scholarly journals Structure of the Brd4 ET domain bound to a C-terminal motif from γ-retroviral integrases reveals a conserved mechanism of interaction

2016 ◽  
Vol 113 (8) ◽  
pp. 2086-2091 ◽  
Author(s):  
Brandon L. Crowe ◽  
Ross C. Larue ◽  
Chunhua Yuan ◽  
Sonja Hess ◽  
Mamuka Kvaratskhelia ◽  
...  
Keyword(s):  
Transcriptional Activation ◽  
Solution Structure ◽  
Focal Point ◽  
Leukemia Virus ◽  
Viral Proteins ◽  
Structural Features ◽  
Peptide Sequence ◽  
Binding Motif ◽  
C Terminus ◽  
Retroviral Integrase

The bromodomain and extraterminal domain (BET) protein family are promising therapeutic targets for a range of diseases linked to transcriptional activation, cancer, viral latency, and viral integration. Tandem bromodomains selectively tether BET proteins to chromatin by engaging cognate acetylated histone marks, and the extraterminal (ET) domain is the focal point for recruiting a range of cellular and viral proteins. BET proteins guide γ-retroviral integration to transcription start sites and enhancers through bimodal interaction with chromatin and the γ-retroviral integrase (IN). We report the NMR-derived solution structure of the Brd4 ET domain bound to a conserved peptide sequence from the C terminus of murine leukemia virus (MLV) IN. The complex reveals a protein–protein interaction governed by the binding-coupled folding of disordered regions in both interacting partners to form a well-structured intermolecular three-stranded β sheet. In addition, we show that a peptide comprising the ET binding motif (EBM) of MLV IN can disrupt the cognate interaction of Brd4 with NSD3, and that substitutions of Brd4 ET residues essential for binding MLV IN also impair interaction of Brd4 with a number of cellular partners involved in transcriptional regulation and chromatin remodeling. This suggests that γ-retroviruses have evolved the EBM to mimic a cognate interaction motif to achieve effective integration in host chromatin. Collectively, our findings identify key structural features of the ET domain of Brd4 that allow for interactions with both cellular and viral proteins.

scholarly journals Solution Structure of the Carbon Storage Regulator Protein CsrA from Escherichia coli

2005 ◽  
Vol 187 (10) ◽  
pp. 3496-3501 ◽  
Author(s):  
Pablo Gutiérrez ◽  
Yan Li ◽  
Michael J. Osborne ◽  
Ekaterina Pomerantseva ◽  
Qian Liu ◽  
...  
Keyword(s):  
Carbon Storage ◽  
Solution Structure ◽  
Rna Binding ◽  
Binding Motif ◽  
Binding Properties ◽  
Nmr Titration ◽  
C Terminus ◽  
Regulator Protein ◽  
Carbon Storage Regulator ◽  
Α Helix

ABSTRACT The carbon storage regulator A (CsrA) is a protein responsible for the repression of a variety of stationary-phase genes in bacteria. In this work, we describe the nuclear magnetic resonance (NMR)-based structure of the CsrA dimer and its RNA-binding properties. CsrA is a dimer of two identical subunits, each composed of five strands, a small α-helix and a flexible C terminus. NMR titration experiments suggest that the β1-β2 and β3-β4 loops and the C-terminal helix are important elements in RNA binding. Even though the β3-β4 loop contains a highly conserved RNA-binding motif, GxxG, typical of KH domains, our structure excludes CsrA from being a member of this protein family, as previously suggested. A mechanism for the recognition of mRNAs downregulated by CsrA is proposed.

