<?xml version="1.0" encoding="UTF-8"?><xmi:XMI xmlns:pos="http:///org/u_compare/shared/label/penn/pos.ecore" xmlns:grammatical="http:///org/u_compare/shared/label/penn/function/grammatical.ecore" xmlns:general="http:///org/u_compare/shared/label/penn/pos/general.ecore" xmlns:cas="http:///uima/cas.ecore" xmlns:stanford="http:///org/u_compare/shared/label/stanford.ecore" xmlns:semantic2="http:///uk/ac/nactem/semantic.ecore" xmlns:bioie="http:///org/u_compare/shared/label/penn/pos/bioie.ecore" xmlns:function="http:///org/u_compare/shared/label/penn/function.ecore" xmlns:tcas="http:///uima/tcas.ecore" xmlns:bio="http:///org/u_compare/shared/semantic/bio.ecore" xmlns:syntactic="http:///org/u_compare/shared/syntactic.ecore" xmlns:comparable="http:///org/u_compare/shared/comparable.ecore" xmlns:examples="http:///org/apache/uima/examples.ecore" xmlns:label="http:///org/u_compare/shared/label.ecore" xmlns:xmi="http://www.omg.org/XMI" xmlns:general2="http:///org/u_compare/shared/label/penn/bracket/general.ecore" xmlns:shared="http:///org/u_compare/shared.ecore" xmlns:fragment="http:///org/u_compare/shared/document/fragment.ecore" xmlns:document="http:///org/u_compare/shared/document.ecore" xmlns:bracket="http:///org/u_compare/shared/label/penn/bracket.ecore" xmlns:text="http:///org/u_compare/shared/label/penn/function/text.ecore" xmlns:structure="http:///org/u_compare/shared/document/structure.ecore" xmlns:text2="http:///org/u_compare/shared/document/text.ecore" xmlns:release="http:///org/u_compare/shared/label/penn/pos/release.ecore" xmlns:semantic="http:///org/u_compare/shared/semantic.ecore" xmlns:nontext="http:///org/u_compare/shared/document/nontext.ecore" xmlns:conll="http:///org/u_compare/shared/label/conll.ecore" xmlns:chemical="http:///org/u_compare/shared/semantic/chemical.ecore" xmlns:semantic3="http:///org/u_compare/shared/label/penn/function/semantic.ecore" xmlns:release2="http:///org/u_compare/shared/label/penn/bracket/release.ecore" xmlns:coindex="http:///org/u_compare/shared/label/penn/coindex.ecore" xmi:version="2.0"><cas:NULL xmi:id="0"/><cas:Sofa xmi:id="1" sofaNum="1" sofaID="_InitialView" mimeType="text" sofaString="Organization and regulation of the D-xylose operons in Escherichia coli K-12: XylR acts as a transcriptional activator. &#10;The metabolism of D-xylose in Escherichia coli K-12 is known to be mediated by the xylAB gene. However, the nearby xylFGHR genes were found by genome sequencing and predicted to be responsible for transport and regulation for xylose based on their sequence similarities to other functionally related genes. Here, we investigated transcriptional organization and functions of the xyl genes. An analysis with random transposon insertions revealed that the xyl genes are organized into two major transcriptional units, xylAB and xylFGHR, governed by the promoters PA and PF, respectively. However, there is an additional weak promoter, PR, which is specific for xylR. Sites of transcription initiation were determined by primer extension analysis. When studied with operon fusions to lacZ, the PA and PF promoters were activated by D-xylose and repressed by glucose. In contrast, the PR promoter was not regulated by these sugars. A mutation in xylR completely abolished expression from the PA and PF promoters, causing a defect in both growth and transport. Binding of XylR to the xyl promoter was enhanced by the presence of D-xylose, suggesting that transcription was