%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % % % GENIC INTERACTION EXPRESSED BY AN EXPLICIT ACTION % % % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% ID 11069677-3 sentence In vivo studies of the activity of four of the kinases, KinA, KinC, KinD (ykvD) and KinE (ykrQ), using abrB transcription as an indicator of Spo0A~P level, revealed that KinC and KinD were responsible for Spo0A~P production during the exponential phase of growth in the absence of KinA and KinB. words word(0,'In',0,1) word(1,'vivo',3,6) word(2,'studies',8,14) word(3,'of',16,17) word(4,'the',19,21) word(5,'activity',23,30) word(6,'of',32,33) word(7,'four',35,38) word(8,'of',40,41) word(9,'the',43,45) word(10,'kinases',47,53) word(11,'KinA',56,59) word(12,'KinC',62,65) word(13,'KinD',68,71) word(14,'ykvD',74,77) word(15,'and',80,82) word(16,'KinE',84,87) word(17,'ykrQ',90,93) word(18,'using',97,101) word(19,'abrB',103,106) word(20,'transcription',108,120) word(21,'as',122,123) word(22,'an',125,126) word(23,'indicator',128,136) word(24,'of',138,139) word(25,'Spo0A~P',141,147) word(26,'level',149,153) word(27,'revealed',156,163) word(28,'that',165,168) word(29,'KinC',170,173) word(30,'and',175,177) word(31,'KinD',179,182) word(32,'were',184,187) word(33,'responsible',189,199) word(34,'for',201,203) word(35,'Spo0A~P',205,211) word(36,'production',213,222) word(37,'during',224,229) word(38,'the',231,233) word(39,'exponential',235,245) word(40,'phase',247,251) word(41,'of',253,254) word(42,'growth',256,261) word(43,'in',263,264) word(44,'the',266,268) word(45,'absence',270,276) word(46,'of',278,279) word(47,'KinA',281,284) word(48,'and',286,288) word(49,'KinB',290,293) lemmas lemma(0,'in') lemma(1,'vivo') lemma(2,'study') lemma(3,'of') lemma(4,'the') lemma(5,'activity') lemma(6,'of') lemma(7,'four') lemma(8,'of') lemma(9,'the') lemma(10,'kinase') lemma(11,'KinA') lemma(12,'KinC') lemma(13,'KinD') lemma(14,'kinD') lemma(15,'and') lemma(16,'KinE') lemma(17,'kinE') lemma(18,'use') lemma(19,'abrB') lemma(20,'transcription') lemma(21,'as') lemma(22,'an') lemma(23,'indicator') lemma(24,'of') lemma(25,'Spo0A-P') lemma(26,'level') lemma(27,'reveal') lemma(28,'that') lemma(29,'KinC') lemma(30,'and') lemma(31,'KinD') lemma(32,'be') lemma(33,'responsible') lemma(34,'for') lemma(35,'Spo0A-P') lemma(36,'production') lemma(37,'during') lemma(38,'the') lemma(39,'exponential') lemma(40,'phase') lemma(41,'of') lemma(42,'growth') lemma(43,'in') lemma(44,'the') lemma(45,'absence') lemma(46,'of') lemma(47,'KinA') lemma(48,'and') lemma(49,'KinB') syntactic_relations relation('comp_in:N-N',2,1) relation('comp_of:N-N',2,5) relation('comp_of:N-N',5,7) relation('comp_of:N-N',7,10) relation('appos',10,11) relation('appos',10,13) relation('appos',10,12) relation('appos',10,16) relation('appos',13,14) relation('appos',16,17) relation('subj:V-N',18,2) relation('obj:V-N',18,20) relation('mod_att:N-N',20,19) relation('comp_as:V-N',18,23) relation('comp_of:N-N',23,26) relation('mod_att:N-N',26,25) relation('subj:V-N',27,2) relation('mod_pred:N-ADJ',29,33) relation('mod_pred:N-ADJ',31,33) relation('comp_for:ADJ-N',33,36) relation('mod_att:N-N',36,35) relation('comp_during:ADJ-N',33,40) relation('comp_of:N-N',40,42) relation('comp_in:ADJ-N',33,45) relation('comp_of:N-N',45,47) relation('comp_of:N-N',45,49) relation('mod_att:N-ADJ',40,39) agents agent(29) agent(31) targets target(35) genic_interactions genic_interaction(29,35) genic_interaction(31,35) ID 11064201-3 sentence In this mutant, expression of the spoIIG gene, whose transcription depends on both sigma(A) and the phosphorylated Spo0A protein, Spo0A~P, a major transcription factor during early stages of sporulation, was greatly reduced at 43 degrees C. words word(0,'In',0,1) word(1,'this',3,6) word(2,'mutant',8,13) word(3,'expression',16,25) word(4,'of',27,28) word(5,'the',30,32) word(6,'spoIIG',34,39) word(7,'gene',41,44) word(8,'whose',47,51) word(9,'transcription',53,65) word(10,'depends',67,73) word(11,'on',75,76) word(12,'both',78,81) word(13,'sigma(A)',83,90) word(14,'and',92,94) word(15,'the',96,98) word(16,'phosphorylated',100,113) word(17,'Spo0A',115,119) word(18,'protein',121,127) word(19,'Spo0A~P',130,136) word(20,'a',139,139) word(21,'major',141,145) word(22,'transcription',147,159) word(23,'factor',161,166) word(24,'during',168,173) word(25,'early',175,179) word(26,'stages',181,186) word(27,'of',188,189) word(28,'sporulation',191,201) word(29,'was',204,206) word(30,'greatly',208,214) word(31,'reduced',216,222) word(32,'at',224,225) word(33,'43',227,228) word(34,'degrees',230,236) word(35,'C',238,238) lemmas lemma(0,'in') lemma(1,'this') lemma(2,'mutant') lemma(3,'expression') lemma(4,'of') lemma(5,'the') lemma(6,'spoIIG') lemma(7,'gene') lemma(8,'whose') lemma(9,'transcription') lemma(10,'depend') lemma(11,'on') lemma(12,'both') lemma(13,'sigA') lemma(14,'and') lemma(15,'the') lemma(16,'phosphorylated') lemma(17,'spo0A') lemma(18,'protein') lemma(19,'Spo0A-P') lemma(20,'a') lemma(21,'major') lemma(22,'transcription') lemma(23,'factor') lemma(24,'during') lemma(25,'early') lemma(26,'stage') lemma(27,'of') lemma(28,'sporulation') lemma(29,'be') lemma(30,'greatly') lemma(31,'reduce') lemma(32,'at') lemma(33,'43') lemma(34,'degree') lemma(35,'C') syntactic_relations relation('subj:V_PASS-N',31,3) relation('mod_att:N-N',7,6) relation('mod_att:N-ADJ',34,33) relation('comp_during:N-N',23,26) relation('comp_of:N-N',26,28) relation('comp_on:V-N',10,13) relation('mod_att:N-N',23,22) relation('mod_att:N-ADJ',18,16) relation('mod:V_PASS-ADV',31,30) relation('mod_att:N-ADJ',26,25) relation('mod_att:N-ADJ',23,21) relation('mod_att:N-N',18,17) relation('comp_on:V-N',10,18) relation('appos',19,23) relation('subj:V-N',10,9) relation('appos',18,19) relation('comp_of:N-N',3,7) relation('comp_in:V-N',31,2) relation('comp_of:N-N',9,7) relation('comp_at:V_PASS-N',31,34) relation('mod_att:N-N',34,35) agents agent(13) agent(17) targets target(6) genic_interactions genic_interaction(13,6) genic_interaction(17,6) ID 11011148-3 sentence Transcription of ydhD was dependent on SigE, and the mRNA was detectable from 2 h after the cessation of logarithmic growth (T2 of sporulation). words word(0,'Transcription',0,12) word(1,'of',14,15) word(2,'ydhD',17,20) word(3,'was',22,24) word(4,'dependent',26,34) word(5,'on',36,37) word(6,'SigE',39,42) word(7,'and',45,47) word(8,'the',49,51) word(9,'mRNA',53,56) word(10,'was',58,60) word(11,'detectable',62,71) word(12,'from',73,76) word(13,'2',78,78) word(14,'h',80,80) word(15,'after',82,86) word(16,'the',88,90) word(17,'cessation',92,100) word(18,'of',102,103) word(19,'logarithmic',105,115) word(20,'growth',117,122) word(21,'T2',125,126) word(22,'of',128,129) word(23,'sporulation',131,141) lemmas lemma(0,'transcription') lemma(1,'of') lemma(2,'ydhD') lemma(3,'be') lemma(4,'dependent') lemma(5,'on') lemma(6,'SigE') lemma(7,'and') lemma(8,'the') lemma(9,'mRNA') lemma(10,'be') lemma(11,'detectable') lemma(12,'from') lemma(13,'2') lemma(14,'h') lemma(15,'after') lemma(16,'the') lemma(17,'cessation') lemma(18,'of') lemma(19,'logarithmic') lemma(20,'growth') lemma(21,'T2') lemma(22,'of') lemma(23,'sporulation') syntactic_relations relation('comp_from:ADJ-N',11,14) relation('mod_pred:N-ADJ',9,11) relation('comp_on:ADJ-N',4,6) relation('comp_of:N-N',17,20) relation('comp_of:N-N',0,2) relation('comp_after:N-N',14,17) relation('mod_att:N-ADJ',14,13) relation('comp_of:N-N',21,23) relation('mod_att:N-ADJ',20,19) relation('appos',20,21) relation('mod_pred:N-ADJ',0,4) agents agent(6) targets target(2) genic_interactions genic_interaction(6,2) ID 11011148-4 sentence ykuD was transcribed by SigK RNA polymerase from T4 of sporulation. words word(0,'ykuD',0,3) word(1,'was',5,7) word(2,'transcribed',9,19) word(3,'by',21,22) word(4,'SigK',24,27) word(5,'RNA',29,31) word(6,'polymerase',33,42) word(7,'from',44,47) word(8,'T4',49,50) word(9,'of',52,53) word(10,'sporulation',55,65) lemmas lemma(0,'ykuD') lemma(1,'be') lemma(2,'transcribe') lemma(3,'by') lemma(4,'SigK') lemma(5,'RNA') lemma(6,'polymerase') lemma(7,'from') lemma(8,'T4') lemma(9,'of') lemma(10,'sporulation') syntactic_relations relation('comp_by:V_PASS-N',2,6) relation('subj:V_PASS-N',2,0) relation('mod_att:N-N',6,5) relation('comp_of:N-N',8,10) relation('mod_att:N-N',6,4) relation('comp_from:V_PASS-N',2,8) agents agent(4) targets target(0) genic_interactions genic_interaction(4,0) ID 11011148-5 sentence Both SigK and GerE were essential for ykvP expression, and this gene was transcribed from T5 of sporulation. words word(0,'Both',0,3) word(1,'SigK',5,8) word(2,'and',10,12) word(3,'GerE',14,17) word(4,'were',19,22) word(5,'essential',24,32) word(6,'for',34,36) word(7,'ykvP',38,41) word(8,'expression',43,52) word(9,'and',55,57) word(10,'this',59,62) word(11,'gene',64,67) word(12,'was',69,71) word(13,'transcribed',73,83) word(14,'from',85,88) word(15,'T5',90,91) word(16,'of',93,94) word(17,'sporulation',96,106) lemmas lemma(0,'both') lemma(1,'SigK') lemma(2,'and') lemma(3,'GerE') lemma(4,'be') lemma(5,'essential') lemma(6,'for') lemma(7,'ykvP') lemma(8,'expression') lemma(9,'and') lemma(10,'this') lemma(11,'gene') lemma(12,'be') lemma(13,'transcribe') lemma(14,'from') lemma(15,'T5') lemma(16,'of') lemma(17,'sporulation') syntactic_relations relation('mod_att:N-N',8,7) relation('mod_pred:N-ADJ',3,5) relation('mod_pred:N-ADJ',1,5) relation('comp_for:ADJ-N',5,8) relation('subj:V_PASS-N',13,11) relation('comp_of:N-N',15,17) relation('comp_from:V_PASS-N',13,15) agents agent(1) agent(3) targets target(7) genic_interactions genic_interaction(1,7) genic_interaction(3,7) ID 10767540-2 sentence Analysis of the expression of a translational ywhE-lacZ fusion showed that ywhE expression is sporulation-specific, and is controlled predominantly by the forespore-specific sigma factor sigma(F), and to a lesser extent by sigma(G). words word(0,'Analysis',0,7) word(1,'of',9,10) word(2,'the',12,14) word(3,'expression',16,25) word(4,'of',27,28) word(5,'a',30,30) word(6,'translational',32,44) word(7,'ywhE',46,49) word(8,'lacZ',51,54) word(9,'fusion',56,61) word(10,'showed',63,68) word(11,'that',70,73) word(12,'ywhE',75,78) word(13,'expression',80,89) word(14,'is',91,92) word(15,'sporulation-specific',94,113) word(16,'and',116,118) word(17,'is',120,121) word(18,'controlled',123,132) word(19,'predominantly',134,146) word(20,'by',148,149) word(21,'the',151,153) word(22,'forespore-specific',155,172) word(23,'sigma',174,178) word(24,'factor',180,185) word(25,'sigma(F)',187,194) word(26,'and',197,199) word(27,'to',201,202) word(28,'a',204,204) word(29,'lesser',206,211) word(30,'extent',213,218) word(31,'by',220,221) word(32,'sigma(G)',223,230) lemmas lemma(0,'analysis') lemma(1,'of') lemma(2,'the') lemma(3,'expression') lemma(4,'of') lemma(5,'a') lemma(6,'translational') lemma(7,'ywhE') lemma(8,'lacZ') lemma(9,'fusion') lemma(10,'show') lemma(11,'that') lemma(12,'ywhE') lemma(13,'expression') lemma(14,'be') lemma(15,'sporulation-specific') lemma(16,'and') lemma(17,'be') lemma(18,'control') lemma(19,'predominantly') lemma(20,'by') lemma(21,'the') lemma(22,'forespore-specific') lemma(23,'sigma') lemma(24,'factor') lemma(25,'sigF') lemma(26,'and') lemma(27,'to') lemma(28,'a') lemma(29,'lesser') lemma(30,'extent') lemma(31,'by') lemma(32,'sigG') syntactic_relations relation('comp_of:N-N',0,3) relation('comp_of:N-N',3,9) relation('mod_att:N-ADJ',9,6) relation('mod_att:N-N',8,7) relation('mod_att:N-N',9,8) relation('subj:V-N',10,0) relation('mod_att:N-N',13,12) relation('mod_pred:N-ADJ',13,15) relation('subj:V_PASS-N',18,13) relation('mod:V_PASS-ADV',18,19) relation('comp_by:V_PASS-N',18,25) relation('mod_att:N-N',25,24) relation('mod_att:N-N',24,23) relation('mod_att:N-ADJ',24,22) relation('comp_by:V_PASS-N',18,32) relation('mod_att:N-ADJ',30,29) relation('comp_to:V_PASS-N',18,30) agents