Biochemical and redox characterization of the Mediator complex and its associated transcription factor GeBPL, a GLABROUS1 enhancer binding protein
The eukaryotic Mediator integrates regulatory signals from promoter-bound transcription factors and transmits them to RNA polymerase II machinery. Although redox signaling is important in adjusting plant metabolism and development, nothing is known about a possible redox regulation of Mediator. Here, using pull-down and yeast two-hybrid assays, we demonstrate the association of MED10a, MED28 and MED32 Mediator subunits with the GLABROUS1 enhancer binding protein-like (GeBPL), a plant-specific transcription factor that binds a promoter containing CryR2 element. All the corresponding recombinant proteins form various types o...
Source: BJ Gene - April 16, 2015 Category: Biochemistry Authors: J Shaikhali, C Davoine, K Brännström, N ROUHIER, J Bygdell, S Björklund, G Wingsle Tags: BJ Plant Source Type: research
ABC50 mutants modify translation start codon selection
This study indicates that interfering with the function of ABC50 influences the accuracy of initiation codon selection. (Source: BJ Gene)
Source: BJ Gene - January 19, 2015 Category: Biochemistry Authors: J D Stewart, J L Cowan, L S Perry, M J Coldwell, C G Proud Tags: BJ Gene Source Type: research
The MAP kinase-interacting kinases regulate cell migration, vimentin expression and eIF4E/CYFIP1 binding
The MAP kinase-interacting kinases (Mnk1 and Mnk2) are activated by ERK and are best known for phosphorylating the translation initiation factor eIF4E. Genetic knockout of the Mnks impaired the migration of embryonic fibroblasts both in two-dimensional wound-healing experiments and in three-dimensional migration assays. Furthermore, a novel and selective Mnk inhibitor, Mnk-I1, which potently blocks eIF4E phosphorylation, blocked the migration of fibroblasts and cancer cells, without exerting ‘off-target’ effects on other signalling pathways such as Erk. Mnk-I1 or genetic knockout of the Mnks decreased the exp...
Source: BJ Gene - January 15, 2015 Category: Biochemistry Authors: J E Beggs, S Tian, G G Jones, J Xie, V Iadevaia, V Jenei, G J Thomas, C Gregory Proud Tags: BJ Signal Source Type: research
STAT2/IRF9 directs a prolonged ISGF3-like transcriptional response and antiviral activity in the absence of STAT1
Evidence is accumulating for the existence of a STAT2/IRF9-dependent, STAT1-independent IFNα signaling pathway. However, no detailed insight exists in the genome-wide transcriptional regulation and the biological implications of STAT2/IRF9 dependent IFNα signaling as compared to ISGF3. In hST2-U3C and mST2-MS1KO cells we observed that the IFNα-induced expression of OAS2 and Ifit1 correlated with the kinetics of STAT2 phosphorylation, and the presence of a STAT2/IRF9 complex requiring STAT2 phosphorylation and the STAT2 transactivation domain. Subsequent microarray analysis of IFNα treated WT and...
Source: BJ Gene - January 7, 2015 Category: Biochemistry Authors: K Blaszczyk, A Olejnik, H Nowicka, L Ozgyin, Y Chen, S Chmielewski, K Kostyrko, J Wesoly, B Laszlo Balint, C Lee, H A.R. Bluyssen Tags: BJ Signal Source Type: research
The regulatory role of Streptomyces coelicolor TamR in central metabolism
Trans-aconitate methyltransferase regulator (TamR) is a member of the ligand-responsive multiple antibiotic resistance regulator (MarR) family of transcription factors. In Streptomyces coelicolor, TamR regulates transcription of tamR (encoding TamR), tam (encoding trans-aconitate methyltransferase) and sacA (encoding aconitase); upregulation of these genes promotes metabolic flux through the citric acid cycle. DNA binding by TamR is attenuated and transcriptional derepression is achieved on binding of ligands such as citrate and trans-aconitate to TamR. Here we show that three additional genes are regulated by S. coelicolo...