positively regulated by XylR. In vivo footprinting analysis revealed that XylR binds to at least two DNA regions, IA and IF, each with a direct repeat. It is very likely that XylR interacts with IA and IF as a dimer. The presumed binding sites are located just upstream of the promoter consensus sequences (-35), while IA is additionally flanked by a cyclic AMP receptor protein-binding site on the other side. The proposed structure of xyl promoters is consistent with the regulation of xyl gene expression and with phenotypes of transposon insertions obtained in the promoter regions. "/><cas:FSArray xmi:id="667" elements="671 680"/><cas:FSArray xmi:id="674" elements="26"/><cas:FSArray xmi:id="683" elements="37"/><cas:FSArray xmi:id="689" elements="693 702"/><cas:FSArray xmi:id="696" elements="55"/><cas:FSArray xmi:id="705" elements="66"/><cas:FSArray xmi:id="711" elements="715 724"/><cas:FSArray xmi:id="718" elements="91"/><cas:FSArray xmi:id="727" elements="77"/><cas:FSArray xmi:id="733" elements="737 747"/><cas:FSArray xmi:id="740" elements="124 135"/><cas:FSArray xmi:id="750" elements="102 113"/><cas:FSArray xmi:id="757" elements="761 770"/><cas:FSArray xmi:id="764" elements="157"/><cas:FSArray xmi:id="773" elements="146"/><cas:FSArray xmi:id="779" elements="783 792"/><cas:FSArray xmi:id="786" elements="164"/><cas:FSArray xmi:id="795" elements="146"/><cas:FSArray xmi:id="801" elements="805 814"/><cas:FSArray xmi:id="808" elements="178"/><cas:FSArray xmi:id="817" elements="171"/><cas:FSArray xmi:id="823" elements="826"/><cas:FSArray xmi:id="829" elements="192"/><cas:FSArray xmi:id="835" elements="839 848"/><cas:FSArray xmi:id="842" elements="185"/><cas:FSArray xmi:id="851" elements="579"/><cas:FSArray xmi:id="857" elements="860"/><cas:FSArray xmi:id="863" elements="203"/><cas:FSArray xmi:id="869" elements="873 882"/><cas:FSArray xmi:id="876" elements="214"/><cas:FSArray xmi:id="885" elements="225"/><cas:FSArray xmi:id="891" elements="895 904"/><cas:FSArray xmi:id="898" elements="236"/><cas:FSArray xmi:id="907" elements="590"/><cas:FSArray xmi:id="913" elements="918 927 936"/><cas:FSArray xmi:id="921" elements="260"/><cas:FSArray xmi:id="930" elements="243"/><cas:FSArray xmi:id="939" elements="253"/><cas:FSArray xmi:id="945" elements="949 958"/><cas:FSArray xmi:id="952" elements="271"/><cas:FSArray xmi:id="961" elements="282 293"/><cas:FSArray xmi:id="968" elements="972 981"/><cas:FSArray xmi:id="975" elements="304"/><cas:FSArray xmi:id="984" elements="315 326"/><cas:FSArray xmi:id="991" elements="994"/><cas:FSArray xmi:id="997" elements="656"/><cas:FSArray xmi:id="1003" elements="1006"/><cas:FSArray xmi:id="1009" elements="337"/><cas:FSArray xmi:id="1018" elements="0 26 37 44 55 66 77 84 91 102 113 124 135 146 157 164 171 178 185 192 203 214 225 236 243 253 260 271 282 293 304 315 326 337 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0"/><tcas:DocumentAnnotation xmi:id="8" sofa="1" begin="0" end="1876" language="x-unspecified"/><tcas:DocumentAnnotation xmi:id="21" sofa="1" begin="0" end="1876"/><examples:SourceDocumentInformation xmi:id="13" sofa="1" begin="0" end="1876" uri="/9371449.txt" offsetInSource="0" documentSize="1876" lastSegment="true"/><semantic:LinkedAnnotationSet xmi:id="671" linkingRelation="677" linkedAnnotations="674"/><semantic:LinkedAnnotationSet xmi:id="680" linkingRelation="686" linkedAnnotations="683"/><semantic:LinkedAnnotationSet