agent(25) agent(32) targets target(12) genic_interactions genic_interaction(25,12) genic_interaction(32,12) ID 10747015-3 sentence Secondly, SpoIIE is essential for the activation of the first compartment-specific transcription factor sigma(F) in the prespore. words word(0,'Secondly',0,7) word(1,'SpoIIE',10,15) word(2,'is',17,18) word(3,'essential',20,28) word(4,'for',30,32) word(5,'the',34,36) word(6,'activation',38,47) word(7,'of',49,50) word(8,'the',52,54) word(9,'first',56,60) word(10,'compartment-specific',62,81) word(11,'transcription',83,95) word(12,'factor',97,102) word(13,'sigma(F)',104,111) word(14,'in',113,114) word(15,'the',116,118) word(16,'prespore',120,127) lemmas lemma(0,'secondly') lemma(1,'SpoIIE') lemma(2,'be') lemma(3,'essential') lemma(4,'for') lemma(5,'the') lemma(6,'activation') lemma(7,'of') lemma(8,'the') lemma(9,'first') lemma(10,'compartment-specific') lemma(11,'transcription') lemma(12,'factor') lemma(13,'sigF') lemma(14,'in') lemma(15,'the') lemma(16,'prespore') syntactic_relations relation('mod_att:N-ADJ',12,9) relation('comp_for:ADJ-N',3,6) relation('comp_of:N-N',6,12) relation('comp_in:N-N',6,16) relation('mod:V-ADV',2,0) relation('mod_att:N-N',12,13) relation('mod_pred:N-ADJ',1,3) relation('mod_att:N-ADJ',12,10) relation('mod_att:N-N',12,11) agents agent(1) targets target(13) genic_interactions genic_interaction(1,13) ID 10648512-3 sentence In the shaA mutant, sigma(H)-dependent expression of spo0A and spoVG at an early stage of sporulation was sensitive to external NaCl. words word(0,'In',0,1) word(1,'the',3,5) word(2,'shaA',7,10) word(3,'mutant',12,17) word(4,'sigma(H)',20,27) word(5,'dependent',29,37) word(6,'expression',39,48) word(7,'of',50,51) word(8,'spo0A',53,57) word(9,'and',59,61) word(10,'spoVG',63,67) word(11,'at',69,70) word(12,'an',72,73) word(13,'early',75,79) word(14,'stage',81,85) word(15,'of',87,88) word(16,'sporulation',90,100) word(17,'was',102,104) word(18,'sensitive',106,114) word(19,'to',116,117) word(20,'external',119,126) word(21,'NaCl',128,131) lemmas lemma(0,'in') lemma(1,'the') lemma(2,'mrpA') lemma(3,'mutant') lemma(4,'sigH') lemma(5,'dependent') lemma(6,'expression') lemma(7,'of') lemma(8,'spo0A') lemma(9,'and') lemma(10,'spoVG') lemma(11,'at') lemma(12,'an') lemma(13,'early') lemma(14,'stage') lemma(15,'of') lemma(16,'sporulation') lemma(17,'be') lemma(18,'sensitive') lemma(19,'to') lemma(20,'external') lemma(21,'NaCl') syntactic_relations relation('comp_at:N-N',6,14) relation('comp_of:N-N',14,16) relation('comp_in:N-N',17,3) relation('comp_of:N-N',6,10) relation('mod_att:N-ADJ',6,5) relation('mod:ADJ-N',5,4) relation('mod_att:N-ADJ',21,20) relation('comp_of:N-N',6,8) relation('mod_att:N-ADJ',14,13) relation('mod_att:N-N',3,2) relation('comp_to:ADJ-N',18,21) relation('mod_pred:N-ADJ',6,18) agents agent(4) targets target(8) target(10) genic_interactions genic_interaction(4,8) genic_interaction(4,10) ID 10629188-5 sentence The expression of rsfA is under the control of both sigma(F) and sigma(G). words word(0,'The',0,2) word(1,'expression',4,13) word(2,'of',15,16) word(3,'rsfA',18,21) word(4,'is',23,24) word(5,'under',26,30) word(6,'the',32,34) word(7,'control',36,42) word(8,'of',44,45) word(9,'both',47,50) word(10,'sigma(F)',52,59) word(11,'and',61,63) word(12,'sigma(G)',65,72) lemmas lemma(0,'the') lemma(1,'expression') lemma(2,'of') lemma(3,'rsfA') lemma(4,'be') lemma(5,'under') lemma(6,'the') lemma(7,'control') lemma(8,'of') lemma(9,'both') lemma(10,'sigF') lemma(11,'and') lemma(12,'sigG') syntactic_relations relation('comp_of:N-N',1,3) relation('subj:V-N',4,1) relation('comp_under:V-N',4,7) relation('comp_of:N-N',7,10) relation('comp_of:N-N',7,12) agents agent(10) agent(12) targets target(3) genic_interactions genic_interaction(10,3) genic_interaction(12,3) ID 10515909-4 sentence Expression of the sigma(K)-dependent cwlH gene depended on gerE. words word(0,'Expression',0,9) word(1,'of',11,12) word(2,'the',14,16) word(3,'sigma(K)',18,25) word(4,'dependent',27,35) word(5,'cwlH',37,40) word(6,'gene',42,45) word(7,'depended',47,54) word(8,'on',56,57) word(9,'gerE',59,62) lemmas lemma(0,'expression') lemma(1,'of') lemma(2,'the') lemma(3,'sigK') lemma(4,'dependent') lemma(5,'cwlH') lemma(6,'gene') lemma(7,'depend') lemma(8,'on') lemma(9,'gerE') syntactic_relations relation('subj:V-N',7,0) relation('mod_att:N-ADJ',6,4) relation('mod:ADJ-N',4,3) relation('mod_att:N-N',6,5) relation('comp_of:N-N',0,6) relation('comp_on:V-N',7,9) agents agent(3) agent(9) targets target(5) genic_interactions genic_interaction(3,5) genic_interaction(9,5) ID 10503549-5 sentence Our results indicate that the level of KatX level in outgrowing spores depends mainly on EsigmaF, because sigB mutants show normal KatX activity in dormant and outgrowing spores. words word(0,'Our',0,2) word(1,'results',4,10) word(2,'indicate',12,19) word(3,'that',21,24) word(4,'the',26,28) word(5,'level',30,34) word(6,'of',36,37) word(7,'KatX',39,42) word(8,'level',44,48) word(9,'in',50,51) word(10,'outgrowing',53,62) word(11,'spores',64,69) word(12,'depends',71,77) word(13,'mainly',79,84) word(14,'on',86,87) word(15,'EsigmaF',89,95) word(16,'because',98,104) word(17,'sigB',106,109) word(18,'mutants',111,117) word(19,'show',119,122) word(20,'normal',124,129) word(21,'KatX',131,134) word(22,'activity',136,143) word(23,'in',145,146) word(24,'dormant',148,154) word(25,'and',156,158) word(26,'outgrowing',160,169) word(27,'spores',171,176) lemmas lemma(0,'our') lemma(1,'result') lemma(2,'indicate') lemma(3,'that') lemma(4,'the') lemma(5,'level') lemma(6,'of') lemma(7,'KatX') lemma(8,'level') lemma(9,'in') lemma(10,'outgrow') lemma(11,'swarm') lemma(12,'depend') lemma(13,'mainly') lemma(14,'on') lemma(15,'EsigmaF') lemma(16,'because') lemma(17,'sigB') lemma(18,'mutant') lemma(19,'show') lemma(20,'normal') lemma(21,'KatX') lemma(22,'activity') lemma(23,'in') lemma(24,'dormant') lemma(25,'and') lemma(26,'outgrow') lemma(27,'swarm') syntactic_relations relation('comp_of:N-N',5,8) relation('mod_att:N-N',18,17) relation('comp_on:V-N',12,15) relation('mod:V-ADV',12,13) relation('comp_in:V-N',19,27) relation('subj:V-N',19,18) relation('mod_att:N-ADJ',11,10) relation('subj:V-N',2,1) relation('mod_att:N-N',22,21) relation('mod_att:N-ADJ',27,26) relation('mod_att:N-ADJ',27,24) relation('obj:V-N',19,22) relation('subj:V-N',12,5) relation('mod_att:N-N',8,7) relation('mod_att:N-ADJ',22,20) relation('comp_in:N-N',8,11) agents agent(15) targets target(7) genic_interactions genic_interaction(15,7) ID 10503549-7 sentence Therefore, the physiological role of sigmaB-dependent katX expression remains obscure. words word(0,'Therefore',0,8) word(1,'the',11,13) word(2,'physiological',15,27) word(3,'role',29,32) word(4,'of',34,35) word(5,'sigmaB',37,42) word(6,'dependent',44,52) word(7,'katX',54,57) word(8,'expression',59,68) word(9,'remains',70,76) word(10,'obscure',78,84) lemmas lemma(0,'therefore') lemma(1,'the') lemma(2,'physiological') lemma(3,'role') lemma(4,'of') lemma(5,'sigB') lemma(6,'dependent') lemma(7,'katX') lemma(8,'expression') lemma(9,'remain') lemma(10,'obscure') syntactic_relations relation('mod_att:N-N',8,7) relation('mod_att:N-ADJ',3,2) relation('mod:ADJ-N',6,5) relation('mod_pred:N-ADJ',3,10) relation('mod_att:N-ADJ',8,6) relation('comp_of:N-N',3,8) relation('mod:V-ADV',9,0) agents agent(5) targets target(7) genic_interactions genic_interaction(5,7) ID 10476035-10 sentence Taken together, the results support the idea that sequestration of SpoIIE protein into the prespore plays an important role in the control of sigmaF activation and in coupling this activation to septation. words word(0,'Taken',0,4) word(1,'together',6,13) word(2,'the',16,18) word(3,'results',20,26) word(4,'support',28,34) word(5,'the',36,38) word(6,'idea',40,43) word(7,'that',45,48) word(8,'sequestration',50,62) word(9,'of',64,65) word(10,'SpoIIE',67,72) word(11,'protein',74,80) word(12,'into',82,85) word(13,'the',87,89) word(14,'prespore',91,98) word(15,'plays',100,104) word(16,'an',106,107) word(17,'important',109,117) word(18,'role',119,122) word(19,'in',124,125) word(20,'the',127,129) word(21,'control',131,137) word(22,'of',139,140) word(23,'sigmaF',142,147) word(24,'activation',149,158) word(25,'and',160,162) word(26,'in',164,165) word(27,'coupling',167,174) word(28,'this',176,179) word(29,'activation',181,190) word(30,'to',192,193) word(31,'septation',195,203) lemmas lemma(0,'take') lemma(1,'together') lemma(2,'the') lemma(3,'result') lemma(4,'support') lemma(5,'the') lemma(6,'idea') lemma(7,'that') lemma(8,'sequestration') lemma(9,'of') lemma(10,'SpoIIE') lemma(11,'protein') lemma(12,'into') lemma(13,'the') lemma(14,'prespore') lemma(15,'play') lemma(16,'an') lemma(17,'important') lemma(18,'role') lemma(19,'in') lemma(20,'the') lemma(21,'control') lemma(22,'of') lemma(23,'sigF') lemma(24,'activation') lemma(25,'and') lemma(26,'in') lemma(27,'coupling') lemma(28,'this') lemma(29,'activation') lemma(30,'to') lemma(31,'septation') syntactic_relations relation('comp_in:N-N',18,21) relation('comp_of:N-N',21,24) relation('subj:V-N',15,8) relation('mod_att:N-N',24,23) relation('mod_att:N-ADJ',18,17) relation('comp_of:N-N',8,11) relation('obj:V-N',27,29) relation('mod_att:N-N',11,10) relation('subj:V-N',4,3) relation('obj:V-N',15,18) relation('obj:V-N',4,6) relation('comp_to:V-N',27,31) relation('comp_into:N-N',8,14) relation('comp_in:N-N',18,27) relation('mod_att:N-ADJ',3,0) relation('mod:ADJ-ADV',0,1) agents agent(10) targets target(23) genic_interactions genic_interaction(10,23) ID 10468601-1 sentence The rocG gene of Bacillus subtilis, encoding a catabolic glutamate dehydrogenase, is transcribed by SigL-containing RNA polymerase and requires for its expression RocR, a member of the NtrC/NifA family of proteins that bind to enhancer-like elements, called upstream activating sequences (UAS). words word(0,'The',0,2) word(1,'rocG',4,7) word(2,'gene',9,12) word(3,'of',14,15) word(4,'Bacillus subtilis',17,33) word(5,'encoding',36,43) word(6,'a',45,45) word(7,'catabolic',47,55) word(8,'glutamate',57,65) word(9,'dehydrogenase',67,79) word(10,'is',82,83) word(11,'transcribed',85,95) word(12,'by',97,98) word(13,'SigL',100,103) word(14,'containing',105,114) word(15,'RNA',116,118) word(16,'polymerase',120,129) word(17,'and',131,133) word(18,'requires',135,142) word(19,'for',144,146) word(20,'its',148,150) word(21,'expression',152,161) word(22,'RocR',163,166) word(23,'a',169,169) word(24,'member',171,176) word(25,'of',178,179) word(26,'the',181,183) word(27,'NtrC/NifA',185,193) word(28,'family',195,200) word(29,'of',202,203) word(30,'proteins',205,212) word(31,'that',214,217) word(32,'bind',219,222) word(33,'to',224,225) word(34,'enhancer-like',227,239) word(35,'elements',241,248) word(36,'called',251,256) word(37,'upstream',258,265) word(38,'activating',267,276) word(39,'sequences',278,286) word(40,'UAS',289,291) lemmas lemma(0,'the') lemma(1,'rocG') lemma(2,'gene') lemma(3,'of') lemma(4,'Bacillus subtilis') lemma(5,'encode') lemma(6,'a') lemma(7,'catabolic') lemma(8,'glutamate') lemma(9,'dehydrogenase') lemma(10,'be') lemma(11,'transcribe') lemma(12,'by') lemma(13,'SigL') lemma(14,'contain') lemma(15,'RNA') lemma(16,'polymerase') lemma(17,'and') lemma(18,'require') lemma(19,'for') lemma(20,'its') lemma(21,'expression') lemma(22,'RocR') lemma(23,'a') lemma(24,'member') lemma(25,'of') lemma(26,'the') lemma(27,'NtrC/NifA') lemma(28,'family') lemma(29,'of') lemma(30,'protein') lemma(31,'that') lemma(32,'bind') lemma(33,'to') lemma(34,'enhancer-like') lemma(35,'element') lemma(36,'call') lemma(37,'upstream') lemma(38,'activate') lemma(39,'sequence') lemma(40,'UAS') syntactic_relations