151
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Micevski D, Dougan DA. Proteolytic regulation of stress response pathways in Escherichia coli. Subcell Biochem 2013; 66:105-28. [PMID: 23479439 DOI: 10.1007/978-94-007-5940-4_5] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Maintaining correct cellular function is a fundamental biological process for all forms of life. A critical aspect of this process is the maintenance of protein homeostasis (proteostasis) in the cell, which is largely performed by a group of proteins, referred to as the protein quality control (PQC) network. This network of proteins, comprised of chaperones and proteases, is critical for maintaining proteostasis not only during favourable growth conditions, but also in response to stress. Indeed proteases play a crucial role in the clearance of unwanted proteins that accumulate during stress, but more importantly, in the activation of various different stress response pathways. In bacteria, the cells response to stress is usually orchestrated by a specific transcription factor (sigma factor). In Escherichia coli there are seven different sigma factors, each of which responds to a particular stress, resulting in the rapid expression of a specific set of genes. The cellular concentration of each transcription factor is tightly controlled, at the level of transcription, translation and protein stability. Here we will focus on the proteolytic regulation of two sigma factors (σ(32) and σ(S)), which control the heat and general stress response pathways, respectively. This review will also briefly discuss the role proteolytic systems play in the clearance of unwanted proteins that accumulate during stress.
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Affiliation(s)
- Dimce Micevski
- Department of Biochemistry, La Trobe Institute for Molecular Science (LIMS), La Trobe University, Melbourne, 3086, Australia
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152
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Trigui H, Mendis N, Li L, Saad M, Faucher SP. Facets of small RNA-mediated regulation in Legionella pneumophila. Curr Top Microbiol Immunol 2013; 376:53-80. [PMID: 23918178 DOI: 10.1007/82_2013_347] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Legionella pneumophila is a water-borne pathogen that causes a severe lung infection in humans. It is able to replicate inside amoeba in the water environment, and inside lung macrophages in humans. Efficient regulation of gene expression is critical for responding to the conditions that L. pneumophila encounters and for intracellular multiplication in host cells. In the last two decades, many reports have contributed to our understanding of the critical importance of small regulatory RNAs (sRNAs) in the regulatory network of bacterial species. This report presents the current state of knowledge about the sRNAs expressed by L. pneumophila and discusses a few regulatory pathways in which sRNAs should be involved in this pathogen.
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Affiliation(s)
- Hana Trigui
- Faculty of Agricultural and Environmental Sciences, Department of Natural Resource Sciences, McGill University, Ste-Anne-de-Bellevue, QC, H9X 3V9, Canada,
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153
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Mackie GA. RNase E: at the interface of bacterial RNA processing and decay. Nat Rev Microbiol 2012; 11:45-57. [DOI: 10.1038/nrmicro2930] [Citation(s) in RCA: 236] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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154
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Rentschler AE, Lovrich SD, Fitton R, Enos-Berlage J, Schwan WR. OmpR regulation of the uropathogenic Escherichia coli fimB gene in an acidic/high osmolality environment. MICROBIOLOGY-SGM 2012; 159:316-327. [PMID: 23175504 DOI: 10.1099/mic.0.059386-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Uropathogenic Escherichia coli (UPEC) causes more than 90 % of all human urinary tract infections through type 1 piliated UPEC cells binding to bladder epithelial cells. The FimB and FimE site-specific recombinases orient the fimS element containing the fimA structural gene promoter. Regulation of fimB and fimE depends on environmental pH and osmolality. The EnvZ/OmpR two-component system affects osmoregulation in E. coli. To ascertain if OmpR directly regulated the fimB gene promoters, gel mobility shift and DNase I footprinting experiments were performed using OmpR or phosphorylated OmpR (OmpR-P) mixed with the fimB promoter regions of UPEC strain NU149. Both OmpR-P and OmpR bound weakly to one fimB promoter. Because there was weak binding to one fimB promoter, strain NU149 was grown in different pH and osmolality environments, and total RNAs were extracted from each population and converted to cDNAs. Quantitative reverse-transcriptase PCR showed no differences in ompR transcription among the different growth conditions. Conversely, Western blots showed a significant increase in OmpR protein in UPEC cells grown in a combined low pH/high osmolality environment versus a neutral pH/high osmolality environment. In a high osmolality environment, the ompR mutant expressed more fimB transcripts and Phase-ON positioning of the fimS element as well as higher type 1 pili levels than wild-type cells. Together these results suggest that OmpR may be post-transcriptionally regulated in UPEC cells growing in a low pH/high osmolality environment, which regulates fimB in UPEC.
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155
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Hayashi G, Hong C, Hagihara M, Nakatani K. Activation of prokaryotic translation by antisense oligonucleotides binding to coding region of mRNA. Biochem Biophys Res Commun 2012; 429:105-10. [PMID: 23111330 DOI: 10.1016/j.bbrc.2012.10.072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Accepted: 10/19/2012] [Indexed: 01/21/2023]
Abstract
A few examples of translational activation by antisense small noncoding RNAs (sRNAs) have already been discovered in prokaryotic cells, and all of them are through a sense-antisense interaction at the 5'-untranslated region (5'-UTR) of target mRNAs. Here, we report a novel phenomenon of translational activation of prokaryotic gene expression with trans-acting antisense oligonucleotides targeting the coding region of mRNA. Screening of antisense oligonucleotides complementary to the coding sequences of GFP or ZsGreen identified antisense sequences that activate translation of the mRNAs in a concentration-dependent manner. We also found that the translational activation highly depends on the hybridization positions of the antisense strands. Translation-activating antisense oligonucleotides (TAOs) tended to bind to the 5'-region rather than the 3'-region of the mRNA coding region. RNA folding simulation suggested that TAOs may disrupt the structured elements around the translation initiation region (TIR) by pairing with complementary sequences in the mRNA coding region, resulting in an increase in translation efficiency. Further, we demonstrate that number and position of locked nucleic acid (LNA) bases in the antisense strands govern the tendency of up- or down-regulation. Our findings described here may lead to the discovery of a new class of antisense sRNA and the development of a tool for activating desired gene expression in the future.
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Affiliation(s)
- Gosuke Hayashi
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Japan
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156
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ncRNAs and thermoregulation: a view in prokaryotes and eukaryotes. FEBS Lett 2012; 586:4061-9. [PMID: 23098758 DOI: 10.1016/j.febslet.2012.10.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Revised: 10/09/2012] [Accepted: 10/10/2012] [Indexed: 11/24/2022]
Abstract
During cellular stress response, a widespread inhibition of transcription and blockade of splicing and other post-transcriptional processing is detected, while certain specific genes are induced. In particular, free-living cells constantly monitor temperature. When the thermal condition changes, they activate a set of genes coding for proteins that participate in the response. Non-coding RNAs, ncRNAs, and conformational changes in specific regions of mRNAs seem also to be crucial regulators that enable the cell to adjust its physiology to environmental changes. They exert their effects following the same principles in all organisms and may affect all steps of gene expression. These ncRNAs and structural elements as related to thermal stress response in bacteria are reviewed. The resemblances to eukaryotic ncRNAs are highlighted.
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157
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Tattersall J, Rao GV, Runac J, Hackstadt T, Grieshaber SS, Grieshaber NA. Translation inhibition of the developmental cycle protein HctA by the small RNA IhtA is conserved across Chlamydia. PLoS One 2012; 7:e47439. [PMID: 23071807 PMCID: PMC3469542 DOI: 10.1371/journal.pone.0047439] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2011] [Accepted: 09/17/2012] [Indexed: 11/18/2022] Open
Abstract
The developmental cycle of the obligate intracellular pathogen Chlamydia trachomatis serovar L2 is controlled in part by the small non-coding RNA (sRNA), IhtA. All Chlamydia alternate in a regulated fashion between the infectious elementary body (EB) and the replicative reticulate body (RB) which asynchronously re-differentiates back to the terminal EB form at the end of the cycle. The histone like protein HctA is central to RB:EB differentiation late in the cycle as it binds to and occludes the genome, thereby repressing transcription and translation. The sRNA IhtA is a critical component of this regulatory loop as it represses translation of hctA until late in infection at which point IhtA transcription decreases, allowing HctA expression to occur and RB to EB differentiation to proceed. It has been reported that IhtA is expressed during infection by the human pathogens C. trachomatis serovars L2, D and L2b and C. pneumoniae. We show in this work that IhtA is also expressed by the animal pathogens C. caviae and C. muridarum. Expression of HctA in E. coli is lethal and co-expression of IhtA relieves this phenotype. To determine if regulation of HctA by IhtA is a conserved mechanism across pathogenic chlamydial species, we cloned hctA and ihtA from C. trachomatis serovar D, C. muridarum, C. caviae and C. pneumoniae and assayed for rescue of growth repression in E. coli co-expression studies. In each case, co-expression of ihtA with the cognate hctA resulted in relief of growth repression. In addition, expression of each chlamydial species IhtA rescued the lethal phenotype of C. trachomatis serovar L2 HctA expression. As biolayer interferometry studies indicate that IhtA interacts directly with hctA message for all species tested, we predict that conserved sequences of IhtA are necessary for function and/or binding.
