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rRNA transcription

Zuopeng Lv, Athaydes Francisco Leite, Hauke Harms, Karin Glaser, Jan Liebetrau, Sabine Kleinsteuber, Marcell Nikolausz
Anaerobic digestion of nitrogen-rich substrate often causes process inhibition due to the susceptibility of the microbial community facing ammonia accumulation. However, the precise response of the microbial community has remained largely unknown. To explore the reasons, bacterial communities in ammonia-stressed reactors and control reactors were studied by amplicon pyrosequencing of 16S rRNA genes and the active methanogens were followed by terminal restriction fragment length polymorphism (T-RFLP) analyses of mcrA/mrtA gene transcripts...
October 17, 2018: Applied Microbiology and Biotechnology
Vijayapalani Paramasivan, Tarek Hewezi, Frederic Pontvianne, Thomas J Baum
Cyst nematodes are plant-pathogenic animals that secrete effector proteins into plant root cells to alter host gene expression and reprogram these cells to form specialized feeding sites, known as syncytia. The molecular mechanisms of these effectors are mostly unknown. We determined that the sugar beet cyst nematode (Heterodera schachtii) 32E03 effector protein strongly inhibits the activities of Arabidopsis thaliana histone deacetylases including the HDT1 enzyme, which has a known function in the regulation of rRNA gene expression through chromatin modifications...
October 17, 2018: Plant Cell
Angela Kranz, Andrea Steinmann, Ursula Degner, Aliye Mengus-Kaya, Susana Matamouros, Michael Bott, Tino Polen
BACKGROUND: Gluconobacter oxydans is a strictly aerobic Gram-negative acetic acid bacterium used industrially for oxidative biotransformations due to its exceptional type of catabolism. It incompletely oxidizes a wide variety of carbohydrates regio- and stereoselectively in the periplasm using membrane-bound dehydrogenases with accumulation of the products in the medium. As a consequence, only a small fraction of the carbon and energy source enters the cell, resulting in a low biomass yield...
October 16, 2018: BMC Genomics
Fabian Bonk, Denny Popp, Sören Weinrich, Heike Sträuber, Sabine Kleinsteuber, Hauke Harms, Florian Centler
Background: Demand-driven biogas production could play an important role for future sustainable energy supply. However, feeding a biogas reactor according to energy demand may lead to organic overloading and, thus, to process failures. To minimize this risk, digesters need to be actively steered towards containing more robust microbial communities. This study focuses on acetogenesis and methanogenesis as crucial process steps for avoiding acidification. We fed lab-scale anaerobic digesters with volatile fatty acids under various feeding regimes and disturbances...
2018: Biotechnology for Biofuels
Danil Pupov, Ivan Petushkov, Daria Esyunina, Katsuhiko S Murakami, Andrey Kulbachinskiy
The σ factor drives promoter recognition by bacterial RNA polymerase (RNAP) and is also essential for later steps of transcription initiation, including RNA priming and promoter escape. Conserved region 3.2 of the primary σ factor ('σ finger') directly contacts the template DNA strand in the open promoter complex and facilitates initiating NTP binding in the active center of RNAP. Ribosomal RNA promoters are responsible for most RNA synthesis during exponential growth but should be silenced during the stationary phase to save cell resources...
October 13, 2018: Nucleic Acids Research
Priyanka Maiti, Hyun-Jung Kim, Ya-Ting Tu, Antoni Barrientos
Most steps on the biogenesis of the mitochondrial ribosome (mitoribosome) occur near the mitochondrial DNA nucleoid, in RNA granules, which contain dedicated RNA metabolism and mitoribosome assembly factors. Here, analysis of the RNA granule proteome identified the presence of a set of small GTPases that belong to conserved families of ribosome assembly factors. We show that GTPBP10, a member of the conserved Obg family of P-loop small G proteins, is a mitochondrial protein and have used gene-editing technologies to create a HEK293T cell line KO for GTPBP10...
October 13, 2018: Nucleic Acids Research
Shenghua Zhang, Lizheng Guo, Kai Yang, Yin Zhang, Chengsong Ye, Sheng Chen, Xin Yu, Wei E Huang, Li Cui
A viable but non-culturable (VBNC) state of bacteria induced by disinfection in water treatment poses serious health risks because of possible resuscitation of VBNC cells during transportation. In this study, a setup using continuous-flow ultraviolet (UVC) irradiation ranging from 0 to 172.2 mJ cm-2 was designed to simulate real-world disinfection in both drinking water (SDW) and reclaimed water (SRW) treatment plants. A systematic investigation of UVC-induced VBNC bacteria, including occurrence, resuscitation, and time-dependent recovery of metabolic activity during post-incubation, was conducted...
