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rRNA transcription

Jipeng Luo, Yuying Liu, Qi Tao, Qiong Hou, Keren Wu, Yuchao Song, Yuankun Liu, Xinyu Guo, Jinxing Li, Muhammad Laeeq Ur Rehman Hashmi, Yongchao Liang, Tingqiang Li
Phytoextraction is an attractive strategy for remediation of soils contaminated by heavy metal (HM), yet the effects of this practice on biochemical processes involved in soil nutrient cycling remain unknown. Here we investigated the impact of successive phytoextraction with a Cd/Zn co-hyperaccumulator Sedum alfredii (Crassulaceae) on potential nitrification rates (PNRs), abundance and composition of nitrifying communities and functional genes associated with nitrification using archaeal and bacterial 16S rRNA gene profiling and quantitative real-time PCR...
January 25, 2019: Science of the Total Environment
Bela Hausmann, Claus Pelikan, Thomas Rattei, Alexander Loy, Michael Pester
Microbial diversity in the environment is mainly concealed within the rare biosphere (all species with <0.1% relative abundance). While dormancy explains a low-abundance state very well, the mechanisms leading to rare but active microorganisms remain elusive. We used environmental systems biology to genomically and transcriptionally characterize " Candidatus Desulfosporosinus infrequens," a low-abundance sulfate-reducing microorganism cosmopolitan to freshwater wetlands, where it contributes to cryptic sulfur cycling...
February 12, 2019: MBio
Chinwe U Chukwudi, Liam Good
In bacteria, RNase III cleaves the initial long primary ribosomal RNA transcripts/precursors (pre-rRNAs), thereby releasing the pre-16S and pre-23S rRNAs for maturation. This cleavage is specified by the double-stranded secondary structures flanking the mature rRNAs, and not necessarily by the nucleotide sequences. Inhibition of this cleavage would lead to a build-up of pre-rRNA molecules. Doxycycline has earlier been shown to bind synthetic double-stranded RNAs and inhibit their cleavage by RNase III. Since bacterial rRNA processing is primarily dependent on RNase III cleavage (which is inhibited by doxycycline), doxycycline could therefore inhibit the normal processing of bacterial rRNA...
February 8, 2019: Journal of Antibiotics
Bo Zhou, Chaoyang Sun, Jia Huang, Meng Xia, Ensong Guo, Na Li, Hao Lu, Wanying Shan, Yifan Wu, Yuan Li, Xiaoyan Xu, Danhui Weng, Li Meng, Junbo Hu, Qinglei Gao, Ding Ma, Gang Chen
Ovarian carcinoma is caused by multiple factors, but its etiology associated with microbes and infection is unknown. Using 16S rRNA high-throughput sequencing methods, the diversity and composition of the microbiota from ovarian cancer tissues (25 samples) and normal distal fallopian tube tissues (25 samples) were analyzed. High-throughput sequencing showed that the diversity and richness indexes were significantly decreased in ovarian cancer tissues compared to tissues from normal distal fallopian tubes. The ratio of the two phyla for Proteobacteria/Firmicutes was notably increased in ovarian cancer, which revealed that microbial composition change might be associated with the process of ovarian cancer development...
February 8, 2019: Scientific Reports
Karissa L Milbury, Biplab Paul, Azra Lari, Claire Fowler, Ben Montpetit, Peter C Stirling
The exosome functions to regulate the cellular transcriptome through RNA biogenesis, surveillance, and decay. Through these activities the exosome contributes to many cellular processes, including ribosome biogenesis, mitosis, transcription, and gene silencing. Mutations in Dis3, a catalytic subunit of the RNA exosome with separable endonuclease and exonuclease activities, have recently been linked to the blood cancer multiple myeloma. Here we report that high-throughput genetic interaction screening of a cancer-associated DIS3 allele, dis3E729K , provides evidence for DIS3 functioning to support mitotic fidelity in yeast...
February 6, 2019: Nucleus
Sarah K Stumper, Harini Ravi, Larry J Friedman, Rachel Anne Mooney, Ivan R Corrêa, Anne Gershenson, Robert Landick, Jeff Gelles
RNA polymerases (RNAPs) contain a conserved 'secondary channel' which binds regulatory factors that modulate transcription initiation. In Escherichia coli , the secondary channel factors (SCFs) GreB and DksA both repress ribosomal RNA (rRNA) transcription, but SCF loading and repression mechanisms are unclear. We observed in vitro fluorescently labeled GreB molecules binding to single RNAPs and initiation of individual transcripts from an rRNA promoter. GreB arrived and departed from promoters only in complex with RNAP...
