Asymmetric arginine dimethylation of RelA provides a repressive mark to modulate TNFα/NF-κB response

Nuclear factor kappa B (NF-κB) is an inducible transcription factor that plays critical roles in immune and stress responses and is often implicated in pathologies, including chronic inflammation and cancer. Although much has been learned about NF-κB–activating pathways, the specific repression of NF-κB is far less well understood. Here we identified the type I protein arginine methyltransferase 1 (PRMT1) as a restrictive factor controlling TNFα-induced activation of NF-κB. PRMT1 forms a cellular complex with NF-κB through direct interaction with the Rel homology domain of RelA. We demonstrate that PRMT1 methylates RelA at evolutionary conserved R30, located in the DNA-binding L1 loop, which is a critical residue required for DNA binding. Asymmetric R30 dimethylation inhibits the binding of RelA to DNA and represses NF-κB target genes in response to TNFα. Molecular dynamics simulations of the DNA-bound RelA:p50 predicted structural changes in RelA caused by R30 methylation or a mutation that interferes with the stability of the DNA–NF-κB complex. Our findings provide evidence for the asymmetric arginine dimethylation of RelA and unveil a unique mechanism controlling TNFα/NF-κB signaling.

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Computational Identification of miRNAs and Temperature Responsive lncRNAs from Mango (Mangifera indica, L.)

10.21203/rs.3.rs-22698/v1 ◽

2020 ◽

Author(s):

Nann Miky Moh Moh ◽

Peijing Zhang ◽

Yujie Chen ◽

Ming Chen

Keyword(s):

Low Temperature ◽

Stress Responses ◽

Target Genes ◽

Mangifera Indica ◽

Enrichment Analysis ◽

Tropical Fruit ◽

Temperature Responsive ◽

New Information ◽

Go Enrichment ◽

The Stability

Abstract Background Mango is a major tropical fruit in the world and is known as the king of fruits because of its flavour, aroma, taste, and nutritional values. Moreover, various parts of mango trees have been used for medical purposes. Although various regulatory roles of miRNAs and lncRNAs have been investigated in many plants, there is yet an absence of study in mango. This is the first study to provide information on ncRNAs of mango with the aim of identifying miRNAs and lncRNAs of mango and discovering of their potential functions by the interaction prediction of the miRNAs, lncRNAs and their target genes. Results In this analysis, 104 miRNAs and 7,610 temperature responsive lncRNAs were identified and the target genes of these ncRNAs were characterized. By analysing the interaction of miRNAs and their target genes, it was observed that miRNAs are mainly involved in growth, development, and stress responses of mango. For the lncRNAs, cold responsive lncRNAs bound to low temperature responsive proteins expressed at low temperature stress. GO enrichment analysis of heat and cold responsive lncRNAs revealed that they involved in all three basic processes; biological process, cellular component, and molecular function. Moreover, mango lncRNAs can target miRNAs to reduce the stability of lncRNAs and can function as molecular decoys or sponges of miRNAs. Conclusion This paper would provide the new information about miRNAs and lncRNAs of mango and would help for the further investigation of mango ncRNAs.

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Distinct roles for the two cGATA-1 finger domains

Molecular and Cellular Biology ◽

10.1128/mcb.12.10.4562-4570.1992 ◽

1992 ◽

Vol 12 (10) ◽

pp. 4562-4570

Author(s):

H Y Yang ◽

T Evans

Keyword(s):

Dna Binding ◽

Target Genes ◽

Dna Binding Domain ◽

Mouse Homolog ◽

Cis Element ◽

Functional Assays ◽

Binding Function ◽

The Family ◽

The Stability ◽

Basic Region

We have generated and analyzed by functional assays mutations of the chicken erythroid transcription factor GATA-1. The cGATA-1 protein contains two related finger domains highly conserved across species and characteristic of the family of GATA-binding factors. We find that mutations in the C-terminal finger or adjacent basic region abolish sequence-specific DNA binding, confirming that this region constitutes a novel DNA-binding domain sufficient to recognize the consensus WGATAR motif. At least three separate regions outside of this finger II domain contribute in a cooperative manner to the trans-activation potential of the protein. As expected from previous results analyzing the mouse homolog, we find that the N-terminal finger plays a role in DNA binding by affecting the stability of the DNA-protein complex. In addition, we find mutations of finger I subtly altered in DNA-binding function which greatly diminish trans-activation. Our results support the notion that the GATA-1 protein must be positioned precisely on the GATA cis element to enable the activation of target genes.

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Modulation of androgen receptor DNA binding activity through direct interaction with the ETS transcription factor ERG

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1922159117 ◽

2020 ◽

Vol 117 (15) ◽

pp. 8584-8592 ◽

Cited By ~ 3

Author(s):

Elizabeth V. Wasmuth ◽

Elizabeth A. Hoover ◽

Albert Antar ◽

Sebastian Klinge ◽

Yu Chen ◽

...

