Base Pairing Interaction between 5′- and 3′-UTRs Controls icaR mRNA Translation in Staphylococcus aureus
Publication Date
December 19, 2013
Journal
PLOS Genetics
Authors
Igor Ruiz De Los Mozos, Marta Vergara Irigaray, Victor Segura, Maite Villanueva, et al
Volume
9
Issue
12
Pages
e1004001
DOI
http://doi.org/10.1371/journal.pgen.1004001
Publisher URL
http://journals.plos.org/plosgenetics/article?id=10.1371%2Fjournal.pgen.1004001
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/24367275
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3868564
Europe PMC
http://europepmc.org/abstract/MED/24367275
Web of Science
000330533300040
Scopus
84892712664
Mendeley
http://www.mendeley.com/research/base-pairing-interaction-between-5-3utrs-controls-icar-mrna-translation-staphylococcus-aureus
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Mendeley | Further Information

{"title"=>"Base Pairing Interaction between 5′- and 3′-UTRs Controls icaR mRNA Translation in Staphylococcus aureus", "type"=>"journal", "authors"=>[{"first_name"=>"Igor", "last_name"=>"Ruiz de los Mozos", "scopus_author_id"=>"56011236900"}, {"first_name"=>"Marta", "last_name"=>"Vergara-Irigaray", "scopus_author_id"=>"8588086600"}, {"first_name"=>"Victor", "last_name"=>"Segura", "scopus_author_id"=>"6603659414"}, {"first_name"=>"Maite", "last_name"=>"Villanueva", "scopus_author_id"=>"54788500600"}, {"first_name"=>"Nerea", "last_name"=>"Bitarte", "scopus_author_id"=>"23007438100"}, {"first_name"=>"Margarida", "last_name"=>"Saramago", "scopus_author_id"=>"37035005600"}, {"first_name"=>"Susana", "last_name"=>"Domingues", "scopus_author_id"=>"6602390240"}, {"first_name"=>"Cecilia M.", "last_name"=>"Arraiano", "scopus_author_id"=>"7003605542"}, {"first_name"=>"Pierre", "last_name"=>"Fechter", "scopus_author_id"=>"6603821666"}, {"first_name"=>"Pascale", "last_name"=>"Romby", "scopus_author_id"=>"7005380859"}, {"first_name"=>"Jaione", "last_name"=>"Valle", "scopus_author_id"=>"7101953213"}, {"first_name"=>"Cristina", "last_name"=>"Solano", "scopus_author_id"=>"7005089610"}, {"first_name"=>"Iñigo", "last_name"=>"Lasa", "scopus_author_id"=>"7003887382"}, {"first_name"=>"Alejandro", "last_name"=>"Toledo-Arana", "scopus_author_id"=>"56009612600"}], "year"=>2013, "source"=>"PLoS Genetics", "identifiers"=>{"issn"=>"15537390", "scopus"=>"2-s2.0-84892712664", "sgr"=>"84892712664", "pui"=>"372170339", "isbn"=>"1553-7404 (Electronic)\\r1553-7390 (Linking)", "pmid"=>"24367275", "doi"=>"10.1371/journal.pgen.1004001"}, "id"=>"e5549f04-84ed-3236-9c63-9bf77c8dd770", "abstract"=>"The presence of regulatory sequences in the 3' untranslated region (3'-UTR) of eukaryotic mRNAs controlling RNA stability and translation efficiency is widely recognized. In contrast, the relevance of 3'-UTRs in bacterial mRNA functionality has been disregarded. Here, we report evidences showing that around one-third of the mapped mRNAs of the major human pathogen Staphylococcus aureus carry 3'-UTRs longer than 100-nt and thus, potential regulatory functions. We selected the long 3'-UTR of icaR, which codes for the repressor of the main exopolysaccharidic compound of the S. aureus biofilm matrix, to evaluate the role that 3'-UTRs may play in controlling mRNA expression. We showed that base pairing between the 3'-UTR and the Shine-Dalgarno (SD) region of icaR mRNA interferes with the translation initiation complex and generates a double-stranded substrate for RNase III. Deletion or substitution of the motif (UCCCCUG) within icaR 3'-UTR was sufficient to abolish this interaction and resulted in the accumulation of IcaR repressor and inhibition of biofilm development. Our findings provide a singular example of a new potential post-transcriptional regulatory mechanism to modulate bacterial gene expression through the interaction of a 3'-UTR with the 5'-UTR of the same