https://tncentral.ncc.unesp.br/TnPedia/index.php?title=IS_Families/ISL3_family&feed=atom&action=historyIS Families/ISL3 family - Revision history2024-03-29T14:56:03ZRevision history for this page on the wikiMediaWiki 1.34.0https://tncentral.ncc.unesp.br/TnPedia/index.php?title=IS_Families/ISL3_family&diff=3071&oldid=prevTnCentral at 12:55, 5 December 20222022-12-05T12:55:05Z<p></p>
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</table>TnCentralhttps://tncentral.ncc.unesp.br/TnPedia/index.php?title=IS_Families/ISL3_family&diff=3013&oldid=prevTnCentral at 14:14, 4 December 20222022-12-04T14:14:58Z<p></p>
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</table>TnCentralhttps://tncentral.ncc.unesp.br/TnPedia/index.php?title=IS_Families/ISL3_family&diff=2722&oldid=prevTnCentral at 17:57, 21 March 20222022-03-21T17:57:30Z<p></p>
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</table>TnCentralhttps://tncentral.ncc.unesp.br/TnPedia/index.php?title=IS_Families/ISL3_family&diff=2288&oldid=prevTnCentral at 23:59, 12 August 20212021-08-12T23:59:08Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>===Original Identification===</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>===Original Identification===</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>'''<big>T</big>'''he founding member [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISLr2 IS''Lr2''] was identified in [[wikipedia:Lactobacillus_delbrueckii_subsp._bulgaricus|''Lactobacillus delbrueckii'' subsp. ''Bulgaricus'']]<ref<del class="diffchange diffchange-inline">><nowiki</del>><pubmed>7565604</pubmed<del class="diffchange diffchange-inline">></nowiki</del>></ref> a bacterium used mainly for production of yogurt in mixed-strain thermophilic culture together with [[wikipedia:Streptococcus_thermophilus|''Streptococcus thermophilu''s]] where is being responsible for the loss of the capacity to ferment lactose. It was noted to be similar to [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=IS1165 IS''1165''] from [[wikipedia:Leuconostoc_mesenteroides|''Leuconostoc mesenteroides'' subsp. ''cremoris'']] strain DB1165 also used in commercial mesophyllic starter cultures<ref<del class="diffchange diffchange-inline">><nowiki</del>><pubmed>1325060</pubmed<del class="diffchange diffchange-inline">></nowiki</del>></ref>.</div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>'''<big>T</big>'''he founding member [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISLr2 IS''Lr2''] was identified in [[wikipedia:Lactobacillus_delbrueckii_subsp._bulgaricus|''Lactobacillus delbrueckii'' subsp. ''Bulgaricus'']]<ref><pubmed>7565604</pubmed></ref> a bacterium used mainly for production of yogurt in mixed-strain thermophilic culture together with [[wikipedia:Streptococcus_thermophilus|''Streptococcus thermophilu''s]] where is being responsible for the loss of the capacity to ferment lactose. It was noted to be similar to [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=IS1165 IS''1165''] from [[wikipedia:Leuconostoc_mesenteroides|''Leuconostoc mesenteroides'' subsp. ''cremoris'']] strain DB1165 also used in commercial mesophyllic starter cultures<ref><pubmed>1325060</pubmed></ref>.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>===Distribution===</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>===Distribution===</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Potential tIS derivatives with passenger genes appear quite common. These include a [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3466566/ mercury resistance operon]<ref name=":0"><pubmed>15907536</pubmed></div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Potential tIS derivatives with passenger genes appear quite common. These include a [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3466566/ mercury resistance operon]<ref name=":0"><pubmed>15907536</pubmed></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline">&lt;/nowiki&gt;</del></ref> in Tnmer1 ([https://www.ncbi.nlm.nih.gov/nuccore/AY351675.1/ AY351675]) from a conjugative plasmid, pPPM1000, in ''[[wikipedia:Enterococcus_faecium|Enterococcus faecium]]'' and in [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISStma11 IS''Stma11''] from ''[[wikipedia:Stenotrophomonas_maltophilia|Stenotrophomonas maltophilia]]'' ([https://www.ncbi.nlm.nih.gov/nuccore/NC_010943 NC_010943]). A number of other '''tIS''' derivatives with additional types of passenger gene such as restriction modification systems in ''[[wikipedia:Acinetobacter_bereziniae|Acinetobacter bereziniae]]'' ([https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISAbe14 IS''Abe14'']; [https://www.ncbi.nlm.nih.gov/nuccore/LKDJ00000000.2 LKDJ01000006]), ''[[wikipedia:Serratia_marcescens|Seratia marcesens]]'' ([https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISSm1 IS''Sm1'']) ''[[wikipedia:Klebsiella_pneumoniae|Klebsiella pneumoniae]]'' ([https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISKpn25 IS''Kpn25'']; [https://www.ncbi.nlm.nih.gov/nuccore/NC_009650.1/ NC_009650]) have also been identified. There are several additional examples of this type of structure: [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISPpu12 IS''Ppu12''] (''[[wikipedia:Pseudomonas_putida|Pseudomonas putida]]''; [https://www.ncbi.nlm.nih.gov/nuccore/AY128707 AY128707]); [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISPst2 IS''Pst2''] (''[[wikipedia:Pseudomonas_stutzeri|Pseudomonas stutzeri]]'' ; [https://www.ncbi.nlm.nih.gov/nuccore/AJ012352 AJ012352]); [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISEc53 IS''Ec53''] (''[[wikipedia:Escherichia_coli|Escherichia coli]]''; [https://www.ncbi.nlm.nih.gov/nuccore/HG941718 HG941718]); [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISRso21 IS''Rso21''] (''[[wikipedia:Ralstonia_solanacearum|Ralstonia solanacearam]]'').</div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div></ref> in Tnmer1 ([https://www.ncbi.nlm.nih.gov/nuccore/AY351675.1/ AY351675]) from a conjugative plasmid, pPPM1000, in ''[[wikipedia:Enterococcus_faecium|Enterococcus faecium]]'' and in [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISStma11 IS''Stma11''] from ''[[wikipedia:Stenotrophomonas_maltophilia|Stenotrophomonas maltophilia]]'' ([https://www.ncbi.nlm.nih.gov/nuccore/NC_010943 NC_010943]). A number of other '''tIS''' derivatives with additional types of passenger gene such as restriction modification systems in ''[[wikipedia:Acinetobacter_bereziniae|Acinetobacter bereziniae]]'' ([https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISAbe14 IS''Abe14'']; [https://www.ncbi.nlm.nih.gov/nuccore/LKDJ00000000.2 LKDJ01000006]), ''[[wikipedia:Serratia_marcescens|Seratia marcesens]]'' ([https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISSm1 IS''Sm1'']) ''[[wikipedia:Klebsiella_pneumoniae|Klebsiella pneumoniae]]'' ([https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISKpn25 IS''Kpn25'']; [https://www.ncbi.nlm.nih.gov/nuccore/NC_009650.1/ NC_009650]) have also been identified. There are several additional examples of this type of structure: [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISPpu12 IS''Ppu12''] (''[[wikipedia:Pseudomonas_putida|Pseudomonas putida]]''; [https://www.ncbi.nlm.nih.gov/nuccore/AY128707 AY128707]); [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISPst2 IS''Pst2''] (''[[wikipedia:Pseudomonas_stutzeri|Pseudomonas stutzeri]]'' ; [https://www.ncbi.nlm.nih.gov/nuccore/AJ012352 AJ012352]); [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISEc53 IS''Ec53''] (''[[wikipedia:Escherichia_coli|Escherichia coli]]''; [https://www.ncbi.nlm.nih.gov/nuccore/HG941718 HG941718]); [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISRso21 IS''Rso21''] (''[[wikipedia:Ralstonia_solanacearum|Ralstonia solanacearam]]'').