TAL Effectors Target the C-Terminal Domain of RNA Polymerase II (CTD) by Inhibiting the Prolyl-Isomerase Activity of a CTD-Associated Cyclophilin. Corrections 1 Jul 2013: Domingues MN, de Campos BM, de Oliveira MLP, de Mello UQ, Benedetti CE (2013)Correction: TAL Effectors Target the C-Terminal Domain of RNA Polymerase II (CTD) by Inhibiting the Prolyl-Isomerase Activity of a CTD-Associated Cyclophilin.PLoS ONE 8(7):10.1371/annotation/43ed8f9b-0e91-4474-b2bb-fadbd163d650. doi: 10.1371/annotation/43ed8f9b-0e91-4474-b2bb-fadbd163d650 | View correction Transcriptional activator-like (TAL) effectors of plant pathogenic bacteria function as transcription factors in plant cells. However, how TAL effectors control transcription in the host is presently unknown. Previously, we showed that TAL effectors of the citrus canker pathogen Xanthomonas citri, named PthAs, targeted the citrus protein complex comprising the thioredoxin CsTdx, ubiquitin-conjugating enzymes CsUev/Ubc13 and cyclophilin CsCyp.
Figures Editor: John W. Received: May 4, 2012; Accepted: June 24, 2012; Published: July 20, 2012 Copyright: © 2012 Domingues et al. Introduction. Global Analysis of the Small RNA Transcriptome in Different Ploidies and Genomic Combinations of a Vertebrate Complex – The Squalius alburnoides. The Squalius alburnoides complex (Steindachner) is one of the most intricate hybrid polyploid systems known in vertebrates. In this complex, the constant switch of the genome composition in consecutive generations, very frequently involving a change on the ploidy level, promotes repetitive situations of potential genomic shock. Previously in this complex, it was showed that in response to the increase in genome dosage, triploids hybrids could regulate gene expression to a diploid state. In this work we compared the small RNA profiles in the different genomic compositions interacting in the complex in order to explore the miRNA involvement in gene expression regulation of triploids.
Using high-throughput arrays and sequencing technologies we were able to verify that diploid and triploid hybrids shared most of their sequences and their miRNA expression profiles were high correlated. Editor: Reiner Albert Veitia, Institut Jacques Monod, France Copyright: © 2012 Inácio et al. Introduction. Evaluation of Four Different Systems for Extraction of RNA from Stool Suspensions Using MS-2 Coliphage as an Exogenous Control for RT-PCR Inhibition. Knowing when, and to what extent co-extracted inhibitors interfere with molecular RNA diagnostic assays is of utmost importance. The QIAamp Viral RNA Mini Kit (A); MagNA Pure LC2.0 Automatic extractor (B); KingFisher (C); and NucliSENS EasyMag (D) RNA extraction systems were evaluated for extraction efficiency and co-purification of inhibitors from stool suspensions. Real-Time Reverse Transcriptase Polymerase Chain Reaction (rRT-PCR) of MS-2 coliphage spiked into each system’s lysis buffer served as an external control for both.
Cycle thresholds (Cts) of the MS2 were determined for RNA extracted from stool suspensions containing unknown (n = 93) or varying amounts of inhibitors (n = 92). Stool suspensions from the latter group were also used to determine whether MS-2 and enterovirus rRT-PCR inhibitions were correlated. Figures Editor: Richard C. Received: March 29, 2012; Accepted: May 21, 2012; Published: July 16, 2012 Copyright: © 2012 Shulman et al. Introduction Results Table 1. 1. 1. Dicer-Dependent Biogenesis of Small RNAs Derived from 7SL RNA. It has been reported that decreased Dicer expression leads to Alu RNAs accumulation in human retinal pigmented epithelium cells, and Dicer may process the endogenous SINE/B1 RNAs (the rodent equivalent of the primate Alu RNAs) into small interfering RNAs (siRNAs). In this study, we aimed to address whether Dicer can process Alu RNAs and their common ancestor, 7SL RNA.
