Alba-Domain Proteins of Trypanosoma brucei Are Cytoplasmic RNA-Binding Proteins That Interact with the Translation Machinery
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{"title"=>"Alba-domain proteins of trypanosoma brucei are cytoplasmic RNA-Binding proteins that interact with the translation machinery", "type"=>"journal", "authors"=>[{"first_name"=>"Jan", "last_name"=>"Mani", "scopus_author_id"=>"15053379000"}, {"first_name"=>"Andreas", "last_name"=>"Güttinger", "scopus_author_id"=>"16241735900"}, {"first_name"=>"Bernd", "last_name"=>"Schimanski", "scopus_author_id"=>"9243145900"}, {"first_name"=>"Manfred", "last_name"=>"Heller", "scopus_author_id"=>"56988578100"}, {"first_name"=>"Alvaro", "last_name"=>"Acosta-Serrano", "scopus_author_id"=>"6602671796"}, {"first_name"=>"Pascale", "last_name"=>"Pescher", "scopus_author_id"=>"6603025089"}, {"first_name"=>"Gerald", "last_name"=>"Späth", "scopus_author_id"=>"7003643165"}, {"first_name"=>"Isabel", "last_name"=>"Roditi", "scopus_author_id"=>"7006565031"}], "year"=>2011, "source"=>"PLoS ONE", "identifiers"=>{"sgr"=>"79960647138", "pmid"=>"21811616", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "pui"=>"362190963", "issn"=>"19326203", "scopus"=>"2-s2.0-79960647138", "doi"=>"10.1371/journal.pone.0022463"}, "id"=>"62cde44e-aca7-324a-a786-b3c97fbec0b3", "abstract"=>"Trypanosoma brucei and related pathogens transcribe most genes as polycistronic arrays that are subsequently processed into monocistronic mRNAs. Expression is frequently regulated post-transcriptionally by cis-acting elements in the untranslated regions (UTRs). GPEET and EP procyclins are the major surface proteins of procyclic (insect midgut) forms of T. brucei. Three regulatory elements common to the 3' UTRs of both mRNAs regulate mRNA turnover and translation. The glycerol-responsive element (GRE) is unique to the GPEET 3' UTR and regulates its expression independently from EP. A synthetic RNA encompassing the GRE showed robust sequence-specific interactions with cytoplasmic proteins in electromobility shift assays. This, combined with column chromatography, led to the identification of 3 Alba-domain proteins. RNAi against Alba3 caused a growth phenotype and reduced the levels of Alba1 and Alba2 proteins, indicative of interactions between family members. Tandem-affinity purification and co-immunoprecipitation verified these interactions and also identified Alba4 in sub-stoichiometric amounts. Alba proteins are cytoplasmic and are recruited to starvation granules together with poly(A) RNA. Concomitant depletion of all four Alba proteins by RNAi specifically reduced translation of a reporter transcript flanked by the GPEET 3' UTR. Pulldown of tagged Alba proteins confirmed interactions with poly(A) binding proteins, ribosomal protein P0 and, in the case of Alba3, the cap-binding protein eIF4E4. In addition, Alba2 and Alba3 partially cosediment with polyribosomes in sucrose gradients. Alba-domain proteins seem to have exhibited great functional plasticity in the course of evolution. First identified as DNA-binding proteins in Archaea, then in association with nuclear RNase MRP/P in yeast and mammalian cells, they were recently described as components of a translationally silent complex containing stage-regulated mRNAs in Plasmodium. Our results are also consistent with stage-specific regulation of translation in trypanosomes, but most likely in the context of initiation.", "link"=>"http://www.mendeley.com/research/albadomain-proteins-trypanosoma-brucei-cytoplasmic-rnabinding-proteins-interact-translation-machiner", "reader_count"=>63, "reader_count_by_academic_status"=>{"Unspecified"=>2, "Professor > Associate Professor"=>4, "Researcher"=>23, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>14, "Student > Postgraduate"=>2, "Student > Master"=>4, "Student > Bachelor"=>6, "Lecturer"=>1, "Professor"=>5}, "reader_count_by_user_role"=>{"Unspecified"=>2, "Professor > Associate Professor"=>4, "Researcher"=>23, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>14, "Student > Postgraduate"=>2, "Student > Master"=>4, "Student > Bachelor"=>6, "Lecturer"=>1, "Professor"=>5}, "reader_count_by_subject_area"=>{"Unspecified"=>5, "Biochemistry, Genetics and Molecular Biology"=>16, "Nursing and Health Professions"=>1, "Agricultural and Biological Sciences"=>37, "Medicine and Dentistry"=>2, "Immunology and Microbiology"=>2}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>2}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>37}, "Nursing and Health Professions"=>{"Nursing and Health Professions"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>16}, "Unspecified"=>{"Unspecified"=>5}}, "reader_count_by_country"=>{"Brazil"=>3, "Denmark"=>1, "United Kingdom"=>2, "France"=>1, "India"=>1}, "group_count"=>1}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/754528"], "description"=>"<p>(A) Ectopic expression of HA-tagged Alba proteins was induced by addition of tetracycline to cell cultures prior to extract preparation and CoIP. Input protein samples (inp) and precipitated proteins (IP) were analyzed by immunoblotting using Alba-specific antibodies. Detection of HA served as a positive control and HSP60 as a negative control for immunoprecipitation. Epitope-tagged Alba3 (HA-Alba3) and endogenous Alba3 (endo Alba3) cross-react with the bivalent anti-Alba4 antibody. lc: light chain of the anti-HA antibody used for the pulldown. (B) Summary of interactions between Alba proteins determined from TAP and CoIP experiments. Full black lines depict interactions that are resistant to RNase A. The dashed line indicates an RNase-sensitive interaction.</p>", "links"=>[], "tags"=>["alba", "proteins", "bridging", "rna"], "article_id"=>424896, "categories"=>["Molecular Biology", "Biochemistry", "Microbiology"], "users"=>["Jan Mani", "Andreas Güttinger", "Bernd Schimanski", "Manfred Heller", "Alvaro Acosta-Serrano", "Pascale Pescher", "Gerald Späth", "Isabel Roditi"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0022463.g008", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Interactions_between_Alba_proteins_are_largely_independent_of_bridging_RNA_molecules_/424896", "title"=>"Interactions between Alba proteins are largely independent of bridging RNA molecules.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-07-21 01:21:36"}
  • {"files"=>["https://ndownloader.figshare.com/files/754600"], "description"=>"<p>(A) Alba3 interacts with eIF4E4 via an RNA bridge. Expression of eIF4E4-HA was induced by addition of tetracycline. Extracts were either left untreated or treated with RNase A prior to performing CoIP. Protein input samples (inp) and precipitated proteins (IP) were analyzed by immunoblotting using Alba-specific antibodies. HA and HSP60 serve as controls for fusion protein expression and loading, respectively. (B–E). Ribosomal protein P0 co-precipitates with Alba proteins. CoIP experiments were performed using cells treated with tetracycline to induce expression of HA-tagged Alba proteins. Input protein samples (inp) and precipitated proteins (IP) were analyzed for the presence of the ribosomal protein P0. Detection of HA served as a positive control and HSP60 as a negative control for immunoprecipitation. HA-Alba1 (B) and HA-Alba4 (C) precipitate P0. Incubation with RNase A (10 µg/ml) abolishes these interactions. HA-Alba2 (D) and HA-Alba3 (E) also associate with P0 but treatment with 40 µg/ml RNase A does not completely abolish the interaction.</p>", "links"=>[], "tags"=>["proteins"], "article_id"=>424969, "categories"=>["Molecular Biology", "Biochemistry", "Microbiology"], "users"=>["Jan Mani", "Andreas Güttinger", "Bernd Schimanski", "Manfred Heller", "Alvaro Acosta-Serrano", "Pascale Pescher", "Gerald Späth", "Isabel Roditi"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0022463.g009", "stats"=>{"downloads"=>1, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Alba_proteins_interact_with_the_translation_machinery_/424969", "title"=>"Alba proteins interact with the translation machinery.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-07-21 01:22:49"}
