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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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2
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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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3
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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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4
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He Y, Yan C, Fang J, Inouye C, Tjian R, Ivanov I, Nogales E. Near-atomic resolution visualization of human transcription promoter opening. Nature 2016; 533:359-65. [PMID: 27193682 PMCID: PMC4940141 DOI: 10.1038/nature17970] [Citation(s) in RCA: 220] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 04/05/2016] [Indexed: 12/11/2022]
Abstract
In eukaryotic transcription initiation, a large multi-subunit pre-initiation complex (PIC) that assembles at the core promoter is required for the opening of the duplex DNA and identification of the start site for transcription by RNA polymerase II. Here we use cryo-electron microscropy (cryo-EM) to determine near-atomic resolution structures of the human PIC in a closed state (engaged with duplex DNA), an open state (engaged with a transcription bubble), and an initially transcribing complex (containing six base pairs of DNA-RNA hybrid). Our studies provide structures for previously uncharacterized components of the PIC, such as TFIIE and TFIIH, and segments of TFIIA, TFIIB and TFIIF. Comparison of the different structures reveals the sequential conformational changes that accompany the transition from each state to the next throughout the transcription initiation process. This analysis illustrates the key role of TFIIB in transcription bubble stabilization and provides strong structural support for a translocase activity of XPB.
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Affiliation(s)
- Yuan He
- Molecular Biophysics and Integrative Bio-Imaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.,Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, USA
| | - Chunli Yan
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30302, USA
| | - Jie Fang
- Howard Hughes Medical Institute, University of California, Berkeley, California 94720, USA
| | - Carla Inouye
- Li Ka Shing Center for Biomedical and Health Sciences, University of California, Berkeley, California 94720, USA
| | - Robert Tjian
- Howard Hughes Medical Institute, University of California, Berkeley, California 94720, USA.,Li Ka Shing Center for Biomedical and Health Sciences, University of California, Berkeley, California 94720, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
| | - Ivaylo Ivanov
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30302, USA
| | - Eva Nogales
- Molecular Biophysics and Integrative Bio-Imaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.,Howard Hughes Medical Institute, University of California, Berkeley, California 94720, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
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5
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Contursi P, Farina B, Pirone L, Fusco S, Russo L, Bartolucci S, Fattorusso R, Pedone E. Structural and functional studies of Stf76 from the Sulfolobus islandicus plasmid-virus pSSVx: a novel peculiar member of the winged helix-turn-helix transcription factor family. Nucleic Acids Res 2014; 42:5993-6011. [PMID: 24682827 PMCID: PMC4027180 DOI: 10.1093/nar/gku215] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The hybrid plasmid–virus pSSVx from Sulfolobus islandicus presents an open reading frame encoding a 76 amino acid protein, namely Stf76, that does not show significant sequence homology with any protein with known 3D structure. The recombinant protein recognizes specifically two DNA-binding sites located in its own promoter, thus suggesting an auto-regulated role of its expression. Circular dichroism, spectrofluorimetric, light scattering and isothermal titration calorimetry experiments indicated a 2:1 molar ratio (protein:DNA) upon binding to the DNA target containing a single site. Furthermore, the solution structure of Stf76, determined by nuclear magnetic resonance (NMR) using chemical shift Rosetta software, has shown that the protein assumes a winged helix–turn–helix fold. NMR chemical shift perturbation analysis has been performed for the identification of the residues responsible for DNA interaction. In addition, a model of the Stf76–DNA complex has been built using as template a structurally related homolog.
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Affiliation(s)
- Patrizia Contursi
- Dipartimento di Biologia, Università degli Studi di Napoli "Federico II", Napoli 80126, Italy
| | - Biancamaria Farina
- Interuniversity Centre for Research on Bioactive Peptides (CIRPEB), University of Naples Federico II, Via Mezzocannone 16, 80134 Naples, Italy
| | | | - Salvatore Fusco
- Dipartimento di Biologia, Università degli Studi di Napoli "Federico II", Napoli 80126, Italy
| | - Luigi Russo
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Seconda Università di Napoli, Caserta 81100, Italy
| | - Simonetta Bartolucci
- Dipartimento di Biologia, Università degli Studi di Napoli "Federico II", Napoli 80126, Italy
| | - Roberto Fattorusso
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Seconda Università di Napoli, Caserta 81100, Italy
| | - Emilia Pedone
- Interuniversity Centre for Research on Bioactive Peptides (CIRPEB), University of Naples Federico II, Via Mezzocannone 16, 80134 Naples, Italy Istituto di Biostrutture e Bioimmagini, C.N.R., Napoli 80134, Italy
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6
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Fujiwara Y, Takeshita K, Nakagawa A, Okamura Y. Structural characteristics of the redox-sensing coiled coil in the voltage-gated H+ channel. J Biol Chem 2013; 288:17968-75. [PMID: 23667254 DOI: 10.1074/jbc.m113.459024] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Oxidation is an important biochemical defense mechanism, but it also elicits toxicity; therefore, oxidation must be under strict control. In phagocytotic events in neutrophils, the voltage-gated H(+) (Hv) channel is a key regulator of the production of reactive oxygen species against invading bacteria. The cytoplasmic domain of the Hv channel forms a dimeric coiled coil underpinning a dimerized functional unit. Importantly, in the alignment of the coiled-coil core, a conserved cysteine residue forms a potential intersubunit disulfide bond. In this study, we solved the crystal structures of the coiled-coil domain in reduced, oxidized, and mutated (Cys → Ser) states. The crystal structures indicate that a pair of Cys residues forms an intersubunit disulfide bond dependent on the redox conditions. CD spectroscopy revealed that the disulfide bond increases the thermal stability of the coiled-coil protein. We also reveal that two thiol modifier molecules are able to bind to Cys in a redox-dependent manner without disruption of the dimeric coiled-coil assembly. Thus, the biochemical properties of the cytoplasmic coiled-coil domain in the Hv channel depend on the redox condition, which may play a role in redox sensing in the phagosome.
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Affiliation(s)
- Yuichiro Fujiwara
- Department of Physiology, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan.
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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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Grünberg S, Warfield L, Hahn S. Architecture of the RNA polymerase II preinitiation complex and mechanism of ATP-dependent promoter opening. Nat Struct Mol Biol 2012; 19:788-96. [PMID: 22751016 PMCID: PMC3414687 DOI: 10.1038/nsmb.2334] [Citation(s) in RCA: 113] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Accepted: 05/28/2012] [Indexed: 01/23/2023]
Abstract
Yeast RNA polymerase (Pol) II general factor TFIIE and the TFIIH subunit Ssl2/XPB function in transition of the preinitiation complex (PIC) to the open complex. We find that the three TFIIE winged helix (WH) domains form a heterodimer, with the Tfa1/TFIIEα WH binding the Pol II clamp and the Tfa2/TFIIEβ tandem WH domain encircling promoter DNA that becomes single stranded in the open complex. Ssl2 lies adjacent to TFIIE, enclosing downstream promoter DNA. In contrast to previous proposals, comparison of the PIC and open complex models strongly suggests that Ssl2 promotes DNA opening by functioning as a double stranded DNA translocase, feeding 15 bp of double stranded DNA into the Pol II cleft. Right-handed threading of DNA through the Ssl2 binding groove, combined with the fixed position of upstream promoter DNA, will lead to DNA unwinding and the open state.
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