1
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Chawra HS, Agarwal M, Mishra A, Chandel SS, Singh RP, Dubey G, Kukreti N, Singh M. MicroRNA-21's role in PTEN suppression and PI3K/AKT activation: Implications for cancer biology. Pathol Res Pract 2024; 254:155091. [PMID: 38194804 DOI: 10.1016/j.prp.2024.155091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Revised: 12/31/2023] [Accepted: 01/01/2024] [Indexed: 01/11/2024]
Abstract
MicroRNA-21 (miR-21) was recognized as a key figure in the intricate web of tumor biology, with a prominent role in regulating the PTEN tumor suppressor gene and the PI3K/AKT cascade. This review elucidates the multifaceted interactions between miR-21, PTEN, and the PI3K/AKT signaling, shedding light on their profound implications in cancer initiation, progression, and therapeutic strategies. The core of this review delves into the mechanical intricacies of miR-21-mediated PTEN suppression and its consequent impact on PI3K/AKT pathway activation. It explores how miR-21, as an oncogenic miRNA, targets PTEN directly or indirectly, resulting in uncontrolled activation of PI3K/AKT, fostering cancerous cell survival, proliferation, and evasion of apoptosis. Furthermore, the abstract emphasizes the clinical relevance of these molecular interactions, discussing their implications in various cancer types, prognostic significance, and potential as therapeutic targets. The review provides insights into ongoing research efforts to develop miR-21 inhibitors and strategies to restore PTEN function, offering new avenues for cancer treatment. This article illuminates the critical function of miR-21 in PTEN suppression and PI3K/AKT activation, offering profound insights into its implications for cancer biology and the potential for targeted interventions.
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Affiliation(s)
| | - Mohit Agarwal
- NIMS Institute of Pharmacy, NIMS University Rajasthan, Jaipur, India
| | - Anurag Mishra
- NIMS Institute of Pharmacy, NIMS University Rajasthan, Jaipur, India
| | | | | | - Gaurav Dubey
- NIMS Institute of Pharmacy, NIMS University Rajasthan, Jaipur, India
| | - Neelima Kukreti
- School of Pharmacy, Graphic Era Hill University, Dehradun 248007, India
| | - Mithilesh Singh
- NIMS Institute of Pharmacy, NIMS University Rajasthan, Jaipur, India.
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2
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Cossa A, Trépout S, Wien F, Groen J, Le Brun E, Turbant F, Besse L, Pereiro E, Arluison V. Cryo soft X-ray tomography to explore Escherichia coli nucleoid remodeling by Hfq master regulator. J Struct Biol 2022; 214:107912. [PMID: 36283630 DOI: 10.1016/j.jsb.2022.107912] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 09/28/2022] [Accepted: 10/18/2022] [Indexed: 11/18/2022]
Abstract
The bacterial chromosomic DNA is packed within a membrane-less structure, the nucleoid, due to the association of DNA with proteins called Nucleoid Associated Proteins (NAPs). Among these NAPs, Hfq is one of the most intriguing as it plays both direct and indirect roles on DNA structure. Indeed, Hfq is best known to mediate post-transcriptional regulation by using small noncoding RNA (sRNA). Although Hfq presence in the nucleoid has been demonstrated for years, its precise role is still unclear. Recently, it has been shown in vitro that Hfq forms amyloid-like structures through its C-terminal region, hence belonging to the bridging family of NAPs. Here, using cryo soft X-ray tomography imaging of native unlabeled cells and using a semi-automatic analysis and segmentation procedure, we show that Hfq significantly remodels the Escherichia coli nucleoid. More specifically, Hfq influences nucleoid density especially during the stationary growth phase when it is more abundant. Our results indicate that Hfq could regulate nucleoid compaction directly via its interaction with DNA, but also at the post-transcriptional level via its interaction with RNAs. Taken together, our findings reveal a new role for this protein in nucleoid remodeling in vivo, that may serve in response to stress conditions and in adapting to changing environments.
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Affiliation(s)
- Antoine Cossa
- Institut Curie, Université PSL, CNRS UAR2016, Inserm US43, Université Paris-Saclay, Multimodal Imaging Center, 91400 Orsay, France; Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris-Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France
| | - Sylvain Trépout
- Institut Curie, Université PSL, CNRS UAR2016, Inserm US43, Université Paris-Saclay, Multimodal Imaging Center, 91400 Orsay, France; Ramaciotti Centre for Cryo-Electron Microscopy, Monash University, Clayton, Victoria 3800, Australia.
| | - Frank Wien
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint Aubin BP48, 91192 Gif-sur-Yvette, France
| | - Johannes Groen
- Mistral Beamline, Alba Light Source, Cerdanyola del Valles, 08290 Barcelona, Spain
| | - Etienne Le Brun
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris-Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France
| | - Florian Turbant
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris-Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France; Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Laetitia Besse
- Institut Curie, Université PSL, CNRS UAR2016, Inserm US43, Université Paris-Saclay, Multimodal Imaging Center, 91400 Orsay, France
| | - Eva Pereiro
- Mistral Beamline, Alba Light Source, Cerdanyola del Valles, 08290 Barcelona, Spain
| | - Véronique Arluison
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris-Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France; Université Paris Cité, UFR Sciences du vivant, 75006 Paris cedex, France.
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3
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Tan CJ, Basak R, Yadav I, van Kan JA, Arluison V, van der Maarel JRC. Mobility of Bacterial Protein Hfq on dsDNA: Role of C-Terminus-Mediated Transient Binding. J Phys Chem B 2022; 126:1477-1482. [PMID: 35166115 DOI: 10.1021/acs.jpcb.1c10234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The mobility of protein is fundamental in the machinery of life. Here, we have investigated the effect of DNA binding in conjunction with DNA segmental fluctuation (internal motion) of the bacterial Hfq master regulator devoid of its amyloid C-terminus domain. Hfq is one of the most abundant nucleoid associated proteins that shape the bacterial chromosome and is involved in several aspects of nucleic acid metabolism. Fluorescence microscopy has been used to track a C-terminus domain lacking mutant form of Hfq on double-stranded DNA, which is stretched by confinement to a rectangular nanofluidic channel. The mobility of the mutant is strongly accelerated with respect to the wild-type variant. Furthermore, it shows a reverse dependence on the internal motion of DNA, in that slower motion results in slower protein diffusion. The results demonstrate the subtle role of DNA internal motion in controlling the mobility of a nucleoid associated protein, and, in particular, the importance of transient binding and moving DNA strands out of the way.
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Affiliation(s)
- Chuan Jie Tan
- Department of Physics, National University of Singapore, Singapore 117542, Singapore
| | - Rajib Basak
- Department of Physics, National University of Singapore, Singapore 117542, Singapore
| | - Indresh Yadav
- Department of Physics, National University of Singapore, Singapore 117542, Singapore
| | - Jeroen A van Kan
- Department of Physics, National University of Singapore, Singapore 117542, Singapore
| | - Véronique Arluison
- Université de Paris, UFR SDV, Paris 75006, France.,Laboratoire Léon Brillouin, CEA, CNRS, Université Paris Saclay, Gif-sur-Yvette 91191, France
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4
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Abstract
To exert their functions, RNAs adopt diverse structures, ranging from simple secondary to complex tertiary and quaternary folds. In vivo, RNA folding starts with RNA transcription, and a wide variety of processes are coupled to co-transcriptional RNA folding events, including the regulation of fundamental transcription dynamics, gene regulation by mechanisms like attenuation, RNA processing or ribonucleoprotein particle formation. While co-transcriptional RNA folding and associated co-transcriptional processes are by now well accepted as pervasive regulatory principles in all organisms, investigations into the role of the transcription machinery in co-transcriptional folding processes have so far largely focused on effects of the order in which RNA regions are produced and of transcription kinetics. Recent structural and structure-guided functional analyses of bacterial transcription complexes increasingly point to an additional role of RNA polymerase and associated transcription factors in supporting co-transcriptional RNA folding by fostering or preventing strategic contacts to the nascent transcripts. In general, the results support the view that transcription complexes can act as RNA chaperones, a function that has been suggested over 30 years ago. Here, we discuss transcription complexes as RNA chaperones based on recent examples from bacterial transcription.
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Affiliation(s)
- Nelly Said
- Freie Universität Berlin, Department Biology, Chemistry, Pharmacy, Institute of Chemistry and Biochemistry, Laboratory of Structural Biochemistry, Berlin, Germany
| | - Markus C Wahl
- Freie Universität Berlin, Department Biology, Chemistry, Pharmacy, Institute of Chemistry and Biochemistry, Laboratory of Structural Biochemistry, Berlin, Germany.,Helmholtz-Zentrum Berlin Für Materialien Und Energie, Macromolecular Crystallography, Berlin, Germany
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5
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Aseev LV, Koledinskaya LS, Bychenko OS, Boni IV. Regulation of Ribosomal Protein Synthesis in Mycobacteria: The Autogenous Control of rpsO. Int J Mol Sci 2021; 22:9679. [PMID: 34575857 PMCID: PMC8470358 DOI: 10.3390/ijms22189679] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/02/2021] [Accepted: 09/03/2021] [Indexed: 01/23/2023] Open
Abstract
The autogenous regulation of ribosomal protein (r-protein) synthesis plays a key role in maintaining the stoichiometry of ribosomal components in bacteria. In this work, taking the rpsO gene as a classic example, we addressed for the first time the in vivo regulation of r-protein synthesis in the mycobacteria M. smegmatis (Msm) and M. tuberculosis (Mtb). We used a strategy based on chromosomally integrated reporters under the control of the rpsO regulatory regions and the ectopic expression of Msm S15 to measure its impact on the reporter expression. Because the use of E. coli as a host appeared inefficient, a fluorescent reporter system was developed by inserting Msm or Mtb rpsO-egfp fusions into the Msm chromosome and expressing Msm S15 or E. coli S15 in trans from a novel replicative shuttle vector, pAMYC. The results of the eGFP expression measurements in Msm cells provided evidence that the rpsO gene in Msm and Mtb was feedback-regulated at the translation level. The mutagenic analysis showed that the folding of Msm rpsO 5'UTR in a pseudoknot appeared crucial for repression by both Msm S15 and E. coli S15, thus indicating a striking resemblance of the rpsO feedback control in mycobacteria and in E. coli.
