<?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="Molecular analysis of the regulation of csiD, a carbon starvation-inducible gene in Escherichia coli that is exclusively dependent on sigma s and requires activation by cAMP-CRP. &#10;The general stress-induced sigma subunit sigma s of Escherichia coli RNA polymerase is closely related to the vegetative sigma factor sigma 70. In view of their very similar promoter specificity in vitro, it is unclear how sigma factor selectivity in the expression of sigma s-dependent genes is generated in vivo. The csiD gene is such a strongly sigma s-dependent gene. In contrast to sigma s, which is induced in response to many different stresses, csiD, whose expression is driven from a single promoter, is induced by carbon starvation only. To our knowledge, the csiD promoter is the first characterized promoter which is not only exclusively dependent on sigma s-containing RNA polymerase (E sigma s), but also requires an activator, cAMP-CRP. In addition, leucine-responsive regulatory protein (Lrp) acts as a positive modulator of csiD expression. Also in vitro, E sigma s is more efficient than E sigma 70 in csiD promoter binding, open complex formation and run-off transcription, which might be due to the poor match of the csiD -35 region to the sigma 70 consensus and to transcription by E sigma s being less dependent on contacts in this region. By DNase I protection experiments, a cAMP-CRP binding site centered at -68.5 nucleotides upstream of the csiD transcriptional start site was identified. While cAMP-CRP stimulates E sigma 70 binding, it does not promote open complex formation by E sigma 70, but does so in conjunction with E sigma s. With linear templates, cAMP-CRP significantly stimulates E sigma s-mediated in vitro transcription, whereas transcription by E sigma 70 is negligible and hardly stimulated by cAMP-CRP. These findings may reflect different or less stringent positional requirements for an activator site for E sigma s than for E sigma 70, and indicate that cAMP-CRP contributes to sigma factor selectivity at the csiD promoter. In vitro transcription experiments with super-coiled templates, however, revealed significant cAMP-CRP-stimulated transcription also by E sigma 70. Yet, under these conditions, H-NS was found to restore E sigma s specificity by strongly interfering with cAMP-CRP/E sigma 70-dependent transcription. Lrp strongly and cooperatively binds to multiple sites located between positions -14 and -102 (in a way that suggests DNA wrapping around multiple Lrp molecules) and moderately stimulates in vitro transcription, especially with E sigma s. In summary, we conclude that the csiD promoter has an intrinsic preference for E sigma s, but that also protein factors such as cAMP-CRP, Lrp and probably H-NS as well as DNA conformation contribute to its strong E sigma s selectivity. Furthermore, this strong E sigma s preference in combination with a requirement for high concentrations of the essential activator cAMP-CRP ensures csiD expression under conditions of carbon starvation, but not other stress conditions. "/><cas:FSArray xmi:id="389" elements="392"/><cas:FSArray xmi:id="395" elements="26"/><cas:FSArray xmi:id="401" elements="405 414"/><cas:FSArray xmi:id="408" elements="279"/><cas:FSArray xmi:id="417" elements="37"/><cas:FSArray xmi:id="423" elements="427 436"/><cas:FSArray xmi:id="430" elements="55"/><cas:FSArray xmi:id="439" elements="44"/><cas:FSArray xmi:id="445" elements="449 458"/><cas:FSArray xmi:id="452" elements="62"/><cas:FSArray xmi:id="461" elements="73"/><cas:FSArray xmi:id="467" elements="471 480"/><cas:FSArray xmi:id="474" elements="84"/><cas:FSArray xmi:id="483" elements="95"/><cas:FSArray xmi:id="489" elements="493 502"/><cas:FSArray xmi:id="496" elements="106"/><cas:FSArray xmi:id="505" elements="117"/><cas:FSArray xmi:id="511" elements="515 524"/><cas:FSArray xmi:id="518" elements="137"/><cas:FSArray xmi:id="527" elements="127"/><cas:FSArray xmi:id="533" elements="537 546"/><cas:FSArray xmi:id="540" elements="148"/><cas:FSArray xmi:id="549" elements="155"/><cas:FSArray xmi:id="555" elements="559 568"/><cas:FSArray xmi:id="562" elements="165"/><cas:FSArray xmi:id="571" elements="172"/><cas:FSArray xmi:id="577" elements="581 590"/><cas:FSArray xmi:id="584" elements="182"/><cas:FSArray