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The Denaturant- and Mutation-Induced Disassembly of Pseudomonas aeruginosa Hexameric Hfq Y55W Mutant. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27123821. [PMID: 35744948 PMCID: PMC9228748 DOI: 10.3390/molecules27123821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 06/10/2022] [Accepted: 06/11/2022] [Indexed: 11/17/2022]
Abstract
Although oligomeric proteins are predominant in cells, their folding is poorly studied at present. This work is focused on the denaturant- and mutation-induced disassembly of the hexameric mutant Y55W of the Qβ host factor (Hfq) from mesophilic Pseudomonas aeruginosa (Pae). Using intrinsic tryptophan fluorescence, dynamic light scattering (DLS), and high-performance liquid chromatography (HPLC), we show that the dissociation of Hfq Y55W occurs either under the effect of GuHCl or during the pre-denaturing transition, when the protein concentration is decreased, with both events proceeding through the accumulation of stable intermediate states. With an extremely low pH of 1.4, a low ionic strength, and decreasing protein concentration, the accumulated trimers and dimers turn into monomers. Also, we report on the structural features of monomeric Hfq resulting from a triple mutation (D9A/V43R/Y55W) within the inter-subunit surface of the protein. This globular and rigidly packed monomer displays a high thermostability and an oligomer-like content of the secondary structure, although its urea resistance is much lower.
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2
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Sonnleitner E, Wulf A, Campagne S, Pei XY, Wolfinger MT, Forlani G, Prindl K, Abdou L, Resch A, Allain FHT, Luisi BF, Urlaub H, Bläsi U. Interplay between the catabolite repression control protein Crc, Hfq and RNA in Hfq-dependent translational regulation in Pseudomonas aeruginosa. Nucleic Acids Res 2019; 46:1470-1485. [PMID: 29244160 PMCID: PMC5815094 DOI: 10.1093/nar/gkx1245] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 12/01/2017] [Indexed: 12/23/2022] Open
Abstract
In Pseudomonas aeruginosa the RNA chaperone Hfq and the catabolite repression control protein (Crc) act as post-transcriptional regulators during carbon catabolite repression (CCR). In this regard Crc is required for full-fledged Hfq-mediated translational repression of catabolic genes. RNAseq based transcriptome analyses revealed a significant overlap between the Crc and Hfq regulons, which in conjunction with genetic data supported a concerted action of both proteins. Biochemical and biophysical approaches further suggest that Crc and Hfq form an assembly in the presence of RNAs containing A-rich motifs, and that Crc interacts with both, Hfq and RNA. Through these interactions, Crc enhances the stability of Hfq/Crc/RNA complexes, which can explain its facilitating role in Hfq-mediated translational repression. Hence, these studies revealed for the first time insights into how an interacting protein can modulate Hfq function. Moreover, Crc is shown to interfere with binding of a regulatory RNA to Hfq, which bears implications for riboregulation. These results are discussed in terms of a working model, wherein Crc prioritizes the function of Hfq toward utilization of favored carbon sources.
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Affiliation(s)
- Elisabeth Sonnleitner
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter, Dr. Bohrgasse 9, 1030 Vienna, Austria
| | - Alexander Wulf
- Biophysical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Sébastien Campagne
- Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland
| | - Xue-Yuan Pei
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Michael T Wolfinger
- Institute of Theoretical Chemistry, University of Vienna, 1090 Vienna, Austria.,Center for Anatomy and Cell Biology, Medical University of Vienna, 1090 Vienna, Austria
| | - Giada Forlani
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter, Dr. Bohrgasse 9, 1030 Vienna, Austria
| | - Konstantin Prindl
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter, Dr. Bohrgasse 9, 1030 Vienna, Austria
| | - Laetitia Abdou
- Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Armin Resch
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter, Dr. Bohrgasse 9, 1030 Vienna, Austria
| | - Frederic H-T Allain
- Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland
| | - Ben F Luisi
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Henning Urlaub
- Biophysical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany.,Bioanalytics, Institute for Clinical Chemistry, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Udo Bläsi
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter, Dr. Bohrgasse 9, 1030 Vienna, Austria
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Stanek KA, Mura C. Producing Hfq/Sm Proteins and sRNAs for Structural and Biophysical Studies of Ribonucleoprotein Assembly. Methods Mol Biol 2019; 1737:273-299. [PMID: 29484599 DOI: 10.1007/978-1-4939-7634-8_16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hfq is a bacterial RNA-binding protein that plays key roles in the post-transcriptional regulation of gene expression. Like other Sm proteins, Hfq assembles into toroidal discs that bind RNAs with varying affinities and degrees of sequence specificity. By simultaneously binding to a regulatory small RNA (sRNA) and an mRNA target, Hfq hexamers facilitate productive RNA∙∙∙RNA interactions; the generic nature of this chaperone-like functionality makes Hfq a hub in many sRNA-based regulatory networks. That Hfq is crucial in diverse cellular pathways-including stress response, quorum sensing, and biofilm formation-has motivated genetic and "RNAomic" studies of its function and physiology (in vivo), as well as biochemical and structural analyses of Hfq∙∙∙RNA interactions (in vitro). Indeed, crystallographic and biophysical studies first established Hfq as a member of the phylogenetically conserved Sm superfamily. Crystallography and other biophysical methodologies enable the RNA-binding properties of Hfq to be elucidated in atomic detail, but such approaches have stringent sample requirements, viz.: reconstituting and characterizing an Hfq·RNA complex requires ample quantities of well-behaved (sufficient purity, homogeneity) specimens of Hfq and RNA (sRNA, mRNA fragments, short oligoribonucleotides, or even single nucleotides). The production of such materials is covered in this chapter, with a particular focus on recombinant Hfq proteins for crystallization experiments.
