bengisucam/LLL_INO-tagged · Datasets at Hugging Face

Unnamed: 0 int64 0 163	Gene1 stringlengths 4 9	Gene2 stringlengths 3 9	Keywords stringlengths 4 47	Direct dependency relations stringlengths 2 63	INO Type stringlengths 9 59	INO ID stringlengths 7 11	Num. Keywords stringclasses 5 values	Sentence stringlengths 108 552
0	KinC	Spo0A~P	responsible, production	nmod(responsible, production)	regulation of translation	INO_0000034	2	In vivo studies of the activity of four of the kinases, KinA, [PROTEIN1] KinC [/PROTEIN1], KinD (ykvD) and KinE (ykrQ), using abrB transcription as an indicator of [PROTEIN2] Spo0A~P [/PROTEIN2] 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.
1	KinD	Spo0A~P	responsible, production	nmod(responsible, production)	regulation of translation	INO_0000034	2	In vivo studies of the activity of four of the kinases, KinA, KinC, [PROTEIN1] KinD [/PROTEIN1] (ykvD) and KinE (ykrQ), using abrB transcription as an indicator of [PROTEIN2] Spo0A~P [/PROTEIN2] 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.
2	sigma(A)	spoIIG	transcription, depends	nsubj(depends, transcription)	regulation of transcription	INO_0000032	2	In this mutant, expression of the [PROTEIN2] spoIIG [/PROTEIN2] gene, whose transcription depends on both [PROTEIN1] sigma(A) [/PROTEIN1] and the phosphorylated Spo0A protein, Spo0A~P, a major transcription factor during early stages of sporulation, was greatly reduced at 43 degrees C.
3	Spo0A	spoIIG	transcription, depends	nsubj(depends, transcription)	regulation of transcription	INO_0000032	2	In this mutant, expression of the [PROTEIN2] spoIIG [/PROTEIN2] gene, whose transcription depends on both sigma(A) and the phosphorylated [PROTEIN1] Spo0A [/PROTEIN1] protein, Spo0A~P, a major transcription factor during early stages of sporulation, was greatly reduced at 43 degrees C.
4	SigE	ydhD	transcription, dependent	nsubj(dependent, transcription)	regulation of transcription	INO_0000032	2	Transcription of [PROTEIN2] ydhD [/PROTEIN2] was dependent on [PROTEIN1] SigE [/PROTEIN1], and the mRNA was detectable from 2 h after the cessation of logarithmic growth (T2 of sporulation).
5	SigK	ykuD	transcribed	ONE WORD	regulation of transcription	INO_0000032	1	[PROTEIN2] ykuD [/PROTEIN2] was transcribed by [PROTEIN1] SigK [/PROTEIN1] RNA polymerase from T4 of sporulation.
6	SigK	ykvP	essential, expression	nmod(essential, expression)	gene expression regulation	INO_0000044	2	Both [PROTEIN1] SigK [/PROTEIN1] and GerE were essential for [PROTEIN2] ykvP [/PROTEIN2] expression, and this gene was transcribed from T5 of sporulation.
7	GerE	ykvP	essential, expression	nmod(essential, expression)	gene expression regulation	INO_0000044	2	Both SigK and [PROTEIN1] GerE [/PROTEIN1] were essential for [PROTEIN2] ykvP [/PROTEIN2] expression, and this gene was transcribed from T5 of sporulation.
8	sigma(F)	ywhE	expression, controlled	-1	gene expression regulation	INO_0000044	2	Analysis of the expression of a translational [PROTEIN1] ywhE [/PROTEIN1]-lacZ fusion showed that ywhE expression is sporulation-specific, and is controlled predominantly by the forespore-specific sigma factor [PROTEIN1] sigma(F) [/PROTEIN1], and to a lesser extent by sigma(G).
10	SpoIIE	sigma(F)	essential, activation	nmod:for(essential, activation)	regulation of gene activation	INO_0000037	2	Secondly, [PROTEIN1] SpoIIE [/PROTEIN1] is essential for the activation of the first compartment-specific transcription factor [PROTEIN2] sigma(F) [/PROTEIN2] in the prespore.
11	FtsZ	SpoIIE	localization, dependent	nsubj(dependent, Localization)	regulation of protein location	INO_0000031	2	Localization of [PROTEIN2] SpoIIE [/PROTEIN2] was shown to be dependent on the essential cell division protein [PROTEIN1] FtsZ [/PROTEIN1].
13	sigma(H)	spoVG	dependent, expression	amod(expression, dependent)	gene expression regulation	INO_0000044	2	In the shaA mutant, [PROTEIN1] sigma(H) [/PROTEIN1]-dependent expression of spo0A and [PROTEIN2] spoVG [/PROTEIN2] at an early stage of sporulation was sensitive to external NaCl.
14	sigma(F)	rsfA	expression, control	nsubj(control, expression)	gene expression regulation	INO_0000044	2	The expression of [PROTEIN2] rsfA [/PROTEIN2] is under the control of both [PROTEIN1] sigma(F) [/PROTEIN1] and sigma(G).
17	gerE	cwlH	expression, depended	-1	gene expression regulation	INO_0000044	2	Expression of the sigma(K)-dependent [PROTEIN2] cwlH [/PROTEIN2] gene depended on [PROTEIN1] gerE [/PROTEIN1].
20	sigmaB	katX	dependent, promoters	amod(promoters, sigmaF-dependent)	promoter-based regulation of transcription	INO_0000079	2	The -10 and -35 sequences of the [PROTEIN1] sigmaB [/PROTEIN1]- and sigmaF-dependent promoters of [PROTEIN2] katX [/PROTEIN2] overlap, and the transcriptional start points used by EsigmaB and EsigmaF differ by only one nucleotide.
21	sigmaF	katX	dependent, promoters	amod(promoters, sigmaF-dependent)	promoter-based regulation of transcription	INO_0000079	2	The -10 and -35 sequences of the sigmaB- and [PROTEIN1] sigmaF [/PROTEIN1]-dependent promoters of [PROTEIN2] katX [/PROTEIN2] overlap, and the transcriptional start points used by EsigmaB and EsigmaF differ by only one nucleotide.
22	sigmaB	katX	dependent	ONE WORD	gene expression regulation	INO_0000044	1	We demonstrated that [PROTEIN2] katX [/PROTEIN2] is also a [PROTEIN1] sigmaB [/PROTEIN1]-dependent general stress gene, since it is strongly induced by heat, salt and ethanol stress, as well as by energy depletion.
23	SpoIIE	sigmaF	control, activation	nmod:of(control, activation)	regulation of gene activation	INO_0000037	2	Taken together, the results support the idea that sequestration of [PROTEIN1] SpoIIE [/PROTEIN1] protein into the prespore plays an important role in the control of [PROTEIN2] sigmaF [/PROTEIN2] activation and in coupling this activation to septation.
25	SpoIIAA	sigmaF	controlled	ONE WORD	controling	INO_0000057	1	[PROTEIN2] sigmaF [/PROTEIN2] is controlled by a regulatory cascade involving an anti-sigma factor, SpoIIAB, an anti-anti-sigma factor, [PROTEIN1] SpoIIAA [/PROTEIN1], and a membrane-bound phosphatase, SpoIIE, which converts the inactive, phosphorylated form of SpoIIAA back to the active form.
26	SpoIIE	sigmaF	controlled	ONE WORD	controling	INO_0000057	1	[PROTEIN2] sigmaF [/PROTEIN2] is controlled by a regulatory cascade involving an anti-sigma factor, SpoIIAB, an anti-anti-sigma factor, SpoIIAA, and a membrane-bound phosphatase, [PROTEIN1] SpoIIE [/PROTEIN1], which converts the inactive, phosphorylated form of SpoIIAA back to the active form.
27	SpoIIE	SpoIIAA	converts, active	-1	regulation of gene activation	INO_0000037	2	sigmaF is controlled by a regulatory cascade involving an anti-sigma factor, SpoIIAB, an anti-anti-sigma factor, [PROTEIN2] SpoIIAA [/PROTEIN2], and a membrane-bound phosphatase, [PROTEIN1] SpoIIE [/PROTEIN1], which converts the inactive, phosphorylated form of SpoIIAA back to the active form.
28	SigL	rocG	transcribed	ONE WORD	gene transcription	INO_0000173	1	The [PROTEIN2] rocG [/PROTEIN2] gene of Bacillus subtilis, encoding a catabolic glutamate dehydrogenase, is transcribed by [PROTEIN1] SigL [/PROTEIN1]-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).
32	E sigma E	yfhS	transcribed	ONE WORD	regulation of transcription	INO_0000032	1	Northern blot and primer extension analyses indicated that [PROTEIN2] yfhS [/PROTEIN2] is transcribed by [PROTEIN1] E sigma E [/PROTEIN1] during sporulation.
33	YfhP	yfhQ	negative regulator, transcription	nmod:for(regulator, transcription); amod(regulator, negative)	negative regulation of transcription	INO_0000074	2	These results suggest that [PROTEIN1] YfhP [/PROTEIN1] may act as a negative regulator for the transcription of [PROTEIN2] yfhQ [/PROTEIN2], yfhR, sspE and yfhP.