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Affiliation(s)
| | | | | | - Irina V. Boni
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997 Moscow, Russia; (L.V.A.); (L.S.K.); (O.S.B.)
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6
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Differential Chromosome- and Plasmid-Borne Resistance of Escherichia coli hfq Mutants to High Concentrations of Various Antibiotics. Int J Mol Sci 2021; 22:ijms22168886. [PMID: 34445592 PMCID: PMC8396180 DOI: 10.3390/ijms22168886] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/15/2021] [Accepted: 08/16/2021] [Indexed: 12/14/2022] Open
Abstract
The Hfq protein is a bacterial RNA chaperone, involved in many molecular interactions, including control of actions of various small RNA regulatory molecules. We found that the presence of Hfq was required for survival of plasmid-containing Escherichia coli cells against high concentrations of chloramphenicol (plasmid p27cmr), tetracycline (pSC101, pBR322) and ampicillin (pBR322), as hfq+ strains were more resistant to these antibiotics than the hfq-null mutant. In striking contrast, production of Hfq resulted in low resistance to high concentrations of kanamycin when the antibiotic-resistance marker was chromosome-borne, with deletion of hfq resulting in increasing bacterial survival. These results were observed both in solid and liquid medium, suggesting that antibiotic resistance is an intrinsic feature of these strains rather than a consequence of adaptation. Despite its major role as RNA chaperone, which also affects mRNA stability, Hfq was not found to significantly affect kan and tet mRNAs turnover. Nevertheless, kan mRNA steady-state levels were higher in the hfq-null mutant compared to the hfq+ strain, suggesting that Hfq can act as a repressor of kan expression.This observation does correlate with the enhanced resistance to high levels of kanamycin observed in the hfq-null mutant. Furthermore, dependency on Hfq for resistance to high doses of tetracycline was found to depend on plasmid copy number, which was only observed when the resistance marker was expressed from a low copy plasmid (pSC101) but not from a medium copy plasmid (pBR322). This suggests that Hfq may influence survival against high doses of antibiotics through mechanisms that remain to be determined. Studies with pBR322Δrom may also suggest an interplay between Hfq and Rom in the regulation of ColE1-like plasmid replication. Results of experiments with a mutant devoid of the part of the hfq gene coding for the C-terminal region of Hfq suggested that this region, as well as the N-terminal region, may be involved in the regulation of expression of antibiotic resistance in E. coli independently.
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7
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Yadav I, Basak R, Yan P, van Kan JA, Arluison V, van der Maarel JRC. Role of Internal DNA Motion on the Mobility of a Nucleoid-Associated Protein. J Phys Chem Lett 2020; 11:8424-8429. [PMID: 32930601 DOI: 10.1021/acs.jpclett.0c02251] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Protein transport on DNA is at the core of the machinery of life. Here we investigated the influence of DNA internal motion on the mobility of Hfq, which is involved in several aspects of nucleic acid metabolism and is one of the nucleoid-associated proteins that shape the bacterial chromosome. Fluorescence microscopy was used to follow Hfq on double-stranded DNA that was stretched by confinement to a channel with a diameter of 125 nm. The protein mobility shows a strong dependence on the internal motion of DNA in that slower motion results in faster protein diffusion. A model of released diffusion is proposed that is based on three-dimensional diffusion through the interior of the DNA coil interspersed by periods in which the protein is immobilized in a bound state. We surmise that the coupling between DNA internal motion and protein mobility has important implications for DNA metabolism and protein-binding-related regulation of gene expression.
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Affiliation(s)
- Indresh Yadav
- Department of Physics, National University of Singapore, Singapore 117542
| | - Rajib Basak
- Department of Physics, National University of Singapore, Singapore 117542
| | - Peiyan Yan
- Department of Physics, National University of Singapore, Singapore 117542
| | - Jeroen A van Kan
- Department of Physics, National University of Singapore, Singapore 117542
| | - Véronique Arluison
- Université de Paris, UFR SDV, 75006 Paris, France
- Laboratoire Léon Brillouin, CEA, CNRS, Université Paris Saclay, 91191 Gif-sur-Yvette, France
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8
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Orans J, Kovach AR, Hoff KE, Horstmann NM, Brennan RG. Crystal structure of an Escherichia coli Hfq Core (residues 2-69)-DNA complex reveals multifunctional nucleic acid binding sites. Nucleic Acids Res 2020; 48:3987-3997. [PMID: 32133526 PMCID: PMC7144919 DOI: 10.1093/nar/gkaa149] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 02/26/2020] [Indexed: 12/13/2022] Open
Abstract
Hfq regulates bacterial gene expression post-transcriptionally by binding small RNAs and their target mRNAs, facilitating sRNA-mRNA annealing, typically resulting in translation inhibition and RNA turnover. Hfq is also found in the nucleoid and binds double-stranded (ds) DNA with a slight preference for A-tracts. Here, we present the crystal structure of the Escherichia coli Hfq Core bound to a 30 bp DNA, containing three 6 bp A-tracts. Although previously postulated to bind to the ‘distal’ face, three statistically disordered double stranded DNA molecules bind across the proximal face of the Hfq hexamer as parallel, straight rods with B-DNA like conformational properties. One DNA duplex spans the diameter of the hexamer and passes over the uridine-binding proximal-face pore, whereas the remaining DNA duplexes interact with the rims and serve as bridges between adjacent hexamers. Binding is sequence-independent with residues N13, R16, R17 and Q41 interacting exclusively with the DNA backbone. Atomic force microscopy data support the sequence-independent nature of the Hfq-DNA interaction and a role for Hfq in DNA compaction and nucleoid architecture. Our structure and nucleic acid-binding studies also provide insight into the mechanism of sequence-independent binding of Hfq to dsRNA stems, a function that is critical for proper riboregulation.
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Affiliation(s)
- Jillian Orans
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Alexander R Kovach
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Kirsten E Hoff
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Nicola M Horstmann
- Department of Infectious Diseases, Infection Control Research, University of Texas MD Anderson Cancer Center, Houston TX 77054, USA
| | - Richard G Brennan
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
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9
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Aseev LV, Koledinskaya LS, Boni IV. Autogenous regulation in vivo of the rpmE gene encoding ribosomal protein L31 (bL31), a key component of the protein-protein intersubunit bridge B1b. RNA (NEW YORK, N.Y.) 2020; 26:814-826. [PMID: 32209634 PMCID: PMC7297116 DOI: 10.1261/rna.074237.119] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 03/22/2020] [Indexed: 06/10/2023]
Abstract
Bacterial ribosomal proteins (r-proteins) encoded by nonessential genes often carry out very important tasks in translation. In particular, this is the case of a small basic bacteria-specific r-protein L31 (bL31). Recent studies revealed a crucial role of bL31 in formation of the protein-protein intersubunit bridge B1b and hence its contribution to ribosome dynamics. Our goal was to study in vivo regulation of the rpmE operon encoding bL31. We used a previously developed approach based on chromosomally integrated fusions with the lacZ reporter. E. coli rpmE is transcribed from two promoter regions, and translation of both mRNA transcripts was shown to be feedback regulated by bL31, indicating that the autogenous operator is located within the shorter transcript. The bL31-mediated control of rpmE is gene-specific, as no regulation was found for rpmE-unrelated reporters. Thus, bL31, as many other r-proteins, possesses dual activity in living cells, acting both as an integral ribosome component and an autogenous repressor. Phylogenetic studies revealed the presence of a highly conserved stem-loop structure in the rpmE 5'UTR, a presumable translational operator targeted by bL31, which was further confirmed by site-directed mutagenesis. This stable operator stem-loop separates an AU-rich translational enhancer from a Shine-Dalgarno element, which is a rare case of a noncontiguous translation initiation region. Sequence/structure computational approaches classify bL31 as an RNA-binding protein, consistent with its repressor function discovered here. Mutational analysis of bL31 showed that its unstructured amino-terminal part enriched in lysine is necessary for the repressor activity.
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Affiliation(s)
- Leonid V Aseev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997 Moscow, Russia
| | | | - Irina V Boni
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997 Moscow, Russia
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10
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Wien F, Martinez D, Le Brun E, Jones NC, Vrønning Hoffmann S, Waeytens J, Berbon M, Habenstein B, Arluison V. The Bacterial Amyloid-Like Hfq Promotes In Vitro DNA Alignment. Microorganisms 2019; 7:microorganisms7120639. [PMID: 31816864 PMCID: PMC6956100 DOI: 10.3390/microorganisms7120639] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Revised: 11/25/2019] [Accepted: 11/28/2019] [Indexed: 12/14/2022] Open
Abstract
The Hfq protein is reported to be involved in environmental adaptation and virulence of several bacteria. In Gram-negative bacteria, Hfq mediates the interaction between regulatory noncoding RNAs and their target mRNAs. Besides these RNA-related functions, Hfq is also associated with DNA and is a part of the bacterial chromatin. Its precise role in DNA structuration is, however, unclear and whether Hfq plays a direct role in DNA-related processes such as replication or recombination is controversial. In previous works, we showed that Escherichia coli Hfq, or more precisely its amyloid-like C-terminal region (CTR), induces DNA compaction into a condensed form. In this paper, we evidence a new property for Hfq; precisely we show that its CTR influences double helix structure and base tilting, resulting in a strong local alignment of nucleoprotein Hfq:DNA fibers. The significance of this alignment is discussed in terms of chromatin structuration and possible functional consequences on evolutionary processes and adaptation to environment.