  • {"files"=>["https://ndownloader.figshare.com/files/754102"], "description"=>"<p>(A) Total RNA from induced (+ Tet) and uninduced (- Tet) RNAi cells was extracted on the days indicated. Blots were hybridised with probes recognizing GPEET mRNA and 18S rRNA, which served as a loading control. (B) Quantification after normalisation to 18S rRNA. Steady-state levels of GPEET mRNA remained constant in the Alba4 and Alba3&4 RNAi cell lines.</p>", "links"=>[], "tags"=>["albas", "gpeet", "mrna"], "article_id"=>424468, "categories"=>["Molecular Biology", "Biochemistry", "Microbiology"], "users"=>["Jan Mani", "Andreas Güttinger", "Bernd Schimanski", "Manfred Heller", "Alvaro Acosta-Serrano", "Pascale Pescher", "Gerald Späth", "Isabel Roditi"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0022463.g003", "stats"=>{"downloads"=>3, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Ablation_of_Albas_has_little_effect_on_GPEET_mRNA_levels_/424468", "title"=>"Ablation of Albas has little effect on GPEET mRNA levels.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-07-21 01:14:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/754202"], "description"=>"<p>(A) Western blot analysis was performed on total lysates (1.5×10<sup>6</sup> cell equivalents per lane). Alba 3&4 RNAi cultures were incubated for 4 days in the presence or absence of tetracycline (+/− Tet). Western blot analysis was performed with antibodies against GPEET and EP. Mitochondrial HSP60 was used as a loading control. Early procyclic forms of AnTat 1.1 (early PCF) possess two copies of GPEET. In Alba3&4 RNAi the coding region of one copy of GPEET is replaced by GFP and the adjacent copy of EP3 is replaced by a puromycin-resistance cassette. (B–E). 2D-DIGE detects a limited number of differences in following knockdown of Alba proteins. Alba3&4 RNAi cells were cultured for 4 days in the presence (+Tet) or absence (−Tet) of tetracycline, which is before the onset of the slow growth phenotype. (B) Merge of a representative pair of gels (one of 4 biological replicates) showing significantly regulated proteins. (C) Enlarged regions of 2D-DIGE gels for Cy3-labeled proteins from induced (+Tet; green) and Cy5-labeled proteins from uninduced (−Tet, red) cultures, and the corresponding 3D views. The lower panel shows a graphic representation of differences in abundance of these proteins across the 4 independent experiments. (D) Protein identities, fold difference (+Tet/−Tet) and statistical significance. (E) Northern blot analysis and quantification of GFP mRNA in Alba3&4 RNAi cells. The entire ORF of GFP was used as a hybridisation probe.</p>", "links"=>[], "tags"=>["alba", "proteins", "gpeet", "ep", "affects"], "article_id"=>424565, "categories"=>["Molecular Biology", "Biochemistry", "Microbiology"], "users"=>["Jan Mani", "Andreas Güttinger", "Bernd Schimanski", "Manfred Heller", "Alvaro Acosta-Serrano", "Pascale Pescher", "Gerald Späth", "Isabel Roditi"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0022463.g004", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Depletion_of_Alba_proteins_does_not_affect_GPEET_and_EP_procyclins_but_affects_translation_of_a_reporter_/424565", "title"=>"Depletion of Alba proteins does not affect GPEET and EP procyclins, but affects translation of a reporter.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-07-21 01:16:05"}
