Dissecting the ATP hydrolysis pathway of bacterial enhancer-binding proteins

2008 ◽  
Vol 36 (1) ◽  
pp. 83-88 ◽  
Author(s):  
Daniel Bose ◽  
Nicolas Joly ◽  
Tillmann Pape ◽  
Mathieu Rappas ◽  
Jorg Schumacher ◽  
...  
Keyword(s):  
Active Site ◽  
Binding Proteins ◽  
Atp Hydrolysis ◽  
Aaa Atpase ◽  
Enhancer Binding Proteins ◽  
Σ Factor ◽  
Hydrolysis Pathway ◽  
Promoter Dna ◽  
Transcription Activators ◽  
Activate Gene

bEBPs (bacterial enhancer-binding proteins) are AAA+ (ATPase associated with various cellular activities) transcription activators that activate gene transcription through a specific bacterial σ factor, σ54. σ54–RNAP (RNA polymerase) binds to promoter DNA sites and forms a stable closed complex, unable to proceed to transcription. The closed complex must be remodelled using energy from ATP hydrolysis provided by bEBPs to melt DNA and initiate transcription. Recently, large amounts of structural and biochemical data have produced insights into how ATP hydrolysis within the active site of bEBPs is coupled to the re-modelling of the closed complex. In the present article, we review some of the key nucleotides, mutations and techniques used and how they have contributed towards our understanding of the function of bEBPs.

scholarly journals Structural basis for transcription activation by Crl through tethering of σS and RNA polymerase

2019 ◽  
Vol 116 (38) ◽  
pp. 18923-18927 ◽  
Author(s):  
Alexis Jaramillo Cartagena ◽  
Amy B. Banta ◽  
Nikhil Sathyan ◽  
Wilma Ross ◽  
Richard L. Gourse ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Transcription Initiation ◽  
Structural Basis ◽  
Functional Importance ◽  
Structural Element ◽  
Cryo Electron Microscopy ◽  
Promoter Complex ◽  
Σ Factor ◽  
Promoter Dna ◽  
Transcription Activators

In bacteria, a primary σ-factor associates with the core RNA polymerase (RNAP) to control most transcription initiation, while alternative σ-factors are used to coordinate expression of additional regulons in response to environmental conditions. Many alternative σ-factors are negatively regulated by anti–σ-factors. In Escherichia coli, Salmonella enterica, and many other γ-proteobacteria, the transcription factor Crl positively regulates the alternative σS-regulon by promoting the association of σS with RNAP without interacting with promoter DNA. The molecular mechanism for Crl activity is unknown. Here, we determined a single-particle cryo-electron microscopy structure of Crl-σS-RNAP in an open promoter complex with a σS-regulon promoter. In addition to previously predicted interactions between Crl and domain 2 of σS (σS2), the structure, along with p-benzoylphenylalanine cross-linking, reveals that Crl interacts with a structural element of the RNAP β′-subunit that we call the β′-clamp-toe (β′CT). Deletion of the β′CT decreases activation by Crl without affecting basal transcription, highlighting the functional importance of the Crl-β′CT interaction. We conclude that Crl activates σS-dependent transcription in part through stabilizing σS-RNAP by tethering σS2 and the β′CT. We propose that Crl, and other transcription activators that may use similar mechanisms, be designated σ-activators.

Comparison of promoter DNA methylation and expression levels of genes encoding CCAAT/enhancer binding proteins in AML patients

2014 ◽  
Vol 38 (7) ◽  
pp. 850-856 ◽  
Author(s):  
Ewa Musialik ◽  
Mateusz Bujko ◽  
Paulina Kober ◽  
Monika Anna Grygorowicz ◽  
Marta Libura ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Binding Proteins ◽  
Expression Levels ◽  
Enhancer Binding Proteins ◽  
Promoter Dna Methylation ◽  
Genes Encoding ◽  
Promoter Dna

Comparison of promoter DNA methylation and expression levels of genes encoding CCAAT/enhancer binding proteins in AML patients