xmi:id="593" elements="189"/><cas:FSArray xmi:id="602" elements="0 26 37 44 55 62 73 84 95 106 117 127 137 148 155 165 172 182 189 0 0 0 0 0 0 0 0 0 0"/><tcas:DocumentAnnotation xmi:id="8" sofa="1" begin="0" end="3062" language="x-unspecified"/><tcas:DocumentAnnotation xmi:id="21" sofa="1" begin="0" end="3062"/><examples:SourceDocumentInformation xmi:id="13" sofa="1" begin="0" end="3062" uri="/9512707.txt" offsetInSource="0" documentSize="3062" lastSegment="true"/><semantic:LinkedAnnotationSet xmi:id="392" linkingRelation="398" linkedAnnotations="395"/><semantic:LinkedAnnotationSet xmi:id="405" linkingRelation="411" linkedAnnotations="408"/><semantic:LinkedAnnotationSet xmi:id="414" linkingRelation="420" linkedAnnotations="417"/><semantic:LinkedAnnotationSet xmi:id="427" linkingRelation="433" linkedAnnotations="430"/><semantic:LinkedAnnotationSet xmi:id="436" linkingRelation="442" linkedAnnotations="439"/><semantic:LinkedAnnotationSet xmi:id="449" linkingRelation="455" linkedAnnotations="452"/><semantic:LinkedAnnotationSet xmi:id="458" linkingRelation="464" linkedAnnotations="461"/><semantic:LinkedAnnotationSet xmi:id="471" linkingRelation="477" linkedAnnotations="474"/><semantic:LinkedAnnotationSet xmi:id="480" linkingRelation="486" linkedAnnotations="483"/><semantic:LinkedAnnotationSet xmi:id="493" linkingRelation="499" linkedAnnotations="496"/><semantic:LinkedAnnotationSet xmi:id="502" linkingRelation="508" linkedAnnotations="505"/><semantic:LinkedAnnotationSet xmi:id="515" linkingRelation="521" linkedAnnotations="518"/><semantic:LinkedAnnotationSet xmi:id="524" linkingRelation="530" linkedAnnotations="527"/><semantic:LinkedAnnotationSet xmi:id="537" linkingRelation="543" linkedAnnotations="540"/><semantic:LinkedAnnotationSet xmi:id="546" linkingRelation="552" linkedAnnotations="549"/><semantic:LinkedAnnotationSet xmi:id="559" linkingRelation="565" linkedAnnotations="562"/><semantic:LinkedAnnotationSet xmi:id="568" linkingRelation="574" linkedAnnotations="571"/><semantic:LinkedAnnotationSet xmi:id="581" linkingRelation="587" linkedAnnotations="584"/><semantic:LinkedAnnotationSet xmi:id="590" linkingRelation="596" linkedAnnotations="593"/><shared:ExternalReference xmi:id="34" namespace="GREC Concepts" ID="Gene"/><shared:ExternalReference xmi:id="52" namespace="GREC Concepts" ID="Gene"/><shared:ExternalReference xmi:id="70" namespace="GREC Concepts" ID="Promoter"/><shared:ExternalReference xmi:id="81" namespace="GREC Concepts" ID="Activator"/><shared:ExternalReference xmi:id="92" namespace="GREC Concepts" ID="Protein"/><shared:ExternalReference xmi:id="103" namespace="GREC Concepts" ID="Regulator"/><shared:ExternalReference xmi:id="114" namespace="GREC Concepts" ID="Protein"/><shared:ExternalReference xmi:id="124" namespace="GREC Concepts" ID="Transcription"/><shared:ExternalReference xmi:id="134" namespace="GREC Concepts" ID="Transcription"/><shared:ExternalReference xmi:id="145" namespace="GREC Concepts" ID="Protein"/><shared:ExternalReference xmi:id="162" namespace="GREC Concepts" ID="Transcription"/><shared:ExternalReference xmi:id="179" namespace="GREC Concepts" ID="Transcription"/><shared:ExternalReference xmi:id="196" namespace="GREC Concepts" ID="Transcription"/><shared:ExternalReference xmi:id="287" namespace="GREC" ID="GRE"/><shared:ExternalReference xmi:id="298" namespace="GREC" ID="GRE"/><shared:ExternalReference xmi:id="309" namespace="GREC" ID="Gene_Activation"/><shared:ExternalReference xmi:id="320" namespace="GREC" ID="GRE"/><shared:ExternalReference xmi:id="331" namespace="GREC" ID="GRE"/><shared:ExternalReference xmi:id="342" namespace="GREC" ID="GRE"/><shared:ExternalReference xmi:id="353" namespace="GREC" ID="GRE"/><shared:ExternalReference xmi:id="364" namespace="GREC" ID="GRE"/><shared:ExternalReference xmi:id="375" namespace="GREC" ID="GRE"/><shared:ExternalReference xmi:id="386" namespace="GREC" ID="GRE"/><shared:ExternalReference xmi:id="398" namespace="GREC Concepts" ID="Agent"/><shared:ExternalReference xmi:id="411" namespace="GREC Concepts" ID="Agent"/><shared:ExternalReference xmi:id="420" namespace="GREC Concepts" ID="Theme"/><shared:ExternalReference xmi:id="433" namespace="GREC Concepts" ID="Agent"/><shared:ExternalReference xmi:id="442" namespace="GREC Concepts" ID="Theme"/><shared:ExternalReference xmi:id="455" namespace="GREC Concepts" ID="Agent"/><shared:ExternalReference