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Affiliation(s)
- Frank Wien
- Synchrotron SOLEIL, 91192 Gif-sur-Yvette, France
- Correspondence: (F.W.); (V.A.); Tel.: +33-(0)1-69-35-96-65 (F.W.); +33-(0)1-69-08-32-82 (V.A.)
| | - Denis Martinez
- Institute of Chemistry and Biology of Membranes and Nano-objects, CBMN UMR5248 CNRS Université de Bordeaux INP, 33607 Pessac, France; (D.M.); (M.B.); (B.H.)
| | - Etienne Le Brun
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France;
| | - Nykola C. Jones
- ISA, Department of Physics and Astronomy, Aarhus University, 8000 Aarhus C, Denmark; (N.C.J.); (S.V.H.)
| | - Søren Vrønning Hoffmann
- ISA, Department of Physics and Astronomy, Aarhus University, 8000 Aarhus C, Denmark; (N.C.J.); (S.V.H.)
| | - Jehan Waeytens
- Structure et Fonction des Membranes Biologiques, Université libre de Bruxelles, B1050 Bruxelles, Belgique;
- Laboratoire de Chimie Physique d’Orsay, CNRS UMR8000, Université Paris-Sud, Université Paris-Saclay 91400 Orsay, France
| | - Melanie Berbon
- Institute of Chemistry and Biology of Membranes and Nano-objects, CBMN UMR5248 CNRS Université de Bordeaux INP, 33607 Pessac, France; (D.M.); (M.B.); (B.H.)
| | - Birgit Habenstein
- Institute of Chemistry and Biology of Membranes and Nano-objects, CBMN UMR5248 CNRS Université de Bordeaux INP, 33607 Pessac, France; (D.M.); (M.B.); (B.H.)
| | - Véronique Arluison
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France;
- Université de Paris, UFR Sciences du vivant, 35 rue Hélène Brion, 75205 Paris cedex, France
- Correspondence: (F.W.); (V.A.); Tel.: +33-(0)1-69-35-96-65 (F.W.); +33-(0)1-69-08-32-82 (V.A.)
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11
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Identification of protein-protein and ribonucleoprotein complexes containing Hfq. Sci Rep 2019; 9:14054. [PMID: 31575967 PMCID: PMC6773851 DOI: 10.1038/s41598-019-50562-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 09/06/2019] [Indexed: 11/08/2022] Open
Abstract
Hfq is a RNA-binding protein that plays a pivotal role in the control of gene expression in bacteria by stabilizing sRNAs and facilitating their pairing with multiple target mRNAs. It has already been shown that Hfq, directly or indirectly, interacts with many proteins: RNase E, Rho, poly(A)polymerase, RNA polymerase… In order to detect more Hfq-related protein-protein interactions we have used two approaches, TAP-tag combined with RNase A treatment to access the role of RNA in these complexes, and protein-protein crosslinking, which freezes protein-protein complexes formed in vivo. In addition, we have performed microscale thermophoresis to evaluate the role of RNA in some of the complexes detected and used far-western blotting to confirm some protein-protein interactions. Taken together, the results show unambiguously a direct interaction between Hfq and EF-Tu. However a very large number of the interactions of proteins with Hfq in E. coli involve RNAs. These RNAs together with the interacting protein, may play an active role in the formation of Hfq-containing complexes with previously unforeseen implications for the riboregulatory functions of Hfq.
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12
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Georg J, Rosana ARR, Chamot D, Migur A, Hess WR, Owttrim GW. Inactivation of the RNA helicase CrhR impacts a specific subset of the transcriptome in the cyanobacterium Synechocystis sp. PCC 6803. RNA Biol 2019; 16:1205-1214. [PMID: 31234711 PMCID: PMC6693541 DOI: 10.1080/15476286.2019.1621622] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
DEAD-box RNA-helicases catalyze the reorganization of structured RNAs and the formation of RNP complexes. The cyanobacterium Synechocystis sp. PCC 6803 encodes a single DEAD-box RNA helicase, CrhR (Slr0083), whose expression is regulated by abiotic stresses that alter the redox potential of the photosynthetic electron transport chain, including temperature downshift. Despite its proposed effect on RNA metabolism and its known relevance in cold-stress adaptation, the reported impact of a CrhR knockout on the cold adaption of the transcriptome only identified eight affected genes. Here, we utilized a custom designed microarray to assess the impact of the absence of CrhR RNA helicase activity on the transcriptome, independent of cold stress. CrhR truncation impacts an RNA subset comprising ~10% of the ncRNA and also ~10% of the mRNA transcripts. While equal numbers of mRNAs showed increased as well as decreased abundance, more than 90% of the ncRNAs showed enhanced expression in the absence of CrhR, indicative of a negative effect on ncRNA transcription or stability. We further tested the effect of CrhR on the stability of strongly responding RNAs that identify examples of post-transcriptional and transcriptional regulation. The data suggest that CrhR impacts multiple aspects of RNA metabolism in Synechocystis.
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Affiliation(s)
- Jens Georg
- a Faculty of Biology, University of Freiburg , Freiburg , Germany
| | | | - Danuta Chamot
- b Department of Biological Sciences, University of Alberta , Edmonton , AB , Canada
| | - Anzhela Migur
- a Faculty of Biology, University of Freiburg , Freiburg , Germany
| | - Wolfgang R Hess
- a Faculty of Biology, University of Freiburg , Freiburg , Germany.,c Freiburg Institute for Advanced Studies, University of Freiburg , Freiburg , Germany
| | - George W Owttrim
- b Department of Biological Sciences, University of Alberta , Edmonton , AB , Canada
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13
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Dos Santos RF, Arraiano CM, Andrade JM. New molecular interactions broaden the functions of the RNA chaperone Hfq. Curr Genet 2019; 65:1313-1319. [PMID: 31104083 DOI: 10.1007/s00294-019-00990-y] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 05/03/2019] [Accepted: 05/06/2019] [Indexed: 01/09/2023]
Abstract
The RNA chaperone Hfq is an important bacterial post-transcriptional regulator. Most studies on Hfq are focused on the role of this protein on small non-coding RNAs (sRNAs) and messenger RNAs (mRNAs). The most well-characterized function of Hfq is its role as RNA matchmaker, promoting the base-pairing between sRNAs and their mRNA targets. However, novel substrates and previous unrecognized functions of Hfq have now been identified, which expanded the regulatory spectrum of this protein. Hfq was recently found to bind rRNA and act as a new ribosome biogenesis factor, affecting rRNA processing, ribosome assembly, translational efficiency and translational fidelity. Hfq was also found to bind tRNAs, which could provide an additional mechanism for its role on the accuracy of protein synthesis. The list of substrates does not include RNA exclusively since Hfq was shown to bind DNA, playing an important role in DNA compaction. Additionally, Hfq is also capable to establish many protein-protein interactions. Overall, the functions of the RNA-binding protein Hfq have been expanded beyond its function in small RNA-mediated regulation. The identification of additional substrates and new functions provides alternative explanations for the importance of the chaperone Hfq as a global regulator.
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Affiliation(s)
- Ricardo F Dos Santos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República, 2780-157, Oeiras, Portugal
| | - Cecília M Arraiano
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República, 2780-157, Oeiras, Portugal.
| | - José M Andrade
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República, 2780-157, Oeiras, Portugal.
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14
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Malabirade A, Partouche D, El Hamoui O, Turbant F, Geinguenaud F, Recouvreux P, Bizien T, Busi F, Wien F, Arluison V. Revised role for Hfq bacterial regulator on DNA topology. Sci Rep 2018; 8:16792. [PMID: 30429520 PMCID: PMC6235962 DOI: 10.1038/s41598-018-35060-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 10/26/2018] [Indexed: 12/11/2022] Open
Abstract
Hfq is a pleiotropic regulator that mediates several aspects of bacterial RNA metabolism. The protein notably regulates translation efficiency and RNA decay in Gram-negative bacteria, usually via its interaction with small regulatory RNA. Besides these RNA-related functions, Hfq has also been described as one of the nucleoid associated proteins shaping the bacterial chromosome. Therefore, Hfq appears as a versatile nucleic acid-binding protein, which functions are probably even more numerous than those initially suggested. For instance, E. coli Hfq, and more precisely its C-terminal region (CTR), has been shown to induce DNA compaction into a condensed form. In this paper, we establish that DNA induces Hfq-CTR amyloidogenesis, resulting in a change of DNA local conformation. Furthermore, we clarify the effect of Hfq on DNA topology. Our results evidence that, even if the protein has a strong propensity to compact DNA thanks to its amyloid region, it does not affect overall DNA topology. We confirm however that hfq gene disruption influences plasmid supercoiling in vivo, indicating that the effect on DNA topology in former reports was indirect. Most likely, this effect is related to small regulatory sRNA-Hfq-based regulation of another protein that influences DNA supercoiling, possibly a nucleoid associated protein such as H-NS or Dps. Finally, we hypothesise that this indirect effect on DNA topology explains, at least partially, the previously reported effect of Hfq on plasmid replication efficiency.
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Affiliation(s)
- Antoine Malabirade
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris Saclay, CEA Saclay, 91191, Gif-sur-Yvette, France
| | - David Partouche
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris Saclay, CEA Saclay, 91191, Gif-sur-Yvette, France.,Synchrotron SOLEIL, L'Orme des Merisiers, Saint Aubin BP48, 91192, Gif-sur-Yvette, France
| | - Omar El Hamoui
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint Aubin BP48, 91192, Gif-sur-Yvette, France
| | - Florian Turbant
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris Saclay, CEA Saclay, 91191, Gif-sur-Yvette, France
| | | | | | - Thomas Bizien
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint Aubin BP48, 91192, Gif-sur-Yvette, France
| | - Florent Busi
- Unité de Biologie Fonctionnelle et Adaptative, CNRS UMR8251, Université Paris Diderot, 75013, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, 75013, Paris, France
| | - Frank Wien
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint Aubin BP48, 91192, Gif-sur-Yvette, France
| | - Véronique Arluison
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris Saclay, CEA Saclay, 91191, Gif-sur-Yvette, France. .,Université Paris Diderot, Sorbonne Paris Cité, 75013, Paris, France.
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15
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Wang C, Pu T, Lou W, Wang Y, Gao Z, Hu B, Fan J. Hfq, a RNA Chaperone, Contributes to Virulence by Regulating Plant Cell Wall-Degrading Enzyme Production, Type VI Secretion System Expression, Bacterial Competition, and Suppressing Host Defense Response in Pectobacterium carotovorum. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2018; 31:1166-1178. [PMID: 30198820 DOI: 10.1094/mpmi-12-17-0303-r] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Hfq is a RNA chaperone and participates in a wide range of cellular processes and pathways. In this study, mutation of hfq gene from Pectobacterium carotovorum subsp. carotovorum PccS1 led to significantly reduced virulence and plant cell wall-degrading enzyme (PCWDE) activities. In addition, the mutant exhibited decreased biofilm formation and motility and greatly attenuated carbapenem production as well as secretion of hemolysin coregulated protein (Hcp) as compared with wild-type strain PccS1. Moreover, a higher level of callose deposition was induced in Nicotiana benthamiana leaves when infiltrated with the mutant. A total of 26 small (s)RNA deletion mutants were obtained among a predicted 27 sRNAs, and three mutants exhibited reduced virulence in the host plant. These results suggest that hfq plays a key role in Pectobacterium virulence by positively impacting PCWDE production, secretion of the type VI secretion system, bacterial competition, and suppression of host plant responses.
