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https://www.readbyqxmd.com/read/28735396/isolation-of-polysomal-rna-for-analyzing-stress-responsive-genes-regulated-at-the-translational-level-in-plants
#1
Yong-Fang Li, Ramamurthy Mahalingam, Ramanjulu Sunkar
Alteration of gene expression is an essential mechanism, which allows plants to respond and adapt to adverse environmental conditions. Transcriptome and proteome analyses in plants exposed to abiotic stresses revealed that protein levels are not correlated with the changes in corresponding mRNAs, indicating regulation at translational level is another major regulator for gene expression. Analysis of translatome, which refers to all mRNAs associated with ribosomes, thus has the potential to bridge the gap between transcriptome and proteome...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28731305/the-role-of-lead-ii-in-nucleic-acids
#2
Joana Palou-Mir, Miquel Barceló-Oliver, Roland K O Sigel
Although lead(II) is naturally not associated with nucleic acids, this metal ions has been applied with DNA and RNA in various contexts. Pb2+ is an excellent hydrolytic metal ion for nucleic acids, which is why it is mainly used as probing agent for secondary structure and to determine metal ion binding sites both in vitro and in vivo. A further application of lead(II) is in structural studies, i.e., NMR, but also in X-ray crystallography, mostly using this heavy metal to solve the phase problem in the latter method...
April 10, 2017: Metal Ions in Life Sciences
https://www.readbyqxmd.com/read/28730145/prokaryotic-rna-associated-to-bacterial-viability-induces-polymorphonuclear-neutrophil-activation
#3
Nahuel Rodriguez-Rodrigues, Luis A Castillo, Verónica I Landoni, Daiana Martire-Greco, M Ayelén Milillo, Paula Barrionuevo, Gabriela C Fernández
Polymorphonuclear neutrophils (PMN) are the first cellular line of antibacterial host defense. They sense pathogens through recognition of pathogen-associated molecular patterns (PAMPs) by innate pattern recognition receptors, such as Toll-like receptors (TLR). The aim of this study was to investigate whether PMN sense bacterial viability and explore which viability factor could be involved in this phenomenon. For this purpose, different functions were evaluated in isolated human PMN using live Escherichia coli (Ec) and heat-killed Ec (HK-Ec)...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/28729959/shot-gun-proteome-and-transcriptome-mapping-of-the-jujube-floral-organ-and-identification-of-a-pollen-specific-s-locus-f-box-gene
#4
Ruihong Chen, Guoliang Chen, Jian Huang
The flower is a plant reproductive organ that forms part of the fruit produced as the flowering season ends. While the number and identity of proteins expressed in a jujube (Ziziphus jujuba Mill.) flower is currently unknown, integrative proteomic and transcriptomic analyses provide a systematic strategy of characterizing the floral biology of plants. We conducted a shotgun proteomic analysis on jujube flowers by using a filter-aided sample preparation tryptic digestion, followed by liquid chromatography-tandem mass spectrometry (LC-MS/MS)...
2017: PeerJ
https://www.readbyqxmd.com/read/28729872/plc-mediated-signaling-pathway-in-pollen-tubes-regulates-the-gametophytic-self-incompatibility-of-pyrus-species
#5
Haiyong Qu, Yaqin Guan, Yongzhang Wang, Shaolin Zhang
Among the Rosaceae species, the gametophytic self-incompatibility (GSI) is controlled by a single multi-allelic S locus, which is composed of the pistil-S and pollen-S genes. The pistil-S gene encodes a polymorphic ribonuclease (S-RNase), which is essential for identifying self-pollen. However, the S-RNase system has not been fully characterized. In this study, the self-S-RNase inhibited the Ca(2+)-permeable channel activity at pollen tube apices and the selectively decreased phospholipase C (PLC) activity in the plasma membrane of Pyrus pyrifolia pollen tubes...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28719000/zc3h12a-mcpip1-regnase-1-related-endonucleases-an-evolutionary-perspective-on-molecular-mechanisms-and-biological-functions
#6
REVIEW
Cornelia Habacher, Rafal Ciosk
The mammalian Zc3h12a/MCPIP1/Regnase-1, an extensively studied regulator of inflammatory response, is the founding member of a ribonuclease family, which includes proteins related by the presence of the so-called Zc3h12a-like NYN domain. Recently, several related proteins have been described in Caenorhabditis elegans, allowing comparative evaluation of molecular functions and biological roles of these ribonucleases. We discuss the structural features of these proteins, which endow some members with ribonuclease (RNase) activity while others with auxiliary or RNA-independent functions...