</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>[https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=IS1167 IS''1167''] copies have been found flanking the ''cap1'' (capsular polysaccharide) locus of type 1 ''[[wikipedia:Streptococcus_pneumoniae|S. pneumoniae]]'' forming a potential compound transposon<ref<del class="diffchange diffchange-inline">><nowiki</del>><pubmed>11902728</pubmed<del class="diffchange diffchange-inline">></nowiki</del>></ref>. It has also used as a tool to distinguish between ''[[wikipedia:Streptococcus_pneumoniae|S. pneumoniae]]'' strains<ref<del class="diffchange diffchange-inline">><nowiki</del>><pubmed>9878026</pubmed<del class="diffchange diffchange-inline">></nowiki</del>></ref> using [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=IS1167 IS''1167''] [[wikipedia:Restriction_fragment_length_polymorphism|'''R'''estriction '''F'''ragment '''L'''ength '''P'''olymorphism (RFLP)]] pattern analysis<ref<del class="diffchange diffchange-inline">><nowiki</del>><pubmed>10747146</pubmed<del class="diffchange diffchange-inline">></nowiki</del>></ref>. The ''[[wikipedia:Pseudomonas_putida|Pseudomonas putida]]'', [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=IS1411 IS''1411''], was discovered by its ability to insertional activate promoter less ''pheBA'' genes by insertion due to an outward-directed promoter(s) at its left end<ref name=":1"><pubmed>9765560</pubmed></div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>[https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=IS1167 IS''1167''] copies have been found flanking the ''cap1'' (capsular polysaccharide) locus of type 1 ''[[wikipedia:Streptococcus_pneumoniae|S. pneumoniae]]'' forming a potential compound transposon<ref><pubmed>11902728</pubmed></ref>. It has also used as a tool to distinguish between ''[[wikipedia:Streptococcus_pneumoniae|S. pneumoniae]]'' strains<ref><pubmed>9878026</pubmed></ref> using [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=IS1167 IS''1167''] [[wikipedia:Restriction_fragment_length_polymorphism|'''R'''estriction '''F'''ragment '''L'''ength '''P'''olymorphism (RFLP)]] pattern analysis<ref><pubmed>10747146</pubmed></ref>. The ''[[wikipedia:Pseudomonas_putida|Pseudomonas putida]]'', [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=IS1411 IS''1411''], was discovered by its ability to insertional activate promoter less ''pheBA'' genes by insertion due to an outward-directed promoter(s) at its left end<ref name=":1"><pubmed>9765560</pubmed></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline">&lt;/nowiki&gt;</del></ref>.</div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div></ref>.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Small sequences (130-340 bp) related to the [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=IS1167 IS''1167''] '''IRs''' have been detected in ''[[wikipedia:Streptococcus_sanguinis|Streptococcus sanguis]]'', ''[[wikipedia:Streptococcus_pneumoniae|S. pneumoniae]]'', and ''[[wikipedia:Streptococcus_agalactiae|S. agalactiae]]''<ref<del class="diffchange diffchange-inline">><nowiki</del>><pubmed>2352474</pubmed<del class="diffchange diffchange-inline">></nowiki</del>></ref><ref<del class="diffchange diffchange-inline">><nowiki</del>><pubmed>7597107</pubmed<del class="diffchange diffchange-inline">></nowiki</del>></ref>.</div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Small sequences (130-340 bp) related to the [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=IS1167 IS''1167''] '''IRs''' have been detected in ''[[wikipedia:Streptococcus_sanguinis|Streptococcus sanguis]]'', ''[[wikipedia:Streptococcus_pneumoniae|S. pneumoniae]]'', and ''[[wikipedia:Streptococcus_agalactiae|S. agalactiae]]''<ref><pubmed>2352474</pubmed></ref><ref><pubmed>7597107</pubmed></ref>.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>===Organization===</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>===Organization===</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Members range in size from 1186 bp to 1553 bp, carry closely related IR of between 15 and 39 bp [[:File:Fig. ISL3.1.png|(Fig.IS''L3'')]] and generate DR of 8 bp. They generally have a single orf of between 400 and 440 amino acids which shows good alignment and includes an α-helical insertion domain<ref<del class="diffchange diffchange-inline">><nowiki</del>><pubmed>20067338</pubmed<del class="diffchange diffchange-inline">></nowiki</del>></ref>. </div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Members range in size from 1186 bp to 1553 bp, carry closely related IR of between 15 and 39 bp [[:File:Fig. ISL3.1.png|(Fig.IS''L3'')]] and generate DR of 8 bp. They generally have a single orf of between 400 and 440 amino acids which shows good alignment and includes an α-helical insertion domain<ref><pubmed>20067338</pubmed></ref>. </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[[Image:Fig. ISL3.1.png|thumb|center|620x620px|'''Fig. IS''L3''.''' '''General IS''L3'' characteristics, average length, and common ends. Top:''' Distribution of IS length (base pairs) of IS''L3'' family members. The number of examples used in the sample is shown above each column. '''Bottom''': Left ('''IRL''') and right '''IRR''' inverted terminal repeats are shown in [http://weblogo.threeplusone.com/ WebLogo] format.|alt=]]</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[[Image:Fig. ISL3.1.png|thumb|center|620x620px|'''Fig. IS''L3''.''' '''General IS''L3'' characteristics, average length, and common ends. Top:''' Distribution of IS length (base pairs) of IS''L3'' family members. The number of examples used in the sample is shown above each column. '''Bottom''': Left ('''IRL''') and right '''IRR''' inverted terminal repeats are shown in [http://weblogo.threeplusone.com/ WebLogo] format.