Using Solexa sequencing technology, we showed that Alu-derived small RNAs accounted for 0.6% of the total cellular small RNAs in HepG2.2.15 cells, and the abundance decreased when Dicer was knocked down. However, Alu-derived small RNAs showed different characteristics from miRNAs and siRNAs, the classic Dicer-processed products. Interestingly, we found that small RNAs derived from 7SL RNA accounted for 3.1% of the total cellular small RNAs in the control cells, and the abundance dropped about 3.4 folds in Dicer knockdown cells. Dicer-dependent biogenesis of 7SL RNA-derived small RNAs was validated by northern blotting. Evidence for a Non-Catalytic Ion-Binding Site in Multiple RNA-Dependent RNA Polymerases. A high-affinity divalent cation-binding site located proximal to the catalytic center has been identified in several RNA-dependent RNA polymerases (RdRps), but the characteristics of such a site have not been systematically studied. Here, all available polymerase structures that follow the hand-like structural motif were screened for the presence of a divalent cation close to the catalytic site but distinct from catalytic metal ions.
Such non-catalytic ions were found in all RNA virus families for which there were high-resolution RdRp structures available. Bound ions were always located in structurally similar locations at an approximate 6-Å distance from the catalytic site. Furthermore, the second aspartate residue in the highly conserved GDD sequence was found to be involved in the coordination of the bound ion in all viral RdRps studied. Citation: Mönttinen HAM, Ravantti JJ, Poranen MM (2012) Evidence for a Non-Catalytic Ion-Binding Site in Multiple RNA-Dependent RNA Polymerases. Conformational Features of Topologically Classified RNA Secondary Structures. Background Current RNA secondary structure prediction approaches predict prevalent pseudoknots such as the H-pseudoknot and kissing hairpin.
The number of possible structures increases drastically when more complex pseudoknots are considered, thus leading to computational limitations. On the other hand, the enormous population of possible structures means not all of them appear in real RNA molecules. Therefore, it is of interest to understand how many of them really exist and the reasons for their preferred existence over the others, as any new findings revealed by this study might enhance the capability of future structure prediction algorithms for more accurate prediction of complex pseudoknots. Methodology/Principal Findings A novel algorithm was devised to estimate the exact number of structural possibilities for a pseudoknot constructed with a specified number of base pair stems.
Conclusions Figures Editor: Hans-Joachim Wieden, University of Lethbridge, Canada Introduction is given by and. T7 RNA Polymerase Functions In Vitro without Clustering. Many nucleic acid polymerases function in clusters known as factories. We investigate whether the RNA polymerase (RNAP) of phage T7 also clusters when active. Using ‘pulldowns’ and fluorescence correlation spectroscopy we find that elongation complexes do not interact in vitro with a Kd<1 µM.
Chromosome conformation capture also reveals that genes located 100 kb apart on the E. coli chromosome do not associate more frequently when transcribed by T7 RNAP. We conclude that if clustering does occur in vivo, it must be driven by weak interactions, or mediated by a phage-encoded protein. Figures Citation: Finan K, Torella JP, Kapanidis AN, Cook PR (2012) T7 RNA Polymerase Functions In Vitro without Clustering. PLoS ONE 7(7): e40207. doi:10.1371/journal.pone.0040207 Editor: Jörg Langowski, German Cancer Research Center, Germany Received: January 12, 2012; Accepted: June 6, 2012; Published: July 2, 2012 Copyright: © 2012 Finan et al. Funding: K.F. was supported by the E.P. Introduction Results A. Isolation of Human Mitotic Protein Phosphatase Complexes: Identification of a Complex between Protein Phosphatase 1 and the RNA Helicase Ddx21. Metazoan mitosis requires remodelling of sub-cellular structures to ensure proper division of cellular and genetic material.