July 18, 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/28717203/genome-wide-identification-and-characterization-of-circular-rnas-by-high-throughput-sequencing-in-soybean
#7
Wei Zhao, Yihui Cheng, Chi Zhang, Qingbo You, Xinjie Shen, Wei Guo, Yongqing Jiao
Circular RNAs (circRNAs) arise during pre-mRNA splicing, in which the 3' and 5' ends are linked to each other by a covalent bond. Soybean is an ancient tetraploid, which underwent two whole genome duplications. Most of soybean genes are paralogous genes with multiple copies. Although many circRNAs have been identified in animals and plants, little is known about soybean circRNAs, especially about circRNAs derived from paralogous genes. Here, we used deep sequencing technology coupled with RNase R enrichment strategy and bioinformatic approach to uncover circRNAs in soybean...
July 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28715256/structural-basis-for-activation-of-an-archaeal-ribonuclease-p-rna-by-protein-cofactors
#8
Makoto Kimura
Ribonuclease P (RNase P) is an endoribonuclease that catalyzes the processing of the 5'-leader sequence of precursor tRNA (pre-tRNA) in all phylogenetic domains. We have found that RNase P in the hyperthermophilic archaeon Pyrococcus horikoshii OT3 consists of RNase P RNA (PhopRNA) and five protein cofactors designated PhoPop5, PhoRpp21, PhoRpp29, PhoRpp30, and PhoRpp38. Biochemical characterizations over the past 10 years have revealed that PhoPop5 and PhoRpp30 fold into a heterotetramer and cooperate to activate a catalytic domain (C-domain) in PhopRNA, whereas PhoRpp21 and PhoRpp29 form a heterodimer and function together to activate a specificity domain (S-domain) in PhopRNA...
July 17, 2017: Bioscience, Biotechnology, and Biochemistry
https://www.readbyqxmd.com/read/28710133/novel-stress-inducible-antisense-rnas-of-protein-coding-loci-are-synthesized-by-rna-dependent-rna-polymerase
#9
Akihiro Matsui, Kei Iida, Maho Tanaka, Katsushi Yamaguchi, Kayoko Mizunashi, Jong-Myong Kim, Satoshi Takahashi, Norio Kobayashi, Shuji Shigenobu, Kazuo Shinozaki, Motoaki Seki
Our previous study identified approximately 6,000 abiotic stress-responsive non-coding transcripts existing on the antisense strand of protein-coding genes, and implied that a type of antisense RNA was synthesized from a sense RNA template by a study of RNA-dependent RNA polymerase (RDR). Expression analyses revealed that the expression of novel abiotic stress-induced antisense RNA on 1,136 gene loci was reduced in the rdr1/2/6 mutants. RNase protection indicated that the RD29A antisense RNA and other RDR1/2/6-dependent antisense RNAs are involved in the formation of double-stranded RNA...
July 14, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28704808/enhanced-reactive-oxygen-species-production-acidic-cytosolic-ph-and-upregulated-na-h-exchanger-nhe-in-dicer-deficient-cd4-t-cells
#10
Yogesh Singh, Yuetao Zhou, Shaqiu Zhang, Khalid N M Abdelazeem, Bernat Elvira, Madhuri S Salker, Florian Lang
BACKGROUND: MicroRNAs (miRNAs) negatively regulate gene expression at a post-transcriptional level. Dicer, a cytoplasmic RNase III enzyme, is required for the maturation of miRNAs from precursor miRNAs. Dicer, therefore, is a critical enzyme involved in the biogenesis and processing of miRNAs. Several biological processes are controlled by miRNAs, including the regulation of T cell development and function. T cells generate reactive oxygen species (ROS) with parallel H+ extrusion accomplished by the Na+/H+-exchanger 1 (NHE1)...