34	YfhP	yfhR	negative regulator, transcription	nmod:for(regulator, transcription); amod(regulator, negative)	negative regulation of transcription	INO_0000074	2	These results suggest that [PROTEIN1] YfhP [/PROTEIN1] may act as a negative regulator for the transcription of yfhQ, [PROTEIN2] yfhR [/PROTEIN2], sspE and yfhP.
35	YfhP	sspE	negative regulator, transcription	nmod:for(regulator, transcription); amod(regulator, negative)	negative regulation of transcription	INO_0000074	2	These results suggest that [PROTEIN1] YfhP [/PROTEIN1] may act as a negative regulator for the transcription of yfhQ, yfhR, [PROTEIN2] sspE [/PROTEIN2] and yfhP.
36	YfhP	yfhP	negative regulator, transcription	nmod:for(regulator, transcription); amod(regulator, negative)	negative regulation of transcription	INO_0000074	2	These results suggest that [PROTEIN1] YfhP [/PROTEIN1] may act as a negative regulator for the transcription of yfhQ, yfhR, sspE and [PROTEIN2] yfhP [/PROTEIN2].
37	sigmaK	Spo0A	production, affect	nsubj(affect, production)	gene expression regulation	INO_0000044	2	Production of [PROTEIN1] sigmaK [/PROTEIN1] about 1 h earlier than normal does affect [PROTEIN2] Spo0A [/PROTEIN2], which when phosphorylated is an activator of sigE transcription.
38	Spo0A	sigE	phosphorylated, activator, transcription	MORE THAN TWO KEYWORDS	activation of gene transcription by phosphorylated protein	INO_0000081	3	Production of sigmaK about 1 h earlier than normal does affect [PROTEIN1] Spo0A [/PROTEIN1], which when phosphorylated is an activator of [PROTEIN2] sigE [/PROTEIN2] transcription.
39	sigmaA	ald	promoter, recognized	nsubjpass(recognized, promoter)	promoter-based regulation of transcription	INO_0000079	2	The [PROTEIN2] ald [/PROTEIN2] promoter, like the sigE promoter, is believed to be recognized by [PROTEIN1] sigmaA [/PROTEIN1] RNA polymerase, suggesting that sigmaK may inhibit sigmaA activity late in sporulation.
40	sigmaA	sigE	promoter, recognized	nsubjpass(recognized, promoter)	promoter-based regulation of transcription	INO_0000079	2	The ald promoter, like the [PROTEIN2] sigE [/PROTEIN2] promoter, is believed to be recognized by [PROTEIN1] sigmaA [/PROTEIN1] RNA polymerase, suggesting that sigmaK may inhibit sigmaA activity late in sporulation.
41	sigmaK	sigmaA	inhibit, activity	dobj(inhibit, activity)	inhibition of protein activity	INO_0000070	2	The ald promoter, like the sigE promoter, is believed to be recognized by [PROTEIN2] sigmaA [/PROTEIN2]RNA polymerase, suggesting that [PROTEIN1] sigmaK [/PROTEIN1] may inhibit sigmaA activity late in sporulation.
42	sigmaK	sigE	expression, negatively regulated	nsubjpass(regulated, expression); advmod(regulated, negatively)	negative regulation of gene expression	INO_0000039	2	In the mother cell compartment of sporulating cells, expression of the [PROTEIN2] sigE [/PROTEIN2] gene, encoding the earlier-acting sigma factor, sigmaE, is negatively regulated by the later-acting sigma factor, [PROTEIN1] sigmaK [/PROTEIN1].
43	FtsZ	SpoIIE	depends	ONE WORD	regulation	INO_0000157	1	The first stage, which involves the phosphatase function of [PROTEIN2] SpoIIE [/PROTEIN2], depends on the cell division protein [PROTEIN1] FtsZ [/PROTEIN1] and could correspond to the FtsZ-dependent assembly of SpoIIE into E-rings.
44	FtsZ	SpoIIE	dependent, assembly	amod(assembly, FtsZ-dependent)	regulation of assembly	INO_0000100	2	The first stage, which involves the phosphatase function of [PROTEIN2] SpoIIE [/PROTEIN2], depends on the cell division protein [PROTEIN1] FtsZ [/PROTEIN1] and could correspond to the FtsZ-dependent assembly of SpoIIE into E-rings.
45	SpoIIE	SpoIIAA	blocks	ONE WORD	inhibition	INO_0000124	1	Evidence based on the use of modified and mutant forms of the phosphatase protein indicates that [PROTEIN1] SpoIIE [/PROTEIN1] blocks the capacity of unphosphorylated [PROTEIN2] SpoIIAA [/PROTEIN2] to activate sigmaF until formation of the polar septum is completed.
46	SpoIIAA	sigmaF	activate	ONE WORD	activation	INO_0000024	1	Evidence based on the use of modified and mutant forms of the phosphatase protein indicates that SpoIIE blocks the capacity of unphosphorylated [PROTEIN1] SpoIIAA [/PROTEIN1] to activate [PROTEIN2] sigmaF [/PROTEIN2] until formation of the polar septum is completed.
47	SpoIIE	sigmaF	activation, requires	nsubj(requires, activation)	regulation of gene activation	INO_0000037	2	Cell-specific activation of transcription factor [PROTEIN2] sigmaF [/PROTEIN2]during sporulation in Bacillus subtilis requires the formation of the polar septum and the activity of a serine phosphatase ([PROTEIN1] SpoIIE [/PROTEIN1]) located in the septum.
48	SpoIIE	SpoIIAA-P	dephosphorylating	ONE WORD	dephosphorylation reaction	MI:0203	1	The [PROTEIN1] SpoIIE [/PROTEIN1] phosphatase indirectly activates sigmaF by dephosphorylating a protein ([PROTEIN2] SpoIIAA-P [/PROTEIN2]) in the pathway that controls the activity of the transcription factor.
49	SpoIIE	sigmaF	activates	ONE WORD	activation	INO_0000024	1	The [PROTEIN1] SpoIIE [/PROTEIN1] phosphatase indirectly activates [PROTEIN2] sigmaF [/PROTEIN2] by dephosphorylating a protein (SpoIIAA-P) in the pathway that controls the activity of the transcription factor.
50	SpoIIAA-P	sigmaF	controls, activity	dobj(controls, activity)	regulation of protein activity	INO_0000055	2	The SpoIIE phosphatase indirectly activates [PROTEIN2] sigmaF [/PROTEIN2] by dephosphorylating a protein ([PROTEIN1] SpoIIAA-P [/PROTEIN1]) in the pathway that controls the activity of the transcription factor.
52	sigmaB	bmrUR	control	ONE WORD	controling	INO_0000057	1	(i) The finding that the [PROTEIN2] bmrUR [/PROTEIN2] operon is under [PROTEIN1] sigmaB [/PROTEIN1] control indicates that the elimination of multidrug compounds might be a new function in multiple stress resistance.
53	sigmaB	ydaP	dependent	ONE WORD	gene expression regulation	INO_0000044	1	The [PROTEIN1] ydaP [/PROTEIN1] gene might belong to the increasing number of [PROTEIN2] sigmaB [/PROTEIN2]-dependent genes whose orthologues are under the control of sigmas in Escherichia coli, indicating that both regulons may fulfil similar functions.
54	sigmaB	ydaE	dependent	ONE WORD	gene expression regulation	INO_0000044	1	Three new [PROTEIN1] sigmaB [/PROTEIN1]-dependent genes ([PROTEIN2] ydaE [/PROTEIN2], ydaG and yfkM) encoding proteins with still unknown functions were also described.
56	sigmaB	yfkM	dependent	ONE WORD	gene expression regulation	INO_0000044	1	Three new [PROTEIN1] sigmaB [/PROTEIN1]-dependent genes (ydaE, ydaG and [PROTEIN2] yfkM [/PROTEIN2]) encoding proteins with still unknown functions were also described.
57	SpoIIE	sigma F	activated, action	nmod:through(activated, action)	gene activation	INO_0000075	2	Cell specificity is first established in the forespore under the control of the [PROTEIN2] sigma F [/PROTEIN2] factor, which is itself activated through the action of the [PROTEIN1] SpoIIE [/PROTEIN1] serine phosphatase, an enzyme targeted to the septum between the two cells.
58	sigmaK	cot	transcribed	ONE WORD	gene transcription	INO_0000173	1	Most [PROTEIN1] cot [/PROTEIN1] genes, and the gerE gene, are transcribed by [PROTEIN2] sigmaK [/PROTEIN2] RNA polymerase.
59	sigmaK	gerE	transcribed	ONE WORD	gene transcription	INO_0000173	1	Most cot genes, and the [PROTEIN1] gerE [/PROTEIN1] gene, are transcribed by [PROTEIN2] sigmaK [/PROTEIN2] RNA polymerase.
60	GerE	sigK	inhibits, transcription	dobj(inhibits, transcription)	inhibition of gene transcription	INO_0000046	2	Previously, it was shown that the [PROTEIN1] GerE [/PROTEIN1] protein inhibits transcription in vitro of the [PROTEIN2] sigK [/PROTEIN2] gene encoding sigmaK.
61	sigmaK	gerE	dependent, transcription	amod(transcription-6, sigmaK-dependent-5)	regulation of transcription	INO_0000032	2	These results demonstrate that [PROTEIN1] sigmaK [/PROTEIN1]-dependent transcription of [PROTEIN2] gerE [/PROTEIN2] initiates a negative feedback loop in which GerE acts as a repressor to limit production of sigmaK.