relation('subj:V-N',32,30) relation('subj:V-N',5,2) relation('comp_of:N-N',24,28) relation('mod_att:N-N',28,27) relation('subj:V-N',18,2) relation('appos',39,40) relation('mod_att:N-ADJ',39,38) relation('mod_att:N-ADJ',39,37) relation('obj:V-N',5,9) relation('mod_att:N-ADJ',16,14) relation('mod:ADJ-N',14,13) relation('comp_of:N-N',2,4) relation('appos',22,24) relation('comp_to:V-N',32,35) relation('comp_by:V_PASS-N',11,16) relation('mod_att:N-N',9,8) relation('mod_att:N-ADJ',35,34) relation('obj:V_PASS-N',36,39) relation('subj:V_PASS-N',36,35) relation('mod_att:N-N',2,1) relation('mod_att:N-N',16,15) relation('subj:V_PASS-N',11,2) relation('obj:V-N',18,22) relation('comp_for:V-N',18,21) relation('comp_of:N-N',28,30) relation('mod_att:N-ADJ',8,7) agents agent(13) agent(22) targets target(1) genic_interactions genic_interaction(13,1) genic_interaction(22,1) ID 10464187-11 sentence In addition to controlling transcription of phrC, sigmaH appears to control expression of at least one other gene required for production of CSF. words word(0,'In',0,1) word(1,'addition',3,10) word(2,'to',12,13) word(3,'controlling',15,25) word(4,'transcription',27,39) word(5,'of',41,42) word(6,'phrC',44,47) word(7,'sigmaH',50,55) word(8,'appears',57,63) word(9,'to',65,66) word(10,'control',68,74) word(11,'expression',76,85) word(12,'of',87,88) word(13,'at',90,91) word(14,'least',93,97) word(15,'one',99,101) word(16,'other',103,107) word(17,'gene',109,112) word(18,'required',114,121) word(19,'for',123,125) word(20,'production',127,136) word(21,'of',138,139) word(22,'CSF',141,143) lemmas lemma(0,'in') lemma(1,'addition') lemma(2,'to') lemma(3,'control') lemma(4,'transcription') lemma(5,'of') lemma(6,'phrC') lemma(7,'sigH') lemma(8,'appear') lemma(9,'to') lemma(10,'control') lemma(11,'expression') lemma(12,'of') lemma(13,'at') lemma(14,'least') lemma(15,'one') lemma(16,'other') lemma(17,'gene') lemma(18,'require') lemma(19,'for') lemma(20,'production') lemma(21,'of') lemma(22,'CSF') syntactic_relations relation('comp_to:N-V',1,3) relation('comp_of:N-N',20,22) relation('subj:V-N',10,7) relation('comp_of:N-N',11,17) relation('comp_for:V_PASS-N',18,20) relation('obj:V-N',10,11) relation('comp_in:V-N',8,1) relation('comp_of:N-N',4,6) relation('obj:V-N',3,4) relation('subj:V_PASS-N',18,17) relation('mod_att:N-ADJ',17,15) agents agent(7) targets target(6) genic_interactions genic_interaction(7,6) ID 10463184-4 sentence Northern blot and primer extension analyses indicated that yfhS is transcribed by E sigma E during sporulation. words word(0,'Northern',0,7) word(1,'blot',9,12) word(2,'and',14,16) word(3,'primer',18,23) word(4,'extension',25,33) word(5,'analyses',35,42) word(6,'indicated',44,52) word(7,'that',54,57) word(8,'yfhS',59,62) word(9,'is',64,65) word(10,'transcribed',67,77) word(11,'by',79,80) word(12,'E sigma E',82,90) word(13,'during',92,97) word(14,'sporulation',99,109) lemmas lemma(0,'northern') lemma(1,'blot') lemma(2,'and') lemma(3,'prime') lemma(4,'extension') lemma(5,'analysis') lemma(6,'indicate') lemma(7,'that') lemma(8,'yfhS') lemma(9,'be') lemma(10,'transcribe') lemma(11,'by') lemma(12,'E sigma E') lemma(13,'during') lemma(14,'sporulation') syntactic_relations relation('comp_by:V_PASS-N',10,12) relation('subj:V-N',6,5) relation('mod_att:N-N',1,0) relation('mod_att:N-N',4,3) relation('mod_att:N-N',5,1) relation('mod_att:N-N',5,4) relation('subj:V_PASS-N',10,8) relation('comp_during:V_PASS-N',10,14) agents agent(12) targets target(8) genic_interactions genic_interaction(12,8) ID 10463184-8 sentence These results suggest that YfhP may act as a negative regulator for the transcription of yfhQ, yfhR, sspE and yfhP. words word(0,'These',0,4) word(1,'results',6,12) word(2,'suggest',14,20) word(3,'that',22,25) word(4,'YfhP',27,30) word(5,'may',32,34) word(6,'act',36,38) word(7,'as',40,41) word(8,'a',43,43) word(9,'negative',45,52) word(10,'regulator',54,62) word(11,'for',64,66) word(12,'the',68,70) word(13,'transcription',72,84) word(14,'of',86,87) word(15,'yfhQ',89,92) word(16,'yfhR',95,98) word(17,'sspE',101,104) word(18,'and',106,108) word(19,'yfhP',110,113) lemmas lemma(0,'these') lemma(1,'result') lemma(2,'suggest') lemma(3,'that') lemma(4,'YfhP') lemma(5,'may') lemma(6,'act') lemma(7,'as') lemma(8,'a') lemma(9,'negative') lemma(10,'regulator') lemma(11,'for') lemma(12,'the') lemma(13,'transcription') lemma(14,'of') lemma(15,'yfhQ') lemma(16,'fabL') lemma(17,'sspE') lemma(18,'and') lemma(19,'yfhP') syntactic_relations relation('comp_as:V-N',6,10) relation('comp_of:N-N',13,19) relation('subj:V-N',6,4) relation('comp_for:N-N',10,13) relation('mod_att:N-ADJ',10,9) relation('subj:V-N',2,1) relation('comp_of:N-N',13,15) relation('comp_of:N-N',13,17) relation('comp_of:N-N',13,16) agents agent(4) targets target(15) target(16) target(17) target(19) genic_interactions genic_interaction(4,15) genic_interaction(4,16) genic_interaction(4,17) genic_interaction(4,19) ID 10383978-4 sentence Production of sigmaK about 1 h earlier than normal does affect Spo0A, which when phosphorylated is an activator of sigE transcription. words word(0,'Production',0,9) word(1,'of',11,12) word(2,'sigmaK',14,19) word(3,'about',21,25) word(4,'1',27,27) word(5,'h',29,29) word(6,'earlier',31,37) word(7,'than',39,42) word(8,'normal',44,49) word(9,'does',51,54) word(10,'affect',56,61) word(11,'Spo0A',63,67) word(12,'which',70,74) word(13,'when',76,79) word(14,'phosphorylated',81,94) word(15,'is',96,97) word(16,'an',99,100) word(17,'activator',102,110) word(18,'of',112,113) word(19,'sigE',115,118) word(20,'transcription',120,132) lemmas lemma(0,'production') lemma(1,'of') lemma(2,'sigK') lemma(3,'about') lemma(4,'1') lemma(5,'h') lemma(6,'early') lemma(7,'than') lemma(8,'normal') lemma(9,'do') lemma(10,'affect') lemma(11,'spo0A') lemma(12,'which') lemma(13,'when') lemma(14,'phosphorylated') lemma(15,'be') lemma(16,'an') lemma(17,'activator') lemma(18,'of') lemma(19,'sigE') lemma(20,'transcription') syntactic_relations relation('mod_att:N-N',20,19) relation('comp_of:N-N',17,20) relation('subj:V-N',10,0) relation('comp_of:N-N',0,2) relation('obj:V-N',10,11) relation('mod_pred:N-N',11,17) relation('mod_post:N-ADJ',0,6) relation('mod:ADJ-N',6,5) relation('mod_att:N-ADJ',5,4) relation('mod:ADJ-ADV',4,3) relation('comp_than:ADJ-N',6,8) relation('subj:V_PASS-N',14,11) agents agent(2) agent(11) targets target(11) target(19) genic_interactions genic_interaction(2,11) genic_interaction(11,19) ID 10323866-7 sentence The first stage, which involves the phosphatase function of SpoIIE, depends on the cell division protein FtsZ and could correspond to the FtsZ-dependent assembly of SpoIIE into E-rings. words word(0,'The',0,2) word(1,'first',4,8) word(2,'stage',10,14) word(3,'which',17,21) word(4,'involves',23,30) word(5,'the',32,34) word(6,'phosphatase',36,46) word(7,'function',48,55) word(8,'of',57,58) word(9,'SpoIIE',60,65) word(10,'depends',68,74) word(11,'on',76,77) word(12,'the',79,81) word(13,'cell',83,86) word(14,'division',88,95) word(15,'protein',97,103) word(16,'FtsZ',105,108) word(17,'and',110,112) word(18,'could',114,118) word(19,'correspond',120,129) word(20,'to',131,132) word(21,'the',134,136) word(22,'FtsZ',138,141) word(23,'dependent',143,151) word(24,'assembly',153,160) word(25,'of',162,163) word(26,'SpoIIE',165,170) word(27,'into',172,175) word(28,'E-rings',177,183) lemmas lemma(0,'the') lemma(1,'first') lemma(2,'stage') lemma(3,'which') lemma(4,'involve') lemma(5,'the') lemma(6,'phosphatase') lemma(7,'function') lemma(8,'of') lemma(9,'SpoIIE') lemma(10,'depend') lemma(11,'on') lemma(12,'the') lemma(13,'cell') lemma(14,'division') lemma(15,'protein') lemma(16,'FtsZ') lemma(17,'and') lemma(18,'could') lemma(19,'correspond') lemma(20,'to') lemma(21,'the') lemma(22,'FtsZ') lemma(23,'dependent') lemma(24,'assembly') lemma(25,'of') lemma(26,'SpoIIE') lemma(27,'into') lemma(28,'E-rings') syntactic_relations relation('comp_of:N-N',24,26) relation('mod_att:N-ADJ',2,1) relation('subj:V-N',19,2) relation('mod_att:N-ADJ',7,6) relation('mod_att:N-N',16,15) relation('mod_att:N-N',14,13) relation('obj:V-N',4,7) relation('subj:V-N',4,2) relation('mod:ADJ-N',23,22) relation('comp_on:V-N',10,16) relation('comp_into:N-N',24,28) relation('comp_of:N-N',7,9) relation('mod_att:N-N',15,14) relation('subj:V-N',10,2) relation('comp_to:V-N',19,24) relation('mod_att:N-ADJ',24,23) agents agent(16) agent(22) targets target(9) target(26) genic_interactions genic_interaction(16,9) genic_interaction(22,26) ID 10323866-9 sentence Evidence based on the use of modified and mutant forms of the phosphatase protein indicates that SpoIIE blocks the capacity of unphosphorylated SpoIIAA to activate sigmaF until formation of the polar septum is completed. words word(0,'Evidence',0,7) word(1,'based',9,13) word(2,'on',15,16) word(3,'the',18,20) word(4,'use',22,24) word(5,'of',26,27) word(6,'modified',29,36) word(7,'and',38,40) word(8,'mutant',42,47) word(9,'forms',49,53) word(10,'of',55,56) word(11,'the',58,60) word(12,'phosphatase',62,72) word(13,'protein',74,80) word(14,'indicates',82,90) word(15,'that',92,95) word(16,'SpoIIE',97,102) word(17,'blocks',104,109) word(18,'the',111,113) word(19,'capacity',115,122) word(20,'of',124,125) word(21,'unphosphorylated',127,142) word(22,'SpoIIAA',144,150) word(23,'to',152,153) word(24,'activate',155,162) word(25,'sigmaF',164,169) word(26,'until',171,175) word(27,'formation',177,185) word(28,'of',187,188) word(29,'the',190,192) word(30,'polar',194,198) word(31,'septum',200,205) word(32,'is',207,208) word(33,'completed',210,218) lemmas lemma(0,'evidence') lemma(1,'base') lemma(2,'on') lemma(3,'the') lemma(4,'use') lemma(5,'of') lemma(6,'modified') lemma(7,'and') lemma(8,'mutant') lemma(9,'form') lemma(10,'of') lemma(11,'the') lemma(12,'phosphatase') lemma(13,'protein') lemma(14,'indicate') lemma(15,'that') lemma(16,'SpoIIE') lemma(17,'block') lemma(18,'the') lemma(19,'capacity') lemma(20,'of') lemma(21,'unphosphorylated') lemma(22,'SpoIIAA') lemma(23,'to') lemma(24,'activate') lemma(25,'sigF') lemma(26,'until') lemma(27,'formation') lemma(28,'of') lemma(29,'the') lemma(30,'polar') lemma(31,'septum') lemma(32,'be') lemma(33,'complete') syntactic_relations relation('comp_of:N-N',19,22) relation('comp_of:N-N',27,31) relation('subj:V-N',17,16) relation('mod_att:N-ADJ',8,9) relation('mod_att:N-ADJ',22,21) relation('mod_att:N-ADJ',31,30) relation('comp_on:V_PASS-N',1,4) relation('comp_of:N-N',9,13) relation('obj:V-N',24,25) relation('mod_att:N-N',13,12) relation('subj:V_PASS-N',33,27) relation('subj:V_PASS-N',1,0) relation('mod_att:N-ADJ',9,6) relation('subj:V-N',14,0) relation('comp_of:N-N',4,9) relation('obj:V-N',17,19) relation('comp_until:V-N',17,27) relation('comp_to:N-V',19,24) agents agent(16) agent(22) targets target(22) target(25) genic_interactions genic_interaction(16,22) genic_interaction(22,25) ID 10234829-1 sentence Dephosphorylation of SpoIIAA-P by SpoIIE is strictly dependent on the presence of the bivalent metal ions Mn2+ or Mg2+. words word(0,'Dephosphorylation',0,16) word(1,'of',18,19) word(2,'SpoIIAA-P',21,29) word(3,'by',31,32) word(4,'SpoIIE',34,39) word(5,'is',41,42) word(6,'strictly',44,51) word(7,'dependent',53,61) word(8,'on',63,64) word(9,'the',66,68) word(10,'presence',70,77) word(11,'of',79,80) word(12,'the',82,84) word(13,'bivalent',86,93) word(14,'metal',95,99) word(15,'ions',101,104) word(16,'Mn2+',106,109) word(17,'or',111,112) word(18,'Mg2+',114,117) lemmas lemma(0,'Dephosphorylation') lemma(1,'of') lemma(2,'SpoIIAA-P') lemma(3,'by') lemma(4,'SpoIIE') lemma(5,'be') lemma(6,'strictly') lemma(7,'dependent') lemma(8,'on') lemma(9,'the') lemma(10,'presence') lemma(11,'of') lemma(12,'the') lemma(13,'bivalent') lemma(14,'metal') lemma(15,'ion') lemma(16,'Mn2+') lemma(17,'or') lemma(18,'Mg2+') syntactic_relations