|alt=]]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>While most carry only a single orf, the transposase, several variants include additional orfs: [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=IS1096 IS''1096''] harbors two orfs: the upstream orf exhibits similarities to the IS''L3'' family Tpases; the second, ''tnpR'', a [https://www.ncbi.nlm.nih.gov/pubmed/12829265 MerR-like transcription factor], is related to orfs from ''[[wikipedia:Rhizobium_rhizogenes|Agrobacterium rhizogenes]]'' and ''[[wikipedia:Rhizobium|Rhizobium]]'' sp. plasmids. TnpR appears to regulate transposition activity of [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISPpu12 IS''Ppu12'']<ref name=":2"><pubmed>20061472</pubmed></div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>While most carry only a single orf, the transposase, several variants include additional orfs: [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=IS1096 IS''1096''] harbors two orfs: the upstream orf exhibits similarities to the IS''L3'' family Tpases; the second, ''tnpR'', a [https://www.ncbi.nlm.nih.gov/pubmed/12829265 MerR-like transcription factor], is related to orfs from ''[[wikipedia:Rhizobium_rhizogenes|Agrobacterium rhizogenes]]'' and ''[[wikipedia:Rhizobium|Rhizobium]]'' sp. plasmids. TnpR appears to regulate transposition activity of [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISPpu12 IS''Ppu12'']<ref name=":2"><pubmed>20061472</pubmed></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline">&lt;/nowiki&gt;</del></ref>; [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISPpu12 IS''Ppu12''] in addition to a ''tnpA'' homologue carries three open reading frames, a PnbR-like regulatory protein of the [https://www.uniprot.org/uniprot/P0A183 MerR family], a putative membrane/transport protein and a putative [https://www.uniprot.org/uniprot/P00804 lipoprotein signal peptide-like protein (''lspA'')]<ref<del class="diffchange diffchange-inline">><nowiki</del>><pubmed>12426346</pubmed<del class="diffchange diffchange-inline">></nowiki</del>></ref><ref<del class="diffchange diffchange-inline">><nowiki</del>><pubmed>12426347</pubmed<del class="diffchange diffchange-inline">></nowiki</del>></ref>.</div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div></ref>; [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISPpu12 IS''Ppu12''] in addition to a ''tnpA'' homologue carries three open reading frames, a PnbR-like regulatory protein of the [https://www.uniprot.org/uniprot/P0A183 MerR family], a putative membrane/transport protein and a putative [https://www.uniprot.org/uniprot/P00804 lipoprotein signal peptide-like protein (''lspA'')]<ref><pubmed>12426346</pubmed></ref><ref><pubmed>12426347</pubmed></ref>.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>In [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=IS1167 IS''1167''], the reading frame appears to be distributed between two consecutive orfs with a potential for translational coupling suggested by overlapping initiation and termination codons (ATGA). </div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>In [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=IS1167 IS''1167''], the reading frame appears to be distributed between two consecutive orfs with a potential for translational coupling suggested by overlapping initiation and termination codons (ATGA). </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>===Mechanism===</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>===Mechanism===</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Transposition of most of these elements has been demonstrated, but no detailed analysis of their transposition mechanism has yet appeared. [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=IS1411 IS''1411''] from ''[[wikipedia:Pseudomonas_putida|Pseudomonas putida]]'' forms a circular species with abutted IS ends separated by 5 bp from the DNA flank of one IS end <ref name=":1" />. Clearly, as is the case in other IS which form circular transposition intermediates, expression of the ''tnp'' gene will be driven by the leftward oriented promoter. Transposon circles are also formed by [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISPst9 IS''Pst9'']<ref<del class="diffchange diffchange-inline">><nowiki</del>><pubmed>18645960</pubmed<del class="diffchange diffchange-inline">></nowiki</del>></ref> and the tIS, Tn''mer1'' <ref name=":0" /> and in both cases the abutted '''IRs''' are also separated by 5 bp. An isoform of [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISPpu12 IS''Ppu12'']''<ref name=":2" />'', [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=IS31831 IS''31831''] and [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=IS1411 IS''1411'']''<ref name=":1" />'' forms DNA species with a size expected for an excised transposon circles. For [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=IS31831 IS''31831''], derivatives of which have been used in [[wikipedia:Mutagenesis|mutagenesis]], the majority of insertions were found to be simple and only rare clones carried accompanying vector DNA<ref<del class="diffchange diffchange-inline">><nowiki</del>><pubmed>8196545</pubmed<del class="diffchange diffchange-inline">></nowiki</del>></ref>.</div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Transposition of most of these elements has been demonstrated, but no detailed analysis of their transposition mechanism has yet appeared. [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=IS1411 IS''1411''] from ''[[wikipedia:Pseudomonas_putida|Pseudomonas putida]]'' forms a circular species with abutted IS ends separated by 5 bp from the DNA flank of one IS end <ref name=":1" />. Clearly, as is the case in other IS which form circular transposition intermediates, expression of the ''tnp'' gene will be driven by the leftward oriented promoter. Transposon circles are also formed by [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISPst9 IS''Pst9'']<ref><pubmed>18645960</pubmed></ref> and the tIS, Tn''mer1'' <ref name=":0" /> and in both cases the abutted '''IRs''' are also separated by 5 bp. An isoform of [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISPpu12 IS''Ppu12'']''<ref name=":2" />'', [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=IS31831 IS''31831''] and [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=IS1411 IS''1411'']''<ref name=":1" />'' forms DNA species with a size expected for an excised transposon circles. For [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=IS31831 IS''31831''], derivatives of which have been used in [[wikipedia:Mutagenesis|mutagenesis]], the majority of insertions were found to be simple and only rare clones carried accompanying vector DNA<ref><pubmed>8196545</pubmed></ref>.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>There is some evidence indicating that transposition of these IS can be induced by a form of zygotic induction following conjugative transfer ''<ref name=":2" />'' although the phenomenon is not understood. [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISPst9 IS''Pst9''] undergoes transposition in the resident ''[[wikipedia:Pseudomonas_stutzeri|Pseudomonas stutzeri]]'' strain when brought into contact with a conjugative ''[[wikipedia:Escherichia_coli|E. coli]]'' strain, ''[[wikipedia:Escherichia_coli|E. coli]]'' S17-1 lambda(pir), and undergoes deletion. Activation requires a second IS''L3'' derivative, [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISPpu12 IS''Ppu12''], in the same strain. </div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>There is some evidence indicating that transposition of these IS can be induced by a form of zygotic induction following conjugative transfer ''<ref name=":2" />'' although the phenomenon is not understood. [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISPst9 IS''Pst9''] undergoes transposition in the resident ''[[wikipedia:Pseudomonas_stutzeri|Pseudomonas stutzeri]]'' strain when brought into contact with a conjugative ''[[wikipedia:Escherichia_coli|E. coli]]'' strain, ''[[wikipedia:Escherichia_coli|E. coli]]'' S17-1 lambda(pir), and undergoes deletion. Activation requires a second IS''L3'' derivative, [https://tncentral.ncc.unesp.br/ISfinder/scripts/ficheIS.php?name=ISPpu12 IS''Ppu12''], in the same strain. </div></td></tr>