Keyword(s):

Prostate Cancer ◽

Androgen Receptor ◽

Dna Binding ◽

Direct Interaction ◽

Binding Activity ◽

Nuclear Hormone Receptor ◽

Type I ◽

Minimal Cell ◽

Normal Prostate ◽

Free System

The androgen receptor (AR) is a type I nuclear hormone receptor and the primary drug target in prostate cancer due to its role as a lineage survival factor in prostate luminal epithelium. In prostate cancer, the AR cistrome is reprogrammed relative to normal prostate epithelium and particularly in cancers driven by oncogenic ETS fusion genes. The molecular basis for this change has remained elusive. Using purified proteins, we report a minimal cell-free system that demonstrates interdomain cooperativity between the ligand (LBD) and DNA binding domains (DBD) of AR, and its autoinhibition by the N terminus of AR. Furthermore, we identify ERG as a cofactor that activates AR’s ability to bind DNA in both high and lower affinity contexts through direct interaction within a newly identified AR-interacting motif (AIM) in the ETS domain, independent of ERG’s own DNA binding ability. Finally, we present evidence that this interaction is conserved among ETS factors whose expression is altered in prostate cancer. Our work highlights, at a biochemical level, how tumor-initiating ETS translocations result in reprogramming of the AR cistrome.

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Sequences flanking the core-binding site modulate glucocorticoid receptor structure and activity

Nature Communications ◽

10.1038/ncomms12621 ◽

2016 ◽

Vol 7 (1) ◽

Cited By ~ 24

Author(s):

Stefanie Schöne ◽

Marcel Jurk ◽

Mahdi Bagherpoor Helabad ◽

Iris Dror ◽

Isabelle Lebars ◽

...

Keyword(s):

Dna Binding ◽

Glucocorticoid Receptor ◽

Binding Site ◽

Structural Changes ◽

Target Genes ◽

Quaternary Structure ◽

Dimensional Structure ◽

Genomic Context ◽

The Core ◽

Induced Changes

Abstract The glucocorticoid receptor (GR) binds as a homodimer to genomic response elements, which have particular sequence and shape characteristics. Here we show that the nucleotides directly flanking the core-binding site, differ depending on the strength of GR-dependent activation of nearby genes. Our study indicates that these flanking nucleotides change the three-dimensional structure of the DNA-binding site, the DNA-binding domain of GR and the quaternary structure of the dimeric complex. Functional studies in a defined genomic context show that sequence-induced changes in GR activity cannot be explained by differences in GR occupancy. Rather, mutating the dimerization interface mitigates DNA-induced changes in both activity and structure, arguing for a role of DNA-induced structural changes in modulating GR activity. Together, our study shows that DNA sequence identity of genomic binding sites modulates GR activity downstream of binding, which may play a role in achieving regulatory specificity towards individual target genes.

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Distinct roles for the two cGATA-1 finger domains.

Molecular and Cellular Biology ◽

10.1128/mcb.12.10.4562 ◽

1992 ◽

Vol 12 (10) ◽

pp. 4562-4570 ◽

Cited By ~ 90

Author(s):

H Y Yang ◽

T Evans

Keyword(s):

Dna Binding ◽

Target Genes ◽

Dna Binding Domain ◽

Mouse Homolog ◽

Cis Element ◽

Functional Assays ◽

Binding Function ◽

The Family ◽

The Stability ◽

Basic Region

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Molecular Basis Distinguishing the DNA Binding Profile of Nrf2-Maf Heterodimer from That of Maf Homodimer

Journal of Biological Chemistry ◽

10.1074/jbc.m706863200 ◽

2007 ◽

Vol 282 (46) ◽

pp. 33681-33690 ◽

Cited By ~ 66

Author(s):

Momoko Kimura ◽

Tae Yamamoto ◽

Jianyong Zhang ◽

Ken Itoh ◽

Motoki Kyo ◽

...