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Affiliation(s)
- Jeremiah Tattersall
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, Florida, United States of America
| | - Geeta Vittal Rao
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, Florida, United States of America
| | - Justin Runac
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, Florida, United States of America
| | - Ted Hackstadt
- Host-Parasite Interactions Section, Laboratory of Intracellular Parasites, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, Montana, United States of America
| | - Scott S. Grieshaber
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, Florida, United States of America
| | - Nicole A. Grieshaber
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, Florida, United States of America
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158
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Horstmann N, Orans J, Valentin-Hansen P, Shelburne SA, Brennan RG. Structural mechanism of Staphylococcus aureus Hfq binding to an RNA A-tract. Nucleic Acids Res 2012; 40:11023-35. [PMID: 22965117 PMCID: PMC3505971 DOI: 10.1093/nar/gks809] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Hfq is a post-transcriptional regulator that plays a key role in bacterial gene expression by binding AU-rich sequences and A-tracts to facilitate the annealing of sRNAs to target mRNAs and to affect RNA stability. To understand how Hfq from the Gram-positive bacterium Staphylococcus aureus (Sa) binds A-tract RNA, we determined the crystal structure of an Sa Hfq–adenine oligoribonucleotide complex. The structure reveals a bipartite RNA-binding motif on the distal face that is composed of a purine nucleotide-specificity site (R-site) and a non-discriminating linker site (L-site). The (R–L)-binding motif, which is also utilized by Bacillus subtilis Hfq to bind (AG)3A, differs from the (A–R–N) tripartite poly(A) RNA-binding motif of Escherichia coli Hfq whereby the Sa Hfq R-site strongly prefers adenosine, is more aromatic and permits deeper insertion of the adenine ring. R-site adenine-stacking residue Phe30, which is conserved among Gram-positive bacterial Hfqs, and an altered conformation about β3 and β4 eliminate the adenosine-specificity site (A-site) and create the L-site. Binding studies show that Sa Hfq binds (AU)3A ≈ (AG)3A ≥ (AC)3A > (AA)3A and L-site residue Lys33 plays a significant role. The (R–L) motif is likely utilized by Hfqs from most Gram-positive bacteria to bind alternating (A–N)n RNA.
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Affiliation(s)
- Nicola Horstmann
- Department of Biochemistry and Molecular Biology, UT MD Anderson Cancer Center, Houston, TX 77030, USA
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159
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de Almeida Ribeiro E, Beich-Frandsen M, Konarev PV, Shang W, Večerek B, Kontaxis G, Hämmerle H, Peterlik H, Svergun DI, Bläsi U, Djinović-Carugo K. Structural flexibility of RNA as molecular basis for Hfq chaperone function. Nucleic Acids Res 2012; 40:8072-84. [PMID: 22718981 PMCID: PMC3439903 DOI: 10.1093/nar/gks510] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Revised: 05/05/2012] [Accepted: 05/09/2012] [Indexed: 12/22/2022] Open
Abstract
In enteric bacteria, many small regulatory RNAs (sRNAs) associate with the RNA chaperone host factor Q (Hfq) and often require the protein for regulation of target mRNAs. Previous studies suggested that the hexameric Escherichia coli Hfq (Hfq(Ec)) binds sRNAs on the proximal site, whereas the distal site has been implicated in Hfq-mRNA interactions. Employing a combination of small angle X-ray scattering, nuclear magnetic resonance and biochemical approaches, we report the structural analysis of a 1:1 complex of Hfq(Ec) with a 34-nt-long subsequence of a natural substrate sRNA, DsrA (DsrA(34)). This sRNA is involved in post-transcriptional regulation of the E. coli rpoS mRNA encoding the stationary phase sigma factor RpoS. The molecular envelopes of Hfq(Ec) in complex with DsrA(34) revealed an overall asymmetric shape of the complex in solution with the protein maintaining its doughnut-like structure, whereas the extended DsrA(34) is flexible and displays an ensemble of different spatial arrangements. These results are discussed in terms of a model, wherein the structural flexibility of RNA ligands bound to Hfq stochastically facilitates base pairing and provides the foundation for the RNA chaperone function inherent to Hfq.
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Affiliation(s)
- Euripedes de Almeida Ribeiro
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria, EMBL-Hamburg c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany, Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Dr. Bohrgasse 9, A-1030 Vienna, Austria, Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria and Department of Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Aškerčeva 5, 1000 Ljubljana, Slovenia
| | - Mads Beich-Frandsen
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria, EMBL-Hamburg c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany, Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Dr. Bohrgasse 9, A-1030 Vienna, Austria, Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria and Department of Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Aškerčeva 5, 1000 Ljubljana, Slovenia
| | - Petr V. Konarev
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria, EMBL-Hamburg c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany, Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Dr. Bohrgasse 9, A-1030 Vienna, Austria, Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria and Department of Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Aškerčeva 5, 1000 Ljubljana, Slovenia
| | - Weifeng Shang
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria, EMBL-Hamburg c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany, Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Dr. Bohrgasse 9, A-1030 Vienna, Austria, Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria and Department of Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Aškerčeva 5, 1000 Ljubljana, Slovenia
| | - Branislav Večerek
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria, EMBL-Hamburg c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany, Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Dr. Bohrgasse 9, A-1030 Vienna, Austria, Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria and Department of Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Aškerčeva 5, 1000 Ljubljana, Slovenia
| | - Georg Kontaxis
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria, EMBL-Hamburg c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany, Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Dr. Bohrgasse 9, A-1030 Vienna, Austria, Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria and Department of Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Aškerčeva 5, 1000 Ljubljana, Slovenia
| | - Hermann Hämmerle
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria, EMBL-Hamburg c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany, Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Dr. Bohrgasse 9, A-1030 Vienna, Austria, Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria and Department of Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Aškerčeva 5, 1000 Ljubljana, Slovenia
| | - Herwig Peterlik
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria, EMBL-Hamburg c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany, Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Dr. Bohrgasse 9, A-1030 Vienna, Austria, Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria and Department of Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Aškerčeva 5, 1000 Ljubljana, Slovenia
| | - Dmitri I. Svergun
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria, EMBL-Hamburg c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany, Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Dr. Bohrgasse 9, A-1030 Vienna, Austria, Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria and Department of Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Aškerčeva 5, 1000 Ljubljana, Slovenia
| | - Udo Bläsi
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria, EMBL-Hamburg c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany, Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Dr. Bohrgasse 9, A-1030 Vienna, Austria, Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria and Department of Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Aškerčeva 5, 1000 Ljubljana, Slovenia
| | - Kristina Djinović-Carugo
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria, EMBL-Hamburg c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany, Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Dr. Bohrgasse 9, A-1030 Vienna, Austria, Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria and Department of Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Aškerčeva 5, 1000 Ljubljana, Slovenia
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160
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Eisenhut M, Georg J, Klähn S, Sakurai I, Mustila H, Zhang P, Hess WR, Aro EM. The antisense RNA As1_flv4 in the Cyanobacterium Synechocystis sp. PCC 6803 prevents premature expression of the flv4-2 operon upon shift in inorganic carbon supply. J Biol Chem 2012; 287:33153-62. [PMID: 22854963 PMCID: PMC3460422 DOI: 10.1074/jbc.m112.391755] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The functional relevance of natural cis-antisense transcripts is mostly unknown. Here we have characterized the association of three antisense RNAs and one intergenically encoded noncoding RNA with an operon that plays a crucial role in photoprotection of photosystem II under low carbon conditions in the cyanobacterium Synechocystis sp. PCC 6803. Cyanobacteria show strong gene expression dynamics in response to a shift of cells from high carbon to low levels of inorganic carbon (Ci), but the regulatory mechanisms are poorly understood. Among the most up-regulated genes in Synechocystis are flv4, sll0218, and flv2, which are organized in the flv4-2 operon. The flavodiiron proteins encoded by this operon open up an alternative electron transfer route, likely starting from the QB site in photosystem II, under photooxidative stress conditions. Our expression analysis of cells shifted from high carbon to low carbon demonstrated an inversely correlated transcript accumulation of the flv4-2 operon mRNA and one antisense RNA to flv4, designated as As1_flv4. Overexpression of As1_flv4 led to a decrease in flv4-2 mRNA. The promoter activity of as1_flv4 was transiently stimulated by Ci limitation and negatively regulated by the AbrB-like transcription regulator Sll0822, whereas the flv4-2 operon was positively regulated by the transcription factor NdhR. The results indicate that the tightly regulated antisense RNA As1_flv4 establishes a transient threshold for flv4-2 expression in the early phase after a change in Ci conditions. Thus, it prevents unfavorable synthesis of the proteins from the flv4-2 operon.