2018: Frontiers in Microbiology
Gongqing Wu, Yunhong Yi
In this study, we describe RNA-seq expression profiling of larval Bombyx mori response to hemocoel injection of Bacillus thuringiensis (Bt). Two transcriptomes were generated from the hemocytes of the PBS- and Bt-injected B. mori larvae. More than 49 million 100-bp paired-end reads, encompassing over 7.3 Gb of sequence data, were generated for each library. After filtering the raw reads and removing the rRNA mapped reads, more than 89% of the reads in each library could be mapped to the silkworm genome reference sequence...
October 10, 2018: Molecular Immunology
Martin Morovic, Olga Østrup, Frantisek Strejcek, Michal Benc, Matej Murin, Katarina Jedlickova, Alexandra Bartkova, Andrea Lucas-Hahn, Lazo Pendovski, Jozef Laurincik
SummaryThe present study examines the role of RNA polymerase I (RPI)-mediated transcription, maternally inherited rRNA and nucleolar proteins in the resumption of fibrillogranular nucleoli during embryonic genome activation (EGA) in porcine embryos. Late 4-cell embryos were incubated in the absence (control) or presence of actinomycin D (AD) (0.2 μg/ml for inhibition of RPI; 2.0 μg/ml for inhibition of total transcription) and late 2-cell embryos were cultured to the late 4-cell stage with 0.2 μg/ml AD to block EGA...
October 12, 2018: Zygote: the Biology of Gametes and Early Embryos
Lukas Trixl, Alexandra Lusser
It is a well-known fact that RNA is the target of a plethora of modifications which currently amount to over a hundred. The vast majority of these modifications was observed in the two most abundant classes of RNA, rRNA and tRNA. With the recent advance in mapping technologies, modifications have been discovered also in mRNA and in less abundant non-coding RNA species. These developments have sparked renewed interest in elucidating the nature and functions of those "epitransciptomic" modifications in RNA...
October 11, 2018: Wiley Interdisciplinary Reviews. RNA
Gabriela T Niemirowicz, Juan J Cazzulo, Vanina E Álvarez, León A Bouvier
Nowadays, most reverse genetics approaches in Trypanosoma brucei, a protozoan parasite of medical and veterinary importance, rely on pre-established cell lines. Consequently, inducible experimentation is reduced to a few laboratory strains. Here we described a new transgene expression system based exclusively on endogenous transcription activities and a minimum set of regulatory components that can easily been adapted to different strains. The pTbFIX vectors are designed to contain the sequence of interest under the control of an inducible rRNA promoter along with a constitutive dicistronic unit encoding a nucleus targeted tetracycline repressor and puromycin resistance genes in a tandem "head-to-tail" configuration...
2018: PloS One
Emma Briggs, Graham Hamilton, Kathryn Crouch, Craig Lapsley, Richard McCulloch
R-loops are stable RNA-DNA hybrids that have been implicated in transcription initiation and termination, as well as in telomere maintenance, chromatin formation, and genome replication and instability. RNA Polymerase (Pol) II transcription in the protozoan parasite Trypanosoma brucei is highly unusual: virtually all genes are co-transcribed from multigene transcription units, with mRNAs generated by linked trans-splicing and polyadenylation, and transcription initiation sites display no conserved promoter motifs...
October 10, 2018: Nucleic Acids Research
F-C Kuo, Y-D Lu, C-T Wu, H-L You, G-B Lee, M S Lee
AIMS: The aim of this study was to compare the results of 16S/28S rRNA sequencing with the erythrocyte sedimentation rate (ESR), C-reactive protein (CRP) level, and synovial fluid analysis in the diagnosis of prosthetic joint infection (PJI). PATIENTS AND METHODS: Between September 2015 and August 2016, 214 consecutive patients were enrolled. In the study population, there were 25 patients with a PJI and 189 controls. Of the PJI patients, 14 (56%) were women, and the mean age at the time of diagnosis was 65 years (38 to 83)...
October 2018: Bone & Joint Journal
Robert Schlaberg, Amanda Barrett, Kornelia Edes, Michael Graves, Litty Paul, Jenna Rychert, Bert K Lopansri, Daniel T Leung
Background: Host factors play an important role in pathogenesis and disease outcome in Clostridium difficile infection (CDI), and characterization of these responses could uncover potential host biomarkers to complement existing microbe-based diagnostics. Methods: We extracted RNA from fecal samples of patients with CDI and profiled human mRNA using amplicon-based next-generation sequencing (NGS). We compared the fecal host mRNA transcript expression profiles of patients with CDI to controls with non-CDI diarrhea...