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Affiliation(s)
- Chunting Wang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Tianxin Pu
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Wangying Lou
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Yujie Wang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Zishu Gao
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Baishi Hu
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Jiaqin Fan
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
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16
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Sudo N, Soma A, Iyoda S, Oshima T, Ohto Y, Saito K, Sekine Y. Small RNA Esr41 inversely regulates expression of LEE and flagellar genes in enterohaemorrhagic Escherichia coli. MICROBIOLOGY-SGM 2018; 164:821-834. [PMID: 29580371 DOI: 10.1099/mic.0.000652] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Enterohaemorrhagic Escherichia coli (EHEC) is a life-threatening human pathogen worldwide. The locus of enterocyte effacement (LEE) in EHEC encodes a type three secretion system and effector proteins, all of which are essential for bacterial adherence to host cells. When LEE expression is activated, flagellar gene expression is down-regulated because bacterial flagella induce the immune responses of host cells at the infection stage. Therefore, this inverse regulation is also important for EHEC infection. We report here that a small regulatory RNA (sRNA), Esr41, mediates LEE repression and flagellar gene activation. Multiple copies of esr41 abolished LEE expression by down-regulating the expression of ler and pch, which encode positive regulators of LEE. This regulation led to reduced EHEC adhesion to host cells. Translational gene-reporter fusion experiments revealed that Esr41 regulates ler expression at a post-transcriptional level, and pch transcription, probably via an unknown target of Esr41. Esr41-mediated ler and pch repression was not observed in cells lacking hfq, which encodes an RNA-binding protein essential for most sRNA functions, indicating that Esr41 acts in an Hfq-dependent manner. We previously reported an increase in cell motility induced by Esr41. This motility enhancement was also observed in EHEC lacking ler, showing that Esr41-mediated enhancement of cell motility is in a ler-independent manner. In addition, Esr41 activated the expression of flagellar Class 3 genes by indirectly inducing the transcription of fliA, which encodes the sigma factor for flagellar synthesis. These results suggest that Esr41 plays important roles in the inverse regulation of LEE and flagellar gene expression.
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Affiliation(s)
- Naoki Sudo
- Department of Life Science, College of Science, Rikkyo University, Toshima, Tokyo, Japan.,Department of Bacteriology I, National Institute of Infectious Diseases, Shinjuku, Tokyo, Japan
| | - Akiko Soma
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba, Japan
| | - Sunao Iyoda
- Department of Bacteriology I, National Institute of Infectious Diseases, Shinjuku, Tokyo, Japan
| | - Taku Oshima
- Department of Biotechnology, Toyama Prefectural University, Imizu, Toyama, Japan
| | - Yui Ohto
- Department of Life Science, College of Science, Rikkyo University, Toshima, Tokyo, Japan
| | - Kenta Saito
- Department of Life Science, College of Science, Rikkyo University, Toshima, Tokyo, Japan
| | - Yasuhiko Sekine
- Department of Life Science, College of Science, Rikkyo University, Toshima, Tokyo, Japan
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17
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Malabirade A, Jiang K, Kubiak K, Diaz-Mendoza A, Liu F, van Kan JA, Berret JF, Arluison V, van der Maarel JRC. Compaction and condensation of DNA mediated by the C-terminal domain of Hfq. Nucleic Acids Res 2017; 45:7299-7308. [PMID: 28521053 PMCID: PMC5499573 DOI: 10.1093/nar/gkx431] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2017] [Accepted: 05/03/2017] [Indexed: 11/28/2022] Open
Abstract
Hfq is a bacterial protein that is involved in several aspects of nucleic acids metabolism. It has been described as one of the nucleoid associated proteins shaping the bacterial chromosome, although it is better known to influence translation and turnover of cellular RNAs. Here, we explore the role of Escherichia coli Hfq's C-terminal domain in the compaction of double stranded DNA. Various experimental methodologies, including fluorescence microscopy imaging of single DNA molecules confined inside nanofluidic channels, atomic force microscopy, isothermal titration microcalorimetry and electrophoretic mobility assays have been used to follow the assembly of the C-terminal and N-terminal regions of Hfq on DNA. Results highlight the role of Hfq's C-terminal arms in DNA binding, change in mechanical properties of the double helix and compaction of DNA into a condensed form. The propensity for bridging and compaction of DNA by the C-terminal domain might be related to aggregation of bound protein and may have implications for protein binding related gene regulation.
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Affiliation(s)
- Antoine Malabirade
- Laboratoire Léon Brillouin, CEA, CNRS, Université Paris Saclay, 91191 Gif-sur-Yvette, France
| | - Kai Jiang
- Department of Physics, National University of Singapore, 2 Science Drive 3, 117542, Singapore
| | - Krzysztof Kubiak
- Laboratoire Léon Brillouin, CEA, CNRS, Université Paris Saclay, 91191 Gif-sur-Yvette, France.,Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | | | - Fan Liu
- Department of Physics, National University of Singapore, 2 Science Drive 3, 117542, Singapore
| | - Jeroen A van Kan
- Department of Physics, National University of Singapore, 2 Science Drive 3, 117542, Singapore
| | | | - Véronique Arluison
- Laboratoire Léon Brillouin, CEA, CNRS, Université Paris Saclay, 91191 Gif-sur-Yvette, France.,Université Paris Diderot, Sorbonne Paris Cité, 75013 Paris, France
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18
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Fontaine F, Gasiorowski E, Gracia C, Ballouche M, Caillet J, Marchais A, Hajnsdorf E. The small RNA SraG participates in PNPase homeostasis. RNA (NEW YORK, N.Y.) 2016; 22:1560-1573. [PMID: 27495318 PMCID: PMC5029454 DOI: 10.1261/rna.055236.115] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 06/24/2016] [Indexed: 06/06/2023]
Abstract
The rpsO-pnp operon encodes ribosomal protein S15 and polynucleotide phosphorylase, a major 3'-5' exoribonuclease involved in mRNA decay in Escherichia coli The gene for the SraG small RNA is located between the coding regions of the rpsO and pnp genes, and it is transcribed in the opposite direction relative to the two genes. No function has been assigned to SraG. Multiple levels of post-transcriptional regulation have been demonstrated for the rpsO-pnp operon. Here we show that SraG is a new factor affecting pnp expression. SraG overexpression results in a reduction of pnp expression and a destabilization of pnp mRNA; in contrast, inhibition of SraG transcription results in a higher level of the pnp transcript. Furthermore, in vitro experiments indicate that SraG inhibits translation initiation of pnp Together, these observations demonstrate that SraG participates in the post-transcriptional control of pnp by a direct antisense interaction between SraG and PNPase RNAs. Our data reveal a new level of regulation in the expression of this major exoribonuclease.
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Affiliation(s)
- Fanette Fontaine
- CNRS UMR8261 (previously FRE3630) associated with University Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, 75005 Paris, France
| | - Elise Gasiorowski
- CNRS UMR8261 (previously FRE3630) associated with University Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, 75005 Paris, France
| | - Celine Gracia
- CNRS UMR8261 (previously FRE3630) associated with University Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, 75005 Paris, France
| | - Mathieu Ballouche
- CNRS UMR8261 (previously FRE3630) associated with University Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, 75005 Paris, France
| | - Joel Caillet
- CNRS UMR8261 (previously FRE3630) associated with University Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, 75005 Paris, France
| | - Antonin Marchais
- Institut de Génétique et Microbiologie, CNRS/UMR 8621, Université Paris Sud, 91405 Orsay, France
| | - Eliane Hajnsdorf
- CNRS UMR8261 (previously FRE3630) associated with University Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, 75005 Paris, France
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19
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Aseev LV, Koledinskaya LS, Boni IV. Regulation of Ribosomal Protein Operons rplM-rpsI, rpmB-rpmG, and rplU-rpmA at the Transcriptional and Translational Levels. J Bacteriol 2016; 198:2494-502. [PMID: 27381917 PMCID: PMC4999927 DOI: 10.1128/jb.00187-16] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 06/30/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED It is widely assumed that in the best-characterized model bacterium Escherichia coli, transcription units encoding ribosomal proteins (r-proteins) and regulation of their expression have been already well defined. However, transcription start sites for several E. coli r-protein operons have been established only very recently, so that information concerning the regulation of these operons at the transcriptional or posttranscriptional level is still missing. This paper describes for the first time the in vivo regulation of three r-protein operons, rplM-rpsI, rpmB-rpmG, and rplU-rpmA The results demonstrate that transcription of all three operons is subject to ppGpp/DksA-dependent negative stringent control under amino acid starvation, in parallel with the rRNA operons. By using single-copy translational fusions with the chromosomal lacZ gene, we show here that at the translation level only one of these operons, rplM-rpsI, is regulated by the mechanism of autogenous repression involving the 5' untranslated region (UTR) of the operon mRNA, while rpmB-rpmG and rplU-rpmA are not subject to this type of regulation. This may imply that translational feedback control is not a general rule for modulating the expression of E. coli r-protein operons. Finally, we report that L13, a primary protein in 50S ribosomal subunit assembly, serves as a repressor of rplM-rpsI expression in vivo, acting at a target within the rplM translation initiation region. Thus, L13 represents a novel example of regulatory r-proteins in bacteria. IMPORTANCE It is important to obtain a deeper understanding of the regulatory mechanisms responsible for coordinated and balanced synthesis of ribosomal components. In this paper, we highlight the major role of a stringent response in regulating transcription of three previously unexplored r-protein operons, and we show that only one of them is subject to feedback regulation at the translational level. Improved knowledge of the regulatory pathways controlling ribosome biogenesis may promote the development of novel antibacterial agents.
