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https://www.readbyqxmd.com/read/28436820/srna-mediated-activation-of-gene-expression-by-inhibition-of-5-3-exonucleolytic-mrna-degradation
#1
Sylvain Durand, Frédérique Braun, Anne-Catherine Helfer, Pascale Romby, Ciarán Condon
Post-transcriptional control by small regulatory RNA (sRNA) is critical for rapid adaptive processes. sRNAs can directly modulate mRNA degradation in Proteobacteria without interfering with translation. However, Firmicutes have a fundamentally different set of ribonucleases for mRNA degradation and whether sRNAs can regulate the activity of these enzymes is an open question. We show that Bacillus subtilis RoxS, a major trans-acting sRNA shared with Staphylococus aureus, prevents degradation of the yflS mRNA, encoding a malate transporter...
April 24, 2017: ELife
https://www.readbyqxmd.com/read/28431495/iron-regulated-small-rna-expression-as-neisseria-gonorrhoeae-fa-1090-transitions-into-stationary-phase-growth
#2
Lydgia A Jackson, Michael Day, Jennie Allen, Edgar Scott, David W Dyer
BACKGROUND: For most pathogens, iron (Fe) homeostasis is crucial for maintenance within the host and the ability to cause disease. The primary transcriptional regulator that controls intracellular Fe levels is the Fur (ferric uptake regulator) protein, which exerts its action on transcription by binding to a promoter-proximal sequence termed the Fur box. Fur-regulated transcriptional responses are often fine-tuned at the post-transcriptional level through the action of small regulatory RNAs (sRNAs)...
April 21, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28405712/emergence-of-new-srnas-in-enteric-bacteria-is-associated-with-low-expression-and-rapid-evolution
#3
Fenil R Kacharia, Jess A Millar, Rahul Raghavan
Non-coding small RNAs (sRNAs) are critical to post-transcriptional gene regulation in bacteria. However, unlike for protein-coding genes, the evolutionary forces that shape sRNAs are not understood. We investigated sRNAs in enteric bacteria and discovered that recently emerged sRNAs evolve at significantly faster rates than older sRNAs. Concomitantly, younger sRNAs are expressed at significantly lower levels than older sRNAs. This process could potentially facilitate the integration of newly emerged sRNAs into bacterial regulatory networks...
April 12, 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/28403818/srnas-as-possible-regulators-of-retrotransposon-activity-in-cryptococcus-gattii-vgii
#4
Patrícia Aline Gröhs Ferrareze, Rodrigo Silva Araujo Streit, Francine Melise Dos Santos, Augusto Schrank, Livia Kmetzsch, Marilene Henning Vainstein, Charley Christian Staats
BACKGROUND: The absence of Argonaute genes in the fungal pathogen Cryptococcus gattii R265 and other VGII strains indicates that yeasts of this genotype cannot have a functional RNAi pathway, an evolutionarily conserved gene silencing mechanism performed by small RNAs. The success of the R265 strain as a pathogen that caused the Pacific Northwest and Vancouver Island outbreaks may imply that RNAi machinery loss could be beneficial under certain circumstances during evolution. As a result, a hypermutant phenotype would be created with high rates of genome retrotransposition, for instance...
April 12, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28401641/a-conserved-%C3%AE-proteobacterial-small-rna-contributes-to-osmoadaptation-and-symbiotic-efficiency-of-rhizobia-on-legume-roots
#5
Marta Robledo, Alexandra Peregrina, Vicenta Millán, Natalia I García-Tomsig, Omar Torres-Quesada, Pedro F Mateos, Anke Becker, José I Jiménez-Zurdo
Small non-coding RNAs (sRNAs) are expected to have pivotal roles in the adaptive responses underlying symbiosis of nitrogen-fixing rhizobia with legumes. Here, we provide primary insights into the function and activity mechanism of the Sinorhizobium meliloti trans-sRNA NfeR1 (Nodule Formation Efficiency RNA). Northern blot probing and transcription tracking with fluorescent promoter-reporter fusions unveiled high nfeR1 expression in response to salt stress and throughout the symbiotic interaction. The strength and differential regulation of nfeR1 transcription are conferred by a motif, which is conserved in nfeR1 promoter regions in α-proteobacteria...