Source: BJ Gene - December 11, 2014 Category: Biochemistry Authors: H Huang, S Sivapragasam, A Grove Tags: BJ Gene Source Type: research
Inositol pyrophosphates regulate RNA polymerase I-mediated rRNA transcription in Saccharomyces cerevisiae
We examined whether inositol pyrophosphates, energy-rich derivatives of inositol which act as metabolic messengers, play a role in ribosome synthesis in the budding yeast, Saccharomyces cerevisiae. Yeast lacking the IP6 kinase Kcs1, which is required for the synthesis of inositol pyrophosphates, display increased sensitivity to translation inhibitors and decreased protein synthesis. These phenotypes are reversed upon the expression of enzymatically active Kcs1, but not the inactive form. kcs1Δ yeast exhibit reduced levels of ribosome subunits, suggesting that they are defective in ribosome biogenesis. The rate of rR...
Source: BJ Gene - November 24, 2014 Category: Biochemistry Authors: S Gowri Thota, C Unnikannan, S R. Thampatty, R Manorama, R Bhandari Tags: BJ Signal Source Type: research
The structural basis of DNA binding by the single stranded DNA binding protein from Sulfolobus solfataricus
Canonical single-stranded DNA binding proteins (SSBs) from the Oligosaccharide/Oligonucleotide Binding (OB) domain family are present in all known organisms and are critical for DNA replication, recombination and repair. The SSB from the hyperthermophilic crenarchaeote Sulfolobus solfataricus (SsoSSB) has a ‘simple’ domain organisation consisting of a single DNA binding OB fold coupled to a flexible C-terminal tail, in contrast to other SSBs in this family that incorporate up to four OB domains. Despite the large differences in the domain organisation within the SSB family, the structure of the OB domain is r...
Source: BJ Gene - November 4, 2014 Category: Biochemistry Authors: R Gamsjaeger, R Kariawasam, A X Gimenez, C Touma, E McIlwain, R E Bernardo, N E Shepherd, S F Ataide, Q Dong, D J Richard, M F White, L Cubeddu Tags: BJ Biomolecules Source Type: research
AP2 suppresses osteoblast differentiation and mineralization through down-regulation of Frizzled-1
Transcription factor activating protein 2 (AP2) plays an important role in cellular differentiation. Although profound craniofacial and long bone developmental abnormalities have been observed in AP2 knockout mice, the molecular effects of AP2 on osteoblasts are poorly defined. We demonstrated that AP2 regulates the expression of human frizzled 1 (FZD1), a co-receptor for the Wnt signaling pathway, in human osteoblast cell lines and primary bone marrow stromal cells (BMSCs). We also identified a putative AP2 binding site in the FZD1 proximal promoter in silico and characterized this binding element further in Saos2 in vitr...
Source: BJ Gene - November 4, 2014 Category: Biochemistry Authors: S Yu, L M Yerges-Armstrong, Y Chu, J M Zmuda, Y Zhang Tags: BJ Gene Source Type: research
Eukaryotic elongation factor 2 kinase regulates the cold stress response by slowing translation elongation
Cells respond to external stress conditions by controlling gene expression, a process which occurs rapidly via post-transcriptional regulation at the level of protein synthesis. Global control of translation is mediated by modification of translation factors to allow reprogramming of the translatome and synthesis of specific proteins that are required for stress protection or initiation of apoptosis. Herein we have investigated how global protein synthesis rates are regulated upon mild cooling. We demonstrate that although there are changes to the factors that control initiation, including phosphorylation of eIF2 on the al...
Source: BJ Gene - October 29, 2014 Category: Biochemistry Authors: J RP Knight, A Bastide, A Roobol, J Roobol, T John Jackson, W Utami, D A Barrett, C Mark Smales, A E Willis Tags: BJ Gene Source Type: research
The architecture of an Okazaki fragment-processing holoenzyme from the archaeon Sulfolobus solfataricus
DNA replication on the lagging strand occurs via the synthesis and maturation of Okazaki fragments. In archaea and eukaryotes the enzymatic activities required for this process are supplied by a replicative DNA polymerase, Flap Endonuclease 1 (Fen1) and DNA ligase 1. These factors interact with the sliding clamp PCNA providing a potential means of coordinating their sequential actions within a higher order assembly. In hyperthermophilic archaea of the Sulfolobus genus PCNA is a defined heterotrimeric assembly and each subunit interacts preferentially with specific client proteins. We have exploited this inherent asymmetry ...
