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Bhowmick A, Bhakta K, Roy M, Gupta S, Das J, Samanta S, Patranabis S, Ghosh A. Heat shock response in Sulfolobus acidocaldarius and first implications for cross-stress adaptation. Res Microbiol 2023; 174:104106. [PMID: 37516156 DOI: 10.1016/j.resmic.2023.104106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 07/15/2023] [Accepted: 07/21/2023] [Indexed: 07/31/2023]
Abstract
Sulfolobus acidocaldarius, a thermoacidophilic crenarchaeon, frequently encounters temperature fluctuations, oxidative stress, and nutrient limitations in its environment. Here, we employed a high-throughput transcriptomic analysis to examine how the gene expression of S. acidocaldarius changes when exposed to high temperatures (92 °C). The data obtained was subsequently validated using quantitative reverse transcription-PCR (qRT-PCR) analysis. Our particular focus was on genes that are involved in the heat shock response, type-II Toxin-Antitoxin systems, and putative transcription factors. To investigate how S. acidocaldarius adapts to multiple stressors, we assessed the expression of these selected genes under oxidative and nutrient stresses using qRT-PCR analysis. The results demonstrated that the gene thβ encoding the β subunit of the thermosome, as well as hsp14 and hsp20, play crucial roles in the majority of stress conditions. Furthermore, we observed overexpression of at least eight different TA pairs belonging to the type II TA systems under all stress conditions. Additionally, four common transcription factors: FadR, TFEβ, CRISPR loci binding protein, and HTH family protein were consistently overexpressed across all stress conditions, indicating their significant role in managing stress. Overall, this work provides the first insight into molecular players involved in the cross-stress adaptation of S. acidocaldarius.
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Affiliation(s)
- Arghya Bhowmick
- Department of Biological Sciences, Bose Institute, EN Block, Sector-V, Kolkata-700091, India
| | - Koustav Bhakta
- Department of Biological Sciences, Bose Institute, EN Block, Sector-V, Kolkata-700091, India
| | - Mousam Roy
- Department of Biological Sciences, Bose Institute, EN Block, Sector-V, Kolkata-700091, India
| | - Sayandeep Gupta
- Department of Biological Sciences, Bose Institute, EN Block, Sector-V, Kolkata-700091, India
| | - Jagriti Das
- Department of Biological Sciences, Bose Institute, EN Block, Sector-V, Kolkata-700091, India
| | - Shirsha Samanta
- Department of Biological Sciences, Bose Institute, EN Block, Sector-V, Kolkata-700091, India
| | | | - Abhrajyoti Ghosh
- Department of Biological Sciences, Bose Institute, EN Block, Sector-V, Kolkata-700091, India.
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2
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Payá G, Bautista V, Camacho M, Esclapez J, Bonete MJ. Comprehensive Bioinformatics Analysis of the Biodiversity of Lsm Proteins in the Archaea Domain. Microorganisms 2023; 11:1196. [PMID: 37317170 DOI: 10.3390/microorganisms11051196] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 04/25/2023] [Accepted: 04/27/2023] [Indexed: 06/16/2023] Open
Abstract
The Sm protein superfamily includes Sm, like-Sm (Lsm), and Hfq proteins. Sm and Lsm proteins are found in the Eukarya and Archaea domains, respectively, while Hfq proteins exist in the Bacteria domain. Even though Sm and Hfq proteins have been extensively studied, archaeal Lsm proteins still require further exploration. In this work, different bioinformatics tools are used to understand the diversity and distribution of 168 Lsm proteins in 109 archaeal species to increase the global understanding of these proteins. All 109 archaeal species analyzed encode one to three Lsm proteins in their genome. Lsm proteins can be classified into two groups based on molecular weight. Regarding the gene environment of lsm genes, many of these genes are located adjacent to transcriptional regulators of the Lrp/AsnC and MarR families, RNA-binding proteins, and ribosomal protein L37e. Notably, only proteins from species of the class Halobacteria conserved the internal and external residues of the RNA-binding site identified in Pyrococcus abyssi, despite belonging to different taxonomic orders. In most species, the Lsm genes show associations with 11 genes: rpl7ae, rpl37e, fusA, flpA, purF, rrp4, rrp41, hel308, rpoD, rpoH, and rpoN. We propose that most archaeal Lsm proteins are related to the RNA metabolism, and the larger Lsm proteins could perform different functions and/or act through other mechanisms of action.
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Affiliation(s)
- Gloria Payá
- Department of Biochemistry and Molecular Biology and Soil Science and Agricultural Chemistry, Faculty of Science, University of Alicante, Ap 99, 03080 Alicante, Spain
| | - Vanesa Bautista
- Department of Biochemistry and Molecular Biology and Soil Science and Agricultural Chemistry, Faculty of Science, University of Alicante, Ap 99, 03080 Alicante, Spain
| | - Mónica Camacho
- Department of Biochemistry and Molecular Biology and Soil Science and Agricultural Chemistry, Faculty of Science, University of Alicante, Ap 99, 03080 Alicante, Spain
| | - Julia Esclapez
- Department of Biochemistry and Molecular Biology and Soil Science and Agricultural Chemistry, Faculty of Science, University of Alicante, Ap 99, 03080 Alicante, Spain
| | - María-José Bonete
- Department of Biochemistry and Molecular Biology and Soil Science and Agricultural Chemistry, Faculty of Science, University of Alicante, Ap 99, 03080 Alicante, Spain
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3
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Abstract
Oxidative stress causes cellular damage, including DNA mutations, protein dysfunction, and loss of membrane integrity. Here, we discovered that a TrmB (transcription regulator of mal operon) family protein (Pfam PF01978) composed of a single winged-helix DNA binding domain (InterPro IPR002831) can function as thiol-based transcriptional regulator of oxidative stress response. Using the archaeon Haloferax volcanii as a model system, we demonstrate that the TrmB-like OxsR is important for recovery of cells from hypochlorite stress. OxsR is shown to bind specific regions of genomic DNA, particularly during hypochlorite stress. OxsR-bound intergenic regions were found proximal to oxidative stress operons, including genes associated with thiol relay and low molecular weight thiol biosynthesis. Further analysis of a subset of these sites revealed OxsR to function during hypochlorite stress as a transcriptional activator and repressor. OxsR was shown to require a conserved cysteine (C24) for function and to use a CG-rich motif upstream of conserved BRE/TATA box promoter elements for transcriptional activation. Protein modeling suggested the C24 is located at a homodimer interface formed by antiparallel α helices, and that oxidation of this cysteine would result in the formation of an intersubunit disulfide bond. This covalent linkage may promote stabilization of an OxsR homodimer with the enhanced DNA binding properties observed in the presence of hypochlorite stress. The phylogenetic distribution TrmB family proteins, like OxsR, that have a single winged-helix DNA binding domain and conserved cysteine residue suggests this type of redox signaling mechanism is widespread in Archaea.
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Rodríguez-Herrero V, Payá G, Bautista V, Vegara A, Cortés-Molina M, Camacho M, Esclapez J, Bonete MJ. Essentiality of the glnA gene in Haloferax mediterranei: gene conversion and transcriptional analysis. Extremophiles 2020; 24:433-446. [PMID: 32296946 DOI: 10.1007/s00792-020-01169-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 03/27/2020] [Indexed: 11/26/2022]
Abstract
Glutamine synthetase is an essential enzyme in ammonium assimilation and glutamine biosynthesis. The Haloferax mediterranei genome has two other glnA-type genes (glnA2 and glnA3) in addition to the glutamine synthetase gene glnA. To determine whether the glnA2 and glnA3 genes can replace glnA in nitrogen metabolism, we generated deletion mutants of glnA. The glnA deletion mutants could not be generated in a medium without glutamine, and thus, glnA is an essential gene in H. mediterranei. The glnA deletion mutant was achieved by adding 40 mM glutamine to the selective medium. This conditional HM26-ΔglnA mutant was characterised with different approaches in the presence of distinct nitrogen sources and nitrogen starvation. Transcriptomic analysis was performed to compare the expression profiles of the strains HM26-ΔglnA and HM26 under different growth conditions. The glnA deletion did not affect the expression of glnA2, glnA3 and nitrogen assimilation genes under nitrogen starvation. Moreover, the results showed that glnA, glnA2 and glnA3 were not expressed under the same conditions. These results indicated that glnA is an essential gene for H. mediterranei and, therefore, glnA2 and glnA3 cannot replace glnA in the conditions analysed.
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Affiliation(s)
- V Rodríguez-Herrero
- División de Bioquímica Y Biología Molecular, Departamento de Agroquímica Y Bioquímica, Universidad de Alicante, Carretera de San Vicente del Raspeig s/n, San Vicente del Raspeig, 03690, Alicante, Spain
| | - G Payá
- División de Bioquímica Y Biología Molecular, Departamento de Agroquímica Y Bioquímica, Universidad de Alicante, Carretera de San Vicente del Raspeig s/n, San Vicente del Raspeig, 03690, Alicante, Spain
| | - V Bautista
- División de Bioquímica Y Biología Molecular, Departamento de Agroquímica Y Bioquímica, Universidad de Alicante, Carretera de San Vicente del Raspeig s/n, San Vicente del Raspeig, 03690, Alicante, Spain
| | - A Vegara
- División de Bioquímica Y Biología Molecular, Departamento de Agroquímica Y Bioquímica, Universidad de Alicante, Carretera de San Vicente del Raspeig s/n, San Vicente del Raspeig, 03690, Alicante, Spain
| | - M Cortés-Molina
- Departamento de Matemática Aplicada, Universidad de Alicante, Carretera de San Vicente del Raspeig s/n, San Vicente del Raspeig, 03690, Alicante, Spain
| | - M Camacho
- División de Bioquímica Y Biología Molecular, Departamento de Agroquímica Y Bioquímica, Universidad de Alicante, Carretera de San Vicente del Raspeig s/n, San Vicente del Raspeig, 03690, Alicante, Spain
| | - J Esclapez
- División de Bioquímica Y Biología Molecular, Departamento de Agroquímica Y Bioquímica, Universidad de Alicante, Carretera de San Vicente del Raspeig s/n, San Vicente del Raspeig, 03690, Alicante, Spain
| | - M J Bonete
- División de Bioquímica Y Biología Molecular, Departamento de Agroquímica Y Bioquímica, Universidad de Alicante, Carretera de San Vicente del Raspeig s/n, San Vicente del Raspeig, 03690, Alicante, Spain.