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Affiliation(s)
- Marion Eisenhut
- Department of Biochemistry and Food Science, Plant Physiology and Molecular Biology, University of Turku, Turku FI-20014, Finland
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161
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Matallana-Surget S, Joux F, Wattiez R, Lebaron P. Proteome analysis of the UVB-resistant marine bacterium Photobacterium angustum S14. PLoS One 2012; 7:e42299. [PMID: 22870314 PMCID: PMC3411663 DOI: 10.1371/journal.pone.0042299] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2012] [Accepted: 07/03/2012] [Indexed: 12/22/2022] Open
Abstract
The proteome of the marine bacterium Photobacterium angustum S14 was exposed to UVB and analyzed by the implementation of both the post-digest ICPL labeling method and 2D-DIGE technique using exponentially growing cells. A total of 40 and 23 proteins were quantified in all replicates using either the ICPL or 2D-DIGE methods, respectively. By combining both datasets from 8 biological replicates (4 biological replicates for each proteomics technique), 55 proteins were found to respond significantly to UVB radiation in P. angustum. A total of 8 UVB biomarkers of P. angustum were quantified in all replicates using both methods. Among them, the protein found to present the highest increase in abundance (almost a 3-fold change) was RecA, which is known to play a crucial role in the so-called recombinational repair process. We also observed a high number of antioxidants, transport proteins, metabolism-related proteins, transcription/translation regulators, chaperonins and proteases. We also discuss and compare the UVB response and global protein expression profiles obtained for two different marine bacteria with trophic lifestyles: the copiotroph P. angustum and oligotroph Sphingopyxis alaskensis.
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Affiliation(s)
- Sabine Matallana-Surget
- UPMC Univ Paris 06, UMR7621, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique, Banyuls/mer, France.
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162
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Hfq influences multiple transport systems and virulence in the plant pathogen Agrobacterium tumefaciens. J Bacteriol 2012; 194:5209-17. [PMID: 22821981 DOI: 10.1128/jb.00510-12] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The Hfq protein mediates gene regulation by small RNAs (sRNAs) in about 50% of all bacteria. Depending on the species, phenotypic defects of an hfq mutant range from mild to severe. Here, we document that the purified Hfq protein of the plant pathogen and natural genetic engineer Agrobacterium tumefaciens binds to the previously described sRNA AbcR1 and its target mRNA atu2422, which codes for the substrate binding protein of an ABC transporter taking up proline and γ-aminobutyric acid (GABA). Several other ABC transporter components were overproduced in an hfq mutant compared to their levels in the parental strain, suggesting that Hfq plays a major role in controlling the uptake systems and metabolic versatility of A. tumefaciens. The hfq mutant showed delayed growth, altered cell morphology, and reduced motility. Although the DNA-transferring type IV secretion system was produced, tumor formation by the mutant strain was attenuated, demonstrating an important contribution of Hfq to plant transformation by A. tumefaciens.
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163
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Antisense RNA that affects Rhodopseudomonas palustris quorum-sensing signal receptor expression. Proc Natl Acad Sci U S A 2012; 109:12141-6. [PMID: 22778415 DOI: 10.1073/pnas.1200243109] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Quorum sensing in the bacterium Rhodopseudomonas palustris involves the RpaI signal synthase, which produces p-coumaroyl-homoserine lactone (pC-HSL) and RpaR, which is a pC-HSL-dependent transcriptional activator. There is also an antisense rpaR transcript (asrpaR) of unknown function. Recent RNAseq studies have revealed that bacterial antisense RNAs are abundant, but little is known about the function of these molecules. Because asrpaR expression is quorum sensing dependent, we sought to characterize its production and function. We show that asrpaR is approximately 300-600 bases and is produced in response to pC-HSL and RpaR. There is an RpaR-binding site centered 51.5 bp from the mapped asrpaR transcript start site. We show that asrpaR overexpression reduces RpaR levels, rpaI expression, and pC-HSL production. We also generated an asrpaR mutant, which shows elevated RpaR levels, and elevated rpaI expression. Thus, asrpaR inhibits rpaR translation, and this inhibition results in suppression of RpaR-dependent rpaI expression and, thus, pC-HSL production. The R. palustris asrpaR represents an antisense RNA for which an activity can be measured and for which a distinct regulatory circuit related to a function is elucidated. It also represents yet another subtle regulatory layer for acyl-homoserine lactone quorum-sensing signal-responsive transcription factors.
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164
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Dong TG, Mekalanos JJ. Characterization of the RpoN regulon reveals differential regulation of T6SS and new flagellar operons in Vibrio cholerae O37 strain V52. Nucleic Acids Res 2012; 40:7766-75. [PMID: 22723378 PMCID: PMC3439928 DOI: 10.1093/nar/gks567] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
The alternative sigma factor RpoN is an essential colonization factor of Vibrio cholerae and controls important cellular functions including motility and type VI secretion (T6SS). The RpoN regulon has yet to be clearly defined in T6SS-active V. cholerae isolates, which use T6SS to target both bacterial competitors and eukaryotic cells. We hypothesize that T6SS-dependent secreted effectors are co-regulated by RpoN. To systemically identify RpoN-controlled genes, we used chromatin immunoprecipitation coupled with sequencing (ChIP-Seq) and transcriptome analysis (RNA-Seq) to determine RpoN-binding sites and RpoN-controlled gene expression. There were 68 RpoN-binding sites and 82 operons positively controlled by RpoN, among which 37 operons had ChIP-identified binding sites. A consensus RpoN-binding motif was identified with a highly conserved thymine (−14) and an AT-rich region in the middle between the hallmark RpoN-recognized motif GG(−24)/GC(−12). There were seven new RpoN-dependent promoters in the flagellar regions. We identified a small RNA, flaX, downstream of the major flagellin gene flaA. Mutation of flaX substantially reduced motility. In contrast to previous results, we report that RpoN positively regulates the expression of hcp operons and vgrG3 that encode T6SS secreted proteins but has no effect on the expression of the main T6SS cluster encoding sheath and other structural components.
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Affiliation(s)
- Tao G Dong
- Department of Microbiology and Immunobiology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
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165
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Salim NN, Faner MA, Philip JA, Feig AL. Requirement of upstream Hfq-binding (ARN)x elements in glmS and the Hfq C-terminal region for GlmS upregulation by sRNAs GlmZ and GlmY. Nucleic Acids Res 2012; 40:8021-32. [PMID: 22661574 PMCID: PMC3439879 DOI: 10.1093/nar/gks392] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Hfq is an important RNA-binding protein that helps bacteria adapt to stress. Its primary function is to promote pairing between trans-acting small non-coding RNAs (sRNAs) and their target mRNAs. Identification of essential Hfq-binding motifs in up-stream regions of rpoS and fhlA led us to ask the question whether these elements are a common occurrence among other Hfq-dependent mRNAs as well. Here, we confirm the presence of a similar (ARN)x motif in glmS RNA, a gene controlled by two sRNAs (GlmZ and GlmY) in an Hfq-dependent manner. GlmZ represents a canonical sRNA:mRNA pairing system, whereas GlmY is non-canonical, interfacing with the RNA processing protein YhbJ. We show that glmS interacts with both Hfq-binding surfaces in the absence of sRNAs. Even though two (ARN)x motifs are present, using a glmS:gfp fusion system, we determined that only one specific (ARN)x element is essential for regulation. Furthermore, we show that residues 66–72 in the C-terminal extension of Escherichia coli Hfq are essential for activation of GlmS expression by GlmY, but not with GlmZ. This result shows that the C-terminal extension of Hfq may be required for some forms of non-canonical sRNA regulation involving ancillary components such as additional RNAs or proteins.
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Affiliation(s)
- Nilshad N Salim
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA
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166
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Stauffer LT, Stauffer GV. The Escherichia coli GcvB sRNA Uses Genetic Redundancy to Control cycA Expression. ISRN MICROBIOLOGY 2012; 2012:636273. [PMID: 23724327 PMCID: PMC3658540 DOI: 10.5402/2012/636273] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2012] [Accepted: 03/19/2012] [Indexed: 11/23/2022]
Abstract
The Escherichia coli sRNA GcvB regulates several genes involved in transport of amino acids and peptides (sstT, oppA, dppA, and cycA). Two regions of GcvB from nt +124 to +161 and from nt +73 to +82 are complementary with essentially the same region of the cycA mRNA. Transcriptional fusions of cycA to lacZ showed the region of cycA mRNA that can pair with either region of GcvB is necessary for regulation by GcvB. However, mutations in either region of gcvB predicted to disrupt pairing between cycA mRNA and GcvB did not alter expression of a cycA-lacZ translational fusion. A genetic analysis identified nts in GcvB necessary for regulation of the cycA-lacZ fusion. The results show that either region of GcvB complementary to cycA mRNA can basepair with and independently repress cycA-lacZ and both regions need to be changed to cause a significant loss of repression.
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167
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Desnoyers G, Massé E. Noncanonical repression of translation initiation through small RNA recruitment of the RNA chaperone Hfq. Genes Dev 2012; 26:726-39. [PMID: 22474262 DOI: 10.1101/gad.182493.111] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The RNA chaperone Hfq is mostly known to help small regulatory RNAs (sRNAs) interact with target mRNAs to block initiating ribosomes. In this model, whereas the sRNA is directly competing with initiating 30S ribosomal subunits, Hfq plays only an indirect role, allowing optimal sRNA-mRNA pairing. Here we report that Hfq is recruited by a sRNA, Spot42, to bind to a precise AU-rich region in the vicinity of the translation initiation region (TIR) of sdhC mRNA and competes directly with 30S ribosomal subunits. We show that the sRNA Spot42 binds sdhC too far upstream of the TIR to directly repress translation initiation in vitro and in vivo. Contrary to the canonical model of sRNA regulation, this suggests a new mechanism where Hfq is directly involved in the translational repression of the target mRNA and where the sRNA acts only as a recruitment factor.
