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rRNA transcription

Andrew S Burns, Cory C Padilla, Zoe A Pratte, Kailen Gilde, Matthew Regensburger, Eric Hall, Alistair D M Dove, Frank J Stewart
Denitrification by sulfur-oxidizing bacteria is an effective nitrate removal strategy in engineered aquatic systems. However, the community taxonomic and metabolic diversity of sulfur-driven denitrification (SDN) systems, as well as the relationship between nitrate removal and SDN community structure, remains underexplored. This is particularly true for SDN reactors applied to marine aquaria, despite increasing use of this technology to supplement filtration. We applied 16S rRNA gene, metagenomic, and metatranscriptomic analysis to explore the microbial basis of SDN reactors operating on Georgia Aquarium's Ocean Voyager , the largest indoor closed-system seawater exhibit in the United States...
August 10, 2018: Applied and Environmental Microbiology
Sudarat Chomwong, Walaiporn Charoensapsri, Piti Amparyup, Anchalee Tassanakajon
Lactic acid bacteria (LAB) are group of beneficial bacteria that have been proposed as relevant probiotics with immunomodulatory functions. In this study, we initially isolated and identified host-derived LAB from the gut of the Pacific white shrimp Litopenaeus vannamei. Analysis of the bacterial 16S rRNA gene sequence revealed two candidate LAB, the Lactobacillus plantarum strain SGLAB01 and the Lactococcus lactis strain SGLAB02, which exhibited 99% identity to the L. plantarum strain LB1-2 and the L. lactis strain R-53658, which were isolated from bee gut, respectively...
August 6, 2018: Developmental and Comparative Immunology
Meghan L Ruebel, Peter Z Schall, Uros Midic, Kailey A Vincent, Benjamin Goheen, Catherine A VandeVoort, Keith E Latham
STUDY QUESTION: Which different pathways and functions are altered in rhesus monkey oocytes that fail to mature after an ovulatory stimulus? SUMMARY ANSWER: FTM oocytes complete a large portion of the transition in transcriptome composition associated with normal maturation, but also manifest numerous differences that indicate incomplete transcriptional repression and cytoplasmic maturation affecting multiple processes. WHAT IS KNOWN ALREADY: Oocyte maturation defects contribute to unexplained female infertility...
August 3, 2018: Molecular Human Reproduction
Stephen M Rawlinson, Tianyue Zhao, Ashley M Rozario, Christina L Rootes, Paul J McMillan, Anthony W Purcell, Amanda Woon, Glenn A Marsh, Kim G Lieu, Lin-Fa Wang, Hans J Netter, Toby D M Bell, Cameron R Stewart, Gregory W Moseley
Recent studies indicate that nucleoli play critical roles in the DNA-damage response (DDR) via interaction of DDR machinery including NBS1 with nucleolar Treacle protein, a key mediator of ribosomal RNA (rRNA) transcription and processing. Here, using proteomics, confocal and single molecule super-resolution imaging, and infection under biosafety level-4 containment, we show that this nucleolar DDR pathway is targeted by infectious pathogens. We find that the matrix proteins of Hendra virus and Nipah virus, highly pathogenic viruses of the Henipavirus genus in the order Mononegavirales, interact with Treacle and inhibit its function, thereby silencing rRNA biogenesis, consistent with mimicking NBS1-Treacle interaction during a DDR...
August 3, 2018: Nature Communications
Farshad Davoodi Mastakani, Gabriel Pagheh, Sajad Rashidi Monfared, Masoud Shams-Bakhsh
Opium poppy (Papaver somniferum L.) is one of the ancient medical crops, which produces several important alkaloids such as morphine, noscapine, sanguinarine and codeine. MicroRNAs are endogenous non-coding RNAs that play important regulatory roles in plant diverse biological processes. Many plant miRNAs are encoded as single transcriptional units, in contrast to animal miRNAs, which are often clustered. Herein, using computational approaches, a total of 22 miRNA precursors were identified, which five of them were located as a clustered in pre-ribosomal RNA...