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5
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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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Denis A, Martínez-Núñez MA, Tenorio-Salgado S, Perez-Rueda E. Dissecting the Repertoire of DNA-Binding Transcription Factors of the Archaeon Pyrococcus furiosus DSM 3638. Life (Basel) 2018; 8:life8040040. [PMID: 30248960 PMCID: PMC6316755 DOI: 10.3390/life8040040] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 09/11/2018] [Accepted: 09/19/2018] [Indexed: 01/06/2023] Open
Abstract
In recent years, there has been a large increase in the amount of experimental evidence for diverse archaeal organisms, and these findings allow for a comprehensive analysis of archaeal genetic organization. However, studies about regulatory mechanisms in this cellular domain are still limited. In this context, we identified a repertoire of 86 DNA-binding transcription factors (TFs) in the archaeon Pyrococcus furiosus DSM 3638, that are clustered into 32 evolutionary families. In structural terms, 45% of these proteins are composed of one structural domain, 41% have two domains, and 14% have three structural domains. The most abundant DNA-binding domain corresponds to the winged helix-turn-helix domain; with few alternative DNA-binding domains. We also identified seven regulons, which represent 13.5% (279 genes) of the total genes in this archaeon. These analyses increase our knowledge about gene regulation in P. furiosus DSM 3638 and provide additional clues for comprehensive modeling of transcriptional regulatory networks in the Archaea cellular domain.
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Affiliation(s)
- Antonia Denis
- Facultad de Medicina, Universidad Juárez Autónoma de Tabasco, C.P. 86100, Tabasco, Mexico.
| | - Mario Alberto Martínez-Núñez
- Facultad de Ciencias, Universidad Nacional Autónoma de México, Unidad Académica de Ciencias y Tecnología de la UNAM en Yucatán, Carretera Sierra Papacal-Chuburna Km. 5, C.P. 97302, Mérida, Yucatán, Mexico.
| | - Silvia Tenorio-Salgado
- Tecnológico Nacional de México, Instituto Tecnológico de Mérida, C.P. 97000, Mérida, Yucatán, Mexico.
| | - Ernesto Perez-Rueda
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Unidad Académica Yucatán, C.P. 97302, Mérida, Yucatán, Mexico.
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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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Sheppard C, Werner F. Structure and mechanisms of viral transcription factors in archaea. Extremophiles 2017; 21:829-838. [PMID: 28681113 PMCID: PMC5569661 DOI: 10.1007/s00792-017-0951-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 06/23/2017] [Indexed: 01/31/2023]
Abstract
Virus-encoded transcription factors have been pivotal in exploring the molecular mechanisms and regulation of gene expression in bacteria and eukaryotes since the birth of molecular biology, while our understanding of viral transcription in archaea is still in its infancy. Archaeal viruses do not encode their own RNA polymerases (RNAPs) and are consequently entirely dependent on their hosts for gene expression; this is fundamentally different from many bacteriophages and requires alternative regulatory strategies. Archaeal viruses wield a repertoire of proteins to expropriate the host transcription machinery to their own benefit. In this short review we summarise our current understanding of gene-specific and global mechanisms that viruses employ to chiefly downregulate host transcription and enable the efficient and temporal expression of the viral transcriptome. Most of the experimentally characterised archaeo-viral transcription regulators possess either ribbon-helix-helix or Zn-finger motifs that allow them to engage with the DNA in a sequence-specific manner, altering the expression of a specific subset of genes. Recently a novel type of regulator was reported that directly binds to the RNAP and shuts down transcription of both host and viral genes in a global fashion.
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Affiliation(s)
- Carol Sheppard
- Division of Biosciences, Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - Finn Werner
- Division of Biosciences, Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK.
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9
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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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10
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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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11
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Carbohydrate metabolism in Archaea: current insights into unusual enzymes and pathways and their regulation. Microbiol Mol Biol Rev 2014; 78:89-175. [PMID: 24600042 DOI: 10.1128/mmbr.00041-13] [Citation(s) in RCA: 200] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The metabolism of Archaea, the third domain of life, resembles in its complexity those of Bacteria and lower Eukarya. However, this metabolic complexity in Archaea is accompanied by the absence of many "classical" pathways, particularly in central carbohydrate metabolism. Instead, Archaea are characterized by the presence of unique, modified variants of classical pathways such as the Embden-Meyerhof-Parnas (EMP) pathway and the Entner-Doudoroff (ED) pathway. The pentose phosphate pathway is only partly present (if at all), and pentose degradation also significantly differs from that known for bacterial model organisms. These modifications are accompanied by the invention of "new," unusual enzymes which cause fundamental consequences for the underlying regulatory principles, and classical allosteric regulation sites well established in Bacteria and Eukarya are lost. The aim of this review is to present the current understanding of central carbohydrate metabolic pathways and their regulation in Archaea. In order to give an overview of their complexity, pathway modifications are discussed with respect to unusual archaeal biocatalysts, their structural and mechanistic characteristics, and their regulatory properties in comparison to their classic counterparts from Bacteria and Eukarya. Furthermore, an overview focusing on hexose metabolic, i.e., glycolytic as well as gluconeogenic, pathways identified in archaeal model organisms is given. Their energy gain is discussed, and new insights into different levels of regulation that have been observed so far, including the transcript and protein levels (e.g., gene regulation, known transcription regulators, and posttranslational modification via reversible protein phosphorylation), are presented.
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13
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Abstract
The ability of organisms to sense and respond to their environment is essential to their survival. This is no different for members of the third domain of life, the Archaea. Archaea are found in diverse and often extreme habitats. However, their ability to sense and respond to their environment at the level of gene expression has been understudied when compared to bacteria and eukaryotes. Over the last decade, the field has expanded, and a variety of unique and interesting regulatory schemes have been unraveled. In this review, the current state of knowledge of archaeal transcription regulation is explored.
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14
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Contursi P, Fusco S, Limauro D, Fiorentino G. Host and viral transcriptional regulators in Sulfolobus: an overview. Extremophiles 2013; 17:881-95. [PMID: 24085522 DOI: 10.1007/s00792-013-0586-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Accepted: 09/16/2013] [Indexed: 12/29/2022]
Abstract
The genus Sulfolobus includes microorganisms belonging to the domain Archaea, sub-kingdom Crenarchaeota, living in geographically distant acidic hot springs. Their adaptation to such particular habitats requires finely regulated mechanisms of gene expression, among which, those modulated by sequence-specific transcription factors (TFs) play a key role. In this review, we summarize the current knowledge on the repertoires of TFs found in Sulfolobus spp. and their viruses, focusing on the description of their DNA-binding domains and their structure-function relationship.
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Affiliation(s)
- Patrizia Contursi
- Dipartimento di Biologia, Università di Napoli Federico II, via Cinthia, Edificio 7, 80126, Napoli, Italy
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15
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Abstract
Biofilms are currently viewed as the most common form in which microorganisms exist in nature. Bacterial biofilms play important roles in disease and industrial applications, and they have been studied in great detail. Although it is well accepted that archaea are not only the extremists they were thought to be as they occupy nearly every habitat where also bacteria are found, it is surprising how little molecular details are known about archaeal biofilm formation. Therefore, we aim to highlight the available information and indicate open questions in this field.
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Affiliation(s)
- Alvaro Orell
- Molecular Biology of Archaea, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany;
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16
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Orell A, Peeters E, Vassen V, Jachlewski S, Schalles S, Siebers B, Albers SV. Lrs14 transcriptional regulators influence biofilm formation and cell motility of Crenarchaea. ISME JOURNAL 2013; 7:1886-98. [PMID: 23657363 DOI: 10.1038/ismej.2013.68] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2012] [Revised: 03/13/2013] [Accepted: 03/15/2013] [Indexed: 11/09/2022]
Abstract
Like bacteria, archaea predominately exist as biofilms in nature. However, the environmental cues and the molecular mechanisms driving archaeal biofilm development are not characterized. Here we provide data suggesting that the transcriptional regulators belonging to the Lrs14-like protein family constitute a key regulatory factor during Sulfolobus biofilm development. Among the six lrs14-like genes encoded by Sulfolobus acidocaldarius, the deletion of three led to markedly altered biofilm phenotypes. Although Δsaci1223 and Δsaci1242 deletion mutants were impaired in biofilm formation, the Δsaci0446 deletion strain exhibited a highly increased extracellular polymeric substance (EPS) production, leading to a robust biofilm structure. Moreover, although the expression of the adhesive pili (aap) genes was upregulated, the genes of the motility structure, the archaellum (fla), were downregulated rendering the Δsaci0446 strain non-motile. Gel shift assays confirmed that Saci0446 bound to the promoter regions of fla and aap thus controlling the expression of both cell surface structures. In addition, genetic epistasis analysis using Δsaci0446 as background strain identified a gene cluster involved in the EPS biosynthetic pathway of S. acidocaldarius. These results provide insights into both the molecular mechanisms that govern biofilm formation in Crenarchaea and the functionality of the Lrs14-like proteins, an archaea-specific class of transcriptional regulators.