</table>TnCentralhttps://tncentral.ncc.unesp.br/TnPedia/index.php?title=IS_Families/ISL3_family&diff=2281&oldid=prevTnCentral at 23:50, 12 August 20212021-08-12T23:50:17Z<p></p>
<a href="https://tncentral.ncc.unesp.br/TnPedia/index.php?title=IS_Families/ISL3_family&diff=2281&oldid=1822">Show changes</a>TnCentralhttps://tncentral.ncc.unesp.br/TnPedia/index.php?title=IS_Families/ISL3_family&diff=1822&oldid=prevTnCentral at 15:12, 7 December 20202020-12-07T15:12:28Z<p></p>
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 15:12, 7 December 2020</td>
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<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>===Mechanism===</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>===Mechanism===</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Transposition of most of these elements has been demonstrated, but no detailed analysis of their transposition mechanism has yet appeared. IS''1411'' from ''Pseudomonas putida'' forms a circular species with<ref name=":1" />. Clearly as is the case in other IS which form circular transposition intermediates, expression of the tnp gene will be driven by the leftward oriented promoter. Transposon circles are also formed by IS''Pst9''<ref><nowiki><pubmed>18645960</pubmed></nowiki></ref> and the tIS, Tn''mer1'' <ref name=":0" /> and in both cases the abutted IRs are also separated by 5 bp. An isoform of IS''Ppu12<ref name=":2" />'', IS''31831'' and IS''1411<ref name=":1" />'' forms DNA species with a size expected for an excised transposon circles. For IS''31831'', derivatives of which have been used in mutagenesis, the majority of insertions were found to be simple and only rare clones carried accompanying vector DNA<ref><nowiki><pubmed>8196545</pubmed></nowiki></ref>.</div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Transposition of most of these elements has been demonstrated, but no detailed analysis of their transposition mechanism has yet appeared. IS''1411'' from ''Pseudomonas putida'' forms a circular species with <ins class="diffchange diffchange-inline">abutted IS ends separated by 5 bp from the DNA flank of one IS end </ins><ref name=":1" />. Clearly as is the case in other IS which form circular transposition intermediates, expression of the tnp gene will be driven by the leftward oriented promoter. Transposon circles are also formed by IS''Pst9''<ref><nowiki><pubmed>18645960</pubmed></nowiki></ref> and the tIS, Tn''mer1'' <ref name=":0" /> and in both cases the abutted IRs are also separated by 5 bp. An isoform of IS''Ppu12<ref name=":2" />'', IS''31831'' and IS''1411<ref name=":1" />'' forms DNA species with a size expected for an excised transposon circles. For IS''31831'', derivatives of which have been used in mutagenesis, the majority of insertions were found to be simple and only rare clones carried accompanying vector DNA<ref><nowiki><pubmed>8196545</pubmed></nowiki></ref>.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>There is some evidence indicating that transposition of these IS can be induced by a form of zygotic induction following conjugative transfer ''<ref name=":2" />'' although the phenomenon is not understood. IS''Pst9'' undergoes transposition in the resident ''Pseudomonas stutzeri'' strain when brought into contact with a conjugative ''E. coli'' strain, ''E. coli'' S17-1 lambda(pir), and undergoes deletion. Activation requires a second IS''L3'' derivative, IS''Ppu12'', in the same strain. Although both IS''L3''-like ISs are similar, they differ in their accompanying genes: Mutation of TnpR, a MerR-like transcriptional regulator present in IS''Ppu12'' but not in IS''Pst9'', reduced the IS''Ppu12'' tnpA transcription and decreased formation of transposon circle transposition intermediates after conjugative interaction. Complementation of TnpR restored the ability to activate transposition but the expression of TnpR in the absence of IS''Ppu12'' did not result in conjugative induction of IS''Pst9''. This suggests that IS''Ppu12'' TnpR activates IS''Ppu12'' ''tnpA'' transcription and raises the possibility that IS''Ppu12'' TnpA might bind IRs of both IS''Ppu12'' and IS''Pst9'' and catalyze transposition of both elements. </div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>There is some evidence indicating that transposition of these IS can be induced by a form of zygotic induction following conjugative transfer ''<ref name=":2" />'' although the phenomenon is not understood. IS''Pst9'' undergoes transposition in the resident ''Pseudomonas stutzeri'' strain when brought into contact with a conjugative ''E. coli'' strain, ''E. coli'' S17-1 lambda(pir), and undergoes deletion. Activation requires a second IS''L3'' derivative, IS''Ppu12'', in the same strain. Although both IS''L3''-like ISs are similar, they differ in their accompanying genes: Mutation of TnpR, a MerR-like transcriptional regulator present in IS''Ppu12'' but not in IS''Pst9'', reduced the IS''Ppu12'' tnpA transcription and decreased formation of transposon circle transposition intermediates after conjugative interaction. Complementation of TnpR restored the ability to activate transposition but the expression of TnpR in the absence of IS''Ppu12'' did not result in conjugative induction of IS''Pst9''. This suggests that IS''Ppu12'' TnpR activates IS''Ppu12'' ''tnpA'' transcription and raises the possibility that IS''Ppu12'' TnpA might bind IRs of both IS''Ppu12'' and IS''Pst9'' and catalyze transposition of both elements. </div></td></tr>
</table>TnCentralhttps://tncentral.ncc.unesp.br/TnPedia/index.php?title=IS_Families/ISL3_family&diff=1651&oldid=prevTnCentral at 19:11, 13 July 20202020-07-13T19:11:51Z<p></p>
<table class="diff diff-contentalign-left" data-mw="interface">
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</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l13" >Line 13:</td>