relation('comp_of:N-N',10,16) relation('comp_by:N-N',0,4) relation('comp_of:N-N',0,2) relation('mod:ADJ-ADV',7,6) relation('mod_att:N-N',15,14) relation('comp_on:ADJ-N',7,10) relation('mod_pred:N-ADJ',0,7) relation('mod_att:N-N',18,15) relation('mod_att:N-ADJ',15,13) relation('mod_att:N-N',16,15) relation('comp_of:N-N',10,18) agents agent(4) targets target(2) genic_interactions genic_interaction(4,2) ID 10220166-7 sentence (i) The finding that the bmrUR operon is under sigmaB control indicates that the elimination of multidrug compounds might be a new function in multiple stress resistance. words word(0,'i',1,1) word(1,'The',4,6) word(2,'finding',8,14) word(3,'that',16,19) word(4,'the',21,23) word(5,'bmrUR',25,29) word(6,'operon',31,36) word(7,'is',38,39) word(8,'under',41,45) word(9,'sigmaB',47,52) word(10,'control',54,60) word(11,'indicates',62,70) word(12,'that',72,75) word(13,'the',77,79) word(14,'elimination',81,91) word(15,'of',93,94) word(16,'multidrug',96,104) word(17,'compounds',106,114) word(18,'might',116,120) word(19,'be',122,123) word(20,'a',125,125) word(21,'new',127,129) word(22,'function',131,138) word(23,'in',140,141) word(24,'multiple',143,150) word(25,'stress',152,157) word(26,'resistance',159,168) lemmas lemma(0,'i') lemma(1,'the') lemma(2,'finding') lemma(3,'that') lemma(4,'the') lemma(5,'bmrUR') lemma(6,'operon') lemma(7,'be') lemma(8,'under') lemma(9,'sigB') lemma(10,'control') lemma(11,'indicate') lemma(12,'that') lemma(13,'the') lemma(14,'elimination') lemma(15,'of') lemma(16,'multidrug') lemma(17,'compound') lemma(18,'might') lemma(19,'be') lemma(20,'a') lemma(21,'new') lemma(22,'function') lemma(23,'in') lemma(24,'multiple') lemma(25,'stress') lemma(26,'resistance') syntactic_relations relation('mod_att:N-ADJ',25,24) relation('mod_att:N-N',6,5) relation('mod_att:N-ADJ',22,21) relation('subj:V-N',7,6) relation('mod_att:N-ADJ',17,16) relation('subj:V-N',11,2) relation('mod_att:N-N',26,25) relation('mod_att:N-N',10,9) relation('comp_of:N-N',14,17) relation('comp_under:V-N',7,10) relation('comp_in:N-N',22,26) relation('mod_pred:N-N',14,22) agents agent(9) targets target(5) genic_interactions genic_interaction(9,5) ID 10200961-2 sentence Cell specificity is first established in the forespore under the control of the sigma F factor, which is itself activated through the action of the SpoIIE serine phosphatase, an enzyme targeted to the septum between the two cells. words word(0,'Cell',0,3) word(1,'specificity',5,15) word(2,'is',17,18) word(3,'first',20,24) word(4,'established',26,36) word(5,'in',38,39) word(6,'the',41,43) word(7,'forespore',45,53) word(8,'under',55,59) word(9,'the',61,63) word(10,'control',65,71) word(11,'of',73,74) word(12,'the',76,78) word(13,'sigma F',80,86) word(14,'factor',88,93) word(15,'which',96,100) word(16,'is',102,103) word(17,'itself',105,110) word(18,'activated',112,120) word(19,'through',122,128) word(20,'the',130,132) word(21,'action',134,139) word(22,'of',141,142) word(23,'the',144,146) word(24,'SpoIIE',148,153) word(25,'serine',155,160) word(26,'phosphatase',162,172) word(27,'an',175,176) word(28,'enzyme',178,183) word(29,'targeted',185,192) word(30,'to',194,195) word(31,'the',197,199) word(32,'septum',201,206) word(33,'between',208,214) word(34,'the',216,218) word(35,'two',220,222) word(36,'cells',224,228) lemmas lemma(0,'cell') lemma(1,'specificity') lemma(2,'be') lemma(3,'first') lemma(4,'establish') lemma(5,'in') lemma(6,'the') lemma(7,'forespore') lemma(8,'under') lemma(9,'the') lemma(10,'control') lemma(11,'of') lemma(12,'the') lemma(13,'sigF') lemma(14,'factor') lemma(15,'which') lemma(16,'be') lemma(17,'itself') lemma(18,'activate') lemma(19,'through') lemma(20,'the') lemma(21,'action') lemma(22,'of') lemma(23,'the') lemma(24,'SpoIIE') lemma(25,'serine') lemma(26,'phosphatase') lemma(27,'an') lemma(28,'enzyme') lemma(29,'target') lemma(30,'to') lemma(31,'the') lemma(32,'septum') lemma(33,'between') lemma(34,'the') lemma(35,'two') lemma(36,'cell') syntactic_relations relation('comp_to:V_PASS-N',29,32) relation('appos',26,28) relation('mod_att:N-ADJ',26,25) relation('mod_att:N-N',14,13) relation('subj:V_PASS-N',18,14) relation('mod_att:N-N',1,0) relation('subj:V_PASS-N',29,28) relation('mod:V_PASS-ADV',4,3) relation('subj:V_PASS-N',4,1) relation('comp_between:N-N',32,36) relation('comp_of:N-N',21,26) relation('comp_of:N-N',10,14) relation('mod_att:N-N',26,24) relation('mod:V_PASS-ADV',18,17) relation('comp_in:V_PASS-N',4,7) relation('comp_under:V_PASS-N',4,10) relation('comp_through:V_PASS-N',18,21) agents agent(24) targets target(13) genic_interactions genic_interaction(24,13) ID 10075739-3 sentence Most cot genes, and the gerE gene, are transcribed by sigmaK RNA polymerase. words word(0,'Most',0,3) word(1,'cot',5,7) word(2,'genes',9,13) word(3,'and',16,18) word(4,'the',20,22) word(5,'gerE',24,27) word(6,'gene',29,32) word(7,'are',35,37) word(8,'transcribed',39,49) word(9,'by',51,52) word(10,'sigmaK',54,59) word(11,'RNA',61,63) word(12,'polymerase',65,74) lemmas lemma(0,'most') lemma(1,'cot') lemma(2,'gene') lemma(3,'and') lemma(4,'the') lemma(5,'gerE') lemma(6,'gene') lemma(7,'be') lemma(8,'transcribe') lemma(9,'by') lemma(10,'sigK') lemma(11,'RNA') lemma(12,'polymerase') syntactic_relations relation('mod_att:N-N',12,10) relation('subj:V_PASS-N',8,6) relation('subj:V_PASS-N',8,2) relation('comp_by:V_PASS-N',8,12) relation('mod_att:N-N',2,1) relation('mod_att:N-N',12,11) relation('mod_att:N-N',6,5) agents agent(10) targets target(1) target(5) genic_interactions genic_interaction(10,1) genic_interaction(10,5) ID 10075739-4 sentence Previously, it was shown that the GerE protein inhibits transcription in vitro of the sigK gene encoding sigmaK. words word(0,'Previously',0,9) word(1,'it',12,13) word(2,'was',15,17) word(3,'shown',19,23) word(4,'that',25,28) word(5,'the',30,32) word(6,'GerE',34,37) word(7,'protein',39,45) word(8,'inhibits',47,54) word(9,'transcription',56,68) word(10,'in',70,71) word(11,'vitro',73,77) word(12,'of',79,80) word(13,'the',82,84) word(14,'sigK',86,89) word(15,'gene',91,94) word(16,'encoding',96,103) word(17,'sigmaK',105,110) lemmas lemma(0,'previously') lemma(1,'it') lemma(2,'be') lemma(3,'show') lemma(4,'that') lemma(5,'the') lemma(6,'GerE') lemma(7,'protein') lemma(8,'inhibit') lemma(9,'transcription') lemma(10,'in') lemma(11,'vitro') lemma(12,'of') lemma(13,'the') lemma(14,'sigK') lemma(15,'gene') lemma(16,'encode') lemma(17,'sigK') syntactic_relations relation('mod_att:N-N',7,6) relation('comp_of:N-N',9,15) relation('obj:V-N',8,9) relation('mod:V-ADV',3,0) relation('subj:V-N',8,7) relation('mod_att:N-N',15,14) relation('subj:V-N',16,15) relation('obj:V-N',16,17) relation('subj:V_PASS-N',3,1) relation('comp_in:N-N',9,11) agents agent(6) targets target(14) genic_interactions genic_interaction(6,14) ID 10075739-8 sentence These results demonstrate that sigmaK-dependent transcription of gerE initiates a negative feedback loop in which GerE acts as a repressor to limit production of sigmaK. words word(0,'These',0,4) word(1,'results',6,12) word(2,'demonstrate',14,24) word(3,'that',26,29) word(4,'sigmaK',31,36) word(5,'dependent',38,46) word(6,'transcription',48,60) word(7,'of',62,63) word(8,'gerE',65,68) word(9,'initiates',70,78) word(10,'a',80,80) word(11,'negative',82,89) word(12,'feedback',91,98) word(13,'loop',100,103) word(14,'in',105,106) word(15,'which',108,112) word(16,'GerE',114,117) word(17,'acts',119,122) word(18,'as',124,125) word(19,'a',127,127) word(20,'repressor',129,137) word(21,'to',139,140) word(22,'limit',142,146) word(23,'production',148,157) word(24,'of',159,160) word(25,'sigmaK',162,167) lemmas lemma(0,'these') lemma(1,'result') lemma(2,'demonstrate') lemma(3,'that') lemma(4,'sigK') lemma(5,'dependent') lemma(6,'transcription') lemma(7,'of') lemma(8,'gerE') lemma(9,'initiate') lemma(10,'a') lemma(11,'negative') lemma(12,'feedback') lemma(13,'loop') lemma(14,'in') lemma(15,'which') lemma(16,'GerE') lemma(17,'act') lemma(18,'as') lemma(19,'a') lemma(20,'represser') lemma(21,'to') lemma(22,'limit') lemma(23,'production') lemma(24,'of') lemma(25,'sigK') syntactic_relations relation('comp_in:V-N',17,13) relation('subj:V-N',2,1) relation('subj:V-N',9,6) relation('obj:V-N',9,13) relation('mod_att:N-N',13,12) relation('mod_att:N-ADJ',12,11) relation('subj:V-N',17,16) relation('comp_of:N-N',23,25) relation('mod_att:N-ADJ',6,5) relation('mod:ADJ-N',5,4) relation('comp_to:V-V',17,22) relation('comp_as:V-N',17,20) relation('comp_of:N-N',6,8) relation('obj:V-N',22,23) agents agent(4) agent(16) targets target(8) target(25) genic_interactions genic_interaction(4,8) genic_interaction(16,25) ID 10075739-11 sentence A low level of GerE activated transcription of cotD by sigmaK RNA polymerase in vitro, but a higher level of GerE repressed cotD transcription. words word(0,'A',0,0) word(1,'low',2,4) word(2,'level',6,10) word(3,'of',12,13) word(4,'GerE',15,18) word(5,'activated',20,28) word(6,'transcription',30,42) word(7,'of',44,45) word(8,'cotD',47,50) word(9,'by',52,53) word(10,'sigmaK',55,60) word(11,'RNA',62,64) word(12,'polymerase',66,75) word(13,'in',77,78) word(14,'vitro',80,84) word(15,'but',87,89) word(16,'a',91,91) word(17,'higher',93,98) word(18,'level',100,104) word(19,'of',106,107) word(20,'GerE',109,112) word(21,'repressed',114,122) word(22,'cotD',124,127) word(23,'transcription',129,141) lemmas lemma(0,'a') lemma(1,'low') lemma(2,'level') lemma(3,'of') lemma(4,'GerE') lemma(5,'activate') lemma(6,'transcription') lemma(7,'of') lemma(8,'cotD') lemma(9,'by') lemma(10,'sigK') lemma(11,'RNA') lemma(12,'polymerase') lemma(13,'in') lemma(14,'vitro') lemma(15,'but') lemma(16,'a') lemma(17,'high') lemma(18,'level') lemma(19,'of') lemma(20,'GerE') lemma(21,'repressed') lemma(22,'cotD') lemma(23,'transcription') syntactic_relations relation('obj:V-N',5,6) relation('comp_by:V-N',5,12) relation('subj:V-N',21,18) relation('comp_of:N-N',2,4) relation('mod_att:N-ADJ',18,17) relation('comp_of:N-N',18,20) relation('mod_att:N-N',12,11) relation('subj:V-N',5,2) relation('comp_of:N-N',6,8) relation('mod_att:N-N',23,22) relation('mod_att:N-ADJ',2,1) relation('obj:V-N',21,23) relation('mod_att:N-N',12,10) relation('comp_in:V-N',5,14) agents agent(4) agent(10) agent(20) targets target(8) target(10) target(22) genic_interactions genic_interaction(4,8) genic_interaction(4,10) genic_interaction(10,8) genic_interaction(20,22) ID 9852018-5 sentence sspG transcription also requires the DNA binding protein GerE. words word(0,'sspG',0,3) word(1,'transcription',5,17) word(2,'also',19,22) word(3,'requires',24,31) word(4,'the',33,35) word(5,'DNA',37,39) word(6,'binding',41,47) word(7,'protein',49,55) word(8,'GerE',57,60) lemmas lemma(0,'sspG') lemma(1,'transcription') lemma(2,'also') lemma(3,'require') lemma(4,'the') lemma(5,'DNA') lemma(6,'binding') lemma(7,'protein') lemma(8,'GerE') syntactic_relations relation('mod:ADJ-N',6,5) relation('obj:V-N',3,8) relation('mod_att:N-N',1,0) relation('mod_att:N-ADJ',7,6) relation('mod_att:N-N',8,7) relation('mod:V-ADV',3,2) relation('subj:V-N',3,1) agents agent(8) targets target(0) genic_interactions genic_interaction(8,0) ID 9852018-6 sentence In contrast, sspJ is transcribed in the forespore compartment by RNA polymerase with the forespore-specific sigmaG and appears to give a monocistronic transcript. words word(0,'In',0,1) word(1,'contrast',3,10) word(2,'sspJ',13,16) word(3,'is',18,19) word(4,'transcribed',21,31) word(5,'in',33,34) word(6,'the',36,38) word(7,'forespore',40,48) word(8,'compartment',50,60) word(9,'by',62,63) word(10,'RNA',65,67) word(11,'polymerase',69,78) word(12,'with',80,83) word(13,'the',85,87) word(14,'forespore-specific',89,106) word(15,'sigmaG',108,113) word(16,'and',115,117) word(17,'appears',119,125) word(18,'to',127,128) word(19,'give',130,133) word(20,'a',135,135) word(21,'monocistronic',137,149) word(22,'transcript',151,160) lemmas