Structure of a dimeric crenarchaeal Cas6 enzyme with an atypical active site for CRISPR RNA processing
The competition between viruses and hosts is played out in all branches of life. Many prokaryotes have an adaptive immune system termed “CRISPR” which is based on the capture of short pieces of viral DNA. The captured DNA is integrated into the genomic DNA of the organism flanked by direct repeats, transcribed and processed to generate CRISPR RNA (crRNA) that is loaded into a variety of effector complexes. These complexes carry out sequence-specific detection and destruction of invading mobile genetic elements. Here we report the structure and activity of a Cas6 enzyme (Sso1437) from Sulfolobus solfataricus r...
Source: BJ Gene - March 25, 2013 Category: Biochemistry Authors: J Reeks, R D Sokolowski, S Graham, H Liu, J H Naismith, M F White Tags: BJ Gene Source Type: research
Single-strand promoter traps for bacterial RNA polymerase
Besides canonical double-strand DNA promoters, multisubunit RNA polymerases (RNAPs) recognize a number of specific single-strand DNA and RNA templates, resulting in synthesis of various types of RNA transcripts. The general recognition principles and the mechanisms of transcription initiation on these templates are not fully understood. To further investigate the molecular mechanisms underlying the transcription of single-strand templates by bacterial RNAP, we selected high affinity single-strand DNA aptamers that are specifically bound by RNAP holoenzyme, and characterized a novel class of aptamer-based transcription temp...
Source: BJ Gene - March 22, 2013 Category: Biochemistry Authors: D Pupov, D Esyunina, A Feklistov, A Kulbachinskiy Tags: BJ Gene Source Type: research
Nuclear Export Factor 3 is involved in regulating the expression of TGF-{beta}3 in an mRNA export activity-independent manner in mouse Sertoli cells
In this study, we found that mouse NXF3, specifically expressed in principal cells in segment II of the caput epididymis, as well as Sertoli cells in the mouse testis, was required to mediate TGF-β-induced down-regulation of TGF-β3 mRNA expression and protein secretion in Sertoli cells. In addition, NXF3 was also involved in TGF-β-induced transcriptional regulation of other genes associated with Sertoli cell maturation and the restructuring of the Sertoli cell blood-testis barrier (BTB), such as GATA1, WT1, Claudin11, and p21. The transcriptional regulation of NXF3 was mediated through physical interac...
Source: BJ Gene - February 25, 2013 Category: Biochemistry Authors: Y Yin, G Wang, N Liang, H Zhang, Z Liu, W Li, F Sun Tags: BJ Signal Source Type: research
Prediction of hammerhead ribozyme intracellular activity with the catalytic core fingerprint
Hammerhead ribozyme is a versatile tool for down-regulation of gene expression in vivo. Due to its small size and high activity, it is used as a model for RNA structure-function relationship studies. Here we describe a new extended hammerhead ribozyme HH-2 with a tertiary stabilizing motif constructed on the basis of the tetraloop receptor sequence. This ribozyme is very active in living cells but shows low activity in vitro. To understand it, we analyzed tertiary structure models of substrate:ribozyme complexes. We calculated six unique catalytic core geometry parameters as distances and angles between particular atoms th...
Source: BJ Gene - February 19, 2013 Category: Biochemistry Authors: M Magdalena Gabryelska, E Wyszko, M Szymański, M Popenda, J Barciszewski Tags: BJ Gene Source Type: research
V101L of human formyl peptide receptor 1 (FPR1) increases the receptor affinity and augments the antagonism mediated by cyclosporins
Genetic variation plays a major role in drug response variability. Cyclosporin A (CsA), a widely used immunosuppressive agent, is a specific antagonist for formyl peptide receptor 1 (FPR1), which is an important G protein-coupled chemoattractant receptor in the innate immune system. In order to study the variable responses of cyclosporins to different FPR1 mutants, we investigated the distribution of human FPR1 haplotypes among 209 healthy Han Chinese subjects. The haplotype pattern in Han Chinese were characterized based on five single nucleotide polymorphisms (SNPs), including rs5030878 (p.T11I), rs2070745 (p.V101L), rs5...
Source: BJ Gene - February 4, 2013 Category: Biochemistry Authors: C Zhou, Y Zhou, J Wang, Y Feng, H Wang, J Xue, Y Chen, R D. Ye, M Wang Tags: BJ Gene Source Type: research
Zc3h12c Inhibits Vascular Inflammation by Repressing NF-{kappa}B Activation and Proinflammatory Gene Expression in Endothelial Cells
Endothelial activation characterized by the expression of multiple chemokines and adhesive molecules is a critical initial step of vascular inflammation which results in recruitment of leukocytes into sub-endothelial layer of vascular wall and triggers vascular inflammatory diseases such as atherosclerosis. Although inhibiting the endothelial inflammation has already been well recognized as a therapeutic strategy in vascular inflammatory diseases, the therapeutic targets are still elusive. In the present study we found that Zc3h12c, a recently discovered CCCH-zinc finger containing protein, significantly inhibited endothel...
Source: BJ Gene - January 29, 2013 Category: Biochemistry Authors: L Liu, Z Zhou, S Huang, Y Guo, Y Fan, J Zhang, J Zhang, M Fu, Y Chen Tags: BJ Signal Source Type: research
The serine/threonine phosphatase PPM1B (PP2C{beta}) selectively modulates PPAR{gamma} activity
Reversible phosphorylation is a widespread molecular mechanism to regulate the function of cellular proteins, including transcription factors. Phosphorylation of the nuclear receptor Peroxisome Proliferator Activated Receptor γ (PPARγ)on two conserved serine residue (S112 and S273) results in altered transcriptional activity of this transcription factor. So far, only a very limited number of cellular enzymatic activities has been described which can dephosphorylate nuclear receptors. Here we used immunoprecipitation assays coupled to tandem mass spectrometry analysis to identify novel PPARγ regulating ...
Source: BJ Gene - January 15, 2013 Category: Biochemistry Authors: I Tasdelen, O van Beekum, O Gorbenko, V Fleskens, N J.F. van den Broek, A Koppen, N Hamers, R Berger, P J Coffer, A B. Brenkman, E Kalkhoven Tags: BJ Metabolism Source Type: research
Mammalian Trit1 is a tRNA[Ser]Sec-isopentenyl-transferase required for full selenoprotein expression
Selenoproteins are proteins carrying the rare amino acid selenocysteine (Sec). Full expression of selenoproteins requires modification of tRNA[Ser]Sec, including N6-isopentenylation of base A37. We show that Trit1 is a dimethylallyl:tRNA[Ser]Sec-transferase. Knockdown of Trit1 reduces expression of selenoproteins. Incubation of in vitro transcribed tRNA[Ser]Sec with recombinant Trit1 transfers [14C]-dimethylallyl pyrophosphate to tRNA[Ser]Sec. A37G tRNA[Ser]Sec is resistant to isopentenylation by Trit1. (Source: BJ Gene)
Source: BJ Gene - January 4, 2013 Category: Biochemistry Authors: N Fradejas, B A Carlson, E Rijntjes, N Becker, R Tobe, U Schweizer Tags: BJ Gene Source Type: research