mRNA.", "link"=>"http://www.mendeley.com/research/base-pairing-interaction-between-5-3utrs-controls-icar-mrna-translation-staphylococcus-aureus", "reader_count"=>63, "reader_count_by_academic_status"=>{"Unspecified"=>2, "Professor > Associate Professor"=>4, "Librarian"=>3, "Researcher"=>13, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>22, "Student > Postgraduate"=>3, "Student > Master"=>5, "Student > Bachelor"=>5, "Professor"=>4}, "reader_count_by_user_role"=>{"Unspecified"=>2, "Professor > Associate Professor"=>4, "Librarian"=>3, "Researcher"=>13, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>22, "Student > Postgraduate"=>3, "Student > Master"=>5, "Student > Bachelor"=>5, "Professor"=>4}, "reader_count_by_subject_area"=>{"Engineering"=>2, "Unspecified"=>3, "Biochemistry, Genetics and Molecular Biology"=>15, "Agricultural and Biological Sciences"=>35, "Medicine and Dentistry"=>1, "Arts and Humanities"=>2, "Pharmacology, Toxicology and Pharmaceutical Science"=>1, "Immunology and Microbiology"=>3, "Social Sciences"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>2}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Social Sciences"=>{"Social Sciences"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>3}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>35}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>15}, "Unspecified"=>{"Unspecified"=>3}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>1}, "Arts and Humanities"=>{"Arts and Humanities"=>2}}, "reader_count_by_country"=>{"Iran"=>1, "Denmark"=>1, "Portugal"=>1}, "group_count"=>1}

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Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1323455"], "description"=>"<p>A transcript ending in a transcriptional terminator located far away from the corresponding protein stop codon generates a <i>bona fide</i> long 3′-UTR. In other cases, despite the presence of a transcriptional terminator (TT) close to the end of the protein stop codon, transcription may continue downstream the predicted TT, generating a terminating-read-through-dependent long 3′-UTR. In addition, several transcripts end at a TT that is part of the expression platform of a riboswitch. In this case the long 3′-UTRs will be generated only when the riboswitch is in an OFF configuration. Otherwise, if the riboswitch is in an ON configuration, a polycistronic transcript is generated.</p>", "links"=>[], "tags"=>["bacterial"], "article_id"=>882658, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Igor Ruiz de los Mozos", "Marta Vergara-Irigaray", "Victor Segura", "Maite Villanueva", "Nerea Bitarte", "Margarida Saramago", "Susana Domingues", "Cecília M. Arraiano", "Pierre Fechter", "Pascale Romby", "Jaione Valle", "Cristina Solano", "Iñigo Lasa", "Alejandro Toledo-Arana"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1004001.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Schematic_representation_of_how_long_bacterial_3_8242_UTRs_can_be_generated_/882658", "title"=>"Schematic representation of how long bacterial 3′-UTRs can be generated.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-12-19 04:02:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/1323457"], "description"=>"<p>(A) Schematic representation of the <i>icaR</i> mRNA molecule, mapped by RACE, showing the length of the 5′-UTR, ORF and 3′-UTR. The nucleotide sequence of the 3′-UTR is shown. The sequence of the transcriptional terminator is underlined and its secondary structure, predicted by Mfold, is shown. (B) Northern blots carried out with two different riboprobes, one targeting the <i>icaR</i> ORF region and the other, the <i>icaR</i> mRNA 3′-UTR.</p>", "links"=>[], "tags"=>["mrna", "contains", "conserved"], "article_id"=>882660, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Igor Ruiz de los Mozos", "Marta Vergara-Irigaray", "Victor Segura", "Maite Villanueva", "Nerea Bitarte", "Margarida Saramago", "Susana Domingues", "Cecília M. Arraiano", "Pierre Fechter", "Pascale Romby", "Jaione Valle", "Cristina Solano", "Iñigo Lasa", "Alejandro Toledo-Arana"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1004001.