62	GerE	sigmaK	repressor, limit production	acl(repressor, limit); dobj(limit, production)	inhibition of gene transcription	INO_0000046	2	These results demonstrate that sigmaK-dependent transcription of gerE initiates a negative feedback loop in which [PROTEIN1] GerE [/PROTEIN1] acts as a repressor to limit production of [PROTEIN2] sigmaK [/PROTEIN1].
63	GerE	sigmaK	activated, transcription	dobj(activated, transcription)	regulation of transcription	INO_0000032	2	A low level of [PROTEIN1] GerE [/PROTEIN1] activated transcription of cotD by [PROTEIN2] sigmaK [/PROTEIN2] RNA polymerase in vitro, but a higher level of GerE repressed cotD transcription.
64	GerE	cotD	low level, activated, transcription	MORE THAN TWO KEYWORDS	activation of gene transcription by low level protein	INO_0000052	3	A low level of GerE activated transcription of cotD by sigmaK RNA polymerase in vitro, but a higher level of [PROTEIN1] GerE [/PROTEIN1] repressed [PROTEIN2] cotD [/PROTEIN2] transcription.
65	sigmaK	cotD	transcription	ONE WORD	regulation of transcription	INO_0000032	1	A low level of GerE activated transcription of [PROTEIN2] cotD [/PROTEIN2] by [PROTEIN1] sigmaK [/PROTEIN1] RNA polymerase in vitro, but a higher level of GerE repressed cotD transcription.
67	GerE	sigK	binds, transcriptional, act, repressor	MORE THAN TWO KEYWORDS	negative regulation of gene transcription	INO_0000042	4	Here, we show that [PROTEIN1] GerE [/PROTEIN1] binds near the [PROTEIN2] sigK [/PROTEIN2] transcriptional start site, to act as a repressor.
68	GerE	cotD	binds, promoter	-1	regulation of transcription by binding to promoter	INO_0000071	2	We show that [PROTEIN1] GerE [/PROTEIN1] binds to two sites that span the -35 region of the [PROTEIN2] cotD [/PROTEIN2] promoter.
69	GerE	cotD	activate, transcription, repress, transcription	dobj(activate, transcription); advmod(transcription, repress)	regulation of transcription	INO_0000032	2 (2 events with two keywords each)	These results suggest that a rising level of [PROTEIN1] GerE [/PROTEIN1] in sporulating cells may first activate [PROTEIN2] cotD [/PROTEIN2] transcription from the upstream site then repress transcription as the downstream site becomes occupied.
70	GerE	sspG	transcription, requires	nsubj(requires,transcription);	regulation of transcription	INO_0000032	2	[PROTEIN2] sspG [/PROTEIN2] transcription also requires the DNA binding protein [PROTEIN1] GerE [/PROTEIN1].
71	sigmaG	sspJ	transcribed	ONE WORD	gene transcription	INO_0000173	1	In contrast, [PROTEIN1] sspJ [/PROTEIN1] is transcribed in the forespore compartment by RNA polymerase with the forespore-specific [PROTEIN2] sigmaG [/PROTEIN2] and appears to give a monocistronic transcript.
72	ComK	FlgM	stimulating, transcription	dobj(stimulating,transcription)	positive regulation of gene transcription	INO_0000049	2	[PROTEIN1] ComK [/PROTEIN1] negatively controls the transcription of hag by stimulating the transcription of comF-flgM, thereby increasing the production of the [PROTEIN2] FlgM [/PROTEIN2] antisigma factor that inhibits sigmaD activity.
73	ComK	hag	negatively controls, transcription	dobj(controls, transcription); advmod(controls, negatively)	negative regulation of gene transcription	INO_0000042	2	[PROTEIN1] ComK [/PROTEIN1] negatively controls the transcription of [PROTEIN2] hag [/PROTEIN2] by stimulating the transcription of comF-flgM, thereby increasing the production of the FlgM antisigma factor that inhibits sigmaD activity.
74	ComK	comF	stimulating, transcription	dobj(stimulating,transcription)	positive regulation of gene transcription	INO_0000049	2	[PROTEIN1] ComK [/PROTEIN1] negatively controls the transcription of hag by stimulating the transcription of [PROTEIN2] comF [/PROTEIN2]-flgM, thereby increasing the production of the FlgM antisigma factor that inhibits sigmaD activity.
76	FlgM	sigmaD	inhibit, activity	dobj(inhibits,activity)	inhibition of protein activity	INO_0000070	2	ComK negatively controls the transcription of hag by stimulating the transcription of comF-flgM, thereby increasing the production of the [PROTEIN1] FlgM [/PROTEIN1] antisigma factor that inhibits [PROTEIN2] sigmaD [/PROTEIN2] activity.
77	sigmaB	ykzA	increase, expression, dependent	MORE THAN TWO KEYWORDS	positive regulation of gene expression	INO_0000038	3	This stress-induced increase in [PROTEIN2] ykzA [/PROTEIN2] expression is absolutely dependent on the alternative sigma factor [PROTEIN1] sigmaB [/PROTEIN1], which controls a large stationary-phase and stress regulon.
78	sigma X	CsbB	contributes, expression	nmod(contributes,expression)	gene expression regulation	INO_0000044	2	[PROTEIN1] sigma X [/PROTEIN1] also contributes to the expression of [PROTEIN2] CsbB [/PROTEIN2], a putative membrane-bound glucosyl transferase that is partially controlled by the sigma B stress response sigma factor.
79	sigma B	CsbB	controlled	ONE WORD	controling	INO_0000057	1	sigma X also contributes to the expression of [PROTEIN2] CsbB [/PROTEIN2], a putative membrane-bound glucosyl transferase that is partially controlled by the [PROTEIN1] sigma B [/PROTEIN1] stress response sigma factor.
80	sigma B	nadE	induced, dependent	-1	positive regulation of gene expression	INO_0000038	2	Transcriptional studies showed that [PROTEIN2] nadE [/PROTEIN2] is strongly induced in response to heat, ethanol and salt stress or after starvation for glucose in a [PROTEIN1] sigma B [/PROTEIN1]-dependent manner.
81	sigma(B)	YtxH	induced, dependent	-1	positive regulation of gene expression	INO_0000038	2	Furthermore, [PROTEIN2] YtxH [/PROTEIN2] and YvyD seemed to be induced after phosphate starvation in the wild type in a [PROTEIN1] sigma(B) [/PROTEIN1]-dependent manner and in the sigB mutant probably via sigma(H).
82	sigma(B)	YvyD	induced, dependent	-1	positive regulation of gene expression	INO_0000038	2	Furthermore, YtxH and [PROTEIN1] YvyD [/PROTEIN1] seemed to be induced after phosphate starvation in the wild type in a [PROTEIN2] sigma(B) [/PROTEIN2]-dependent manner and in the sigB mutant probably via sigma(H).
83	sigma(H)	YtxH	induced, via	-1	induction	INO_0000122	2	Furthermore, [PROTEIN1] YtxH [/PROTEIN1] 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 [PROTEIN2] sigma(H) [/PROTEIN2].
84	sigma(H)	YvyD	induced, via	-1	induction	INO_0000122	2	Furthermore, YtxH and [PROTEIN2] YvyD [/PROTEIN2] seemed to be induced after phosphate starvation in the wild type in a sigma(B)-dependent manner and in the sigB mutant probably via [PROTEIN1] sigma(H) [/PROTEIN1].
86	ComK	sigmaD	preventing, transcription	dobj(preventing,transcription)	inhibition of gene transcription	INO_0000046	2	From these results we conclude that [PROTEIN1] ComK [/PROTEIN1] negatively regulates degR expression by preventing [PROTEIN2] sigmaD [/PROTEIN2]-driven transcription of degR, possibly through interaction with the control region.
87	ComK	degR	negatively regulates, expression	dobj(regulates,expression)	negative regulation of gene expression	INO_0000039	2	From these results we conclude that [PROTEIN1] ComK [/PROTEIN1] negatively regulates [PROTEIN2] degR [/PROTEIN2] expression by preventing sigmaD-driven transcription of degR, possibly through interaction with the control region.
88	ComK	degR	preventing, transcription	dobj(preventing,transcription)	inhibition of gene transcription	INO_0000046	2	From these results we conclude that [PROTEIN1] ComK [/PROTEIN1] negatively regulates [PROTEIN2] degR [/PROTEIN2] expression by preventing sigmaD-driven transcription of degR, possibly through interaction with the control region.
89	sigmaD	degR	driven, transcription	amod(transcription, sigmaD-driven)	positive regulation of gene transcription	INO_0000049	2	From these results we conclude that ComK negatively regulates degR expression by preventing [PROTEIN1] sigmaD [/PROTEIN1]-driven transcription of [PROTEIN2] degR [/PROTEIN2], possibly through interaction with the control region.
