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rRNA transcription

Jemaneh Habtewold, Robert Gordon, Vera Sokolov, Andrew VanderZaag, Claudia Wagner-Riddle, Kari Dunfield
Liquid dairy manure treated with sulfuric acid was stored in duplicate pilot-scale storage tanks for 120 days with continuous monitoring of CH4 emissions and concurrent examination of changes in the structure of bacterial and methanogenic communities. Methane emissions were monitored at the site using laser-based Trace Gas Analyzer whereas quantitative real-time polymerase chain reaction and massively parallel sequencing were employed to study bacterial and methanogenic communities using 16S rRNA and methyl-coenzyme M Reductase A ( mcrA ) genes/transcripts, respectively...
2018: Frontiers in Microbiology
Long Chen, Lichao Huang, Liping Dai, Yihong Gao, Weiwei Zou, Xueli Lu, Changjian Wang, Guangheng Zhang, Deyong Ren, Jiang Hu, Lan Shen, Guojun Dong, Zhenyu Gao, Guang Chen, Dawei Xue, Longbiao Guo, Yongzhong Xing, Qian Qian, Li Zhu, Dali Zeng
Pentatricopeptide repeat (PPR) proteins regulate organellar gene expression in plants, through their involvement in organellar RNA metabolism. In rice (Oryza sativa), 477 genes are predicted to encode PPR proteins; however, the majority of their functions remain unknown. In this study, we identified and characterized a rice mutant, pale-green leaf12 (pgl12); at the seedling stage, pgl12 mutants had yellow-green leaves, which gradually turned pale green as the plants grew. The pgl12 mutant had significantly reduced chlorophyll contents and increased sensitivity to changes in temperature...
November 30, 2018: Plant & Cell Physiology
Barak Rotblat, Massimiliano Agostini, Maria Victoria Niklison-Chirou, Ivano Amelio, Anne E Willis, Gerry Melino
The transcription factor p73 is a member of the p53 family, of which the transactivation domain containing isoform (TAp73) plays key roles in brain development and neuronal stem cells. TAp73 also facilitates homoeostasis and prevents oxidative damage in vivo by inducing the expression of its target genes. Recently, we found that in addition to its role in regulation of transcription, TAp73 also affects mRNA translation. In cultured cells, acute TAp73 depletion activates eEF2K, which phosphorylates eEF2 reducing mRNA translation elongation...
December 3, 2018: Cell Cycle
Milka Popova, Jessie Guyader, Mathieu Silberberg, Ahmad Reza Seradj, Cristina Saro, Aurélien Bernard, Christine Gérard, Cécile Martin, Diego P Morgavi
Dietary supplementation with linseed, saponins and nitrate is a promising methane mitigation strategy in ruminant production. Here we aimed to assess the effects of these additives on the rumen microbiota in order to understand underlying microbial mechanisms of methane abatement. Two 2 × 2 factorial design studies were conducted simultaneously, which also allowed us to make a broad-based assessment of microbial responses. Eight non-lactating cows were fed diets supplemented with linseed or saponin in order to decrease hydrogen production and nitrate to deviate hydrogen consumption; also, combinations of linseed plus nitrate or saponin plus nitrate were used to explore the interaction between dietary treatments...
November 30, 2018: Applied and Environmental Microbiology
Feng He, Alper Celik, Richard Baker, Allan Jacobson
Contemporary high-throughput sequencing methods, notably RNA-Seq, permit the systematic identification and characterization of transcripts whose levels change significantly in response to altered biological states. We have described methods for the application of this methodology to a definition of the transcripts regulated by the NMD pathway in the yeast Saccharomyces cerevisiae. In short, we outline methods for growing cells of wild-type or NMD-deficient yeast, isolating RNA from the different strains, depleting rRNA from each sample, preparing and sequencing the respective RNA-Seq libraries, and employing multiple software packages to characterize the resulting sequence reads meaningfully...
2018: Methods in Enzymology
Lauren M Bradford, Gisle Vestergaard, András Táncsics, Baoli Zhu, Michael Schloter, Tillmann Lueders
While most studies using RNA-stable isotope probing (SIP) to date have focused on ribosomal RNA, the detection of 13 C-labeled mRNA has rarely been demonstrated. This approach could alleviate some of the major caveats of current non-target environmental "omics." Here, we demonstrate the feasibility of total RNA-SIP in an experiment where hydrocarbon-degrading microbes from a BTEX-contaminated aquifer were studied in microcosms with 13 C-labeled toluene under microoxic conditions. From the total sequencing reads (∼30 mio...
2018: Frontiers in Microbiology
Natalia Borowska-Zuchowska, Ewa Robaszkiewicz, Elzbieta Wolny, Alexander Betekhtin, Robert Hasterok
Nucleolar dominance (ND) is an epigenetic phenomenon that occurs in some plant and animal allopolyploids and hybrids, whereby only one ancestral set of 35S rRNA genes retains the ability to form the nucleolus, whilst the rDNA loci derived from the other progenitor are transcriptionally silenced. Since there is substantial evidence that ND is regulated developmentally, this study focusses upon the establishment and/or maintenance of ND during different stages of development in the model grass allotetraploid, Brachypodium hybridum...