xmi:id="693" linkingRelation="699" linkedAnnotations="696"/><semantic:LinkedAnnotationSet xmi:id="702" linkingRelation="708" linkedAnnotations="705"/><semantic:LinkedAnnotationSet xmi:id="715" linkingRelation="721" linkedAnnotations="718"/><semantic:LinkedAnnotationSet xmi:id="724" linkingRelation="730" linkedAnnotations="727"/><semantic:LinkedAnnotationSet xmi:id="737" linkingRelation="744" linkedAnnotations="740"/><semantic:LinkedAnnotationSet xmi:id="747" linkingRelation="754" linkedAnnotations="750"/><semantic:LinkedAnnotationSet xmi:id="761" linkingRelation="767" linkedAnnotations="764"/><semantic:LinkedAnnotationSet xmi:id="770" linkingRelation="776" linkedAnnotations="773"/><semantic:LinkedAnnotationSet xmi:id="783" linkingRelation="789" linkedAnnotations="786"/><semantic:LinkedAnnotationSet xmi:id="792" linkingRelation="798" linkedAnnotations="795"/><semantic:LinkedAnnotationSet xmi:id="805" linkingRelation="811" linkedAnnotations="808"/><semantic:LinkedAnnotationSet xmi:id="814" linkingRelation="820" linkedAnnotations="817"/><semantic:LinkedAnnotationSet xmi:id="826" linkingRelation="832" linkedAnnotations="829"/><semantic:LinkedAnnotationSet xmi:id="839" linkingRelation="845" linkedAnnotations="842"/><semantic:LinkedAnnotationSet xmi:id="848" linkingRelation="854" linkedAnnotations="851"/><semantic:LinkedAnnotationSet xmi:id="860" linkingRelation="866" linkedAnnotations="863"/><semantic:LinkedAnnotationSet xmi:id="873" linkingRelation="879" linkedAnnotations="876"/><semantic:LinkedAnnotationSet xmi:id="882" linkingRelation="888" linkedAnnotations="885"/><semantic:LinkedAnnotationSet xmi:id="895" linkingRelation="901" linkedAnnotations="898"/><semantic:LinkedAnnotationSet xmi:id="904" linkingRelation="910" linkedAnnotations="907"/><semantic:LinkedAnnotationSet xmi:id="918" linkingRelation="924" linkedAnnotations="921"/><semantic:LinkedAnnotationSet xmi:id="927" linkingRelation="933" linkedAnnotations="930"/><semantic:LinkedAnnotationSet xmi:id="936" linkingRelation="942" linkedAnnotations="939"/><semantic:LinkedAnnotationSet xmi:id="949" linkingRelation="955" linkedAnnotations="952"/><semantic:LinkedAnnotationSet xmi:id="958" linkingRelation="965" linkedAnnotations="961"/><semantic:LinkedAnnotationSet xmi:id="972" linkingRelation="978" linkedAnnotations="975"/><semantic:LinkedAnnotationSet xmi:id="981" linkingRelation="988" linkedAnnotations="984"/><semantic:LinkedAnnotationSet xmi:id="994" linkingRelation="1000" linkedAnnotations="997"/><semantic:LinkedAnnotationSet xmi:id="1006" linkingRelation="1012" linkedAnnotations="1009"/><shared:ExternalReference xmi:id="34" namespace="GREC Concepts" ID="Operon"/><shared:ExternalReference xmi:id="52" namespace="GREC Concepts" ID="Bacteria"/><shared:ExternalReference xmi:id="63" namespace="GREC Concepts" ID="Activator"/><shared:ExternalReference xmi:id="74" namespace="GREC Concepts" ID="Activator"/><shared:ExternalReference xmi:id="99" namespace="GREC Concepts" ID="Gene"/><shared:ExternalReference xmi:id="110" namespace="GREC Concepts" ID="Gene"/><shared:ExternalReference xmi:id="121" namespace="GREC Concepts" ID="Gene"/><shared:ExternalReference xmi:id="132" namespace="GREC Concepts" ID="Promoter"/><shared:ExternalReference xmi:id="143" namespace="GREC Concepts" ID="Promoter"/><shared:ExternalReference xmi:id="154" namespace="GREC Concepts" ID="Promoter"/><shared:ExternalReference xmi:id="200" namespace="GREC Concepts" ID="Gene"/><shared:ExternalReference xmi:id="211" namespace="GREC