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<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>===Organization===</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>===Organization===</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Members range in size from 1186 bp to 1553 bp, carry closely related IR of between 15 and 39 bp [[:File:Fig. ISL3.1.png|(Fig.IS''L3'')]] and generate DR of 8 bp. They generally have a single orf of between 400 and 440 amino acids which shows good alignment and includes an α-helical insertion domain<ref><nowiki><pubmed>20067338</pubmed></nowiki></ref>. </div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Members range in size from 1186 bp to 1553 bp, carry closely related IR of between 15 and 39 bp [[:File:Fig. ISL3.1.png|(Fig.IS''L3'')]] and generate DR of 8 bp. They generally have a single orf of between 400 and 440 amino acids which shows good alignment and includes an α-helical insertion domain<ref><nowiki><pubmed>20067338</pubmed></nowiki></ref>. </div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>[[Image:Fig. ISL3.1.png|thumb|center|<del class="diffchange diffchange-inline">500x500px</del>|'''Fig. IS''L3''.''' General IS''L3'' characteristics, average length and common ends.|alt=]]</div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>[[Image:Fig. ISL3.1.png|thumb|center|<ins class="diffchange diffchange-inline">620x620px</ins>|'''Fig. IS''L3''.<ins class="diffchange diffchange-inline">''' </ins>'''General IS''L3'' characteristics, average length<ins class="diffchange diffchange-inline">, </ins>and common ends<ins class="diffchange diffchange-inline">. Top:''' Distribution of IS length (base pairs) of IS''L3'' family members. The number of examples used in the sample is shown above each column. '''Bottom''': Left (IRL) and right IRR inverted terminal repeats are shown in WebLogo format (Crooks et al., 2004)</ins>.|alt=]]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>While most carry only a single orf, the transposase, several variants include additional orfs: IS''1096'' harbors two orfs: the upstream orf exhibits similarities to the IS''L3'' family Tpases; the second, ''tnpR'', a [https://www.ncbi.nlm.nih.gov/pubmed/12829265 MerR-like transcription factor], is related to orfs from ''[[wikipedia:Rhizobium_rhizogenes|Agrobacterium rhizogenes]]'' and ''[[wikipedia:Rhizobium|Rhizobium]]'' sp. plasmids. TnpR appears to regulate transposition activity of IS''Ppu12''<ref name=":2"><pubmed>20061472</pubmed></nowiki></ref>; ISPpu12 in addition to a tnpA homologue carries three open reading frames, a PnbR-like regulatory protein of the MerR family, a putative membrane/transport protein and a putative lipoprotein signal peptide-like protein (lspA)<ref><nowiki><pubmed>12426346</pubmed></nowiki></ref><ref><nowiki><pubmed>12426347</pubmed></nowiki></ref>.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>While most carry only a single orf, the transposase, several variants include additional orfs: IS''1096'' harbors two orfs: the upstream orf exhibits similarities to the IS''L3'' family Tpases; the second, ''tnpR'', a [https://www.ncbi.nlm.nih.gov/pubmed/12829265 MerR-like transcription factor], is related to orfs from ''[[wikipedia:Rhizobium_rhizogenes|Agrobacterium rhizogenes]]'' and ''[[wikipedia:Rhizobium|Rhizobium]]'' sp. plasmids. TnpR appears to regulate transposition activity of IS''Ppu12''<ref name=":2"><pubmed>20061472</pubmed></nowiki></ref>; ISPpu12 in addition to a tnpA homologue carries three open reading frames, a PnbR-like regulatory protein of the MerR family, a putative membrane/transport protein and a putative lipoprotein signal peptide-like protein (lspA)<ref><nowiki><pubmed>12426346</pubmed></nowiki></ref><ref><nowiki><pubmed>12426347</pubmed></nowiki></ref>.</div></td></tr>
</table>TnCentralhttps://tncentral.ncc.unesp.br/TnPedia/index.php?title=IS_Families/ISL3_family&diff=1365&oldid=prevTnCentral: /* Organization */2020-06-23T14:05:57Z<p><span dir="auto"><span class="autocomment">Organization</span></span></p>
<table class="diff diff-contentalign-left" data-mw="interface">
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</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l13" >Line 13:</td>
<td colspan="2" class="diff-lineno">Line 13:</td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>===Organization===</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>===Organization===</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Members range in size from 1186 bp to 1553 bp, carry closely related IR of between 15 and 39 bp [[:File:Fig. ISL3.1.png|(Fig.IS''L3'')]] and generate DR of 8 bp. They generally have a single orf of between 400 and 440 amino acids which shows good alignment and includes an α-helical insertion domain<ref><nowiki><pubmed>20067338</pubmed></nowiki></ref>. </div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Members range in size from 1186 bp to 1553 bp, carry closely related IR of between 15 and 39 bp [[:File:Fig. ISL3.1.png|(Fig.IS''L3'')]] and generate DR of 8 bp. They generally have a single orf of between 400 and 440 amino acids which shows good alignment and includes an α-helical insertion domain<ref><nowiki><pubmed>20067338</pubmed></nowiki></ref>. </div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>[[Image:Fig. ISL3.1.png|thumb|center|500x500px|'''Fig. IS''L3''.'''|alt=]]</div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>[[Image:Fig. ISL3.1.png|thumb|center|500x500px|'''Fig. IS''L3''.''' <ins class="diffchange diffchange-inline">General IS''L3'' characteristics, average length and common ends.</ins>|alt=]]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>While most carry only a single orf, the transposase, several variants include additional orfs: IS''1096'' harbors two orfs: the upstream orf exhibits similarities to the IS''L3'' family Tpases; the second, ''tnpR'', a [https://www.ncbi.nlm.nih.gov/pubmed/12829265 MerR-like transcription factor], is related to orfs from ''[[wikipedia:Rhizobium_rhizogenes|Agrobacterium rhizogenes]]'' and ''[[wikipedia:Rhizobium|Rhizobium]]'' sp. plasmids. TnpR appears to regulate transposition activity of IS''Ppu12''<ref name=":2"><pubmed>20061472</pubmed></nowiki></ref>; ISPpu12 in addition to a tnpA homologue carries three open reading frames, a PnbR-like regulatory protein of the MerR family, a putative membrane/transport protein and a putative lipoprotein signal peptide-like protein (lspA)<ref><nowiki><pubmed>12426346</pubmed></nowiki></ref><ref><nowiki><pubmed>12426347</pubmed></nowiki></ref>.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>While most carry only a single orf, the transposase, several variants include additional orfs: IS''1096'' harbors two orfs: the upstream orf exhibits similarities to the IS''L3'' family Tpases; the second, ''tnpR'', a [https://www.ncbi.nlm.nih.gov/pubmed/12829265 MerR-like transcription factor], is related to orfs from ''[[wikipedia:Rhizobium_rhizogenes|Agrobacterium rhizogenes]]'' and ''[[wikipedia:Rhizobium|Rhizobium]]'' sp. plasmids. TnpR appears to regulate transposition activity of IS''Ppu12''<ref name=":2"><pubmed>20061472</pubmed></nowiki></ref>; ISPpu12 in addition to a tnpA homologue carries three open reading frames, a PnbR-like regulatory protein of the MerR family, a putative membrane/transport protein and a putative lipoprotein signal peptide-like protein (lspA)<ref><nowiki><pubmed>12426346</pubmed></nowiki></ref><ref><nowiki><pubmed>12426347</pubmed></nowiki></ref>.</div></td></tr>
</table>TnCentralhttps://tncentral.ncc.unesp.br/TnPedia/index.php?title=IS_Families/ISL3_family&diff=1323&oldid=prevTnCentral at 18:54, 22 June 20202020-06-22T18:54:59Z<p></p>
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 18:54, 22 June 2020</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l5" >Line 5:</td>