Keyword(s):

Surface Plasmon Resonance ◽

Dna Binding ◽

Surface Plasmon ◽

Plasmon Resonance ◽

Stress Responses ◽

Molecular Basis ◽

Target Genes ◽

Binding Specificity ◽

Critical Determinant ◽

Binding Profile

Nrf2-small Maf heterodimer activates the transcription of many cytoprotective genes through the antioxidant response element and serves as a key factor in xenobiotic and oxidative stress responses. Our surface plasmon resonance-microarray binding analysis revealed that both Nrf2-MafG heterodimer and MafG homodimer bind to the consensus Maf recognition element with high affinity but bind differentially to the suboptimal binding sequences degenerated from the consensus. We examined the molecular basis distinguishing the binding profile of Nrf2-MafG heterodimer from that of MafG homodimer and found that the Ala-502 residue in the basic region of Nrf2 is a critical determinant of its binding specificity. In Maf proteins, a tyrosine resides in the position corresponding to Ala-502 in Nrf2. We prepared a mutant Nrf2 molecule in which Ala-502 was replaced with tyrosine. In surface plasmon resonance-microarray analysis, heterodimer of Nrf2(A502Y) and MafG displayed a binding specificity similar to that of MafG homodimer. The target genes activated by mutant Nrf2(A502Y)-small Maf heterodimer were largely different, albeit with some overlap, from those activated by wild-type Nrf2-small Maf, indicating that the array of target genes regulated by Nrf2-small Maf heterodimer differs substantially from that regulated by Maf homodimer in vivo. These results suggest that the distinct DNA binding profile of Nrf2-Maf heterodimer is biologically significant for Nrf2 to function as a key regulator of cytoprotective genes. Our contention is supported that the differential DNA binding specificity between Maf homodimers and Nrf2-Maf heterodimers establishes the differential gene regulation by these dimer-forming transcription factors.

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Protein Phosphatases Type 2C Group A Interact with and Regulate the Stability of ACC Synthase 7 in Arabidopsis

Cells ◽

10.3390/cells9040978 ◽

2020 ◽

Vol 9 (4) ◽

pp. 978 ◽

Cited By ~ 4

Author(s):

Małgorzata Marczak ◽

Agata Cieśla ◽

Maciej Janicki ◽

Anna Kasprowicz-Maluśki ◽

Piotr Kubiak ◽

...

Keyword(s):

Stress Responses ◽

Acc Synthase ◽

Ethylene Biosynthesis ◽

Negative Regulator ◽

Type I ◽

Amino Acid Residues ◽

Regulatory Domains ◽

Group A ◽

A Cell ◽

The Stability

Ethylene is an important plant hormone that controls growth, development, aging and stress responses. The rate-limiting enzymes in ethylene biosynthesis, the 1-aminocyclopropane-1-carboxylate synthases (ACSs), are strictly regulated at many levels, including posttranslational control of protein half-life. Reversible phosphorylation/dephosphorylation events play a pivotal role as signals for ubiquitin-dependent degradation. We showed previously that ABI1, a group A protein phosphatase type 2C (PP2C) and a key negative regulator of abscisic acid signaling regulates type I ACS stability. Here we provide evidence that ABI1 also contributes to the regulation of ethylene biosynthesis via ACS7, a type III ACS without known regulatory domains. Using various approaches, we show that ACS7 interacts with ABI1, ABI2 and HAB1. We use molecular modeling to predict the amino acid residues involved in ABI1/ACS7 complex formation and confirm these predictions by mcBiFC–FRET–FLIM analysis. Using a cell-free degradation assay, we show that proteasomal degradation of ACS7 is delayed in protein extracts prepared from PP2C type A knockout plants, compared to a wild-type extract. This study therefore shows that ACS7 undergoes complex regulation governed by ABI1, ABI2 and HAB1. Furthermore, this suggests that ACS7, together with PP2Cs, plays an essential role in maintaining appropriate levels of ethylene in Arabidopsis.

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Fine-tuning the Spike: Role of the nature and topology of the glycan shield structure and dynamics of SARS-CoV-2 S

10.1101/2021.04.01.438036 ◽

2021 ◽

Author(s):

Aoife M Harbison ◽

Carl A Fogarty ◽

Toan K Phung ◽

Akash Satheesan ◽

Benjamin L. Schulz ◽

...

Keyword(s):

