Communication between Eσ<sup>54</sup>, promoter DNA and the conserved threonine residue in the GAFTGA motif of the PspF σ<sup>54</sup>‐dependent activator during transcription activation

Bordes, Patricia; Wigneshweraraj, Sivaramesh; Chaney, Matthew; Dago, Angel E.; Morett, Enrique; Buck, Martin

doi:10.1111/j.1365-2958.2004.04280.x

Cited by 27 publications

(33 citation statements)

References 41 publications

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“…Interactions of a bEBP and a 54 from two distinct microorganisms have already been demonstrated (50). This is made possible by the high degree of conservation between the 54 binding region of E. coli bEBPs and the bEBPs used in this study: the central domain, including the GAFTGA sequence, which mediates bEBP binding to 54 , is conserved among all the bEBPs used in this study (8,43,49,65) (see Fig. S2 in the supplemental material).…”

Section: Discussionmentioning

confidence: 94%

Regulation of Type VI Secretion Gene Clusters by σ ⁵⁴ and Cognate Enhancer Binding Proteins

et al. 2011

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Type VI secretion systems (T6SS) are bacteriophage-derived macromolecular machines responsible for the release of at least two proteins in the milieu, which are thought to form an extracellular appendage. Although several T6SS have been shown to be involved in the virulence of animal and plant pathogens, clusters encoding these machines are found in the genomes of most species of Gram-negative bacteria, including soil, marine, and environmental isolates. T6SS have been associated with several phenotypes, ranging from virulence to biofilm formation or stress sensing. Their various environmental niches and large diversity of functions are correlated with their broad variety of regulatory mechanisms. Using a bioinformatic approach, we identified several clusters, including those of Vibrio cholerae, Aeromonas hydrophila, Pectobacterium atrosepticum, Pseudomonas aeruginosa, Pseudomonas syringae pv. tomato, and a Marinomonas sp., which possess typical ؊24/؊12 sequences, recognized by the alternate sigma factor sigma 54 ( 54 or N ). 54 , which directs the RNA polymerase to these promoters, requires the action of a bacterial enhancer binding protein (bEBP), which binds to cis-acting upstream activating sequences. Putative bEBPs are encoded within the T6SS gene clusters possessing 54 boxes. Using in vitro binding experiments and in vivo reporter fusion assays, we showed that the expression of these clusters is dependent on both 54 and bEBPs.

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Section: Discussionmentioning

confidence: 94%

Regulation of Type VI Secretion Gene Clusters by σ ⁵⁴ and Cognate Enhancer Binding Proteins

et al. 2011

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“…Extensive mutagenesis studies suggest that bEBPs remodel s54 protein via interactions with region I, the protein's N-terminal domain (Gonzalez et al 1998;Bordes et al 2004;Dago et al 2007;Schumacher et al 2007;Zhang et al 2009). Region I spans ;50 amino acids that are predicted to form an a helix; it possesses two short motifs that are suggested to make direct contact with the GAFTGA motifs of the ATPase (Merrick 1993;Zhang et al 2012).…”

Section: The Gap Interface Of the Ntrc1 Atpase As A Nucleotide Releasmentioning

confidence: 99%

Nucleotide-induced asymmetry within ATPase activator ring drives σ54–RNAP interaction and ATP hydrolysis

et al. 2013

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It is largely unknown how the typical homomeric ring geometry of ATPases associated with various cellular activities enables them to perform mechanical work. Small-angle solution X-ray scattering, crystallography, and electron microscopy (EM) reconstructions revealed that partial ATP occupancy caused the heptameric closed ring of the bacterial enhancer-binding protein (bEBP) NtrC1 to rearrange into a hexameric split ring of striking asymmetry. The highly conserved and functionally crucial GAFTGA loops responsible for interacting with s54-RNA polymerase formed a spiral staircase. We propose that splitting of the ensemble directs ATP hydrolysis within the oligomer, and the ring's asymmetry guides interaction between ATPase and the complex of s54 and promoter DNA. Similarity between the structure of the transcriptional activator NtrC1 and those of distantly related helicases Rho and E1 reveals a general mechanism in homomeric ATPases whereby complex allostery within the ring geometry forms asymmetric functional states that allow these biological motors to exert directional forces on their target macromolecules.

