Domain orientation in the RNA helicase YxiN and the role of conformational changes for RNA unwinding [PDF]
, 2010 The RNA helicase YxiN from Bacillus subtilis is a member of the family of DEAD box proteins. YxiN is able to unwind RNA double strands in an ATP-dependent manner. The ability to catalyse RNA rearrangement is in vivo presumably necessary for the bacterial
Karow, Anne R.
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Structured RNA Contaminants in Bacterial Ribo-Seq
mSphere, 2020 Ribosome profiling (Ribo-Seq) is a powerful method to study translation in bacteria. However, Ribo-Seq signal can be observed across RNAs that one would not expect to be bound by ribosomes.
Brayon J. Fremin, Ami S. Bhatt
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Structural insights into the dynamics and function of the C-terminus of the E. coli RNA chaperone Hfq [PDF]
, 2011 The hexameric Escherichia coli RNA chaperone Hfq (Hfq(Ec)) is involved in riboregulation of target mRNAs by small trans-encoded RNAs. Hfq proteins of different bacteria comprise an evolutionarily conserved core, whereas the C-terminus is variable in ...
Beich-Frandsen, Mads (Department of Structural and Computational Biology, Centre for Molecular Biology, University of Vienna) +46 more
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Evaluation of rRNA depletion methods for capturing the RNA virome from environmental surfaces
BMC Research Notes, 2023 Objective Metatranscriptomic analysis of RNA viromes on built-environment surfaces is hampered by low RNA yields and high abundance of rRNA. Therefore, we evaluated the quality of libraries, efficiency of rRNA depletion, and viral detection sensitivity ...
Yuh Shiwa +5 more
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RNA Dynamics in Aging Bacterial Spores [PDF]
Cell, 2012 Upon starvation, the bacterium Bacillus subtilis enters the process of sporulation, lasting several hours and culminating in formation of a spore, the most resilient cell type known. We show that a few days following sporulation, the RNA profile of spores is highly dynamic.
Segev, Einat +2 more
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Detection of genome-scale ordered RNA structure (GORS) in genomes of positive-stranded RNA viruses:Implications for virus evolution and host persistence [PDF]
, 2004 Discrete RNA secondary and higher-order structures, typically local in extent, play a fundamental role in RNA virus replication. Using new bioinformatics analysis methods, we have identified genome-scale ordered RNA structure (GORS) in many genera and ...
Evans, David J +5 more
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RNA‐Seq for Bacterial Gene Expression [PDF]
Current Protocols in Nucleic Acid Chemistry, 2018 AbstractRNA sequencing (RNA‐seq) has become the preferred method for global quantification of bacterial gene expression. With the continued improvements in sequencing technology and data analysis tools, the most labor‐intensive and expensive part of an RNA‐seq experiment is the preparation of sequencing libraries, which is also essential for the ...
Poulsen, Line Dahl, Vinther, Jeppe
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In planta Transcriptome Analysis of Pseudomonas syringae
Bio-Protocol, 2018 Profiling bacterial transcriptome in planta is challenging due to the low abundance of bacterial RNA in infected plant tissues. Here, we describe a protocol to profile transcriptome of a foliar bacterial pathogen, Pseudomonas syringae pv.
Tatsuya Nobori, Kenichi Tsuda
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Comparison of DNA and RNA sequencing of total nucleic acids from human cervix for metagenomics
Scientific Reports, 2021 Although metagenomics and metatranscriptomics are commonly used to identify bacteria and viruses in human samples, few studies directly compare these strategies.
Laila Sara Arroyo Mühr +4 more
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Maf1-mediated repression of RNA polymerase III transcription inhibits tRNA degradation via RTD pathway [PDF]
, 2012 tRNA precursors, which are transcribed by RNA polymerase III, undergo end-maturation, splicing and base modifications. Hypomodified tRNAs, such as tRNAVal(AAC), lacking 7-methylguanosine and 5-methylcytidine modifications, are subject to degradation by a
Boguta, Magdalena +3 more
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