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Affiliation(s)
- Alvaro Orell
- Molecular Biology of Archaea, Max Planck Institute for terrestrial Microbiology, Marburg, Germany
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Lassak K, Ghosh A, Albers SV. Diversity, assembly and regulation of archaeal type IV pili-like and non-type-IV pili-like surface structures. Res Microbiol 2012; 163:630-44. [PMID: 23146836 DOI: 10.1016/j.resmic.2012.10.024] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Accepted: 10/04/2012] [Indexed: 11/25/2022]
Abstract
Archaea have evolved fascinating surface structures allowing rapid adaptation to changing environments. The archaeal surface appendages display such diverse biological roles as motility, adhesion, biofilm formation, exchange of genetic material and species-specific interactions and, in turn, increase fitness of the cells. Intriguingly, despite sharing the same functions with their bacterial counterparts, the assembly mechanism of many archaeal surface structures is rather related to assembly of bacterial type IV pili. This review summarizes our state-of-the-art knowledge about unique structural and biochemical properties of archaeal surface appendages with a particular focus on archaeal type IV pili-like structures. The latter comprise not only widely distributed archaella (formerly known as archaeal flagella), but also different highly specialized archaeal pili, which are often restricted to certain species. Recent findings regarding assembly mechanisms, structural aspects and physiological roles of these type IV pili-like structures will be discussed in detail. Recently, first regulatory proteins involved in transition from both planktonic to sessile lifestyle and in assembly of archaella were identified. To conclude, we provide novel insights into regulatory mechanisms underlying the assembly of archaeal surface structures.
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Affiliation(s)
- Kerstin Lassak
- Max Planck Institute for Terrestrial Microbiology, Molecular Biology of Archaea, Karl-von-Frisch-Strasse 10, 35043 Marburg, Germany
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Deng W, Wang H, Xie J. Regulatory and pathogenesis roles of Mycobacterium Lrp/AsnC family transcriptional factors. J Cell Biochem 2012; 112:2655-62. [PMID: 21608015 DOI: 10.1002/jcb.23193] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Lrp/AsnC (leucine-responsive regulatory protein/asparagine synthase C products) family transcriptional regulators, widespread among bacteria and archaea, is also known as feast/famine regulatory protein (FFRPs). They regulate multiple cellular metabolisms globally (Lrp) or specifically (AsnC), such as amino acid metabolism, pili synthesis, DNA transactions during DNA repair and recombination, and also might be implicated in persistence. To better understanding of the pathogenesis of M. tuberculosis, based on our lab's work on this transcriptional factor family, these progresses are summarized, with special focus on that of Mycobacterium via comparative genomics.
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Affiliation(s)
- Wanyan Deng
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three GorgesArea, School of Life Sciences, Southwest University, Chongqing 400715, China
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Abstract
Archaea represent an important and vast domain of life. This cellular domain includes a large diversity of organisms characterized as prokaryotes with basal transcriptional machinery similar to eukarya. In this work we explore the most recent findings concerning the transcriptional regulatory organization in archaeal genomes since the perspective of the DNA-binding transcription factors (TFs), such as the high proportion of archaeal TFs homologous to bacteria, the apparent deficit of TFs, only comparable to the proportion of TFs in parasites or intracellular pathogenic bacteria, suggesting a deficit in this class of proteins. We discuss an appealing hypothesis to explain the apparent deficit of TFs in archaea, based on their characteristics, such as their small length sizes. The hypothesis suggests that a large fraction of these small-sized TFs could supply the deficit of TFs in archaea, by forming different combinations of monomers similar to that observed in eukaryotic transcriptional machinery, where a wide diversity of protein-protein interactions could act as mediators of regulatory feedback, indicating a chimera of bacterial and eukaryotic TFs' functionality. Finally, we discuss how global experiments can help to understand in a global context the role of TFs in these organisms.
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Cordone A, Lucchini S, Felice M, Ricca E. Direct and indirect control of Lrp on LEE pathogenicity genes of Citrobacter rodentium. FEMS Microbiol Lett 2011; 325:64-70. [DOI: 10.1111/j.1574-6968.2011.02411.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2011] [Revised: 07/11/2011] [Accepted: 09/05/2011] [Indexed: 11/29/2022] Open
Affiliation(s)
- Angelina Cordone
- Dipartimento di Biologia Strutturale e Funzionale; Università Federico II; Napoli; Italy
| | | | - Maurilio Felice
- Dipartimento di Biologia Strutturale e Funzionale; Università Federico II; Napoli; Italy
| | - Ezio Ricca
- Dipartimento di Biologia Strutturale e Funzionale; Università Federico II; Napoli; Italy
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Koerdt A, Orell A, Pham TK, Mukherjee J, Wlodkowski A, Karunakaran E, Biggs CA, Wright PC, Albers SV. Macromolecular fingerprinting of sulfolobus species in biofilm: a transcriptomic and proteomic approach combined with spectroscopic analysis. J Proteome Res 2011; 10:4105-19. [PMID: 21761944 PMCID: PMC3166137 DOI: 10.1021/pr2003006] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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Microorganisms in nature often live in surface-associated sessile communities, encased in a self-produced matrix, referred to as biofilms. Biofilms have been well studied in bacteria but in a limited way for archaea. We have recently characterized biofilm formation in three closely related hyperthermophilic crenarchaeotes: Sulfolobus acidocaldarius, S. solfataricus, and S. tokodaii. These strains form different communities ranging from simple carpet structures in S. solfataricus to high density tower-like structures in S. acidocaldarius under static condition. Here, we combine spectroscopic, proteomic, and transcriptomic analyses to describe physiological and regulatory features associated with biofilms. Spectroscopic analysis reveals that in comparison to planktonic life-style, biofilm life-style has distinctive influence on the physiology of each Sulfolobus spp. Proteomic and transcriptomic data show that biofilm-forming life-style is strain specific (eg ca. 15% of the S. acidocaldarius genes were differently expressed, S. solfataricus and S. tokodaii had ∼3.4 and ∼1%, respectively). The -omic data showed that regulated ORFs were widely distributed in basic cellular functions, including surface modifications. Several regulated genes are common to biofilm-forming cells in all three species. One of the most striking common response genes include putative Lrs14-like transcriptional regulators, indicating their possible roles as a key regulatory factor in biofilm development. S. acidocaldarius, S. solfataricus, and S. tokodaii strains were grown independently as biofilms. Comparison between planktonic and biofilm cell popupations of all three strains was performed by spectroscopic analysis (FTIR and XPS), iTRAQ proteomics, and RNA microarrays. To highlight common features in biofilm formation among the Sulfolobus strains, the data is presented as a comparative analysis. One of the most striking common response genes include putative Lrs14-like transcriptional regulators, suggesting their roles as key regulatory factor in biofilm development.
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Affiliation(s)
- Andrea Koerdt
- Molecular Biology of Archaea, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse, 35043 Marburg, Germany
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22
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Payankaulam S, Li LM, Arnosti DN. Transcriptional repression: conserved and evolved features. Curr Biol 2011; 20:R764-71. [PMID: 20833321 DOI: 10.1016/j.cub.2010.06.037] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The regulation of gene expression by transcriptional repression is an ancient and conserved mechanism that manifests itself in diverse ways. Here we summarize conserved pathways for transcriptional repression prevalent throughout all forms of life, as well as indirect mechanisms that appear to have originated in eukaryotes, consistent with the unique chromatin environment of eukaryotic genes. The direct interactions between transcriptional repressors and the core transcriptional machinery in bacteria and archaea are sufficient to generate a sophisticated suite of mechanisms that provide flexible control. These direct interactions contrast with the activity of corepressors, which provide an additional regulatory control in eukaryotes. Their modulation of chromatin structure represents an indirect pathway to downregulate transcription, and their diversity and modulation provide additional complexity suited to the requirements of elaborate eukaryotic repression patterns. New findings indicate that corepressors are not necessarily restricted to generating a single stereotypic output, but can rather exhibit diverse functional responses depending on the context in which they are recruited, providing a hitherto unsuspected additional source of diversity in transcriptional control. Mechanisms within eukaryotes appear to be highly conserved, with novel aspects chiefly represented by addition of lineage-specific corepressor scaffolds that provide additional opportunities for recruiting the same core machinery.
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Affiliation(s)
- Sandhya Payankaulam
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48910, USA
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23
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Schwaiger R, Schwarz C, Furtwängler K, Tarasov V, Wende A, Oesterhelt D. Transcriptional control by two leucine-responsive regulatory proteins in Halobacterium salinarum R1. BMC Mol Biol 2010; 11:40. [PMID: 20509863 PMCID: PMC2894021 DOI: 10.1186/1471-2199-11-40] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2010] [Accepted: 05/28/2010] [Indexed: 12/26/2022] Open
Abstract
Background Archaea combine bacterial-as well as eukaryotic-like features to regulate cellular processes. Halobacterium salinarum R1 encodes eight leucine-responsive regulatory protein (Lrp)-homologues. The function of two of them, Irp (OE3923F) and lrpA1 (OE2621R), were analyzed by gene deletion and overexpression, including genome scale impacts using microarrays. Results It was shown that Lrp affects the transcription of multiple target genes, including those encoding enzymes involved in amino acid synthesis, central metabolism, transport processes and other regulators of transcription. In contrast, LrpA1 regulates transcription in a more specific manner. The aspB3 gene, coding for an aspartate transaminase, was repressed by LrpA1 in the presence of L-aspartate. Analytical DNA-affinity chromatography was adapted to high salt, and demonstrated binding of LrpA1 to its own promoter, as well as L-aspartate dependent binding to the aspB3 promoter. Conclusion The gene expression profiles of two archaeal Lrp-homologues report in detail their role in H. salinarum R1. LrpA1 and Lrp show similar functions to those already described in bacteria, but in addition they play a key role in regulatory networks, such as controlling the transcription of other regulators. In a more detailed analysis ligand dependent binding of LrpA1 was demonstrated to its target gene aspB3.