Solution structure of the Taf14 YEATS domain and its roles in cell growth of Saccharomyces cerevisiae

2011 ◽  
Vol 436 (1) ◽  
pp. 83-90 ◽  
Author(s):  
Wen Zhang ◽  
Jiahai Zhang ◽  
Xuecheng Zhang ◽  
Chao Xu ◽  
Xiaoming Tu
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Cell Growth ◽  
Transcriptional Activation ◽  
Solution Structure ◽  
Protein Complexes ◽  
Domain Family ◽  
Functional Studies ◽  
C Terminus ◽  
Eukaryotic Species ◽  
Negative Role

Chromatin modifications play important roles in cellular biological process. A novel conserved domain family, YEATS, has been discovered in a variety of eukaryotic species ranging from yeasts to humans. Taf14, which is involved in a few protein complexes of chromatin remodelling and gene transcription, and is essential for keeping chromosome stability, regular cell growth and transcriptional regulation, contains a YEATS domain at its N-terminus. In the present study, we determined the solution structure of the Taf14 YEATS domain using NMR spectroscopy. The Taf14 YEATS domain adopts a global fold of an elongated β-sandwich, similar to the Yaf9 YEATS domain. However, the Taf14 YEATS domain differs significantly from the Yaf9 YEATS domain in some aspects, which might indicate different structural classes of the YEATS domain family. Functional studies indicate that the YEATS domain is critical for the function of Taf14 in inhibiting cell growth under stress conditions. In addition, our results show that the C-terminus of Taf14 is responsible for its interaction with Sth1, which is an essential component of the RSC complex. Taken together, this implies that Taf14 is involved in transcriptional activation of Saccharomyces cerevisiae and the YEATS domain of Taf14 might play a negative role in cell growth.

scholarly journals A common binding motif in the ET domain of BRD3 forms polymorphic structural interfaces with host and viral proteins

2020 ◽  
Author(s):  
Sriram Aiyer ◽  
G.V.T. Swapna ◽  
Li-Chung Ma ◽  
Gaohua Liu ◽  
Jingzhou Hao ◽  
...  
Keyword(s):  
Molecular Recognition ◽  
Protein Interactions ◽  
Leukemia Virus ◽  
Cost Effective ◽  
Viral Proteins ◽  
Potential Range ◽  
Binding Motif ◽  
List Type ◽  
Nmr Studies ◽  
Β Sheet

SummaryThe extra-terminal (ET) domain of BRD3 is conserved among BET proteins (BRD2, BRD3, BRD4), interacting with multiple host and viral protein-protein networks. Solution NMR structures of complexes formed between BRD3-ET domain with either the 79-residue murine leukemia virus integrase (IN) C-terminal domain (IN329-408), or its 22-residue IN tail peptide (TP) (IN386-407) alone, reveal similar intermolecular three-stranded β-sheet formation. 15N relaxation studies reveal a 10-residue linker region (IN379-388) tethering the SH3 domain (IN329-378) to the ET-binding motif (IN389-405)-ET complex. This linker has restricted flexibility, impacting its potential range of orientations in the IN - nucleosome complex. The complex of the ET-binding peptide of host NSD3 protein (NSD3148-184) and BRD3-ET domain includes a similar three-stranded β-sheet interaction, but the orientation of the β−hairpin is flipped compared to the two IN : ET complexes. These studies expand our understanding of molecular recognition polymorphism in complexes of ET-binding motifs with viral and host proteins.HighlightsThe BRD3 ET domain binds to key peptide motifs of diverse host and viral proteins.These complexes reveal conformational plasticity in molecular recognition.NMR studies demonstrate restricted interdomain motion in the IN CTD / ET complex.A cost-effective approach is described for producing isotopically-labeled peptides.Etoc BlurbWe address structurally how the MLV Integrase (IN) usurps the host function of the BET protein through comparative studies of the IN : Brd3 ET complex with that of the host NSD3. MLV integration and thus its pathogenesis is driven through protein interactions of the IN : BET family.