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Affiliation(s)
- Leonid V Aseev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia
| | | | - Irina V Boni
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia
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20
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Cech GM, Szalewska-Pałasz A, Kubiak K, Malabirade A, Grange W, Arluison V, Węgrzyn G. The Escherichia Coli Hfq Protein: An Unattended DNA-Transactions Regulator. Front Mol Biosci 2016; 3:36. [PMID: 27517037 PMCID: PMC4963395 DOI: 10.3389/fmolb.2016.00036] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 07/13/2016] [Indexed: 11/17/2022] Open
Abstract
The Hfq protein was discovered in Escherichia coli as a host factor for bacteriophage Qβ RNA replication. Subsequent studies indicated that Hfq is a pleiotropic regulator of bacterial gene expression. The regulatory role of Hfq is ascribed mainly to its function as an RNA-chaperone, facilitating interactions between bacterial non-coding RNA and its mRNA target. Thus, it modulates mRNA translation and stability. Nevertheless, Hfq is able to interact with DNA as well. Its role in the regulation of DNA-related processes has been demonstrated. In this mini-review, it is discussed how Hfq interacts with DNA and what is the role of this protein in regulation of DNA transactions. Particularly, Hfq has been demonstrated to be involved in the control of ColE1 plasmid DNA replication, transposition, and possibly also transcription. Possible mechanisms of these Hfq-mediated regulations are described and discussed.
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Affiliation(s)
- Grzegorz M Cech
- Department of Molecular Biology, University of Gdańsk Gdańsk, Poland
| | | | - Krzysztof Kubiak
- Department of Molecular Biology, University of GdańskGdańsk, Poland; Laboratoire Léon Brillouin, CEA, Centre National de la Recherche Scientifique, Université Paris Saclay, CEA SaclayGif-sur-Yvette, France; IPCMS/Centre National de la Recherche ScientifiqueStrasbourg, France
| | - Antoine Malabirade
- Laboratoire Léon Brillouin, CEA, Centre National de la Recherche Scientifique, Université Paris Saclay, CEA Saclay Gif-sur-Yvette, France
| | - Wilfried Grange
- IPCMS/Centre National de la Recherche ScientifiqueStrasbourg, France; Universite Paris Diderot, UFR Science du VivantParis, France
| | - Veronique Arluison
- Laboratoire Léon Brillouin, CEA, Centre National de la Recherche Scientifique, Université Paris Saclay, CEA SaclayGif-sur-Yvette, France; Universite Paris Diderot, UFR Science du VivantParis, France
| | - Grzegorz Węgrzyn
- Department of Molecular Biology, University of Gdańsk Gdańsk, Poland
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21
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Cayrol B, Fortas E, Martret C, Cech G, Kloska A, Caulet S, Barbet M, Trépout S, Marco S, Taghbalout A, Busi F, Wegrzyn G, Arluison V. Riboregulation of the bacterial actin-homolog MreB by DsrA small noncoding RNA. Integr Biol (Camb) 2015; 7:128-41. [PMID: 25407044 DOI: 10.1039/c4ib00102h] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The bacterial actin-homolog MreB is a key player in bacterial cell-wall biosynthesis and is required for the maintenance of the rod-like morphology of Escherichia coli. However, how MreB cellular levels are adjusted to growth conditions is poorly understood. Here, we show that DsrA, an E. coli small noncoding RNA (sRNA), is involved in the post-transcriptional regulation of mreB. DsrA is required for the downregulation of MreB cellular concentration during environmentally induced slow growth-rates, mainly growth at low temperature and during the stationary phase. DsrA interacts in an Hfq-dependent manner with the 5' region of mreB mRNA, which contains signals for translation initiation and thereby affects mreB translation and stability. Moreover, as DsrA is also involved in the regulation of two transcriptional regulators, σ(S) and the nucleoid associated protein H-NS, which negatively regulate mreB transcription, it also indirectly contributes to mreB transcriptional down-regulation. By using quantitative analyses, our results evidence the complexity of this regulation and the tangled interplay between transcriptional and post-transcriptional control. As transcription factors and sRNA-mediated post-transcriptional regulators use different timescales, we propose that the sRNA pathway helps to adapt to changes in temperature, but also indirectly mediates long-term regulation of MreB concentration. The tight regulation and fine-tuning of mreB gene expression in response to cellular stresses is discussed in regard to the effect of the MreB protein on cell elongation.
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Affiliation(s)
- Bastien Cayrol
- Laboratoire Léon Brillouin, CEA - Centre de Saclay, 91191 Gif-sur-Yvette, France.
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22
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Panda G, Tanwer P, Ansari S, Khare D, Bhatnagar R. Regulation and RNA-binding properties of Hfq-like RNA chaperones in Bacillus anthracis. Biochim Biophys Acta Gen Subj 2015; 1850:1661-8. [DOI: 10.1016/j.bbagen.2015.03.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Revised: 03/05/2015] [Accepted: 03/31/2015] [Indexed: 10/23/2022]
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23
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Aseev LV, Bylinkina NS, Boni IV. Regulation of the rplY gene encoding 5S rRNA binding protein L25 in Escherichia coli and related bacteria. RNA (NEW YORK, N.Y.) 2015; 21:851-61. [PMID: 25749694 PMCID: PMC4408793 DOI: 10.1261/rna.047381.114] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 12/22/2014] [Indexed: 05/09/2023]
Abstract
Ribosomal protein (r-protein) L25 is one of the three r-proteins (L25, L5, L18) that interact with 5S rRNA in eubacteria. Specific binding of L25 with a certain domain of 5S r-RNA, a so-called loop E, has been studied in detail, but information about regulation of L25 synthesis has remained totally lacking. In contrast to the rplE (L5) and rplR (L18) genes that belong to the polycistronic spc-operon and are regulated at the translation level by r-protein S8, the rplY (L25) gene forms an independent transcription unit. The main goal of this work was to study the regulation of the rplY expression in vivo. We show that the rplY promoter is down-regulated by ppGpp and its cofactor DksA in response to amino acid starvation. At the level of translation, the rplY expression is subjected to the negative feedback control. The 5'-untranslated region of the rplY mRNA comprises specific sequence/structure features, including an atypical SD-like sequence, which are highly conserved in a subset of gamma-proteobacterial families. Despite the lack of a canonical SD element, the rplY'-'lacZ single-copy reporter showed unusually high translation efficiency. Expression of the rplY gene in trans decreased the translation yield, indicating the mechanism of autogenous repression. Site-directed mutagenesis of the rplY 5' UTR revealed an important role of the conserved elements in the translation control. Thus, the rplY expression regulation represents one more example of regulatory pathways that control ribosome biogenesis in Escherichia coli and related bacteria.
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Affiliation(s)
- Leonid V Aseev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997, Moscow, Russia
| | - Natalia S Bylinkina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997, Moscow, Russia Moscow Institute of Physics and Technology, 141700, Moscow Region, Dolgoprudny, Russia
| | - Irina V Boni
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997, Moscow, Russia
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24
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Jiang K, Zhang C, Guttula D, Liu F, van Kan JA, Lavelle C, Kubiak K, Malabirade A, Lapp A, Arluison V, van der Maarel JRC. Effects of Hfq on the conformation and compaction of DNA. Nucleic Acids Res 2015; 43:4332-41. [PMID: 25824948 PMCID: PMC4417175 DOI: 10.1093/nar/gkv268] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 03/18/2015] [Indexed: 12/14/2022] Open
Abstract
Hfq is a bacterial pleiotropic regulator that mediates several aspects of nucleic acids metabolism. The protein notably influences translation and turnover of cellular RNAs. Although most previous contributions concentrated on Hfq's interaction with RNA, its association to DNA has also been observed in vitro and in vivo. Here, we focus on DNA-compacting properties of Hfq. Various experimental technologies, including fluorescence microscopy imaging of single DNA molecules confined inside nanofluidic channels, atomic force microscopy and small angle neutron scattering have been used to follow the assembly of Hfq on DNA. Our results show that Hfq forms a nucleoprotein complex, changes the mechanical properties of the double helix and compacts DNA into a condensed form. We propose a compaction mechanism based on protein-mediated bridging of DNA segments. The propensity for bridging is presumably related to multi-arm functionality of the Hfq hexamer, resulting from binding of the C-terminal domains to the duplex. Results are discussed in regard to previous results obtained for H-NS, with important implications for protein binding related gene regulation.
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Affiliation(s)
- Kai Jiang
- Department of Physics, National University of Singapore, 2 Science Drive 3, 117542, Singapore
| | - Ce Zhang
- Department of Physics, National University of Singapore, 2 Science Drive 3, 117542, Singapore
| | - Durgarao Guttula
- Department of Physics, National University of Singapore, 2 Science Drive 3, 117542, Singapore
| | - Fan Liu
- Department of Physics, National University of Singapore, 2 Science Drive 3, 117542, Singapore
| | - Jeroen A van Kan
- Department of Physics, National University of Singapore, 2 Science Drive 3, 117542, Singapore
| | - Christophe Lavelle
- Genomes Structure and Instability, Sorbonne Universities, National Museum of Natural History, Inserm U 1154, CNRS UMR 7196, 75005 Paris, France
| | - Krzysztof Kubiak
- Laboratoire Léon Brillouin, UMR 12 CEA/CNRS, CEA-Saclay, Gif sur Yvette Cedex 91191, France Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Antoine Malabirade
- Laboratoire Léon Brillouin, UMR 12 CEA/CNRS, CEA-Saclay, Gif sur Yvette Cedex 91191, France
| | - Alain Lapp
- Laboratoire Léon Brillouin, UMR 12 CEA/CNRS, CEA-Saclay, Gif sur Yvette Cedex 91191, France
| | - Véronique Arluison
- Laboratoire Léon Brillouin, UMR 12 CEA/CNRS, CEA-Saclay, Gif sur Yvette Cedex 91191, France Université Paris Diderot, Sorbonne Paris Cité, 75013 Paris, France
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Van Assche E, Van Puyvelde S, Vanderleyden J, Steenackers HP. RNA-binding proteins involved in post-transcriptional regulation in bacteria. Front Microbiol 2015; 6:141. [PMID: 25784899 PMCID: PMC4347634 DOI: 10.3389/fmicb.2015.00141] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Accepted: 02/06/2015] [Indexed: 11/19/2022] Open
Abstract
Post-transcriptional regulation is a very important mechanism to control gene expression in changing environments. In the past decade, a lot of interest has been directed toward the role of small RNAs (sRNAs) in bacterial post-transcriptional regulation. However, sRNAs are not the only molecules controlling gene expression at this level, RNA-binding proteins (RBPs) play an important role as well. CsrA and Hfq are the two best studied bacterial proteins of this type, but recently, additional proteins involved in post-transcriptional control have been identified. This review focuses on the general working mechanisms of post-transcriptionally active RBPs, which include (i) adaptation of the susceptibility of mRNAs and sRNAs to RNases, (ii) modulating the accessibility of the ribosome binding site of mRNAs, (iii) recruiting and assisting in the interaction of mRNAs with other molecules and (iv) regulating transcription terminator/antiterminator formation, and gives an overview of both the well-studied and the newly identified proteins that are involved in post-transcriptional regulatory processes. Additionally, the post-transcriptional mechanisms by which the expression or the activity of these proteins is regulated, are described. For many of the newly identified proteins, however, mechanistic questions remain. Most likely, more post-transcriptionally active proteins will be identified in the future.
