Doyle
- Guelph-Waterloo Centre for Graduate Studies in Chemistry and Biochemistry, and Department of Chemistry, University of Waterloo, 200 University Ave. West, Waterloo, ON, Canada
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Hsu CH, Wang AHJ. The DNA-recognition fold of Sso7c4 suggests a new member of SpoVT-AbrB superfamily from archaea. Nucleic Acids Res 2011; 39:6764-74. [PMID: 21546550 PMCID: PMC3159460 DOI: 10.1093/nar/gkr283] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Organisms growing at elevated temperatures face the challenge of maintaining the integrity of their genetic materials. Archaea possess unique chromatin proteins for gene organization and information processing. We present the solution structure of Sso7c4 from Sulfolobus solfataricus, which has a homodimeric DNA-binding fold forming a swapped β-loop-β ‘Tai-Chi’ topology. The fold is reminiscent of the N-terminal DNA-binding domain of AbrB and MazE. In addition, several amide resonances in the heteronuclear single quantum coherence spectra of Sso7c4 are shifted and broadened with the addition of small amounts of duplex DNA oligomers. The locations of the corresponding amides in the Sso7c4 structure define its DNA-interacting surface. NMR spectra of DNA titrated with the protein further indicated that Sso7c4 interacts with DNA in the major groove. Taken together, a plausible model for the Sso7c4–DNA complex is presented, in which the DNA double helix is curved around the protein dimer.
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Affiliation(s)
- Chun-Hua Hsu
- Department of Agricultural Chemistry, National Taiwan University, Taipei, Taiwan
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Andrésen C, Jalal S, Aili D, Wang Y, Islam S, Jarl A, Liedberg B, Wretlind B, Mårtensson LG, Sunnerhagen M. Critical biophysical properties in the Pseudomonas aeruginosa efflux gene regulator MexR are targeted by mutations conferring multidrug resistance. Protein Sci 2010; 19:680-92. [PMID: 20095047 DOI: 10.1002/pro.343] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The self-assembling MexA-MexB-OprM efflux pump system, encoded by the mexO operon, contributes to facile resistance of Pseudomonas aeruginosa by actively extruding multiple antimicrobials. MexR negatively regulates the mexO operon, comprising two adjacent MexR binding sites, and is as such highly targeted by mutations that confer multidrug resistance (MDR). To understand how MDR mutations impair MexR function, we studied MexR-wt as well as a selected set of MDR single mutants distant from the proposed DNA-binding helix. Although DNA affinity and MexA-MexB-OprM repression were both drastically impaired in the selected MexR-MDR mutants, MexR-wt bound its two binding sites in the mexO with high affinity as a dimer. In the MexR-MDR mutants, secondary structure content and oligomerization properties were very similar to MexR-wt despite their lack of DNA binding. Despite this, the MexR-MDR mutants showed highly varying stabilities compared with MexR-wt, suggesting disturbed critical interdomain contacts, because mutations in the DNA-binding domains affected the stability of the dimer region and vice versa. Furthermore, significant ANS binding to MexR-wt in both free and DNA-bound states, together with increased ANS binding in all studied mutants, suggest that a hydrophobic cavity in the dimer region already shown to be involved in regulatory binding is enlarged by MDR mutations. Taken together, we propose that the biophysical MexR properties that are targeted by MDR mutations-stability, domain interactions, and internal hydrophobic surfaces-are also critical for the regulation of MexR DNA binding.
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Affiliation(s)
- Cecilia Andrésen
- Division of Molecular Biotechnology, Department of Physics, Chemistry and Biology, Linköping University, SE-58183 Linköping, Sweden
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21
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Shinkai A, Sekine SI, Urushibata A, Terada T, Shirouzu M, Yokoyama S. The putative DNA-binding protein Sto12a from the thermoacidophilic archaeon Sulfolobus tokodaii contains intrachain and interchain disulfide bonds. J Mol Biol 2007; 372:1293-304. [PMID: 17720190 DOI: 10.1016/j.jmb.2007.07.051] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2007] [Revised: 07/20/2007] [Accepted: 07/23/2007] [Indexed: 11/24/2022]
Abstract
The Sto12a protein, from the thermoacidophilic archaeon Sulfolobus tokodaii, has been identified as a small putative DNA-binding protein. Most of the proteins with a high level of amino acid sequence homology to this protein are derived from members of the Sulfolobaceae family, including a transcriptional regulator. We determined the crystal structure of Sto12a at 2.05 A resolution by multiple-wavelength anomalous dispersion phasing from the selenomethionine-containing protein crystal. This is the first structure of a member of this family of DNA-binding proteins. The Sto12a protein forms a homodimer, and the structure is composed of an N-terminal alpha-helix, a winged-helix-turn-helix domain, and a C-terminal alpha-helix that forms an interchain antiparallel coiled coil. The two winged-helix domains are located at both ends of the coiled coil, with putative DNA-recognition helices separated by approximately 34 A. A structural homology search indicated that the winged-helix domain shared a high level of homology with those found in B-DNA- or Z-DNA-binding proteins from various species, including archaea, bacteria, and human, despite a low level of sequence similarity. The unique structural features of the Sto12a protein include intrachain and interchain disulfide bonds, which stabilize the chain and homodimer structures. There are three cysteine residues: Cys15 and Cys16 in the N-terminal alpha-helix, and Cys100 in the C-terminal alpha-helix. Cys15 is involved in an interchain disulfide bridge with the other Cys15, and Cys16 forms an intrachain disulfide bridge with Cys100. This is a novel fold among winged-helix DNA-binding proteins. Possible DNA-binding interactions of the Sto12a protein are discussed based on the crystal structure of Sto12a and comparisons to other winged-helix DNA-binding proteins.