Molecular characterization of two Schistosoma mansoni proteins sharing common motifs with the vif protein of HIV-1

Parasitology ◽  
1994 ◽  
Vol 108 (5) ◽  
pp. 533-542 ◽  
Author(s):  
J. Khalife ◽  
R. J. Pierce ◽  
C. Godin ◽  
A. Capron
Keyword(s):  
Schistosoma Mansoni ◽  
Consensus Sequence ◽  
Structural Features ◽  
Surface Proteins ◽  
Peptide Sequence ◽  
Major Band ◽  
C Terminus ◽  
Vif Protein ◽  
Hiv 1

SummaryWe have previously described a rat mAb directed against a peptide derived from the vif protein of HIV-1 that recognized two Schistosoma mansoni (Sm) antigens with a major band at 65 kDa. Epitope mapping of this mAb using overlapping hexapeptides derived from the vif peptide revealed that the motif recognized was PLPSVT. The screening of a Sm cDNA library led to the identification of two clones, Sm70 and Sm65. The two deduced protein sequences did not share any common structural features apart from the epitope recognized by the mAb (see below), and did not show significant identity to sequences present in the data bases. However, the N terminus of the deduced sequence of the Sm70 protein exhibits a consensus sequence known to be an ATP/GTP binding site. Furthermore, the C terminus of the deduced Sm65 protein sequence was found to contain a conserved hexapeptide with a consensus sequence LPETGE reported to be an important motif of the surface proteins of gram-positive cocci. Both proteins exhibit a peptide sequence (PLRSVT for Sm70 and PVGSVT for Sm65) similar to the epitope recognized by the mAb anti-vif. Western blotting experiments showed that the mAb anti-vif reacted with both proteins. However, only Sm65 was recognized by sera from HIV-1- seropositive individuals, whereas both proteins were recognized by S. mansoni-infected patients.

scholarly journals Identification of a Second CtBP Binding Site in Adenovirus Type 5 E1A Conserved Region 3

2008 ◽  
Vol 82 (17) ◽  
pp. 8476-8486 ◽  
Author(s):  
Rachel K. Bruton ◽  
Peter Pelka ◽  
Katie L. Mapp ◽  
Gregory J. Fonseca ◽  
Joseph Torchia ◽  
...  
Keyword(s):  
Transcriptional Activation ◽  
Adenovirus Type ◽  
Stable Complex ◽  
Binding Motif ◽  
Transcriptional Activation Domain ◽  
C Terminus ◽  
Reporter Assays ◽  
Conserved Region ◽  
Adenovirus Type 5 ◽  
Repressor Activity

ABSTRACT C-terminal binding protein (CtBP) binds to adenovirus early region 1A (AdE1A) through a highly conserved PXDLS motif close to the C terminus. We now have demonstrated that CtBP1 also interacts directly with the transcriptional activation domain (conserved region 3 [CR3]) of adenovirus type 5 E1A (Ad5E1A) and requires the integrity of the entire CR3 region for optimal binding. The interaction appears to be at least partially mediated through a sequence (161RRNTGDP167) very similar to a recently characterized novel CtBP binding motif in ZNF217 as well as other regions of CR3. Using reporter assays, we further demonstrated that CtBP1 represses Ad5E1A CR3-dependent transcriptional activation. Ad5E1A also appears to be recruited to the E-cadherin promoter through its interaction with CtBP. Significantly, Ad5E1A, CtBP1, and ZNF217 form a stable complex which requires CR3 and the PLDLS motif. It has been shown that Ad513SE1A, containing the CR3 region, is able to overcome the transcriptional repressor activity of a ZNF217 polypeptide fragment in a GAL4 reporter assay through recruitment of CtBP1. These results suggest a hitherto-unsuspected complexity in the association of Ad5E1A with CtBP, with the interaction resulting in transcriptional activation by recruitment of CR3-bound factors to CtBP1-containing complexes.

