{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,9,13]],"date-time":"2023-09-13T16:23:38Z","timestamp":1694622218519},"reference-count":37,"publisher":"Cold Spring Harbor Laboratory","issue":"12","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["RNA"],"published-print":{"date-parts":[[2003,12]]},"abstract":"<jats:p>Expression of the <jats:italic>trpEDCFBA<\/jats:italic> operon of <jats:italic>Bacillus subtilis<\/jats:italic> is regulated by transcription attenuation and translation control mechanisms. We recently determined that the <jats:italic>B. subtilis trp<\/jats:italic> leader readthrough transcript can adopt a Mg<jats:sup>2+<\/jats:sup>-dependent tertiary structure that appears to interfere with TRAP-mediated translation control of <jats:italic>trpE<\/jats:italic>. In the present study, sequence comparisons to <jats:italic>trp<\/jats:italic> leaders from three other <jats:italic>Bacillus<\/jats:italic> sp. were made, suggesting that RNA secondary and tertiary structures are phylogenetically conserved. To test this hypothesis, experiments were carried out with the <jats:italic>trp<\/jats:italic> leader transcript from <jats:italic>Bacillus stearothermophilus<\/jats:italic>. Structure mapping experiments confirmed the predicted secondary structure. Native gel experiments identified a faster mobility species in the presence of Mg<jats:sup>2+<\/jats:sup>, suggesting that a Mg<jats:sup>2+<\/jats:sup>-dependent tertiary structure forms. Mg<jats:sup>2+<\/jats:sup>-dependent protection of residues within the first five triplet repeats of the TRAP binding target and a pyrimidine-rich internal loop were observed, consistent with tertiary structure formation between these regions. Structure mapping in the presence of a competitor DNA oligonucleotide allowed the interacting partners to be identified as a single-stranded portion of the purine-rich TRAP binding target and the large downstream pyrimidine-rich internal loop. Thermal denaturation experiments revealed a Mg<jats:sup>2+<\/jats:sup>- and pH-dependent unfolding transition that was absent for a transcript missing the first five triplet repeats. The stability of several mutant transcripts allowed a large portion of the base-pairing register for the tertiary interaction to be determined. These data indicate that RNA secondary and tertiary structures involved in TRAP-mediated translation control are conserved in at least four <jats:italic>Bacillus<\/jats:italic> species.<\/jats:p>","DOI":"10.1261\/rna.5149603","type":"journal-article","created":{"date-parts":[[2003,11,17]],"date-time":"2003-11-17T19:26:25Z","timestamp":1069097185000},"page":"1502-1515","source":"Crossref","is-referenced-by-count":2,"title":["Phylogenetic conservation of RNA secondary and tertiary structure in the <i>trpEDCFBA<\/i> operon leader transcript in <i>Bacillus<\/i>"],"prefix":"10.1261","volume":"9","author":[{"given":"JANELL E.","family":"SCHAAK","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"PAUL","family":"BABITZKE","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"PHILIP C.","family":"BEVILACQUA","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"246","published-online":{"date-parts":[[2003,11,17]]},"reference":[{"key":"2021112105340846000_9.12.1502.1","doi-asserted-by":"publisher","DOI":"10.1006\/jmbi.1994.1698"},{"key":"2021112105340846000_9.12.1502.2","doi-asserted-by":"publisher","DOI":"10.1038\/374693a0"},{"key":"2021112105340846000_9.12.1502.3","doi-asserted-by":"publisher","DOI":"10.1038\/45730"},{"key":"2021112105340846000_9.12.1502.4","doi-asserted-by":"publisher","DOI":"10.1128\/JB.183.20.5795-5802.2001"},{"key":"2021112105340846000_9.12.1502.5","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.90.1.133"},{"key":"2021112105340846000_9.12.1502.6","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.270.21.12452"},{"key":"2021112105340846000_9.12.1502.7","doi-asserted-by":"crossref","first-page":"16597","DOI":"10.1016\/S0021-9258(19)89431-0","volume":"269","year":"1994","journal-title":"J. 