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Affiliation(s)
- Kimberly A Stanek
- Department of Chemistry, University of Virginia, Charlottesville, VA, USA.
| | - Cameron Mura
- Department of Chemistry, University of Virginia, Charlottesville, VA, USA.
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Stanek KA, Patterson-West J, Randolph PS, Mura C. Crystal structure and RNA-binding properties of an Hfq homolog from the deep-branching Aquificae: conservation of the lateral RNA-binding mode. Acta Crystallogr D Struct Biol 2017; 73:294-315. [PMID: 28375142 PMCID: PMC5379935 DOI: 10.1107/s2059798317000031] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 01/02/2017] [Indexed: 11/10/2022] Open
Abstract
The host factor Hfq, as the bacterial branch of the Sm family, is an RNA-binding protein involved in the post-transcriptional regulation of mRNA expression and turnover. Hfq facilitates pairing between small regulatory RNAs (sRNAs) and their corresponding mRNA targets by binding both RNAs and bringing them into close proximity. Hfq homologs self-assemble into homo-hexameric rings with at least two distinct surfaces that bind RNA. Recently, another binding site, dubbed the `lateral rim', has been implicated in sRNA·mRNA annealing; the RNA-binding properties of this site appear to be rather subtle, and its degree of evolutionary conservation is unknown. An Hfq homolog has been identified in the phylogenetically deep-branching thermophile Aquifex aeolicus (Aae), but little is known about the structure and function of Hfq from basal bacterial lineages such as the Aquificae. Therefore, Aae Hfq was cloned, overexpressed, purified, crystallized and biochemically characterized. Structures of Aae Hfq were determined in space groups P1 and P6, both to 1.5 Å resolution, and nanomolar-scale binding affinities for uridine- and adenosine-rich RNAs were discovered. Co-crystallization with U6 RNA reveals that the outer rim of the Aae Hfq hexamer features a well defined binding pocket that is selective for uracil. This Aae Hfq structure, combined with biochemical and biophysical characterization of the homolog, reveals deep evolutionary conservation of the lateral RNA-binding mode, and lays a foundation for further studies of Hfq-associated RNA biology in ancient bacterial phyla.
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Affiliation(s)
- Kimberly A. Stanek
- Department of Chemistry, University of Virginia, 409 McCormick Road, Charlottesville, VA 22904, USA
| | - Jennifer Patterson-West
- Department of Chemistry, University of Virginia, 409 McCormick Road, Charlottesville, VA 22904, USA
| | - Peter S. Randolph
- Department of Chemistry, University of Virginia, 409 McCormick Road, Charlottesville, VA 22904, USA
| | - Cameron Mura
- Department of Chemistry, University of Virginia, 409 McCormick Road, Charlottesville, VA 22904, USA
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Murina VN, Nikulin AD. Bacterial Small Regulatory RNAs and Hfq Protein. BIOCHEMISTRY (MOSCOW) 2016; 80:1647-54. [PMID: 26878571 DOI: 10.1134/s0006297915130027] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Small regulatory RNA (sRNA) is a unique noncoding RNA involved in regulation of gene expression in both eukaryotic and bacterial cells. This short review discusses examples of positive and negative translation regulation by sRNAs in bacteria and participation of Hfq in these processes. The importance of structure investigation of nucleotide-protein and RNA-protein complexes for designing a model of Hfq interaction with both mRNA and sRNA simultaneously is demonstrated.
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Affiliation(s)
- V N Murina
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.