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<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>There are more than 150 members from nearly 80 bacterial species. The family also includes archaeal members, particularly in the [[wikipedia:Methanomicrobia|Methanomicrobia]]. </div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>There are more than 150 members from nearly 80 bacterial species. The family also includes archaeal members, particularly in the [[wikipedia:Methanomicrobia|Methanomicrobia]]. </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Potential tIS derivatives with passenger genes appear quite common. These include a mercury resistance operon<ref<del class="diffchange diffchange-inline">><nowiki</del>><pubmed>15907536</pubmed></nowiki></ref> in Tnmer1 ([https://www.ncbi.nlm.nih.gov/nuccore/AY351675.1/ AY351675]) from a conjugative plasmid, pPPM1000, in ''[[wikipedia:Enterococcus_faecium|Enterococcus faecium]]'' and in IS''Stma11'' from ''[[wikipedia:Stenotrophomonas_maltophilia|Stenotrophomonas maltophilia]]'' ([https://www.ncbi.nlm.nih.gov/nuccore/NC_010943 NC_010943]). A number of other tIS derivatives with additional types of passenger gene such as restriction modification systems in ''[[wikipedia:Acinetobacter_bereziniae|Acinetobacter bereziniae]]'' (IS''Abe14''; [https://www.ncbi.nlm.nih.gov/nuccore/LKDJ00000000.2 LKDJ01000006]), ''[[wikipedia:Serratia_marcescens|Seratia marcesens]]'' (IS''Sm1'') ''[[wikipedia:Klebsiella_pneumoniae|Klebsiella pneumoniae]]'' (IS''Kpn25''; [https://www.ncbi.nlm.nih.gov/nuccore/NC_009650.1/ NC_009650]) have also been identified. There are several additional examples of this type of structure: IS''Ppu12'' (''[[wikipedia:Pseudomonas_putida|Pseudomonas putida]]''; [https://www.ncbi.nlm.nih.gov/nuccore/AY128707 AY128707]); IS''Pst2'' (''[[wikipedia:Pseudomonas_stutzeri|Pseudomonas stutzeri]]'' ; [https://www.ncbi.nlm.nih.gov/nuccore/AJ012352 AJ012352]); IS''Ec53'' (''[[wikipedia:Escherichia_coli|Escherichia coli]]''; [https://www.ncbi.nlm.nih.gov/nuccore/HG941718 HG941718]); IS''Rso21'' (''[[wikipedia:Ralstonia_solanacearum|Ralstonia solanacearam]]'').</div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Potential tIS derivatives with passenger genes appear quite common. These include a mercury resistance operon<ref <ins class="diffchange diffchange-inline">name=":0"</ins>><pubmed>15907536</pubmed></nowiki></ref> in Tnmer1 ([https://www.ncbi.nlm.nih.gov/nuccore/AY351675.1/ AY351675]) from a conjugative plasmid, pPPM1000, in ''[[wikipedia:Enterococcus_faecium|Enterococcus faecium]]'' and in IS''Stma11'' from ''[[wikipedia:Stenotrophomonas_maltophilia|Stenotrophomonas maltophilia]]'' ([https://www.ncbi.nlm.nih.gov/nuccore/NC_010943 NC_010943]). A number of other tIS derivatives with additional types of passenger gene such as restriction modification systems in ''[[wikipedia:Acinetobacter_bereziniae|Acinetobacter bereziniae]]'' (IS''Abe14''; [https://www.ncbi.nlm.nih.gov/nuccore/LKDJ00000000.2 LKDJ01000006]), ''[[wikipedia:Serratia_marcescens|Seratia marcesens]]'' (IS''Sm1'') ''[[wikipedia:Klebsiella_pneumoniae|Klebsiella pneumoniae]]'' (IS''Kpn25''; [https://www.ncbi.nlm.nih.gov/nuccore/NC_009650.1/ NC_009650]) have also been identified. There are several additional examples of this type of structure: IS''Ppu12'' (''[[wikipedia:Pseudomonas_putida|Pseudomonas putida]]''; [https://www.ncbi.nlm.nih.gov/nuccore/AY128707 AY128707]); IS''Pst2'' (''[[wikipedia:Pseudomonas_stutzeri|Pseudomonas stutzeri]]'' ; [https://www.ncbi.nlm.nih.gov/nuccore/AJ012352 AJ012352]); IS''Ec53'' (''[[wikipedia:Escherichia_coli|Escherichia coli]]''; [https://www.ncbi.nlm.nih.gov/nuccore/HG941718 HG941718]); IS''Rso21'' (''[[wikipedia:Ralstonia_solanacearum|Ralstonia solanacearam]]'').</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>IS''1167'' copies have been found flanking the ''cap1'' (capsular polysaccharide) locus of type 1 ''[[wikipedia:Streptococcus_pneumoniae|S. pneumoniae]]'' forming a potential compound transposon<ref><nowiki><pubmed>11902728</pubmed></nowiki></ref>. It has also used as a tool to distinguish between ''S. pneumoniae'' strains<ref><nowiki><pubmed>9878026</pubmed></nowiki></ref> using IS''1167'' '''R'''estriction '''F'''ragment '''L'''ength '''P'''olymorphism (RFLP) pattern analysis<ref><nowiki><pubmed>10747146</pubmed></nowiki></ref>. The ''Pseudomonas putida'', IS''1411'', was discovered by its ability to insertional activate promoter less ''pheBA'' genes by insertion due to an outward-directed promoter(s) at its left end<ref<del class="diffchange diffchange-inline">><nowiki</del>><pubmed>9765560</pubmed></nowiki></ref>.</div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>IS''1167'' copies have been found flanking the ''cap1'' (capsular polysaccharide) locus of type 1 ''[[wikipedia:Streptococcus_pneumoniae|S. pneumoniae]]'' forming a potential compound transposon<ref><nowiki><pubmed>11902728</pubmed></nowiki></ref>. It has also used as a tool to distinguish between ''S. pneumoniae'' strains<ref><nowiki><pubmed>9878026</pubmed></nowiki></ref> using IS''1167'' '''R'''estriction '''F'''ragment '''L'''ength '''P'''olymorphism (RFLP) pattern analysis<ref><nowiki><pubmed>10747146</pubmed></nowiki></ref>. The ''Pseudomonas putida'', IS''1411'', was discovered by its ability to insertional activate promoter less ''pheBA'' genes by insertion due to an outward-directed promoter(s) at its left end<ref <ins class="diffchange diffchange-inline">name=":1"</ins>><pubmed>9765560</pubmed></nowiki></ref>.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Small sequences (130-340 bp) related to the IS''1167'' IRs have been detected in ''[[wikipedia:Streptococcus_sanguinis|Streptococcus sanguis]]'', ''S. pneumoniae'', and ''[[wikipedia:Streptococcus_agalactiae|S. agalactiae]]''<ref><nowiki><pubmed>2352474</pubmed></nowiki></ref><ref><nowiki><pubmed>7597107</pubmed></nowiki></ref>.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Small sequences (130-340 bp) related to the IS''1167'' IRs have been detected in ''[[wikipedia:Streptococcus_sanguinis|Streptococcus sanguis]]'', ''S. pneumoniae'', and ''[[wikipedia:Streptococcus_agalactiae|S. agalactiae]]''<ref><nowiki><pubmed>2352474</pubmed></nowiki></ref><ref><nowiki><pubmed>7597107</pubmed></nowiki></ref>.</div></td></tr>