Glycosylation Site ◽

Fine Tuning ◽

Type I ◽

Functional Roles ◽

Functional Sites ◽

Structure And Dynamics ◽

Fusion Glycoprotein ◽

Sequence Reconstruction ◽

The Stability ◽

Dynamics Simulations

The SARS-CoV-2 spike (S) is a type I fusion glycoprotein, responsible for initiating the infection leading to COVID19. As a feature unique of SARS-CoV-2, the thick glycan shield covering the S protein is not only essential for hiding the virus from immune detection, but it also plays multiple functional roles, stabilising the S prefusion open conformation, which is competent for binding the ACE2 primary receptor, and gating the open-to-close transitions. This newly discovered functions of the glycan shield suggest the evolution of its sites of glycosylation is potentially intertwined with the evolution of the overall protein sequence to affect optimal activity. Furthermore, recent studies indicate that the occupancy and structures of SARS-CoV-2 S glycosylation depends not only on the host-cell, but also on the structural stability of the prefusion trimer; a point that raises important questions about the relative binding competence of different glycoforms. In this work we use multi-microsecond molecular dynamics simulations to characterize the structure and dynamics of different SARS-CoV-2 S models with different N-glycans at key functional sites, namely N234, N165 and N343. We also assessed the effect of a change in the SARS-CoV-2 S glycan shield topology at N370, due to the recently acquired T372A mutation. Our results indicate that the structures of the N-glycans at N234, N165 and N343 affect the stability of the active (or open) S conformation, and thus its exposure and accessibility. Furthermore, while glycosylation at N370 stabilizes the open S conformation, we find that the N370 glycan binds the closed receptor binding domain (RBD) surface, essentially tying the closed protomers together. These results suggest that the loss of the N370 glycosylation site in SARS-CoV-2 may have increased the availability of the open S form, perhaps contributing to its higher infectivity relative to CoV1 and other variants carrying the sequon. Finally, we discuss these specific changes to the topology of the SARS-CoV-2 S glycan shield through ancestral sequence reconstruction of select SARS strains and discuss how they may have evolved to affect S activity.

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PGAM5-MAVS interaction regulates TBK1/ IRF3 dependent antiviral responses

Scientific Reports ◽

10.1038/s41598-020-65155-1 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Yu-qiang Yu ◽

Marta Zielinska ◽

Wei Li ◽

Dominic B. Bernkopf ◽

Christiane Silke Heilingloh ◽

...

Keyword(s):

Defense Mechanisms ◽

Cellular Response ◽

Target Genes ◽

Viral Infections ◽

Mitochondrial Protein ◽

Direct Interaction ◽

Type I Interferons ◽

Poly I:C ◽

Phosphoglycerate Mutase ◽

Type I

Abstract Viral infections trigger host innate immune responses, characterized by the production of type-I interferons (IFN) including IFNβ. IFNβ induces cellular antiviral defense mechanisms and thereby contributes to pathogen clearance. Accumulating evidence suggests that mitochondria constitute a crucial platform for the induction of antiviral immunity. Here we demonstrate that the mitochondrial protein phosphoglycerate mutase family member 5 (PGAM5) is important for the antiviral cellular response. Following challenge of HeLa cells with the dsRNA-analog poly(I:C), PGAM5 oligomers and high levels of PGAM5 were found in mitochondrial aggregates. Using immunoprecipitation, a direct interaction of PGAM5 with the mitochondrial antiviral-signaling protein (MAVS) was demonstrated. In addition, PGAM5 deficient cells showed diminished expression of IFNβ and IFNβ target genes as compared to WT cells. Moreover, PGAM5 deficient mouse embryonic fibroblasts (MEFs) exhibited decreased phosphorylation levels of IRF3 and TBK1 when challenged with poly(I:C) intracellularly. Finally, PGAM5 deficient MEFs, upon infection with vesicular stomatitis virus (VSV), revealed diminished IFNβ expression and increased VSV replication. Collectively, our study highlights PGAM5 as an important regulator for IFNβ production mediated via the TBK1/IRF3 signaling pathway in response to viral infection.

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The Role of Hydrophobicity in the Stability and pH-Switchability of (RXDX)4 and Coumarin-RXDX Conjugate β-Sheets

10.26434/chemrxiv.11493060 ◽

2020 ◽

Author(s):

Ryan Weber ◽

Martin McCullagh

Keyword(s):

Biological Imaging ◽

Ph Sensing ◽

Hydrophobic Residue ◽

Ideal Candidate ◽

Self Assembling ◽

Sensing Applications ◽

Β Sheets ◽

The Stability ◽

Dynamics Simulations

pH-switchable, self-assembling materials are of interest in biological imaging and sensing applications. Here we propose that combining the pH-switchability of RXDX (X=Ala, Val, Leu, Ile, Phe) peptides and the optical properties of coumarin creates an ideal candidate for these materials. This suggestion is tested with a thorough set of all-atom molecular dynamics simulations. We first investigate the dependence of pH-switchabiliy on the identity of the hydrophobic residue, X, in the bare (RXDX)4 systems. Increasing the hydrophobicity stabilizes the fiber which, in turn, reduces the pH-switchabilty of the system. This behavior is found to be somewhat transferable to systems in which a single hydrophobic residue is replaced with a coumarin containing amino acid. In this case, conjugates with X=Ala are found to be unstable and both pHs while conjugates with X=Val, Leu, Ile and Phe are found to form stable β-sheets at least at neutral pH. The (RFDF)4-coumarin conjugate is found to have the largest relative entropy value of 0.884 +/- 0.001 between neutral and acidic coumarin ordering distributions. Thus, we posit that coumarin-(RFDF)4 containing peptide sequences are ideal candidates for pH-sensing bioelectronic materials.

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