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_icaR_mRNA_contains_a_conserved_long_3_UTR_/882660", "title"=>"<i>icaR</i> mRNA contains a conserved long 3′-UTR.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-12-19 04:02:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/1323458"], "description"=>"<p>(A) Schematic representation of chromosomal 3′-UTR deletion. Note that the transcriptional terminator is not affected by the deletion. (B) qRT-PCR analysis of <i>icaR</i> mRNA levels in <i>S. aureus</i> 15981 wild type and Δ3′-UTR strains grown in TSB-gluc at 37°C until exponential phase (OD<sub>600 nm</sub> = 0.8). The <i>gyrB</i> transcript was used as an endogenous control, and the results were expressed as the n-fold difference relative to the control gene (2<sup>−ΔCt</sup>, where ΔCt represents the difference in threshold cycle between the target and control genes). (C) A representative Northern blot showing <i>icaR</i> mRNA of wild type and Δ3′UTR strains grown in TSB-gluc at 37°C until exponential phase (OD<sub>600 nm</sub> = 0.8). Lower panel shows 16S ribosome band stained with ethidium bromide as loading control. (D) A representative Western blot showing IcaR protein levels expressed from strains shown in panel A. The 3XFLAG tagged IcaR protein was detected with commercial anti-3XFLAG antibodies. Numbers below the image show relative band quantification according to densitometry analysis performed with ImageJ (<a href=\"http://rsbweb.nih.gov/ij/\" target=\"_blank\">http://rsbweb.nih.gov/ij/</a>). A Coomassie stained gel portion is shown as loading control. (E) Schematic representation of plasmid constructions constitutively expressing the 3XFLAG tagged IcaR protein from the whole <i>icaR</i> mRNA or the mRNA carrying the 3′-UTR deletion. (F) A representative Western blot showing IcaR protein levels of strains shown in panel E. The 3XFLAG tagged IcaR protein was detected with commercial anti-3XFLAG antibodies. Densitometry analysis is also shown. On the left, a Coomassie stained gel portion is shown as loading control.</p>", "links"=>[], "tags"=>["post-transcriptionally", "modulates", "icar"], "article_id"=>882661, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Igor Ruiz de los Mozos", "Marta Vergara-Irigaray", "Victor Segura", "Maite Villanueva", "Nerea Bitarte", "Margarida Saramago", "Susana Domingues", "Cecília M. Arraiano", "Pierre Fechter", "Pascale Romby", "Jaione Valle", "Cristina Solano", "Iñigo Lasa", "Alejandro Toledo-Arana"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1004001.g003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_icaR_3_UTR_post_transcriptionally_modulates_IcaR_expression_/882661", "title"=>"<i>icaR</i> 3′-UTR post-transcriptionally modulates IcaR expression.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-12-19 04:02:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/1323459"], "description"=>"<p>(A) Half-life measurement of <i>icaR</i> wild type and Δ3′-UTR mRNAs constitutively expressed in the wild type and Δ<i>rnc</i> mutant strains. These strains were grown in TSB-gluc at 37°C until exponential phase (OD<sub>600 nm</sub> = 0.8) and then rifampicin (300 µg/ml) was added. Samples for RNA extraction were taken at the indicated time points (min). The experiment was repeated three times and representative images are shown. (B) Levels of <i>icaR</i> mRNA were quantified by densitometry of Northern blot autoradiographies using ImageJ (<a href=\"http://rsbweb.nih.gov/ij/\" target=\"_blank\">http://rsbweb.nih.gov/ij/</a>). Each of mRNA levels was relativized to mRNA levels at time 0. The logarithm values of relative mRNA