Concepts" ID="Promoter"/><shared:ExternalReference xmi:id="222" namespace="GREC Concepts" ID="Activator"/><shared:ExternalReference xmi:id="233" namespace="GREC Concepts" ID="Promoter"/><shared:ExternalReference xmi:id="250" namespace="GREC Concepts" ID="Transcription"/><shared:ExternalReference xmi:id="268" namespace="GREC Concepts" ID="Activator"/><shared:ExternalReference xmi:id="279" namespace="GREC Concepts" ID="Activator"/><shared:ExternalReference xmi:id="290" namespace="GREC Concepts" ID="Transcription_Binding_Site"/><shared:ExternalReference xmi:id="301" namespace="GREC Concepts" ID="Transcription_Binding_Site"/><shared:ExternalReference xmi:id="312" namespace="GREC Concepts" ID="Activator"/><shared:ExternalReference xmi:id="323" namespace="GREC Concepts" ID="Transcription_Binding_Site"/><shared:ExternalReference xmi:id="334" namespace="GREC Concepts" ID="Transcription_Binding_Site"/><shared:ExternalReference xmi:id="488" namespace="GREC" ID="Regulation"/><shared:ExternalReference xmi:id="499" namespace="GREC" ID="GRE"/><shared:ExternalReference xmi:id="510" namespace="GREC" ID="GRE"/><shared:ExternalReference xmi:id="521" namespace="GREC" ID="GRE"/><shared:ExternalReference xmi:id="532" namespace="GREC" ID="Gene_Activation"/><shared:ExternalReference xmi:id="543" namespace="GREC" ID="Gene_Repression"/><shared:ExternalReference xmi:id="554" namespace="GREC" ID="Regulation"/><shared:ExternalReference xmi:id="565" namespace="GREC" ID="Mutation"/><shared:ExternalReference xmi:id="576" namespace="GREC" ID="GRE"/><shared:ExternalReference xmi:id="587" namespace="GREC" ID="Gene_Expression"/><shared:ExternalReference xmi:id="598" namespace="GREC" ID="GRE"/><shared:ExternalReference xmi:id="609" namespace="GREC" ID="GRE"/><shared:ExternalReference xmi:id="620" namespace="GREC" ID="Regulation"/><shared:ExternalReference xmi:id="631" namespace="GREC" ID="GRE"/><shared:ExternalReference xmi:id="642" namespace="GREC" ID="GRE"/><shared:ExternalReference xmi:id="653" namespace="GREC" ID="Regulation"/><shared:ExternalReference xmi:id="664" namespace="GREC" ID="Gene_Expression"/><shared:ExternalReference xmi:id="677" namespace="GREC Concepts" ID="Theme"/><shared:ExternalReference xmi:id="686" namespace="GREC Concepts" ID="Location"/><shared:ExternalReference xmi:id="699" namespace="GREC Concepts" ID="Theme"/><shared:ExternalReference xmi:id="708" namespace="GREC Concepts" ID="Descriptive-Theme"/><shared:ExternalReference xmi:id="721" namespace="GREC Concepts" ID="Agent"/><shared:ExternalReference xmi:id="730" namespace="GREC Concepts" ID="Theme"/><shared:ExternalReference xmi:id="744" namespace="GREC Concepts" ID="Agent"/><shared:ExternalReference xmi:id="754" namespace="GREC Concepts" ID="Theme"/><shared:ExternalReference xmi:id="767" namespace="GREC Concepts" ID="Agent"/><shared:ExternalReference xmi:id="776" namespace="GREC Concepts" ID="Theme"/><shared:ExternalReference xmi:id="789" namespace="GREC Concepts" ID="Agent"/><shared:ExternalReference xmi:id="798" namespace="GREC Concepts" ID="Theme"/><shared:ExternalReference xmi:id="811" namespace="GREC Concepts" ID="Agent"/><shared:ExternalReference xmi:id="820" namespace="GREC Concepts" ID="Theme"/><shared:ExternalReference xmi:id="832" namespace="GREC Concepts" ID="Location"/><shared:ExternalReference xmi:id="845" namespace="GREC Concepts" ID="Agent"/><shared:ExternalReference xmi:id="854" namespace="GREC Concepts" ID="Theme"/><shared:ExternalReference