April 12, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28381573/potato-virus-y-hcpro-suppression-of-antiviral-silencing-in-nicotiana-benthamiana-plants-correlates-with-its-ability-to-bind-in-vivo-to-21-and-22-nucleotide-small-rnas-of-viral-sequence
#6
Francisco J Del Toro, Livia Donaire, Emmanuel Aguilar, Bong-Nam Chung, Francisco Tenllado, Tomás Canto
We have investigated short and small RNAs (sRNAs) that were bound to a biologically active hexahistidine-tagged Potato virus Y (PVY) HCPro suppressor of silencing, expressed from a heterologous virus vector in Nicotiana benthamiana plants, and purified under non-denaturing conditions. We found that RNAs in purified preparations were differentially enriched in sRNAs of 21 and to a much lesser extent of 22 nucleotides (nt) in length and of viral sequence (vsRNAs) when compared to those found in a control plant protein background bound to the nickel resin in the absence of HCPro, or in a purified alanine substitution HCPro mutant (HCPro mutB) control that lacked suppressor of silencing activity...
April 5, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28379505/the-rna-targetome-of-staphylococcus-aureus-non-coding-rna-rsaa-impact-on-cell-surface-properties-and-defense-mechanisms
#7
Arnaud Tomasini, Karen Moreau, Johana Chicher, Thomas Geissmann, François Vandenesch, Pascale Romby, Stefano Marzi, Isabelle Caldelari
The virulon of Staphyloccocus aureus is controlled by intricate connections between transcriptional and post-transcriptional regulators including proteins and small non-coding RNAs (sRNAs). Many of the sRNAs regulate gene expression through base-pairings with mRNAs. However, characterization of the direct sRNA targets in Gram-positive bacteria remained a difficult challenge. Here, we have applied and adapted the MS2-affinity purification approach coupled to RNA sequencing (MAPS) to determine the targetome of RsaA sRNA of S...
April 3, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28378154/plant-derived-phosphocholine-facilitates-cellular-uptake-of-anti-pulmonary-fibrotic-hjt-srna-m7
#8
Jianchao Du, Zhu Liang, Jiantao Xu, Yan Zhao, Xiaoyun Li, Yanli Zhang, Dandan Zhao, Ruxuan Chen, Yang Liu, Trupti Joshi, Jiahui Chang, Zhiqing Wang, Yanxu Zhang, Jindong Zhu, Qiang Liu, Dong Xu, Chengyu Jiang
Pulmonary fibrosis, a progressive chronic disease with a high mortality rate, has limited treatment options. Currently, lung transplantation remains the only effective treatment. Here we report that a small RNA, HJT-sRNA-m7, from a Chinese herbal medicine Hong Jing Tian (HJT, Rhodiola crenulata can effectively reduce the expressions of fibrotic hallmark genes and proteins both in alveolar in vitro and in mouse lung tissues in vivo. We also discovered over one hundred oil-soluble chemicals from HJT decoctions, most of which are found in lipid extracts from other Chinese herbals decoctions, including Pu Gong Ying (PGY, Taraxacum mongolicum), Chuan Xin Lian (CXL, Andrographis paniculata), and Jin Yin Hua (JYH, lonicera japonica or Honeysuckle)...
March 31, 2017: Science China. Life Sciences
https://www.readbyqxmd.com/read/28375142/crystal-structure-and-rna-binding-properties-of-an-hfq-homolog-from-the-deep-branching-aquificae-conservation-of-the-lateral-rna-binding-mode
#9
Kimberly A Stanek, Jennifer Patterson-West, Peter S Randolph, Cameron Mura
The host factor Hfq, as the bacterial branch of the Sm family, is an RNA-binding protein involved in the post-transcriptional regulation of mRNA expression and turnover. Hfq facilitates pairing between small regulatory RNAs (sRNAs) and their corresponding mRNA targets by binding both RNAs and bringing them into close proximity. Hfq homologs self-assemble into homo-hexameric rings with at least two distinct surfaces that bind RNA. Recently, another binding site, dubbed the `lateral rim', has been implicated in sRNA·mRNA annealing; the RNA-binding properties of this site appear to be rather subtle, and its degree of evolutionary conservation is unknown...