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Affiliation(s)
- Guillaume Desnoyers
- RNA Group, Department of Biochemistry, University of Sherbrooke, Sherbrooke, Quebec J1H 5N4, Canada
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168
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Bardill JP, Hammer BK. Non-coding sRNAs regulate virulence in the bacterial pathogen Vibrio cholerae. RNA Biol 2012; 9:392-401. [PMID: 22546941 DOI: 10.4161/rna.19975] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Vibrio cholerae is the waterborne bacterium responsible for worldwide outbreaks of the acute, potentially fatal cholera diarrhea. The primary factors this human pathogen uses to cause the disease are controlled by a complex regulatory program linking extracellular signaling inputs to changes in expression of several critical virulence genes. Recently it has been uncovered that many non-coding regulatory sRNAs are important components of the V. cholerae virulence regulon. Most of these sRNAs appear to require the RNA-binding protein, Hfq, to interact with and alter the expression of target genes, while a few sRNAs appear to function by an Hfq-independent mechanism. Direct base-pairing between the sRNAs and putative target mRNAs has been shown in a few cases but the extent of each sRNAs regulon is not fully known. Genetic and biochemical methods, coupled with computational and genomics approaches, are being used to validate known sRNAs and also to identify many additional putative sRNAs that may play a role in the pathogenic lifestyle of V. cholerae.
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Affiliation(s)
- J Patrick Bardill
- School of Biology, Georgia Institute of Technology, Atlanta, GA, USA
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169
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Hébrard M, Kröger C, Srikumar S, Colgan A, Händler K, Hinton JCD. sRNAs and the virulence of Salmonella enterica serovar Typhimurium. RNA Biol 2012; 9:437-45. [PMID: 22546935 PMCID: PMC3384567 DOI: 10.4161/rna.20480] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The combination of genomics and high-throughput cDNA sequencing technologies has facilitated the identification of many small RNAs (sRNAs) that play a central role in the post-transcriptional gene regulation of Salmonella enterica serovar Typhimurium. To date, most of the functionally characterized sRNAs have been involved in the regulation of processes which are not directly linked to virulence. Just five sRNAs have been found to affect the ability of Salmonella to replicate within mammalian cells, but the precise regulatory mechanisms that are used by sRNAs to control Salmonella pathogenicity at the post-transcriptional level remain to be identified. It is anticipated that an improved understanding of sRNA biology will shed new light on the virulence of Salmonella.
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Affiliation(s)
- Magali Hébrard
- Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin, Ireland
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170
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Guantes R, Cayrol B, Busi F, Arluison V. Positive regulatory dynamics by a small noncoding RNA: speeding up responses under temperature stress. MOLECULAR BIOSYSTEMS 2012; 8:1707-15. [PMID: 22456827 DOI: 10.1039/c2mb05479e] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Recent discoveries of noncoding regulatory RNAs have led to further understanding of the elements controlling genetic expression. In E. coli, most of those ncRNAs for which functional knowledge is available were shown to be dependent on the Hfq RNA chaperone and to act as inhibitors of translation by base pairing with their mRNA target. Nevertheless, there are also some examples where the sRNA plays a role of a translational activator, structurally enhancing ribosome binding to mRNA. In this work, we seek to understand the dynamics of DsrA-based positive regulation of rpoS mRNA, encoding the σ(S) RNA polymerase subunit, and to understand how it helps to mitigate environmental stress in bacteria. Our analysis is based on the first absolute quantification of the copy number of both the sRNA and of its corresponding mRNA in combination with mathematical models for post-transcriptional regulation. We show that on average, DsrA is present at a ratio of 3 to 24 copies per cell, while an rpoS transcript is present at a level of 1 to 4 copies per cell, both levels increasing when temperature is decreased. Our analysis supports the idea that temperature dependency of DsrA degradation is not a crucial condition for the attainment of observed DsrA steady levels, but highlights that this may have a marked influence on the dynamics of the regulation, notably to speed up the time of recovery to normal RNA levels after ending the stress signal. Further, our analysis also reveals how reversibility of RNA complex formation and σ(S)-regulated degradation act to reduce intrinsic noise in σ(S) induction. Taking into account the importance of this master regulator, which allows E. coli as well as other important pathogens to survive their environment, the present work contributes to complete the panel of multiple signals used to regulate bacterial transcription.
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Affiliation(s)
- Raúl Guantes
- Department of Condensed Matter Physics and Materials Science Institute Nicolás Cabrera, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain.
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171
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Thermodynamic and kinetic analysis of an RNA kissing interaction and its resolution into an extended duplex. Biophys J 2012; 102:1097-107. [PMID: 22404932 DOI: 10.1016/j.bpj.2011.12.052] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2011] [Revised: 12/22/2011] [Accepted: 12/30/2011] [Indexed: 11/22/2022] Open
Abstract
Kissing hairpin interactions form when the loop residues of two hairpins have Watson-Crick complementarity. In a unimolecular context, kissing interactions are important for tertiary folding and pseudoknot formation, whereas in a bimolecular context, they provide a basis for molecular recognition. In some cases, kissing complexes can be a prelude to strand displacement reactions where the two hairpins resolve to form a stable extended intermolecular duplex. The kinetics and thermodynamics of kissing-complex formation and their subsequent strand-displacement reactions are poorly understood. Here, biophysical techniques including isothermal titration calorimetry, surface plasmon resonance, and single-molecule fluorescence have been employed to probe the factors that govern the stability of kissing complexes and their subsequent structural rearrangements. We show that the general understanding of RNA duplex formation can be extended to kissing complexes but that kissing complexes display an unusual level of stability relative to simple duplexes of the same sequence. These interactions form and break many times at room temperature before becoming committed to a slow, irreversible forward transition to the strand-displaced form. Furthermore, using smFRET we show that the primary difference between stable and labile kissing complexes is based almost completely on their off rates. Both stable and labile complexes form at the same rate within error, but less stable species dissociate rapidly, allowing us to understand how these complexes can help generate specificity along a folding pathway or during a gene regulation event.
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172
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Monteiro C, Papenfort K, Hentrich K, Ahmad I, Le Guyon S, Reimann R, Grantcharova N, Römling U. Hfq and Hfq-dependent small RNAs are major contributors to multicellular development in Salmonella enterica serovar Typhimurium. RNA Biol 2012; 9:489-502. [PMID: 22336758 DOI: 10.4161/rna.19682] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The RNA chaperone Hfq and its associated small RNAs (sRNAs) regulate a variety of phenotypes in bacteria. In this work, we show that Hfq is a master regulator of biofilm formation in Salmonella enterica serovar Typhimurium. Hfq and two Hfq-dependent sRNAs (ArcZ and SdsR) are required for rdar morphotype expression in S. typhimurium. Hfq controls rdar biofilm formation through the major biofilm regulator CsgD. While csgD mRNA steady-state levels are altered in a sdsR mutant, ArcZ seems to work mainly at the post-transcriptional level. Overexpression of ArcZ complemented rdar morphotype formation of an hfq mutant under plate-grown conditions. Although ArcZ activates rpoS expression, its effect on csgD expression is mainly independent of RpoS. ArcZ does not only regulate rdar morphotype expression, but also the transition between sessility and motility and the timing of type 1 fimbriae vs. curli fimbriae surface-attachment at ambient temperature. Consequently, ArcZ is a major regulator of rdar biofilm development.
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Affiliation(s)
- Claudia Monteiro
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden
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173
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Holmqvist E, Unoson C, Reimegård J, Wagner EGH. A mixed double negative feedback loop between the sRNA MicF and the global regulator Lrp. Mol Microbiol 2012; 84:414-27. [PMID: 22324810 DOI: 10.1111/j.1365-2958.2012.07994.x] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Roughly 10% of all genes in Escherichia coli are controlled by the global transcription factor Lrp, which responds to nutrient availability. Bioinformatically, we identified lrp as one of several putative targets for the sRNA MicF, which is transcriptionally downregulated by Lrp. Deleting micF results in higher Lrp levels, while overexpression of MicF inhibits Lrp synthesis. This effect is by antisense; mutations in the predicted interaction region relieve MicF-dependent repression of Lrp synthesis, and regulation is restored by compensatory mutations. In vitro, MicF sterically interferes with initiation complex formation and inhibits lrp mRNA translation. In vivo, MicF indirectly activates genes in the Lrp regulon by repressing Lrp, and causes severely impaired growth in minimal medium, a phenotype characteristic of lrp deletion strains. The double negative feedback between MicF and Lrp may promote a switch for adequate Lrp-dependent adaptation to nutrient availability. Lrp adds to the growing list of transcription factors that are targeted by sRNAs, thus indicating that perhaps the majority of all bacterial genes may be directly or indirectly controlled by sRNAs.
