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https://www.readbyqxmd.com/read/29159897/identification-and-characterization-of-two-variants-of-the-hfq-srna-chaperone-in-the-fish-pathogen-piscirickettsia-salmonis
#1
S H Marshall, P Flores-Herrera, F A Henríquez, F A Gómez
Small RNA and chaperone proteins form synergistic duos that play pivotal roles in controlling gene expression in bacteria. This is the case for Hfq, a highly pleiotropic pretranslational modulator of general protein expression, which responds to harsh environmental conditions and influences fitness and virulence in a wide range of pathogenic Enterobacteria. Given this relevancy, we evaluated the presence and potential role of Hfq in the fish pathogen Piscirickettsia salmonis, a Gram-negative bacterium that threatens the sustainability of Chilean salmon production...
November 21, 2017: Journal of Fish Diseases
https://www.readbyqxmd.com/read/29157225/identification-of-drought-responsive-mirnas-and-physiological-characterization-of-tea-plant-camellia-sinensis-l-under-drought-stress
#2
Yuqiong Guo, Shanshan Zhao, Chen Zhu, Xiaojun Chang, Chuan Yue, Zhong Wang, Yuling Lin, Zhongxiong Lai
BACKGROUND: Drought stress is one of the major natural challenges in the main tea-producing regions of China. The tea plant (Camellia sinensis) is a traditional beverage plant whose growth status directly affects tea quality. Recent studies have revealed that microRNAs (miRNAs) play key functions in plant growth and development. Although some miRNAs have been identified in C. sinensis, little is known about their roles in the drought stress response of tea plants. RESULTS: Physiological characterization of Camellia sinensis 'Tieguanyin' under drought stress showed that the malondialdehyde concentration and electrical conductivity of leaves of drought-stressed plants increased when the chlorophyll concentration decreased under severe drought stress...
November 21, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/29145803/unraveling-the-evolution-and-coevolution-of-small-regulatory-rnas-and-coding-genes-in-listeria
#3
Franck Cerutti, Ludovic Mallet, Anaïs Painset, Claire Hoede, Annick Moisan, Christophe Bécavin, Mélodie Duval, Olivier Dussurget, Pascale Cossart, Christine Gaspin, Hélène Chiapello
BACKGROUND: Small regulatory RNAs (sRNAs) are widely found in bacteria and play key roles in many important physiological and adaptation processes. Studying their evolution and screening for events of coevolution with other genomic features is a powerful way to better understand their origin and assess a common functional or adaptive relationship between them. However, evolution and coevolution of sRNAs with coding genes have been sparsely investigated in bacterial pathogens. RESULTS: We designed a robust and generic phylogenomics approach that detects correlated evolution between sRNAs and protein-coding genes using their observed and inferred patterns of presence-absence in a set of annotated genomes...
November 16, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29145635/trex-a-web-portal-for-exploration-of-trna-derived-fragments-in-arabidopsis-thaliana
#4
Agnieszka Thompson, Andrzej Zielezinski, Patrycja Plewka, Maciej Szymanski, Przemyslaw Nuc, Zofia Szweykowska-Kulinska, Artur Jarmolowski, Wojciech M Karlowski
tRNA-derived fragments (tRFs) constitute a new class of short regulatory RNAs that are a product of nascent or mature tRNA processing. tRF sequences have been identified in all domains of life; however, most published research pertains to human, yeast and some bacterial organisms. Despite growing interest in plant tRFs and accumulating evidence of their function in plant development and stress responses, no public, web-based repository dedicated to these molecules is currently available. Here, we introduce tRex (http://combio...
November 14, 2017: Plant & Cell Physiology
https://www.readbyqxmd.com/read/29142288/identification-of-small-rnas-abundant-in-burkholderia-cenocepacia-biofilms-reveal-putative-regulators-with-a-potential-role-in-carbon-and-iron-metabolism
#5
Andrea Sass, Sanne Kiekens, Tom Coenye
Small RNAs play a regulatory role in many central metabolic processes of bacteria, as well as in developmental processes such as biofilm formation. Small RNAs of Burkholderia cenocepacia, an opportunistic pathogenic beta-proteobacterium, are to date not well characterised. To address that, we performed genome-wide transcriptome structure analysis of biofilm grown B. cenocepacia J2315. 41 unannotated short transcripts were identified in intergenic regions of the B. cenocepacia genome. 15 of these short transcripts, highly abundant in biofilms, widely conserved in Burkholderia sp...