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Affiliation(s)
- Akeo Shinkai
- RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
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Cianci M, Helliwell JR, Helliwell M, Kaucic V, Logar NZ, Mali G, Tusar NN. Anomalous scattering in structural chemistry and biology¶. CRYSTALLOGR REV 2005. [DOI: 10.1080/08893110500421268] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Kahsai MA, Vogler B, Clark AT, Edmondson SP, Shriver JW. Solution structure, stability, and flexibility of Sso10a: a hyperthermophile coiled-coil DNA-binding protein. Biochemistry 2005; 44:2822-32. [PMID: 15723526 DOI: 10.1021/bi047669t] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Sso10a is one of a number of DNA-binding proteins from the hyperthermophile Sulfolobus solfataricus that has been associated with DNA packaging and chromatin regulation. Sequence analysis indicates that it is a member of a conserved group of archaeal transcription regulators (COG3432). We have determined the solution structure of Sso10a and show that it is a homodimer of winged-helix DNA-binding domains. The dimer interface consists of an extended antiparallel coiled coil, with the globular DNA-binding domains positioned at opposite ends of a solvent-exposed coiled-coil rod. NMR structure refinement of the elongated structure benefited not only from the inclusion of residual dipolar couplings from partially aligned samples but also the influence of anisotropic rotational diffusion on heteronuclear relaxation. An analysis of backbone mobility using (15)N relaxation rates indicated that the overall tertiary and quaternary structure is largely inflexible on the nanosecond to picosecond time scale. Amide hydrogen exchange data demonstrated that the most stable region of the protein extends from the core of the winged helices into the coiled coil. The positions of the globular heads relative to the coiled coil in solution deviate only slightly from that observed in a crystal structure. The most significant difference between the solution and crystal structures occurs in the putative DNA-binding helix-turn-helix (HTH) motif. This is the region of lowest stability in solution and a point of protein-protein contact in the crystal. Alternative conformations of the HTH motif may permit adjustment of the structure for optimal DNA binding.
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Affiliation(s)
- Mebrahtu A Kahsai
- Biomolecular Nuclear Magnetic Resonance Laboratory, Department of Chemistry, Graduate Program in Biotechnology Science and Engineering, University of Alabama in Huntsville, Huntsville, Alabama 35899, USA
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Edmondson SP, Kahsai MA, Gupta R, Shriver JW. Characterization of Sac10a, a hyperthermophile DNA-binding protein from Sulfolobus acidocaldarius. Biochemistry 2004; 43:13026-36. [PMID: 15476396 DOI: 10.1021/bi0491752] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Sac10a is a member of a group of basic DNA-binding proteins thought to be important in chromatin structure and regulation in the archaeon Sulfolobus. We describe here the isolation, gene identification, and biophysical characterization of native Sac10a. The protein exists as a 23.8 kDa homodimer at pH 7 and unfolds with a T degrees of 122 degrees C. Dissociation of the dimer into folded globular subunits is promoted by decreased pH and salt concentration. Thermal unfolding of the monomeric subunits occurred with two transitions, indicating two independent domains. The dimer demonstrated a high affinity for duplex poly(dAdT) with a K(D) of 5 x 10(-)(10) M and a site size of 17 bp (in 0.15 M KCl, pH 7), with only weak binding (K(D) > 5 x 10(-)(6) M) to poly(dA)-poly(dT), poly(dGdC), poly(dG)-poly(dC), and Escherichia coli DNA under similar conditions. Binding to poly(dAdT) resulted in distortions in the DNA duplex that were consistent with overwinding as indicated by inversion of the CD spectrum of the DNA. The monomeric subunits are predicted to adopt a winged helix DNA-binding motif which dimerizes through formation of a two-stranded coiled coil involving an extended C-terminal helix with more than four heptad repeats (about 45 A in length). This is the first example of the conserved archaeal transcription regulator domain COG3432 to be characterized. Sequences for homologous proteins containing both COG3432 and predicted coiled coil domains occur in the genomes of both crenarchaeota (Sulfolobus, Pyrobaculum, Aeropyrum) and euryarchaeota (Methanosarcina, Methanococcus, Archaeoglobus, Thermoplasma), with multiple genes in some species. Sac10a shows no sequence similarity to the other Sulfolobus chromatin proteins Sac7d, Sac8, Sso10b2, and Alba.
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Affiliation(s)
- Stephen P Edmondson
- Laboratory for Structural Biology, Department of Chemistry, Graduate Program in Biotechnology and Bioengineering, University of Alabama in Huntsville, Huntsville, Alabama 35899, USA
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