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Affiliation(s)
- Erik Holmqvist
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Box 596, S-75124 Uppsala, Sweden. SciLifeLab, Uppsala, Sweden
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174
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Thomason MK, Fontaine F, De Lay N, Storz G. A small RNA that regulates motility and biofilm formation in response to changes in nutrient availability in Escherichia coli. Mol Microbiol 2012; 84:17-35. [PMID: 22289118 DOI: 10.1111/j.1365-2958.2012.07965.x] [Citation(s) in RCA: 158] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In bacteria, many small regulatory RNAs (sRNAs) are induced in response to specific environmental signals or stresses and act by base-pairing with mRNA targets to affect protein translation or mRNA stability. In Escherichia coli, the gene for the sRNA IS061/IsrA, here renamed McaS, was predicted to reside in an intergenic region between abgR, encoding a transcription regulator and ydaL, encoding a small MutS-related protein. We show that McaS is a ∼95nt transcript whose expression increases over growth, peaking in early-to-mid stationary phase, or when glucose is limiting. McaS uses three discrete single-stranded regions to regulate mRNA targets involved in various aspects of biofilm formation. McaS represses csgD, the transcription regulator of curli biogenesis and activates flhD, the master transcription regulator of flagella synthesis leading to increased motility, a process not previously reported to be regulated by sRNAs. McaS also regulates pgaA, a porin required for the export of the polysaccharide poly β-1,6-N-acetyl-d-glucosamine. Consequently, high levels of McaS result in increased biofilm formation while a strain lacking mcaS shows reduced biofilm formation. Based on our observations, we propose that, in response to limited nutrient availability, increasing levels of McaS modulate steps in the progression to a sessile lifestyle.
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Affiliation(s)
- Maureen K Thomason
- Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, USA
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175
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Battesti A, Majdalani N, Gottesman S. The RpoS-mediated general stress response in Escherichia coli. Annu Rev Microbiol 2012; 65:189-213. [PMID: 21639793 DOI: 10.1146/annurev-micro-090110-102946] [Citation(s) in RCA: 631] [Impact Index Per Article: 52.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Under conditions of nutrient deprivation or stress, or as cells enter stationary phase, Escherichia coli and related bacteria increase the accumulation of RpoS, a specialized sigma factor. RpoS-dependent gene expression leads to general stress resistance of cells. During rapid growth, RpoS translation is inhibited and any RpoS protein that is synthesized is rapidly degraded. The complex transition from exponential growth to stationary phase has been partially dissected by analyzing the induction of RpoS after specific stress treatments. Different stress conditions lead to induction of specific sRNAs that stimulate RpoS translation or to induction of small-protein antiadaptors that stabilize the protein. Recent progress has led to a better, but still far from complete, understanding of how stresses lead to RpoS induction and what RpoS-dependent genes help the cell deal with the stress.
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Affiliation(s)
- Aurelia Battesti
- Laboratory of Molecular Biology, National Cancer Institute, Bethesda, Maryland 20892, USA.
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176
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Shao Y, Bassler BL. Quorum-sensing non-coding small RNAs use unique pairing regions to differentially control mRNA targets. Mol Microbiol 2012; 83:599-611. [PMID: 22229925 PMCID: PMC3262071 DOI: 10.1111/j.1365-2958.2011.07959.x] [Citation(s) in RCA: 88] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Quorum sensing is a mechanism of cell–cell communication that bacteria use to control collective behaviours including bioluminescence, biofilm formation and virulence factor production. In the Vibrio harveyi and Vibrio cholerae quorum-sensing circuits, multiple non-coding small regulatory RNAs called the quorum-regulated small RNAs (Qrr sRNAs) function to establish the global quorum-sensing gene expression pattern by modulating translation of multiple mRNAs encoding quorum-sensing regulatory factors. Here we show that the Qrr sRNAs post-transcriptionally activate production of the low cell density master regulator AphA through base pairing to aphA mRNA, and this is crucial for the accumulation of appropriate levels of AphA protein at low cell density. We find that the Qrr sRNAs use unique pairing regions to discriminate between their different targets. Qrr1 is not as effective as Qrr2–5 in activating aphA because Qrr1 lacks one of two required pairing regions. However, Qrr1 is equally effective as the other Qrr sRNAs at controlling targets like luxR and luxO because it harbours all of the required pairing regions for these targets. Sequence comparisons reveal that Vibrionaceae species possessing only qrr1 do not have the aphA gene under Qrr sRNA control. Our findings suggest co-evolving relationships between particular Qrr sRNAs and particular mRNA targets.
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Affiliation(s)
- Yi Shao
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
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177
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Madhugiri R, Pessi G, Voss B, Hahn J, Sharma CM, Reinhardt R, Vogel J, Hess WR, Fischer HM, Evguenieva-Hackenberg E. Small RNAs of the Bradyrhizobium/Rhodopseudomonas lineage and their analysis. RNA Biol 2012; 9:47-58. [PMID: 22258152 DOI: 10.4161/rna.9.1.18008] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Small RNAs (sRNAs) play a pivotal role in bacterial gene regulation. However, the sRNAs of the vast majority of bacteria with sequenced genomes still remain unknown since sRNA genes are usually difficult to recognize and thus not annotated. Here, expression of seven sRNAs (BjrC2a, BjrC2b, BjrC2c, BjrC68, BjrC80, BjrC174 and BjrC1505) predicted by genome comparison of Bradyrhizobium and Rhodopseudomonas members, was verified by RNA gel blot hybridization, microarray and deep sequencing analyses of RNA from the soybean symbiont Bradyrhizobium japonicum USDA 110. BjrC2a, BjrC2b and BjrC2c belong to the RNA family RF00519, while the other sRNAs are novel. For some of the sRNAs we observed expression differences between free-living bacteria and bacteroids in root nodules. The amount of BjrC1505 was decreased in nodules. By contrast, the amount of BjrC2a, BjrC68, BjrC80, BjrC174 and the previously described 6S RNA was increased in nodules, and accumulation of truncated forms of these sRNAs was observed. Comparative genomics and deep sequencing suggest that BjrC2a is an antisense RNA regulating the expression of inositol-monophosphatase. The analyzed sRNAs show a different degree of conservation in Rhizobiales, and expression of homologs of BjrC2, BjrC68, BjrC1505, and 6S RNA was confirmed in the free-living purple bacterium Rhodopseudomonas palustris 5D.
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MESH Headings
- Bradyrhizobium/enzymology
- Bradyrhizobium/genetics
- Bradyrhizobium/metabolism
- Computational Biology
- Culture Media/metabolism
- Databases, Genetic
- Gene Expression Regulation, Bacterial
- Gene Expression Regulation, Enzymologic
- Genome, Bacterial
- High-Throughput Nucleotide Sequencing/methods
- Oligonucleotide Array Sequence Analysis
- Phosphoric Monoester Hydrolases/genetics
- Phosphoric Monoester Hydrolases/metabolism
- RNA, Antisense/genetics
- RNA, Antisense/metabolism
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Untranslated
- Rhodopseudomonas/enzymology
- Rhodopseudomonas/genetics
- Rhodopseudomonas/metabolism
- Root Nodules, Plant/genetics
- Root Nodules, Plant/metabolism
- Root Nodules, Plant/microbiology
- Glycine max/microbiology
- Symbiosis
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178
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Abstract
Four different mechanisms have evolved in eubacteria to comply with changes in the environmental temperature. The underlying genetic mechanisms regulate gene expression at transcriptional, translational and posttranslational level. The high temperature response (HTR) is a reaction on increases in temperature and is mainly used by pathogenic bacteria when they enter their mammalian host. The temperature of 37°C causes induction of the virulent genes the products of which are only needed in this environment. The heat shock response (HSR) is induced by any sudden increase in temperature, allows the bacterial cell to adapt to this environmental stress factor and is shut off after adaptation. In a similar way the low temperature response (LTR) is a reaction to a new environment and leads to the constant expression of appropriate genes. In contrast, the cold shock response (CSR) includes turn off of the cold shock genes after adaptation to the low temperature. Sensors of temperature changes are specific DNA regions, RNA molecules or proteins and conformational changes have been identified as a common motif.
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179
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Peng Y, Soper TJ, Woodson SA. RNase footprinting of protein binding sites on an mRNA target of small RNAs. Methods Mol Biol 2012; 905:213-24. [PMID: 22736006 DOI: 10.1007/978-1-61779-949-5_13] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Endoribonuclease footprinting is an important technique for probing RNA-protein interactions with single nucleotide resolution. The susceptibility of RNA residues to enzymatic digestion gives information about the RNA secondary structure, the location of protein binding sites, and the effects of protein binding on the RNA structure. Here we present a detailed protocol for using RNase T2, which cleaves single stranded RNA with a preference for A nucleotides, to footprint the protein Hfq on the rpoS mRNA leader. This protocol covers how to form the RNP complex, determine the correct dose of enzyme, footprint the protein, and analyze the cleavage pattern using primer extension.