90	sigmaD	degR	transcription, driven	nsubjpass(driven,transcription)	positive regulation of gene transcription	INO_0000049	2	We have shown previously that the transcription of [PROTEIN2] degR [/PROTEIN2] is driven by an alternative sigma factor, [PROTEIN1] sigmaD [/PROTEIN1].
91	SpoIIID	cotC	binds	ONE WORD	direct interaction	MI_0407	1	DNase I footprinting showed that [PROTEIN1] SpoIIID [/PROTEIN1] binds strongly to two sites in the [PROTEIN2] cotC [/PROTEIN2] promoter region, binds weakly to one site in the cotX promoter, and does not bind specifically to cotB.
92	SpoIIID	cotX	binds	ONE WORD	direct interaction	MI_0407	1	DNase I footprinting showed that [PROTEIN1] SpoIIID [/PROTEIN1] binds strongly to two sites in the cotC promoter region, binds weakly to one site in the [PROTEIN2] cotX [/PROTEIN2] promoter, and does not bind specifically to cotB.
93	SpoIIID	cotB	bind	ONE WORD	direct interaction	MI_0407	1	DNase I footprinting showed that [PROTEIN1] SpoIIID [/PROTEIN1] 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 [PROTEIN2] cotB [/PROTEIN2].
94	sigma(K)	cotB	transcription	ONE WORD	gene transcription	INO_0000173	1	Transcription of the [PROTEIN1] cotB [/PROTEIN1], cotC, and cotX genes by final [PROTEIN2] sigma(K) [/PROTEIN2] RNA polymerase is activated by a small, DNA-binding protein called GerE.
96	sigma(K)	cotX	transcription	ONE WORD	gene transcription	INO_0000173	1	Transcription of the cotB, cotC, and [PROTEIN1] cotX [/PROTEIN1] genes by final [PROTEIN2] sigma(K) [/PROTEIN2] RNA polymerase is activated by a small, DNA-binding protein called GerE.
97	GerE	cotB	transcription, activated	nsubjpass(activated,transcription)	activation of gene transcription	INO_0000051	2	Transcription of the [PROTEIN2] cotB [/PROTEIN2], cotC, and cotX genes by final sigma(K) RNA polymerase is activated by a small, DNA-binding protein called [PROTEIN1] GerE [/PROTEIN1].
98	GerE	cotC	transcription ,activated	nsubjpass(activated,transcription)	activation of gene transcription	INO_0000051	2	Transcription of the cotB, [PROTEIN2] cotC [/PROTEIN2], and cotX genes by final sigma(K) RNA polymerase is activated by a small, DNA-binding protein called [PROTEIN1] GerE [/PROTEIN1].
99	GerE	cotX	transcription, activated	nsubjpass(activated,transcription)	activation of gene transcription	INO_0000051	2	Transcription of the cotB, cotC, and [PROTEIN2] cotX [/PROTEIN2] genes by final sigma(K) RNA polymerase is activated by a small, DNA-binding protein called [PROTEIN1] GerE [/PROTEIN1].
100	GerE	cot	gene expression, action	-1	gene expression regulation	INO_0000044	2	In vitro transcription experiments suggest that the differential pattern of [PROTEIN2] cot [/PROTEIN2] gene expression results from the combined action of [PROTEIN1] GerE [/PROTEIN1] and another transcription factor, SpoIIID.
102	GerE	sigma(K)	low concentration, activated, transcription	MORE THAN TWO KEYWORDS	regulation of transcription	INO_0000032	3	A low concentration of [PROTEIN1] GerE [/PROTEIN1] activated cotB transcription by final [PROTEIN2] sigma(K) [/PROTEIN2] RNA polymerase, whereas a higher concentration was needed to activate transcription of cotX or cotC.
103	GerE	cotB	low concentration, activated, transcription	MORE THAN TWO KEYWORDS	activation of gene transcription by low level protein	INO_0000052	3	A low concentration of [PROTEIN1] GerE [/PROTEIN1] activated [PROTEIN2] cotB [/PROTEIN2] transcription by final sigma(K) RNA polymerase, whereas a higher concentration was needed to activate transcription of cotX or cotC.
104	GerE	cotX	activate, transcription	amod(transcription, activate)	activation of gene transcription	INO_0000051	2	A low concentration of [PROTEIN1] GerE [/PROTEIN1] activated cotB transcription by final sigma(K) RNA polymerase, whereas a higher concentration was needed to activate transcription of [PROTEIN2] cotX [/PROTEIN2] or cotC.
106	sigma(K)	cotB	activated, transcription	dobj(activated,transcription)	activation of gene transcription	INO_0000051	2	A low concentration of GerE activated [PROTEIN2] cotB [/PROTEIN2] transcription by final [PROTEIN1] sigma(K) [/PROTEIN1] RNA polymerase, whereas a higher concentration was needed to activate transcription of cotX or cotC.
107	SpoIIID	cotC	repressed, transcription	dobj(repressed,transcription)	inhibition of gene transcription	INO_0000046	2	[PROTEIN1] SpoIIID [/PROTEIN1] at low concentration repressed [PROTEIN2] cotC [/PROTEIN2] transcription, whereas a higher concentration only partially repressed cotX transcription and had little effect on cotB transcription.
108	SpoIIID	cotX	repressed, transcription	dobj(repressed,transcription)	inhibition of gene transcription	INO_0000046	2	[PROTEIN1] SpoIIID [/PROTEIN1] at low concentration repressed cotC transcription, whereas a higher concentration only partially repressed [PROTEIN2] cotX [/PROTEIN2] transcription and had little effect on cotB transcription.
109	SpoIIID	cotB	repressed, transcription	dobj(repressed,transcription)	inhibition of gene transcription	INO_0000046	2	[PROTEIN1] SpoIIID [/PROTEIN1] at low concentration repressed cotC transcription, whereas a higher concentration only partially repressed cotX transcription and had little effect on [PROTEIN2] cotB [/PROTEIN2] transcription.
110	sigmaA	kdgR	dependent, promoter	amod(promoter, sigmaA-dependent)	promoter-based regulation of transcription	INO_0000079	2	Primer extension experiments and Northern blot analysis show that an active [PROTEIN1] sigmaA [/PROTEIN1]-dependent promoter precedes [PROTEIN2] kdgR [/PROTEIN2] and transcription is terminated at the putative p-independent terminator downstream of kdgT.
111	sigmaW	sigW	dependent, promoter, precedes	MORE THAN TWO KEYWORDS	promoter-based regulation of transcription	INO_0000079	3	A [PROTEIN1] sigmaW [/PROTEIN1]-dependent promoter (PW) precedes [PROTEIN2] sigW [/PROTEIN2], demonstrating that this transcription factor is positively autoregulated.
112	sigma(A)	sigX	recognize, promoter	-1	promoter-based regulation of transcription	INO_0000079	2	We overproduced and purified sigma(X) from Escherichia coli and demonstrate that in vitro, both [PROTEIN1] sigma(A) [/PROTEIN1] and sigma(X) holoenzymes recognize promoter elements within the [PROTEIN2] sigX [/PROTEIN2]-ypuN control region.
113	sigma(A)	ypuN	recognize, promoter	-1	promoter-based regulation of transcription	INO_0000079	2	We overproduced and purified sigma(X) from Escherichia coli and demonstrate that in vitro, both [PROTEIN1] sigma(A) [/PROTEIN1] and sigma(X) holoenzymes recognize promoter elements within the sigX-[PROTEIN2] ypuN [/PROTEIN2] control region.
114	sigma(X)	sigX	recognize, promoter	-1	promoter-based regulation of transcription	INO_0000079	2	We overproduced and purified [PROTEIN1] sigma(X) [/PROTEIN1] from Escherichia coli and demonstrate that in vitro, both sigma(A) and sigma(X) holoenzymes recognize promoter elements within the [PROTEIN2] sigX [/PROTEIN2]-ypuN control region.
116	PhoP~P	tagA	repress, transcription	dobj(repress,transcription)	inhibition of gene transcription	INO_0000046	2	The results indicate that [PROTEIN1] PhoP~P [/PROTEIN1] is sufficient to repress the transcription of the [PROTEIN2] tagA [/PROTEIN2] and tagD promoters and also to activate the transcription of the tuaA promoter.
117	PhoP~P	tagD	repress, transcription	dobj(repress,transcription)	inhibition of gene transcription	INO_0000046	2	The results indicate that [PROTEIN1] PhoP~P [/PROTEIN1] is sufficient to repress the transcription of the tagA and [PROTEIN2] tagD [/PROTEIN2] promoters and also to activate the transcription of the tuaA promoter.
118	PhoP~P	tuaA	activate, transcription	dobj(activate,transcription)	activation of gene transcription	INO_0000051	2	The results indicate that [PROTEIN1] PhoP~P [/PROTEIN1] is sufficient to repress the transcription of the tagA and tagD promoters and also to activate the transcription of the [PROTEIN2] tuaA [/PROTEIN2] promoter.