Faults often lead to genomic instability, cell cycle arrests and disease onset. These key structural changes are under tight spatial-temporal and post-translational control, with crucial roles for reversible protein phosphorylation. The phosphoprotein phosphatases PP1 and PP2A are paramount for the timely execution of mitotic entry and exit but their interaction partners and substrates are still largely unresolved. High throughput, mass-spectrometry based studies have limited sensitivity for the detection of low-abundance and transient complexes, a typical feature of many protein phosphatase complexes. Moreover, the limited timeframe during which mitosis takes place reduces the likelihood of identifying mitotic phosphatase complexes in asynchronous cells. Hence, numerous mitotic protein phosphatase complexes still await identification.
Figures Editor: Beata G. Reconstruction of Ribosomal RNA Genes from Metagenomic Data. Direct sequencing of environmental DNA (metagenomics) has a great potential for describing the 16S rRNA gene diversity of microbial communities. However current approaches using this 16S rRNA gene information to describe community diversity suffer from low taxonomic resolution or chimera problems. Here we describe a new strategy that involves stringent assembly and data filtering to reconstruct full-length 16S rRNA genes from metagenomicpyrosequencing data.
Simulations showed that reconstructed 16S rRNA genes provided a true picture of the community diversity, had minimal rates of chimera formation and gave taxonomic resolution down to genus level. The strategy was furthermore compared to PCR-based methods to determine the microbial diversity in two marine sponges. This showed that about 30% of the abundant phylotypes reconstructed from metagenomic data failed to be amplified by PCR. Figures Editor: Francisco Rodriguez-Valera, Universidad Miguel Hernandez, Spain Introduction Results. FusionFinder: A Software Tool to Identify Expressed Gene Fusion Candidates from RNA-Seq Data. Citation: Francis RW, Thompson-Wicking K, Carter KW, Anderson D, Kees UR, et al. (2012) FusionFinder: A Software Tool to Identify Expressed Gene Fusion Candidates from RNA-Seq Data. PLoS ONE 7(6): e39987. doi:10.1371/journal.pone.0039987 Editor: Steve Horvath, University of California, Los Angeles, United States of America Received: April 18, 2012; Accepted: May 30, 2012; Published: June 27, 2012 Copyright: © 2012 Francis et al.
This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: The study was funded by the WA State Government Centres of Excellence Program, the Children’s Leukaemia and Cancer Research Foundation, Perth and the Mike Schon-Hegrad Memorial Fund. Competing interests: The authors have declared that no competing interests exist. Introduction Results Figure 1. Step 1. Step 2. Step 3. Step 4. The RNA Binding Protein SAM68 Transiently Localizes in the Chromatoid Body of Male Germ Cells and Influences Expression of Select MicroRNAs. The chromatoid body (CB) is a unique structure of male germ cells composed of thin filaments that condense into a perinuclear organelle after meiosis.
Due to the presence of proteins involved in different steps of RNA metabolism and of different classes of RNAs, including microRNAs (miRNAs), the CB has been recently suggested to function as an RNA processing centre. Herein, we show that the RNA binding protein SAM68 transiently localizes in the CB, in concomitance with the meiotic divisions of mouse spermatocytes. Precise staging of the seminiferous tubules and co-localization studies with MVH and MILI, two well recognized CB markers, documented that SAM68 transiently associates with the CB in secondary spermatocytes and early round spermatids.
Furthermore, although SAM68 co-immunoprecipitated with MVH in secondary spermatocytes, its ablation did not affect the proper localization of MVH in the CB. Figures Received: April 2, 2012; Accepted: May 25, 2012; Published: June 22, 2012 Results. Fragile Mental Retardation Protein Interacts with the RNA-Binding Protein Caprin1 in Neuronal RiboNucleoProtein Complexes. Corrections 27 Sep 2012: El Fatimy R, Tremblay S, Dury AY, Solomon S, De Koninck P, et al. (2012)Correction: Fragile Mental Retardation Protein Interacts with the RNA-Binding Protein Caprin1 in Neuronal RiboNucleoProtein Complexes.PLoS ONE 7(9):10.1371/annotation/05374d07-34cf-483f-80f4-ec87374cbeb6. doi: 10.1371/annotation/05374d07-34cf-483f-80f4-ec87374cbeb6 | View correction Fragile X syndrome is caused by the absence of the Fragile X Mental Retardation Protein (FMRP), an RNA-binding protein.