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Affiliation(s)
- Rita Schwaiger
- Max Planck Institute of Biochemistry, Department of Membrane Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
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Pérez-Rueda E, Janga SC. Identification and genomic analysis of transcription factors in archaeal genomes exemplifies their functional architecture and evolutionary origin. Mol Biol Evol 2010; 27:1449-59. [PMID: 20123795 PMCID: PMC2872624 DOI: 10.1093/molbev/msq033] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Archaea, which represent a large fraction of the phylogenetic diversity of organisms, are prokaryotes with eukaryote-like basal transcriptional machinery. This organization makes the study of their DNA-binding transcription factors (TFs) and their transcriptional regulatory networks particularly interesting. In addition, there are limited experimental data regarding their TFs. In this work, 3,918 TFs were identified and exhaustively analyzed in 52 archaeal genomes. TFs represented less than 5% of the gene products in all the studied species comparable with the number of TFs identified in parasites or intracellular pathogenic bacteria, suggesting a deficit in this class of proteins. A total of 75 families were identified, of which HTH_3, AsnC, TrmB, and ArsR families were universally and abundantly identified in all the archaeal genomes. We found that archaeal TFs are significantly small compared with other protein-coding genes in archaea as well as bacterial TFs, suggesting that a large fraction of these small-sized TFs could supply the probable deficit of TFs in archaea, by possibly forming different combinations of monomers similar to that observed in eukaryotic transcriptional machinery. Our results show that although the DNA-binding domains of archaeal TFs are similar to bacteria, there is an underrepresentation of ligand-binding domains in smaller TFs, which suggests that protein–protein interactions may act as mediators of regulatory feedback, indicating a chimera of bacterial and eukaryotic TFs’ functionality. The analysis presented here contributes to the understanding of the details of transcriptional apparatus in archaea and provides a framework for the analysis of regulatory networks in these organisms.
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Affiliation(s)
- Ernesto Pérez-Rueda
- Departamento de Ingeniería Celular y Biocatálisis, IBT-UNAM, AP 565-A, Cuernavaca, Morelos, México.
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Peeters E, Albers SV, Vassart A, Driessen AJM, Charlier D. Ss-LrpB, a transcriptional regulator fromSulfolobus solfataricus, regulates a gene cluster with a pyruvate ferredoxin oxidoreductase-encoding operon and permease genes. Mol Microbiol 2009; 71:972-88. [DOI: 10.1111/j.1365-2958.2008.06578.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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26
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Kumarevel T, Nakano N, Ponnuraj K, Gopinath SCB, Sakamoto K, Shinkai A, Kumar PKR, Yokoyama S. Crystal structure of glutamine receptor protein from Sulfolobus tokodaii strain 7 in complex with its effector L-glutamine: implications of effector binding in molecular association and DNA binding. Nucleic Acids Res 2008; 36:4808-20. [PMID: 18653535 PMCID: PMC2504300 DOI: 10.1093/nar/gkn456] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2008] [Revised: 06/30/2008] [Accepted: 07/02/2008] [Indexed: 11/15/2022] Open
Abstract
Genome analyses have revealed that members of the Lrp/AsnC family of transcriptional regulators are widely distributed among prokaryotes, including both bacteria and archaea. These regulatory proteins are involved in cellular metabolism in both global and specific manners, depending on the availability of the exogenous amino acid effectors. Here we report the first crystal structure of glutamine receptor protein (Grp) from Sulfolobus tokodaii strain 7, in the ligand-free and glutamine-bound (Grp-Gln) forms. Although the overall structures of both molecules are similar, a significant conformational change was observed at the ligand [L-glutamine (Gln)] binding site in the effector domain, which may be essential for further stabilization of the octameric structure, and in turn for facilitating DNA binding. In addition, we predicted promoter for the grp gene, and these analyses suggested the importance of cooperative binding to the protein. To gain insights into the ligand-induced conformational changes, we mutated all of the ligand-binding residues in Grp, and revealed the importance of Gln binding by biochemical and structural analyses. Further structural analyses showed that Y77 is crucial for ligand binding, and that the residues T132 and T134, which are highly conserved among the Lrp family of proteins, fluctuates between the active and inactive conformations, thus affecting protein oligomerization for DNA binding.
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Affiliation(s)
- Thirumananseri Kumarevel
- RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan, Center of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600 025, Tamil Nadu, India, Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Tsukuba, Ibaraki 305-8566, Systems and Structural Biology Center, Yokohama Institute, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045 and Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Noboru Nakano
- RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan, Center of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600 025, Tamil Nadu, India, Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Tsukuba, Ibaraki 305-8566, Systems and Structural Biology Center, Yokohama Institute, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045 and Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Karthe Ponnuraj
- RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan, Center of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600 025, Tamil Nadu, India, Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Tsukuba, Ibaraki 305-8566, Systems and Structural Biology Center, Yokohama Institute, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045 and Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Subash C. B. Gopinath
- RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan, Center of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600 025, Tamil Nadu, India, Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Tsukuba, Ibaraki 305-8566, Systems and Structural Biology Center, Yokohama Institute, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045 and Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Keiko Sakamoto
- RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan, Center of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600 025, Tamil Nadu, India, Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Tsukuba, Ibaraki 305-8566, Systems and Structural Biology Center, Yokohama Institute, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045 and Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Akeo Shinkai
- RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan, Center of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600 025, Tamil Nadu, India, Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Tsukuba, Ibaraki 305-8566, Systems and Structural Biology Center, Yokohama Institute, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045 and Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Penmetcha K. R. Kumar
- RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan, Center of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600 025, Tamil Nadu, India, Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Tsukuba, Ibaraki 305-8566, Systems and Structural Biology Center, Yokohama Institute, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045 and Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Shigeyuki Yokoyama
- RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan, Center of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600 025, Tamil Nadu, India, Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Tsukuba, Ibaraki 305-8566, Systems and Structural Biology Center, Yokohama Institute, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045 and Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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Kawashima T, Aramaki H, Oyamada T, Makino K, Yamada M, Okamura H, Yokoyama K, Ishijima SA, Suzuki M. Transcription Regulation by Feast/Famine Regulatory Proteins, FFRPs, in Archaea and Eubacteria. Biol Pharm Bull 2008; 31:173-86. [DOI: 10.1248/bpb.31.173] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Tsuyoshi Kawashima
- National Institute of Advanced Industrial Science and Technology
- Japan Science and Technology Agency, Core Research for Evolutionary Science and Technology
- Yokohama College of Pharmacy, Laboratory of Molecular Biology
| | - Hironori Aramaki
- Department of Molecular Biology, Daiichi College of Pharmaceutical Sciences
| | - Tomoya Oyamada
- Department of Applied Chemistry, National Defense Academy
| | - Kozo Makino
- Department of Applied Chemistry, National Defense Academy
| | - Mitsugu Yamada
- National Institute of Advanced Industrial Science and Technology
- Japan Science and Technology Agency, Core Research for Evolutionary Science and Technology
| | - Hideyasu Okamura
- National Institute of Advanced Industrial Science and Technology
- Japan Science and Technology Agency, Core Research for Evolutionary Science and Technology
| | - Katsushi Yokoyama
- National Institute of Advanced Industrial Science and Technology
- Japan Science and Technology Agency, Core Research for Evolutionary Science and Technology
| | - Sanae Arakawa Ishijima
- National Institute of Advanced Industrial Science and Technology
- Japan Science and Technology Agency, Core Research for Evolutionary Science and Technology
| | - Masashi Suzuki
- National Institute of Advanced Industrial Science and Technology
- Japan Science and Technology Agency, Core Research for Evolutionary Science and Technology
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28
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Abella M, Rodríguez S, Paytubi S, Campoy S, White MF, Barbé J. The Sulfolobus solfataricus radA paralogue sso0777 is DNA damage inducible and positively regulated by the Sta1 protein. Nucleic Acids Res 2007; 35:6788-97. [PMID: 17921500 PMCID: PMC2175319 DOI: 10.1093/nar/gkm782] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Little is known about the regulation of the DNA damage-mediated gene expression in archaea. Here we report that the addition of actinomycin D to Sulfolobus solfataricus cultures triggers the expression of the radA paralogue sso0777. Furthermore, a specific retarded band is observed when electrophoretic mobility shift assays (EMSAs) with crude S. solfataricus cell extracts and the sso0777 promoter were carried out. The protein that binds to this promoter was isolated and identified as Sta1. Footprinting experiments have shown that the Sta1 DNA-binding site is included in the ATTTTTTATTTTCACATGTAAGATGTTTATT sequence, which is located upstream the putative TTG translation starting codon of the sso0777 gene. Additionally, gel electrophoretic mobility retardation experiments using mutant sso0777 promoter derivatives show the presence of three essential motifs (TTATT, CANGNA and TTATT) that are absolutely required for Sta1 DNA binding. Finally, in vitro transcription experiments confirm that Sta1 functions as an activator for sso0777 gene expression being the first identified archaeal regulatory protein associated with the DNA damage-mediated induction of gene expression.