0

KinC

Spo0A~P

responsible, production

nmod(responsible, production)

regulation of translation

INO_0000034

2

In vivo studies of the activity of four of the kinases, KinA, [PROTEIN1] KinC [/PROTEIN1], KinD (ykvD) and KinE (ykrQ), using abrB transcription as an indicator of [PROTEIN2] Spo0A~P [/PROTEIN2] 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.

1

KinD

Spo0A~P

responsible, production

nmod(responsible, production)

regulation of translation

INO_0000034

2

In vivo studies of the activity of four of the kinases, KinA, KinC, [PROTEIN1] KinD [/PROTEIN1] (ykvD) and KinE (ykrQ), using abrB transcription as an indicator of [PROTEIN2] Spo0A~P [/PROTEIN2] 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.

2

sigma(A)

spoIIG

transcription, depends

nsubj(depends, transcription)

regulation of transcription

INO_0000032

2

In this mutant, expression of the [PROTEIN2] spoIIG [/PROTEIN2] gene, whose transcription depends on both [PROTEIN1] sigma(A) [/PROTEIN1] and the phosphorylated Spo0A protein, Spo0A~P, a major transcription factor during early stages of sporulation, was greatly reduced at 43 degrees C.

3

Spo0A

spoIIG

transcription, depends

nsubj(depends, transcription)

regulation of transcription

INO_0000032

2

In this mutant, expression of the [PROTEIN2] spoIIG [/PROTEIN2] gene, whose transcription depends on both sigma(A) and the phosphorylated [PROTEIN1] Spo0A [/PROTEIN1] protein, Spo0A~P, a major transcription factor during early stages of sporulation, was greatly reduced at 43 degrees C.

4

SigE

ydhD

transcription, dependent

nsubj(dependent, transcription)

regulation of transcription

INO_0000032

2

Transcription of [PROTEIN2] ydhD [/PROTEIN2] was dependent on [PROTEIN1] SigE [/PROTEIN1], and the mRNA was detectable from 2 h after the cessation of logarithmic growth (T2 of sporulation).

5

SigK

ykuD

transcribed

ONE WORD

regulation of transcription

INO_0000032

1

[PROTEIN2] ykuD [/PROTEIN2] was transcribed by [PROTEIN1] SigK [/PROTEIN1] RNA polymerase from T4 of sporulation.

6

SigK

ykvP

essential, expression

nmod(essential, expression)

gene expression regulation

INO_0000044

2

Both [PROTEIN1] SigK [/PROTEIN1] and GerE were essential for [PROTEIN2] ykvP [/PROTEIN2] expression, and this gene was transcribed from T5 of sporulation.

7

GerE

ykvP

essential, expression

nmod(essential, expression)

gene expression regulation

INO_0000044

2

Both SigK and [PROTEIN1] GerE [/PROTEIN1] were essential for [PROTEIN2] ykvP [/PROTEIN2] expression, and this gene was transcribed from T5 of sporulation.

8

sigma(F)

ywhE

expression, controlled

-1

gene expression regulation

INO_0000044

2

Analysis of the expression of a translational [PROTEIN1] ywhE [/PROTEIN1]-lacZ fusion showed that ywhE expression is sporulation-specific, and is controlled predominantly by the forespore-specific sigma factor [PROTEIN1] sigma(F) [/PROTEIN1], and to a lesser extent by sigma(G).

10

SpoIIE

sigma(F)

essential, activation

nmod:for(essential, activation)

regulation of gene activation

INO_0000037

2

Secondly, [PROTEIN1] SpoIIE [/PROTEIN1] is essential for the activation of the first compartment-specific transcription factor [PROTEIN2] sigma(F) [/PROTEIN2] in the prespore.

11

FtsZ

SpoIIE

localization, dependent

nsubj(dependent, Localization)

regulation of protein location

INO_0000031

2

Localization of [PROTEIN2] SpoIIE [/PROTEIN2] was shown to be dependent on the essential cell division protein [PROTEIN1] FtsZ [/PROTEIN1].

13

sigma(H)

spoVG

dependent, expression

amod(expression, dependent)

gene expression regulation

INO_0000044

2

In the shaA mutant, [PROTEIN1] sigma(H) [/PROTEIN1]-dependent expression of spo0A and [PROTEIN2] spoVG [/PROTEIN2] at an early stage of sporulation was sensitive to external NaCl.

14

sigma(F)

rsfA

expression, control

nsubj(control, expression)

gene expression regulation

INO_0000044

2

The expression of [PROTEIN2] rsfA [/PROTEIN2] is under the control of both [PROTEIN1] sigma(F) [/PROTEIN1] and sigma(G).

17

gerE

cwlH

expression, depended

-1

gene expression regulation

INO_0000044

2

Expression of the sigma(K)-dependent [PROTEIN2] cwlH [/PROTEIN2] gene depended on [PROTEIN1] gerE [/PROTEIN1].

20

sigmaB

katX

dependent, promoters

amod(promoters, sigmaF-dependent)

promoter-based regulation of transcription

INO_0000079

2

The -10 and -35 sequences of the [PROTEIN1] sigmaB [/PROTEIN1]- and sigmaF-dependent promoters of [PROTEIN2] katX [/PROTEIN2] overlap, and the transcriptional start points used by EsigmaB and EsigmaF differ by only one nucleotide.

21

sigmaF

katX

dependent, promoters

amod(promoters, sigmaF-dependent)

promoter-based regulation of transcription

INO_0000079

2

The -10 and -35 sequences of the sigmaB- and [PROTEIN1] sigmaF [/PROTEIN1]-dependent promoters of [PROTEIN2] katX [/PROTEIN2] overlap, and the transcriptional start points used by EsigmaB and EsigmaF differ by only one nucleotide.

22

sigmaB

katX

dependent

ONE WORD

gene expression regulation

INO_0000044

1

We demonstrated that [PROTEIN2] katX [/PROTEIN2] is also a [PROTEIN1] sigmaB [/PROTEIN1]-dependent general stress gene, since it is strongly induced by heat, salt and ethanol stress, as well as by energy depletion.

23

SpoIIE

sigmaF

control, activation

nmod:of(control, activation)

regulation of gene activation

INO_0000037

2

Taken together, the results support the idea that sequestration of [PROTEIN1] SpoIIE [/PROTEIN1] protein into the prespore plays an important role in the control of [PROTEIN2] sigmaF [/PROTEIN2] activation and in coupling this activation to septation.

25

SpoIIAA

sigmaF

controlled

ONE WORD

controling

INO_0000057

1

[PROTEIN2] sigmaF [/PROTEIN2] is controlled by a regulatory cascade involving an anti-sigma factor, SpoIIAB, an anti-anti-sigma factor, [PROTEIN1] SpoIIAA [/PROTEIN1], and a membrane-bound phosphatase, SpoIIE, which converts the inactive, phosphorylated form of SpoIIAA back to the active form.

26

SpoIIE

sigmaF

controlled

ONE WORD

controling

INO_0000057

1

[PROTEIN2] sigmaF [/PROTEIN2] is controlled by a regulatory cascade involving an anti-sigma factor, SpoIIAB, an anti-anti-sigma factor, SpoIIAA, and a membrane-bound phosphatase, [PROTEIN1] SpoIIE [/PROTEIN1], which converts the inactive, phosphorylated form of SpoIIAA back to the active form.

27

SpoIIE

SpoIIAA

converts, active

-1

regulation of gene activation

INO_0000037

2

sigmaF is controlled by a regulatory cascade involving an anti-sigma factor, SpoIIAB, an anti-anti-sigma factor, [PROTEIN2] SpoIIAA [/PROTEIN2], and a membrane-bound phosphatase, [PROTEIN1] SpoIIE [/PROTEIN1], which converts the inactive, phosphorylated form of SpoIIAA back to the active form.

28

SigL

rocG

transcribed

ONE WORD

gene transcription

INO_0000173

1

The [PROTEIN2] rocG [/PROTEIN2] gene of Bacillus subtilis, encoding a catabolic glutamate dehydrogenase, is transcribed by [PROTEIN1] SigL [/PROTEIN1]-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).

32

E sigma E

yfhS

transcribed

ONE WORD

regulation of transcription

INO_0000032

1

Northern blot and primer extension analyses indicated that [PROTEIN2] yfhS [/PROTEIN2] is transcribed by [PROTEIN1] E sigma E [/PROTEIN1] during sporulation.

33

YfhP

yfhQ

negative regulator, transcription

nmod:for(regulator, transcription); amod(regulator, negative)

negative regulation of transcription

INO_0000074

2

These results suggest that [PROTEIN1] YfhP [/PROTEIN1] may act as a negative regulator for the transcription of [PROTEIN2] yfhQ [/PROTEIN2], yfhR, sspE and yfhP.