February 5, 2019: ELife
Xuguang Hu, Fan Yu, Yongji Huang, Lei Sun, Xueting Li, Shan Yang, Ke Chen, Fei Huang, Kai Zeng, Muqing Zhang, Zuhu Deng
The 35S ribosomal DNA (rDNA) units that occur in tandem repeat are separated by an intergenic spacer (IGS) that plays an important role in rRNA transcription. Moreover, IGS is an important molecular marker for evolutionary research in plants. In the present study, the IGS sequence of Erianthus arundinaceus was isolated and sequenced for the first time. Structure analysis indicated the entire IGS sequence of three typical E. arundinaceus genotypes was highly conserved, with approximately 3087 bp and 67.1% mean GC content...
February 1, 2019: Gene
Caroline Fromont, Karen L Adair, Angela E Douglas
Resident microorganisms are known to influence the fitness and traits of animals under controlled laboratory conditions, but, the relevance of these findings to wild animals is uncertain. This study investigated the host functional correlates of microbiota composition in a wild community of three sympatric species of mycophagous drosophilid flies, Drosophila falleni, D. neotestacea and D. putrida. Specifically, we quantified bacterial communities and host transcriptomes by parallel 16S rRNA gene amplicon sequencing and RNA-Seq of individual flies...
February 3, 2019: Molecular Ecology
Lijuan Du, Fan Yang, Houshun Fang, Huiying Sun, Yao Chen, Yan Xu, Hui Li, Liang Zheng, Bin-Bing S Zhou
It has been shown that 5-amino-4-imidazolecarboxamide riboside (AICAr) can inhibit cell proliferation and induce apoptosis in childhood acute lymphoblastic leukemia (ALL) cells. Although AICAr could regulate cellular energy metabolism by activating AMPK, the cytotoxic mechanisms of AICAr are still unclear. Here, we knocked out TP53 or PRKAA1 gene (encoding AMPKα1) in NALM-6 and Reh cells by using the clustered regularly interspaced short palindromic repeats/Cas9 system and found that AICAr-induced proliferation inhibition was independent of AMPK activation but dependent on p53...
January 31, 2019: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
Davinder Sharma, Naresh Golla, Sudhakar Singh, Pankaj Kumar Singh, Dheer Singh, Suneel Kumar Onteru
The next-generation RNA sequencing technologies expedite the discovery of a large number of novel transcripts and genes associated with various pathophysiological conditions. These technologies involve poly(A) enrichment, which in turn requires micrograms of high-quality total RNA. Unfortunately, the available RNA isolation approaches produce poor quality total RNA from difficult-to-isolate animal tissues, such as the liver with high glycogen content. Moreover, the extraction efficiencies of these approaches vary significantly depending on the animal species...
January 29, 2019: Journal of Cellular Physiology
Wenli Li, Andrea Edwards, Christina Riehle, Madison Cox, Sarah Raabis, Joseph Skarlupka, Andrew Steinberger, Jason Walling, Derek Bickhart, Garret Suen
In mammals, microbial colonization of the digestive tract (GIT) occurs right after birth by several bacterial phyla. Numerous human and mouse studies have reported the importance of early gut microbial inhabitants on host health. However, few attempts have been undertaken to directly interrogate the role of early gut/rumen microbial colonization on GIT development or host health in neonatal ruminants through artificial manipulation of the rumen microbiome. Thus, the molecular changes associated with bacterial colonization are largely unknown in cattle...
January 28, 2019: Scientific Reports
Samuel B Sondalle, Simonne Longerich, Lisa M Ogawa, Patrick Sung, Susan J Baserga
Fanconi anemia (FA) is a disease of DNA repair characterized by bone marrow failure and a reduced ability to remove DNA interstrand cross-links. Here, we provide evidence that the FA protein FANCI also functions in ribosome biogenesis, the process of making ribosomes that initiates in the nucleolus. We show that FANCI localizes to the nucleolus and is functionally and physically tied to the transcription of pre-ribosomal RNA (pre-rRNA) and to large ribosomal subunit (LSU) pre-rRNA processing independent of FANCD2...
January 28, 2019: Proceedings of the National Academy of Sciences of the United States of America
Deepesh Kumar Neelam, Akhil Agrawal, Anuj Kumar Tomer, Shreetama Bandyopadhayaya, Ankit Sharma, Medicharla V Jagannadham, Chandi C Mandal, Pawan K Dadheech
Microorganisms thrive in extreme environments and are known for synthesizing valuable metabolites. Salt-loving microorganisms can flourish in saline environments which inhibit the growth of other microbial life, and they possess the potential to produce stable and novel biomolecules for the use in biotechnological applications, including anticancer compounds. Sambhar Lake is the largest inland soda lake in India and is an appropriate habitat for halophilic bacterial and archaeal strains in terms of diversity and potential production of bioactive compounds...