FMRP is associated with messenger RiboNucleoParticles (mRNPs) present in polyribosomes and its absence in neurons leads to alteration in synaptic plasticity as a result of translation regulation defects. The molecular mechanisms by which FMRP plays a role in translation regulation remain elusive. Using immunoprecipitation approaches with monoclonal Ab7G1-1 and a new generation of chicken antibodies, we identified Caprin1 as a novel FMRP-cellular partner. Figures Copyright: © 2012 El Fatimy et al. Cohesin Proteins Promote Ribosomal RNA Production and Protein Translation in Yeast and Human Cells.
Abstract Cohesin is a protein complex known for its essential role in chromosome segregation. However, cohesin and associated factors have additional functions in transcription, DNA damage repair, and chromosome condensation. The human cohesinopathy diseases are thought to stem not from defects in chromosome segregation but from gene expression. The role of cohesin in gene expression is not well understood. Author Summary Cohesin is a protein complex known for its essential role in chromosome segregation. Figures Citation: Bose T, Lee KK, Lu S, Xu B, Harris B, et al. (2012) Cohesin Proteins Promote Ribosomal RNA Production and Protein Translation in Yeast and Human Cells.
Editor: Nancy B. Received: October 6, 2011; Accepted: April 19, 2012; Published: June 14, 2012 Copyright: © 2012 Bose et al. Funding: This work was supported by the Stowers Institute for Medical Research. Competing interests: The authors have declared that no competing interests exist. Introduction Results Figure 1. A. p180 Promotes the Ribosome-Independent Localization of a Subset of mRNA to the Endoplasmic Reticulum. Abstract In metazoans, the majority of mRNAs coding for secreted and membrane-bound proteins are translated on the surface of the endoplasmic reticulum (ER).
Although the targeting of these transcripts to the surface of the ER can be mediated by the translation of a signal sequence and their maintenance is mediated by interactions between the ribosome and the translocon, it is becoming increasingly clear that additional ER-localization pathways exist. Here we demonstrate that many of these mRNAs can be targeted to, and remain associated with, the ER independently of ribosomes and translation. Using a mass spectrometry analysis of proteins that associate with ER-bound polysomes, we identified putative mRNA receptors that may mediate this alternative mechanism, including p180, an abundant, positively charged membrane-bound protein.
Author Summary Figures Academic Editor: Michael A. Received: July 14, 2011; Accepted: April 12, 2012; Published: May 29, 2012 Copyright: © 2012 Cui et al. Results. Microbial Biogeography of Public Restroom Surfaces. We spend the majority of our lives indoors where we are constantly exposed to bacteria residing on surfaces. However, the diversity of these surface-associated communities is largely unknown. We explored the biogeographical patterns exhibited by bacteria across ten surfaces within each of twelve public restrooms.
Using high-throughput barcoded pyrosequencing of the 16 S rRNA gene, we identified 19 bacterial phyla across all surfaces. Most sequences belonged to four phyla: Actinobacteria, Bacteriodetes, Firmicutes and Proteobacteria. The communities clustered into three general categories: those found on surfaces associated with toilets, those on the restroom floor, and those found on surfaces routinely touched with hands. On toilet surfaces, gut-associated taxa were more prevalent, suggesting fecal contamination of these surfaces. Floor surfaces were the most diverse of all communities and contained several taxa commonly found in soils. Figures Editor: Mark R. Introduction Figure 1. Identification of Short Hairpin RNA Targeting Foot-And-Mouth Disease Virus with Transgenic Bovine Fetal Epithelium Cells.
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