34

YfhP

yfhR

negative regulator, transcription

nmod:for(regulator, transcription); amod(regulator, negative)

negative regulation of transcription

INO_0000074

2

These results suggest that [PROTEIN1] YfhP [/PROTEIN1] may act as a negative regulator for the transcription of yfhQ, [PROTEIN2] yfhR [/PROTEIN2], sspE and yfhP.

35

YfhP

sspE

negative regulator, transcription

nmod:for(regulator, transcription); amod(regulator, negative)

negative regulation of transcription

INO_0000074

2

These results suggest that [PROTEIN1] YfhP [/PROTEIN1] may act as a negative regulator for the transcription of yfhQ, yfhR, [PROTEIN2] sspE [/PROTEIN2] and yfhP.

36

YfhP

yfhP

negative regulator, transcription

nmod:for(regulator, transcription); amod(regulator, negative)

negative regulation of transcription

INO_0000074

2

These results suggest that [PROTEIN1] YfhP [/PROTEIN1] may act as a negative regulator for the transcription of yfhQ, yfhR, sspE and [PROTEIN2] yfhP [/PROTEIN2].

37

sigmaK

Spo0A

production, affect

nsubj(affect, production)

gene expression regulation

INO_0000044

2

Production of [PROTEIN1] sigmaK [/PROTEIN1] about 1 h earlier than normal does affect [PROTEIN2] Spo0A [/PROTEIN2], which when phosphorylated is an activator of sigE transcription.

38

Spo0A

sigE

phosphorylated, activator, transcription

MORE THAN TWO KEYWORDS

activation of gene transcription by phosphorylated protein

INO_0000081

3

Production of sigmaK about 1 h earlier than normal does affect [PROTEIN1] Spo0A [/PROTEIN1], which when phosphorylated is an activator of [PROTEIN2] sigE [/PROTEIN2] transcription.

39

sigmaA

ald

promoter, recognized

nsubjpass(recognized, promoter)

promoter-based regulation of transcription

INO_0000079

2

The [PROTEIN2] ald [/PROTEIN2] promoter, like the sigE promoter, is believed to be recognized by [PROTEIN1] sigmaA [/PROTEIN1] RNA polymerase, suggesting that sigmaK may inhibit sigmaA activity late in sporulation.

40

sigmaA

sigE

promoter, recognized

nsubjpass(recognized, promoter)

promoter-based regulation of transcription

INO_0000079

2

The ald promoter, like the [PROTEIN2] sigE [/PROTEIN2] promoter, is believed to be recognized by [PROTEIN1] sigmaA [/PROTEIN1] RNA polymerase, suggesting that sigmaK may inhibit sigmaA activity late in sporulation.

41

sigmaK

sigmaA

inhibit, activity

dobj(inhibit, activity)

inhibition of protein activity

INO_0000070

2

The ald promoter, like the sigE promoter, is believed to be recognized by [PROTEIN2] sigmaA [/PROTEIN2]RNA polymerase, suggesting that [PROTEIN1] sigmaK [/PROTEIN1] may inhibit sigmaA activity late in sporulation.

42

sigmaK

sigE

expression, negatively regulated

nsubjpass(regulated, expression); advmod(regulated, negatively)

negative regulation of gene expression

INO_0000039

2

In the mother cell compartment of sporulating cells, expression of the [PROTEIN2] sigE [/PROTEIN2] gene, encoding the earlier-acting sigma factor, sigmaE, is negatively regulated by the later-acting sigma factor, [PROTEIN1] sigmaK [/PROTEIN1].

43

FtsZ

SpoIIE

depends

ONE WORD

regulation

INO_0000157

1

The first stage, which involves the phosphatase function of [PROTEIN2] SpoIIE [/PROTEIN2], depends on the cell division protein [PROTEIN1] FtsZ [/PROTEIN1] and could correspond to the FtsZ-dependent assembly of SpoIIE into E-rings.

44

FtsZ

SpoIIE

dependent, assembly

amod(assembly, FtsZ-dependent)

regulation of assembly

INO_0000100

2

The first stage, which involves the phosphatase function of [PROTEIN2] SpoIIE [/PROTEIN2], depends on the cell division protein [PROTEIN1] FtsZ [/PROTEIN1] and could correspond to the FtsZ-dependent assembly of SpoIIE into E-rings.

45

SpoIIE

SpoIIAA

blocks

ONE WORD

inhibition

INO_0000124

1

Evidence based on the use of modified and mutant forms of the phosphatase protein indicates that [PROTEIN1] SpoIIE [/PROTEIN1] blocks the capacity of unphosphorylated [PROTEIN2] SpoIIAA [/PROTEIN2] to activate sigmaF until formation of the polar septum is completed.

46

SpoIIAA

sigmaF

activate

ONE WORD

activation

INO_0000024

1

Evidence based on the use of modified and mutant forms of the phosphatase protein indicates that SpoIIE blocks the capacity of unphosphorylated [PROTEIN1] SpoIIAA [/PROTEIN1] to activate [PROTEIN2] sigmaF [/PROTEIN2] until formation of the polar septum is completed.

47

SpoIIE

sigmaF

activation, requires

nsubj(requires, activation)

regulation of gene activation

INO_0000037

2

Cell-specific activation of transcription factor [PROTEIN2] sigmaF [/PROTEIN2]during sporulation in Bacillus subtilis requires the formation of the polar septum and the activity of a serine phosphatase ([PROTEIN1] SpoIIE [/PROTEIN1]) located in the septum.

48

SpoIIE

SpoIIAA-P

dephosphorylating

ONE WORD

dephosphorylation reaction

MI:0203

1

The [PROTEIN1] SpoIIE [/PROTEIN1] phosphatase indirectly activates sigmaF by dephosphorylating a protein ([PROTEIN2] SpoIIAA-P [/PROTEIN2]) in the pathway that controls the activity of the transcription factor.

49

SpoIIE

sigmaF

activates

ONE WORD

activation

INO_0000024

1

The [PROTEIN1] SpoIIE [/PROTEIN1] phosphatase indirectly activates [PROTEIN2] sigmaF [/PROTEIN2] by dephosphorylating a protein (SpoIIAA-P) in the pathway that controls the activity of the transcription factor.

50

SpoIIAA-P

sigmaF

controls, activity

dobj(controls, activity)

regulation of protein activity

INO_0000055

2

The SpoIIE phosphatase indirectly activates [PROTEIN2] sigmaF [/PROTEIN2] by dephosphorylating a protein ([PROTEIN1] SpoIIAA-P [/PROTEIN1]) in the pathway that controls the activity of the transcription factor.

52

sigmaB

bmrUR

control

ONE WORD

controling

INO_0000057

1

(i) The finding that the [PROTEIN2] bmrUR [/PROTEIN2] operon is under [PROTEIN1] sigmaB [/PROTEIN1] control indicates that the elimination of multidrug compounds might be a new function in multiple stress resistance.

53

sigmaB

ydaP

dependent

ONE WORD

gene expression regulation

INO_0000044

1

The [PROTEIN1] ydaP [/PROTEIN1] gene might belong to the increasing number of [PROTEIN2] sigmaB [/PROTEIN2]-dependent genes whose orthologues are under the control of sigmas in Escherichia coli, indicating that both regulons may fulfil similar functions.

54

sigmaB

ydaE

dependent

ONE WORD

gene expression regulation

INO_0000044

1

Three new [PROTEIN1] sigmaB [/PROTEIN1]-dependent genes ([PROTEIN2] ydaE [/PROTEIN2], ydaG and yfkM) encoding proteins with still unknown functions were also described.

56

sigmaB

yfkM

dependent

ONE WORD

gene expression regulation

INO_0000044

1

Three new [PROTEIN1] sigmaB [/PROTEIN1]-dependent genes (ydaE, ydaG and [PROTEIN2] yfkM [/PROTEIN2]) encoding proteins with still unknown functions were also described.

57

SpoIIE

sigma F

activated, action

nmod:through(activated, action)

gene activation

INO_0000075

2

Cell specificity is first established in the forespore under the control of the [PROTEIN2] sigma F [/PROTEIN2] factor, which is itself activated through the action of the [PROTEIN1] SpoIIE [/PROTEIN1] serine phosphatase, an enzyme targeted to the septum between the two cells.

58

sigmaK

cot

transcribed

ONE WORD

gene transcription

INO_0000173

1

Most [PROTEIN1] cot [/PROTEIN1] genes, and the gerE gene, are transcribed by [PROTEIN2] sigmaK [/PROTEIN2] RNA polymerase.

59

sigmaK

gerE

transcribed

ONE WORD

gene transcription

INO_0000173

1

Most cot genes, and the [PROTEIN1] gerE [/PROTEIN1] gene, are transcribed by [PROTEIN2] sigmaK [/PROTEIN2] RNA polymerase.

60

GerE

sigK

inhibits, transcription

dobj(inhibits, transcription)

inhibition of gene transcription

INO_0000046

2

Previously, it was shown that the [PROTEIN1] GerE [/PROTEIN1] protein inhibits transcription in vitro of the [PROTEIN2] sigK [/PROTEIN2] gene encoding sigmaK.