  • {"files"=>["https://ndownloader.figshare.com/files/754389"], "description"=>"<p>(A) Protein extracts from wild type AnTat1.1 were separated on sucrose gradients. Absorption at 254 nm was recorded during fractionation of the gradient. Fractions were separated by SDS-PAGE and analyzed by immunoblotting. The ribosomal protein P0 served as a ribosome marker and the endoplasmic reticulum protein BiP as a marker for proteins not associated with ribosomes. (B) Fractionation of extracts after treatment with 50 mM EDTA, which disrupts polysomes.</p>", "links"=>[], "tags"=>["alba3"], "article_id"=>424756, "categories"=>["Molecular Biology", "Biochemistry", "Microbiology"], "users"=>["Jan Mani", "Andreas Güttinger", "Bernd Schimanski", "Manfred Heller", "Alvaro Acosta-Serrano", "Pascale Pescher", "Gerald Späth", "Isabel Roditi"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0022463.g006", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Alba2_and_Alba3_partially_associate_with_polysomes_/424756", "title"=>"Alba2 and Alba3 partially associate with polysomes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-07-21 01:19:16"}
  • {"files"=>["https://ndownloader.figshare.com/files/754004"], "description"=>"<p>(A) A panel of RNAi cell lines was constructed to knock down single Alba proteins or combinations of Alba proteins. A derivative of AnTat 90-13 <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0022463#pone.0022463-Engstler1\" target=\"_blank\">[36]</a>, in which one copy of the GPEET coding region was replaced by enhanced GFP, was used as the parental line for Alba 1, Alba2, Alba1&2 and Alba3&4 RNAi cells. Unmodified AnTat 90-13 was used as the parental line for Alba 3 and Alba4 RNAi cells. RNAi was induced by addition of tetracycline to the cultures 3 days prior to the preparation of protein extracts. Band shift assays with <sup>32</sup>P-labeled GPEET were performed as described in the legend to <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0022463#pone-0022463-g001\" target=\"_blank\">Figure 1</a>. - Tet: uninduced; + Tet: induced; RNA only: incubation of GPEETLII without protein extract. (B) and (C): Alba1 and Alba2 proteins are dependent on Alba3. Western blot analysis of Alba proteins after knockdown of Alba3 (B) or Alba4 (C) by RNAi. Protein extracts of uninduced (- Tet) and induced (+Tet) cells were prepared every second or third day for 12 days and Alba proteins were detected with specific antibodies. HSP60 served as a loading control.</p>", "links"=>[], "tags"=>["proteins", "components", "complexes", "s2"], "article_id"=>424368, "categories"=>["Molecular Biology", "Biochemistry", "Microbiology"], "users"=>["Jan Mani", "Andreas Güttinger", "Bernd Schimanski", "Manfred Heller", "Alvaro Acosta-Serrano", "Pascale Pescher", "Gerald Späth", "Isabel Roditi"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0022463.g002", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Alba_proteins_are_components_of_complexes_S2_and_S3_/424368", "title"=>"Alba proteins are components of complexes S2 and S3.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-07-21 01:12:48"}
  • {"files"=>["https://ndownloader.figshare.com/files/380087", "https://ndownloader.figshare.com/files/380117", "https://ndownloader.figshare.com/files/380151", "https://ndownloader.figshare.com/files/380176", "https://ndownloader.figshare.com/files/380199", "https://ndownloader.figshare.com/files/380226", "https://ndownloader.figshare.com/files/380249", "https://ndownloader.figshare.com/files/380274", "https://ndownloader.figshare.com/files/380304", "https://ndownloader.figshare.com/files/380323", "https://ndownloader.figshare.com/files/380362", "https://ndownloader.figshare.com/files/380388", "https://ndownloader.figshare.com/files/380416", "https://ndownloader.figshare.com/files/380432"], "description"=>"<div><p><em>Trypanosoma brucei</em> and related pathogens transcribe most genes as polycistronic arrays that are subsequently processed into monocistronic mRNAs. Expression is frequently regulated post-transcriptionally by <em>cis</em>-acting elements in the untranslated regions (UTRs). GPEET and EP procyclins are the major surface proteins of procyclic (insect midgut) forms of <em>T. brucei.