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<td colspan="2" class="diff-lineno">Line 15:</td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[[Image:Fig. ISL3.1.png|thumb|center|500x500px|'''Fig. IS''L3''.'''|alt=]]</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[[Image:Fig. ISL3.1.png|thumb|center|500x500px|'''Fig. IS''L3''.'''|alt=]]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>While most carry only a single orf, the transposase, several variants include additional orfs: IS''1096'' harbors two orfs: the upstream orf exhibits similarities to the IS''L3'' family Tpases; the second, ''tnpR'', a [https://www.ncbi.nlm.nih.gov/pubmed/12829265 MerR-like transcription factor], is related to orfs from ''[[wikipedia:Rhizobium_rhizogenes|Agrobacterium rhizogenes]]'' and ''[[wikipedia:Rhizobium|Rhizobium]]'' sp. plasmids. TnpR appears to regulate transposition activity of IS''Ppu12''<ref<del class="diffchange diffchange-inline">><nowiki</del>><pubmed>20061472</pubmed></nowiki></ref>; ISPpu12 in addition to a tnpA homologue carries three open reading frames, a PnbR-like regulatory protein of the MerR family, a putative membrane/transport protein and a putative lipoprotein signal peptide-like protein (lspA)<ref><nowiki><pubmed>12426346</pubmed></nowiki></ref><ref><nowiki><pubmed>12426347</pubmed></nowiki></ref>.</div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>While most carry only a single orf, the transposase, several variants include additional orfs: IS''1096'' harbors two orfs: the upstream orf exhibits similarities to the IS''L3'' family Tpases; the second, ''tnpR'', a [https://www.ncbi.nlm.nih.gov/pubmed/12829265 MerR-like transcription factor], is related to orfs from ''[[wikipedia:Rhizobium_rhizogenes|Agrobacterium rhizogenes]]'' and ''[[wikipedia:Rhizobium|Rhizobium]]'' sp. plasmids. TnpR appears to regulate transposition activity of IS''Ppu12''<ref <ins class="diffchange diffchange-inline">name=":2"</ins>><pubmed>20061472</pubmed></nowiki></ref>; ISPpu12 in addition to a tnpA homologue carries three open reading frames, a PnbR-like regulatory protein of the MerR family, a putative membrane/transport protein and a putative lipoprotein signal peptide-like protein (lspA)<ref><nowiki><pubmed>12426346</pubmed></nowiki></ref><ref><nowiki><pubmed>12426347</pubmed></nowiki></ref>.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>In IS1167, the reading frame appears to be distributed between two consecutive orfs with a potential for translational coupling suggested by overlapping initiation and termination codons (ATGA). </div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>In IS1167, the reading frame appears to be distributed between two consecutive orfs with a potential for translational coupling suggested by overlapping initiation and termination codons (ATGA). </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>===Mechanism===</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>===Mechanism===</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Transposition of most of these elements has been demonstrated, but no detailed analysis of their transposition mechanism has yet appeared. IS''1411'' from ''Pseudomonas putida'' forms a circular species with<ref<del class="diffchange diffchange-inline">><nowiki><pubmed>9765560</pubmed></nowiki><</del>/<del class="diffchange diffchange-inline">ref</del>>. Clearly as is the case in other IS which form circular transposition intermediates, expression of the tnp gene will be driven by the leftward oriented promoter. Transposon circles are also formed by IS''Pst9''<ref><nowiki><pubmed>18645960</pubmed></nowiki></ref> and the tIS, <del class="diffchange diffchange-inline">Tnmer1</del><ref<del class="diffchange diffchange-inline">><nowiki><pubmed>15907536</pubmed></nowiki><</del>/<del class="diffchange diffchange-inline">ref</del>> and in both cases the abutted IRs are also separated by 5 bp. An isoform of IS''Ppu12<del class="diffchange diffchange-inline">''</del><ref<del class="diffchange diffchange-inline">><nowiki><pubmed>20061472<</del>/<del class="diffchange diffchange-inline">pubmed></nowiki></ref</del>>, IS''31831'' and IS''1411<del class="diffchange diffchange-inline">''</del><ref<del class="diffchange diffchange-inline">><nowiki><pubmed>9765560</pubmed><</del>/<del class="diffchange diffchange-inline">nowiki></ref</del>> forms DNA species with a size expected for an excised transposon circles. For IS''31831'', derivatives of which have been used in mutagenesis, the majority of insertions were found to be simple and only rare clones carried accompanying vector DNA<ref><nowiki><pubmed>8196545</pubmed></nowiki></ref>.</div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Transposition of most of these elements has been demonstrated, but no detailed analysis of their transposition mechanism has yet appeared. IS''1411'' from ''Pseudomonas putida'' forms a circular species with<ref <ins class="diffchange diffchange-inline">name=":1" </ins>/>. Clearly as is the case in other IS which form circular transposition intermediates, expression of the tnp gene will be driven by the leftward oriented promoter. Transposon circles are also formed by IS''Pst9''<ref><nowiki><pubmed>18645960</pubmed></nowiki></ref> and the tIS, <ins class="diffchange diffchange-inline">Tn''mer1'' </ins><ref <ins class="diffchange diffchange-inline">name=":0" </ins>/> and in both cases the abutted IRs are also separated by 5 bp. An isoform of IS''Ppu12<ref <ins class="diffchange diffchange-inline">name=":2" </ins>/><ins class="diffchange diffchange-inline">''</ins>, IS''31831'' and IS''1411<ref <ins class="diffchange diffchange-inline">name=":1" </ins>/><ins class="diffchange diffchange-inline">'' </ins>forms DNA species with a size expected for an excised transposon circles. For IS''31831'', derivatives of which have been used in mutagenesis, the majority of insertions were found to be simple and only rare clones carried accompanying vector DNA<ref><nowiki><pubmed>8196545</pubmed></nowiki></ref>.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>There is some evidence indicating that transposition of these IS can be induced by a form of zygotic induction following conjugative transfer<ref<del class="diffchange diffchange-inline">><nowiki><pubmed>20061472<</del>/<del class="diffchange diffchange-inline">pubmed></nowiki></ref</del>> although the phenomenon is not understood. IS''Pst9'' undergoes transposition in the resident ''Pseudomonas stutzeri'' strain when brought into contact with a conjugative ''E. coli'' strain, ''E. coli'' S17-1 lambda(pir), and undergoes deletion. Activation requires a second IS''L3'' derivative, IS''Ppu12'', in the same strain. Although both IS''L3''-like ISs are similar, they differ in their accompanying genes: Mutation of TnpR, a MerR-like transcriptional regulator present in IS''Ppu12'' but not in IS''Pst9'', reduced the IS''Ppu12'' tnpA transcription and decreased formation of transposon circle transposition intermediates after conjugative interaction. Complementation of TnpR restored the ability to activate transposition but the expression of TnpR in the absence of IS''Ppu12'' did not result in conjugative induction of IS''Pst9''. This suggests that IS''Ppu12'' TnpR activates IS''Ppu12'' ''tnpA'' transcription and raises the possibility that IS''Ppu12'' TnpA might bind IRs of both IS''Ppu12'' and IS''Pst9'' and catalyze transposition of both elements. </div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>There is some evidence indicating that transposition of these IS can be induced by a form of zygotic induction following conjugative transfer <ins class="diffchange diffchange-inline">''</ins><ref <ins class="diffchange diffchange-inline">name=":2" </ins>/><ins class="diffchange diffchange-inline">'' </ins>although the phenomenon is not understood. IS''Pst9'' undergoes transposition in the resident ''Pseudomonas stutzeri'' strain when brought