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Affiliation(s)
- Yi Peng
- T. C. Jenkins Department of Biophysics and CMDB Program, Johns Hopkins University, Baltimore, MD, USA
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180
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Wilf NM, Salmond GPC. The stationary phase sigma factor, RpoS, regulates the production of a carbapenem antibiotic, a bioactive prodigiosin and virulence in the enterobacterial pathogen Serratia sp. ATCC 39006. MICROBIOLOGY-SGM 2011; 158:648-658. [PMID: 22194349 DOI: 10.1099/mic.0.055780-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Serratia sp. ATCC 39006 (S39006) is a Gram-negative bacterium that is virulent in plant (potato) and invertebrate animal (Caenorhabditis elegans) models. It produces two secondary metabolite antibiotics, a prodigiosin and a carbapenem, and the exoenzymes pectate lyase and cellulase. We showed previously that deletion of the RNA chaperone Hfq abolished antibiotic production and attenuated virulence in both animal and plant hosts. Hfq and dependent small RNAs (sRNAs) are known to regulate the post-transcriptional expression of rpoS, which encodes σ(S), the stationary phase sigma factor subunit of RNA polymerase. An S39006 hfq deletion mutant showed decreased transcript levels of rpoS. Therefore, in this study we investigated whether the phenotypes regulated by Hfq were mediated through its control of rpoS. Whereas loss of Hfq abolished prodigiosin and carbapenem production and attenuated virulence in both C. elegans and potato, characterization of an S39006 rpoS mutant showed unexpectedly elevated prodigiosin and carbapenem production. Furthermore, the rpoS mutant exhibited attenuated animal pathogenesis, but not plant pathogenesis. Additionally, a homologue of the Hfq-dependent sRNA, RprA, was identified and shown to regulate prodigiosin production in a manner consistent with its role in positively regulating translation of rpoS mRNA. Combined, these results demonstrate that Hfq regulation of secondary metabolism and plant pathogenesis is independent of RpoS and establishes RpoS and RprA as regulators of antibiotic production.
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Affiliation(s)
- Nabil M Wilf
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, UK
| | - George P C Salmond
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, UK
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181
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Fröhlich KS, Papenfort K, Berger AA, Vogel J. A conserved RpoS-dependent small RNA controls the synthesis of major porin OmpD. Nucleic Acids Res 2011; 40:3623-40. [PMID: 22180532 PMCID: PMC3333887 DOI: 10.1093/nar/gkr1156] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
A remarkable feature of many small non-coding RNAs (sRNAs) of Escherichia coli and Salmonella is their accumulation in the stationary phase of bacterial growth. Several stress response regulators and sigma factors have been reported to direct the transcription of stationary phase-specific sRNAs, but a widely conserved sRNA gene that is controlled by the major stationary phase and stress sigma factor, σ(S) (RpoS), has remained elusive. We have studied in Salmonella the conserved SdsR sRNA, previously known as RyeB, one of the most abundant stationary phase-specific sRNAs in E. coli. Alignments of the sdsR promoter region and genetic analysis strongly suggest that this sRNA gene is selectively transcribed by σ(S). We show that SdsR down-regulates the synthesis of the major Salmonella porin OmpD by Hfq-dependent base pairing; SdsR thus represents the fourth sRNA to regulate this major outer membrane porin. Similar to the InvR, MicC and RybB sRNAs, SdsR recognizes the ompD mRNA in the coding sequence, suggesting that this mRNA may be primarily targeted downstream of the start codon. The SdsR-binding site in ompD was localized by 3'-RACE, an experimental approach that promises to be of use in predicting other sRNA-target interactions in bacteria.
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Affiliation(s)
- Kathrin S Fröhlich
- RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, Josef-Schneider-Strasse 2, D-97080 Würzburg, Germany
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182
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Abstract
In their stressful natural environments, bacteria often are in stationary phase and use their limited resources for maintenance and stress survival. Underlying this activity is the general stress response, which in Escherichia coli depends on the σS (RpoS) subunit of RNA polymerase. σS is closely related to the vegetative sigma factor σ70 (RpoD), and these two sigmas recognize similar but not identical promoter sequences. During the postexponential phase and entry into stationary phase, σS is induced by a fine-tuned combination of transcriptional, translational, and proteolytic control. In addition, regulatory "short-cuts" to high cellular σS levels, which mainly rely on the rapid inhibition of σS proteolysis, are triggered by sudden starvation for various nutrients and other stressful shift conditons. σS directly or indirectly activates more than 500 genes. Additional signal input is integrated by σS cooperating with various transcription factors in complex cascades and feedforward loops. Target gene products have stress-protective functions, redirect metabolism, affect cell envelope and cell shape, are involved in biofilm formation or pathogenesis, or can increased stationary phase and stress-induced mutagenesis. This review summarizes these diverse functions and the amazingly complex regulation of σS. At the molecular level, these processes are integrated with the partitioning of global transcription space by sigma factor competition for RNA polymerase core enzyme and signaling by nucleotide second messengers that include cAMP, (p)ppGpp, and c-di-GMP. Physiologically, σS is the key player in choosing between a lifestyle associated with postexponential growth based on nutrient scavenging and motility and a lifestyle focused on maintenance, strong stress resistance, and increased adhesiveness. Finally, research with other proteobacteria is beginning to reveal how evolution has further adapted function and regulation of σS to specific environmental niches.
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183
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Bacterial small RNA regulators: versatile roles and rapidly evolving variations. Cold Spring Harb Perspect Biol 2011; 3:cshperspect.a003798. [PMID: 20980440 DOI: 10.1101/cshperspect.a003798] [Citation(s) in RCA: 534] [Impact Index Per Article: 41.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Small RNA regulators (sRNAs) have been identified in a wide range of bacteria and found to play critical regulatory roles in many processes. The major families of sRNAs include true antisense RNAs, synthesized from the strand complementary to the mRNA they regulate, sRNAs that also act by pairing but have limited complementarity with their targets, and sRNAs that regulate proteins by binding to and affecting protein activity. The sRNAs with limited complementarity are akin to eukaryotic microRNAs in their ability to modulate the activity and stability of multiple mRNAs. In many bacterial species, the RNA chaperone Hfq is required to promote pairing between these sRNAs and their target mRNAs. Understanding the evolution of regulatory sRNAs remains a challenge; sRNA genes show evidence of duplication and horizontal transfer but also could be evolved from tRNAs, mRNAs or random transcription.
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184
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Wang W, Wang L, Zou Y, Zhang J, Gong Q, Wu J, Shi Y. Cooperation of Escherichia coli Hfq hexamers in DsrA binding. Genes Dev 2011; 25:2106-17. [PMID: 21979921 DOI: 10.1101/gad.16746011] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Hfq is a bacterial post-transcriptional regulator. It facilitates base-pairing between sRNA and target mRNA. Hfq mediates DsrA-dependent translational activation of rpoS mRNA at low temperatures. rpoS encodes the stationary-phase σ factor σ(S), which is the central regulator in general stress response. However, structural information on Hfq-DsrA interaction is not yet available. Although Hfq is reported to hydrolyze ATP, the ATP-binding site is still unknown. Here, we report a ternary crystal complex structure of Escherichia coli Hfq bound to a major Hfq recognition region on DsrA (AU(6)A) together with ADP, and a crystal complex structure of Hfq bound to ADP. AU(6)A binds to the proximal and distal sides of two Hfq hexamers. ADP binds to a purine-selective site on the distal side and contacts conserved arginine or glutamine residues on the proximal side of another hexamer. This binding mode is different from previously postulated. The cooperation of two different Hfq hexamers upon nucleic acid binding in solution is verified by fluorescence polarization and solution nuclear magnetic resonance (NMR) experiments using fragments of Hfq and DsrA. Fluorescence resonance energy transfer conducted with full-length Hfq and DsrA also supports cooperation of Hfq hexamers upon DsrA binding. The implications of Hfq hexamer cooperation have been discussed.
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Affiliation(s)
- Weiwei Wang
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China
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185
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Abstract
A major class of small bacterial RNAs (sRNAs) regulate translation and mRNA stability by pairing with target mRNAs, dependent upon the RNA chaperone Hfq. Hfq, related to the Lsm/Sm families of splicing proteins, binds the sRNAs and stabilizes them in vivo and stimulates pairing with mRNAs in vitro. Although Hfq is abundant, the sRNAs, when induced, are similarly abundant. Therefore, Hfq may be limiting for sRNA function. We find that, when overexpressed, a number of sRNAs competed with endogenous sRNAs for binding to Hfq. This correlated with lower accumulation of the sRNAs (presumably a reflection of the loss of Hfq binding), and lower activity of the sRNAs in regulating gene expression. Hfq was limiting for both positive and negative regulation by the sRNAs. In addition, deletion of the gene for an expressed and particularly effective competitor sRNA improved the regulation of genes by other sRNAs, suggesting that Hfq is limiting during normal growth conditions. These results support the existence of a hierarchy of sRNA competition for Hfq, modulating the function of some sRNAs.
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Affiliation(s)
- Kyung Moon
- Laboratory of Molecular Biology, National Cancer Institute, Bethesda, MD 20892, USA
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186
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The Vibrio cholerae mannitol transporter is regulated posttranscriptionally by the MtlS small regulatory RNA. J Bacteriol 2011; 194:598-606. [PMID: 22101846 DOI: 10.1128/jb.06153-11] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Vibrio cholerae continues to pose a health threat in many developing nations and regions of the world struck by natural disasters. It is a pathogen that rapidly adapts to aquatic environments and the human small intestine. Small regulatory RNAs (sRNAs) may contribute to this adaptability. Specifically, the mannitol operon sRNA (MtlS sRNA; previously designated the IGR7 sRNA) is transcribed antisense to the 5' untranslated region of the mtl operon, encoding the mannitol-specific phosphotransferase system. Mannitol is a six-carbon sugar alcohol that accumulates in the human small intestine, the primary site of V. cholerae colonization. To better understand the V. cholerae mtl operon at a molecular level, we investigated mtlA expression in the presence of various carbon sources and the role of the MtlS sRNA. We observed that MtlA protein is present only in cells grown on mannitol sugar, whereas MtlS sRNA is expressed during growth on all sugars other than mannitol. In contrast, mtlA mRNA is expressed in similar amounts regardless of the carbon source used for bacterial growth. These observations suggest that the regulation of MtlA protein expression is a posttranscriptional event. We further demonstrate that MtlS sRNA overexpression repressed MtlA synthesis without affecting the stability of the messenger and that this process is largely independent of Hfq. We propose a model in which, when carbon sources other than mannitol are present, MtlS sRNA is transcribed, base pairs with the 5' untranslated region of the mtlA mRNA, occluding the ribosome binding site, and inhibits the synthesis of the mannitol-specific phosphotransferase system.
