<?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="Evolution of transcriptional regulation system through promiscuous coupling of regulatory proteins with operons; suggestion from protein sequence similarities in Escherichia coli. &#10;As an advanced molecular study of the problems of the evolution of organisms, the transcriptional regulation system is studied by investigating the amino acid sequence similarities between the proteins in the regulation system of Escherichia coli in which the data of sequenced proteins as well as of regulator-regulon relationships are accumulated. The similarities between the proteins are calculated by the FASTA algorithm and their homology is also evaluated in terms of statistical significance with the use of the RDF2 program. This investigation reveals that the similarity between the regulatory protein and the regulated protein is hardly found, but many similarities are found between regulatory proteins and between regulated proteins. These similarity relations are compared with the regulator-regulon relationships ascertained experimentally. From this comparison, it is found that similar regulatory proteins rarely regulate the transcription of similar protein genes. As most of the highly similar proteins are considered to have diverged from a common ancestral protein, this finding strongly suggests the possibility that descendant regulatory proteins have been promiscuously coupled with descendant operons, independently of their ancestral regulator-regulon relationship, and that some of the couplings have been fixed by selection to form the present system of transcriptional regulation. The compatibility of such promiscuous coupling with regulatory organization is illustrated in the carbohydrate transport systems and the succeeding metabolic pathways, whose organization is comprehensive in sending nutritious substances to the central path of glycolysis under different environmental conditions. The benefit of flexibility in regulator-regulon relationships in evolutionary processes is also discussed in connection with the punctuational divergence of species in macroevolution and the cell differentiation in multicellular organisms. "/><cas:FSArray xmi:id="293" elements="298 307 316"/><cas:FSArray xmi:id="301" elements="33"/><cas:FSArray xmi:id="310" elements="44"/><cas:FSArray xmi:id="319" elements="26"/><cas:FSArray xmi:id="325" elements="330 339 348"/><cas:FSArray xmi:id="333" elements="55"/><cas:FSArray xmi:id="342" elements="227"/><cas:FSArray xmi:id="351" elements="66"/><cas:FSArray xmi:id="357" elements="360"/><cas:FSArray xmi:id="363" elements="73"/><cas:FSArray xmi:id="369" elements="374 383 392"/><cas:FSArray xmi:id="377" elements="84"/><cas:FSArray xmi:id="386" elements="102"/><cas:FSArray xmi:id="395" elements="95"/><cas:FSArray xmi:id="401" elements="404"/><cas:FSArray xmi:id="407" elements="260"/><cas:FSArray xmi:id="413" elements="416"/><cas:FSArray xmi:id="419" elements="113"/><cas:FSArray xmi:id="425" elements="428"/><cas:FSArray xmi:id="431" elements="120"/><cas:FSArray xmi:id="437" elements="441 450"/><cas:FSArray xmi:id="444" elements="134"/><cas:FSArray xmi:id="453" elements="127"/><cas:FSArray xmi:id="462" elements="0 26 33 44 55 66 73 84 95 102 113 120 127 134 0 0 0 0 0 0 0 0"/><tcas:DocumentAnnotation xmi:id="8" sofa="1" begin="0" end="2144" language="x-unspecified"/><tcas:DocumentAnnotation xmi:id="21" sofa="1" begin="0" end="2144"/><examples:SourceDocumentInformation xmi:id="13" sofa="1" begin="0" end="2144" uri="/8729576.txt" offsetInSource="0" documentSize="2144" lastSegment="true"/><semantic:LinkedAnnotationSet xmi:id="298" linkingRelation="304" linkedAnnotations="301"/><semantic:LinkedAnnotationSet xmi:id="307" linkingRelation="313" linkedAnnotations="310"/><semantic:LinkedAnnotationSet xmi:id="316" linkingRelation="322" linkedAnnotations="319"/><semantic:LinkedAnnotationSet xmi:id="330" linkingRelation="336" linkedAnnotations="333"/><semantic:LinkedAnnotationSet xmi:id="339" linkingRelation="345" linkedAnnotations="342"/><semantic:LinkedAnnotationSet xmi:id="348" linkingRelation="354" linkedAnnotations="351"/><semantic:LinkedAnnotationSet xmi:id="360" linkingRelation="366" linkedAnnotations="363"/><semantic:LinkedAnnotationSet xmi:id="374" linkingRelation="380" linkedAnnotations="377"/><semantic:LinkedAnnotationSet xmi:id="383" linkingRelation="389" linkedAnnotations="386"/><semantic:LinkedAnnotationSet xmi:id="392" linkingRelation="398" linkedAnnotations="395"/><semantic:LinkedAnnotationSet xmi:id="404" linkingRelation="410" linkedAnnotations="407"/><semantic:LinkedAnnotationSet xmi:id="416" linkingRelation="422" linkedAnnotations="419"/><semantic:LinkedAnnotationSet xmi:id="428" linkingRelation="434" linkedAnnotations="431"/><semantic:LinkedAnnotationSet