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Affiliation(s)
- Marc Abella
- Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona 08193 Bellaterra, Spain
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29
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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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30
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Kessler A, Sezonov G, Guijarro JI, Desnoues N, Rose T, Delepierre M, Bell SD, Prangishvili D. A novel archaeal regulatory protein, Sta1, activates transcription from viral promoters. Nucleic Acids Res 2006; 34:4837-45. [PMID: 16973899 PMCID: PMC1635249 DOI: 10.1093/nar/gkl502] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
While studying gene expression of the rudivirus SIRV1 in cells of its host, the hyperthermophilic crenarchaeon Sulfolobus, a novel archaeal transcriptional regulator was isolated. The 14 kDa protein, termed Sulfolobus transcription activator 1, Sta1, is encoded on the host chromosome. Its activating effect on transcription initiation from viral promoters was demonstrated in in vitro transcription experiments using a reconstituted host system containing the RNA polymerase, TATA-binding protein (TBP) and transcription factor B (TFB). Most pronounced activation was observed at low concentrations of either of the two transcription factors, TBP or TFB. Sta1 was able to bind viral promoters independently of any component of the host pre-initiation complex. Two binding sites were revealed by footprinting, one located in the core promoter region and the second ∼30 bp upstream of it. Comparative modeling, NMR and circular dichroism of Sta1 indicated that the protein contained a winged helix–turn–helix motif, most probably involved in DNA binding. This strategy of the archaeal virus to co-opt a host cell regulator to promote transcription of its genes resembles eukaryal virus–host relationships.
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Affiliation(s)
- Alexandra Kessler
- Unité de Biologie Moléculaire du Gène chez les Extrêmophiles, Institut Pasteur25-28 rue du Dr Roux, 75724 Paris Cedex 15, France
- Department of Microbiology, University of RegensburgUniversitäts strasse, 31, D-93053 Regensburg, Germany
| | - Guennadi Sezonov
- Unité de Biologie Moléculaire du Gène chez les Extrêmophiles, Institut Pasteur25-28 rue du Dr Roux, 75724 Paris Cedex 15, France
| | - J. Iñaki Guijarro
- Unité de RMN des Biomolécules (CNRS URA 2185), Institut Pasteur25-28 rue du Dr Roux, 75724 Paris Cedex 15, France
| | - Nicole Desnoues
- Unité de Biologie Moléculaire du Gène chez les Extrêmophiles, Institut Pasteur25-28 rue du Dr Roux, 75724 Paris Cedex 15, France
| | - Thierry Rose
- Unité d'Immunogénétique Cellulaire, Institut Pasteur25-28 rue du Dr Roux, 75724 Paris Cedex 15, France
| | - Muriel Delepierre
- Unité de RMN des Biomolécules (CNRS URA 2185), Institut Pasteur25-28 rue du Dr Roux, 75724 Paris Cedex 15, France
| | - Stephen D. Bell
- MRC Cancer Cell Unit Hutchison/MRC Research Centre, Hills RoadCambridge CB2 2XZ, UK
| | - David Prangishvili
- Unité de Biologie Moléculaire du Gène chez les Extrêmophiles, Institut Pasteur25-28 rue du Dr Roux, 75724 Paris Cedex 15, France
- To whom correspondence should be addressed. Tel: +33 144 38 9119; Fax: +33 145 68 8834;
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31
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Yokoyama K, Ishijima SA, Clowney L, Koike H, Aramaki H, Tanaka C, Makino K, Suzuki M. Feast/famine regulatory proteins (FFRPs): Escherichia coli Lrp, AsnC and related archaeal transcription factors. FEMS Microbiol Rev 2006; 30:89-108. [PMID: 16438681 DOI: 10.1111/j.1574-6976.2005.00005.x] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Feast/famine regulatory proteins comprise a diverse family of transcription factors, which have been referred to in various individual identifications, including Escherichia coli leucine-responsive regulatory protein and asparagine synthase C gene product. A full length feast/famine regulatory protein consists of the N-terminal DNA-binding domain and the C-domain, which is involved in dimerization and further assembly, thereby producing, for example, a disc or a chromatin-like cylinder. Various ligands of the size of amino acids bind at the interface between feast/famine regulatory protein dimers, thereby altering their assembly forms. Also, the combination of feast/famine regulatory protein subunits forming the same assembly is altered. In this way, a small number of feast/famine regulatory proteins are able to regulate a large number of genes in response to various environmental changes. Because feast/famine regulatory proteins are shared by archaea and eubacteria, the genome-wide regulation by feast/famine regulatory proteins is traceable back to their common ancestor, being the prototype of highly differentiated transcription regulatory mechanisms found in organisms nowadays.
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Affiliation(s)
- Katsushi Yokoyama
- National Institute of Advanced Industrial Science and Technology, AIST Tsukuba Center, Tsukuba, Japan
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32
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Thaw P, Sedelnikova SE, Muranova T, Wiese S, Ayora S, Alonso JC, Brinkman AB, Akerboom J, van der Oost J, Rafferty JB. Structural insight into gene transcriptional regulation and effector binding by the Lrp/AsnC family. Nucleic Acids Res 2006; 34:1439-49. [PMID: 16528101 PMCID: PMC1401507 DOI: 10.1093/nar/gkl009] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2005] [Revised: 02/10/2006] [Accepted: 02/10/2006] [Indexed: 12/03/2022] Open
Abstract
The Lrp/AsnC family of transcriptional regulatory proteins is found in both archaea and bacteria. Members of the family influence cellular metabolism in both a global (Lrp) and specific (AsnC) manner, often in response to exogenous amino acid effectors. In the present study we have determined both the first bacterial and the highest resolution structures for members of the family. Escherichia coli AsnC is a specific gene regulator whose activity is triggered by asparagine binding. Bacillus subtilis LrpC is a global regulator involved in chromosome condensation. Our AsnC-asparagine structure is the first for a regulator-effector complex and is revealed as an octameric disc. Key ligand recognition residues are identified together with a route for ligand access. The LrpC structure reveals a stable octamer supportive of a topological role in dynamic DNA packaging. The structures yield significant clues to the functionality of Lrp/AsnC-type regulators with respect to ligand binding and oligomerization states as well as to their role in specific and global DNA regulation.
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Affiliation(s)
- Paul Thaw
- Department of Molecular Biology and Biotechnology, Krebs Institute, University of SheffieldWestern Bank, Sheffield S10 2TN, UK
- Departamento de Biologia Molecular, Universidad Autonoma de MadridCantoblanco, 28049 Madrid, Spain
- Departamento de Biotecnologia Microbiana, Centro Nacional de Biotecnologia, CSIC, Campus Universidad Autonoma de MadridCantoblanco, 28049 Madrid, Spain
- Department of Molecular Biology, NCMLS M850/3.79Geert Grooteplein 30, 6525 GA, Nijmegen, The Netherlands
- Laboratory of Microbiology, Wageningen UniversityHesselink van Suchtelenweg 4, 6307 CT Wageningen, The Netherlands
| | - Svetlana E. Sedelnikova
- Department of Molecular Biology and Biotechnology, Krebs Institute, University of SheffieldWestern Bank, Sheffield S10 2TN, UK
- Departamento de Biologia Molecular, Universidad Autonoma de MadridCantoblanco, 28049 Madrid, Spain
- Departamento de Biotecnologia Microbiana, Centro Nacional de Biotecnologia, CSIC, Campus Universidad Autonoma de MadridCantoblanco, 28049 Madrid, Spain
- Department of Molecular Biology, NCMLS M850/3.79Geert Grooteplein 30, 6525 GA, Nijmegen, The Netherlands
- Laboratory of Microbiology, Wageningen UniversityHesselink van Suchtelenweg 4, 6307 CT Wageningen, The Netherlands
| | - Tatyana Muranova
- Department of Molecular Biology and Biotechnology, Krebs Institute, University of SheffieldWestern Bank, Sheffield S10 2TN, UK
- Departamento de Biologia Molecular, Universidad Autonoma de MadridCantoblanco, 28049 Madrid, Spain
- Departamento de Biotecnologia Microbiana, Centro Nacional de Biotecnologia, CSIC, Campus Universidad Autonoma de MadridCantoblanco, 28049 Madrid, Spain
- Department of Molecular Biology, NCMLS M850/3.79Geert Grooteplein 30, 6525 GA, Nijmegen, The Netherlands
- Laboratory of Microbiology, Wageningen UniversityHesselink van Suchtelenweg 4, 6307 CT Wageningen, The Netherlands
| | - Sebastian Wiese
- Department of Molecular Biology and Biotechnology, Krebs Institute, University of SheffieldWestern Bank, Sheffield S10 2TN, UK
- Departamento de Biologia Molecular, Universidad Autonoma de MadridCantoblanco, 28049 Madrid, Spain
- Departamento de Biotecnologia Microbiana, Centro Nacional de Biotecnologia, CSIC, Campus Universidad Autonoma de MadridCantoblanco, 28049 Madrid, Spain
- Department of Molecular Biology, NCMLS M850/3.79Geert Grooteplein 30, 6525 GA, Nijmegen, The Netherlands
- Laboratory of Microbiology, Wageningen UniversityHesselink van Suchtelenweg 4, 6307 CT Wageningen, The Netherlands
| | - Sylvia Ayora
- Departamento de Biologia Molecular, Universidad Autonoma de MadridCantoblanco, 28049 Madrid, Spain
- Departamento de Biotecnologia Microbiana, Centro Nacional de Biotecnologia, CSIC, Campus Universidad Autonoma de MadridCantoblanco, 28049 Madrid, Spain
| | - Juan C. Alonso
- Departamento de Biotecnologia Microbiana, Centro Nacional de Biotecnologia, CSIC, Campus Universidad Autonoma de MadridCantoblanco, 28049 Madrid, Spain
| | - Arie B. Brinkman
- Department of Molecular Biology, NCMLS M850/3.79Geert Grooteplein 30, 6525 GA, Nijmegen, The Netherlands
| | - Jasper Akerboom
- Laboratory of Microbiology, Wageningen UniversityHesselink van Suchtelenweg 4, 6307 CT Wageningen, The Netherlands
| | - John van der Oost
- Laboratory of Microbiology, Wageningen UniversityHesselink van Suchtelenweg 4, 6307 CT Wageningen, The Netherlands
| | - John B. Rafferty
- To whom correspondence should be addressed. Tel: +44 (114) 222 2809; Fax: +44 (114) 222 2800;
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Peeters E, Willaert R, Maes D, Charlier D. Ss-LrpB from Sulfolobus solfataricus condenses about 100 base pairs of its own operator DNA into globular nucleoprotein complexes. J Biol Chem 2006; 281:11721-8. [PMID: 16522627 DOI: 10.1074/jbc.m600383200] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Ss-LrpB from the hyperthermoacidophilic crenarchaeote Sulfolobus solfataricus P2 is a member of the Lrp-like family of Bacterial/Archaeal transcription regulators that binds its own control region at three regularly spaced and partially conserved 15-bp-long imperfect palindromes. We have used atomic force microscopy to analyze the architecture of Ss-LrpB.DNA complexes with a different stoichiometry formed with the wild type operator and with an operator mutant. Binding of dimeric Ss-LrpB to all three target sites is accompanied by the formation of globular complexes, in which the protein induces strong DNA deformations. Furthermore, DNA contour length foreshortening of these complexes indicates DNA wrapping, with about 100 bp being condensed. The average bending angle is 260 degrees . The establishment of protein-protein contacts between Ss-LrpB dimers in these globular complexes will contribute to the cooperativity of the binding. The profound remodeling of the control region is expected to have a strong impact on gene expression and might constitute the key element in the autoregulatory process.