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“…Specifically, an invariant threonine residue in L1 (Thr 86 in PspF) (see Fig. 1C) is thought to engage with 54 Region I during the energy-coupling process (10,11). The ATP hydrolysis-dependent movements of L1 and L2 have also been observed in the AAA activator Aquifex aeolicus NtrC1 (nitrogen regulatory protein C1) (12).…”

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confidence: 98%

A Role for the Conserved GAFTGA Motif of AAA+ Transcription Activators in Sensing Promoter DNA Conformation

Dago

Wigneshweraraj

Buck

et al. 2007

Journal of Biological Chemistry

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Gene transcription in bacteria is catalyzed by the multisubunit DNA-dependent RNA polymerase (RNAP).5 The catalytically competent core form of bacterial RNAP is a five-subunit enzyme (␣ 2 ␤␤Ј; E), which has to associate with a sixth subunit, the factor, for promoter-specific and regulated initiation of gene transcription. On the basis of differences in mechanism of action and amino acid sequence, bacterial factors are classified into two families. Most bacterial factors belong to the 70 family, named after the prototypical housekeeping factor, 70 , of Escherichia coli. The major variant bacterial factor belongs to the 54 class. Transcription initiation by RNAP containing 70 (E 70 ) and 54 (E 54 ) is mechanistically distinct. E 70 recognizes promoters that contain consensus sequences centered at DNA positions Ϫ35 and Ϫ10, respectively, from the transcription start site (at ϩ1). The initial transcriptionally inactive E 70 ⅐DNA complex, called the closed complex, can spontaneously isomerize to form the transcriptionally active open complex, in which the DNA strands are separated and the RNAP is poised for RNA synthesis. In contrast, E 54 forms closed complexes on promoters that contain consensus sequences centered at DNA positions Ϫ24 and Ϫ12 (1). Closed complexes formed by E 54 remain inactive for transcription unless activated by a specialized type of transcription activator protein that belongs to the AAA (ATPases associated with various cellular activities) protein family (2). E 54 -dependent transcription activators (from now on referred to as AAA activators) bind to DNA sites located (ϳ150 -200 bases) upstream of the promoter (known as upstream activating sequences) and use the energy derived from ATP binding and hydrolysis to remodel the E 54 closed complex (2). The ATP hydrolysis-dependent binding interactions between the AAA activator and E 54 closed complex trigger a series of protein and DNA isomerization events in the E 54 closed complex, which result in the formation of the open complex. The major energetically favorable binding site for the AAA activator within the E 54 closed complex is the N-terminal Region I domain of 54 (see Fig. 1A) (3), which, in the closed complex, is located at the Ϫ12 consensus promoter region, where DNA opening for open complex formation nucleates (4). At the Ϫ12 promoter region, 54 Region I meditates tight binding to a repressive fork junction structure and so prevents open complex formation in the absence of activation. Region I of 54 is associated with a range of properties of E 54 (1). These include maintaining the closed complex transcriptionally silent prior to activation (5), stabilizing the open complex once it is formed (6), and conformational signaling to a structurally conserved DNA-interacting domain(s) of the catalytic ␤Ј subunit of RNAP (7) required for stable open complex formation. Region I of 54 has been shown to make extensive interactions with the catalytic ␤ and ␤Ј subunits of RNAP (8).The AAA activators of E 54 are mechanochemical P-loop ATPases of th...

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Communication between Eσ⁵⁴, promoter DNA and the conserved threonine residue in the GAFTGA motif of the PspF σ⁵⁴‐dependent activator during transcription activation

Abstract: Summary Conversion of E

Cited by 27 publications

References 41 publications

Regulation of Type VI Secretion Gene Clusters by σ ⁵⁴ and Cognate Enhancer Binding Proteins

Regulation of Type VI Secretion Gene Clusters by σ ⁵⁴ and Cognate Enhancer Binding Proteins

Nucleotide-induced asymmetry within ATPase activator ring drives σ54–RNAP interaction and ATP hydrolysis

A Role for the Conserved GAFTGA Motif of AAA+ Transcription Activators in Sensing Promoter DNA Conformation

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Communication between Eσ54, promoter DNA and the conserved threonine residue in the GAFTGA motif of the PspF σ54‐dependent activator during transcription activation

Abstract: Summary Conversion of E

Cited by 27 publications

References 41 publications

Regulation of Type VI Secretion Gene Clusters by σ 54 and Cognate Enhancer Binding Proteins

Regulation of Type VI Secretion Gene Clusters by σ 54 and Cognate Enhancer Binding Proteins

Nucleotide-induced asymmetry within ATPase activator ring drives σ54–RNAP interaction and ATP hydrolysis

A Role for the Conserved GAFTGA Motif of AAA+ Transcription Activators in Sensing Promoter DNA Conformation

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Communication between Eσ⁵⁴, promoter DNA and the conserved threonine residue in the GAFTGA motif of the PspF σ⁵⁴‐dependent activator during transcription activation

Regulation of Type VI Secretion Gene Clusters by σ ⁵⁴ and Cognate Enhancer Binding Proteins

Regulation of Type VI Secretion Gene Clusters by σ ⁵⁴ and Cognate Enhancer Binding Proteins