2018: Pathogens & Immunity
Piero Lo Monaco, Virginie Marcel, Jean-Jacques Diaz, Frédéric Catez
Ribosomal RNA (rRNA) undergoes post-transcriptional modification of over 200 nucleotides, predominantly 2'-O-methylation (2'-O-Me). 2'-O-Methylation protects RNA from hydrolysis and modifies RNA strand flexibility but does not contribute to Watson-Crick base pairing. The contribution of 2'-O-Me to the translational capacity of ribosomes has been established. Yet, how 2'-O-Me participates in ribosome biogenesis and ribosome functioning remains unclear. The development of 2'-O-Me quantitative mapping methods has contributed to the demonstration that these modifications are not constitutive but rather provide heterogeneity to the ribosomal population...
October 3, 2018: Biomolecules
Kim D Allen, Matthew J Regier, Changchi Hsieh, Panayiotis Tsokas, Maya Barnard, Shwetha Phatarpekar, Jason Wolk, Todd C Sacktor, André A Fenton, A Iván Hernández
The transition from short-term to long-term forms of synaptic plasticity requires protein synthesis and new gene expression. Most efforts to understand experience-induced changes in neuronal gene expression have focused on the transcription products of RNA polymerase II-primarily mRNAs and the proteins they encode. We recently showed that nucleolar integrity and activity-dependent ribosomal RNA (rRNA) synthesis are essential for the maintenance of hippocampal long-term potentiation (LTP). Consequently, the synaptic plasticity and memory hypothesis predicts that nucleolar integrity and activity dependent rRNA synthesis would be required for Long-term memory (LTM)...
2018: PloS One
Rina Hamajima, Aya Saito, Shizuka Makino, Michihiro Kobayashi, Motoko Ikeda
Lepidopteran cells rely on multiple antiviral responses to defend against baculovirus infections, including apoptosis, global protein synthesis shutdown, and rRNA degradation. Here, we characterized apoptosis and rRNA degradation in Autographa californica multiple nucleopolyhedrovirus (AcMNPV)-infected Bombyx mori cells, a system resulting in abortive infection, in relation to viral DNA replication and viral late gene expression. RNAi-mediated silencing of viral DNA replication-related genes prevented apoptosis, but not rRNA degradation, in B...
September 26, 2018: Virus Research
Elena López-Jiménez, Ana M Rojas, Eduardo Andrés-León
Circular RNAs (circRNAs) are noncoding and single-stranded RNA transcripts able to form covalently circular-closed structures. They are generated through alternative splicing events and widely expressed from human to viruses. CircRNAs have been appointed as potential regulators of microRNAs (miRNAs), RNA-binding proteins (RPBs), and lineal protein-coding transcripts. Although their mechanism of action remains unclear, the deregulation of circular RNAs has been confirmed in different diseases such as Alzheimer or cancer...
2018: Advances in Experimental Medicine and Biology
Massimiliano Cardinale, Christian Suarez, Diedrich Steffens, Stefan Ratering, Sylvia Schnell
Phosphate is a macronutrient and often the limiting growing factor of many ecosystems. The aim of this work was to assess the effect of various phosphate sources on the active bacterial microbiota of barley rhizosphere and endorhiza. Barley was grown on poor soil supplemented with either Ca(H2 PO4 )2 (CaP), Gafsa rock phosphate (Gafsa), sodium hexaphytate (NaHex), or not amended (P0). RNA was extracted and cDNA synthesized via reverse transcription from both rhizosphere and endorhiza of barley roots; the obtained 16S rRNA cDNA was sequenced by Ion Torrent and analyzed with QIIME and co-occurrence network analysis...
September 26, 2018: Microbial Ecology
Yu-Hang Xing, Ling-Ling Chen
Small nucleolar RNAs (snoRNAs) are a family of conserved nuclear RNAs that function in the modification of small nuclear RNAs (snRNAs) or ribosomal RNAs (rRNAs), or participate in the processing of rRNAs during ribosome subunit maturation. Eukaryotic DNA transcription and RNA processing produce many long noncoding RNA (lncRNA) species. Although most lncRNAs are processed like typical mRNAs to be 5' capped and 3' polyadenylated, other types of lncRNAs are stabilized from primary Pol II transcripts by alternative mechanisms...
September 25, 2018: Critical Reviews in Biochemistry and Molecular Biology
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