xmi:id="866" namespace="GREC Concepts" ID="Source"/><shared:ExternalReference xmi:id="879" namespace="GREC Concepts" ID="Agent"/><shared:ExternalReference xmi:id="888" namespace="GREC Concepts" ID="Destination"/><shared:ExternalReference xmi:id="901" namespace="GREC Concepts" ID="Agent"/><shared:ExternalReference xmi:id="910" namespace="GREC Concepts" ID="Theme"/><shared:ExternalReference xmi:id="924" namespace="GREC Concepts" ID="Agent"/><shared:ExternalReference xmi:id="933" namespace="GREC Concepts" ID="Theme"/><shared:ExternalReference xmi:id="942" namespace="GREC Concepts" ID="Manner"/><shared:ExternalReference xmi:id="955" namespace="GREC Concepts" ID="Agent"/><shared:ExternalReference xmi:id="965" namespace="GREC Concepts" ID="Destination"/><shared:ExternalReference xmi:id="978" namespace="GREC Concepts" ID="Theme"/><shared:ExternalReference xmi:id="988" namespace="GREC Concepts" ID="Descriptive-Theme"/><shared:ExternalReference xmi:id="1000" namespace="GREC Concepts" ID="Theme"/><shared:ExternalReference xmi:id="1012" namespace="GREC Concepts" ID="Theme"/><semantic:EventAnnotation xmi:id="480" sofa="1" begin="17" end="27" externalReference="488" linkedAnnotationSets="667"/><semantic:EventAnnotation xmi:id="491" sofa="1" begin="83" end="87" externalReference="499" linkedAnnotationSets="689"/><semantic:EventAnnotation xmi:id="502" sofa="1" begin="188" end="196" externalReference="510" linkedAnnotationSets="711"/><semantic:EventAnnotation xmi:id="513" sofa="1" begin="656" end="664" externalReference="521" linkedAnnotationSets="733"/><semantic:EventAnnotation xmi:id="524" sofa="1" begin="937" end="946" externalReference="532" linkedAnnotationSets="757"/><semantic:EventAnnotation xmi:id="535" sofa="1" begin="963" end="972" externalReference="543" linkedAnnotationSets="779"/><semantic:EventAnnotation xmi:id="546" sofa="1" begin="1022" end="1031" externalReference="554" linkedAnnotationSets="801"/><semantic:EventAnnotation xmi:id="557" sofa="1" begin="1051" end="1059" externalReference="565" linkedAnnotationSets="823"/><semantic:EventAnnotation xmi:id="568" sofa="1" begin="1079" end="1088" externalReference="576" linkedAnnotationSets="835"/><semantic:EventAnnotation xmi:id="579" sofa="1" begin="1089" end="1099" externalReference="587" linkedAnnotationSets="857"/><semantic:EventAnnotation xmi:id="590" sofa="1" begin="1177" end="1184" externalReference="598" linkedAnnotationSets="869"/><semantic:EventAnnotation xmi:id="601" sofa="1" begin="1217" end="1225" externalReference="609" linkedAnnotationSets="891"/><semantic:EventAnnotation xmi:id="612" sofa="1" begin="1300" end="1309" externalReference="620" linkedAnnotationSets="913"/><semantic:EventAnnotation xmi:id="623" sofa="1" begin="1368" end="1373" externalReference="631" linkedAnnotationSets="945"/><semantic:EventAnnotation xmi:id="634" sofa="1" begin="1469" end="1478" externalReference="642" linkedAnnotationSets="968"/><semantic:EventAnnotation xmi:id="645" sofa="1" begin="1763" end="1773" externalReference="653" linkedAnnotationSets="991"/><semantic:EventAnnotation xmi:id="656" sofa="1" begin="1786" end="1796" externalReference="664" linkedAnnotationSets="1003"/><comparable:IDArray xmi:id="1015" array="1018" idType="t"/><semantic2:NucleicAcids xmi:id="26" sofa="1" begin="31" end="51" externalReference="34"/><semantic2:NucleicAcids xmi:id="91" sofa="1" begin="200" end="214" externalReference="99"/><semantic2:NucleicAcids