2013 ◽  
Vol 41 (8) ◽  
pp. S27
Author(s):  
Ewa Musialik ◽  
Mateusz Bujko ◽  
Paulina Kober ◽  
Monika Grygorowicz ◽  
Marta Libura ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Binding Proteins ◽  
Expression Levels ◽  
Enhancer Binding Proteins ◽  
Promoter Dna Methylation ◽  
Genes Encoding ◽  
Promoter Dna

scholarly journals Bacterial Enhancer Binding Proteins—AAA+ Proteins in Transcription Activation

Biomolecules ◽  
2020 ◽  
Vol 10 (3) ◽  
pp. 351 ◽  
Author(s):  
Forson Gao ◽  
Amy E. Danson ◽  
Fuzhou Ye ◽  
Milija Jovanovic ◽  
Martin Buck ◽  
...  
Keyword(s):  
Transcription Initiation ◽  
Bound States ◽  
Binding Proteins ◽  
Structural Models ◽  
Transcription Activation ◽  
Transcriptional Activators ◽  
Enhancer Binding Proteins ◽  
Promoter Complex ◽  
Promoter Dna ◽  
Aaa Atpases

Bacterial enhancer-binding proteins (bEBPs) are specialised transcriptional activators. bEBPs are hexameric AAA+ ATPases and use ATPase activities to remodel RNA polymerase (RNAP) complexes that contain the major variant sigma factor, σ54 to convert the initial closed complex to the transcription competent open complex. Earlier crystal structures of AAA+ domains alone have led to proposals of how nucleotide-bound states are sensed and propagated to substrate interactions. Recently, the structure of the AAA+ domain of a bEBP bound to RNAP-σ54-promoter DNA was revealed. Together with structures of the closed complex, an intermediate state where DNA is partially loaded into the RNAP cleft and the open promoter complex, a mechanistic understanding of how bEBPs use ATP to activate transcription can now be proposed. This review summarises current structural models and the emerging understanding of how this special class of AAA+ proteins utilises ATPase activities to allow σ54-dependent transcription initiation.

scholarly journals Structural, functional, and genetic analyses of the actinobacterial transcription factor RbpA

2015 ◽  
Vol 112 (23) ◽  
pp. 7171-7176 ◽  
Author(s):  
Elizabeth A. Hubin ◽  
Aline Tabib-Salazar ◽  
Laurence J. Humphrey ◽  
Joshua E. Flack ◽  
Paul Dominic B. Olinares ◽  
...  
Keyword(s):  
Transcription Initiation ◽  
Critical Role ◽  
Transcription Activator ◽  
Functional Studies ◽  
Σ Factor ◽  
Group 2 ◽  
Promoter Dna ◽  
Transcription Activators

Gene expression is highly regulated at the step of transcription initiation, and transcription activators play a critical role in this process. RbpA, an actinobacterial transcription activator that is essential inMycobacterium tuberculosis(Mtb), binds selectively to group 1 and certain group 2 σ-factors. To delineate the molecular mechanism of RbpA, we show that theMtbRbpA σ-interacting domain (SID) and basic linker are sufficient for transcription activation. We also present the crystal structure of theMtbRbpA-SID in complex with domain 2 of the housekeeping σ-factor, σA. The structure explains the basis of σ-selectivity by RbpA, showing that RbpA interacts with conserved regions of σAas well as the nonconserved region (NCR), which is present only in housekeeping σ-factors. Thus, the structure is the first, to our knowledge, to show a protein interacting with the NCR of a σ-factor. We confirm the basis of selectivity and the observed interactions using mutagenesis and functional studies. In addition, the structure allows for a model of the RbpA-SID in the context of a transcription initiation complex. Unexpectedly, the structural modeling suggests that RbpA contacts the promoter DNA, and we present in vivo and in vitro studies supporting this finding. Our combined data lead to a better understanding of the mechanism of RbpA function as a transcription activator.

scholarly journals A functional assay for enhancer-binding proteins

1988 ◽  
Vol 16 (20) ◽  
pp. 9870-9870 ◽  
Author(s):  
M. Hallupp ◽  
W.H. Strãtling
Keyword(s):  
Binding Proteins ◽  
Functional Assay ◽  
Enhancer Binding Proteins
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