61

sigmaK

gerE

dependent, transcription

amod(transcription-6, sigmaK-dependent-5)

regulation of transcription

INO_0000032

2

These results demonstrate that [PROTEIN1] sigmaK [/PROTEIN1]-dependent transcription of [PROTEIN2] gerE [/PROTEIN2] initiates a negative feedback loop in which GerE acts as a repressor to limit production of sigmaK.

62

GerE

sigmaK

repressor, limit production

acl(repressor, limit); dobj(limit, production)

inhibition of gene transcription

INO_0000046

2

These results demonstrate that sigmaK-dependent transcription of gerE initiates a negative feedback loop in which [PROTEIN1] GerE [/PROTEIN1] acts as a repressor to limit production of [PROTEIN2] sigmaK [/PROTEIN1].

63

GerE

sigmaK

activated, transcription

dobj(activated, transcription)

regulation of transcription

INO_0000032

2

A low level of [PROTEIN1] GerE [/PROTEIN1] activated transcription of cotD by [PROTEIN2] sigmaK [/PROTEIN2] RNA polymerase in vitro, but a higher level of GerE repressed cotD transcription.

64

GerE

cotD

low level, activated, transcription

MORE THAN TWO KEYWORDS

activation of gene transcription by low level protein

INO_0000052

3

A low level of GerE activated transcription of cotD by sigmaK RNA polymerase in vitro, but a higher level of [PROTEIN1] GerE [/PROTEIN1] repressed [PROTEIN2] cotD [/PROTEIN2] transcription.

65

sigmaK

cotD

transcription

ONE WORD

regulation of transcription

INO_0000032

1

A low level of GerE activated transcription of [PROTEIN2] cotD [/PROTEIN2] by [PROTEIN1] sigmaK [/PROTEIN1] RNA polymerase in vitro, but a higher level of GerE repressed cotD transcription.

67

GerE

sigK

binds, transcriptional, act, repressor

MORE THAN TWO KEYWORDS

negative regulation of gene transcription

INO_0000042

4

Here, we show that [PROTEIN1] GerE [/PROTEIN1] binds near the [PROTEIN2] sigK [/PROTEIN2] transcriptional start site, to act as a repressor.

68

GerE

cotD

binds, promoter

-1

regulation of transcription by binding to promoter

INO_0000071

2

We show that [PROTEIN1] GerE [/PROTEIN1] binds to two sites that span the -35 region of the [PROTEIN2] cotD [/PROTEIN2] promoter.

69

GerE

cotD

activate, transcription, repress, transcription

dobj(activate, transcription); advmod(transcription, repress)

regulation of transcription

INO_0000032

2 (2 events with two keywords each)

These results suggest that a rising level of [PROTEIN1] GerE [/PROTEIN1] in sporulating cells may first activate [PROTEIN2] cotD [/PROTEIN2] transcription from the upstream site then repress transcription as the downstream site becomes occupied.

70

GerE

sspG

transcription, requires

nsubj(requires,transcription);

regulation of transcription

INO_0000032

2

[PROTEIN2] sspG [/PROTEIN2] transcription also requires the DNA binding protein [PROTEIN1] GerE [/PROTEIN1].

71

sigmaG

sspJ

transcribed

ONE WORD

gene transcription

INO_0000173

1

In contrast, [PROTEIN1] sspJ [/PROTEIN1] is transcribed in the forespore compartment by RNA polymerase with the forespore-specific [PROTEIN2] sigmaG [/PROTEIN2] and appears to give a monocistronic transcript.

72

ComK

FlgM

stimulating, transcription

dobj(stimulating,transcription)

positive regulation of gene transcription

INO_0000049

2

[PROTEIN1] ComK [/PROTEIN1] negatively controls the transcription of hag by stimulating the transcription of comF-flgM, thereby increasing the production of the [PROTEIN2] FlgM [/PROTEIN2] antisigma factor that inhibits sigmaD activity.

73

ComK

hag

negatively controls, transcription

dobj(controls, transcription); advmod(controls, negatively)

negative regulation of gene transcription

INO_0000042

2

[PROTEIN1] ComK [/PROTEIN1] negatively controls the transcription of [PROTEIN2] hag [/PROTEIN2] by stimulating the transcription of comF-flgM, thereby increasing the production of the FlgM antisigma factor that inhibits sigmaD activity.

74

ComK

comF

stimulating, transcription

dobj(stimulating,transcription)

positive regulation of gene transcription

INO_0000049

2

[PROTEIN1] ComK [/PROTEIN1] negatively controls the transcription of hag by stimulating the transcription of [PROTEIN2] comF [/PROTEIN2]-flgM, thereby increasing the production of the FlgM antisigma factor that inhibits sigmaD activity.

76

FlgM

sigmaD

inhibit, activity

dobj(inhibits,activity)

inhibition of protein activity

INO_0000070

2

ComK negatively controls the transcription of hag by stimulating the transcription of comF-flgM, thereby increasing the production of the [PROTEIN1] FlgM [/PROTEIN1] antisigma factor that inhibits [PROTEIN2] sigmaD [/PROTEIN2] activity.

77

sigmaB

ykzA

increase, expression, dependent

MORE THAN TWO KEYWORDS

positive regulation of gene expression

INO_0000038

3

This stress-induced increase in [PROTEIN2] ykzA [/PROTEIN2] expression is absolutely dependent on the alternative sigma factor [PROTEIN1] sigmaB [/PROTEIN1], which controls a large stationary-phase and stress regulon.

78

sigma X

CsbB

contributes, expression

nmod(contributes,expression)

gene expression regulation

INO_0000044

2

[PROTEIN1] sigma X [/PROTEIN1] also contributes to the expression of [PROTEIN2] CsbB [/PROTEIN2], a putative membrane-bound glucosyl transferase that is partially controlled by the sigma B stress response sigma factor.

79

sigma B

CsbB

controlled

ONE WORD

controling

INO_0000057

1

sigma X also contributes to the expression of [PROTEIN2] CsbB [/PROTEIN2], a putative membrane-bound glucosyl transferase that is partially controlled by the [PROTEIN1] sigma B [/PROTEIN1] stress response sigma factor.

80

sigma B

nadE

induced, dependent

-1

positive regulation of gene expression

INO_0000038

2

Transcriptional studies showed that [PROTEIN2] nadE [/PROTEIN2] is strongly induced in response to heat, ethanol and salt stress or after starvation for glucose in a [PROTEIN1] sigma B [/PROTEIN1]-dependent manner.

81

sigma(B)

YtxH

induced, dependent

-1

positive regulation of gene expression

INO_0000038

2

Furthermore, [PROTEIN2] YtxH [/PROTEIN2] and YvyD seemed to be induced after phosphate starvation in the wild type in a [PROTEIN1] sigma(B) [/PROTEIN1]-dependent manner and in the sigB mutant probably via sigma(H).

82

sigma(B)

YvyD

induced, dependent

-1

positive regulation of gene expression

INO_0000038

2

Furthermore, YtxH and [PROTEIN1] YvyD [/PROTEIN1] seemed to be induced after phosphate starvation in the wild type in a [PROTEIN2] sigma(B) [/PROTEIN2]-dependent manner and in the sigB mutant probably via sigma(H).

83

sigma(H)

YtxH

induced, via

-1

induction

INO_0000122

2

Furthermore, [PROTEIN1] YtxH [/PROTEIN1] 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 [PROTEIN2] sigma(H) [/PROTEIN2].

84

sigma(H)

YvyD

induced, via

-1

induction

INO_0000122

2

Furthermore, YtxH and [PROTEIN2] YvyD [/PROTEIN2] seemed to be induced after phosphate starvation in the wild type in a sigma(B)-dependent manner and in the sigB mutant probably via [PROTEIN1] sigma(H) [/PROTEIN1].

86

ComK

sigmaD

preventing, transcription

dobj(preventing,transcription)

inhibition of gene transcription

INO_0000046

2

From these results we conclude that [PROTEIN1] ComK [/PROTEIN1] negatively regulates degR expression by preventing [PROTEIN2] sigmaD [/PROTEIN2]-driven transcription of degR, possibly through interaction with the control region.

87

ComK

degR

negatively regulates, expression

dobj(regulates,expression)

negative regulation of gene expression

INO_0000039

2

From these results we conclude that [PROTEIN1] ComK [/PROTEIN1] negatively regulates [PROTEIN2] degR [/PROTEIN2] expression by preventing sigmaD-driven transcription of degR, possibly through interaction with the control region.

88

ComK

degR

preventing, transcription

dobj(preventing,transcription)

inhibition of gene transcription

INO_0000046

2

From these results we conclude that [PROTEIN1] ComK [/PROTEIN1] negatively regulates [PROTEIN2] degR [/PROTEIN2] expression by preventing sigmaD-driven transcription of degR, possibly through interaction with the control region.

89

sigmaD

degR

driven, transcription

amod(transcription, sigmaD-driven)

positive regulation of gene transcription

INO_0000049

2

From these results we conclude that ComK negatively regulates degR expression by preventing [PROTEIN1] sigmaD [/PROTEIN1]-driven transcription of [PROTEIN2] degR [/PROTEIN2], possibly through interaction with the control region.

