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Malecka EM, Bassani F, Dendooven T, Sonnleitner E, Rozner M, Albanese TG, Resch A, Luisi B, Woodson S, Bläsi U. Stabilization of Hfq-mediated translational repression by the co-repressor Crc in Pseudomonas aeruginosa. Nucleic Acids Res 2021; 49:7075-7087. [PMID: 34139006 PMCID: PMC8266614 DOI: 10.1093/nar/gkab510] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 05/26/2021] [Accepted: 06/15/2021] [Indexed: 01/02/2023] Open
Abstract
In Pseudomonas aeruginosa the RNA chaperone Hfq and the catabolite repression control protein (Crc) govern translation of numerous transcripts during carbon catabolite repression. Here, Crc was shown to enhance Hfq-mediated translational repression of several mRNAs. We have developed a single-molecule fluorescence assay to quantitatively assess the cooperation of Hfq and Crc to form a repressive complex on a RNA, encompassing the translation initiation region and the proximal coding sequence of the P. aeruginosa amiE gene. The presence of Crc did not change the amiE RNA-Hfq interaction lifetimes, whereas it changed the equilibrium towards more stable repressive complexes. This observation is in accord with Cryo-EM analyses, which showed an increased compactness of the repressive Hfq/Crc/RNA assemblies. These biophysical studies revealed how Crc protein kinetically stabilizes Hfq/RNA complexes, and how the two proteins together fold a large segment of the mRNA into a more compact translationally repressive structure. In fact, the presence of Crc resulted in stronger translational repression in vitro and in a significantly reduced half-life of the target amiE mRNA in vivo. Although Hfq is well-known to act with small regulatory RNAs, this study shows how Hfq can collaborate with another protein to down-regulate translation of mRNAs that become targets for the degradative machinery.
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Affiliation(s)
- Ewelina M Malecka
- Department of Biophysics, 3400 N. Charles Street, Johns Hopkins University, Baltimore, MD-21218, USA
| | - Flavia Bassani
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Dr. Bohrgasse 9/4, 1030 Vienna, Austria
| | - Tom Dendooven
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Elisabeth Sonnleitner
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Dr. Bohrgasse 9/4, 1030 Vienna, Austria
| | - Marlena Rozner
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Dr. Bohrgasse 9/4, 1030 Vienna, Austria
| | - Tanino G Albanese
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Dr. Bohrgasse 9/4, 1030 Vienna, Austria
| | - Armin Resch
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Dr. Bohrgasse 9/4, 1030 Vienna, Austria
| | - Ben Luisi
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Sarah Woodson
- Department of Biophysics, 3400 N. Charles Street, Johns Hopkins University, Baltimore, MD-21218, USA
| | - Udo Bläsi
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Dr. Bohrgasse 9/4, 1030 Vienna, Austria
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2
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Ahmed F, Sharma M, Al-Ghamdi AA, Al-Yami SM, Al-Salami AM, Refai MY, Warsi MK, Howladar SM, Baeshen MN. A Comprehensive Analysis of cis-Acting RNA Elements in the SARS-CoV-2 Genome by a Bioinformatics Approach. Front Genet 2020; 11:572702. [PMID: 33424918 PMCID: PMC7786107 DOI: 10.3389/fgene.2020.572702] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 10/14/2020] [Indexed: 01/08/2023] Open
Abstract
The emergence of a new coronavirus (CoV), severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), responsible for severe respiratory disease in humans termed coronavirus disease of 2019 (COVID-19), became a new global threat for health and the economy. The SARS-CoV-2 genome is about a 29,800-nucleotide-long plus-strand RNA that can form functionally important secondary and higher-order structures called cis-acting RNA elements. These elements can interact with viral proteins, host proteins, or other RNAs and be involved in regulating translation and replication processes of the viral genome and encapsidation of the virus. However, the cis-acting RNA elements and their biological roles in SARS-CoV-2 as well as their comparative analysis in the closely related viral genome have not been well explored, which is very important to understand the molecular mechanism of viral infection and pathogenies. In this study, we used a bioinformatics approach to identify the cis-acting RNA elements in the SARS-CoV-2 genome. Initially, we aligned the full genomic sequence of six different CoVs, and a phylogenetic analysis was performed to understand their evolutionary relationship. Next, we predicted the cis-acting RNA elements in the SARS-CoV-2 genome using the structRNAfinder tool. Then, we annotated the location of these cis-acting RNA elements in different genomic regions of SARS-CoV-2. After that, we analyzed the sequence conservation patterns of each cis-acting RNA element among the six CoVs. Finally, the presence of cis-acting RNA elements across different CoV genomes and their comparative analysis was performed. Our study identified 12 important cis-acting RNA elements in the SARS-CoV-2 genome; among them, Corona_FSE, Corona_pk3, and s2m are highly conserved across most of the studied CoVs, and Thr_leader, MAT2A_D, and MS2 are uniquely present in SARS-CoV-2. These RNA structure elements can be involved in viral translation, replication, and encapsidation and, therefore, can be potential targets for better treatment of COVID-19. It is imperative to further characterize these cis-acting RNA elements experimentally for a better mechanistic understanding of SARS-CoV-2 infection and therapeutic intervention.