2018: PloS One
O I Coleman, E M Lobner, S Bierwirth, A Sorbie, N Waldschmitt, E Rath, E Berger, I Lagkouvardos, T Clavel, K D McCoy, A Weber, M Heikenwalder, K P Janssen, D Haller
BACKGROUND & AIMS: Activating transcription factor 6 (ATF6) regulates endoplasmic reticulum stress. We studied whether ATF6 contributes to the development of colorectal cancer (CRC) using tissue from patients and transgenic mice. METHODS: We analyzed data from 541 patients with CRC in the TCGA database for genetic variants and aberrant expression levels of unfolded protein response genes. Findings were validated in a cohort of 83 patients with CRC in Germany...
July 28, 2018: Gastroenterology
Himanshu S Raje, Molly E Lieux, Patrick J DiMario
The ribosomal RNA genes (rDNA) of Drosophila melanogaster reside within centromere-proximal nucleolar organizers on both the X and Y chromosomes. Each locus contains between 200-300 tandem repeat rDNA units that encode 18S, 5.8S, 2S, and 28S ribosomal RNAs (rRNAs) necessary for ribosome biogenesis. In arthropods like Drosophila, about 60% of the rDNA genes have R1 and/or R2 retrotransposons inserted at specific sites within their 28S regions; these units likely fail to produce functional 28S rRNA. We showed earlier that R2 expression increases upon nucleolar stress caused by the loss of the ribosome assembly factor, Nucleolar Phosphoprotein of 140 kDa (Nopp140)...
July 31, 2018: Transcription
Li-Chin Tsai, Chih-Wen Su, James Chun-I Lee, Yu-Sheng Lu, Hsuan-Chen Chen, Yu-Chih Lin, Adrian Linacre, Hsing-Mei Hsieh
We report on a novel method for saliva identification by reverse transcription-loop-mediated isothermal amplification (RT-LAMP). In our previous report, real-time RT-LAMP was used for blood identification by using HBB detection as a model but in this advanced study, this method was refined for the identification of the more challenging body fluid of saliva. Expression of the18S rRNA gene was used as the internal control and the Statherin (STATH) gene as the saliva-specific marker. A turbidimeter was used for real-time detection of the RT-LAMP products, and confirmation was obtained that the real products were generated using: agarose gel electrophoresis, calcein fluorescence detection and/or enzymatic digestion...
July 30, 2018: Forensic Science, Medicine, and Pathology
Pedro J Alcolea, Ana Alonso, Vicente Larraga
The kinetoplastid parasite Leishmania infantum is responsible for zoonotic visceral leishmaniasis in the mediterranean basin, where dogs are the reservoir. Differential gene expression analysis by whole genome DNA microarray hybridization revealed up-regulation of genes involved in infectivity of metacyclic promastigotes in axenic culture, together with two unidentified genes that had not been annotated in the parasite's genome sequences. Sequence analysis revealed that these genes encode for guide RNAs (gRNAs), which are located in the kinetoplast and participate in the kinetoplastid-specific uridine insertion/deletion RNA editing process...
July 25, 2018: Acta Tropica
Sean C Murphy, Andrew S Ishizuka, Zachary P Billman, Tayla M Olsen, Annette M Seilie, Ming Chang, Nahum Smith, Vorada Chuenchob, Sumana Chakravarty, B Kim Lee Sim, Stefan H I Kappe, Stephen L Hoffman, Robert A Seder
BACKGROUND: Plasmodium 18S rRNA is a biomarker used to monitor blood-stage infections in malaria clinical trials. Plasmodium sporozoites also express this biomarker, and there is conflicting evidence about how long sporozoite-derived 18S rRNA persists in peripheral blood. If present in blood for an extended timeframe, sporozoite-derived 18S rRNA could complicate use as a blood-stage biomarker. METHODS: Blood samples from Plasmodium yoelii infected mice were tested for Plasmodium 18S rRNA and their coding genes (rDNA) using sensitive quantitative reverse transcription PCR and quantitative PCR assays, respectively...