November 27, 2018: Journal of Experimental Botany
Heinrich Schäfer, Anja Heinz, Petra Sudzinová, Michelle Voß, Ingo Hantke, Libor Krásný, Kürşad Turgay
Spx is a Bacillus subtilis transcription factor that interacts with the alpha subunits of RNA polymerase. It can activate the thiol stress response regulon and interfere with the activation of many developmental processes. Here, we show that Spx is a central player orchestrating the heat shock response by up-regulating relevant stress response genes as revealed by comparative transcriptomic experiments. Moreover, these experiments revealed the potential of Spx to inhibit transcription of translation-related genes...
November 27, 2018: Molecular Microbiology
Meiping Ye, Liyun Xu, Yuzhen Zou, Bing Li, Qi Guo, Yongjie Zhang, Mengling Zhan, Benyong Xu, Fangyou Yu, Zhemin Zhang, Haiqing Chu
A total of 194 Mycobacterium abscessus isolates were collected from patients and the whole genomes were sequenced. Eighty-five (43.8%) showed linezolid (LZD) resistant. Only 8.2% of resistant isolates harbored 23S rRNA mutations. qRT-PCR revealed higher transcriptional levels of efflux pumps lmrS and mmpL9 in LZD-resistant isolates. Genome comparative analysis identified several new LZD resistance-associated genes. This study highlights the role of efflux pumps in LZD-resistant M. abscessus and proposes potential target genes for further studies...
November 26, 2018: Antimicrobial Agents and Chemotherapy
Laura J Myhill, Sophie Stolzenbach, Tina V A Hansen, Kerstin Skovgaard, C Rune Stensvold, Lee O'Brien Andersen, Peter Nejsum, Helena Mejer, Stig M Thamsborg, Andrew R Williams
Diet composition may play a crucial role in shaping host immune responses and commensal gut microbiota populations. Bioactive dietary components, such as inulin, have been extensively studied for their bioactive properties, particularly in modulating gut immune function and reducing inflammation. It has been shown that colonization with gastrointestinal parasitic worms (helminths) may alleviate chronic inflammation through promotion of T-helper cell type (Th) 2 and T-regulatory immune responses and alterations in the gut microbiome...
2018: Frontiers in Immunology
Aina E Fossum Moen, Jonas Christoffer Lindstrøm, Tone Møller Tannæs, Simen Vatn, Petr Ricanek, Morten H Vatn, Jørgen Jahnsen
Active microbes likely have larger impact on gut health status compared to inactive or dormant microbes. We investigate the composition of active and total mucosal microbiota of treatment-naïve ulcerative colitis (UC) patients to determine the microbial picture at the start-up phase of disease, using both a 16S rRNA transcript and gene amplicon sequencing. DNA and RNA were isolated from the same mucosal colonic biopsies. Our aim was to identify active microbial members of the microbiota in early stages of disease and reveal which members are present, but do not act as major players...
November 22, 2018: Scientific Reports
S A Bengesser, S Mörkl, A Painold, N Dalkner, A Birner, F T Fellendorf, M Platzer, R Queissner, C Hamm, A Maget, R Pilz, A Rieger, J Wagner-Skacel, B Reininghaus, H P Kapfhammer, E Petek, K Kashofer, B Halwachs, P Holzer, A Waha, E Z Reininghaus
Objectives The gut microbiome harbors substantially more genetic material than our body cells and has an impact on a huge variety of physiological mechanisms including the production of neurotransmitters and the interaction with brain functions through the gut-brain-axis. Products of microbiota can affect methylation according to preclinical studies. The current investigation aimed at analyzing the correlation between gut microbiome diversity and the methylation of the clock gene ARNTL in individuals with Bipolar Disorder (BD)...
November 10, 2018: Psychoneuroendocrinology
Margarita Lopez-Fernandez, Domenico Simone, Xiaofen Wu, Lucile Soler, Emelie Nilsson, Karin Holmfeldt, Henrik Lantz, Stefan Bertilsson, Mark Dopson
The continental subsurface is suggested to contain a significant part of the earth's total biomass. However, due to the difficulty of sampling, the deep subsurface is still one of the least understood ecosystems. Therefore, microorganisms inhabiting this environment might profoundly influence the global nutrient and energy cycles. In this study, in situ fixed RNA transcripts from two deep continental groundwaters from the Äspö Hard Rock Laboratory (a Baltic Sea-influenced water with a residence time of <20 years, defined as "modern marine," and an "old saline" groundwater with a residence time of thousands of years) were subjected to metatranscriptome sequencing...
