{"id":{"repo_id":"uiuc","oai_identifier":"oai:www.ideals.illinois.edu:2142/106189"},"canonical_url":"https://search.dev.ndltd.org/etd/uiuc/oai:www.ideals.illinois.edu:2142/106189","repository":{"repo_id":"uiuc","name":"University of Illinois - Urbana-Champaign","base_url":"https://www.ideals.illinois.edu/oai-pmh"},"display":{"title":"An E. coli small RNA inhibits translation initiation from a distance","abstract":"In bacterial systems, small RNA (sRNA)-dependent translational repression is commonly carried out via sRNA-mRNA base pairing interactions near the Shine-Dalgarno (SD) region. In this so-called “canonical” mechanism, the sRNA is the direct regulator; it competes with the initiating ribosomes while the chaperone protein Hfq plays a supporting role. Contrary to this widely accepted model, there are a few examples in the literature where the sRNA base pairs far from the SD region, yet translation of the target mRNA is still inhibited. Mechanistically, non-canonical translation regulation is one of the least understood aspects of sRNA biology. In the targetome of an E. coli sRNA SgrS, manXYZ is a non-canonical target where SgrS base pairs at two distinct sites that are far from the SD regions of manX and manY, yet translation of these two cistrons are repressed by SgrS. We found that manX translation is controlled by a molecular role-reversal mechanism where an Hfq binding site is directly adjacent to the manX ribosome binding site. In this regulatory mechanism, SgrS plays the role of a guide to recruit Hfq to the appropriate binding site to form the silencing complex. We also report that SgrS forms a duplex with a uridine-rich translation-enhancing element in the manY 5' untranslated region. Notably, we show that the enhancer is ribosome-dependent and that the small ribosomal subunit protein S1 interacts with the enhancer to promote translation of manY. In collaboration with the chaperone protein Hfq, SgrS interferes with the interaction between the translation enhancer and the r-protein S1 to repress translation of manY mRNA. Since bacterial translation is often initiated from a nonlinear ribosome binding site, sRNA-mediated enhancer silencing could be a common mode of gene regulation.","abstract_html":"In bacterial systems, small RNA (sRNA)-dependent translational repression is commonly carried out via sRNA-mRNA base pairing interactions near the Shine-Dalgarno (SD) region. In this so-called “canonical” mechanism, the sRNA is the direct regulator; it competes with the initiating ribosomes while the chaperone protein Hfq plays a supporting role. Contrary to this widely accepted model, there are a few examples in the literature where the sRNA base pairs far from the SD region, yet translation of the target mRNA is still inhibited. Mechanistically, non-canonical translation regulation is one of the least understood aspects of sRNA biology. In the targetome of an E. coli sRNA SgrS, manXYZ is a non-canonical target where SgrS base pairs at two distinct sites that are far from the SD regions of manX and manY, yet translation of these two cistrons are repressed by SgrS. We found that manX translation is controlled by a molecular role-reversal mechanism where an Hfq binding site is directly adjacent to the manX ribosome binding site. In this regulatory mechanism, SgrS plays the role of a guide to recruit Hfq to the appropriate binding site to form the silencing complex. We also report that SgrS forms a duplex with a uridine-rich translation-enhancing element in the manY 5' untranslated region. Notably, we show that the enhancer is ribosome-dependent and that the small ribosomal subunit protein S1 interacts with the enhancer to promote translation of manY. In collaboration with the chaperone protein Hfq, SgrS interferes with the interaction between the translation enhancer and the r-protein S1 to repress translation of manY mRNA. Since bacterial translation is often initiated from a nonlinear ribosome binding site, sRNA-mediated enhancer silencing could be a common mode of gene regulation.","abstract_has_math":false,"creators":["Azam, Muhammad Shafiul"],"institution":"University of Illinois at Urbana-Champaign","degree_name":"Ph.D.","degree_level":"Dissertation","degree_discipline":"Microbiology","degree_department":null,"school":null,"contributors":["Vanderpool, Carin K.","Whitaker, Rachel J.","Slauch, James M.","Olsen, Gary J."],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2020,"date_issued":"2020-03-02T21:58:11Z","date_published":"2020-03-02T21:58:11Z","updated_at":"2026-07-22T22:24:45Z","subjects":["sRNA, Hfq, Enhancer"],"languages":["en"],"rights":["Copyright 2019 Muhammad Shafiul Azam"],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"http://hdl.handle.net/2142/106189","outbound_label":"Handle","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Vanderpool, Carin K.","Whitaker, Rachel J.","Slauch, James M.","Olsen, Gary J."]},{"key":"dc:creator","label":"Author","values":["Azam, Muhammad Shafiul"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2020-03-02T21:58:11Z","2019-11-15","2019-12"]},{"key":"dc:type","label":"Dc Type","values":["text"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Microbiology"]},{"key":"thesis:degree_level","label":"Degree Level","values":["Dissertation"]},{"key":"thesis:degree_name","label":"Degree Name","values":["Ph.D."]