lemma(0,'in') lemma(1,'contrast') lemma(2,'sspJ') lemma(3,'be') lemma(4,'transcribe') lemma(5,'in') lemma(6,'the') lemma(7,'forespore') lemma(8,'compartment') lemma(9,'by') lemma(10,'RNA') lemma(11,'polymerase') lemma(12,'with') lemma(13,'the') lemma(14,'forespore-specific') lemma(15,'sigG') lemma(16,'and') lemma(17,'appear') lemma(18,'to') lemma(19,'give') lemma(20,'a') lemma(21,'monocistronic') lemma(22,'transcript') syntactic_relations relation('comp_in:V_PASS-N',4,1) relation('comp_in:V_PASS-N',4,8) relation('comp_with:V_PASS-N',4,15) relation('mod_att:N-ADJ',15,14) relation('mod_att:N-ADJ',22,21) relation('obj:V-N',19,22) relation('mod_att:N-N',8,7) relation('comp_by:V_PASS-N',4,11) relation('mod_att:N-N',11,10) relation('subj:V_PASS-N',4,2) relation('subj:V-N',19,2) agents agent(15) targets target(2) genic_interactions genic_interaction(15,2) ID 9696775-12 sentence ComK negatively controls the transcription of hag by stimulating the transcription of comF-flgM, thereby increasing the production of the FlgM antisigma factor that inhibits sigmaD activity. words word(0,'ComK',0,3) word(1,'negatively',5,14) word(2,'controls',16,23) word(3,'the',25,27) word(4,'transcription',29,41) word(5,'of',43,44) word(6,'hag',46,48) word(7,'by',50,51) word(8,'stimulating',53,63) word(9,'the',65,67) word(10,'transcription',69,81) word(11,'of',83,84) word(12,'comF',86,89) word(13,'flgM',91,94) word(14,'thereby',97,103) word(15,'increasing',105,114) word(16,'the',116,118) word(17,'production',120,129) word(18,'of',131,132) word(19,'the',134,136) word(20,'FlgM',138,141) word(21,'antisigma',143,151) word(22,'factor',153,158) word(23,'that',160,163) word(24,'inhibits',165,172) word(25,'sigmaD',174,179) word(26,'activity',181,188) lemmas lemma(0,'ComK') lemma(1,'negatively') lemma(2,'control') lemma(3,'the') lemma(4,'transcription') lemma(5,'of') lemma(6,'hag') lemma(7,'by') lemma(8,'stimulate') lemma(9,'the') lemma(10,'transcription') lemma(11,'of') lemma(12,'comF') lemma(13,'flgM') lemma(14,'thereby') lemma(15,'increase') lemma(16,'the') lemma(17,'production') lemma(18,'of') lemma(19,'the') lemma(20,'FlgM') lemma(21,'antisigma') lemma(22,'factor') lemma(23,'that') lemma(24,'inhibit') lemma(25,'sigD') lemma(26,'activity') syntactic_relations relation('mod:V-ADV',15,14) relation('subj:V-N',2,0) relation('subj:V-N',15,0) relation('obj:V-N',15,17) relation('mod_att:N-N',22,20) relation('mod_att:N-N',22,21) relation('obj:V-N',24,26) relation('comp_of:N-N',17,22) relation('obj:V-N',8,10) relation('subj:V-N',24,22) relation('comp_by:V-V',2,8) relation('mod:V-ADV',2,1) relation('obj:V-N',2,4) relation('comp_of:N-N',10,12) relation('comp_of:N-N',10,13) relation('comp_of:N-N',4,6) relation('mod_att:N-N',26,25) agents agent(0) agent(20) targets target(6) target(12) target(13) target(20) target(25) genic_interactions genic_interaction(0,6) genic_interaction(0,12) genic_interaction(0,13) genic_interaction(0,20) genic_interaction(20,25) ID 9696771-4 sentence This stress-induced increase in ykzA expression is absolutely dependent on the alternative sigma factor sigmaB, which controls a large stationary-phase and stress regulon. words word(0,'This',0,3) word(1,'stress-induced',5,18) word(2,'increase',20,27) word(3,'in',29,30) word(4,'ykzA',32,35) word(5,'expression',37,46) word(6,'is',48,49) word(7,'absolutely',51,60) word(8,'dependent',62,70) word(9,'on',72,73) word(10,'the',75,77) word(11,'alternative',79,89) word(12,'sigma',91,95) word(13,'factor',97,102) word(14,'sigmaB',104,109) word(15,'which',112,116) word(16,'controls',118,125) word(17,'a',127,127) word(18,'large',129,133) word(19,'stationary-phase',135,150) word(20,'and',152,154) word(21,'stress',156,161) word(22,'regulon',163,169) lemmas lemma(0,'this') lemma(1,'stress-induced') lemma(2,'increase') lemma(3,'in') lemma(4,'ykzA') lemma(5,'expression') lemma(6,'be') lemma(7,'absolutely') lemma(8,'dependent') lemma(9,'on') lemma(10,'the') lemma(11,'alternative') lemma(12,'sigma') lemma(13,'factor') lemma(14,'sigB') lemma(15,'which') lemma(16,'control') lemma(17,'a') lemma(18,'large') lemma(19,'stationary-phase') lemma(20,'and') lemma(21,'stress') lemma(22,'regulon') syntactic_relations relation('mod:ADJ-ADV',8,7) relation('comp_on:ADJ-N',8,14) relation('mod_att:N-N',13,12) relation('mod_att:N-ADJ',2,1) relation('comp_in:N-N',2,5) relation('mod_att:N-N',5,4) relation('mod_pred:N-ADJ',2,8) relation('mod_att:N-ADJ',13,11) relation('mod_att:N-N',14,13) relation('obj:V-N',16,19) relation('subj:V-N',16,14) relation('mod_att:N-ADJ',19,18) relation('obj:V-N',16,22) relation('mod_att:N-N',22,21) agents agent(14) targets target(4) genic_interactions genic_interaction(14,4) ID 9636707-8 sentence sigma X also contributes to the expression of CsbB, a putative membrane-bound glucosyl transferase that is partially controlled by the sigma B stress response sigma factor. words word(0,'sigma X',0,6) word(1,'also',8,11) word(2,'contributes',13,23) word(3,'to',25,26) word(4,'the',28,30) word(5,'expression',32,41) word(6,'of',43,44) word(7,'CsbB',46,49) word(8,'a',52,52) word(9,'putative',54,61) word(10,'membrane-bound',63,76) word(11,'glucosyl',78,85) word(12,'transferase',87,97) word(13,'that',99,102) word(14,'is',104,105) word(15,'partially',107,115) word(16,'controlled',117,126) word(17,'by',128,129) word(18,'the',131,133) word(19,'sigma B',135,141) word(20,'stress',143,148) word(21,'response',150,157) word(22,'sigma',159,163) word(23,'factor',165,170) lemmas lemma(0,'sigX') lemma(1,'also') lemma(2,'contribute') lemma(3,'to') lemma(4,'the') lemma(5,'expression') lemma(6,'of') lemma(7,'CsbB') lemma(8,'a') lemma(9,'putative') lemma(10,'membrane-bound') lemma(11,'glucosyl') lemma(12,'transferase') lemma(13,'that') lemma(14,'be') lemma(15,'partially') lemma(16,'control') lemma(17,'by') lemma(18,'the') lemma(19,'sigB') lemma(20,'stress') lemma(21,'response') lemma(22,'sigma') lemma(23,'factor') syntactic_relations relation('subj:V-N',2,0) relation('comp_to:V-N',2,5) relation('mod:V-ADV',2,1) relation('comp_of:N-N',5,7) relation('appos',7,12) relation('mod_att:N-ADJ',12,9) relation('mod_att:N-ADJ',12,11) relation('mod_att:N-ADJ',12,10) relation('subj:V_PASS-N',16,12) relation('mod:V_PASS-ADV',16,15) relation('comp_by:V_PASS-N',16,23) relation('mod_att:N-N',23,19) relation('mod_att:N-N',23,22) relation('mod_att:N-N',23,21) relation('mod_att:N-N',21,20) agents agent(0) agent(19) targets target(7) genic_interactions genic_interaction(0,7) genic_interaction(19,7) ID 9271869-4 sentence Transcriptional studies showed that nadE is strongly induced in response to heat, ethanol and salt stress or after starvation for glucose in a sigma B-dependent manner. words word(0,'Transcriptional',0,14) word(1,'studies',16,22) word(2,'showed',24,29) word(3,'that',31,34) word(4,'nadE',36,39) word(5,'is',41,42) word(6,'strongly',44,51) word(7,'induced',53,59) word(8,'in',61,62) word(9,'response',64,71) word(10,'to',73,74) word(11,'heat',76,79) word(12,'ethanol',82,88) word(13,'and',90,92) word(14,'salt',94,97) word(15,'stress',99,104) word(16,'or',106,107) word(17,'after',109,113) word(18,'starvation',115,124) word(19,'for',126,128) word(20,'glucose',130,136) word(21,'in',138,139) word(22,'a',141,141) word(23,'sigma B',143,149) word(24,'dependent',151,159) word(25,'manner',161,166) lemmas lemma(0,'transcriptional') lemma(1,'study') lemma(2,'show') lemma(3,'that') lemma(4,'nadE') lemma(5,'be') lemma(6,'strongly') lemma(7,'induce') lemma(8,'in') lemma(9,'response') lemma(10,'to') lemma(11,'heat') lemma(12,'ethanol') lemma(13,'and') lemma(14,'salt') lemma(15,'stress') lemma(16,'or') lemma(17,'after') lemma(18,'starvation') lemma(19,'for') lemma(20,'glucose') lemma(21,'in') lemma(22,'a') lemma(23,'sigB') lemma(24,'dependent') lemma(25,'manner') syntactic_relations relation('mod:ADJ-N',24,23) relation('comp_in:V_PASS-N',7,9) relation('comp_to:N-N',9,15) relation('comp_after:V_PASS-N',7,18) relation('comp_for:N-N',18,20) relation('comp_in:V_PASS-N',7,25) relation('subj:V_PASS-N',7,4) relation('mod_att:N-ADJ',1,0) relation('mod_att:N-N',15,14) relation('mod:V_PASS-ADV',7,6) relation('subj:V-N',2,1) relation('mod_att:N-N',15,12) relation('mod_att:N-N',15,11) relation('mod_att:N-ADJ',25,24) agents agent(23) targets target(4) genic_interactions genic_interaction(23,4) ID 10913081-11 sentence Furthermore, YtxH and YvyD seemed to be induced after phosphate starvation in the wild type in a sigma(B)-dependent manner and in the sigB mutant probably via sigma(H). words word(0,'Furthermore',0,10) word(1,'YtxH',13,16) word(2,'and',18,20) word(3,'YvyD',22,25) word(4,'seemed',27,32) word(5,'to',34,35) word(6,'be',37,38) word(7,'induced',40,46) word(8,'after',48,52) word(9,'phosphate',54,62) word(10,'starvation',64,73) word(11,'in',75,76) word(12,'the',78,80) word(13,'wild',82,85) word(14,'type',87,90) word(15,'in',92,93) word(16,'a',95,95) word(17,'sigma(B)',97,104) word(18,'dependent',106,114) word(19,'manner',116,121) word(20,'and',123,125) word(21,'in',127,128) word(22,'the',130,132) word(23,'sigB',134,137) word(24,'mutant',139,144) word(25,'probably',146,153) word(26,'via',155,157) word(27,'sigma(H)',159,166) lemmas lemma(0,'furthermore') lemma(1,'YtxH') lemma(2,'and') lemma(3,'YvyD') lemma(4,'seem') lemma(5,'to') lemma(6,'be') lemma(7,'induce') lemma(8,'after') lemma(9,'phosphate') lemma(10,'starvation') lemma(11,'in') lemma(12,'the') lemma(13,'wild') lemma(14,'type') lemma(15,'in') lemma(16,'a') lemma(17,'sigB') lemma(18,'dependent') lemma(19,'manner') lemma(20,'and') lemma(21,'in') lemma(22,'the') lemma(23,'sigB') lemma(24,'mutant') lemma(25,'probably') lemma(26,'via') lemma(27,'sigH') syntactic_relations relation('comp_in:V_PASS-N',7,24) relation('comp_in:V_PASS-N',7,19) relation('comp_in:V_PASS-N',7,14) relation('mod_att:N-N',10,9) relation('mod_att:N-ADJ',19,18) relation('mod_att:N-N',24,23) relation('mod:V-ADV',4,0) relation('mod_att:N-ADJ',14,13) relation('comp_via:V_PASS-N',7,27) relation('comp_after:V_PASS-N',7,10) relation('subj:V_PASS-N',1,7) relation('subj:V_PASS-N',3,7) relation('mod:V-ADV',7,25) relation('mod:ADJ-N',18,17) agents agent(17) agent(27) targets target(1) target(3) genic_interactions genic_interaction(17,1) genic_interaction(17,3) genic_interaction(27,1) genic_interaction(27,3) ID 10747015-5 sentence Localization of SpoIIE was shown to be dependent on the essential cell division protein FtsZ. words word(0,'Localization',0,11) word(1,'of',13,14) word(2,'SpoIIE',16,21) word(3,'was',23,25) word(4,'shown',27,31) word(5,'to',33,34) word(6,'be',36,37) word(7,'dependent',39,47) word(8,'on',49,50) word(9,'the',52,54) word(10,'essential',56,64) word(11,'cell',66,69) word(12,'division',71,78) word(13,'protein',80,86) word(14,'FtsZ',88,91) lemmas lemma(0,'localization') lemma(1,'of') lemma(2,'SpoIIE') lemma(3,'be') lemma(4,'show') lemma(5,'to') lemma(6,'be') lemma(7,'dependent') lemma(8,'on') lemma(9,'the') lemma(10,'essential') lemma(11,'cell') lemma(12,'division') lemma(13,'protein') lemma(14,'FtsZ') syntactic_relations relation('comp_of:N-N',0,2) relation('mod_att:N-ADJ',13,10) relation('mod_pred:N-ADJ',0,7) relation('mod_att:N-N',14,13) relation('mod_att:N-N',12,11) relation('mod_att:N-N',13,12) relation('comp_on:ADJ-N',7,14) agents agent(14) targets target(2) genic_interactions genic_interaction(14,2) ID 10094682-7 sentence The expression of the bkd operon was induced by the presence of isoleucine or valine in the growth medium and depended upon the presence of the sigma factor SigL, a member of the sigma 54 family. words word(0,'The',0,2) word(1,'expression',4,13) word(2,'of',15,16) word(3,'the',18,20) word(4,'bkd',22,24) word(5,'operon',26,31) word(6,'was',33,35) word(7,'induced',37,43) word(8,'by',45,46) word(9,'the',48,50) word(10,'presence',52,59) word(11,'of',61,62) word(12,'isoleucine',64,73) word(13,'or',75,76) word(14,'valine',78,83) word(15,'in',85,86) word(16,'the',88,90) word(17,'growth',92,97) word(18,'medium',99,104) word(19,'and',106,108) word(20,'depended',110,117) word(21,'upon',119,122) word(22,'the',124,126) word(23,'presence',128,135) word(24,'of',137,138) word(25,'the',140,142) word(26,'sigma',144,148) word(27,'factor',150,155) word(28,'SigL',157,160) word(29,'a',163,163) word(30,'member',165,170) word(31,'of',172,173) word(32,'the',175,177) word(33,'sigma 