SAC3B is a target of CML19, the centrin 2 of Arabidopsis thaliana

2020 ◽  
Vol 477 (1) ◽  
pp. 173-189 ◽  
Author(s):  
Marco Pedretti ◽  
Carolina Conter ◽  
Paola Dominici ◽  
Alessandra Astegno
Keyword(s):  
Excision Repair ◽  
Complex Structure ◽  
Binding Motif ◽  
C Terminus ◽  
Repair Protein ◽  
Nucleotide Excision ◽  
Ef Hand ◽  
Molecular Determinants ◽  
Structure In Solution

Arabidopsis centrin 2, also known as calmodulin-like protein 19 (CML19), is a member of the EF-hand superfamily of calcium (Ca2+)-binding proteins. In addition to the notion that CML19 interacts with the nucleotide excision repair protein RAD4, CML19 was suggested to be a component of the transcription export complex 2 (TREX-2) by interacting with SAC3B. However, the molecular determinants of this interaction have remained largely unknown. Herein, we identified a CML19-binding site within the C-terminus of SAC3B and characterized the binding properties of the corresponding 26-residue peptide (SAC3Bp), which exhibits the hydrophobic triad centrin-binding motif in a reversed orientation (I8W4W1). Using a combination of spectroscopic and calorimetric experiments, we shed light on the SAC3Bp–CML19 complex structure in solution. We demonstrated that the peptide interacts not only with Ca2+-saturated CML19, but also with apo-CML19 to form a protein–peptide complex with a 1 : 1 stoichiometry. Both interactions involve hydrophobic and electrostatic contributions and include the burial of Trp residues of SAC3Bp. However, the peptide likely assumes different conformations upon binding to apo-CML19 or Ca2+-CML19. Importantly, the peptide dramatically increases the affinity for Ca2+ of CML19, especially of the C-lobe, suggesting that in vivo the protein would be Ca2+-saturated and bound to SAC3B even at resting Ca2+-levels. Our results, providing direct evidence that Arabidopsis SAC3B is a CML19 target and proposing that CML19 can bind to SAC3B through its C-lobe independent of a Ca2+ stimulus, support a functional role for these proteins in TREX-2 complex and mRNA export.

scholarly journals Comparison of two Turnip mosaic virus P1 proteins in their ability to co-localize with the Arabidopsis thaliana G3BP-2 protein

Virus Genes ◽  
2021 ◽  
Vol 57 (2) ◽  
pp. 233-237
Author(s):  
Hendrik Reuper ◽  
Björn Krenz
Keyword(s):  
Arabidopsis Thaliana ◽  
Mosaic Virus ◽  
Specific Interaction ◽  
Viral Proteins ◽  
Turnip Mosaic Virus ◽  
Stress Conditions ◽  
C Terminus ◽  
Positive Sense ◽  
Key Factor ◽  
Large Host

AbstractTurnip mosaic virus (TuMV), belonging to the genus Potyvirus (family Potyviridae), has a large host range and consists of a single-stranded positive sense RNA genome encoding 12 proteins, including the P1 protease. This protein which is separated from the polyprotein by cis cleavage at its respective C-terminus, has been attributed with different functions during potyviral infection of plants. P1 of Turnip mosaic virus (P1-TuMV) harbors an FGSF-motif and FGSL-motif at its N-terminus. This motif is predicted to be a binding site for the host Ras GTPase-activating protein-binding protein (G3BP), which is a key factor for stress granule (SG) formation in mammalian systems and often targeted by viruses to inhibit SG formation. We therefore hypothesized that P1-TuMV might interact with G3BP to control and regulate plant SGs to optimize cellular conditions for the production of viral proteins. Here, we analyzed the co-localization of the Arabidopsis thaliana G3BP-2 with the P1 of two TuMV isolates, namely UK 1 and DEU 2. Surprisingly, P1-TuMV-DEU 2 co-localized with AtG3BP-2 under abiotic stress conditions, whereas P1-TuMV-UK 1 did not. AtG3BP-2::RFP showed strong SGs formation after stress, while P1-UK 1::eGFP maintained a chloroplastic signal under stress conditions, the signal of P1-DEU 2::eGFP co-localized with that of AtG3BP-2::RFP. This indicates a specific interaction between P1-DEU 2 and the AtG3BP family which is not solely based on the canonical interaction motifs.

scholarly journals Elevated Expression of Toxin TisB Protects Persister Cells against Ciprofloxacin but Enhances Susceptibility to Mitomycin C