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(in press).","DOI":"10.1016\/S0076-6879(03)71030-1"},{"key":"2021112105340846000_9.12.1502.10","doi-asserted-by":"publisher","DOI":"10.1021\/bi981732v"},{"key":"2021112105340846000_9.12.1502.11","doi-asserted-by":"publisher","DOI":"10.1146\/annurev.biophys.26.1.113"},{"key":"2021112105340846000_9.12.1502.12","doi-asserted-by":"publisher","DOI":"10.1006\/jmbi.1999.2834"},{"key":"2021112105340846000_9.12.1502.13","doi-asserted-by":"publisher","DOI":"10.1126\/science.7513905"},{"key":"2021112105340846000_9.12.1502.14","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.273.32.20494"},{"key":"2021112105340846000_9.12.1502.15","doi-asserted-by":"crossref","first-page":"2582","DOI":"10.1128\/jb.179.8.2582-2586.1997","volume":"179","year":"1997","journal-title":"J. Bacteriol."},{"key":"2021112105340846000_9.12.1502.16","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.87.22.8726"},{"key":"2021112105340846000_9.12.1502.17","doi-asserted-by":"crossref","unstructured":"Gollnick, P., Babitzke, P., Merino, E., and Yanofsky, C. 2002. Aromatic amino acid metabolism in Bacillus subtilis. In Bacillus subtilis and its closest relatives: From genes to cells, pp. 233\u2013244. ASM Press, Washington, DC.","DOI":"10.1128\/9781555817992.ch17"},{"key":"2021112105340846000_9.12.1502.18","doi-asserted-by":"crossref","first-page":"839","DOI":"10.1128\/jb.177.3.839-842.1995","volume":"177","year":"1995","journal-title":"J. Bacteriol."},{"key":"2021112105340846000_9.12.1502.19","doi-asserted-by":"crossref","first-page":"3080","DOI":"10.1128\/jb.170.7.3080-3088.1988","volume":"170","year":"1988","journal-title":"J. Bacteriol."},{"key":"2021112105340846000_9.12.1502.20","doi-asserted-by":"publisher","DOI":"10.1006\/jmbi.1994.1256"},{"key":"2021112105340846000_9.12.1502.21","doi-asserted-by":"publisher","DOI":"10.1021\/ja9640051"},{"key":"2021112105340846000_9.12.1502.22","doi-asserted-by":"publisher","DOI":"10.1006\/jmbi.1999.2700"},{"key":"2021112105340846000_9.12.1502.23","doi-asserted-by":"crossref","first-page":"6362","DOI":"10.1128\/jb.177.22.6362-6370.1995","volume":"177","year":"1995","journal-title":"J. Bacteriol."},{"key":"2021112105340846000_9.12.1502.24","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.90.1.128"},{"key":"2021112105340846000_9.12.1502.25","unstructured":"Pleij, C.W. 1993. Appendix 2: RNA pseudoknot. In The RNA world: The nature of modern RNA suggests a prebiotic RNA world, pp. 609\u2013613. 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Bacteriol."},{"key":"2021112105340846000_9.12.1502.32","doi-asserted-by":"publisher","DOI":"10.1006\/jmbi.1999.3001"},{"key":"2021112105340846000_9.12.1502.33","unstructured":"Tinoco Jr., I. and Schmitz, M. 2000. Thermodynamics of formation of secondary structure in nucleic acids. In Thermodynamics in biology, pp. 131\u2013176. Oxford University Press, New York."},{"key":"2021112105340846000_9.12.1502.34","doi-asserted-by":"publisher","DOI":"10.1021\/ja00014a068"},{"key":"2021112105340846000_9.12.1502.35","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.162373299"},{"key":"2021112105340846000_9.12.1502.36","doi-asserted-by":"crossref","first-page":"4272","DOI":"10.1128\/jb.177.15.4272-4278.1995","volume":"177","year":"1995","journal-title":"J. Bacteriol."},{"key":"2021112105340846000_9.12.1502.37","doi-asserted-by":"crossref","unstructured":"Zuker, M., Mathews, D.H., and Turner, D.H. 1999. Algorithms and thermodynamics for RNA secondary structure prediction: A practical guide. 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