xmi:id="102" sofa="1" begin="637" end="642" externalReference="110"/><semantic2:NucleicAcids xmi:id="113" sofa="1" begin="647" end="654" externalReference="121"/><semantic2:NucleicAcids xmi:id="124" sofa="1" begin="682" end="684" externalReference="132"/><semantic2:NucleicAcids xmi:id="135" sofa="1" begin="689" end="691" externalReference="143"/><semantic2:NucleicAcids xmi:id="146" sofa="1" begin="908" end="931" externalReference="154"/><semantic2:NucleicAcids xmi:id="192" sofa="1" begin="1063" end="1067" externalReference="200"/><semantic2:NucleicAcids xmi:id="203" sofa="1" begin="1105" end="1128" externalReference="211"/><semantic2:NucleicAcids xmi:id="225" sofa="1" begin="1196" end="1212" externalReference="233"/><semantic2:NucleicAcids xmi:id="282" sofa="1" begin="1403" end="1405" externalReference="290"/><semantic2:NucleicAcids xmi:id="293" sofa="1" begin="1410" end="1412" externalReference="301"/><semantic2:NucleicAcids xmi:id="315" sofa="1" begin="1484" end="1486" externalReference="323"/><semantic2:NucleicAcids xmi:id="326" sofa="1" begin="1491" end="1493" externalReference="334"/><semantic2:Proteins xmi:id="55" sofa="1" begin="78" end="82" externalReference="63"/><semantic2:Proteins xmi:id="66" sofa="1" begin="91" end="118" externalReference="74"/><semantic2:Proteins xmi:id="214" sofa="1" begin="1188" end="1192" externalReference="222"/><semantic2:Proteins xmi:id="260" sofa="1" begin="1313" end="1317" externalReference="268"/><semantic2:Proteins xmi:id="271" sofa="1" begin="1363" end="1367" externalReference="279"/><semantic2:Proteins xmi:id="304" sofa="1" begin="1464" end="1468" externalReference="312"/><semantic2:LivingSystems xmi:id="44" sofa="1" begin="55" end="76" externalReference="52"/><semantic2:Processes xmi:id="243" sofa="1" begin="1271" end="1284" externalReference="250"/><semantic2:EventArgumentSpan xmi:id="37" sofa="1" begin="52" end="76"/><semantic2:EventArgumentSpan xmi:id="77" sofa="1" begin="121" end="147"/><semantic2:EventArgumentSpan xmi:id="84" sofa="1" begin="139" end="147"/><semantic2:EventArgumentSpan xmi:id="157" sofa="1" begin="950" end="958"/><semantic2:EventArgumentSpan xmi:id="164" sofa="1" begin="976" end="983"/><semantic2:EventArgumentSpan xmi:id="171" sofa="1" begin="998" end="1013"/><semantic2:EventArgumentSpan xmi:id="178" sofa="1" begin="1035" end="1047"/><semantic2:EventArgumentSpan xmi:id="185" sofa="1" begin="1049" end="1067"/><semantic2:EventArgumentSpan xmi:id="236" sofa="1" begin="1245" end="1253"/><semantic2:EventArgumentSpan xmi:id="253" sofa="1" begin="1289" end="1299"/><semantic2:EventArgumentSpan xmi:id="337" sofa="1" begin="1777" end="1785"/><cas:View sofa="1" members="667 674 683 689 696 705 711 718 727 733 740 750 757 764 773 779 786 795 801 808 817 823 829 835 842 851 857 863 869 876 885 891 898 907 913 921 930 939 945 952 961 968 975 984 991 997 1003 1009 1018 8 21 13 671 680 693 702 715 724 737 747 761 770 783 792 805 814 826 839 848 860 873 882 895 904 918 927 936 949 958 972 981 994 1006 34 52 63 74 99 110 121 132 143 154 200 211 222 233 250 268 279 290 301 312 323 334 488 499 510 521 532 543 554 565 576 587 598 609 620 631 642 653 664 677 686 699 708 721 730 744 754 767 776 789 798 811 820 832 845 854 866 879 888 901 910 924 933 942 955 965 978 988 1000 1012 480 491 502 513 524 535 546 557 568 579 590 601 612 623 634 645 656 1015 26 91 102 113 124 135 146 192 203 225 282 293 315 326 55 66 214 260 271 304 44 243 37 77 84 157 164 171 178 185 236 253 337"/></xmi:XMI>