2021 ◽  
Vol 9 (5) ◽  
pp. 943
Author(s):  
Daniel Edelmann ◽  
Florian H. Leinberger ◽  
Nicole E. Schmid ◽  
Markus Oberpaul ◽  
Till F. Schäberle ◽  
...  
Keyword(s):  
Dna Damage ◽  
Mitomycin C ◽  
Transcriptional Activation ◽  
Structural Features ◽  
Atp Depletion ◽  
Transcriptional Level ◽  
Persister Cells ◽  
Sos Induction ◽  
Bacterial Chromosomes ◽  
Elevated Expression

Bacterial chromosomes harbor toxin-antitoxin (TA) systems, some of which are implicated in the formation of multidrug-tolerant persister cells. In Escherichia coli, toxin TisB from the tisB/istR-1 TA system depolarizes the inner membrane and causes ATP depletion, which presumably favors persister formation. Transcription of tisB is induced upon DNA damage due to activation of the SOS response by LexA degradation. Transcriptional activation of tisB is counteracted on the post-transcriptional level by structural features of tisB mRNA and RNA antitoxin IstR-1. Deletion of the regulatory RNA elements (mutant Δ1-41 ΔistR) uncouples TisB expression from LexA-dependent SOS induction and causes a ‘high persistence’ (hip) phenotype upon treatment with different antibiotics. Here, we demonstrate by the use of fluorescent reporters that TisB overexpression in mutant Δ1-41 ΔistR inhibits cellular processes, including the expression of SOS genes. The failure in SOS gene expression does not affect the hip phenotype upon treatment with the fluoroquinolone ciprofloxacin, likely because ATP depletion avoids strong DNA damage. By contrast, Δ1-41 ΔistR cells are highly susceptible to the DNA cross-linker mitomycin C, likely because the expression of SOS-dependent repair systems is impeded. Hence, the hip phenotype of the mutant is conditional and strongly depends on the DNA-damaging agent.

scholarly journals The Human T-Cell Leukemia Virus Type 1 Tax Protein Confers CBP/p300 Recruitment and Transcriptional Activation Properties to Phosphorylated CREB

2007 ◽  
Vol 28 (4) ◽  
pp. 1383-1392 ◽  
Author(s):  
Timothy R. Geiger ◽  
Neelam Sharma ◽  
Young-Mi Kim ◽  
Jennifer K. Nyborg
Keyword(s):  
T Cell ◽  
Transcriptional Activation ◽  
Leukemia Virus ◽  
Full Length ◽  
Viral Transcription ◽  
Physical Interaction ◽  
Cell Leukemia ◽  
Human T Cell ◽  
T Cell Leukemia Virus ◽  
P300 Recruitment

ABSTRACT The human T-cell leukemia virus-encoded oncoprotein Tax is a potent activator of viral transcription. Tax function is strictly dependent upon the cellular transcription factor CREB, and together they bind cAMP response elements within the viral promoter and mediate high-level viral transcription. Signal-dependent CREB phosphorylation at Ser133 (pCREB) correlates with the activation of transcription. This activation has been attributed to recruitment of the coactivators CBP/p300 via physical interaction with the KIX domain. Here we show that the promoter-bound Tax/pCREB complex strongly recruits the recombinant, purified full-length coactivators CBP and p300. Additionally, the promoter-bound Tax/pCREB (but not Tax/CREB) complex recruits native p300 and potently activates transcription from chromatin templates. Unexpectedly, pCREB alone failed to detectably recruit the full-length coactivators, despite strong binding to KIX. These observations are in marked contrast to those in published studies that have characterized the physical interaction between KIX and pCREB and extrapolated these results to the full-length proteins. Consistent with our observation that pCREB is deficient for binding of CBP/p300, pCREB alone failed to support transcriptional activation. These data reveal that phosphorylation of CREB is not sufficient for CBP/p300 recruitment and transcriptional activation. The regulation of transcription by pCREB is therefore more complex than is generally recognized, and coregulators, such as Tax, likely play a critical role in the modulation of pCREB function.

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