},{"key":"thesis:institution_name","label":"Thesis Institution Name","values":["University of Illinois at Urbana-Champaign"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["sRNA, Hfq, Enhancer"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["en"]},{"key":"dc:rights","label":"Dc Rights","values":["Copyright 2019 Muhammad Shafiul Azam"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["http://hdl.handle.net/2142/106189"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["In bacterial systems, small RNA (sRNA)-dependent translational repression is commonly carried out via sRNA-mRNA base pairing interactions near the Shine-Dalgarno (SD) region. In this so-called “canonical” mechanism, the sRNA is the direct regulator; it competes with the initiating ribosomes while the chaperone protein Hfq plays a supporting role. Contrary to this widely accepted model, there are a few examples in the literature where the sRNA base pairs far from the SD region, yet translation of the target mRNA is still inhibited. Mechanistically, non-canonical translation regulation is one of the least understood aspects of sRNA biology. In the targetome of an E. coli sRNA SgrS, manXYZ is a non-canonical target where SgrS base pairs at two distinct sites that are far from the SD regions of manX and manY, yet translation of these two cistrons are repressed by SgrS. We found that manX translation is controlled by a molecular role-reversal mechanism where an Hfq binding site is directly adjacent to the manX ribosome binding site. In this regulatory mechanism, SgrS plays the role of a guide to recruit Hfq to the appropriate binding site to form the silencing complex. We also report that SgrS forms a duplex with a uridine-rich translation-enhancing element in the manY 5' untranslated region. Notably, we show that the enhancer is ribosome-dependent and that the small ribosomal subunit protein S1 interacts with the enhancer to promote translation of manY. In collaboration with the chaperone protein Hfq, SgrS interferes with the interaction between the translation enhancer and the r-protein S1 to repress translation of manY mRNA. Since bacterial translation is often initiated from a nonlinear ribosome binding site, sRNA-mediated enhancer silencing could be a common mode of gene regulation.","Submission original under an indefinite embargo labeled 'Open Access'. The submission was exported from vireo on 2020-02-28 without embargo terms","The student, Muhammad Shafiul Azam, accepted the attached license on 2019-11-14 at 12:38.","The student, Muhammad Shafiul Azam, submitted this Dissertation for approval on 2019-11-14 at 12:43.","This Dissertation was approved for publication on 2019-11-15 at 15:01.","DSpace SAF Submission Ingestion Package generated from Vireo submission #14551 on 2020-02-28 at 17:13:39","Made available in DSpace on 2020-03-02T21:58:11Z (GMT). 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Contrary to this widely accepted model, there are a few examples in the literature where the sRNA base pairs far from the SD region, yet translation of the target mRNA is still inhibited. Mechanistically, non-canonical translation regulation is one of the least understood aspects of sRNA biology. In the targetome of an E. coli sRNA SgrS, manXYZ is a non-canonical target where SgrS base pairs at two distinct sites that are far from the SD regions of manX and manY, yet translation of these two cistrons are repressed by SgrS. We found that manX translation is controlled by a molecular role-reversal mechanism where an Hfq binding site is directly adjacent to the manX ribosome binding site. In this regulatory mechanism, SgrS plays the role of a guide to recruit Hfq to the appropriate binding site to form the silencing complex. We also report that SgrS forms a duplex with a uridine-rich translation-enhancing element in the manY 5' untranslated region. Notably, we show that the enhancer is ribosome-dependent and that the small ribosomal subunit protein S1 interacts with the enhancer to promote translation of manY. In collaboration with the chaperone protein Hfq, SgrS interferes with the interaction between the translation enhancer and the r-protein S1 to repress translation of manY mRNA. Since bacterial translation is often initiated from a nonlinear ribosome binding site, sRNA-mediated enhancer silencing could be a common mode of gene regulation.","Submission original under an indefinite embargo labeled 'Open Access'. The submission was exported from vireo on 2020-02-28 without embargo terms","The student, Muhammad Shafiul Azam, accepted the attached license on 2019-11-14 at 12:38.","The student, Muhammad Shafiul Azam, submitted this Dissertation for approval on 2019-11-14 at 12:43.","This Dissertation was approved for publication on 2019-11-15 at 15:01.","DSpace SAF Submission Ingestion Package generated from Vireo submission #14551 on 2020-02-28 at 17:13:39","Made available in DSpace on 2020-03-02T21:58:11Z (GMT). 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