54',179,186) word(34,'family',188,193) lemmas lemma(0,'the') lemma(1,'expression') lemma(2,'of') lemma(3,'the') lemma(4,'bkd') lemma(5,'operon') lemma(6,'be') lemma(7,'induce') lemma(8,'by') lemma(9,'the') lemma(10,'presence') lemma(11,'of') lemma(12,'isoleucine') lemma(13,'or') lemma(14,'valine') lemma(15,'in') lemma(16,'the') lemma(17,'growth') lemma(18,'medium') lemma(19,'and') lemma(20,'depend') lemma(21,'upon') lemma(22,'the') lemma(23,'presence') lemma(24,'of') lemma(25,'the') lemma(26,'sigma') lemma(27,'factor') lemma(28,'SigL') lemma(29,'a') lemma(30,'member') lemma(31,'of') lemma(32,'the') lemma(33,'sigN') lemma(34,'family') syntactic_relations relation('comp_by:V_PASS-N',7,10) relation('comp_of:N-N',10,12) relation('comp_of:N-N',10,14) relation('subj:V-N',20,1) relation('mod_att:N-N',34,33) relation('comp_of:N-N',30,34) relation('mod_att:N-N',5,4) relation('comp_of:N-N',23,28) relation('mod_att:N-N',27,26) relation('mod_att:N-N',18,17) relation('comp_of:N-N',1,5) relation('mod_att:N-N',28,27) relation('subj:V_PASS-N',7,1) relation('appos',28,30) relation('comp_upon:V_PASS-N',20,23) relation('comp_in:N-N',10,18) agents agent(28) targets target(4) genic_interactions genic_interaction(28,4) ID 9108277-9 sentence From these results we conclude that ComK negatively regulates degR expression by preventing sigmaD-driven transcription of degR, possibly through interaction with the control region. words word(0,'From',0,3) word(1,'these',5,9) word(2,'results',11,17) word(3,'we',19,20) word(4,'conclude',22,29) word(5,'that',31,34) word(6,'ComK',36,39) word(7,'negatively',41,50) word(8,'regulates',52,60) word(9,'degR',62,65) word(10,'expression',67,76) word(11,'by',78,79) word(12,'preventing',81,90) word(13,'sigmaD',92,97) word(14,'driven',99,104) word(15,'transcription',106,118) word(16,'of',120,121) word(17,'degR',123,126) word(18,'possibly',129,136) word(19,'through',138,144) word(20,'interaction',146,156) word(21,'with',158,161) word(22,'the',163,165) word(23,'control',167,173) word(24,'region',175,180) lemmas lemma(0,'from') lemma(1,'these') lemma(2,'result') lemma(3,'we') lemma(4,'conclude') lemma(5,'that') lemma(6,'ComK') lemma(7,'negatively') lemma(8,'regulate') lemma(9,'degR') lemma(10,'expression') lemma(11,'by') lemma(12,'prevent') lemma(13,'sigD') lemma(14,'drive') lemma(15,'transcription') lemma(16,'of') lemma(17,'degR') lemma(18,'possibly') lemma(19,'through') lemma(20,'interaction') lemma(21,'with') lemma(22,'the') lemma(23,'control') lemma(24,'region') syntactic_relations relation('mod_att:N-N',10,9) relation('comp_by:V-V',8,12) relation('mod:V-ADV',8,7) relation('comp_with:N-N',20,24) relation('comp_of:N-N',15,17) relation('subj:V-N',4,3) relation('obj:V-N',12,15) relation('comp_from:V-N',4,2) relation('obj:V-N',8,10) relation('subj:V-N',8,6) relation('mod:ADJ-N',14,13) relation('mod_att:N-ADJ',15,14) relation('mod_att:N-N',24,23) relation('comp_through:V-N',12,20) relation('mod:V-ADV',12,18) agents agent(6) agent(13) targets target(9) target(13) target(17) genic_interactions genic_interaction(6,9) genic_interaction(6,13) genic_interaction(13,17) genic_interaction(6,17) %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % % % GENIC INTERACTION EXPRESSED BY A PROTEIN BINDING TO A TARGET GENE PROMOTER % % % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% ID 9139908-4 sentence We overproduced and purified sigma(X) from Escherichia coli and demonstrate that in vitro, both sigma(A) and sigma(X) holoenzymes recognize promoter elements within the sigX-ypuN control region. words word(0,'We',0,1) word(1,'overproduced',3,14) word(2,'and',16,18) word(3,'purified',20,27) word(4,'sigma(X)',29,36) word(5,'from',38,41) word(6,'Escherichia coli',43,58) word(7,'and',60,62) word(8,'demonstrate',64,74) word(9,'that',76,79) word(10,'in',81,82) word(11,'vitro',84,88) word(12,'both',91,94) word(13,'sigma(A)',96,103) word(14,'and',105,107) word(15,'sigma(X)',109,116) word(16,'holoenzymes',118,128) word(17,'recognize',130,138) word(18,'promoter',140,147) word(19,'elements',149,156) word(20,'within',158,163) word(21,'the',165,167) word(22,'sigX',169,172) word(23,'ypuN',174,177) word(24,'control',179,185) word(25,'region',187,192) lemmas lemma(0,'we') lemma(1,'overproduce') lemma(2,'and') lemma(3,'purify') lemma(4,'sigX') lemma(5,'from') lemma(6,'Escherichia coli') lemma(7,'and') lemma(8,'demonstrate') lemma(9,'that') lemma(10,'in') lemma(11,'vitro') lemma(12,'both') lemma(13,'sigA') lemma(14,'and') lemma(15,'sigX') lemma(16,'holoenzyme') lemma(17,'recognize') lemma(18,'promoter') lemma(19,'element') lemma(20,'within') lemma(21,'the') lemma(22,'sigX') lemma(23,'ypuN') lemma(24,'control') lemma(25,'region') syntactic_relations relation('comp_in:V-N',17,11) relation('mod_att:N-N',25,24) relation('subj:V-N',8,0) relation('comp_from:V-N',3,6) relation('comp_from:V-N',1,6) relation('mod_att:N-N',19,18) relation('obj:V-N',17,19) relation('mod_att:N-N',16,13) relation('subj:V-N',1,0) relation('comp_within:N-N',19,25) relation('obj:V-N',1,4) relation('obj:V-N',3,4) relation('subj:V-N',3,0) relation('subj:V-N',17,16) relation('mod_att:N-N',16,15) relation('mod_att:N-N',23,22) relation('mod_att:N-N',25,23) agents agent(13) agent(15) targets target(22) target(23) genic_interactions genic_interaction(13,22) genic_interaction(15,22) genic_interaction(13,23) genic_interaction(15,23) ID 9401028-7 sentence Transcriptional studies demonstrated that the expression from the araE promoter is induced by L-arabinose, repressed by glucose, and negatively regulated by AraR. words word(0,'Transcriptional',0,14) word(1,'studies',16,22) word(2,'demonstrated',24,35) word(3,'that',37,40) word(4,'the',42,44) word(5,'expression',46,55) word(6,'from',57,60) word(7,'the',62,64) word(8,'araE',66,69) word(9,'promoter',71,78) word(10,'is',80,81) word(11,'induced',83,89) word(12,'by',91,92) word(13,'L-arabinose',94,104) word(14,'repressed',107,115) word(15,'by',117,118) word(16,'glucose',120,126) word(17,'and',129,131) word(18,'negatively',133,142) word(19,'regulated',144,152) word(20,'by',154,155) word(21,'AraR',157,160) lemmas lemma(0,'transcriptional') lemma(1,'study') lemma(2,'demonstrate') lemma(3,'that') lemma(4,'the') lemma(5,'expression') lemma(6,'from') lemma(7,'the') lemma(8,'araE') lemma(9,'promoter') lemma(10,'be') lemma(11,'induce') lemma(12,'by') lemma(13,'L-arabinose') lemma(14,'repress') lemma(15,'by') lemma(16,'glucose') lemma(17,'and') lemma(18,'negatively') lemma(19,'regulate') lemma(20,'by') lemma(21,'AraR') syntactic_relations relation('mod:V_PASS-ADV',19,18) relation('subj:V_PASS-N',11,5) relation('comp_by:V_PASS-N',14,16) relation('mod_att:N-ADJ',1,0) relation('mod_att:N-N',9,8) relation('subj:V-N',2,1) relation('subj:V_PASS-N',19,5) relation('subj:V_PASS-N',14,5) relation('comp_by:V_PASS-N',19,21) relation('comp_by:V_PASS-N',11,13) relation('comp_from:N-N',5,9) agents agent(21) targets target(8) genic_interactions genic_interaction(21,8) ID 9683469-3 sentence A sigmaW-dependent promoter (PW) precedes sigW, demonstrating that this transcription factor is positively autoregulated. words word(0,'A',0,0) word(1,'sigmaW',2,7) word(2,'dependent',9,17) word(3,'promoter',19,26) word(4,'PW',29,30) word(5,'precedes',33,40) word(6,'sigW',42,45) word(7,'demonstrating',48,60) word(8,'that',62,65) word(9,'this',67,70) word(10,'transcription',72,84) word(11,'factor',86,91) word(12,'is',93,94) word(13,'positively',96,105) word(14,'autoregulated',107,119) lemmas lemma(0,'a') lemma(1,'sigW') lemma(2,'dependent') lemma(3,'promoter') lemma(4,'PW') lemma(5,'precede') lemma(6,'sigW') lemma(7,'demonstrate') lemma(8,'that') lemma(9,'this') lemma(10,'transcription') lemma(11,'factor') lemma(12,'be') lemma(13,'positively') lemma(14,'autoregulated') syntactic_relations relation('obj:V-N',5,6) relation('mod_att:N-ADJ',3,2) relation('appos',3,4) relation('subj:V-N',5,3) relation('subj:V_PASS-N',14,11) relation('mod:V_PASS-ADV',14,13) relation('mod:ADJ-N',2,1) relation('mod_att:N-N',11,10) agents agent(1) targets target(6) genic_interactions genic_interaction(1,6) ID 9683503-1 sentence The results indicate that PhoP~P is sufficient to repress the transcription of the tagA and tagD promoters and also to activate the transcription of the tuaA promoter. words word(0,'The',0,2) word(1,'results',4,10) word(2,'indicate',12,19) word(3,'that',21,24) word(4,'PhoP~P',26,31) word(5,'is',33,34) word(6,'sufficient',36,45) word(7,'to',47,48) word(8,'repress',50,56) word(9,'the',58,60) word(10,'transcription',62,74) word(11,'of',76,77) word(12,'the',79,81) word(13,'tagA',83,86) word(14,'and',88,90) word(15,'tagD',92,95) word(16,'promoters',97,105) word(17,'and',107,109) word(18,'also',111,114) word(19,'to',116,117) word(20,'activate',119,126) word(21,'the',128,130) word(22,'transcription',132,144) word(23,'of',146,147) word(24,'the',149,151) word(25,'tuaA',153,156) word(26,'promoter',158,165) lemmas lemma(0,'the') lemma(1,'result') lemma(2,'indicate') lemma(3,'that') lemma(4,'PhoP~P') lemma(5,'be') lemma(6,'sufficient') lemma(7,'to') lemma(8,'repress') lemma(9,'the') lemma(10,'transcription') lemma(11,'of') lemma(12,'the') lemma(13,'tagA') lemma(14,'and') lemma(15,'tagD') lemma(16,'promoter') lemma(17,'and') lemma(18,'also') lemma(19,'to') lemma(20,'activate') lemma(21,'the') lemma(22,'transcription') lemma(23,'of') lemma(24,'the') lemma(25,'tuaA') lemma(26,'promoter') syntactic_relations relation('obj:V-N',20,22) relation('comp_of:N-N',10,16) relation('comp_of:N-N',22,26) relation('mod_pred:N-ADJ',4,6) relation('obj:V-N',8,10) relation('subj:V-N',2,1) relation('mod_att:N-N',16,13) relation('mod_att:N-N',16,15) relation('mod_att:N-N',26,25) relation('comp_to:ADJ-V',6,8) relation('comp_to:ADJ-V',6,20) relation('mod:ADJ-ADV',6,18) agents agent(4) targets target(13) target(15) target(25) genic_interactions genic_interaction(4,13) genic_interaction(4,15) genic_interaction(4,25) ID 9846747-4 sentence Primer extension experiments and Northern blot analysis show that an active sigmaA-dependent promoter precedes kdgR and transcription is terminated at the putative p-independent terminator downstream of kdgT. words word(0,'Primer',0,5) word(1,'extension',7,15) word(2,'experiments',17,27) word(3,'and',29,31) word(4,'Northern',33,40) word(5,'blot',42,45) word(6,'analysis',47,54) word(7,'show',56,59) word(8,'that',61,64) word(9,'an',66,67) word(10,'active',69,74) word(11,'sigmaA',76,81) word(12,'dependent',83,91) word(13,'promoter',93,100) word(14,'precedes',102,109) word(15,'kdgR',111,114) word(16,'and',116,118) word(17,'transcription',120,132) word(18,'is',134,135) word(19,'terminated',137,146) word(20,'at',148,149) word(21,'the',151,153) word(22,'putative',155,162) word(23,'p-independent',164,176) word(24,'terminator',178,187) word(25,'downstream',189,198) word(26,'of',200,201) word(27,'kdgT',203,206) lemmas lemma(0,'prime') lemma(1,'extension') lemma(2,'experiment') lemma(3,'and') lemma(4,'northern') lemma(5,'blot') lemma(6,'analysis') lemma(7,'show') lemma(8,'that') lemma(9,'an') lemma(10,'active') lemma(11,'sigA') lemma(12,'dependent') lemma(13,'promoter') lemma(14,'precede') lemma(15,'kdgR') lemma(16,'and') lemma(17,'transcription') lemma(18,'be') lemma(19,'terminate') lemma(20,'at') lemma(21,'the') lemma(22,'putative') lemma(23,'p-independent') lemma(24,'terminator') lemma(25,'downstream') lemma(26,'of') lemma(27,'kdgT') syntactic_relations