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Affiliation(s)
- Elke Van Assche
- Centre of Microbial and Plant Genetics, Department of Molecular and Microbial Systems, KU Leuven Leuven, Belgium
| | - Sandra Van Puyvelde
- Centre of Microbial and Plant Genetics, Department of Molecular and Microbial Systems, KU Leuven Leuven, Belgium
| | - Jos Vanderleyden
- Centre of Microbial and Plant Genetics, Department of Molecular and Microbial Systems, KU Leuven Leuven, Belgium
| | - Hans P Steenackers
- Centre of Microbial and Plant Genetics, Department of Molecular and Microbial Systems, KU Leuven Leuven, Belgium
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26
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Abstract
ABSTRACT
The study of the bacterial transposons Tn
10
and Tn
5
has provided a wealth of information regarding steps in nonreplicative DNA transposition, transpososome dynamics and structure, as well as mechanisms employed to regulate transposition. The focus of ongoing research on these transposons is mainly on host regulation and the use of the Tn
10
antisense system as a platform to develop riboregulators for applications in synthetic biology. Over the past decade two new regulators of both Tn
10
and Tn
5
transposition have been identified, namely H-NS and Hfq proteins. These are both global regulators of gene expression in enteric bacteria with functions linked to stress-response pathways and virulence and potentially could link the Tn
10
and Tn
5
systems (and thus the transfer of antibiotic resistance genes) to environmental cues. Work summarized here is consistent with the H-NS protein working directly on transposition complexes to upregulate both Tn
10
and Tn
5
transposition. In contrast, evidence is discussed that is consistent with Hfq working at the level of transposase expression to downregulate both systems. With regard to Tn
10
and synthetic biology, some recent work that incorporates the Tn
10
antisense RNA into both transcriptional and translational riboswitches is summarized.
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27
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Ross JA, Trussler RS, Black MD, McLellan CR, Haniford DB. Tn5 transposition in Escherichia coli is repressed by Hfq and activated by over-expression of the small non-coding RNA SgrS. Mob DNA 2014; 5:27. [PMID: 25506402 PMCID: PMC4265352 DOI: 10.1186/s13100-014-0027-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 11/11/2014] [Indexed: 12/31/2022] Open
Abstract
Background Hfq functions in post-transcriptional gene regulation in a wide range of bacteria, usually by promoting base pairing of mRNAs with trans-encoded sRNAs. It was previously shown that Hfq down-regulates Tn10 transposition by inhibiting IS10 transposase expression at the post-transcriptional level. This provided the first example of Hfq playing a role in DNA transposition and led us to ask if a related transposon, Tn5, is similarly regulated. Results We show that Hfq strongly suppresses Tn5 transposition in Escherichia coli by inhibiting IS50 transposase expression. However, in contrast to the situation for Tn10, Hfq primarily inhibits IS50 transposase transcription. As Hfq does not typically function directly in transcription, we searched for a transcription factor that also down-regulated IS50 transposase transcription and is itself under Hfq control. We show that Crp (cyclic AMP receptor protein) fits these criteria as: (1) disruption of the crp gene led to an increase in IS50 transposase expression and the magnitude of this increase was comparable to that observed for an hfq disruption; and (2) Crp expression decreased in hfq−. We also demonstrate that IS50 transposase expression and Tn5 transposition are induced by over-expression of the sRNA SgrS and link this response to glucose limitation. Conclusions Tn5 transposition is negatively regulated by Hfq primarily through inhibition of IS50 transposase transcription. Preliminary results support the possibility that this regulation is mediated through Crp. We also provide evidence that glucose limitation activates IS50 transposase transcription and transposition. Electronic supplementary material The online version of this article (doi:10.1186/s13100-014-0027-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Joseph A Ross
- Department of Biochemistry, University of Western Ontario, London, ONN6A 5C1 Canada
| | - Ryan S Trussler
- Department of Biochemistry, University of Western Ontario, London, ONN6A 5C1 Canada
| | - Morgan D Black
- Department of Biochemistry, University of Western Ontario, London, ONN6A 5C1 Canada
| | - Crystal R McLellan
- Department of Biochemistry, University of Western Ontario, London, ONN6A 5C1 Canada
| | - David B Haniford
- Department of Biochemistry, University of Western Ontario, London, ONN6A 5C1 Canada
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Caillet J, Gracia C, Fontaine F, Hajnsdorf E. Clostridium difficile Hfq can replace Escherichia coli Hfq for most of its function. RNA (NEW YORK, N.Y.) 2014; 20:1567-1578. [PMID: 25147238 PMCID: PMC4174439 DOI: 10.1261/rna.043372.113] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Accepted: 05/31/2014] [Indexed: 06/03/2023]
Abstract
A gene for the Hfq protein is present in the majority of sequenced bacterial genomes. Its characteristic hexameric ring-like core structure is formed by the highly conserved N-terminal regions. In contrast, the C-terminal forms an extension, which varies in length, lacks homology, and is predicted to be unstructured. In Gram-negative bacteria, Hfq facilitates the pairing of sRNAs with their mRNA target and thus affects gene expression, either positively or negatively, and modulates sRNA degradation. In Gram-positive bacteria, its role is still poorly characterized. Numerous sRNAs have been detected in many Gram-positive bacteria, but it is not yet known whether these sRNAs act in association with Hfq. Compared with all other Hfqs, the C. difficile Hfq exhibits an unusual C-terminal sequence with 75% asparagine and glutamine residues, while the N-terminal core part is more conserved. To gain insight into the functionality of the C. difficile Hfq (Cd-Hfq) protein in processes regulated by sRNAs, we have tested the ability of Cd-Hfq to fulfill the functions of the E. coli Hfq (Ec-Hfq) by examining various functions associated with Hfq in both positive and negative controls of gene expression. We found that Cd-Hfq substitutes for most but not all of the tested functions of the Ec-Hfq protein. We also investigated the role of the C-terminal part of the Hfq proteins. We found that the C-terminal part of both Ec-Hfq and Cd-Hfq is not essential but contributes to some functions of both the E. coli and C. difficile chaperons.
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Affiliation(s)
- Joel Caillet
- CNRS FRE3630 (previously UPR9073), University Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, 75005 Paris, France
| | - Céline Gracia
- CNRS FRE3630 (previously UPR9073), University Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, 75005 Paris, France
| | - Fanette Fontaine
- CNRS FRE3630 (previously UPR9073), University Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, 75005 Paris, France
| | - Eliane Hajnsdorf
- CNRS FRE3630 (previously UPR9073), University Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, 75005 Paris, France
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29
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Jost D, Nowojewski A, Levine E. Regulating the many to benefit the few: role of weak small RNA targets. Biophys J 2013; 104:1773-82. [PMID: 23601324 DOI: 10.1016/j.bpj.2013.02.020] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Revised: 01/19/2013] [Accepted: 02/19/2013] [Indexed: 12/31/2022] Open
Abstract
Small regulatory RNAs are central players in the regulation of many cellular processes across all kingdoms of life. Experiments in mouse and human have shown that a typical small RNA may regulate the expression of many different genes, suggesting that small RNAs act as global regulators. It is noted though that most targets respond only weakly to the presence of the small RNA. At the same time, evidence in bacteria and animals suggest that the phenotypes associated with small RNA mutants are only due to a few of their targets. Here we assume that targets regulated by a small RNA to control function is in fact small, and propose that the role of the many other weak targets is to confer robustness to the regulation of these few principal targets. Through mathematical modeling we show that auxiliary targets may significantly buffer both number and kinetic fluctuations of the principal targets, with only minor slowdown in the kinetics of response. Analysis of genomic data suggests that auxiliary targets experience a nonspecific evolutionary pressure, playing a role at the system level. Our work is of importance for studies on small RNA functions, and impacts on the understanding of small RNA evolution.
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Affiliation(s)
- Daniel Jost
- Department of Physics and FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts, USA
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30
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Régnier P, Hajnsdorf E. The interplay of Hfq, poly(A) polymerase I and exoribonucleases at the 3' ends of RNAs resulting from Rho-independent termination: A tentative model. RNA Biol 2013; 10:602-9. [PMID: 23392248 DOI: 10.4161/rna.23664] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Discovered in eukaryotes as a modification essential for mRNA function, polyadenylation was then identified as a means used by all cells to destabilize RNA. In Escherichia coli, most accessible 3' RNA extremities are believed to be potential targets of poly(A) polymerase I. However, some RNAs might be preferentially adenylated. After a short statement of the current knowledge of poly(A) metabolism, we discuss how Hfq could affect recognition and polyadenylation of RNA terminated by Rho-independent terminators. Comparison of RNA terminus leads to the proposal that RNAs harboring 3' terminal features required for Hfq binding are not polyadenylated, whereas those lacking these structural elements can gain the oligo(A) tails that initiate exonucleolytic degradation. We also speculate that Hfq stimulates the synthesis of longer tails that could be used as Hfq-binding sites involved in non-characterized functions of Hfq-dependent sRNAs.
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Affiliation(s)
- Philippe Régnier
- University Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, Paris, France.