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Nikulin A, Mikhailina A, Lekontseva N, Balobanov V, Nikonova E, Tishchenko S. Characterization of RNA-binding properties of the archaeal Hfq-like protein from Methanococcus jannaschii. J Biomol Struct Dyn 2016; 35:1615-1628. [PMID: 27187760 DOI: 10.1080/07391102.2016.1189849] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The Sm and Sm-like proteins are widely distributed among bacteria, archaea and eukarya. They participate in many processes related to RNA-processing and regulation of gene expression. While the function of the bacterial Lsm protein Hfq and eukaryotic Sm/Lsm proteins is rather well studied, the role of Lsm proteins in Archaea is investigated poorly. In this work, the RNA-binding ability of an archaeal Hfq-like protein from Methanococcus jannaschii has been studied by X-ray crystallography, anisotropy fluorescence and surface plasmon resonance. It has been found that MjaHfq preserves the proximal RNA-binding site that usually recognizes uridine-rich sequences. Distal adenine-binding and lateral RNA-binding sites show considerable structural changes as compared to bacterial Hfq. MjaHfq did not bind mononucleotides at these sites and would not recognize single-stranded RNA as its bacterial homologues. Nevertheless, MjaHfq possesses affinity to poly(A) RNA that seems to bind at the unstructured positive-charged N-terminal tail of the protein.
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Affiliation(s)
- Alexey Nikulin
- a Institute of Protein Research , Russian Academy of Sciences , Pushchino , Moscow region , 142290 , Russia
| | - Alisa Mikhailina
- a Institute of Protein Research , Russian Academy of Sciences , Pushchino , Moscow region , 142290 , Russia
| | - Natalia Lekontseva
- a Institute of Protein Research , Russian Academy of Sciences , Pushchino , Moscow region , 142290 , Russia
| | - Vitalii Balobanov
- a Institute of Protein Research , Russian Academy of Sciences , Pushchino , Moscow region , 142290 , Russia
| | - Ekaterina Nikonova
- a Institute of Protein Research , Russian Academy of Sciences , Pushchino , Moscow region , 142290 , Russia
| | - Svetlana Tishchenko
- a Institute of Protein Research , Russian Academy of Sciences , Pushchino , Moscow region , 142290 , Russia
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Vrentas C, Ghirlando R, Keefer A, Hu Z, Tomczak A, Gittis AG, Murthi A, Garboczi DN, Gottesman S, Leppla SH. Hfqs in Bacillus anthracis: Role of protein sequence variation in the structure and function of proteins in the Hfq family. Protein Sci 2015; 24:1808-19. [PMID: 26271475 DOI: 10.1002/pro.2773] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 08/13/2015] [Indexed: 11/10/2022]
Abstract
Hfq proteins in Gram-negative bacteria play important roles in bacterial physiology and virulence, mediated by binding of the Hfq hexamer to small RNAs and/or mRNAs to post-transcriptionally regulate gene expression. However, the physiological role of Hfqs in Gram-positive bacteria is less clear. Bacillus anthracis, the causative agent of anthrax, uniquely expresses three distinct Hfq proteins, two from the chromosome (Hfq1, Hfq2) and one from its pXO1 virulence plasmid (Hfq3). The protein sequences of Hfq1 and 3 are evolutionarily distinct from those of Hfq2 and of Hfqs found in other Bacilli. Here, the quaternary structure of each B. anthracis Hfq protein, as produced heterologously in Escherichia coli, was characterized. While Hfq2 adopts the expected hexamer structure, Hfq1 does not form similarly stable hexamers in vitro. The impact on the monomer-hexamer equilibrium of varying Hfq C-terminal tail length and other sequence differences among the Hfqs was examined, and a sequence region of the Hfq proteins that was involved in hexamer formation was identified. It was found that, in addition to the distinct higher-order structures of the Hfq homologs, they give rise to different phenotypes. Hfq1 has a disruptive effect on the function of E. coli Hfq in vivo, while Hfq3 expression at high levels is toxic to E. coli but also partially complements Hfq function in E. coli. These results set the stage for future studies of the roles of these proteins in B. anthracis physiology and for the identification of sequence determinants of phenotypic complementation.
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Affiliation(s)
- Catherine Vrentas
- NIAID, National Institutes of Health (NIH), 33 North Drive, Bethesda, Maryland
| | | | - Andrea Keefer
- NIAID, National Institutes of Health (NIH), 33 North Drive, Bethesda, Maryland
| | - Zonglin Hu
- NIAID, National Institutes of Health (NIH), 33 North Drive, Bethesda, Maryland
| | | | - Apostolos G Gittis
- Structural Biology Section, Research Technologies Branch, NIAID, NIH, Twinbrook II, 12441 Parklawn Drive, Rockville, Maryland
| | - Athulaprabha Murthi
- NIAID, National Institutes of Health (NIH), 33 North Drive, Bethesda, Maryland
| | - David N Garboczi
- Structural Biology Section, Research Technologies Branch, NIAID, NIH, Twinbrook II, 12441 Parklawn Drive, Rockville, Maryland
| | | | - Stephen H Leppla
- NIAID, National Institutes of Health (NIH), 33 North Drive, Bethesda, Maryland
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Murina VN, Selivanova OM, Mikhaylina AO, Kazakov AS, Nikonova EY, Lekontseva NV, Tishchenko SV, Nikulin AD. Supramolecular organization of Hfq-like proteins. BIOCHEMISTRY (MOSCOW) 2015; 80:441-8. [DOI: 10.1134/s0006297915040070] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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