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Affiliation(s)
- Firoz Ahmed
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah, Saudi Arabia
- University of Jeddah Center for Scientific and Medical Research, University of Jeddah, Jeddah, Saudi Arabia
| | - Monika Sharma
- Department of Chemical Sciences, Indian Institute of Science Education and Research, Mohali, India
| | | | | | | | - Mohammed Y. Refai
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah, Saudi Arabia
- University of Jeddah Center for Scientific and Medical Research, University of Jeddah, Jeddah, Saudi Arabia
| | - Mohiuddin Khan Warsi
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah, Saudi Arabia
- University of Jeddah Center for Scientific and Medical Research, University of Jeddah, Jeddah, Saudi Arabia
| | - Saad M. Howladar
- Department of Biology, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Mohammed N. Baeshen
- Department of Biology, College of Science, University of Jeddah, Jeddah, Saudi Arabia
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3
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Barquist L, Langridge GC, Turner DJ, Phan MD, Turner AK, Bateman A, Parkhill J, Wain J, Gardner PP. A comparison of dense transposon insertion libraries in the Salmonella serovars Typhi and Typhimurium. Nucleic Acids Res 2013; 41:4549-64. [PMID: 23470992 PMCID: PMC3632133 DOI: 10.1093/nar/gkt148] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Salmonella Typhi and Typhimurium diverged only ∼50 000 years ago, yet have very different host ranges and pathogenicity. Despite the availability of multiple whole-genome sequences, the genetic differences that have driven these changes in phenotype are only beginning to be understood. In this study, we use transposon-directed insertion-site sequencing to probe differences in gene requirements for competitive growth in rich media between these two closely related serovars. We identify a conserved core of 281 genes that are required for growth in both serovars, 228 of which are essential in Escherichia coli. We are able to identify active prophage elements through the requirement for their repressors. We also find distinct differences in requirements for genes involved in cell surface structure biogenesis and iron utilization. Finally, we demonstrate that transposon-directed insertion-site sequencing is not only applicable to the protein-coding content of the cell but also has sufficient resolution to generate hypotheses regarding the functions of non-coding RNAs (ncRNAs) as well. We are able to assign probable functions to a number of cis-regulatory ncRNA elements, as well as to infer likely differences in trans-acting ncRNA regulatory networks.
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Affiliation(s)
- Lars Barquist
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK.
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4
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Abstract
Regulatory 5' untranslated regions (r5'UTRs) of mRNAs such as riboswitches modulate the expression of genes involved in varied biological processes in both bacteria and eukaryotes. New high-throughput sequencing technologies could provide powerful tools for discovery of novel r5'UTRs, but the size and complexity of the datasets generated by these technologies makes it difficult to differentiate r5'UTRs from the multitude of other types of RNAs detected. Here, we developed and implemented a bioinformatic approach to identify putative r5'UTRs from within large datasets of RNAs recently identified by pyrosequencing of the Vibrio cholerae small transcriptome. This screen yielded only approximately 1% of all non-overlapping RNAs along with 75% of previously annotated r5'UTRs and 69 candidate V. cholerae r5'UTRs. These candidates include several putative functional homologues of diverse r5'UTRs characterized in other species as well as numerous candidates upstream of genes involved in pathways not known to be regulated by r5'UTRs, such as fatty acid oxidation and peptidoglycan catabolism. Two of these novel r5'UTRs were experimentally validated using a GFP reporter-based approach. Our findings suggest that the number and diversity of pathways regulated by r5'UTRs has been underestimated and that deep sequencing-based transcriptomics will be extremely valuable in the search for novel r5'UTRs.
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Affiliation(s)
- Jonathan Livny
- The Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA.