April 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28370647/adaptive-sequence-evolution-is-driven-by-biotic-stress-in-a-pair-of-orchid-species-dactylorhiza-with-distinct-ecological-optima
#10
Francisco Balao, Emiliano Trucchi, Thomas Wolfe, Bao-Hai Hao, Maria Teresa Lorenzo, Juliane Baar, Laura Sedman, Carolin Kosiol, Fabian Amman, Mark W Chase, Mikael Hedrén, Ovidiu Paun
The orchid family is the largest in the angiosperms, but little is known about the molecular basis of the significant variation they exhibit. We investigate here the transcriptomic divergence between two European terrestrial orchids, Dactylorhiza incarnata and D. fuchsii, and integrate these results in the context of their distinct ecologies that we also document. Clear signals of lineage-specific adaptive evolution of protein-coding sequences are identified, notably targeting elements of biotic defence, including both physical and chemical adaptations in the context of divergent pools of pathogens and herbivores...
March 30, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28370625/proq-fino-domain-proteins-another-ubiquitous-family-of-rna-matchmakers
#11
REVIEW
Mikolaj Olejniczak, Gisela Storz
Small RNAs (sRNAs), particularly those that act by limited base pairing with mRNAs, are part of most regulatory networks in bacteria. In many cases, the base-pairing interaction is facilitated by the RNA chaperone Hfq. However, not all bacteria encode Hfq and some base-pairing sRNAs do not require Hfq raising the possibility of other RNA chaperones. Candidates are proteins with homology to FinO, a factor that promotes base pairing between the FinP antisense sRNA and the traJ mRNA to control F plasmid transfer...
March 30, 2017: Molecular Microbiology
https://www.readbyqxmd.com/read/28369640/an-in-vivo-reporter-assay-for-srna-directed-gene-control-in-gram-positive-bacteria-identifying-a-novel-srna-target-in-staphylococcus-aureus
#12
Lorraine Ivain, Valérie Bordeau, Alex Eyraud, Marc Hallier, Stéphane Dreano, Pierre Tattevin, Brice Felden, Svetlana Chabelskaya
Bacterial small regulatory RNAs (sRNAs) play a major role in the regulation of various cellular functions. Most sRNAs interact with mRNA targets via an antisense mechanism, modifying their translation and/or degradation. Despite considerable progresses in discovering sRNAs in Gram-positive bacteria, their functions, for the most part, are unknown. This is mainly due to difficulties in identifying their targets. To aid in the identification of sRNA targets in Gram-positive bacteria, we set up an in vivo method for fast analysis of sRNA-mediated post-transcriptional control at the 5΄ regions of target mRNAs...
March 21, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28367405/synaptic-vesicles-isolated-from-the-electric-organ-of-torpedo-californica-and-from-the-central-nervous-system-of-mus-musculus-contain-small-ribonucleic-acids-srnas
#13
Huinan Li, Cheng Wu, Rodolfo Aramayo, Matthew S Sachs, Mark L Harlow
Synaptic vesicles (SVs) are presynaptic organelles that load and release small molecule neurotransmitters at chemical synapses. In addition to classic neurotransmitters, we have demonstrated that SVs isolated from the Peripheral Nervous Systems (PNS) of the electric organ of Torpedo californica, a model cholinergic synapse, and SVs isolated from the Central Nervous System (CNS) of Mus musculus (mouse) contain small ribonucleic acids (sRNAs; ≤ 50 nucleotides) (Scientific Reports, 5:1-14(14918) Li et al. (2015) [1])...
June 2017: Genomics Data
https://www.readbyqxmd.com/read/28350301/sub-cellular-mrna-localization-modulates-the-regulation-of-gene-expression-by-small-rnas-in-bacteria
#14
Hamid Teimouri, Elgin Korkmazhan, Joel Stavans, Erel Levine
Small non-coding RNAs can exert significant regulatory activity on gene expression in bacteria. In recent years, substantial progress has been made in understanding bacterial gene expression by sRNAs. However, recent findings that demonstrate that families of mRNAs show non-trivial sub-cellular distributions raise the question of how localization may affect the regulatory activity of sRNAs. Here we address this question within a simple mathematical model. We show that the non-uniform spatial distributions of mRNA can alter the threshold-linear response that characterizes sRNAs that act stoichiometrically, and modulate the hierarchy among targets co-regulated by the same sRNA...