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31
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Small RNA modules confer different stabilities and interact differently with multiple targets. PLoS One 2013; 8:e52866. [PMID: 23349691 PMCID: PMC3551931 DOI: 10.1371/journal.pone.0052866] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Accepted: 11/22/2012] [Indexed: 01/08/2023] Open
Abstract
Bacterial Hfq-associated small regulatory RNAs (sRNAs) parallel animal microRNAs in their ability to control multiple target mRNAs. The small non-coding MicA RNA represses the expression of several genes, including major outer membrane proteins such as ompA, tsx and ecnB. In this study, we have characterised the RNA determinants involved in the stability of MicA and analysed how they influence the expression of its targets. Site-directed mutagenesis was used to construct MicA mutated forms. The 5′linear domain, the structured region with two stem-loops, the A/U-rich sequence or the 3′ poly(U) tail were altered without affecting the overall secondary structure of MicA. The stability and the target regulation abilities of the wild-type and the different mutated forms of MicA were then compared. The 5′ domain impacted MicA stability through an RNase III-mediated pathway. The two stem-loops showed different roles and disruption of stem-loop 2 was the one that mostly affected MicA stability and abundance. Moreover, STEM2 was found to be more important for the in vivo repression of both ompA and ecnB mRNAs while STEM1 was critical for regulation of tsx mRNA levels. The A/U-rich linear sequence is not the only Hfq-binding site present in MicA and the 3′ poly(U) sequence was critical for sRNA stability. PNPase was shown to be an important exoribonuclease involved in sRNA degradation. In addition to the 5′ domain of MicA, the stem-loops and the 3′ poly(U) tail are also shown to affect target-binding. Disruption of the 3′U-rich sequence greatly affects all targets analysed. In conclusion, our results have shown that it is important to understand the “sRNA anatomy” in order to modulate its stability. Furthermore, we have demonstrated that MicA RNA can use different modules to regulate its targets. This knowledge can allow for the engineering of non-coding RNAs that interact differently with multiple targets.
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32
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Insights into dynamics of mobile genetic elements in hyperthermophilic environments from five new Thermococcus plasmids. PLoS One 2013; 8:e49044. [PMID: 23326305 PMCID: PMC3543421 DOI: 10.1371/journal.pone.0049044] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Accepted: 10/03/2012] [Indexed: 12/04/2022] Open
Abstract
Mobilome of hyperthermophilic archaea dwelling in deep-sea hydrothermal vents is poorly characterized. To gain insight into genetic diversity and dynamics of mobile genetic elements in these environments we have sequenced five new plasmids from different Thermococcus strains that have been isolated from geographically remote hydrothermal vents. The plasmids were ascribed to two subfamilies, pTN2-like and pEXT9a-like. Gene content and phylogenetic analyses illuminated a robust connection between pTN2-like plasmids and Pyrococcus abyssi virus 1 (PAV1), with roughly half of the viral genome being composed of genes that have homologues in plasmids. Unexpectedly, pEXT9a-like plasmids were found to be closely related to the previously sequenced plasmid pMETVU01 from Methanocaldococcus vulcanius M7. Our data suggests that the latter observation is most compatible with an unprecedented horizontal transfer of a pEXT9a-like plasmid from Thermococcales to Methanococcales. Gene content analysis revealed that thermococcal plasmids encode Hfq-like proteins and toxin-antitoxin (TA) systems of two different families, VapBC and RelBE. Notably, although abundant in archaeal genomes, to our knowledge, TA and hfq-like genes have not been previously found in archaeal plasmids or viruses. Finally, the plasmids described here might prove to be useful in developing new genetic tools for hyperthermophiles.
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33
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Aseev LV, Chugunov AO, Efremov RG, Boni IV. A single missense mutation in a coiled-coil domain of Escherichia coli ribosomal protein S2 confers a thermosensitive phenotype that can be suppressed by ribosomal protein S1. J Bacteriol 2013; 195:95-104. [PMID: 23104805 PMCID: PMC3536177 DOI: 10.1128/jb.01305-12] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2012] [Accepted: 10/21/2012] [Indexed: 01/01/2023] Open
Abstract
Ribosomal protein S2 is an essential component of translation machinery, and its viable mutated variants conferring distinct phenotypes serve as a valuable tool in studying the role of S2 in translation regulation. One of a few available rpsB mutants, rpsB1, shows thermosensitivity and ensures enhanced expression of leaderless mRNAs. In this study, we identified the nature of the rpsB1 mutation. Sequencing of the rpsB1 allele revealed a G-to-A transition in the part of the rpsB gene which encodes a coiled-coil domain of S2. The resulting E132K substitution resides in a highly conserved site, TKKE, a so-called N-terminal capping box, at the beginning of the second alpha helix. The protruding coiled-coil domain of S2 is known to provide binding with 16S rRNA in the head of the 30S subunit and, in addition, to interact with a key mRNA binding protein, S1. Molecular dynamics simulations revealed a detrimental impact of the E132K mutation on the coiled-coil structure and thereby on the interactions between S2 and 16S rRNA, providing a clue for the thermosensitivity of the rpsB1 mutant. Using a strain producing a leaderless lacZ transcript from the chromosomal lac promoter, we demonstrated that not only the rpsB1 mutation generating S2/S1-deficient ribosomes but also the rpsA::IS10 mutation leading to partial deficiency in S1 alone increased translation efficiency of the leaderless mRNA by about 10-fold. Moderate overexpression of S1 relieved all these effects and, moreover, suppressed the thermosensitive phenotype of rpsB1, indicating the role of S1 as an extragenic suppressor of the E132K mutation.
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Affiliation(s)
- Leonid V Aseev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia
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34
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Multiple activities of RNA-binding proteins S1 and Hfq. Biochimie 2012; 94:1544-53. [DOI: 10.1016/j.biochi.2012.02.010] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Accepted: 02/10/2012] [Indexed: 01/16/2023]
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35
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Sobrero P, Valverde C. The bacterial protein Hfq: much more than a mere RNA-binding factor. Crit Rev Microbiol 2012; 38:276-99. [DOI: 10.3109/1040841x.2012.664540] [Citation(s) in RCA: 116] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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36
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Abstract
Hfq is an RNA-binding protein that is common to diverse bacterial lineages and has key roles in the control of gene expression. By facilitating the pairing of small RNAs with their target mRNAs, Hfq affects the translation and turnover rates of specific transcripts and contributes to complex post-transcriptional networks. These functions of Hfq can be attributed to its ring-like oligomeric architecture, which presents two non-equivalent binding surfaces that are capable of multiple interactions with RNA molecules. Distant homologues of Hfq occur in archaea and eukaryotes, reflecting an ancient origin for the protein family and hinting at shared functions. In this Review, we describe the salient structural and functional features of Hfq and discuss possible mechanisms by which this protein can promote RNA interactions to catalyse specific and rapid regulatory responses in vivo.
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Affiliation(s)
- Jörg Vogel
- Institute for Molecular Infection Biology, University of Würzburg, Joseph-Schneider-Strasse 2, D-97080 Würzburg, Germany.
| | - Ben F. Luisi
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK.
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37
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Chiang MK, Lu MC, Liu LC, Lin CT, Lai YC. Impact of Hfq on global gene expression and virulence in Klebsiella pneumoniae. PLoS One 2011; 6:e22248. [PMID: 21779404 PMCID: PMC3136514 DOI: 10.1371/journal.pone.0022248] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2011] [Accepted: 06/17/2011] [Indexed: 11/18/2022] Open
Abstract
Klebsiella pneumoniae is responsible for a wide range of clinical symptoms. How this bacterium adapts itself to ever-changing host milieu is still a mystery. Recently, small non-coding RNAs (sRNAs) have received considerable attention for their functions in fine-tuning gene expression at a post-transcriptional level to promote bacterial adaptation. Here we demonstrate that Hfq, an RNA-binding protein, which facilitates interactions between sRNAs and their mRNA targets, is critical for K. pneumoniae virulence. A K. pneumoniae mutant lacking hfq (Δhfq) failed to disseminate into extra-intestinal organs and was attenuated on induction of a systemic infection in a mouse model. The absence of Hfq was associated with alteration in composition of envelope proteins, increased production of capsular polysaccharides, and decreased resistance to H2O2, heat shock, and UV irradiation. Microarray-based transcriptome analyses revealed that 897 genes involved in numerous cellular processes were deregulated in the Δhfq strain. Interestingly, Hfq appeared to govern expression of many genes indirectly by affecting sigma factor RpoS and RpoE, since 19.5% (175/897) and 17.3% (155/897) of Hfq-dependent genes belong to the RpoE- and RpoS-regulon, respectively. These results indicate that Hfq regulates global gene expression at multiple levels to modulate the physiological fitness and virulence potential of K. pneumoniae.
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Affiliation(s)
- Ming-Ko Chiang
- Department of Life Science, National Chung-Cheng University, Chia-Yi, Taiwan
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38
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Rabhi M, Espéli O, Schwartz A, Cayrol B, Rahmouni AR, Arluison V, Boudvillain M. The Sm-like RNA chaperone Hfq mediates transcription antitermination at Rho-dependent terminators. EMBO J 2011; 30:2805-16. [PMID: 21673658 DOI: 10.1038/emboj.2011.192] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2010] [Accepted: 05/26/2011] [Indexed: 11/09/2022] Open
Abstract
In Escherichia coli, the essential motor protein Rho promotes transcription termination in a tightly controlled manner that is not fully understood. Here, we show that the general post-transcriptional regulatory protein Hfq associates with Rho to regulate Rho function. The Hfq:Rho complex can be further stabilized by RNA bridging both factors in a configuration that inhibits the ATP hydrolysis and duplex unwinding activities of Rho and that mediates transcription antitermination at Rho-dependent terminators in vitro and in vivo. Antitermination at a prototypical terminator (λtR1) requires Hfq binding to an A/U-rich transcript region directly upstream from the terminator. Antitermination is modulated by trans-acting factors (NusG or nucleic acid competitors) that affect Hfq association with Rho or RNA. These data unveil a new Hfq function and a novel transcription regulatory mechanism with potentially important implications for bacterial RNA metabolism, gene silencing, and pathogenicity.