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5
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Ulvé VM, Sevin EW, Chéron A, Barloy-Hubler F. Identification of chromosomal alpha-proteobacterial small RNAs by comparative genome analysis and detection in Sinorhizobium meliloti strain 1021. BMC Genomics 2007; 8:467. [PMID: 18093320 PMCID: PMC2245857 DOI: 10.1186/1471-2164-8-467] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2007] [Accepted: 12/19/2007] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Small untranslated RNAs (sRNAs) seem to be far more abundant than previously believed. The number of sRNAs confirmed in E. coli through various approaches is above 70, with several hundred more sRNA candidate genes under biological validation. Although the total number of sRNAs in any one species is still unclear, their importance in cellular processes has been established. However, unlike protein genes, no simple feature enables the prediction of the location of the corresponding sequences in genomes. Several approaches, of variable usefulness, to identify genomic sequences encoding sRNA have been described in recent years. RESULTS We used a combination of in silico comparative genomics and microarray-based transcriptional profiling. This approach to screening identified ~60 intergenic regions conserved between Sinorhizobium meliloti and related members of the alpha-proteobacteria sub-group 2. Of these, 14 appear to correspond to novel non-coding sRNAs and three are putative peptide-coding or 5' UTR RNAs (ORF smaller than 100 aa). The expression of each of these new small RNA genes was confirmed by Northern blot hybridization. CONCLUSION Small non coding RNA (sra) genes can be found in the intergenic regions of alpha-proteobacteria genomes. Some of these sra genes are only present in S. meliloti, sometimes in genomic islands; homologues of others are present in related genomes including those of the pathogens Brucella and Agrobacterium.
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Affiliation(s)
- Vincent M Ulvé
- CNRS UMR6061 Génétique et Développement, Groupe Modèles Génétiques, Université de Rennes 1, IFR140 GFAS, Faculté de médecine, 2 avenue du Professeur Léon Bernard, CS 34317, 35043 Rennes Cedex, France.
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6
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Laursen BS, Sørensen HP, Mortensen KK, Sperling-Petersen HU. Initiation of protein synthesis in bacteria. Microbiol Mol Biol Rev 2005; 69:101-23. [PMID: 15755955 PMCID: PMC1082788 DOI: 10.1128/mmbr.69.1.101-123.2005] [Citation(s) in RCA: 415] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Valuable information on translation initiation is available from biochemical data and recently solved structures. We present a detailed description of current knowledge about the structure, function, and interactions of the individual components involved in bacterial translation initiation. The first section describes the ribosomal features relevant to the initiation process. Subsequent sections describe the structure, function, and interactions of the mRNA, the initiator tRNA, and the initiation factors IF1, IF2, and IF3. Finally, we provide an overview of mechanisms of regulation of the translation initiation event. Translation occurs on ribonucleoprotein complexes called ribosomes. The ribosome is composed of a large subunit and a small subunit that hold the activities of peptidyltransfer and decode the triplet code of the mRNA, respectively. Translation initiation is promoted by IF1, IF2, and IF3, which mediate base pairing of the initiator tRNA anticodon to the mRNA initiation codon located in the ribosomal P-site. The mechanism of translation initiation differs for canonical and leaderless mRNAs, since the latter is dependent on the relative level of the initiation factors. Regulation of translation occurs primarily in the initiation phase. Secondary structures at the mRNA ribosomal binding site (RBS) inhibit translation initiation. The accessibility of the RBS is regulated by temperature and binding of small metabolites, proteins, or antisense RNAs. The future challenge is to obtain atomic-resolution structures of complete initiation complexes in order to understand the mechanism of translation initiation in molecular detail.
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Affiliation(s)
- Brian Søgaard Laursen
- Department of Molecular Biology, Aarhus University, Gustav Wieds vej 10C, DK-8000 Aarhus C, Denmark
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7
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Abstract
Translational repression results from a complex choreography of macromolecular interactions interfering with the formation of translational initiation complexes. The relationship between the rate and extent of formation of these interactions to form repressed mRNA complexes determines the extent of repression. A novel analysis of repression mechanisms is presented here and it indicates that the reversibility of repressed complex formation influences the steady state balance of the distribution of translationally active and inactive complexes and therefore has an impact on the efficiency of repression. Reviewed here is evidence for three distinct translational repression mechanisms, regulating expression of the transcription factor sigma32, threonine tRNA synthetase and ribosomal proteins on the alpha operon in Escherichia coli. Efficient regulation of expression in these systems makes use of specific mRNA structures in quite different ways.
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Affiliation(s)
- Paula Jean Schlax
- Department of Chemistry, Program in Biological Chemistry, Bates College, 5 Andrews Road, Lewiston, Maine 04240, USA.