July 27, 2018: Malaria Journal
Albert L Müller, Claus Pelikan, Julia R de Rezende, Kenneth Wasmund, Martina Putz, Clemens Glombitza, Kasper U Kjeldsen, Bo Barker Jørgensen, Alexander Loy
Seafloor microorganisms impact global carbon cycling by mineralizing vast quantities of organic matter (OM) from pelagic primary production, which is predicted to increase in the Arctic because of diminishing sea ice cover. We studied microbial interspecies-carbon-flow during anaerobic OM degradation in arctic marine sediment using stable isotope probing. We supplemented sediment incubations with 13 C-labeled cyanobacterial necromass (spirulina), mimicking fresh OM input, or acetate, an important OM degradation intermediate, and monitored sulfate reduction rates and concentrations of volatile fatty acids (VFAs) during substrate degradation...
July 26, 2018: Environmental Microbiology
Melody R Lindsay, Maximiliano J Amenabar, Kristopher M Fecteau, Randal V Debes, Maria C Fernandes Martins, Kirsten E Fristad, Huifang Xu, Tori M Hoehler, Everett L Shock, Eric S Boyd
The geochemistry of hot springs and the availability of oxidants capable of supporting microbial metabolisms are influenced by subsurface processes including the separation of hydrothermal fluids into vapor and liquid phases. Here, we characterized the influence of geochemical variation and oxidant availability on the abundance, composition, and activity of hydrogen (H2 )-dependent chemoautotrophs along the outflow channels of two-paired hot springs in Yellowstone National Park. The hydrothermal fluid at Roadside East (RSE; 82...
July 23, 2018: Geobiology
Thomas P Quinn, Tamsyn M Crowley, Mark F Richardson
BACKGROUND: Count data generated by next-generation sequencing assays do not measure absolute transcript abundances. Instead, the data are constrained to an arbitrary "library size" by the sequencing depth of the assay, and typically must be normalized prior to statistical analysis. The constrained nature of these data means one could alternatively use a log-ratio transformation in lieu of normalization, as often done when testing for differential abundance (DA) of operational taxonomic units (OTUs) in 16S rRNA data...
July 18, 2018: BMC Bioinformatics
Maria G Iacovella, Michael Bremang, Omer Basha, Luciano Giacò, Walter Carotenuto, Cristina Golfieri, Barnabas Szakal, Marianna Dal Maschio, Valentina Infantino, Galina V Beznoussenko, Chinnu R Joseph, Clara Visintin, Alexander A Mironov, Rosella Visintin, Dana Branzei, Sébastien Ferreira-Cerca, Esti Yeger-Lotem, Peter De Wulf
The Saccharomyces cerevisiae kinase/adenosine triphosphatase Rio1 regulates rDNA transcription and segregation, pre-rRNA processing and small ribosomal subunit maturation. Other roles are unknown. When overexpressed, human ortholog RIOK1 drives tumor growth and metastasis. Likewise, RIOK1 promotes 40S ribosomal subunit biogenesis and has not been characterized globally. We show that Rio1 manages directly and via a series of regulators, an essential signaling network at the protein, chromatin and RNA levels...
July 16, 2018: Nucleic Acids Research
Nhan van Tran, Leslie Muller, Robert L Ross, Roxane Lestini, Juliette Létoquart, Nathalie Ulryck, Patrick A Limbach, Valérie de Crécy-Lagard, Sarah Cianférani, Marc Graille
Protein synthesis is a complex and highly coordinated process requiring many different protein factors as well as various types of nucleic acids. All translation machinery components require multiple maturation events to be functional. These include post-transcriptional and post-translational modification steps and methylations are the most frequent among these events. In eukaryotes, Trm112, a small protein (COG2835) conserved in all three domains of life, interacts and activates four methyltransferases (Bud23, Trm9, Trm11 and Mtq2) that target different components of the translation machinery (rRNA, tRNAs, release factors)...