July 14, 2017: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/28698277/deep-sea-hydrothermal-vent-viruses-compensate-for-microbial-metabolism-in-virus-host-interactions
#11
Tianliang He, Hongyun Li, Xiaobo Zhang
Viruses are believed to be responsible for the mortality of host organisms. However, some recent investigations reveal that viruses may be essential for host survival. To date, it remains unclear whether viruses are beneficial or harmful to their hosts. To reveal the roles of viruses in the virus-host interactions, viromes and microbiomes of sediment samples from three deep-sea hydrothermal vents were explored in this study. To exclude the influence of exogenous DNAs on viromes, the virus particles were purified with nuclease (DNase I and RNase A) treatments and cesium chloride density gradient centrifugation...
July 11, 2017: MBio
https://www.readbyqxmd.com/read/28697848/roles-of-rnase-p-and-its-subunits
#12
REVIEW
Nayef Jarrous
Recent studies show that nuclear RNase P is linked to chromatin structure and function. Thus, variants of this ribonucleoprotein (RNP) complex bind to chromatin of small noncoding RNA genes; integrate into initiation complexes of RNA polymerase (Pol) III; repress histone H3.3 nucleosome deposition; control tRNA and PIWI-interacting RNA (piRNA) gene clusters for genome defense; and respond to Werner syndrome helicase (WRN)-related replication stress and DNA double-strand breaks (DSBs). Likewise, the related RNase MRP and RMRP-TERT (telomerase reverse transcriptase) are implicated in RNA-dependent RNA polymerization for chromatin silencing, whereas the telomerase carries out RNA-dependent DNA polymerization for telomere lengthening...
July 8, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28696260/biophysical-analysis-of-arabidopsis-protein-only-rnase-p-alone-and-in-complex-with-trna-provides-a-refined-model-of-trna-binding
#13
Franziska Pinker, Cédric Schelcher, Pablo Fernández-Millán, Anthony Gobert, Catherine Birck, Aurélien Thureau, Pierre Roblin, Philippe Giegé, Claude Sauter
RNase P is a universal enzyme that removes 5' leader sequences from tRNA precursors. The enzyme is therefore essential for maturation of functional tRNAs and mRNA translation. RNase P represents a unique example of an enzyme that can occur either as ribonucleoprotein or as protein alone. The latter form of the enzyme called PRORP (PRotein-Only RNase P) is widespread in eukaryotes, in which it can provide organellar or nuclear RNase P activities. Here, we have focused on Arabidopsis nuclear PRORP2 and its interaction with tRNA substrates...
July 10, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28694664/mir-382-functions-as-a-tumor-suppressor-against-esophageal-squamous-cell-carcinoma
#14
Jie Feng, Bo Qi, Ling Guo, Ling-Yun Chen, Xiu-Feng Wei, Yu-Zhen Liu, Bao-Sheng Zhao
AIM: To explore the effect of miR-382 on esophageal squamous cell carcinoma (ESCC) in vitro and its possible molecular mechanism. METHODS: Eca109 cells derived from human ESCC and Het-1A cells derived from human normal esophageal epithelium were used. Lentivirus-mediated miR-382 was overexpressed in Eca109 cells. The effect of miR-382 on cell proliferation was evaluated by MTT and colony formation assay. For cell cycle analysis, cells were fixed and stained for 30 min with propidium iodide (PI) staining buffer containing 10 mg/mL PI and 100 mg/mL RNase A, and analyzed by BD FACSCalibur™ flow cytometer...
June 21, 2017: World Journal of Gastroenterology: WJG
https://www.readbyqxmd.com/read/28694328/the-contribution-of-the-c5-protein-subunit-of-escherichia-coli-ribonuclease-p-to-specificity-for-precursor-trna-is-modulated-by-proximal-5-leader-sequences
#15
Courtney Nicole Niland, David R Anderson, Eckhard Jankowsky, Michael E Harris
Molecular recognition of RNA by RNA processing enzymes and RNA binding proteins often involves the cooperation between multiple subunits. However, the interdependent contributions of RNA and protein subunits to molecular recognition by ribonucleoproteins and protein-protein complexes is relatively unexplored. RNase P is an endonuclease that removes 5' leaders from precursor tRNAs and functions in bacteria as dimer formed by a catalytic RNA subunit (P RNA) and a protein subunit (C5 in E. coli). The P RNA subunit contacts the tRNA body and proximal 5' leader sequences (N(-1) and N(-2)) while C5 binds distal 5' leader sequences (N(-3) to N(-6))...