</em> Three regulatory elements common to the 3′ UTRs of both mRNAs regulate mRNA turnover and translation. The glycerol-responsive element (GRE) is unique to the GPEET 3′ UTR and regulates its expression independently from EP. A synthetic RNA encompassing the GRE showed robust sequence-specific interactions with cytoplasmic proteins in electromobility shift assays. This, combined with column chromatography, led to the identification of 3 Alba-domain proteins. RNAi against Alba3 caused a growth phenotype and reduced the levels of Alba1 and Alba2 proteins, indicative of interactions between family members. Tandem-affinity purification and co-immunoprecipitation verified these interactions and also identified Alba4 in sub-stoichiometric amounts. Alba proteins are cytoplasmic and are recruited to starvation granules together with poly(A) RNA. Concomitant depletion of all four Alba proteins by RNAi specifically reduced translation of a reporter transcript flanked by the GPEET 3′ UTR. Pulldown of tagged Alba proteins confirmed interactions with poly(A) binding proteins, ribosomal protein P0 and, in the case of Alba3, the cap-binding protein eIF4E4. In addition, Alba2 and Alba3 partially cosediment with polyribosomes in sucrose gradients. Alba-domain proteins seem to have exhibited great functional plasticity in the course of evolution. First identified as DNA-binding proteins in <em>Archaea,</em> then in association with nuclear RNase MRP/P in yeast and mammalian cells, they were recently described as components of a translationally silent complex containing stage-regulated mRNAs in <em>Plasmodium</em>. Our results are also consistent with stage-specific regulation of translation in trypanosomes, but most likely in the context of initiation.</p> </div>", "links"=>[], "tags"=>["alba-domain", "proteins", "are", "cytoplasmic", "rna-binding", "machinery"], "article_id"=>135100, "categories"=>["Molecular Biology", "Biochemistry", "Microbiology"], "users"=>["Jan Mani", "Andreas Güttinger", "Bernd Schimanski", "Manfred Heller", "Alvaro Acosta-Serrano", "Pascale Pescher", "Gerald Späth", "Isabel Roditi"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0022463.s001", "https://dx.doi.org/10.1371/journal.pone.0022463.s002", "https://dx.doi.org/10.1371/journal.pone.0022463.s003", "https://dx.doi.org/10.1371/journal.pone.0022463.s004", "https://dx.doi.org/10.1371/journal.pone.0022463.s005", "https://dx.doi.org/10.1371/journal.pone.0022463.s006", "https://dx.doi.org/10.1371/journal.pone.0022463.s007", "https://dx.doi.org/10.1371/journal.pone.0022463.s008", "https://dx.doi.org/10.1371/journal.pone.0022463.s009", "https://dx.doi.org/10.1371/journal.pone.0022463.s010", "https://dx.doi.org/10.1371/journal.pone.0022463.s011", "https://dx.doi.org/10.1371/journal.pone.0022463.s012", "https://dx.doi.org/10.1371/journal.pone.0022463.s013", "https://dx.doi.org/10.1371/journal.pone.0022463.s014"], "stats"=>{"downloads"=>14, "page_views"=>16, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Alba_Domain_Proteins_of_Trypanosoma_brucei_Are_Cytoplasmic_RNA_Binding_Proteins_That_Interact_with_the_Translation_Machinery/135100", "title"=>"Alba-Domain Proteins of <em>Trypanosoma brucei</em> Are Cytoplasmic RNA-Binding Proteins That Interact with the Translation Machinery", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2011-07-21 01:25:00"}
