{"id":806,"date":"2023-03-16T14:19:46","date_gmt":"2023-03-16T07:19:46","guid":{"rendered":"https:\/\/conf.icgbio.ru\/bgrs98\/?page_id=806"},"modified":"2023-04-12T12:30:57","modified_gmt":"2023-04-12T05:30:57","slug":"063_computer-analysis-of-base-pairing-free-energy-between-shine-dalgarno-sequence-and-16s-rrna-sequence-in-various-procaryotes","status":"publish","type":"page","link":"https:\/\/conf.icgbio.ru\/bgrs98\/abstracts\/abstract-list\/063_computer-analysis-of-base-pairing-free-energy-between-shine-dalgarno-sequence-and-16s-rrna-sequence-in-various-procaryotes\/","title":{"rendered":"COMPUTER ANALYSIS OF BASE PAIRING FREE-ENERGY BETWEEN SHINE-DALGARNO SEQUENCE AND 16S RRNA SEQUENCE IN VARIOUS PROCARYOTES"},"content":{"rendered":"<p><a href=\"https:\/\/conf.icgbio.ru\/bgrs98\/abstracts\/authors-index\/#yuko\">OSADA YUKO<\/a>,\u00a0<a href=\"https:\/\/conf.icgbio.ru\/bgrs98\/abstracts\/authors-index\/#saito\">RINTARO SAITO<\/a>,\u00a0<a href=\"https:\/\/conf.icgbio.ru\/bgrs98\/abstracts\/authors-index\/#tomita\">TOMITA MASARU<\/a><\/p>\n<p>Laboratory for Bioinformatics<\/p>\n<p>Keio University<\/p>\n<p><a href=\"https:\/\/conf.icgbio.ru\/bgrs98\/abstracts\/keywords-index\/\">Keywords<\/a>: computer analysis, base pairing free energy, Shine-Dalgarno sequence, 16S rRNA<\/p>\n<p>&nbsp;<\/p>\n<p>It is well accepted that the 3&#8242; end of 16S rRNA is directly involved in the procaryotic translation initiation by pairing with the Shine-Dalgarno (SD) sequence, which is located in the ribosome-binding site of mRNA. We comprehensively calculated free-energy values of the base pairing between the 3&#8242; end of 16S rRNA and the 5&#8242; UTR of mRNA, in order to detect the mRNA binding sequence in 16S rRNA for various procaryotes.<\/p>\n<p>The average free-energy values are sharply dropped a few bps upstream of the start codon in\u00a0<i>E. coli<\/i>, which is consistent with the model that the 3&#8242; end of 16S rRNA interacts with the SD sequence.<br \/>\n<i>H. influenzae<\/i>\u00a0shows quite a similar pattern, indicating that the organism has basically the same translation initiation mechanism. Other species, such as\u00a0<i>Mycoplasma pneumoniae<\/i>,<i>Helicobacter pylori<\/i>, and\u00a0<i>Synecholystis\u00a0<\/i>PCC6803, also show free-energy drops, although the drops are less evident and the shape of the drops is significantly different from that of\u00a0<i>E.coli<\/i>\u00a0and\u00a0<i>H. influenzae<\/i>.<\/p>\n<p>No free-energy drops can be seen in the genomes of\u00a0<i>Aquifex aeolicus<\/i>\u00a0and the three archibacteria (<i>Archaeoglobus fulgibus<\/i>,\u00a0<i>Methanobacterium thermoautotrophicum<\/i>, and\u00a0<i>Methanococcus jannaschii<\/i>), suggesting that 16S rRNA of those procaryotes does not base pair with a specific region of mRNA.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>OSADA YUKO,\u00a0RINTARO SAITO,\u00a0TOMITA MASARU Laboratory for Bioinformatics Keio University Keywords: computer analysis, base pairing free energy, Shine-Dalgarno sequence, 16S rRNA &nbsp; It is well accepted that the 3&#8242; end of 16S rRNA is directly involved in the procaryotic translation initiation &hellip; <a href=\"https:\/\/conf.icgbio.ru\/bgrs98\/abstracts\/abstract-list\/063_computer-analysis-of-base-pairing-free-energy-between-shine-dalgarno-sequence-and-16s-rrna-sequence-in-various-procaryotes\/\">Continue reading <span class=\"meta-nav\">&rarr;<\/span><\/a><\/p>\n","protected":false},"author":13,"featured_media":0,"parent":97,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":[],"_links":{"self":[{"href":"https:\/\/conf.icgbio.ru\/bgrs98\/wp-json\/wp\/v2\/pages\/806"}],"collection":[{"href":"https:\/\/conf.icgbio.ru\/bgrs98\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/conf.icgbio.ru\/bgrs98\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/conf.icgbio.ru\/bgrs98\/wp-json\/wp\/v2\/users\/13"}],"replies":[{"embeddable":true,"href":"https:\/\/conf.icgbio.ru\/bgrs98\/wp-json\/wp\/v2\/comments?post=806"}],"version-history":[{"count":3,"href":"https:\/\/conf.icgbio.ru\/bgrs98\/wp-json\/wp\/v2\/pages\/806\/revisions"}],"predecessor-version":[{"id":1401,"href":"https:\/\/conf.icgbio.ru\/bgrs98\/wp-json\/wp\/v2\/pages\/806\/revisions\/1401"}],"up":[{"embeddable":true,"href":"https:\/\/conf.icgbio.ru\/bgrs98\/wp-json\/wp\/v2\/pages\/97"}],"wp:attachment":[{"href":"https:\/\/conf.icgbio.ru\/bgrs98\/wp-json\/wp\/v2\/media?parent=806"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}