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187
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Conservation and Occurrence of Trans-Encoded sRNAs in the Rhizobiales. Genes (Basel) 2011; 2:925-56. [PMID: 24710299 PMCID: PMC3927594 DOI: 10.3390/genes2040925] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Revised: 10/24/2011] [Accepted: 10/26/2011] [Indexed: 12/13/2022] Open
Abstract
Post-transcriptional regulation by trans-encoded sRNAs, for example via base-pairing with target mRNAs, is a common feature in bacteria and influences various cell processes, e.g., response to stress factors. Several studies based on computational and RNA-seq approaches identified approximately 180 trans-encoded sRNAs in Sinorhizobium meliloti. The initial point of this report is a set of 52 trans-encoded sRNAs derived from the former studies. Sequence homology combined with structural conservation analyses were applied to elucidate the occurrence and distribution of conserved trans-encoded sRNAs in the order of Rhizobiales. This approach resulted in 39 RNA family models (RFMs) which showed various taxonomic distribution patterns. Whereas the majority of RFMs was restricted to Sinorhizobium species or the Rhizobiaceae, members of a few RFMs were more widely distributed in the Rhizobiales. Access to this data is provided via the RhizoGATE portal [1,2].
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188
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Kang Z, Wang X, Li Y, Wang Q, Qi Q. Small RNA RyhB as a potential tool used for metabolic engineering in Escherichia coli. Biotechnol Lett 2011; 34:527-31. [PMID: 22083717 DOI: 10.1007/s10529-011-0794-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2011] [Accepted: 11/03/2011] [Indexed: 11/25/2022]
Abstract
Small RNA (RyhB) was overexpressed artificially using an arabinose-inducible system in Escherichia coli and resulted in more succinate (7-fold) accumulation, which suggested that RyhB had a strong effect on sdhCDAB genes. Acetate was also increased indicating that RyhB had a comprehensive influence on glucose central metabolism. RyhB might therefore be useful for metabolic engineering of E. coli.
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Affiliation(s)
- Zhen Kang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, People's Republic of China
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189
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Good L, Stach JEM. Synthetic RNA silencing in bacteria - antimicrobial discovery and resistance breaking. Front Microbiol 2011; 2:185. [PMID: 21941522 PMCID: PMC3170882 DOI: 10.3389/fmicb.2011.00185] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2011] [Accepted: 08/20/2011] [Indexed: 12/30/2022] Open
Abstract
The increasing incidence and prevalence of antibiotic resistance in bacteria threatens the “antibiotic miracle.” Conventional antimicrobial drug development has failed to replace the armamentarium needed to combat this problem, and novel solutions are urgently required. Here we review both natural and synthetic RNA silencing and its potential to provide new antibacterials through improved target selection, evaluation, and screening. Furthermore, we focus on synthetic RNA silencers as a novel class of antibacterials and review their unique properties.
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Affiliation(s)
- Liam Good
- Department of Pathology and Infectious Diseases, Royal Veterinary College, University of London London, UK
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190
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Updegrove TB, Wartell RM. The influence of Escherichia coli Hfq mutations on RNA binding and sRNA•mRNA duplex formation in rpoS riboregulation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2011; 1809:532-40. [PMID: 21889623 DOI: 10.1016/j.bbagrm.2011.08.006] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2011] [Revised: 08/12/2011] [Accepted: 08/16/2011] [Indexed: 11/16/2022]
Abstract
The Escherichia coli RNA binding protein Hfq plays an important role in regulating mRNA translation through its interactions with small non-coding RNAs (sRNAs) and specific mRNAs sites. The rpoS mRNA, which codes for a transcription factor, is regulated by several sRNAs. DsrA and RprA enhance translation by pairing to a site on this mRNA, while OxyS represses rpoS mRNA translation. To better understand how Hfq interacts with these sRNAs and rpoS mRNA, the binding of wt Hfq and eleven mutant Hfqs to DsrA, RprA, OxyS and rpoS mRNA was examined. Nine of the mutant Hfq had single-residue mutations located on the proximal, distal, and outer-edge surfaces of the Hfq hexamer, while two Hfq had truncated C-terminal ends. Hfq with outer-edge mutations and truncated C-terminal ends behaved similar to wt Hfq with regard to binding the sRNAs, rpoS mRNA segments, and stimulating DsrA•rpoS mRNA formation. Proximal surface mutations decreased Hfq binding to the three sRNAs and the rpoS mRNA segment containing the translation initiation region. Distal surface mutations lowered Hfq's affinity for the rpoS mRNA segment containing the (ARN)(4) sequence. Strong Hfq binding to both rpoS mRNA segments appears to be needed for maximum enhancement of DsrA•rpoS mRNA annealing. OxyS bound tightly to Hfq but exhibited weak affinity for rpoS mRNA containing the leader region and 75 nt of coding sequence in the absence or presence of Hfq. This together with other results suggest OxyS represses rpoS mRNA translation by sequestering Hfq rather than binding to rpoS mRNA.
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Affiliation(s)
- Taylor B Updegrove
- School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
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191
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Abstract
A substantial amount of antisense transcription is a hallmark of gene expression in eukaryotes. However, antisense transcription was first demonstrated in bacteria almost 50 years ago. The transcriptomes of bacteria as different as Helicobacter pylori, Bacillus subtilis, Escherichia coli, Synechocystis sp. strain PCC6803, Mycoplasma pneumoniae, Sinorhizobium meliloti, Geobacter sulfurreducens, Vibrio cholerae, Chlamydia trachomatis, Pseudomonas syringae, and Staphylococcus aureus have now been reported to contain antisense RNA (asRNA) transcripts for a high percentage of genes. Bacterial asRNAs share functional similarities with trans-acting regulatory RNAs, but in addition, they use their own distinct mechanisms. Among their confirmed functional roles are transcription termination, codegradation, control of translation, transcriptional interference, and enhanced stability of their respective target transcripts. Here, we review recent publications indicating that asRNAs occur as frequently in simple unicellular bacteria as they do in higher organisms, and we provide a comprehensive overview of the experimentally confirmed characteristics of asRNA actions and intimately linked quantitative aspects. Emerging functional data suggest that asRNAs in bacteria mediate a plethora of effects and are involved in far more processes than were previously anticipated. Thus, the functional impact of asRNAs should be considered when developing new strategies against pathogenic bacteria and when optimizing bacterial strains for biotechnology.
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192
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Sharma CM, Papenfort K, Pernitzsch SR, Mollenkopf HJ, Hinton JCD, Vogel J. Pervasive post-transcriptional control of genes involved in amino acid metabolism by the Hfq-dependent GcvB small RNA. Mol Microbiol 2011; 81:1144-65. [PMID: 21696468 DOI: 10.1111/j.1365-2958.2011.07751.x] [Citation(s) in RCA: 163] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
GcvB is one of the most highly conserved Hfq-associated small RNAs in Gram-negative bacteria and was previously reported to repress several ABC transporters for amino acids. To determine the full extent of GcvB-mediated regulation in Salmonella, we combined a genome-wide experimental approach with biocomputational target prediction. Comparative pulse expression of wild-type versus mutant sRNA variants revealed that GcvB governs a large post-transcriptional regulon, impacting ~1% of all Salmonella genes via its conserved G/U-rich domain R1. Complementary predictions of C/A-rich binding sites in mRNAs and gfp reporter fusion experiments increased the number of validated GcvB targets to more than 20, and doubled the number of regulated amino acid transporters. Unlike the previously described targeting via the single R1 domain, GcvB represses the glycine transporter CycA by exceptionally redundant base-pairing. This novel ability of GcvB is focused upon the one target that could feedback-regulate the glycine-responsive synthesis of GcvB. Several newly discovered mRNA targets involved in amino acid metabolism, including the global regulator Lrp, question the previous assumption that GcvB simply acts to limit unnecessary amino acid uptake. Rather, GcvB rewires primary transcriptional control circuits and seems to act as a distinct regulatory node in amino acid metabolism.