relation('mod_att:N-N',1,0) relation('mod_att:N-N',2,1) relation('mod_att:N-N',5,4) relation('mod_att:N-N',6,5) relation('mod:V_PASS-ADV',19,25) relation('mod:ADJ-N',12,11) relation('mod_att:N-ADJ',13,12) relation('mod_att:N-ADJ',13,10) relation('comp_of:ADV-N',25,27) relation('subj:V-N',7,6) relation('subj:V-N',7,2) relation('obj:V-N',14,15) relation('mod_att:N-ADJ',24,22) relation('subj:V-N',14,13) relation('mod_att:N-ADJ',24,23) relation('subj:V_PASS-N',19,17) relation('comp_at:V-N',19,24) agents agent(11) targets target(15) genic_interactions genic_interaction(11,15) ID 9852014-4 sentence The sigmaB-dependent promoter drives expression of yvyD under stress conditions and after glucose starvation, whereas a sigmaH-dependent promoter is responsible for yvyD transcription following amino acid limitation. words word(0,'The',0,2) word(1,'sigmaB',4,9) word(2,'dependent',11,19) word(3,'promoter',21,28) word(4,'drives',30,35) word(5,'expression',37,46) word(6,'of',48,49) word(7,'yvyD',51,54) word(8,'under',56,60) word(9,'stress',62,67) word(10,'conditions',69,78) word(11,'and',80,82) word(12,'after',84,88) word(13,'glucose',90,96) word(14,'starvation',98,107) word(15,'whereas',110,116) word(16,'a',118,118) word(17,'sigmaH',120,125) word(18,'dependent',127,135) word(19,'promoter',137,144) word(20,'is',146,147) word(21,'responsible',149,159) word(22,'for',161,163) word(23,'yvyD',165,168) word(24,'transcription',170,182) word(25,'following',184,192) word(26,'amino',194,198) word(27,'acid',200,203) word(28,'limitation',205,214) lemmas lemma(0,'the') lemma(1,'sigB') lemma(2,'dependent') lemma(3,'promoter') lemma(4,'drive') lemma(5,'expression') lemma(6,'of') lemma(7,'yvyD') lemma(8,'under') lemma(9,'stress') lemma(10,'condition') lemma(11,'and') lemma(12,'after') lemma(13,'glucose') lemma(14,'starvation') lemma(15,'whereas') lemma(16,'a') lemma(17,'sigH') lemma(18,'dependent') lemma(19,'promoter') lemma(20,'be') lemma(21,'responsible') lemma(22,'for') lemma(23,'yvyD') lemma(24,'transcription') lemma(25,'follow') lemma(26,'amino') lemma(27,'acid') lemma(28,'limitation') syntactic_relations relation('mod:ADJ-N',18,17) relation('mod_att:N-ADJ',19,18) relation('mod:ADJ-N',2,1) relation('mod_att:N-ADJ',3,2) relation('mod_att:N-N',28,27) relation('mod_att:N-ADJ',27,26) relation('obj:V-N',4,5) relation('comp_after:V-N',4,14) relation('mod_att:N-N',10,9) relation('mod_att:N-N',14,13) relation('subj:V-N',4,3) relation('obj:V-N',25,28) relation('comp_of:N-N',5,7) relation('mod_att:N-N',24,23) relation('comp_under:V-N',4,10) relation('comp_for:ADJ-N',21,24) relation('subj:V-N',25,24) relation('mod_pred:N-ADJ',19,21) agents agent(1) agent(17) targets target(7) target(23) genic_interactions genic_interaction(1,7) genic_interaction(17,23) ID 9852015-1 sentence The Bacillus subtilis clpC operon is regulated by two stress induction pathways relying on either sigmaB or a class III stress induction mechanism acting at a sigmaA-like promoter. words word(0,'The',0,2) word(1,'Bacillus subtilis',4,20) word(2,'clpC',22,25) word(3,'operon',27,32) word(4,'is',34,35) word(5,'regulated',37,45) word(6,'by',47,48) word(7,'two',50,52) word(8,'stress',54,59) word(9,'induction',61,69) word(10,'pathways',71,78) word(11,'relying',80,86) word(12,'on',88,89) word(13,'either',91,96) word(14,'sigmaB',98,103) word(15,'or',105,106) word(16,'a',108,108) word(17,'class',110,114) word(18,'III',116,118) word(19,'stress',120,125) word(20,'induction',127,135) word(21,'mechanism',137,145) word(22,'acting',147,152) word(23,'at',154,155) word(24,'a',157,157) word(25,'sigmaA',159,164) word(26,'like',166,169) word(27,'promoter',171,178) lemmas lemma(0,'the') lemma(1,'Bacillus subtilis') lemma(2,'mecB') lemma(3,'operon') lemma(4,'be') lemma(5,'regulate') lemma(6,'by') lemma(7,'two') lemma(8,'stress') lemma(9,'induction') lemma(10,'pathway') lemma(11,'rely') lemma(12,'on') lemma(13,'either') lemma(14,'sigB') lemma(15,'or') lemma(16,'a') lemma(17,'class') lemma(18,'III') lemma(19,'stress') lemma(20,'induction') lemma(21,'mechanism') lemma(22,'act') lemma(23,'at') lemma(24,'a') lemma(25,'sigA') lemma(26,'like') lemma(27,'promoter') syntactic_relations relation('subj:V-N',22,21) relation('mod_att:N-N',10,9) relation('mod_att:N-N',9,8) relation('mod_att:N-N',21,20) relation('subj:V-N',11,10) relation('mod_att:N-N',21,17) relation('comp_on:V-N',11,14) relation('mod_att:N-ADJ',27,26) relation('mod:ADJ-N',26,25) relation('comp_by:V_PASS-N',5,10) relation('mod_att:N-N',20,19) relation('comp_at:V-N',22,27) relation('mod_att:N-N',3,1) relation('subj:V_PASS-N',5,3) relation('mod_post:N-ADJ',17,18) relation('comp_on:V-N',11,21) relation('mod_att:N-N',3,2) agents agent(14) agent(25) targets target(2) genic_interactions genic_interaction(14,2) genic_interaction(25,2) ID 10075739-5 sentence Here, we show that GerE binds near the sigK transcriptional start site, to act as a repressor. words word(0,'Here',0,3) word(1,'we',6,7) word(2,'show',9,12) word(3,'that',14,17) word(4,'GerE',19,22) word(5,'binds',24,28) word(6,'near',30,33) word(7,'the',35,37) word(8,'sigK',39,42) word(9,'transcriptional',44,58) word(10,'start',60,64) word(11,'site',66,69) word(12,'to',72,73) word(13,'act',75,77) word(14,'as',79,80) word(15,'a',82,82) word(16,'repressor',84,92) lemmas lemma(0,'here') lemma(1,'we') lemma(2,'show') lemma(3,'that') lemma(4,'GerE') lemma(5,'bind') lemma(6,'near') lemma(7,'the') lemma(8,'sigK') lemma(9,'transcriptional') lemma(10,'start') lemma(11,'site') lemma(12,'to') lemma(13,'act') lemma(14,'as') lemma(15,'a') lemma(16,'represser') syntactic_relations relation('subj:V-N',5,4) relation('subj:V-N',13,4) relation('comp_as:V-N',13,16) relation('mod:V-ADV',2,0) relation('mod_att:N-N',11,8) relation('comp_near:V-N',5,11) relation('mod_att:N-N',11,10) relation('mod_att:N-ADJ',11,9) relation('subj:V-N',2,1) relation('comp_to:V-V',5,13) agents agent(4) targets target(8) genic_interactions genic_interaction(4,8) ID 10075739-9 sentence We show that GerE binds to two sites that span the -35 region of the cotD promoter. words word(0,'We',0,1) word(1,'show',3,6) word(2,'that',8,11) word(3,'GerE',13,16) word(4,'binds',18,22) word(5,'to',24,25) word(6,'two',27,29) word(7,'sites',31,35) word(8,'that',37,40) word(9,'span',42,45) word(10,'the',47,49) word(11,'-35',51,53) word(12,'region',55,60) word(13,'of',62,63) word(14,'the',65,67) word(15,'cotD',69,72) word(16,'promoter',74,81) lemmas lemma(0,'we') lemma(1,'show') lemma(2,'that') lemma(3,'GerE') lemma(4,'bind') lemma(5,'to') lemma(6,'two') lemma(7,'site') lemma(8,'that') lemma(9,'span') lemma(10,'the') lemma(11,'-35') lemma(12,'region') lemma(13,'of') lemma(14,'the') lemma(15,'cotD') lemma(16,'promoter') syntactic_relations relation('mod_att:N-N',16,15) relation('subj:V-N',9,7) relation('comp_to:V-N',4,7) relation('subj:V-N',4,3) relation('comp_of:N-N',12,16) relation('subj:V-N',1,0) relation('obj:V-N',9,12) relation('mod_att:N-ADJ',12,11) relation('mod_att:N-ADJ',7,6) agents agent(3) targets target(15) genic_interactions genic_interaction(3,15) ID 10383978-8 sentence The ald promoter, like the sigE promoter, is believed to be recognized by sigmaA RNA polymerase, suggesting that sigmaK may inhibit sigmaA activity late in sporulation. words word(0,'The',0,2) word(1,'ald',4,6) word(2,'promoter',8,15) word(3,'like',18,21) word(4,'the',23,25) word(5,'sigE',27,30) word(6,'promoter',32,39) word(7,'is',42,43) word(8,'believed',45,52) word(9,'to',54,55) word(10,'be',57,58) word(11,'recognized',60,69) word(12,'by',71,72) word(13,'sigmaA',74,79) word(14,'RNA',81,83) word(15,'polymerase',85,94) word(16,'suggesting',97,106) word(17,'that',108,111) word(18,'sigmaK',113,118) word(19,'may',120,122) word(20,'inhibit',124,130) word(21,'sigmaA',132,137) word(22,'activity',139,146) word(23,'late',148,151) word(24,'in',153,154) word(25,'sporulation',156,166) lemmas lemma(0,'the') lemma(1,'ald') lemma(2,'promoter') lemma(3,'like') lemma(4,'the') lemma(5,'sigE') lemma(6,'promoter') lemma(7,'be') lemma(8,'believe') lemma(9,'to') lemma(10,'be') lemma(11,'recognize') lemma(12,'by') lemma(13,'sigA') lemma(14,'RNA') lemma(15,'polymerase') lemma(16,'suggest') lemma(17,'that') lemma(18,'sigK') lemma(19,'may') lemma(20,'inhibit') lemma(21,'sigA') lemma(22,'activity') lemma(23,'late') lemma(24,'in') lemma(25,'sporulation') syntactic_relations relation('comp_by:V_PASS-N',11,15) relation('mod_att:N-N',22,21) relation('obj:V-N',20,22) relation('mod_att:N-N',15,14) relation('mod_att:N-N',15,13) relation('subj:V-N',20,18) relation('subj:V_PASS-N',11,2) relation('mod_att:N-N',2,1) relation('mod_att:N-N',6,5) relation('comp_like:V_PASS-N',11,6) relation('mod:V-ADV',20,23) relation('comp_in:ADV-N',23,25) agents agent(13) agent(18) targets target(1) target(21) genic_interactions genic_interaction(13,1) genic_interaction(18,21) ID 10400595-1 sentence During endospore formation in Bacillus subtilis, the DNA binding protein GerE stimulates transcription from several promoters that are used by RNA polymerase containing sigmaK words word(0,'During',0,5) word(1,'endospore',7,15) word(2,'formation',17,25) word(3,'in',27,28) word(4,'Bacillus subtilis',30,46) word(5,'the',49,51) word(6,'DNA',53,55) word(7,'binding',57,63) word(8,'protein',65,71) word(9,'GerE',73,76) word(10,'stimulates',78,87) word(11,'transcription',89,101) word(12,'from',103,106) word(13,'several',108,114) word(14,'promoters',116,124) word(15,'that',126,129) word(16,'are',131,133) word(17,'used',135,138) word(18,'by',140,141) word(19,'RNA',143,145) word(20,'polymerase',147,156) word(21,'containing',158,167) word(22,'sigmaK',169,174) lemmas lemma(0,'during') lemma(1,'endospore') lemma(2,'formation') lemma(3,'in') lemma(4,'Bacillus subtilis') lemma(5,'the') lemma(6,'DNA') lemma(7,'binding') lemma(8,'protein') lemma(9,'GerE') lemma(10,'stimulate') lemma(11,'transcription') lemma(12,'from') lemma(13,'several') lemma(14,'promoter') lemma(15,'that') lemma(16,'be') lemma(17,'use') lemma(18,'by') lemma(19,'RNA') lemma(20,'polymerase') lemma(21,'contain') lemma(22,'sigK') syntactic_relations relation('subj:V-N',21,20) relation('mod_att:N-N',9,8) relation('obj:V-N',21,22) relation('mod_att:N-N',20,19) relation('comp_during:V-N',10,2) relation('mod:ADJ-N',7,6) relation('subj:V_PASS-N',17,14) relation('comp_in:N-N',2,4) relation('comp_by:V_PASS-N',17,20) relation('mod_att:N-ADJ',2,1) relation('obj:V-N',10,11) relation('comp_from:N-N',11,14) relation('subj:V-N',10,9) relation('mod_att:N-ADJ',8,7) relation('mod_att:N-ADJ',14,13) agents agent(9) targets target(22) genic_interactions genic_interaction(9,22) ID 10503549-4 sentence The -10 and -35 sequences of the sigmaB- and sigmaF-dependent promoters of katX overlap, and the transcriptional start points used by EsigmaB and EsigmaF differ by only one nucleotide. words word(0,'The',0,2) word(1,'-10',4,6) word(2,'and',8,10) word(3,'-35',12,14) word(4,'sequences',16,24) word(5,'of',26,27) word(6,'the',29,31) word(7,'sigmaB',33,38) word(8,'and',41,43) word(9,'sigmaF',45,50) word(10,'dependent',52,60) word(11,'promoters',62,70) word(12,'of',72,73) word(13,'katX',75,78) word(14,'overlap',80,86) word(15,'and',89,91) word(16,'the',93,95) word(17,'transcriptional',97,111) word(18,'start',113,117) word(19,'points',119,124) word(20,'used',126,129) word(21,'by',131,132) word(22,'EsigmaB',134,140) word(23,'and',142,144) word(24,'EsigmaF',146,152) word(25,'differ',154,159) word(26,'by',161,162) word(27,'only',164,167) word(28,'one',169,171) word(29,'nucleotide',173,182) lemmas lemma(0,'the') lemma(1,'-10') lemma(2,'and') lemma(3,'-35') lemma(4,'sequence') lemma(5,'of') lemma(6,'the') lemma(7,'sigB') lemma(8,'and') lemma(9,'sigF') lemma(10,'dependent') lemma(11,'promoter') lemma(12,'of') lemma(13,'katX') lemma(14,'overlap') lemma(15,'and') lemma(16,'the') lemma(17,'transcriptional') lemma(18,'start') lemma(19,'point') lemma(20,'use') lemma(21,'by') lemma(22,'EsigmaB') lemma(23,'and') lemma(24,'EsigmaF') lemma(25,'differ') lemma(26,'by') lemma(27,'only') lemma(28,'one') lemma(29,'nucleotide') syntactic_relations