Source: BJ Gene - October 9, 2014 Category: Biochemistry Authors: G Cannone, Y Xu, T R. Beattie, S D Bell, L Spagnolo Tags: BJ Gene Source Type: research
Trace analysis of methylated and hydroxymethylated cytosines in DNA by isotope-dilution LC-MS/MS: first evidence of DNA methylation in Caenorhabditis elegans
Since 1986 till now, the popular research model organism Caenorhabditis elegans has been thought to completely lack DNA methylation and seems to lost DNA methylation enzymes from its genomes. Here we report the development of a sensitive and selective assay based on LC-MS/MS to simultaneously measure 5-methyl-2′-deoxycytidine (5-mdC) and 5-hydroxymethyl-2′-deoxycytidine (5-hmdC) in DNA hydrolysates. With the use of isotope internal standards (d3-5-mdC and d3-5-hmdC) and online solid-phase extraction, the detection limits of 5-mdC and 5-hmdC were estimated to be 0.01 and 0.02 pg, respectively, which correspond...
Source: BJ Gene - October 9, 2014 Category: Biochemistry Authors: C Hu, J Chen, Y Hsu, C Yen, M Chao Tags: BJ Biomolecules Source Type: research
DNA polymerase eta is regulated by poly(rC)-binding protein 1 via mRNA stability
In this study, we found that the levels of both POLH transcript and protein were decreased upon knockdown of the transcript encoding poly(rC)-binding protein 1 (PCBP1). We also found that the half-life of POLH mRNA was markedly decreased upon knockdown of PCBP1. Moreover, we found that PCBP1 directly bound to POLH 3'UTR and the PCBP1-binding site in POLH mRNA is an atypical AU-rich element. Finally, we showed that the AU-rich element in POLH 3'UTR was responsive to PCBP1 and sufficient for PCBP1 to regulate POLH expression. Altogether, we uncovered a novel mechanism by which POLH expression is controlled by PCBP1 via mRNA ...
Source: BJ Gene - September 30, 2014 Category: Biochemistry Authors: C Ren, S Cho, Y Jung, X Chen Tags: BJ Gene Source Type: research
Unlocked nucleic acids: implications of increased conformational flexibility for RNA/DNA triplex formation
Unlocked nucleic acids (UNAs) have been introduced at specific positions in short model DNA hairpins and RNA/DNA triplexes for the first time. UNA residues destabilize the hairpins and decrease triplex thermodynamic stability or suppress triplex formation for most of the evaluated structures. Nevertheless, the incorporation of UNA residues at certain positions of dsDNA was found to be energetically favorable or at least did not affect triplex stability. Notably, the most thermodynamically stable UNA-modified triplexes exhibited improved stability at both acidic and physiological pH. The specificity of the interactions betw...
Source: BJ Gene - September 16, 2014 Category: Biochemistry Authors: W Kotkowiak, M Kotkowiak, R Kierzek, A Pasternak Tags: BJ Biomolecules Source Type: research
Structural and functional features of Crl proteins and identification of conserved surface residues required for interaction with the RpoS/{sigma}S subunit of RNA polymerase
In many γ-proteobacteria, the RpoS/σS sigma factor associates with the core RNA polymerase (RNAP) to modify global gene transcription in stationary phase and under stress conditions. The small regulatory protein Crl stimulates the association of σS with the core RNAP in Escherichia coli and Salmonella enterica serovarTyphimurium (S. Typhimurium), through direct and specific interaction with σS. The structural determinants of Crl involved in σS binding are unknown. Here, we report the X-ray crystal structure of the Proteus mirabilis Crl protein (CrlPM) and a structural model for S. Typhimu...
Source: BJ Gene - July 24, 2014 Category: Biochemistry Authors: P Cavaliere, F Levi-Acobas, C Mayer, F A Saul, P England, P Weber, B Raynal, V Monteil, J Bellalou, A Haouz, F Norel Tags: BJ Gene Source Type: research
Pdx1 and USF transcription factors coordinately regulate Alx3 gene expression in pancreatic {beta} cells
In this study, we investigated the mechanisms that regulate expression of Alx3 in pancreatic islets at the transcriptional level. We found that the Alx3 promoter contains at least eight putative regulatory elements with an E-box consensus sequence, three of which were determined to be functional and required for Alx3 promoter activity by mutational analysis in transfected MIN6 b cells. We determined that these E-box elements are recognized by the basic helix–loop–helix transcription factors USF (upstream stimulatory factor) 1 and USF2. We also identified a highly conserved A-box in the Alx3 promoter that is r...
Source: BJ Gene - July 21, 2014 Category: Biochemistry Authors: A Fernández-Pérez, M Vallejo Tags: BJ Gene Source Type: research
