Gene1: sigmaB

Gene2: yvyD

Keywords: dependent, inducible

INO Type: induction

Sentence: In addition to the typical [PROTEIN1] sigmaB [/PROTEIN1]-dependent, stress- and starvation-inducible pattern, [PROTEIN2] yvyD [/PROTEIN2] is also induced in response to amino acid depletion.


Gene1: sigma(X)

Gene2: ypuN

Keywords: recognize, promoter

INO Type: promoter-based regulation of transcription

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


Gene1: sigmaH

Keywords: dependent, drives, expression, promoter

Direct dependency relations: MORE THAN TWO KEYWORDS

INO Type: positive regulation of transcription by binding to promoter

Sentence: The sigmaB-dependent promoter drives expression of yvyD under stress conditions and after glucose starvation, whereas a [PROTEIN1] sigmaH [/PROTEIN1]-dependent promoter is responsible for [PROTEIN2] yvyD [/PROTEIN2] transcription following amino acid limitation.


Gene2: ydaG

Keywords: dependent

Direct dependency relations: ONE WORD

INO Type: gene expression regulation

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


Gene1: sigma(K)

Gene2: cotC

Keywords: transcription

INO Type: gene transcription

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


Gene1: RocR

Gene2: rocG

Keywords: requires, expression

Sentence: The [PROTEIN2] rocG [/PROTEIN2] gene of Bacillus subtilis, encoding a catabolic glutamate dehydrogenase, is transcribed by SigL-containing RNA polymerase and requires for its expression [PROTEIN1] RocR [/PROTEIN1], a member of the NtrC/NifA family of proteins that bind to enhancer-like elements, called upstream activating sequences (UAS).


Gene1: sigma W

Keywords: regulon, includes

Direct dependency relations: nsubj(includes,regulon)

Sentence: The [PROTEIN1] sigma W [/PROTEIN1] regulon includes a penicillin binding protein ([PROTEIN2] PBP4* [/PROTEIN2]) and a co-transcribed amino acid racemase (RacX), homologues of signal peptide peptidase (YteI), flotillin (YuaG), ABC transporters (YknXYZ), non-haem bromoperoxidase (YdjP), epoxide hydrolase (YfhM) and three small peptides with structural similarities to bacteriocin precursor polypeptides.


Gene1: SpoIIE

Gene2: SpoIIAA-P

Keywords: dephosphorylation

INO Type: dephosphorylation reaction

Sentence: Dephosphorylation of [PROTEIN2] SpoIIAA-P [/PROTEIN2] by [PROTEIN1] SpoIIE [/PROTEIN1] is strictly dependent on the presence of the bivalent metal ions Mn2+ or Mg2+.


Gene1: SpoIIID

Gene2: cot

Keywords: gene expression, action

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


Gene1: SpoIIAB

Gene2: sigma F

Keywords: inhibits

INO Type: inhibition

Sentence: The class includes AsiA form bacteriophage T4, which inhibits Escherichia coli sigma 70; FlgM, present in both gram-positive and gram-negative bacteria, which inhibits the flagella sigma factor sigma 28; [PROTEIN1] SpoIIAB [/PROTEIN1], which inhibits the sporulation-specific sigma factor,[PROTEIN2] sigma F [/PROTEIN2]and sigma G, of Bacillus subtilis; RbsW of B. subtilis, which inhibits stress response sigma factor sigma B; and DnaK, a general regulator of the heat shock response, which in bacteria inhibits the heat shock sigma factor sigma 32.


Gene2: katX

Keywords: dependent, expression

Direct dependency relations: amod(expression, sigmaB-dependent)

Sentence: Therefore, the physiological role of [PROTEIN1] sigmaB [/PROTEIN1]-dependent [PROTEIN2] katX [/PROTEIN2] expression remains obscure.


Gene1: SigL

Gene2: bkd

Keywords: expression, induced, depended, presence

INO Type: positive regulation of gene expression

Sentence: The expression of the [PROTEIN2] bkd [/PROTEIN2] operon was induced by the presence of isoleucine or valine in the growth medium and depended upon the presence of the sigma factor [PROTEIN1] SigL [/PROTEIN1], a member of the sigma 54 family.


Gene1: sigma(G)

Gene2: rsfA

Keywords: expression, control

Direct dependency relations: nsubj(control, expression)

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


Gene1: GerE

Gene2: cotD

Keywords: repressed, transcription

INO Type: negative regulation of gene transcription

Sentence: 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.


Gene2: sigmaF

Keywords: controlled

INO Type: controling

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


Sentence: Unlike the case for other [PROTEIN1] sigma(54) [/PROTEIN1]-dependent genes, [PROTEIN2] rocG [/PROTEIN2] has no UAS; instead, its expression depends on a sequence located 1.5 kilobases downstream of the rocG promoter, beyond the end of the rocG coding region.


Keywords: member of, regulons

Direct dependency relations: nmod:of(member, regulons)

Sentence: This indicates that the [PROTEIN2] yvyD [/PROTEIN2] gene product, being a member of both the [PROTEIN1] sigmaB [/PROTEIN1] and sigmaH regulons, might negatively regulate the activity of the sigmaL regulon.


Keywords: activate, transcription

Direct dependency relations: amod(transcription, activate)

INO Type: activation of gene transcription

Sentence: 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 cotX or [PROTEIN2] cotC [/PROTEIN2].


Gene1: sigmaG

Gene2: sspL

Keywords: recognized

INO Type: association

Sentence: The sspH and [PROTEIN2] sspL [/PROTEIN2] genes are recognized primarily by the forespore-specific sigma factor for RNA polymerase, [PROTEIN1] sigmaG [/PROTEIN1]; the sspN-tlp operon is recognized equally well by sigmaG and the other forespore-specific sigma factor, sigmaF.


Gene2: cwlH

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


Gene1: ComK

Gene2: flgM

Keywords: increasing, production

Direct dependency relations: dobj(increasing,production)

INO Type: positive regulation of protein translation

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


Gene1: EsigmaF

Gene2: KatX

Keywords: level, depends

Direct dependency relations: nsubj(depends, level)

Sentence: Our results indicate that the level of [PROTEIN2] KatX [/PROTEIN2] level in outgrowing spores depends mainly on [PROTEIN1] EsigmaF [/PROTEIN1], because sigB mutants show normal KatX activity in dormant and outgrowing spores.


Gene1: sigma(H)

Direct dependency relations: amod(expression, dependent)

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


Gene2: ywhE

Keywords: expression, controlled

Sentence: Analysis of the expression of a translational ywhE-lacZ fusion showed that [PROTEIN2] ywhE [PROTEIN2] expression is sporulation-specific, and is controlled predominantly by the forespore-specific sigma factor sigma(F), and to a lesser extent by [PROTEIN1] sigma(G) [/PROTEIN1].


Gene2: phrC

Keywords: controlling, transcription

Direct dependency relations: amod(transcription, controlling)

INO Type: regulation of transcription

Sentence: In addition to controlling transcription of [PROTEIN2] phrC [/PROTEIN2], [PROTEIN1] sigmaH [/PROTEIN1] appears to control expression of at least one other gene required for production of CSF.