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Affiliation(s)
- Eveline Peeters
- Erfelijkheidsleer en Microbiologie, Vrije Universiteit Brussel (VUB), Pleinlaan 2, B-1050 Brussels, Belgium
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34
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Cordone A, Mauriello EMF, Pickard DJ, Dougan G, De Felice M, Ricca E. The lrp gene and its role in type I fimbriation in Citrobacter rodentium. J Bacteriol 2005; 187:7009-17. [PMID: 16199571 PMCID: PMC1251604 DOI: 10.1128/jb.187.20.7009-7017.2005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Citrobacter rodentium is a murine pathogen that is now widely used as an in vivo model for gastrointestinal infections due to its similarities with human enteropathogens, such as the possession of a locus for enterocyte effacement (the LEE island). We studied the lrp gene of C. rodentium and found that it encodes a product highly similar to members of the Lrp (leucine-responsive regulatory protein) family of transcriptional regulators, able to recognize leucine as an effector and to repress the expression of its own structural gene. In enterobacteria, Lrp is a global regulator of gene expression, as it controls a large variety of genes, including those coding for cell appendages and other potential virulence factors. Based on the well-established role of Lrp on the expression of pilus genes in Escherichia coli, we also studied the role of Lrp in controlling the formation of the type I pilus in C. rodentium. Type I pili, produced by the fim system, are virulence factors of uropathogens, involved in mediating bacterial adhesion to bladder epithelial cells. Yeast agglutination assays showed that Lrp is needed for type I pilus formation and real-time PCR experiments indicated that Lrp has a strong leucine-mediated effect on the expression of the fimAICDFGH operon. Mutant studies indicated that this positive action is exerted mainly through a positive control of Lrp on the phase variation mechanism that regulates fimAICDFGH expression. A quantitative analysis of its expression suggested that this operon may also be negatively regulated at the level of transcription.
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Affiliation(s)
- Angela Cordone
- Dipartimento di Biologia Strutturale e Funzionale, Università Federico II, via Cinthia, Complesso Monte S. Angelo, 80126, Naples, Italy
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Xie Y, Reeve JN. Regulation of tryptophan operon expression in the archaeon Methanothermobacter thermautotrophicus. J Bacteriol 2005; 187:6419-29. [PMID: 16159776 PMCID: PMC1236654 DOI: 10.1128/jb.187.18.6419-6429.2005] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2005] [Accepted: 07/07/2005] [Indexed: 11/20/2022] Open
Abstract
Conserved trp genes encode enzymes that catalyze tryptophan biosynthesis in all three biological domains, and studies of their expression in Bacteria and eukaryotes have revealed a variety of different regulatory mechanisms. The results reported here provide the first detailed description of an archaeal trp gene regulatory system. We have established that the trpEGCFBAD operon in Methanothermobacter thermautotrophicus is transcribed divergently from a gene (designated trpY) that encodes a tryptophan-sensitive transcription regulator. TrpY binds to TRP box sequences (consensus, TGTACA) located in the overlapping promoter regions between trpY and trpE, inhibiting trpY transcription in the absence of tryptophan and both trpY and trpEGCFBAD transcription in the presence of tryptophan. TrpY apparently inhibits trpY transcription by blocking RNA polymerase access to the site of trpY transcription initiation and represses trpEGCFBAD transcription by preventing TATA box binding protein (TBP) binding to the TATA box sequence. Given that residue 2 (W2) is the only tryptophan in TrpY and in TrpY homologues in other Euryarchaea and that there is only one tryptophan codon in the entire trpEGCFBAD operon (trpB encodes W175), expression of the trp operon may also be regulated in vivo by the supply of charged tRNA(Trp) available to translate the second codon of the trpY mRNA.
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Affiliation(s)
- Yunwei Xie
- Department of Microbiology, Ohio State University, Columbus, Ohio 43210-1292, USA
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36
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Bell SD. Archaeal transcriptional regulation – variation on a bacterial theme? Trends Microbiol 2005; 13:262-5. [PMID: 15936657 DOI: 10.1016/j.tim.2005.03.015] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2005] [Revised: 03/17/2005] [Accepted: 03/31/2005] [Indexed: 10/25/2022]
Abstract
There is now an increasing body of data available on the DNA-binding properties of several putative transcriptional regulators in the Archaeal domain of life. The evidence points to simple models of promoter occlusion or facilitated recruitment of basal machinery for repressors and activators, respectively. However, little is known about the co-factor requirements, in vivo mechanisms and targets of many of these regulators. It is anticipated that the application of post-genomic technologies will begin to shed light on this fascinating area.
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Affiliation(s)
- Stephen D Bell
- MRC Cancer Cell Unit, Hutchison MRC Research Centre, Hills Road, Cambridge, CB2 2XZ, UK.
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37
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Peeters E, Thia-Toong TL, Gigot D, Maes D, Charlier D. Ss-LrpB, a novel Lrp-like regulator of Sulfolobus solfataricus P2, binds cooperatively to three conserved targets in its own control region. Mol Microbiol 2005; 54:321-36. [PMID: 15469506 DOI: 10.1111/j.1365-2958.2004.04274.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Ss-LrpB, a novel Lrp-like DNA-binding protein from the hyperthermophilic crenarchaeon Sulfolobus solfataricus, was shown to bind cooperatively to three regularly spaced targets in its own control region, with as consensus the 15 bp palindrome 5'-TTGYAW WWWWTRCAA-3'. Binding to the border sites occurred with high affinity; the target in the middle proved to be a low affinity site which is stably bound only when both flanking sites are occupied. Ss-LrpB contacts two major groove segments and the intervening minor groove of each site, all aligned on one face of the helix. The operator shows intrinsic bending and is increasingly deformed upon binding of Ss-LrpB to one, two and three targets. Complex formation relies therefore on DNA conformability, protein-DNA and protein-protein contacts. Mobility-shift assays and in gel footprinting indicate that Ss-LrpB and the transcription factors TATA-box binding protein (TBP) and transcription factor B (TFB) can bind simultaneously to the control region. Based on these findings we present a model for the construction of the higher order nucleoprotein complexes and a hypothesis for the autoregulatory process. The latter is based on the concentration-dependent formation of distinct complexes exhibiting different stoichiometries and conformations, which could positively and negatively affect promoter activity.
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Affiliation(s)
- Eveline Peeters
- Erfelijkheidsleer en Microbiologie, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
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38
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Pérez-Rueda E, Collado-Vides J, Segovia L. Phylogenetic distribution of DNA-binding transcription factors in bacteria and archaea. Comput Biol Chem 2004; 28:341-50. [PMID: 15556475 DOI: 10.1016/j.compbiolchem.2004.09.004] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2004] [Revised: 09/13/2004] [Accepted: 09/15/2004] [Indexed: 11/21/2022]
Abstract
We have addressed the distribution and abundance of 75 transcription factor (TF) families in complete genomes from 90 different bacterial and archaeal species. We found that the proportion of TFs increases with genome size. The deficit of TFs in some genomes might be compensated by the presence of proteins organizing and compacting DNA, such as histone-like proteins. Nine families are represented in all the bacteria and archaea we analyzed, whereas 17 families are specific to bacteria, providing evidence for regulon specialization at an early stage of evolution between the bacterial and archeal lineages. Ten of the 17 families identified in bacteria belong exclusively to the proteobacteria defining a specific signature for this taxonomical group. In bacteria, 10 families are lost mostly in intracellular pathogens and endosymbionts, while 9 families seem to have been horizontally transferred to archaea. The winged helix-turn-helix (HTH) is by far the most abundant structure (motif) in prokaryotes, and might have been the earliest HTH motif to appear as shown by its distribution and abundance in both bacterial and archaeal cellular domains. Horizontal gene transfer and lineage-specific gene losses suggest a progressive elimination of TFs in the course of archaeal and bacterial evolution. This analysis provides a framework for discussing the selective forces directing the evolution of the transcriptional machinery in prokaryotes.