levels were subjected to linear regression analysis and plotted as a function of time. Error bars indicate the standard deviation of mRNA levels from three independent experiments. Dashed lines indicate the time at which 50% of mRNA remained. The half-life of mRNAs is shown above of X-axis. (C) Representative Western blot showing IcaR protein levels in different mutant strains constitutively expressing the 3XFLAG tagged IcaR from the P<i>blaZ</i> promoter. Tagged IcaR protein was detected with commercial anti-3XFLAG antibodies. On the left, a Coomassie stained gel portion is shown as loading control. <i>rnc</i>, double-stranded endoribonuclease RNase III; <i>pnp</i>, polynucleotide phosphorylase PNPase; <i>yqfR</i>, (SAOUHSC_01659), ATP-dependent RNA helicase containing a DEAD box domain; <i>hfq</i>, RNA chaperone, host factor-1 protein.</p>", "links"=>[], "tags"=>["encodes", "stranded", "endoribonuclease", "rnase", "mrna", "icar"], "article_id"=>882662, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Igor Ruiz de los Mozos", "Marta Vergara-Irigaray", "Victor Segura", "Maite Villanueva", "Nerea Bitarte", "Margarida Saramago", "Susana Domingues", "Cecília M. Arraiano", "Pierre Fechter", "Pascale Romby", "Jaione Valle", "Cristina Solano", "Iñigo Lasa", "Alejandro Toledo-Arana"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1004001.g004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Deletion_of_rnc_gene_which_encodes_the_double_stranded_endoribonuclease_RNase_III_affects_icaR_mRNA_stability_and_IcaR_protein_levels_/882662", "title"=>"Deletion of <i>rnc</i> gene, which encodes the double stranded endoribonuclease RNase III, affects <i>icaR</i> mRNA stability and IcaR protein levels.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-12-19 04:02:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/1323461"], "description"=>"<p>(A) Schematic representation of the 5′-3′-UTRs interaction. A UCCCCUG motif located at the 3′-UTR pairs the UAGGGGG Shine-Dalgarno region located at the 5′-UTR. The numbers indicate the relative position of the nucleotides in the full-length <i>icaR</i> mRNA (B) Substitution of the <sup>894</sup>UCCCCUG<sup>900</sup> motif by <sup>894</sup>AGGGGAC<sup>900</sup>, disrupts the pairing predicted by Mfold program. (C) <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004001#s1\" target=\"_blank\">Introduction</a> of a compensatory mutation sequence (<sup>57</sup>GUCCCCU<sup>63</sup>) in the 5′-UTR, complementary to the substituted <sup>894</sup>AGGGGAC<sup>900</sup> motif, restores complex formation. (D) Gel shift analysis of the 5′ and 3′-UTR <i>icaR</i> mRNA interaction. The <sup>32</sup>P-labeled 5′-UTR fragment (1–117-nt) was incubated with increasing concentrations of unlabeled 3′-UTR (3′-UTR WT) or substituted 3′-UTR (3′-UTR-AGGGGAC) (838–957-nt). (E) Similarly, the <sup>32</sup>P-labeled compensatory-5′-UTR fragment (<sup>32</sup>P-5′-UTR-GUCCCCU) was incubated with increasing concentrations of unlabeled 3′-UTR (3′-UTR WT) or substituted 3′-UTR (3′-UTR-AGGGGAC). After 30 min of incubation at 37°C, the mixture was analysed by electrophoresis in a native 5% polyacrylamide gel and PhosphorImager (Molecular Dynamics).</p>", "links"=>[], "tags"=>["motif", "shine-dalgarno", "mrna"], "article_id"=>882664, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Igor Ruiz de los Mozos", "Marta Vergara-Irigaray", "Victor Segura", "Maite Villanueva", "Nerea Bitarte", "Margarida Saramago", "Susana Domingues", "Cecília M. Arraiano", "Pierre Fechter", "Pascale Romby", "Jaione Valle", "Cristina Solano", "Iñigo Lasa", "Alejandro Toledo-Arana"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1004001.g005"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_A_UCCCCUG_motif_is_necessary_for_the_interaction_between_the_3_8242_UTR_and_the_Shine_Dalgarno_region_of_icaR_mRNA_in_vitro_/882664", "title"=>"A