relation('comp_by:V_PASS-N',20,24) relation('mod_att:N-ADJ',4,1) relation('mod_att:N-ADJ',4,3) relation('comp_of:N-N',4,11) relation('mod_att:N-N',19,18) relation('comp_of:N-N',11,13) relation('subj:V-N',25,19) relation('mod_att:N-ADJ',19,17) relation('subj:V-N',14,4) relation('comp_by:V-N',25,29) relation('comp_by:V_PASS-N',20,22) relation('subj:V_PASS-N',20,19) relation('mod_att:N-ADJ',11,10) relation('mod:ADJ-N',10,9) relation('mod:ADJ-N',10,7) relation('mod:ADJ-ADV',28,27) relation('mod_att:N-ADJ',29,28) agents agent(7) agent(9) targets target(13) genic_interactions genic_interaction(7,13) genic_interaction(9,13) ID 10788508-10 sentence DNase I footprinting showed that SpoIIID binds strongly to two sites in the cotC promoter region, binds weakly to one site in the cotX promoter, and does not bind specifically to cotB. words word(0,'DNase',0,4) word(1,'I',6,6) word(2,'footprinting',8,19) word(3,'showed',21,26) word(4,'that',28,31) word(5,'SpoIIID',33,39) word(6,'binds',41,45) word(7,'strongly',47,54) word(8,'to',56,57) word(9,'two',59,61) word(10,'sites',63,67) word(11,'in',69,70) word(12,'the',72,74) word(13,'cotC',76,79) word(14,'promoter',81,88) word(15,'region',90,95) word(16,'binds',98,102) word(17,'weakly',104,109) word(18,'to',111,112) word(19,'one',114,116) word(20,'site',118,121) word(21,'in',123,124) word(22,'the',126,128) word(23,'cotX',130,133) word(24,'promoter',135,142) word(25,'and',145,147) word(26,'does',149,152) word(27,'not',154,156) word(28,'bind',158,161) word(29,'specifically',163,174) word(30,'to',176,177) word(31,'cotB',179,182) lemmas lemma(0,'DNase') lemma(1,'I') lemma(2,'footprinting') lemma(3,'show') lemma(4,'that') lemma(5,'SpoIIID') lemma(6,'bind') lemma(7,'strongly') lemma(8,'to') lemma(9,'two') lemma(10,'site') lemma(11,'in') lemma(12,'the') lemma(13,'cotC') lemma(14,'promoter') lemma(15,'region') lemma(16,'bind') lemma(17,'weakly') lemma(18,'to') lemma(19,'one') lemma(20,'site') lemma(21,'in') lemma(22,'the') lemma(23,'cotX') lemma(24,'promoter') lemma(25,'and') lemma(26,'do') lemma(27,'not') lemma(28,'bind') lemma(29,'specifically') lemma(30,'to') lemma(31,'cotB') syntactic_relations relation('subj:V-N',28,5) relation('subj:V-N',6,5) relation('comp_in:N-N',10,15) relation('mod:V-ADV',6,7) relation('mod_att:N-N',2,0) relation('mod:V-ADV',28,29) relation('mod:V-ADV',16,17) relation('mod_att:N-N',24,23) relation('comp_in:N-N',20,24) relation('mod_att:N-N',15,14) relation('mod_att:N-N',15,13) relation('subj:V-N',16,5) relation('mod_post:N-ADJ',0,1) relation('comp_to:V-N',28,31) relation('comp_to:V-N',16,20) relation('comp_to:V-N',6,10) relation('subj:V-N',3,2) relation('neg',28,27) relation('mod_att:N-ADJ',10,9) relation('mod_att:N-ADJ',20,19) agents agent(5) targets target(13) target(23) target(31) genic_interactions genic_interaction(5,13) genic_interaction(5,23) genic_interaction(5,31) ID 10801786-5 sentence However, the mutant was unable to stimulate transcription by final sigma(A)-RNA polymerase from the Spo0A-dependent spoIIG operon promoter. words word(0,'However',0,6) word(1,'the',9,11) word(2,'mutant',13,18) word(3,'was',20,22) word(4,'unable',24,29) word(5,'to',31,32) word(6,'stimulate',34,42) word(7,'transcription',44,56) word(8,'by',58,59) word(9,'final',61,65) word(10,'sigma(A)',67,74) word(11,'RNA',76,78) word(12,'polymerase',80,89) word(13,'from',91,94) word(14,'the',96,98) word(15,'Spo0A',100,104) word(16,'dependent',106,114) word(17,'spoIIG',116,121) word(18,'operon',123,128) word(19,'promoter',130,137) lemmas lemma(0,'however') lemma(1,'the') lemma(2,'mutant') lemma(3,'be') lemma(4,'unable') lemma(5,'to') lemma(6,'stimulate') lemma(7,'transcription') lemma(8,'by') lemma(9,'final') lemma(10,'sigA') lemma(11,'RNA') lemma(12,'polymerase') lemma(13,'from') lemma(14,'the') lemma(15,'spo0A') lemma(16,'dependent') lemma(17,'spoIIG') lemma(18,'operon') lemma(19,'promoter') syntactic_relations relation('mod_att:N-ADJ',19,16) relation('mod:ADJ-N',16,15) relation('comp_from:N-N',7,19) relation('mod:V-ADV',3,0) relation('obj:V-N',6,7) relation('mod_att:N-N',19,18) relation('mod_att:N-ADJ',12,11) relation('mod_att:N-ADJ',12,10) relation('mod_pred:N-ADJ',2,4) relation('mod_att:N-N',18,17) relation('comp_by:N-N',7,12) relation('comp_to:ADJ-V',4,6) relation('mod_att:N-ADJ',12,9) agents agent(15) agent(10) targets target(17) target(10) genic_interactions genic_interaction(15,17) genic_interaction(10,17) genic_interaction(15,10) ID 11021934-4 sentence Therefore, ftsY is solely expressed during sporulation from a sigma(K)- and GerE-controlled promoter that is located immediately upstream of ftsY inside the smc gene. words word(0,'Therefore',0,8) word(1,'ftsY',11,14) word(2,'is',16,17) word(3,'solely',19,24) word(4,'expressed',26,34) word(5,'during',36,41) word(6,'sporulation',43,53) word(7,'from',55,58) word(8,'a',60,60) word(9,'sigma(K)',62,69) word(10,'and',72,74) word(11,'GerE',76,79) word(12,'controlled',81,90) word(13,'promoter',92,99) word(14,'that',101,104) word(15,'is',106,107) word(16,'located',109,115) word(17,'immediately',117,127) word(18,'upstream',129,136) word(19,'of',138,139) word(20,'ftsY',141,144) word(21,'inside',146,151) word(22,'the',153,155) word(23,'smc',157,159) word(24,'gene',161,164) lemmas lemma(0,'therefore') lemma(1,'ftsY') lemma(2,'be') lemma(3,'solely') lemma(4,'express') lemma(5,'during') lemma(6,'sporulation') lemma(7,'from') lemma(8,'a') lemma(9,'sigK') lemma(10,'and') lemma(11,'GerE') lemma(12,'controlled') lemma(13,'promoter') lemma(14,'that') lemma(15,'be') lemma(16,'locate') lemma(17,'immediately') lemma(18,'upstream') lemma(19,'of') lemma(20,'ftsY') lemma(21,'inside') lemma(22,'the') lemma(23,'smc') lemma(24,'gene') syntactic_relations relation('mod:ADJ-N',12,11) relation('mod:ADJ-N',12,9) relation('mod_att:N-ADJ',13,12) relation('mod_att:N-N',24,23) relation('comp_of:ADV-N',18,20) relation('comp_inside:V_PASS-N',16,24) relation('comp_during:V_PASS-N',4,6) relation('mod:ADV-ADV',18,17) relation('mod:V_PASS-ADV',16,18) relation('mod:V_PASS-ADV',4,0) relation('mod:V_PASS-ADV',4,3) relation('subj:V_PASS-N',4,1) relation('subj:V_PASS-N',16,13) relation('comp_from:V_PASS-N',4,13) agents agent(9) agent(11) targets target(1) genic_interactions genic_interaction(9,1) genic_interaction(11,1) %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % % % GENIC INTERACTION EXPRESSED BY MEMBERSHIP TO REGULON FAMILY % % % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% ID 10220166-10 sentence The ydaP gene might belong to the increasing number of sigmaB-dependent genes whose orthologues are under the control of sigmas in Escherichia coli, indicating that both regulons may fulfil similar functions. words word(0,'The',0,2) word(1,'ydaP',4,7) word(2,'gene',9,12) word(3,'might',14,18) word(4,'belong',20,25) word(5,'to',27,28) word(6,'the',30,32) word(7,'increasing',34,43) word(8,'number',45,50) word(9,'of',52,53) word(10,'sigmaB',55,60) word(11,'dependent',62,70) word(12,'genes',72,76) word(13,'whose',78,82) word(14,'orthologues',84,94) word(15,'are',96,98) word(16,'under',100,104) word(17,'the',106,108) word(18,'control',110,116) word(19,'of',118,119) word(20,'sigmas',121,126) word(21,'in',128,129) word(22,'Escherichia coli',131,146) word(23,'indicating',149,158) word(24,'that',160,163) word(25,'both',165,168) word(26,'regulons',170,177) word(27,'may',179,181) word(28,'fulfil',183,188) word(29,'similar',190,196) word(30,'functions',198,206) lemmas lemma(0,'the') lemma(1,'ydaP') lemma(2,'gene') lemma(3,'might') lemma(4,'belong') lemma(5,'to') lemma(6,'the') lemma(7,'increase') lemma(8,'number') lemma(9,'of') lemma(10,'sigB') lemma(11,'dependent') lemma(12,'gene') lemma(13,'whose') lemma(14,'orthologues') lemma(15,'be') lemma(16,'under') lemma(17,'the') lemma(18,'control') lemma(19,'of') lemma(20,'sigma') lemma(21,'in') lemma(22,'Escherichia coli') lemma(23,'indicate') lemma(24,'that') lemma(25,'both') lemma(26,'regulons') lemma(27,'may') lemma(28,'fulfill') lemma(29,'similar') lemma(30,'function') syntactic_relations relation('comp_in:V-N',15,22) relation('mod:ADJ-N',11,10) relation('comp_under:V-N',15,18) relation('mod_att:N-ADJ',8,7) relation('subj:V-N',28,26) relation('comp_to:V-N',4,8) relation('mod_att:N-ADJ',12,11) relation('subj:V-N',4,2) relation('comp_of:N-N',18,20) relation('subj:V-N',15,14) relation('mod_att:N-N',2,1) relation('comp_of:N-N',8,12) relation('comp_of:N-N',14,12) relation('obj:V-N',28,30) relation('mod_att:N-ADJ',30,29) agents agent(10) targets target(1) genic_interactions genic_interaction(10,1) ID 9852014-10 sentence This indicates that the yvyD gene product, being a member of both the sigmaB and sigmaH regulons, might negatively regulate the activity of the sigmaL regulon. words word(0,'This',0,3) word(1,'indicates',5,13) word(2,'that',15,18) word(3,'the',20,22) word(4,'yvyD',24,27) word(5,'gene',29,32) word(6,'product',34,40) word(7,'being',43,47) word(8,'a',49,49) word(9,'member',51,56) word(10,'of',58,59) word(11,'both',61,64) word(12,'the',66,68) word(13,'sigmaB',70,75) word(14,'and',77,79) word(15,'sigmaH',81,86) word(16,'regulons',88,95) word(17,'might',98,102) word(18,'negatively',104,113) word(19,'regulate',115,122) word(20,'the',124,126) word(21,'activity',128,135) word(22,'of',137,138) word(23,'the',140,142) word(24,'sigmaL',144,149) word(25,'regulon',151,157) lemmas lemma(0,'this') lemma(1,'indicate') lemma(2,'that') lemma(3,'the') lemma(4,'yvyD') lemma(5,'gene') lemma(6,'product') lemma(7,'being') lemma(8,'a') lemma(9,'member') lemma(10,'of') lemma(11,'both') lemma(12,'the') lemma(13,'sigB') lemma(14,'and') lemma(15,'sigH') lemma(16,'regulons') lemma(17,'might') lemma(18,'negatively') lemma(19,'regulate') lemma(20,'the') lemma(21,'activity') lemma(22,'of') lemma(23,'the') lemma(24,'sigL') lemma(25,'regulon') syntactic_relations relation('mod:V-ADV',19,18) relation('mod_att:N-N',16,13) relation('mod_att:N-N',6,5) relation('mod_att:N-N',5,4) relation('mod_att:N-N',25,24) relation('comp_of:N-N',21,25) relation('obj:V-N',19,21) relation('subj:V-N',19,6) relation('mod_att:N-N',16,15) relation('mod_pred:N-N',6,9) relation('comp_of:N-N',9,16) agents agent(13) agent(15) agent(4) targets target(4) target(24) genic_interactions genic_interaction(13,4) genic_interaction(15,4) genic_interaction(4,24) ID 9841221-4 sentence In that respect sigB is similar to the previously described gene gsiB which is also a member of the sigmaB regulon. words word(0,'In',0,1) word(1,'that',3,6) word(2,'respect',8,14) word(3,'sigB',16,19) word(4,'is',21,22) word(5,'similar',24,30) word(6,'to',32,33) word(7,'the',35,37) word(8,'previously',39,48) word(9,'described',50,58) word(10,'gene',60,63) word(11,'gsiB',65,68) word(12,'which',70,74) word(13,'is',76,77) word(14,'also',79,82) word(15,'a',84,84) word(16,'member',86,91) word(17,'of',93,94) word(18,'the',96,98) word(19,'sigmaB',100,105) word(20,'regulon',107,113) lemmas lemma(0,'in') lemma(1,'that') lemma(2,'respect') lemma(3,'sigB') lemma(4,'be') lemma(5,'similar') lemma(6,'to') lemma(7,'the') lemma(8,'previously') lemma(9,'describe') lemma(10,'gene') lemma(11,'gsiB') lemma(12,'which') lemma(13,'be') lemma(14,'also') lemma(15,'a') lemma(16,'member') lemma(17,'of') lemma(18,'the') lemma(19,'sigB') lemma(20,'regulon') syntactic_relations relation('mod:V-ADV',13,14) relation('mod_att:N-N',11,10) relation('mod_att:N-N',20,19) relation('comp_in:V-N',4,2) relation('comp_of:N-N',16,20) relation('mod_att:N-ADJ',10,9) relation('comp_to:ADJ-N',5,11) relation('mod_pred:N-ADJ',3,5) relation('mod_pred:N-N',11,16) relation('mod:ADJ-ADV',9,8) agents agent(19) targets target(11) target(3) genic_interactions genic_interaction(19,11) genic_interaction(19,3)