  • {"files"=>["https://ndownloader.figshare.com/files/754302"], "description"=>"<p>Alba proteins were expressed as GFP fusion proteins. Cells expressing unfused GFP were used as a control. Poly(A) RNA was detected by fluorescence <i>in situ</i> hybridisation using a Cy3-labeled oligo(dT)<sub>30</sub> probe. Cells were incubated for 2 h in PBS, PBS + glucose (PBSG) or in complete medium prior to fixation and analysis. Merge refers to the overlay of GFP and Cy3 signals in combination with signals from the DNA stain DAPI.</p>", "links"=>[], "tags"=>["proteins", "localise", "cytoplasm", "granules", "cells", "deprived"], "article_id"=>424665, "categories"=>["Molecular Biology", "Biochemistry", "Microbiology"], "users"=>["Jan Mani", "Andreas Güttinger", "Bernd Schimanski", "Manfred Heller", "Alvaro Acosta-Serrano", "Pascale Pescher", "Gerald Späth", "Isabel Roditi"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0022463.g005", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Alba_proteins_localise_to_the_cell_cytoplasm_and_become_part_of_stress_granules_SG_when_cells_are_deprived_of_nutrients_/424665", "title"=>"Alba proteins localise to the cell cytoplasm and become part of stress granules (SG) when cells are deprived of nutrients.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-07-21 01:17:45"}
  • {"files"=>["https://ndownloader.figshare.com/files/754457"], "description"=>"<p>(A) Coomassie blue-stained polyacrylamide gels of purified complexes. Alba proteins were tagged <i>in situ</i> with a PTP tag and protein complexes isolated under native conditions. Proteins were treated with trypsin and the resulting peptides identified by LC-MS/MS. ProtC (black triangle) identifies the respective tagged Alba protein after removal of the protein A moiety with AcTev protease. Alba proteins co-purifying with the tagged proteins are highlighted as follows: Alba1 (red diamond), Alba2 (yellow circle), Alba3 (blue square) and Alba4 (green pentagon). (B) List of proteins that were identified independently in at least two TAP experiments in the size range indicated by the dashed lines in (A). α and β tubulin are likely to be contaminants as reported by others.</p>", "links"=>[], "tags"=>["affinity", "purification", "reveals", "interactions", "alba"], "article_id"=>424819, "categories"=>["Molecular Biology", "Biochemistry", "Microbiology"], "users"=>["Jan Mani", "Andreas Güttinger", "Bernd Schimanski", "Manfred Heller", "Alvaro Acosta-Serrano", "Pascale Pescher", "Gerald Späth", "Isabel Roditi"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0022463.g007", "stats"=>{"downloads"=>2, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Tandem_affinity_purification_TAP_reveals_interactions_between_Alba_proteins_/424819", "title"=>"Tandem affinity purification (TAP) reveals interactions between Alba proteins.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-07-21 01:20:19"}
  • {"files"=>["https://ndownloader.figshare.com/files/753910"], "description"=>"<p>(A) Band shift assay of radiolabeled GPEETLII RNA with protein extracts from procyclic form trypanosomes reveals three shifts: S1, S2 and S3 (B) Competition experiment in which a ∼100-fold excess of unlabeled yeast tRNA, GPEETLII, EPLII or GPEETM234 <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0022463#pone.0022463-Vassella4\" target=\"_blank\">[24]</a> was added to the binding reaction. (C) Phylogenetic tree classifying <i>T. brucei</i> Alba proteins within the Rpp20/Pop7 and Rpp25/Pop6 Alba protein subfamilies. The Alba superfamily of proteins is divided into three major subfamilies <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0022463#pone.0022463-Aravind1\" target=\"_blank\">[32]</a>. All archaeal proteins group together in one branch (pink). Eukaryotic Alba proteins belong to either one of two branches typified by Rpp20/Pop7 (blue) and Rpp25/Pop6 (green). Phylogenetic analysis based on isolated Alba-domains of a set of Alba proteins