UCCCCUG motif is necessary for the interaction between the 3′-UTR and the Shine-Dalgarno region of <i>icaR</i> mRNA <i>in vitro</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-12-19 04:02:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/1323464"], "description"=>"<p>(A) <i>In vitro</i> RNase III activity assay. A <sup>32</sup>P-labelled 5′-UTR fragment was incubated with purified recombinant <i>S. aureus</i> RNase III during different times in the absence or presence of either the 3′-UTR fragment or the substituted 3′-UTR fragment. The two RNA bands that are generated by the presence of the wild type 3′-UTR are indicated with arrows. (B) Schematic representation showing <i>in vivo</i> mRACE results. Mapping of <i>icaR</i> mRNA fragments naturally generated <i>in vivo</i> was carried out with circularized RNAs and two outward primers (RT and PCR) that pair next to the transcriptional terminator. Black and white triangles indicate <i>in vivo</i> processing sites identified in the <i>icaR</i> mRNA wild type and the <i>icaR</i> mRNA with the UCCCC substitution respectively.</p>", "links"=>[], "tags"=>["rnase", "iii-mediated", "stranded", "generated"], "article_id"=>882667, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Igor Ruiz de los Mozos", "Marta Vergara-Irigaray", "Victor Segura", "Maite Villanueva", "Nerea Bitarte", "Margarida Saramago", "Susana Domingues", "Cecília M. Arraiano", "Pierre Fechter", "Pascale Romby", "Jaione Valle", "Cristina Solano", "Iñigo Lasa", "Alejandro Toledo-Arana"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1004001.g006"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_In_vitro_and_in_vivo_RNase_III_mediated_processing_of_the_double_stranded_region_generated_by_icaR_5_3_UTRs_interaction_/882667", "title"=>"<i>In vitro</i> and <i>in vivo</i> RNase III-mediated processing of the double stranded region generated by <i>icaR</i> 5′-3′-UTRs interaction.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-12-19 04:02:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/1323465"], "description"=>"<p>(A, B) Formation of the ternary complex between <i>icaR</i> 5′-UTR fragment (5 nM), <i>S. aureus</i> 30S ribosomal subunit, and initiator tRNA was monitored in the absence or in the presence of increasing concentrations of wild-type 3′-UTR fragment and substituted 3′-UTR fragment. The toeprint at position +16 is indicated. The quantification of the toeprint (B) was first normalized according to the full-length extension product bands using the SAFA software <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004001#pgen.1004001-Laederach1\" target=\"_blank\">[79]</a>, and the toeprint signal (given in %) represents the yield of the toeprint obtained in the presence of the competitor RNA versus the yield of the toeprint obtained in the absence of the competitor RNA. (C, D) Formation of the ternary complex with the 5′-UTR fragment and the full-length <i>icaR</i> mRNA molecule was monitored using different <i>S. aureus</i> 30S concentrations. A reverse transcriptase pause at the Shine-Dalgarno (SD) sequence occurring in the full-length <i>icaR</i> mRNA molecule is indicated with an arrow. The quantification of toeprint experiment (D) is described above in B. (E) Schematic representation of plasmid constructions constitutively expressing the 3XFLAG tagged IcaR protein from the different <i>icaR</i> mRNA alleles. (F) A representative Western blot showing IcaR protein levels in strains shown in panel E. The 3XFLAG tagged IcaR protein was detected with commercial anti-3XFLAG antibodies. Band quantification according to densitometry analysis is shown. A Coomassie stained gel portion is shown as loading control.