March 28, 2017: Physical Biology
https://www.readbyqxmd.com/read/28348860/transcriptomic-analysis-of-staphylococcal-srnas-insights-into-species-specific-adaption-and-the-evolution-of-pathogenesis
#15
William H Broach, Andy Weiss, Lindsey N Shaw
Next-generation sequencing technologies have dramatically increased the rate at which new genomes are sequenced. Accordingly, automated annotation programs have become adept at identifying and annotating protein coding regions, as well as common and conserved RNAs. Additionally, RNAseq techniques have advanced our ability to identify and annotate regulatory RNAs (sRNAs), which remain significantly understudied. Recently, our group catalogued and annotated all previously known and newly identified sRNAs in several Staphylococcus aureus strains...
July 2016: Microbial Genomics
https://www.readbyqxmd.com/read/28342817/complete-genome-sequence-of-streptomyces-griseochromogenes-atcc-14511-t-a-producer-of-nucleoside-compounds-and-diverse-secondary-metabolites
#16
Lijuan Wu, Guoqing Chen, Guozhong Feng
ATCC 14511(T) (=DSM 40499, =NBRC 13413) is a type strain of Streptomyces griseochromogenes. It is known as a producer of nucleoside antibiotic, blasticidin S. In this report we present the complete genome sequence of S. griseochromogenes ATCC 14511(T), which consists of 10,764,674bp with a linear chromosome, 9822 protein-coding genes, 6 rRNA operons, 74 tRNA and 3 sRNA. The genomic analysis revealed that 52 putative gene clusters are involved in the biosynthesis of secondary metabolites, including four gene clusters of nucleoside antibiotics...
March 22, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28338079/dissecting-mirna-gene-repression-on-single-cell-level-with-an-advanced-fluorescent-reporter-system
#17
Nicolas Lemus-Diaz, Kai O Böker, Ignacio Rodriguez-Polo, Michael Mitter, Jasmin Preis, Maximilian Arlt, Jens Gruber
Despite major advances on miRNA profiling and target predictions, functional readouts for endogenous miRNAs are limited and frequently lead to contradicting conclusions. Numerous approaches including functional high-throughput and miRISC complex evaluations suggest that the functional miRNAome differs from the predictions based on quantitative sRNA profiling. To resolve the apparent contradiction of expression versus function, we generated and applied a fluorescence reporter gene assay enabling single cell analysis...
March 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28336682/molecular-mechanism-of-mrna-repression-in-trans-by-a-proq-dependent-small-rna
#18
Alexandre Smirnov, Chuan Wang, Lisa L Drewry, Jörg Vogel
Research into post-transcriptional control of mRNAs by small noncoding RNAs (sRNAs) in the model bacteria Escherichia coli and Salmonella enterica has mainly focused on sRNAs that associate with the RNA chaperone Hfq. However, the recent discovery of the protein ProQ as a common binding partner that stabilizes a distinct large class of structured sRNAs suggests that additional RNA regulons exist in these organisms. The cellular functions and molecular mechanisms of these new ProQ-dependent sRNAs are largely unknown...
April 13, 2017: EMBO Journal
https://www.readbyqxmd.com/read/28335718/rnav-2-0-a-visualization-tool-for-bacterial-srna-mediated-regulatory-networks-mining
#19
Romain Bourqui, Isabelle Dutour, Jonathan Dubois, William Benchimol, Patricia Thébault
BACKGROUND: Bacterial sRNA-mediated regulatory networks has been introduced as a powerful way to analyze the fast rewiring capabilities of a bacteria in response to changing environmental conditions. The identification of mRNA targets of bacterial sRNAs is essential to investigate their functional activities. However, this step remains challenging with the lack of knowledge of the topological and biological constraints behind the formation of sRNA-mRNA duplexes. Even with the most sophisticated bioinformatics target prediction tools, the large proportion of false predictions may be prohibitive for further analyses...
March 23, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28335027/a-transposon-derived-small-rna-regulates-gene-expression-in-salmonella-typhimurium
#20
Michael J Ellis, Ryan S Trussler, Onella Charles, David B Haniford
Bacterial sRNAs play an important role in regulating many cellular processes including metabolism, outer membrane homeostasis and virulence. Although sRNAs were initially found in intergenic regions, there is emerging evidence that protein coding regions of the genome are a rich reservoir of sRNAs. Here we report that the 5΄UTR of IS200 transposase mRNA (tnpA) is processed to produce regulatory RNAs that affect expression of over 70 genes in Salmonella Typhimurium. We provide evidence that the tnpA derived sRNA base-pairs with invF mRNA to repress expression...
February 21, 2017: Nucleic Acids Research
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