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Affiliation(s)
- Ernesto Pérez-Rueda
- Facultad de Ciencias, UAEM, Av. Universidad 1001, CP. 62210, Col. Chamilpa, Cuernavaca, Morelos, México.
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39
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Robinson NP, Dionne I, Lundgren M, Marsh VL, Bernander R, Bell SD. Identification of two origins of replication in the single chromosome of the archaeon Sulfolobus solfataricus. Cell 2004; 116:25-38. [PMID: 14718164 DOI: 10.1016/s0092-8674(03)01034-1] [Citation(s) in RCA: 220] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Eukaryotic chromosomes possess multiple origins of replication, whereas bacterial chromosomes are replicated from a single origin. The archaeon Pyrococcus abyssi also appears to have a single origin, suggesting a common rule for prokaryotes. However, in the current work, we describe the identification of two active origins of replication in the single chromosome of the hyperthermophilic archaeon Sulfolobus solfataricus. Further, we identify conserved sequence motifs within the origins that are recognized by a family of three Sulfolobus proteins that are homologous to the eukaryotic initiator proteins Orc1 and Cdc6. We demonstrate that the two origins are recognized by distinct subsets of these Orc1/Cdc6 homologs. These data, in conjunction with an analysis of the levels of the three Orc1/Cdc6 proteins in different growth phases and cell cycle stages, lead us to propose a model for the roles for these proteins in modulating origin activity.
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Affiliation(s)
- Nicholas P Robinson
- Medical Research Council Cancer Cell Unit, Hutchison MRC Research Centre, Hills Road, Cambridge CB2 2XZ, United Kingdom
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40
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Salerno V, Napoli A, White MF, Rossi M, Ciaramella M. Transcriptional response to DNA damage in the archaeon Sulfolobus solfataricus. Nucleic Acids Res 2003; 31:6127-38. [PMID: 14576299 PMCID: PMC275473 DOI: 10.1093/nar/gkg831] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Exposure of cells to DNA-damaging agents triggers a complex biological response involving cell cycle arrest and modulation of gene expression. Genomic sequencing has revealed the presence of archaeal genes homologous to components of the eucaryal nucleotide excision repair (NER) pathway, which is involved in the repair of ultraviolet (UV) light-induced DNA damage. However, the events involved in the cell response to UV irradiation and their regulation have not been studied in Archaea. We show here that UV radiation induces the formation of cyclobutane pyrimidine dimers (CPDs) in the hyperthermophilic archaeon Sulfolobus solfataricus, and that these lesions are efficiently repaired in vivo in the dark, suggesting that a NER pathway is active. DNA damage is a signal for concomitant growth arrest and transcriptional induction of the NER genes XPF, XPG and XPB. The cell response to UV irradiation includes transcriptional regulation of genes encoding two DNA binding proteins involved in chromosome dynamics. Moreover, several of these genes are also strongly induced by the intercalating agent actinomycin D. Thus, response to DNA damage in S.solfataricus has features essentially conserved in all three domains of life.
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Affiliation(s)
- Vincenzo Salerno
- Institute of Protein Biochemistry, Consiglio Nazionale delle Ricerche, Via P. Castellino, 80131 Naples, Italy
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41
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Fiorentino G, Cannio R, Rossi M, Bartolucci S. Transcriptional regulation of the gene encoding an alcohol dehydrogenase in the archaeon Sulfolobus solfataricus involves multiple factors and control elements. J Bacteriol 2003; 185:3926-34. [PMID: 12813087 PMCID: PMC161585 DOI: 10.1128/jb.185.13.3926-3934.2003] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A transcriptionally active region has been identified in the 5' flanking region of the alcohol dehydrogenase gene of the crenarchaeon Sulfolobus solfataricus through the evaluation of the activity of putative transcriptional regulators and the role of the region upstream of the gene under specific metabolic circumstances. Electrophoretic mobility shift assays with crude extracts revealed protein complexes that most likely contain TATA box-associated factors. When the TATA element was deleted from the region, binding sites for both DNA binding proteins, such as the small chromatin structure-modeling Sso7d and Sso10b (Alba), and transcription factors, such as the repressor Lrs14, were revealed. To understand the molecular mechanisms underlying the substrate-induced expression of the adh gene, the promoter was analyzed for the presence of cis-acting elements recognized by specific transcription factors upon exposure of the cell to benzaldehyde. Progressive dissection of the identified promoter region restricted the analysis to a minimal responsive element (PAL) located immediately upstream of the transcription factor B-responsive element-TATA element, resembling typical bacterial regulatory sequences. A benzaldehyde-activated transcription factor (Bald) that specifically binds to the PAL cis-acting element was also identified. This protein was purified from heparin-fractionated extracts of benzaldehyde-induced cells and was shown to have a molecular mass of approximately 16 kDa. The correlation between S. solfataricus adh gene activation and benzaldehyde-inducible occupation of a specific DNA sequence in its promoter suggests that a molecular signaling mechanism is responsible for the switch of the aromatic aldehyde metabolism as a response to environmental changes.
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Affiliation(s)
- Gabriella Fiorentino
- Dipartimento di Chimica Biologica, Università degli Studi di Napoli Federico II, Naples, Italy
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42
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Abstract
Archaea contain a variety of sequence-independent DNA binding proteins consistent with the evolution of several different, sometimes overlapping and exchangeable solutions to the problem of genome compaction. Some of these proteins undergo residue-specific post-translational lysine acetylation or methylation, hinting at analogues of the histone modifications that regulate eukaryotic chromatin structure and transcription. Archaeal transcription initiation most closely resembles the eukaryotic RNA polymerase II (RNAPII) system, but Archaea do not appear to have homologues of the multisubunit complexes that remodel eukaryotic chromatin and activate RNAPII initiation. In contrast, they have sequence-specific regulators that repress and perhaps activate archaeal transcription by mechanisms superficially similar to the bacterial paradigm of regulating promoter binding by RNAP. Repressors compete with archaeal TATA-box binding protein (TBP) and TFB for the TATA-box and TFB-recognition elements (BRE) of the archaeal promoter, or with archaeal RNAP for the site of transcription initiation. Transcript-specific regulation by repressors binding to sites of transcript initiation is consistent with such sites having very little sequence conservation. However, most Archaea have only one TBP and/or TFB that presumably must therefore bind to similar TATA-box and BRE sequences upstream of most genes. Repressors that function by competing with TBP and/or TFB binding must therefore also make additional contacts with transcript-specific regulatory sites adjacent or remote from the TATA-box/BRE region. The fate of the archaeal TBP and TFB following transcription initiation remains to be determined. Based on functional homology with their eukaryotic RNAPII-system counterparts, archaeal TBP and possibly also TFB should remain bound to the TATA-box/BRE region after transcription initiation. However, this seems unlikely as it might limit repressor competition at this site to only the first round of transcription initiation.
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Affiliation(s)
- John N Reeve
- Department of Microbiology, Ohio State University, Columbus, OH 43210-1292, USA.
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43
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Abstract
Genome analysis has revealed that members of the Lrp family of transcriptional regulators are widely distributed among prokaryotes, both bacteria and archaea. The archetype Leucine-responsive Regulatory Protein from Escherichia coli is a global regulator involved in modulating a variety of metabolic functions, including the catabolism and anabolism of amino acids as well as pili synthesis. Most Lrp homologues, however, appear to act as specific regulators of amino acid metabolism-related genes. Like most prokaryotic transcriptional regulators, Lrp-like regulators consist of a DNA-binding domain and a ligand-binding domain. The crystal structure of the Pyrococcus furiosus LrpA revealed an N-terminal domain with a common helix-turn-helix fold, and a C-terminal domain with a typical alphabeta-sandwich fold. The latter regulatory domain constitutes a novel ligand-binding site and has been designated RAM. Database analysis reveals that the RAM domain is present in many prokaryotic genomes, potentially encoding (1) Lrp-homologues, when fused to a DNA-binding domain (2) enzymes, when fused as a potential regulatory domain to a catalytic domain, and (3) stand-alone RAM modules with unknown function. The architecture of Lrp regulators with two distinct domains that harbour the regulatory (effector-binding) site and the active (DNA-binding) site, and their separation by a flexible hinge region, suggests a general allosteric switch of Lrp-like regulators.