</p>", "links"=>[], "tags"=>["interferes", "translational", "initiation"], "article_id"=>882668, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Igor Ruiz de los Mozos", "Marta Vergara-Irigaray", "Victor Segura", "Maite Villanueva", "Nerea Bitarte", "Margarida Saramago", "Susana Domingues", "Cecília M. Arraiano", "Pierre Fechter", "Pascale Romby", "Jaione Valle", "Cristina Solano", "Iñigo Lasa", "Alejandro Toledo-Arana"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1004001.g007"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_5_8242_3_8242_UTRs_interaction_interferes_with_the_translational_initiation_complex_/882668", "title"=>"The 5′-3′-UTRs interaction interferes with the translational initiation complex.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-12-19 04:02:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/1323466"], "description"=>"<p>(A) β-galatosidase assays measuring <i>icaA</i> promoter activity in the wild type and Δ3′-UTR strains grown in TSB-gluc at 37°C until exponential phase (OD<sub>600 nm</sub> = 0.8). Each bar represents the average of three independent assays. (B) Consequences of <i>icaR</i> mRNA 3′-UTR deletion on PIA-PNAG exopolysaccharide synthesis and biofilm production of <i>S. aureus</i> 15981 and 132 strains. (C) <i>In vivo</i> effects of either the mutation or the substitution of the <sup>894</sup>UCCCCUG<sup>900</sup> motif on PIA-PNAG synthesis. Quantification of PIA-PNAG exopolysaccharide biosynthesis by dot-blot. Serial dilutions (1/5) of the samples were spotted onto nitrocellulose membranes and PIA-PNAG production was detected with specific anti-PIA-PNAG antibodies. (D) Biofilm development of the wild type and Δ3′-UTR strains grown in microfermentors under continuous flow for 8 h at 37°C. The glass slides where bacteria form the biofilm are shown. (E) Biofilm development of the <i>S. aureus</i> 15981 with the pCN40, pIcaRm_WT and pIcaRm_SUBST plasmids grown in microfermentors under continuous flow for 8 h at 37°C.</p>", "links"=>[], "tags"=>["relevance", "shine-dalgarno"], "article_id"=>882669, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Igor Ruiz de los Mozos", "Marta Vergara-Irigaray", "Victor Segura", "Maite Villanueva", "Nerea Bitarte", "Margarida Saramago", "Susana Domingues", "Cecília M. Arraiano", "Pierre Fechter", "Pascale Romby", "Jaione Valle", "Cristina Solano", "Iñigo Lasa", "Alejandro Toledo-Arana"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1004001.g008"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_In_vivo_relevance_of_the_interaction_between_the_3_UTR_and_the_Shine_Dalgarno_region_of_icaR_mRNA_/882669", "title"=>"<i>In vivo</i> relevance of the interaction between the 3′-UTR and the Shine-Dalgarno region of <i>icaR</i> mRNA.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-12-19 04:02:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/1323467"], "description"=>"<p>A model of the potential post-transcriptional regulatory mechanism controlling IcaR expression mediated by the 3′-UTR interaction with the Shine-Dalgarno region is shown. Once <i>icaR</i> gene is transcribed, the 3′-UTR interacts either in <i>trans</i> or <i>cis</i> with the 5′-UTR through the anti-SD UCCCCUG motif. This interaction has two main consequences: i) it interferes with ribosome access to the SD region to inhibit the formation of the translational initiation complex and ii) it promotes RNase III-dependent mRNA decay. In consequence, IcaR repressor is less expressed and thus <i>icaADBC</i> transcription occurs, favouring PIA-PNAG biosynthesis and biofilm development. When the interaction between <i>icaR</i> 3′- and 5′-UTR regions does not happen, ribosome binds the SD and proceeds with IcaR protein translation. The resulting IcaR protein binds to <i>icaADBC</i> operon promoter inhibiting its transcription and consequently biofilm formation.