July 10, 2017: RNA
https://www.readbyqxmd.com/read/28690630/lack-of-s-rnase-based-gametophytic-self-incompatibility-in-orchids-suggests-that-this-system-evolved-after-the-monocot-eudicot-split
#16
Shan-Ce Niu, Jie Huang, Yong-Qiang Zhang, Pei-Xing Li, Guo-Qiang Zhang, Qing Xu, Li-Jun Chen, Jie-Yu Wang, Yi-Bo Luo, Zhong-Jian Liu
Self-incompatibility (SI) is found in approximately 40% of flowering plant species and at least 100 families. Although orchids belong to the largest angiosperm family, only 10% of orchid species present SI and have gametophytic SI (GSI). Furthermore, a majority (72%) of Dendrobium species, which constitute one of the largest Orchidaceae genera, show SI and have GSI. However, nothing is known about the molecular mechanism of GSI. The S-determinants of GSI have been well characterized at the molecular level in Solanaceae, Rosaceae, and Plantaginaceae, which use an S-ribonuclease (S-RNase)-based system...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28679714/rnase-h-10-mg-ml-dnase-free
#17
(no author information available yet)
No abstract text is available yet for this article.
July 5, 2017: Cold Spring Harbor Protocols
https://www.readbyqxmd.com/read/28675355/induction-of-interferon-and-interferon-induced-antiviral-effector-genes-following-a-primary-bovine-herpesvirus-1-bhv-1-respiratory-infection
#18
Rahwa Osman, Patricia Gonzalez-Cano, Robert Brownlie, Philip J Griebel
Invitro investigations have identified a variety of mechanisms by which herpesviruses evade interferon-stimulated antiviral effector mechanisms. However, these immune evasion mechanisms have not been evaluated during a bovine herpesvirus-1 (BHV-1) infection. This study investigated the transcription and secretion of type I and II interferons (IFNs) and the transcription of IFN-stimulated genes (ISGs) during a primary BHV-1 infection of the upper respiratory tract (URT) in naïve calves. IFN-α, -β and -γ transcription in nasal turbinates and protein levels in nasal secretions increased following infection...
July 5, 2017: Journal of General Virology
https://www.readbyqxmd.com/read/28673541/a-novel-rna-phosphorylation-state-enables-5-end-dependent-degradation-in-escherichia-coli
#19
Daniel J Luciano, Nikita Vasilyev, Jamie Richards, Alexander Serganov, Joel G Belasco
RNA modifications that once escaped detection are now thought to be pivotal for governing RNA lifetimes in both prokaryotes and eukaryotes. For example, converting the 5'-terminal triphosphate of bacterial transcripts to a monophosphate triggers 5' end-dependent degradation by RNase E. However, the existence of diphosphorylated RNA in bacteria has never been reported, and no biological role for such a modification has ever been proposed. By using a novel assay, we show here for representative Escherichia coli mRNAs that ∼35%-50% of each transcript is diphosphorylated...
June 17, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28669526/attenuating-staphylococcus-aureus-virulence-by-targeting-flotillin-protein-scaffold-activity
#20
Gudrun Koch, Charlotte Wermser, Ivan C Acosta, Lara Kricks, Stephanie T Stengel, Ana Yepes, Daniel Lopez
Scaffold proteins are ubiquitous chaperones that bind proteins and facilitate physical interaction of multi-enzyme complexes. Here we used a biochemical approach to dissect the scaffold activity of the flotillin-homolog protein FloA of the multi-drug-resistant human pathogen Staphylococcus aureus. We show that FloA promotes oligomerization of membrane protein complexes, such as the membrane-associated RNase Rny, which forms part of the RNA-degradation machinery called the degradosome. Cells lacking FloA had reduced Rny function and a consequent increase in the targeted sRNA transcripts that negatively regulate S...
July 20, 2017: Cell Chemical Biology
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