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Affiliation(s)
- Cynthia M Sharma
- Institute for Molecular Infection Biology, Research Centre of Infectious Diseases, University of Würzburg, Germany
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193
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Quantifying the sequence-function relation in gene silencing by bacterial small RNAs. Proc Natl Acad Sci U S A 2011; 108:12473-8. [PMID: 21742981 DOI: 10.1073/pnas.1100432108] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Sequence-function relations for small RNA (sRNA)-mediated gene silencing were quantified for the sRNA RyhB and some of its mRNA targets in Escherichia coli. Numerous mutants of RyhB and its targets were generated and their in vivo functions characterized at various levels of target and RyhB expression. Although a core complementary region is required for repression by RyhB, variations in the complementary sequences of the core region gave rise to a continuum of repression strengths, correlated exponentially with the computed free energy of RyhB-target duplex formation. Moreover, sequence variations in the linker region known to interact with the RNA chaperone Hfq also gave rise to a continuum of repression strengths, correlated exponentially with the computed energy cost of keeping the linker region open. These results support the applicability of the thermodynamic model in predicting sRNA-mRNA interaction and suggest that sequences at these locations may be used to fine-tune the degree of repression. Surprisingly, a truncated RyhB without the Hfq-binding region is found to repress multiple targets of the wild-type RyhB effectively, both in the presence and absence of Hfq, even though the former is required for the activity of wild-type RyhB itself. These findings challenge the commonly accepted model concerning the function of Hfq in gene silencing-both in providing stability to the sRNAs and in catalyzing the target mRNAs to take on active conformations-and raise the intriguing question of why many endogenous sRNAs subject their functions to Hfq-dependences.
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194
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Silva IJ, Saramago M, Dressaire C, Domingues S, Viegas SC, Arraiano CM. Importance and key events of prokaryotic RNA decay: the ultimate fate of an RNA molecule. WILEY INTERDISCIPLINARY REVIEWS-RNA 2011; 2:818-36. [PMID: 21976285 DOI: 10.1002/wrna.94] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Inês Jesus Silva
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Apartado 127, Oeiras, Portugal
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195
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De Lay N, Gottesman S. Role of polynucleotide phosphorylase in sRNA function in Escherichia coli. RNA (NEW YORK, N.Y.) 2011; 17:1172-89. [PMID: 21527671 PMCID: PMC3096048 DOI: 10.1261/rna.2531211] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2010] [Accepted: 03/21/2011] [Indexed: 05/22/2023]
Abstract
In Escherichia coli, many small noncoding regulatory RNAs (sRNAs) post-transcriptionally regulate gene expression by base-pairing to mRNAs in a process that is mediated by the RNA chaperone Hfq. Binding of the sRNA to the mRNA can lead to increased or decreased mRNA stability and/or translation. It is not known if proteins other than Hfq are necessary for this process. In order to identify additional genes required for the post-transcriptional regulation of gene expression by Hfq-dependent sRNAs, we developed a novel combined genetic selection and screen for mutants defective in sRNA regulation. In our combined genetic selection and screen, we isolated hfq mutants and mutants in pnp, encoding polynucleotide phosphorylase (PNPase). We show that loss-of-function mutations in pnp result in a decreased stability of several sRNAs including RyhB, SgrS, and CyaR and also decrease both the negative and positive regulation by sRNAs. The defect in stability of CyaR and in negative and positive regulation are suppressed by deletion mutations in RNase E. Altogether, our results suggest that the lack of sRNA-mediated regulation in the absence of an active form of PNPase is due to the rapid turnover of sRNA resulting from an increase in RNase E activity and/or an increase in access of other ribonucleases to sRNAs.
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Affiliation(s)
- Nicholas De Lay
- Laboratory of Molecular Biology, National Cancer Institute, Bethesda, Maryland 20892, USA
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196
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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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197
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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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198
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Rutherford ST, van Kessel JC, Shao Y, Bassler BL. AphA and LuxR/HapR reciprocally control quorum sensing in vibrios. Genes Dev 2011; 25:397-408. [PMID: 21325136 DOI: 10.1101/gad.2015011] [Citation(s) in RCA: 198] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Bacteria cycle between periods when they perform individual behaviors and periods when they perform group behaviors. These transitions are controlled by a cell-cell communication process called quorum sensing, in which extracellular signal molecules, called autoinducers (AIs), are released, accumulate, and are synchronously detected by a group of bacteria. AI detection results in community-wide changes in gene expression, enabling bacteria to collectively execute behaviors such as bioluminescence, biofilm formation, and virulence factor production. In this study, we show that the transcription factor AphA is a master regulator of quorum sensing that operates at low cell density (LCD) in Vibrio harveyi and Vibrio cholerae. In contrast, LuxR (V. harveyi)/HapR (V. cholerae) is the master regulator that operates at high cell density (HCD). At LCD, redundant small noncoding RNAs (sRNAs) activate production of AphA, and AphA and the sRNAs repress production of LuxR/HapR. Conversely, at HCD, LuxR/HapR represses aphA. This network architecture ensures maximal AphA production at LCD and maximal LuxR/HapR production at HCD. Microarray analyses reveal that 300 genes are regulated by AphA at LCD in V. harveyi, a subset of which is also controlled by LuxR. We propose that reciprocal gradients of AphA and LuxR/HapR establish the quorum-sensing LCD and HCD gene expression patterns, respectively.
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Affiliation(s)
- Steven T Rutherford
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
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199
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Nielsen JS, Larsen MH, Lillebæk EMS, Bergholz TM, Christiansen MHG, Boor KJ, Wiedmann M, Kallipolitis BH. A small RNA controls expression of the chitinase ChiA in Listeria monocytogenes. PLoS One 2011; 6:e19019. [PMID: 21533114 PMCID: PMC3078929 DOI: 10.1371/journal.pone.0019019] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2011] [Accepted: 03/14/2011] [Indexed: 02/04/2023] Open
Abstract
In recent years, more than 60 small RNAs (sRNAs) have been identified in the gram-positive human pathogen Listeria monocytogenes, but their putative roles and mechanisms of action remain largely unknown. The sRNA LhrA was recently shown to be a post-transcriptional regulator of a single gene, lmo0850, which encodes a small protein of unknown function. LhrA controls the translation and degradation of the lmo0850 mRNA by an antisense mechanism, and it depends on the RNA chaperone Hfq for efficient binding to its target. In the present study, we sought to gain more insight into the functional role of LhrA in L. monocytogenes. To this end, we determined the effects of LhrA on global-wide gene expression. We observed that nearly 300 genes in L. monocytogenes are either positively or negatively affected by LhrA. Among these genes, we identified lmo0302 and chiA as direct targets of LhrA, thus establishing LhrA as a multiple target regulator. Lmo0302 encodes a hypothetical protein with no known function, whereas chiA encodes one of two chitinases present in L. monocytogenes. We show here that LhrA acts as a post-transcriptional regulator of lmo0302 and chiA by interfering with ribosome recruitment, and we provide evidence that both LhrA and Hfq act to down-regulate the expression of lmo0302 and chiA. Furthermore, in vitro binding experiments show that Hfq stimulates the base pairing of LhrA to chiA mRNA. Finally, we demonstrate that LhrA has a negative effect on the chitinolytic activity of L. monocytogenes. In marked contrast to this, we found that Hfq has a stimulating effect on the chitinolytic activity, suggesting that Hfq plays multiple roles in the complex regulatory pathways controlling the chitinases of L. monocytogenes.
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Affiliation(s)
- Jesper S. Nielsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Marianne Halberg Larsen
- Department of Veterinary Disease Biology, Faculty of Life Sciences, University of Copenhagen, Frederiksberg, Denmark
| | | | - Teresa M. Bergholz
- Department of Food Science, Cornell University, Ithaca, New York, United States of America
| | - Mie H. G. Christiansen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Kathryn J. Boor
- Department of Food Science, Cornell University, Ithaca, New York, United States of America
| | - Martin Wiedmann
- Department of Food Science, Cornell University, Ithaca, New York, United States of America
| | - Birgitte H. Kallipolitis
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
- * E-mail:
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Mulley G, White JP, Karunakaran R, Prell J, Bourdes A, Bunnewell S, Hill L, Poole PS. Mutation of GOGAT prevents pea bacteroid formation and N2 fixation by globally downregulating transport of organic nitrogen sources. Mol Microbiol 2011; 80:149-67. [PMID: 21276099 DOI: 10.1111/j.1365-2958.2011.07565.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Mutation of gltB (encoding glutamate oxoglutarate amidotransferase or GOGAT) in RU2307 increased the intracellular Gln:Glu ratio and inhibited amino acid transport via Aap and Bra. The mechanism probably involves global post-translational inhibition independent of Ntr. Transport was separately restored by increased gene expression of Aap or heterologous transporters. Likewise, second site suppressor mutations in the RNA chaperone Hfq elevated transport by Aap and Bra by increasing mRNA levels. Microarrays showed Hfq regulates 34 ABC transporter genes, including aap, bra and opp. The genes coding for integral membrane proteins and ABC subunits aapQMP braDEFGC were more strongly elevated in the hfq mutants than solute-binding proteins (aapJ braC). aapQMP and braDEFG are immediately downstream of stem-loops, indicating Hfq attenuates downstream translation and stability of mRNA, explaining differential expression of ABC genes. RU2307 nodulated peas and bacteria grew down infection threads, but bacteroid development was arrested and N(2) was not fixed. This probably results from an inability to synthesize or transport amino acids. However, GOGAT and GOGAT/AldA double mutants carrying suppressor mutations that increased amino acid uptake fixed N(2) on pea plants. Thus de novo ammonium assimilation into amino acids is unnecessary in bacteroids demonstrating sufficient amino acids are supplied by plants.
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Affiliation(s)
- G Mulley
- Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
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