January 26, 2019: Microorganisms
Yangyang Jia, Marcus H Y Leung, Xinzhao Tong, David Wilkins, Patrick K H Lee
Microbial communities are composed of populations with vastly different abundances and levels of metabolic and replicative activity, ranging from actively metabolizing and dividing to dormant or nonviable. The 16S rRNA/rDNA ratio is an emerging tool for evaluating cell-level metabolic activity independent of abundance. In this study, we used five long-term enriched model anaerobic digestion (AD) communities to investigate community composition, diversity, structure, and in particular activity based on the rRNA/rDNA ratio...
January 2019: MSystems
Helen Y Buse, Brian Morris, Ian T Struewing, Jeffrey G Szabo
Building water systems promote the regrowth and survival of opportunistic pathogens, such as Legionella pneumophila , especially within biofilms, where most drinking water microbes reside. However, compared to their planktonic form, disinfection efficacy for the biofilm-associated forms of water-based pathogens is unclear. The aim of this study was to determine the effectiveness of free chlorine and monochloramine in the inactivation of biofilm-associated L. pneumophila strain Philadelphia-1 serogroup 1 (Lp)...
January 25, 2019: Applied and Environmental Microbiology
Michael BenIsrael, Philipp Wanner, Ramon Aravena, Beth L Parker, Elizabeth A Haack, David T Tsao, Kari E Dunfield
Biodegradation is an important mechanism of action of phytoremediation systems, but performance evaluation is challenging. We applied metagenomic molecular approaches and compound-specific stable carbon isotope analysis to assess biodegradation of toluene in the vadose zone at an urban pilot field system where hybrid poplars were planted to remediate legacy impacts to an underlying shallow fractured bedrock aquifer. Carbon isotope ratios were compared spatio-temporally between toluene dissolved in groundwater and in the vapor phase...
January 16, 2019: International Journal of Phytoremediation
Fuyong Li, Thomas C A Hitch, Yanhong Chen, Christopher J Creevey, Le Luo Guan
BACKGROUND: Microorganisms are responsible for fermentation within the rumen and have been reported to contribute to the variation in feed efficiency of cattle. However, to what extent the breed affects the rumen microbiome and its association with host feed efficiency is unknown. Here, rumen microbiomes of beef cattle (n = 48) from three breeds (Angus, Charolais, Kinsella composite hybrid) with high and low feed efficiency were explored using metagenomics and metatranscriptomics, aiming to identify differences between functional potentials and activities of same rumen microbiomes and to evaluate the effects of host breed and feed efficiency on the rumen microbiome...
January 14, 2019: Microbiome
Feng Sun, Wei Tian, Fei Zhang, Yan Chen, Xue-Min Ren, Fa-Hu Pang, Yu-Ying Li, Lun-Guang Yao, Zhao-Jin Chen
Microbial communities play crucial roles in the global biogeochemical nitrogen cycle. To our knowledge, the compositions and functions of rhizosphere communities in riparian buffer strips have not been reported. In this study, rhizosphere soil samples were collected from herbs ( Vetiveria zizanioides and Phragmites australis ), trees ( Pyrus betulifolia ), and shrubs ( Discocleidion rufescens ) in the Danjiangkou Reservoir in June 2017. High-throughput sequencing was performed to analyze the community structure and diversity of bacteria...
January 8, 2019: Huan Jing Ke Xue= Huanjing Kexue
Philipp Girke, Wolfgang Seufert
The nucleolus is a membrane-less organelle of the nucleus and the site of ribosomal RNA synthesis, maturation and assembly into pre-ribosomal particles. The nucleolus, organized around arrays of ribosomal RNA genes (rDNA), dissolves during prophase of mitosis in metazoans, when rDNA transcription ceases, and reforms in telophase, when rDNA transcription resumes. No such dissolution and reformation cycle exists in budding yeast, and the precise course of nucleolar segregation remains unclear. By quantitative live cell imaging we observed that the yeast nucleolus is reorganized in its protein composition during mitosis...
January 9, 2019: Molecular Biology of the Cell
Zhenjun Zhao, Linmei Wang, Dongmei Yue, Bo Ye, Peipei Li, Bo Zhang, Qi Fan
Baculovirus infection impacts global gene expression in the host cell, including the expression of housekeeping genes. Evaluation of candidate reference genes during a viral infection will inform the selection of appropriate reference gene(s) for the normalization of expression data generated by Reverse Transcription Quantitative Real-timePolymerase Chain Reaction (RT-qPCR). Antheraea pernyi multicapsid nucleopolyhedrovirus (AnpeNPV) is able to infect the High Five cells (Tn-Hi5). In the present study, 10 candidate reference genes were evaluated in AnpeNPV-infected Tn-Hi5 cells...
January 1, 2019: Journal of Insect Science
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