places Alba1 and Alba2 in the Rpp20/Pop7 subfamiliy and Alba3 and Alba4 in the Rpp25/Pop6 subfamily. Proteins are indicated with an abbreviation for the species name followed by their UniProt accession number: Af: <i>Archaeoglobus fulgidus;</i> Ap: <i>Aeropyrum pernix;</i> At: <i>Arabidopsis thaliana;</i> Hs: <i>Homo sapiens;</i> Lb: <i>Leishmania braziliensis;</i> Li: <i>Leishmania infantum;</i> Lm: <i>Leishmania major;</i> Mj: <i>Methanocaldococcus jannaschii;</i> Pb: <i>Plasmodium berghei;</i> Ph: <i>Pyrococcus horikoshii;</i> Sc: <i>Saccharomyces cerevisiae;</i> Sl: <i>Stylonychia lemnae;</i> Ssh: <i>Sulfolobus shibatae;</i> Sso: <i>Sulfolobus solfataricus;</i> Tb: <i>Trypanosoma brucei;</i> Tc : <i>Trypanosoma cruzi.</i> Particularly: Tb_Q385X1 is Alba1; Tb_Q385X2 is Alba2; Tb_Q583I9 is Alba3; Tb_Q583J0 is Alba4; Sc_A6ZLB0 is Pop7; Hs_O75817 is Rpp20; Sc_Q45U55 is Pop6; Hs_Q9BUL9 is Rpp25 and Sl_Q8ISG7 is Mdp2. Proteins marked with an asterisk contain RGG repeats in their C-termini.</p>", "links"=>[], "tags"=>["gpeetlii", "interacts", "proteins"], "article_id"=>424274, "categories"=>["Molecular Biology", "Biochemistry", "Microbiology"], "users"=>["Jan Mani", "Andreas Güttinger", "Bernd Schimanski", "Manfred Heller", "Alvaro Acosta-Serrano", "Pascale Pescher", "Gerald Späth", "Isabel Roditi"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0022463.g001", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_cis_regulatory_element_GPEETLII_specifically_interacts_with_proteins_from_T_brucei_/424274", "title"=>"The <i>cis</i>-regulatory element GPEETLII specifically interacts with proteins from <i>T. brucei</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-07-21 01:11:14"}

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  • {"unique-ip"=>"12", "full-text"=>"5", "pdf"=>"5", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"18", "cited-by"=>"0", "year"=>"2020", "month"=>"3"}
  • {"unique-ip"=>"14", "full-text"=>"23", "pdf"=>"6", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2020", "month"=>"4"}
  • {"unique-ip"=>"18", "full-text"=>"21", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"1", "cited-by"=>"1", "year"=>"2020", "month"=>"5"}
  • {"unique-ip"=>"17", "full-text"=>"16", "pdf"=>"4", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"6"}
  • {"unique-ip"=>"10", "full-text"=>"10", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"7"}
  • {"unique-ip"=>"16", "full-text"=>"12", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"8"}

Relative Metric

{"start_date"=>"2011-01-01T00:00:00Z", "end_date"=>"2011-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Biology and life sciences", "average_usage"=>[304, 568, 702, 818, 927, 1027, 1118, 1206, 1285, 1357, 1427, 1500, 1564, 1636, 1705, 1773, 1840, 1909, 1974, 2039, 2106, 2170, 2234, 2296, 2358, 2423, 2484, 2546, 2606, 2673, 2734, 2795, 2857, 2921, 2984, 3046, 3100]}, {"subject_area"=>"/Biology and life sciences/Biochemistry", "average_usage"=>[290, 559, 698, 813, 927, 1028, 1121, 1206, 1289, 1360, 1433, 1501, 1569, 1637, 1707, 1774, 1841, 1911, 1974, 2038, 2103, 2161, 2219, 2280, 2345, 2406, 2466, 2529, 2592, 2654, 2713, 2772, 2835, 2893, 2954, 3020, 3071]}, {"subject_area"=>"/Biology and life sciences/Microbiology", "average_usage"=>[313, 585, 721, 833, 946, 1049, 1147, 1230, 1307, 1383, 1462, 1528, 1592, 1667, 1726, 1794, 1857, 1918, 1993, 2070, 2137, 2194, 2258, 2314, 2370, 2432, 2497, 2555, 2619, 2676, 2741, 2801, 2861, 2914, 2971, 3017, 3072]}, {"subject_area"=>"/Medicine and health sciences/Pharmacology", "average_usage"=>[337, 604, 750, 875, 1001, 1107, 1205, 1299, 1391, 1468, 1552, 1629, 1709, 1785, 1862, 1935, 2013, 2081, 2140, 2212, 2281, 2352, 2422, 2489, 2564, 2629, 2698, 2752, 2833, 2880, 2925, 2983, 3042, 3111, 3183, 3250, 3311]}]}
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