xmi:id="464" namespace="GREC Concepts" ID="Theme"/><shared:ExternalReference xmi:id="477" namespace="GREC Concepts" ID="Agent"/><shared:ExternalReference xmi:id="486" namespace="GREC Concepts" ID="Descriptive-Agent"/><shared:ExternalReference xmi:id="499" namespace="GREC Concepts" ID="Agent"/><shared:ExternalReference xmi:id="508" namespace="GREC Concepts" ID="Theme"/><shared:ExternalReference xmi:id="521" namespace="GREC Concepts" ID="Agent"/><shared:ExternalReference xmi:id="530" namespace="GREC Concepts" ID="Theme"/><shared:ExternalReference xmi:id="543" namespace="GREC Concepts" ID="Agent"/><shared:ExternalReference xmi:id="552" namespace="GREC Concepts" ID="Theme"/><shared:ExternalReference xmi:id="565" namespace="GREC Concepts" ID="Agent"/><shared:ExternalReference xmi:id="574" namespace="GREC Concepts" ID="Theme"/><shared:ExternalReference xmi:id="587" namespace="GREC Concepts" ID="Agent"/><shared:ExternalReference xmi:id="596" namespace="GREC Concepts" ID="Theme"/><semantic:EventAnnotation xmi:id="279" sofa="1" begin="26" end="36" externalReference="287" linkedAnnotationSets="389"/><semantic:EventAnnotation xmi:id="290" sofa="1" begin="146" end="154" externalReference="298" linkedAnnotationSets="401"/><semantic:EventAnnotation xmi:id="301" sofa="1" begin="693" end="700" externalReference="309" linkedAnnotationSets="423"/><semantic:EventAnnotation xmi:id="312" sofa="1" begin="899" end="907" externalReference="320" linkedAnnotationSets="445"/><semantic:EventAnnotation xmi:id="323" sofa="1" begin="989" end="993" externalReference="331" linkedAnnotationSets="467"/><semantic:EventAnnotation xmi:id="334" sofa="1" begin="1688" end="1698" externalReference="342" linkedAnnotationSets="489"/><semantic:EventAnnotation xmi:id="345" sofa="1" begin="1803" end="1813" externalReference="353" linkedAnnotationSets="511"/><semantic:EventAnnotation xmi:id="356" sofa="1" begin="2125" end="2133" externalReference="364" linkedAnnotationSets="533"/><semantic:EventAnnotation xmi:id="367" sofa="1" begin="2289" end="2300" externalReference="375" linkedAnnotationSets="555"/><semantic:EventAnnotation xmi:id="378" sofa="1" begin="2528" end="2538" externalReference="386" linkedAnnotationSets="577"/><comparable:IDArray xmi:id="599" array="602" idType="t"/><semantic2:NucleicAcids xmi:id="26" sofa="1" begin="40" end="44" externalReference="34"/><semantic2:NucleicAcids xmi:id="44" sofa="1" begin="633" end="637" externalReference="52"/><semantic2:NucleicAcids xmi:id="62" sofa="1" begin="746" end="763" externalReference="70"/><semantic2:Proteins xmi:id="73" sofa="1" begin="908" end="920" externalReference="81"/><semantic2:Proteins xmi:id="84" sofa="1" begin="984" end="987" externalReference="92"/><semantic2:Proteins xmi:id="95" sofa="1" begin="997" end="1017" externalReference="103"/><semantic2:Proteins xmi:id="106" sofa="1" begin="1665" end="1673" externalReference="114"/><semantic2:Proteins xmi:id="137" sofa="1" begin="1817" end="1825" externalReference="145"/><semantic2:Processes xmi:id="117" sofa="1" begin="1699" end="1740" externalReference="124"/><semantic2:Processes xmi:id="127" sofa="1" begin="1750" end="1763" externalReference="134"/><semantic2:Processes xmi:id="155" sofa="1" begin="2134" end="2179" externalReference="162"/><semantic2:Processes xmi:id="172" sofa="1" begin="2306" end="2349" externalReference="179"/><semantic2:Processes xmi:id="189" sofa="1" begin="2539" end="2561" externalReference="196"/><semantic2:EventArgumentSpan xmi:id="37" sofa="1" begin="155" end="165"/><semantic2:EventArgumentSpan xmi:id="55" sofa="1" begin="704" end="721"/><semantic2:EventArgumentSpan xmi:id="148" sofa="1" begin="2052" end="2086"/><semantic2:EventArgumentSpan xmi:id="165" sofa="1" begin="2229" end="2233"/><semantic2:EventArgumentSpan xmi:id="182" sofa="1" begin="2351" end="2354"/><cas:View sofa="1" members="389 395 401 408 417 423 430 439 445 452 461 467 474 483 489 496 505 511 518 527 533 540 549 555 562 571 577 584 593 602 8 21 13 392 405 414 427 436 449 458 471 480 493 502 515 524 537 546 559 568 581 590 34 52 70 81 92 103 114 124 134 145 162 179 196 287 298 309 320 331 342 353 364 375 386 398 411 420 433 442 455 464 477 486 499 508 521 530 543 552 565 574 587 596 279 290 301 312 323 334 345 356 367 378 599 26 44 62 73 84 95 106 137 117 127 155 172 189 37 55 148 165 182"/></xmi:XMI>