90

sigmaD

degR

transcription, driven

nsubjpass(driven,transcription)

positive regulation of gene transcription

INO_0000049

2

We have shown previously that the transcription of [PROTEIN2] degR [/PROTEIN2] is driven by an alternative sigma factor, [PROTEIN1] sigmaD [/PROTEIN1].

91

SpoIIID

cotC

binds

ONE WORD

direct interaction

MI_0407

1

DNase I footprinting showed that [PROTEIN1] SpoIIID [/PROTEIN1] binds strongly to two sites in the [PROTEIN2] cotC [/PROTEIN2] promoter region, binds weakly to one site in the cotX promoter, and does not bind specifically to cotB.

92

SpoIIID

cotX

binds

ONE WORD

direct interaction

MI_0407

1

DNase I footprinting showed that [PROTEIN1] SpoIIID [/PROTEIN1] binds strongly to two sites in the cotC promoter region, binds weakly to one site in the [PROTEIN2] cotX [/PROTEIN2] promoter, and does not bind specifically to cotB.

93

SpoIIID

cotB

bind

ONE WORD

direct interaction

MI_0407

1

DNase I footprinting showed that [PROTEIN1] SpoIIID [/PROTEIN1] 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 [PROTEIN2] cotB [/PROTEIN2].

94

sigma(K)

cotB

transcription

ONE WORD

gene transcription

INO_0000173

1

Transcription of the [PROTEIN1] cotB [/PROTEIN1], cotC, and cotX genes by final [PROTEIN2] sigma(K) [/PROTEIN2] RNA polymerase is activated by a small, DNA-binding protein called GerE.

96

sigma(K)

cotX

transcription

ONE WORD

gene transcription

INO_0000173

1

Transcription of the cotB, cotC, and [PROTEIN1] cotX [/PROTEIN1] genes by final [PROTEIN2] sigma(K) [/PROTEIN2] RNA polymerase is activated by a small, DNA-binding protein called GerE.

97

GerE

cotB

transcription, activated

nsubjpass(activated,transcription)

activation of gene transcription

INO_0000051

2

Transcription of the [PROTEIN2] cotB [/PROTEIN2], cotC, and cotX genes by final sigma(K) RNA polymerase is activated by a small, DNA-binding protein called [PROTEIN1] GerE [/PROTEIN1].

98

GerE

cotC

transcription ,activated

nsubjpass(activated,transcription)

activation of gene transcription

INO_0000051

2

Transcription of the cotB, [PROTEIN2] cotC [/PROTEIN2], and cotX genes by final sigma(K) RNA polymerase is activated by a small, DNA-binding protein called [PROTEIN1] GerE [/PROTEIN1].

99

GerE

cotX

transcription, activated

nsubjpass(activated,transcription)

activation of gene transcription

INO_0000051

2

Transcription of the cotB, cotC, and [PROTEIN2] cotX [/PROTEIN2] genes by final sigma(K) RNA polymerase is activated by a small, DNA-binding protein called [PROTEIN1] GerE [/PROTEIN1].

100

GerE

cot

gene expression, action

-1

gene expression regulation

INO_0000044

2

In vitro transcription experiments suggest that the differential pattern of [PROTEIN2] cot [/PROTEIN2] gene expression results from the combined action of [PROTEIN1] GerE [/PROTEIN1] and another transcription factor, SpoIIID.

102

GerE

sigma(K)

low concentration, activated, transcription

MORE THAN TWO KEYWORDS

regulation of transcription

INO_0000032

3

A low concentration of [PROTEIN1] GerE [/PROTEIN1] activated cotB transcription by final [PROTEIN2] sigma(K) [/PROTEIN2] RNA polymerase, whereas a higher concentration was needed to activate transcription of cotX or cotC.

103

GerE

cotB

low concentration, activated, transcription

MORE THAN TWO KEYWORDS

activation of gene transcription by low level protein

INO_0000052

3

A low concentration of [PROTEIN1] GerE [/PROTEIN1] activated [PROTEIN2] cotB [/PROTEIN2] transcription by final sigma(K) RNA polymerase, whereas a higher concentration was needed to activate transcription of cotX or cotC.

104

GerE

cotX

activate, transcription

amod(transcription, activate)

activation of gene transcription

INO_0000051

2

A low concentration of [PROTEIN1] GerE [/PROTEIN1] activated cotB transcription by final sigma(K) RNA polymerase, whereas a higher concentration was needed to activate transcription of [PROTEIN2] cotX [/PROTEIN2] or cotC.

106

sigma(K)

cotB

activated, transcription

dobj(activated,transcription)

activation of gene transcription

INO_0000051

2

A low concentration of GerE activated [PROTEIN2] cotB [/PROTEIN2] transcription by final [PROTEIN1] sigma(K) [/PROTEIN1] RNA polymerase, whereas a higher concentration was needed to activate transcription of cotX or cotC.

107

SpoIIID

cotC

repressed, transcription

dobj(repressed,transcription)

inhibition of gene transcription

INO_0000046

2

[PROTEIN1] SpoIIID [/PROTEIN1] at low concentration repressed [PROTEIN2] cotC [/PROTEIN2] transcription, whereas a higher concentration only partially repressed cotX transcription and had little effect on cotB transcription.

108

SpoIIID

cotX

repressed, transcription

dobj(repressed,transcription)

inhibition of gene transcription

INO_0000046

2

[PROTEIN1] SpoIIID [/PROTEIN1] at low concentration repressed cotC transcription, whereas a higher concentration only partially repressed [PROTEIN2] cotX [/PROTEIN2] transcription and had little effect on cotB transcription.

109

SpoIIID

cotB

repressed, transcription

dobj(repressed,transcription)

inhibition of gene transcription

INO_0000046

2

[PROTEIN1] SpoIIID [/PROTEIN1] at low concentration repressed cotC transcription, whereas a higher concentration only partially repressed cotX transcription and had little effect on [PROTEIN2] cotB [/PROTEIN2] transcription.

110

sigmaA

kdgR

dependent, promoter

amod(promoter, sigmaA-dependent)

promoter-based regulation of transcription

INO_0000079

2

Primer extension experiments and Northern blot analysis show that an active [PROTEIN1] sigmaA [/PROTEIN1]-dependent promoter precedes [PROTEIN2] kdgR [/PROTEIN2] and transcription is terminated at the putative p-independent terminator downstream of kdgT.

111

sigmaW

sigW

dependent, promoter, precedes

MORE THAN TWO KEYWORDS

promoter-based regulation of transcription

INO_0000079

3

A [PROTEIN1] sigmaW [/PROTEIN1]-dependent promoter (PW) precedes [PROTEIN2] sigW [/PROTEIN2], demonstrating that this transcription factor is positively autoregulated.

112

sigma(A)

sigX

recognize, promoter

-1

promoter-based regulation of transcription

INO_0000079

2

We overproduced and purified sigma(X) from Escherichia coli and demonstrate that in vitro, both [PROTEIN1] sigma(A) [/PROTEIN1] and sigma(X) holoenzymes recognize promoter elements within the [PROTEIN2] sigX [/PROTEIN2]-ypuN control region.

113

sigma(A)

ypuN

recognize, promoter

-1

promoter-based regulation of transcription

INO_0000079

2

We overproduced and purified sigma(X) from Escherichia coli and demonstrate that in vitro, both [PROTEIN1] sigma(A) [/PROTEIN1] and sigma(X) holoenzymes recognize promoter elements within the sigX-[PROTEIN2] ypuN [/PROTEIN2] control region.

114

sigma(X)

sigX

recognize, promoter

-1

promoter-based regulation of transcription

INO_0000079

2

We overproduced and purified [PROTEIN1] sigma(X) [/PROTEIN1] from Escherichia coli and demonstrate that in vitro, both sigma(A) and sigma(X) holoenzymes recognize promoter elements within the [PROTEIN2] sigX [/PROTEIN2]-ypuN control region.

116

PhoP~P

tagA

repress, transcription

dobj(repress,transcription)

inhibition of gene transcription

INO_0000046

2

The results indicate that [PROTEIN1] PhoP~P [/PROTEIN1] is sufficient to repress the transcription of the [PROTEIN2] tagA [/PROTEIN2] and tagD promoters and also to activate the transcription of the tuaA promoter.

117

PhoP~P

tagD

repress, transcription

dobj(repress,transcription)

inhibition of gene transcription

INO_0000046

2

The results indicate that [PROTEIN1] PhoP~P [/PROTEIN1] is sufficient to repress the transcription of the tagA and [PROTEIN2] tagD [/PROTEIN2] promoters and also to activate the transcription of the tuaA promoter.

118

PhoP~P

tuaA

activate, transcription

dobj(activate,transcription)

activation of gene transcription

INO_0000051

2

The results indicate that [PROTEIN1] PhoP~P [/PROTEIN1] is sufficient to repress the transcription of the tagA and tagD promoters and also to activate the transcription of the [PROTEIN2] tuaA [/PROTEIN2] promoter.