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Affiliation(s)
- Makhlouf Rabhi
- Centre de Biophysique Moléculaire, CNRS UPR4301, rue Charles Sadron, Orléans Cedex 2, France
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39
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Hfq is required for optimal nitrate assimilation in the Cyanobacterium Anabaena sp. strain PCC 7120. J Bacteriol 2011; 193:3546-55. [PMID: 21602329 DOI: 10.1128/jb.00254-11] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Hfq is an RNA binding protein involved in posttranscriptional regulation of gene expression in bacteria. It acts by binding to regulatory small RNAs (sRNAs), which confer specificity for the regulation. Recently, orthologues of the Hfq protein were annotated in cyanobacterial genomes, although its capacity to regulate gene expression by interacting with sRNAs has not been yet demonstrated. Anabaena sp. strain PCC 7120 is a filamentous cyanobacterium that, in the absence of combined nitrogen, is able to fix atmospheric nitrogen by differentiating specialized cells called heterocysts. We have generated an hfq knockout mutant of Anabaena sp. PCC 7120. Deletion of this gene results in differentiation of heterocysts in the presence of nitrate, suggesting a defect in nitrate assimilation. We show that hfq mutant cells are affected in transport and use of nitrate and nitrite. An analysis of the expression of several genes in the nir operon, encoding different elements of the nitrate assimilation pathway, demonstrates a downregulation of their transcription in mutant cells. We also observed that genes ntcB and cnaT, involved in the regulation of the nir operon, show a lower expression in cells lacking Hfq. Finally, when hfq was reintroduced in the mutant, heterocyst differentiation was no longer observed in the presence of nitrate. Therefore, our results indicate that the RNA chaperone Hfq is involved in the regulation of the nir operon, although the mechanism for this regulation is still unknown.
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40
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Mitchell RJ, Lee SK, Kim T, Ghim CM. Microbial linguistics: perspectives and applications of microbial cell-to-cell communication. BMB Rep 2011; 44:1-10. [PMID: 21266100 DOI: 10.5483/bmbrep.2011.44.1.1] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Inter-cellular communication via diffusible small molecules is a defining character not only of multicellular forms of life but also of single-celled organisms. A large number of bacterial genes are regulated by the change of chemical milieu mediated by the local population density of its own species or others. The cell density-dependent "autoinducer" molecules regulate the expression of those genes involved in genetic competence, biofilm formation and persistence, virulence, sporulation, bioluminescence, antibiotic production, and many others. Recent innovations in recombinant DNA technology and micro-/nano-fluidics systems render the genetic circuitry responsible for cell-to-cell communication feasible to and malleable via synthetic biological approaches. Here we review the current understanding of the molecular biology of bacterial intercellular communication and the novel experimental protocols and platforms used to investigate this phenomenon. A particular emphasis is given to the genetic regulatory circuits that provide the standard building blocks which constitute the syntax of the biochemical communication network. Thus, this review gives focus to the engineering principles necessary for rewiring bacterial chemo-communication for various applications, ranging from population-level gene expression control to the study of host-pathogen interactions.
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Affiliation(s)
- Robert J Mitchell
- School of Nano-Bioscience and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Korea
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41
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Abstract
During the last decade small regulatory RNA (srRNA) emerged as central players in the regulation of gene expression in all kingdoms of life. Multiple pathways for srRNA biogenesis and diverse mechanisms of gene regulation may indicate that srRNA regulation evolved independently multiple times. However, small RNA pathways share numerous properties, including the ability of a single srRNA to regulate multiple targets. Some of the mechanisms of gene regulation by srRNAs have significant effect on the abundance of free srRNAs that are ready to interact with new targets. This results in indirect interactions among seemingly unrelated genes, as well as in a crosstalk between different srRNA pathways. Here we briefly review and compare the major srRNA pathways, and argue that the impact of srRNA is always at the system level. We demonstrate how a simple mathematical model can ease the discussion of governing principles. To demonstrate these points we review a few examples from bacteria and animals.
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Affiliation(s)
- Daniel Jost
- Department of Physics, FAS Center for Systems Biology, Harvard University, Cambridge MA 02138, USA
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Updegrove TB, Correia JJ, Chen Y, Terry C, Wartell RM. The stoichiometry of the Escherichia coli Hfq protein bound to RNA. RNA (NEW YORK, N.Y.) 2011; 17:489-500. [PMID: 21205841 PMCID: PMC3039148 DOI: 10.1261/rna.2452111] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2010] [Accepted: 11/24/2010] [Indexed: 05/30/2023]
Abstract
The Escherichia coli RNA binding protein Hfq is involved in many aspects of post-transcriptional gene expression. Tight binding of Hfq to polyadenylate sequences at the 3' end of mRNAs influences exonucleolytic degradation, while Hfq binding to small noncoding RNAs (sRNA) and their targeted mRNAs facilitate their hybridization which in turn effects translation. Hfq binding to an A-rich tract in the 5' leader region of the rpoS mRNA and to the sRNA DsrA have been shown to be important for DsrA enhanced translation initiation of this mRNA. The complexes of Hfq-A(18) and Hfq-DsrA provide models for understanding how Hfq interacts with these two RNA sequence/structure motifs. Different methods have reported different values for the stoichiometry of Hfq-A(18) and Hfq-DsrA. In this work, mass spectrometry and analytical ultracentrifugation provide direct evidence that the strong binding mode of the Hfq hexamer (Hfq(6)) for A(18) and domain II of DsrA (DsrA(DII)) involve 1:1 complexes. This stoichiometry was also supported by fluorescence anisotropy and a competition gel mobility shift experiment using wild-type and truncated Hfq. More limited studies of Hfq binding to DsrA as well as to the sRNAs RprA, OxyS, and an 18-nt segment of OxyS were also consistent with 1:1 stoichiometry. Mass spectrometry of cross-linked samples of Hfq(6), A(18), and DsrA(DII) exhibit intensity corresponding to a ternary 1:1:1 complex; however, the small intensity of this peak and fluorescence anisotropy experiments did not provide evidence that this ternary complex is stable in solution.
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Affiliation(s)
- Taylor B Updegrove
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
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Geinguenaud F, Calandrini V, Teixeira J, Mayer C, Liquier J, Lavelle C, Arluison V. Conformational transition of DNA bound to Hfq probed by infrared spectroscopy. Phys Chem Chem Phys 2011; 13:1222-9. [DOI: 10.1039/c0cp01084g] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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E. coli DNA associated with isolated Hfq interacts with Hfq's distal surface and C-terminal domain. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2010; 1799:588-96. [PMID: 20619373 DOI: 10.1016/j.bbagrm.2010.06.007] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2010] [Revised: 06/15/2010] [Accepted: 06/29/2010] [Indexed: 11/20/2022]
Abstract
The RNA-binding protein Hfq has been studied extensively for its function as a modulator of gene expression at the post-transcriptional level. While most Hfq studies have focused on the protein's interaction with sRNAs and mRNAs, Hfq binding to DNA has been observed but is less explored. During the isolation of Hfq from Escherichiacoli, we found genomic DNA fragments associated with the protein after multiple steps of purification. Sequences of 41 amplified segments from the DNA fragments associated with Hfq were determined. A large fraction of the DNA segments were predicted to have significant helical axis curvature and were from genes associated with membrane proteins, characteristics unexpected for non-specific binding. Analysis by analytical ultracentrifugation indicated that rA(18) binding to Hfq disrupts Hfq-DNA interactions. The latter observation suggests Hfq binding to DNA involves its distal surface. This was supported by a gel mobility shift assay that showed single amino acid mutations on the distal surface of Hfq inhibited Hfq binding to duplex DNA, while six of seven mutations on the proximal surface and outer circumference of the hexamer did not prevent Hfq binding. Two mutated Hfq which have portions of their C-terminal domain removed also failed to bind to DNA. The apparent K(d) for binding wild type Hfq to several duplex DNA was estimated from a gel mobility shift assay to be ~400nM.
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Arraiano CM, Andrade JM, Domingues S, Guinote IB, Malecki M, Matos RG, Moreira RN, Pobre V, Reis FP, Saramago M, Silva IJ, Viegas SC. The critical role of RNA processing and degradation in the control of gene expression. FEMS Microbiol Rev 2010; 34:883-923. [PMID: 20659169 DOI: 10.1111/j.1574-6976.2010.00242.x] [Citation(s) in RCA: 260] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The continuous degradation and synthesis of prokaryotic mRNAs not only give rise to the metabolic changes that are required as cells grow and divide but also rapid adaptation to new environmental conditions. In bacteria, RNAs can be degraded by mechanisms that act independently, but in parallel, and that target different sites with different efficiencies. The accessibility of sites for degradation depends on several factors, including RNA higher-order structure, protection by translating ribosomes and polyadenylation status. Furthermore, RNA degradation mechanisms have shown to be determinant for the post-transcriptional control of gene expression. RNases mediate the processing, decay and quality control of RNA. RNases can be divided into endonucleases that cleave the RNA internally or exonucleases that cleave the RNA from one of the extremities. Just in Escherichia coli there are >20 different RNases. RNase E is a single-strand-specific endonuclease critical for mRNA decay in E. coli. The enzyme interacts with the exonuclease polynucleotide phosphorylase (PNPase), enolase and RNA helicase B (RhlB) to form the degradosome. However, in Bacillus subtilis, this enzyme is absent, but it has other main endonucleases such as RNase J1 and RNase III. RNase III cleaves double-stranded RNA and family members are involved in RNA interference in eukaryotes. RNase II family members are ubiquitous exonucleases, and in eukaryotes, they can act as the catalytic subunit of the exosome. RNases act in different pathways to execute the maturation of rRNAs and tRNAs, and intervene in the decay of many different mRNAs and small noncoding RNAs. In general, RNases act as a global regulatory network extremely important for the regulation of RNA levels.
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Affiliation(s)
- Cecília M Arraiano
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Apartado 127, 2781-901 Oeiras, Portugal.
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The small RNA Aar in Acinetobacter baylyi: a putative regulator of amino acid metabolism. Arch Microbiol 2010; 192:691-702. [PMID: 20559624 DOI: 10.1007/s00203-010-0592-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2010] [Revised: 05/20/2010] [Accepted: 05/24/2010] [Indexed: 10/19/2022]
Abstract
Small non-coding RNAs (sRNAs) are key players in prokaryotic metabolic circuits, allowing the cell to adapt to changing environmental conditions. Regulatory interference by sRNAs in cellular metabolism is often facilitated by the Sm-like protein Hfq. A search for novel sRNAs in A. baylyi intergenic regions was performed by a biocomputational screening. One candidate, Aar, encoded between trpS and sucD showed Hfq dependency in Northern blot analysis. Aar was expressed strongly during stationary growth phase in minimal medium; in contrast, in complex medium, strongest expression was in the exponential growth phase. Whereas over-expression of Aar in trans did not affect bacterial growth, seven mRNA targets predicted by two in silico approaches were upregulated in stationary growth phase. All seven mRNAs are involved in A. baylyi amino acid metabolism. A putative binding site for Lrp, the global regulator of branched-chain amino acids in E. coli, was observed within the aar gene. Both facts imply an Aar participation in amino acid metabolism.
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