xmi:id="441" linkingRelation="447" linkedAnnotations="444"/><semantic:LinkedAnnotationSet xmi:id="450" linkingRelation="456" linkedAnnotations="453"/><shared:ExternalReference xmi:id="41" namespace="GREC Concepts" ID="Regulator"/><shared:ExternalReference xmi:id="52" namespace="GREC Concepts" ID="Operon"/><shared:ExternalReference xmi:id="63" namespace="GREC Concepts" ID="Regulator"/><shared:ExternalReference xmi:id="81" namespace="GREC Concepts" ID="Gene"/><shared:ExternalReference xmi:id="92" namespace="GREC Concepts" ID="Regulator"/><shared:ExternalReference xmi:id="110" namespace="GREC Concepts" ID="Operon"/><shared:ExternalReference xmi:id="213" namespace="GREC" ID="GRE"/><shared:ExternalReference xmi:id="224" namespace="GREC" ID="GRE"/><shared:ExternalReference xmi:id="235" namespace="GREC" ID="Transcription"/><shared:ExternalReference xmi:id="246" namespace="GREC" ID="GRE"/><shared:ExternalReference xmi:id="257" namespace="GREC" ID="GRE"/><shared:ExternalReference xmi:id="268" namespace="GREC" ID="GRE"/><shared:ExternalReference xmi:id="279" namespace="GREC" ID="Regulation"/><shared:ExternalReference xmi:id="290" namespace="GREC" ID="GRE"/><shared:ExternalReference xmi:id="304" namespace="GREC Concepts" ID="Theme"/><shared:ExternalReference xmi:id="313" namespace="GREC Concepts" ID="Theme"/><shared:ExternalReference xmi:id="322" namespace="GREC Concepts" ID="Manner"/><shared:ExternalReference xmi:id="336" namespace="GREC Concepts" ID="Agent"/><shared:ExternalReference xmi:id="345" namespace="GREC Concepts" ID="Theme"/><shared:ExternalReference xmi:id="354" namespace="GREC Concepts" ID="Manner"/><shared:ExternalReference xmi:id="366" namespace="GREC Concepts" ID="Theme"/><shared:ExternalReference xmi:id="380" namespace="GREC Concepts" ID="Theme"/><shared:ExternalReference xmi:id="389" namespace="GREC Concepts" ID="Theme"/><shared:ExternalReference xmi:id="398" namespace="GREC Concepts" ID="Manner"/><shared:ExternalReference xmi:id="410" namespace="GREC Concepts" ID="Purpose"/><shared:ExternalReference xmi:id="422" namespace="GREC Concepts" ID="Theme"/><shared:ExternalReference xmi:id="434" namespace="GREC Concepts" ID="Manner"/><shared:ExternalReference xmi:id="447" namespace="GREC Concepts" ID="Theme"/><shared:ExternalReference xmi:id="456" namespace="GREC Concepts" ID="Manner"/><semantic:EventAnnotation xmi:id="205" sofa="1" begin="55" end="75" externalReference="213" linkedAnnotationSets="293"/><semantic:EventAnnotation xmi:id="216" sofa="1" begin="1111" end="1119" externalReference="224" linkedAnnotationSets="325"/><semantic:EventAnnotation xmi:id="227" sofa="1" begin="1124" end="1137" externalReference="235" linkedAnnotationSets="357"/><semantic:EventAnnotation xmi:id="238" sofa="1" begin="1375" end="1382" externalReference="246" linkedAnnotationSets="369"/><semantic:EventAnnotation xmi:id="249" sofa="1" begin="1523" end="1532" externalReference="257" linkedAnnotationSets="401"/><semantic:EventAnnotation xmi:id="260" sofa="1" begin="1536" end="1540" externalReference="268" linkedAnnotationSets="413"/><semantic:EventAnnotation xmi:id="271" sofa="1" begin="1579" end="1589" externalReference="279" linkedAnnotationSets="425"/><semantic:EventAnnotation xmi:id="282" sofa="1" begin="1629" end="1637" externalReference="290" linkedAnnotationSets="437"/><comparable:IDArray xmi:id="459" array="462" idType="t"/><semantic2:NucleicAcids xmi:id="44" sofa="1" begin="104" end="111" externalReference="52"/><semantic2:NucleicAcids xmi:id="73" sofa="1" begin="1141" end="1162" externalReference="81"/><semantic2:NucleicAcids xmi:id="102" sofa="1" begin="1388" end="1406" externalReference="110"/><semantic2:Proteins xmi:id="33" sofa="1" begin="79" end="98" externalReference="41"/><semantic2:Proteins xmi:id="55" sofa="1" begin="1076" end="1103" externalReference="63"/><semantic2:Proteins xmi:id="84" sofa="1" begin="1320" end="1350" externalReference="92"/><semantic2:EventArgumentSpan xmi:id="26" sofa="1" begin="55" end="66"/><semantic2:EventArgumentSpan xmi:id="66" sofa="1" begin="1104" end="1110"/><semantic2:EventArgumentSpan xmi:id="95" sofa="1" begin="1361" end="1374"/><semantic2:EventArgumentSpan xmi:id="113" sofa="1" begin="1541" end="1559"/><semantic2:EventArgumentSpan xmi:id="120" sofa="1" begin="1563" end="1578"/><semantic2:EventArgumentSpan xmi:id="127" sofa="1" begin="1617" end="1628"/><semantic2:EventArgumentSpan xmi:id="134" sofa="1" begin="1643" end="1666"/><cas:View sofa="1" members="293 301 310 319 325 333 342 351 357 363 369 377 386 395 401 407 413 419 425 431 437 444 453 462 8 21 13 298 307 316 330 339 348 360 374 383 392 404 416 428 441 450 41 52 63 81 92 110 213 224 235 246 257 268 279 290 304 313 322 336 345 354 366 380 389 398 410 422 434 447 456 205 216 227 238 249 260 271 282 459 44 73 102 33 55 84 26 66 95 113 120 127 134"/></xmi:XMI>