November 20, 2018: MBio
Irene Cano, Nick Gh Taylor, Amanda Bayley, Susie Gunning, Robin McCullough, Kelly Bateman, Barbara F Nowak, Richard Paley
An in vitro model to study the host response to Neoparamoeba perurans, the causative agent of amoebic gill disease (AGD), was evaluated. The rainbow trout gill derived cell line, RTgill-W1, was seeded onto permeable cell culture supports and maintained asymmetrically with apical seawater. Cells were inoculated with either a passage attenuated or a recent wild clone of N. perurans. Amoebae, loaded with phagocytosed fluorescent beads, were observed associated with host cells within 20 min post inoculation (pi)...
November 17, 2018: Fish & Shellfish Immunology
Dawei Song, Guoqing Chen, Sihui Liu, Maqsood Ahmed Khaskheli, Lijuan Wu
Burkholderia sp. JP2-270, a bacterium with a strong ability to inhibit the growth of Rhizoctonia solani, was isolated from the rhizosphere of rice. The phylogenetic analysis based on 16S rRNA gene revealed that JP2-270 belonged to Burkholderia cepacia complex. Here, we present the complete genome sequence of Burkholderia sp. JP2-270, which consists of three circular chromosomes (Chr1 3,723,585 bp, Chr2 3,274,969 bp, Chr3 1,483,367 bp) and two plasmids (Plas1 15,126 bp, Plas2 428,263 bp). A total of 8193 protein coding genes were predicted in the genome, including 67 tRNA genes, 18 rRNA genes and 4 ncRNA genes...
November 17, 2018: Microbial Pathogenesis
Bijoy K Mohanty, Sidney R Kushner
Post-transcriptional RNA metabolic pathways play important roles in permitting prokaryotes to operate under a variety of environmental conditions. Although significant progress has been made during the last decade in deciphering RNA processing pathways in a number of bacteria, a complete understanding of post-transcriptional RNA metabolism in any single microorganism is far from reality. Here we describe multiple experimental approaches that can be used to study mRNA stability, tRNA and rRNA processing, sRNA metabolism, and polyadenylation in prokaryotes...
November 15, 2018: Methods: a Companion to Methods in Enzymology
Jennifer E G Gallagher
Ribosomes are synthesized by large ribonucleoprotein complexes cleaving and properly assembling highly structured rRNAs with ribosomal proteins. Transcription and processing of pre-rRNAs are linked by the transcription-Utp sub-complex (t-Utps), a sub-complex of the small subunit (SSU) processome and prompted the investigations for the requirements of t-Utp formation and transition into the SSU processome. The rDNA promoter, the first 44 nucleotides of the 5΄ETS, and active transcription by pol I were sufficient to recruit the t-Utps to the rDNA...
January 1, 2019: FEMS Yeast Research
Ian M Willis, Robyn D Moir, Nouria Hernandez
As a master negative regulator of RNA polymerase (Pol) III, Maf1 modulates transcription in response to nutrients and stress to balance the production of highly abundant tRNAs, 5S rRNA, and other small noncoding RNAs with cell growth and maintenance. This regulation of Pol III transcription is important for energetic economy as mice lacking Maf1 are lean and resist weight gain on normal and high fat diets. The lean phenotype of Maf1 knockout (KO) mice is attributed in part to metabolic inefficiencies which increase the demand for cellular energy and elevate catabolic processes, including autophagy/lipophagy and lipolysis...
November 27, 2018: Proceedings of the National Academy of Sciences of the United States of America
Yun Xia, Jianmeng Cao, Miao Wang, Maixin Lu, Gang Chen, Fengying Gao, Zhigang Liu, Defeng Zhang, Xiaoli Ke, Mengmeng Yi
The administration of probiotics during early ontogenetic stages can be an effective way to manipulate the gut microbiota of animals. Specifically, the administration of probiotics can enhance gut-colonization success and regulate the immune response. In this study, the effects of early contact with probiotic Lactococcus lactis subsp. lactis JCM5805 on the gut microbial assembly of larvae Nile tilapia were examined. The effects of JCM5805 on IFNα expression through the TLR7 and TLR9-dependent signal transduction pathway as well as larval disease resistance were studied...
November 11, 2018: Fish & Shellfish Immunology
Michaela Šiková, Martina Janoušková, Olga Ramaniuk, Petra Páleníková, Jiří Pospíšil, Pavel Bartl, Agnieszka Suder, Petr Pajer, Pavla Kubičková, Ota Pavliš, Miluše Hradilová, Dragana Vítovská, Hana Šanderová, Martin Převorovský, Jarmila Hnilicová, Libor Krásný
Ms1 is a sRNA recently found in mycobacteria and several other actinobacterial species. Ms1 interacts with the RNA polymerase (RNAP) core devoid of sigma factors, which differs from 6S RNA that binds to RNAP holoenzymes containing the primary sigma factor. Here we show that Ms1 is the most abundant non-rRNA transcript in stationary phase in Mycobacterium smegmatis. The accumulation of Ms1 stems from its high-level synthesis combined with decreased degradation. We identify the Ms1 promoter, PM s1 , and cis-acting elements important for its activity...
November 14, 2018: Molecular Microbiology
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