into contact with a conjugative ''E. coli'' strain, ''E. coli'' S17-1 lambda(pir), and undergoes deletion. Activation requires a second IS''L3'' derivative, IS''Ppu12'', in the same strain. Although both IS''L3''-like ISs are similar, they differ in their accompanying genes: Mutation of TnpR, a MerR-like transcriptional regulator present in IS''Ppu12'' but not in IS''Pst9'', reduced the IS''Ppu12'' tnpA transcription and decreased formation of transposon circle transposition intermediates after conjugative interaction. Complementation of TnpR restored the ability to activate transposition but the expression of TnpR in the absence of IS''Ppu12'' did not result in conjugative induction of IS''Pst9''. This suggests that IS''Ppu12'' TnpR activates IS''Ppu12'' ''tnpA'' transcription and raises the possibility that IS''Ppu12'' TnpA might bind IRs of both IS''Ppu12'' and IS''Pst9'' and catalyze transposition of both elements. </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>No obvious target sequence specificity has yet been observed although there is some suggestion that there may be a preference for AT-rich regions.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>No obvious target sequence specificity has yet been observed although there is some suggestion that there may be a preference for AT-rich regions.</div></td></tr>
</table>TnCentralhttps://tncentral.ncc.unesp.br/TnPedia/index.php?title=IS_Families/ISL3_family&diff=1050&oldid=prevTnCentral at 18:59, 2 June 20202020-06-02T18:59:05Z<p></p>
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</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l22" >Line 22:</td>
<td colspan="2" class="diff-lineno">Line 22:</td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Transposition of most of these elements has been demonstrated, but no detailed analysis of their transposition mechanism has yet appeared. IS''1411'' from ''Pseudomonas putida'' forms a circular species with<ref><nowiki><pubmed>9765560</pubmed></nowiki></ref>. Clearly as is the case in other IS which form circular transposition intermediates, expression of the tnp gene will be driven by the leftward oriented promoter. Transposon circles are also formed by IS''Pst9''<ref><nowiki><pubmed>18645960</pubmed></nowiki></ref> and the tIS, Tnmer1<ref><nowiki><pubmed>15907536</pubmed></nowiki></ref> and in both cases the abutted IRs are also separated by 5 bp. An isoform of IS''Ppu12''<ref><nowiki><pubmed>20061472</pubmed></nowiki></ref>, IS''31831'' and IS''1411''<ref><nowiki><pubmed>9765560</pubmed></nowiki></ref> forms DNA species with a size expected for an excised transposon circles. For IS''31831'', derivatives of which have been used in mutagenesis, the majority of insertions were found to be simple and only rare clones carried accompanying vector DNA<ref><nowiki><pubmed>8196545</pubmed></nowiki></ref>.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Transposition of most of these elements has been demonstrated, but no detailed analysis of their transposition mechanism has yet appeared. IS''1411'' from ''Pseudomonas putida'' forms a circular species with<ref><nowiki><pubmed>9765560</pubmed></nowiki></ref>. Clearly as is the case in other IS which form circular transposition intermediates, expression of the tnp gene will be driven by the leftward oriented promoter. Transposon circles are also formed by IS''Pst9''<ref><nowiki><pubmed>18645960</pubmed></nowiki></ref> and the tIS, Tnmer1<ref><nowiki><pubmed>15907536</pubmed></nowiki></ref> and in both cases the abutted IRs are also separated by 5 bp. An isoform of IS''Ppu12''<ref><nowiki><pubmed>20061472</pubmed></nowiki></ref>, IS''31831'' and IS''1411''<ref><nowiki><pubmed>9765560</pubmed></nowiki></ref> forms DNA species with a size expected for an excised transposon circles. For IS''31831'', derivatives of which have been used in mutagenesis, the majority of insertions were found to be simple and only rare clones carried accompanying vector DNA<ref><nowiki><pubmed>8196545</pubmed></nowiki></ref>.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>There is some evidence indicating that transposition of these IS can be induced by a form of zygotic induction following conjugative transfer<ref><nowiki><pubmed>20061472</pubmed></nowiki></ref> although the phenomenon is not understood. IS''Pst9'' undergoes transposition in the resident ''Pseudomonas stutzeri'' strain when brought into contact with a conjugative ''E. coli'' strain, ''E. coli'' S17-1 lambda(pir), and undergoes deletion. Activation requires a second IS''L3'' derivative, IS''Ppu12'', in the same strain. Although both IS''L3''-like ISs are similar, they differ in their accompanying genes: Mutation of TnpR, a MerR-like transcriptional regulator present in IS''Ppu12'' but not in IS''Pst9'', reduced the IS''Ppu12'' tnpA transcription and decreased formation of transposon circle transposition intermediates after conjugative interaction. Complementation of TnpR restored the ability to activate transposition but expression of TnpR in the absence of IS''Ppu12'' did not result in conjugative induction of IS''Pst9''. This suggests that IS''Ppu12'' TnpR activates IS''Ppu12'' ''tnpA'' transcription and raises the possibility that IS''Ppu12'' TnpA might bind IRs of both IS''Ppu12'' and IS''Pst9'' and catalyze transposition of both elements. </div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>There is some evidence indicating that transposition of these IS can be induced by a form of zygotic induction following conjugative transfer<ref><nowiki><pubmed>20061472</pubmed></nowiki></ref> although the phenomenon is not understood. IS''Pst9'' undergoes transposition in the resident ''Pseudomonas stutzeri'' strain when brought into contact with a conjugative ''E. coli'' strain, ''E. coli'' S17-1 lambda(pir), and undergoes deletion. Activation requires a second IS''L3'' derivative, IS''Ppu12'', in the same strain. Although both IS''L3''-like ISs are similar, they differ in their accompanying genes: Mutation of TnpR, a MerR-like transcriptional regulator present in IS''Ppu12'' but not in IS''Pst9'', reduced the IS''Ppu12'' tnpA transcription and decreased formation of transposon circle transposition intermediates after conjugative interaction. Complementation of TnpR restored the ability to activate transposition but <ins class="diffchange diffchange-inline">the </ins>expression of TnpR in the absence of IS''Ppu12'' did not result in conjugative induction of IS''Pst9''. This suggests that IS''Ppu12'' TnpR activates IS''Ppu12'' ''tnpA'' transcription and raises the possibility that IS''Ppu12'' TnpA might bind IRs of both IS''Ppu12'' and IS''Pst9'' and catalyze transposition of both elements. </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>No obvious target sequence specificity has yet been observed although there is some suggestion that there may be a preference for AT-rich regions.</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>No obvious target sequence specificity has yet been observed although there is some suggestion that there may be a preference for AT-rich regions.</div></td></tr>
</table>TnCentral