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Affiliation(s)
- Arie B Brinkman
- Laboratory of Microbiology, Wageningen University, Hesselink van Suchtelenweg 4, NL-6307 CT Wageningen, The Netherlands
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44
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Lee SJ, Engelmann A, Horlacher R, Qu Q, Vierke G, Hebbeln C, Thomm M, Boos W. TrmB, a sugar-specific transcriptional regulator of the trehalose/maltose ABC transporter from the hyperthermophilic archaeon Thermococcus litoralis. J Biol Chem 2003; 278:983-90. [PMID: 12426307 DOI: 10.1074/jbc.m210236200] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We report the characterization of TrmB, a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of a gene cluster in Thermococcus litoralis, malE malF malG orf trmB malK, encoding a binding protein-dependent ABC transporter for trehalose and maltose. TrmB binds maltose and trehalose half-maximally at 20 microm and 0.5 mm sugar concentration, respectively. Binding of maltose but not of trehalose showed indications of sigmoidality and quenched the intrinsic tryptophan fluorescence by 15%, indicating a conformational change on maltose binding. TrmB causes a shift in electrophoretic mobility of DNA fragments harboring the promoter and upstream regulatory motif identified by footprinting. Band shifting by TrmB can be prevented by maltose. In vitro transcription assays with purified components from Pyrococcus furiosus have been established to show pmalE promoter-dependent transcription at 80 degrees C. TrmB specifically inhibits transcription, and this inhibition is counteracted by maltose and trehalose. These data characterize TrmB as a maltose-specific repressor for the trehalose/maltose transport operon of Thermococcus litoralis.
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Affiliation(s)
- Sung-Jae Lee
- Department of Biology, University of Konstanz, Germany
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45
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Lie TJ, Leigh JA. A novel repressor of nif and glnA expression in the methanogenic archaeon Methanococcus maripaludis. Mol Microbiol 2003; 47:235-46. [PMID: 12492867 DOI: 10.1046/j.1365-2958.2003.03293.x] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Nitrogen assimilation in the methanogenic archaeon Methanococcus maripaludis is regulated by transcriptional repression involving a palindromic 'nitrogen operator' repressor binding sequence. Here we report the isolation of the nitrogen repressor, NrpR, from M. maripaludis using DNA affinity purification. Deletion of the nrpR gene resulted in loss of nitrogen operator binding activity in cell extracts and loss of repression of nif (nitrogen-fixation) and glnA (glutamine synthetase) gene expression in vivo. Genetic complementation of the nrpR mutation restored all functions. NrpR contained a putative N-terminal winged helix-turn-helix motif followed by two mutually homologous domains of unknown function. Comparison of the migration of NrpR in gel-filtration chromatography with its subunit molecular weight (60 kDa) suggested that NrpR was a tetramer. Several lines of evidence suggested that the level of NrpR itself is not regulated, and the binding affinity of NrpR to the nitrogen operator is controlled by an unknown mechanism. Homologues of NrpR were found only in certain species in the kingdom Euryarchaeota. Full length homologues were found in Methanocaldococcus jannaschii and Methanothermobacter thermoautotrophicus, and homologues lacking one or more of the three polypeptide domains were found in Archaeoglobus fulgidus, Methanopyrus kandleri, Methanosarcina acetivorans, and Methanosarcina mazei. NrpR represents a new family of regulators unique to the Euryarchaeota.
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Affiliation(s)
- Thomas J Lie
- Department of Microbiology, University of Washington, Seattle, Washington 98195, USA
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46
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Enoru-Eta J, Gigot D, Glansdorff N, Charlier D. High resolution contact probing of the Lrp-like DNA-binding protein Ss-Lrp from the hyperthermoacidophilic crenarchaeote Sulfolobus solfataricus P2. Mol Microbiol 2002; 45:1541-55. [PMID: 12354224 DOI: 10.1046/j.1365-2958.2002.03136.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Ss-Lrp, from Sulfolobus solfataricus, is an archaeal homologue of the global bacterial regulator Lrp (Leucine-responsive regulatory protein), which out of all genome-encoded proteins is most similar to Escherichia coli Lrp (E-value of 5.6 e-14). The recombinant protein has been purified as a 68 kDa homotetramer. The specific binding of Ss-Lrp to its own control region is suggestive of negative autoregulation. A high resolution contact map of Ss-Lrp binding was established by DNase I and hydroxyl radical footprinting, small non-intercalating groove-specific ligand-binding interference, and various base-specific premodification and base removal binding interference techniques. We show that Ss-Lrp binds one face of the DNA helix and establishes the most salient contacts with two major groove segments and the intervening minor groove, in a region that overlaps the TATA-box and BRE promoter elements. Therefore, Ss-Lrp most likely exerts autoregulation by preventing promoter recognition by TBP and TFB. Moreover, the results demonstrate profound Ss-Lrp induced structural alterations of sequence stretches flanking the core contact site, and reveal that the deformability of these regions significantly contributes to binding selectivity.
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Affiliation(s)
- Julius Enoru-Eta
- Erfelijkheidsleer en Microbiologie, Vrije Universiteit Brussels, Belgium
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47
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Brinkman AB, Bell SD, Lebbink RJ, de Vos WM, van der Oost J. The Sulfolobus solfataricus Lrp-like protein LysM regulates lysine biosynthesis in response to lysine availability. J Biol Chem 2002; 277:29537-49. [PMID: 12042311 DOI: 10.1074/jbc.m203528200] [Citation(s) in RCA: 83] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Although the archaeal transcription apparatus resembles the eukaryal RNA polymerase II system, many bacterial-like regulators can be found in archaea. Particularly, all archaeal genomes sequenced to date contain genes encoding homologues of Lrp (leucine-responsive regulatory protein). Whereas Lrp-like proteins in bacteria are involved in regulation of amino acid metabolism, their physiological role in archaea is unknown. Although several archaeal Lrp-like proteins have been characterized recently, no target genes apart from their own coding genes have been discovered yet, and no ligands for these regulators have been identified so far. In this study, we show that the Lrp-like protein LysM from Sulfolobus solfataricus is involved in the regulation of lysine and possibly also arginine biosynthesis, encoded by the lys gene cluster. Exogenous lysine is the regulatory signal for lys gene expression and specifically serves as a ligand for LysM by altering its DNA binding affinity. LysM binds directly upstream of the TFB-responsive element of the intrinsically weak lysW promoter, and DNA binding is favored in the absence of lysine, when lysWXJK transcription is maximal. The combined in vivo and in vitro data are most compatible with a model in which the bacterial-like LysM activates the eukarya-like transcriptional machinery. As with transcriptional activation by Escherichia coli Lrp, activation by LysM is apparently dependent on a co-activator, which remains to be identified.
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Affiliation(s)
- Arie B Brinkman
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Hesselink van Suchtelenweg 4, 6703 CT Wageningen, The Netherlands.
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48
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Napoli A, Zivanovic Y, Bocs C, Buhler C, Rossi M, Forterre P, Ciaramella M. DNA bending, compaction and negative supercoiling by the architectural protein Sso7d of Sulfolobus solfataricus. Nucleic Acids Res 2002; 30:2656-62. [PMID: 12060682 PMCID: PMC117289 DOI: 10.1093/nar/gkf377] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Members of the Sso7d/Sac7d family are small, abundant, non-specific DNA-binding proteins of the hyperthermophilic Archaea SULFOLOBUS: Crystal structures of these proteins in complex with oligonucleotides showed that they induce changes in the helical twist and marked DNA bending. On this basis they have been suggested to play a role in organising chromatin structures in these prokaryotes, which lack histones. We report functional in vitro assays to investigate the effects of the observed Sso7d-induced structural modifications on DNA geometry and topology. We show that binding of multiple Sso7d molecules to short DNA fragments induces significant curvature and reduces the stiffness of the complex. Sso7d induces negative supercoiling of DNA molecules of any topology (relaxed, positively or negatively supercoiled) and in physiological conditions of temperature and template topology. Binding of Sso7d induces compaction of positively supercoiled and relaxed DNA molecules, but not of negatively supercoiled ones. Finally, Sso7d inhibits the positive supercoiling activity of the thermophile-specific enzyme reverse gyrase. The proposed biological relevance of these observations is that these proteins might model the behaviour of DNA in constrained chromatin environments.
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Affiliation(s)
- Alessandra Napoli
- Institute of Protein Biochemistry and Enzymology, Consiglio Nazionale delle Ricerche, Via Pietro Castellino 111, 80131 Naples, Italy
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49
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Affiliation(s)
- J Soppa
- Institute for Microbiology, Biocentre Niederursel, J. W. Goethe University Frankfurt, D-60439 Frankfurt, Germany
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50
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Dahlke I, Thomm M. A Pyrococcus homolog of the leucine-responsive regulatory protein, LrpA, inhibits transcription by abrogating RNA polymerase recruitment. Nucleic Acids Res 2002; 30:701-10. [PMID: 11809882 PMCID: PMC100285 DOI: 10.1093/nar/30.3.701] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The genomes of Archaea harbor homologs of the global bacterial regulator leucine-responsive regulatory protein (Lrp). Archaeal Lrp homologs are helix-turn-helix DNA-binding proteins that specifically repress the transcription of their own genes in vitro. Here, we analyze the interaction of Pyrococcus LrpA with components of the archaeal transcriptional machinery at the lrpA promoter. DNA-protein complexes can be isolated by electrophoretic mobility shift assays that contain both LrpA and the two archaeal transcription factors TBP and TFB. Phenanthroline-copper footprinting experiments showed that the DNA-binding sites of LrpA and TBP/TFB do not overlap. These results and the finding that association of RNA polymerase with the TBP-TFB promoter complex was inhibited in the presence of LrpA indicate that Pyrococcus LrpA interferes with RNA polymerase recruitment. A DNA motif required for the LrpA-DNA interaction was inferred from dimethylsulfate methylation interference experiments.
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Affiliation(s)
- Isabell Dahlke
- Institut für Allgemeine Mikrobiologie, Universität Kiel, Am Botanischen Garten 1-9, 24118 Kiel, Germany
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