</p>", "links"=>[], "tags"=>["icar"], "article_id"=>882670, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Igor Ruiz de los Mozos", "Marta Vergara-Irigaray", "Victor Segura", "Maite Villanueva", "Nerea Bitarte", "Margarida Saramago", "Susana Domingues", "Cecília M. Arraiano", "Pierre Fechter", "Pascale Romby", "Jaione Valle", "Cristina Solano", "Iñigo Lasa", "Alejandro Toledo-Arana"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1004001.g009"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Modulation_of_IcaR_expression_by_5_8242_3_8242_UTRs_interaction_/882670", "title"=>"Modulation of IcaR expression by 5′-3′-UTRs interaction.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-12-19 04:02:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/1323468", "https://ndownloader.figshare.com/files/1323469", "https://ndownloader.figshare.com/files/1323470", "https://ndownloader.figshare.com/files/1323471", "https://ndownloader.figshare.com/files/1323472", "https://ndownloader.figshare.com/files/1323473", "https://ndownloader.figshare.com/files/1323474", "https://ndownloader.figshare.com/files/1323475", "https://ndownloader.figshare.com/files/1323476", "https://ndownloader.figshare.com/files/1323477"], "description"=>"<div><p>The presence of regulatory sequences in the 3′ untranslated region (3′-UTR) of eukaryotic mRNAs controlling RNA stability and translation efficiency is widely recognized. In contrast, the relevance of 3′-UTRs in bacterial mRNA functionality has been disregarded. Here, we report evidences showing that around one-third of the mapped mRNAs of the major human pathogen <i>Staphylococcus aureus</i> carry 3′-UTRs longer than 100-nt and thus, potential regulatory functions. We selected the long 3′-UTR of <i>icaR</i>, which codes for the repressor of the main exopolysaccharidic compound of the <i>S. aureus</i> biofilm matrix, to evaluate the role that 3′-UTRs may play in controlling mRNA expression. We showed that base pairing between the 3′-UTR and the Shine-Dalgarno (SD) region of <i>icaR</i> mRNA interferes with the translation initiation complex and generates a double-stranded substrate for RNase III. Deletion or substitution of the motif (UCCCCUG) within <i>icaR</i> 3′-UTR was sufficient to abolish this interaction and resulted in the accumulation of IcaR repressor and inhibition of biofilm development. Our findings provide a singular example of a new potential post-transcriptional regulatory mechanism to modulate bacterial gene expression through the interaction of a 3′-UTR with the 5′-UTR of the same mRNA.</p></div>", "links"=>[], "tags"=>["pairing", "controls", "mrna"], "article_id"=>882671, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Igor Ruiz de los Mozos", "Marta Vergara-Irigaray", "Victor Segura", "Maite Villanueva", "Nerea Bitarte", "Margarida Saramago", "Susana Domingues", "Cecília M. Arraiano", "Pierre Fechter", "Pascale Romby", "Jaione Valle", "Cristina Solano", "Iñigo Lasa", "Alejandro Toledo-Arana"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1004001.s001", "https://dx.doi.org/10.1371/journal.pgen.1004001.s002", "https://dx.doi.org/10.1371/journal.pgen.1004001.s003", "https://dx.doi.org/10.1371/journal.pgen.1004001.s004", "https://dx.doi.org/10.1371/journal.pgen.1004001.s005", "https://dx.doi.org/10.1371/journal.pgen.1004001.s006", "https://dx.doi.org/10.1371/journal.pgen.1004001.s007", "https://dx.doi.org/10.1371/journal.pgen.1004001.s008", "https://dx.doi.org/10.1371/journal.pgen.1004001.s009", "https://dx.doi.org/10.1371/journal.pgen.1004001.s010"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Base_Pairing_Interaction_between_5_and_3_UTRs_Controls_icaR_mRNA_Translation_in_Staphylococcus_aureus_/882671", "title"=>"Base Pairing Interaction between 5′- and 3′-UTRs Controls <i>icaR</i> mRNA Translation in <i>Staphylococcus aureus</i>", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-12-19 04:02:08"}

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Relative Metric

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