July 13, 2018: Nucleic Acids Research
Hirokazu Tsuji, Kazunori Matsuda, Koji Nomoto
Over the past decade, the advent of next-generation-sequencing tools has revolutionized our approach to understanding the human gut microbiota. However, numerical data on the gut bacterial groups-particularly low-cell-count microbiota, such as indigenous pathobionts, that are otherwise important components of the microbiota-are relatively limited and disparate. As a result, the comprehensive quantitative structure of the human gut microbiota still needs to be fully defined and standardized. With the aim of filling this knowledge gap, we have established a highly sensitive quantitative analytical system that is based on reverse transcription-quantitative PCR and targets microbial rRNA molecules...
2018: Frontiers in Microbiology
Allison M Veach, Natalie A Griffiths
Aquatic biofilms are hotspots of biogeochemical activity due to concentrated microbial biomass (Battin, Kaplan, Newbold, & Hansen, ). However, biofilms are often considered a single entity when their role in biogeochemical transformations is assessed, even though these biofilms harbour functionally diverse microbial communities (Battin, Besemer, Bengtsson, Romani, & Packmann, ; Veach, Stegen, Brown, Dodds, & Jumpponen, ). Often overlooked are the biotic interactions among biofilm components that can affect ecosystem-scale processes such as primary production and nutrient cycling...
July 2018: Molecular Ecology
Tong Chen, Xuwu Xiang, Haijun Xu, Xuechao Zhang, Bibi Zhou, Youyun Yang, Yongliang Lou, X Frank Yang
Little is known about how Borrelia burgdorferi, the Lyme disease pathogen, adapts and survives in the tick vector. We previously identified a bacterial CarD N-terminal-like (CdnL) protein, LtpA (BB0355), in B. burgdorferi that is preferably expressed at lower temperatures, which is a surrogate condition mimicking the tick portion of the enzootic cycle of B. burgdorferi. CdnL-family proteins, an emerging class of bacterial RNAP-interacting transcription factors, are essential for the viability of Mycobacterium tuberculosis and Myxococcus xanthus...
July 9, 2018: Emerging Microbes & Infections
H P S U Chandrarathna, Chamilani Nikapitiya, S H S Dananjaya, C U B Wijerathne, S H M P Wimalasena, Hyo Jung Kwun, Gang-Joon Heo, Jehee Lee, Mahanama De Zoysa
Fish can be potentially co-infected by two or more bacterial strains, which can make synergistic influence on the virulence of infection. In this study, two opportunistic and multidrug resistant Aeromonas strains were isolated from wounds of morbid zebrafish with typical deep skin lesions similar to Motile Aeromonas Septicemia. Isolates were genetically identified as A. hydrophila and A. veronii by 16 S rRNA sequencing and phylogenetic analysis. Both isolates were positive for virulent genes (aerA, lip, ser, exu gcaT) and selected phenotypic tests (DNase, protease, gelatinase, lipase, biofilm production and β-haemolysis)...
September 2018: Fish & Shellfish Immunology
Michelle Percharde, Chih-Jen Lin, Yafei Yin, Juan Guan, Gabriel A Peixoto, Aydan Bulut-Karslioglu, Steffen Biechele, Bo Huang, Xiaohua Shen, Miguel Ramalho-Santos
Transposable elements represent nearly half of mammalian genomes and are generally described as parasites, or "junk DNA." The LINE1 retrotransposon is the most abundant class and is thought to be deleterious for cells, yet it is paradoxically highly expressed during early development. Here, we report that LINE1 plays essential roles in mouse embryonic stem cells (ESCs) and pre-implantation embryos. In ESCs, LINE1 acts as a nuclear RNA scaffold that recruits Nucleolin and Kap1/Trim28 to repress Dux, the master activator of a transcriptional program specific to the 2-cell embryo...
July 12, 2018: Cell
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