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8
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Scott LG, Williamson JR. Interaction of the Bacillus stearothermophilus ribosomal protein S15 with its 5'-translational operator mRNA. J Mol Biol 2001; 314:413-22. [PMID: 11846555 DOI: 10.1006/jmbi.2001.5165] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The Bacillus stearothermophilus ribosomal protein S15 (BS15) binds both a three-helix junction in the central domain of 16 S ribosomal RNA and its cognate mRNA. Native gel mobility-shift assays show that BS15 interacts specifically and with high affinity to the 5'-untranslated region (5'-UTR) of this cognate mRNA with an apparent dissociation constant of 3(+/-0.3) nM. In order to localize the structural elements that are essential for BS15 recognition, a series of deletion mutants of the full cognate mRNA were prepared and tested in the same gel-shift assay. The minimal binding site for BS15 is a 50 nucleotide RNA showing a close secondary structure resemblance to the BS15 binding region from 16 S rRNA. There are two major structural motifs that must be maintained for high-affinity binding. The first being a purine-rich three-helix junction, and the second being an internal loop. The sequence identity of the internal loops differs greatly between the BS15 mRNA and rRNA sites, and this difference is correlated to discrimination between wild-type BS15 and a BS15(H45R) mutant. The association and dissociation kinetics measured for the 5'-UTR-BS15 interaction are quite slow, but are typical for a ribosomal protein-RNA interaction. The BS15 mRNA and 16 S rRNA binding sites share a common secondary structure yet have little sequence identity. The mRNA and rRNA may in fact present similar if not identical structural elements that confer BS15 recognition.
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MESH Headings
- 5' Untranslated Regions/chemistry
- 5' Untranslated Regions/genetics
- 5' Untranslated Regions/metabolism
- Amino Acid Sequence
- Base Sequence
- Cloning, Molecular
- Electrophoretic Mobility Shift Assay
- Geobacillus stearothermophilus/genetics
- Geobacillus stearothermophilus/metabolism
- Kinetics
- Models, Molecular
- Molecular Sequence Data
- Mutation/genetics
- Nucleic Acid Conformation
- Operator Regions, Genetic/genetics
- Protein Biosynthesis/genetics
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 16S/metabolism
- RNA-Binding Proteins/isolation & purification
- RNA-Binding Proteins/metabolism
- Ribosomal Proteins/isolation & purification
- Ribosomal Proteins/metabolism
- Substrate Specificity
- Titrimetry
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Affiliation(s)
- L G Scott
- Department of Molecular Biology and Skaggs Institute for Chemical Biology, MB33, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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9
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Affiliation(s)
- E Fuchs
- Institute of Molecular Genetics, University of Heidelberg, Germany
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10
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Choquet Y, Stern DB, Wostrikoff K, Kuras R, Girard-Bascou J, Wollman FA. Translation of cytochrome f is autoregulated through the 5' untranslated region of petA mRNA in Chlamydomonas chloroplasts. Proc Natl Acad Sci U S A 1998; 95:4380-5. [PMID: 9539745 PMCID: PMC22497 DOI: 10.1073/pnas.95.8.4380] [Citation(s) in RCA: 100] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
A process that we refer to as control by epistasy of synthesis (CES process) occurs during chloroplast protein biogenesis in Chlamydomonas reinhardtii: the synthesis of some chloroplast-encoded subunits, the CES subunits, is strongly attenuated when some other subunits from the same complex, the dominant subunits, are missing. Herein we investigate the molecular basis of the CES process for the biogenesis of the cytochrome b6f complex and show that negative autoregulation of cytochrome f translation occurs in the absence of other complex subunits. This autoregulation is mediated by an interaction, either direct or indirect, between the 5' untranslated region of petA mRNA, which encodes cytochrome f, and the C-terminal domain of the unassembled protein. This model for the regulation of cytochrome f translation explains both the decreased rate of cytochrome f synthesis in vivo in the absence of its assembly partners and its increase in synthesis when significant accumulation of the C-terminal domain of the protein is prevented. When expressed from a chimeric mRNA containing the atpA 5' untranslated region, cytochrome f no longer showed an assembly-dependent regulation of translation. Conversely, the level of antibiotic resistance conferred by a chimeric petA-aadA-rbcL gene was shown to depend on the state of assembly of cytochrome b6f complexes and on the accumulation of the C-terminal domain of cytochrome f. We discuss the possible ubiquity of the CES process in organellar protein biogenesis.
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Affiliation(s)
- Y Choquet
- Unité Propre de Recherche 9072/Centre National de la Recherche Scientifique, Institut de Biologie Physico-Chimique, 13, rue P. et M. Curie, 75005 Paris, France
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