November 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29140461/a-bacterial-three-hybrid-assay-detects-escherichia-coli-hfq-srna-interactions-in-vivo
#6
Katherine E Berry, Ann Hochschild
The interaction of RNA molecules with proteins is a critical aspect of gene regulation across all domains of life. Here, we report the development of a bacterial three-hybrid (B3H) assay to genetically detect RNA-protein interactions. The basis for this three-hybrid assay is a transcription-based bacterial two-hybrid assay that has been used widely to detect and dissect protein-protein interactions. In the three-hybrid assay, a DNA-bound protein with a fused RNA-binding moiety (the coat protein of bacteriophage MS2 (MS2CP)) is used to recruit a hybrid RNA upstream of a test promoter...
November 11, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29134727/a-srna-in-a-reduced-mutualistic-symbiont-genome-regulates-its-own-gene-expression
#7
Margaret W Thairu, Siyuan Cheng, Allison K Hansen
Similar to other nutritional endosymbionts that are obligate for host survival, the mutualistic aphid endosymbiont, Buchnera, has a highly reduced genome with few regulatory elements. Until recently, it was thought that aphid hosts were primarily responsible for regulating their symbiotic relationship. However, we recently revealed that Buchnera displays differential protein regulation, but not mRNA expression. We also identified a number of conserved small RNAs (sRNAs) that are expressed among Buchnera taxa...
November 13, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/29133885/a-conserved-stem-of-the-myxococcus-xanthus-srna-pxr-controls-srna-accumulation-and-multicellular-development
#8
Yuen-Tsu N Yu, Elizabeth Cooper, Gregory J Velicer
The small RNA (sRNA) Pxr negatively controls multicellular fruiting body formation in the bacterium Myxococcus xanthus, inhibiting the transition from growth to development when nutrients are abundant. Like many other prokaryotic sRNAs, Pxr is predicted to fold into three stem loops (SL1-SL3). SL1 and SL2 are highly conserved across the myxobacteria, whereas SL3 is much more variable. SL1 is necessary for the regulatory function of Pxr but the importance of SL3 in this regard is unknown. To test for cis genetic elements required for Pxr function, we deleted the entire pxr gene from a developmentally defective strain that fails to remove Pxr-mediated blockage of development and reintroduced variably truncated fragments of the pxr region to test for their ability to block development...
November 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29133823/identification-of-mirna-mediated-drought-responsive-multi-tiered-regulatory-network-in-drought-tolerant-rice-nagina-22
#9
Sonia Balyan, Mukesh Kumar, Roseeta Devi Mutum, Utkarsh Raghuvanshi, Priyanka Agarwal, Saloni Mathur, Saurabh Raghuvanshi
Comparative characterization of microRNA-mediated stress regulatory networks in contrasting rice cultivars is critical to decipher plant stress response. Consequently, a multi-level comparative analysis, using sRNA sequencing, degradome analysis, enzymatic and metabolite assays and metal ion analysis, in drought tolerant and sensitive rice cultivars was conducted. The study identified a group of miRNAs "Cultivar-specific drought responsive" (CSDR)-miRNAs (osa-miR159f, osa-miR1871, osa-miR398b, osa-miR408-3p, osa-miR2878-5p, osa-miR528-5p and osa-miR397a) that were up-regulated in the flag-leaves of tolerant cultivar, Nagina 22 (N22) and Vandana, but down-regulated in the sensitive cultivar, Pusa Basmati 1 (PB1) and IR64, during drought...
November 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29133345/small-rna-teg49-is-derived-from-a-sara-transcript-and-regulates-virulence-genes-independent-of-sara-in-staphylococcus-aureus
#10
Adhar C Manna, Samin Kim, Liviu Cengher, Anna Corvaglia, Stefano Leo, Patrice Francois, Ambrose L Cheung
Expression of virulence factors in S. aureus is regulated by a wide range of transcriptional regulators including proteins and small RNAs (sRNAs) at the level of transcription and/or translation. The sarA locus consists of three overlapping transcripts generated from three distinct promoters, all encoding the sarA ORF. The 5' UTRs of these transcripts contain three separate regions at ∼711, 409, and 146-nt upstream of the sarA translation start, the functions of which remain unknown. Recent RNA-Seq analysis and subsequent characterization indicated that two sRNA, teg49 and teg48, are processed and likely produced from the sarA P3 and sarA P1 transcripts of the sarA locus, respectively...
November 13, 2017: Infection and Immunity
https://www.readbyqxmd.com/read/29126230/a-survey-of-software-tools-for-microrna-discovery-and-characterization-using-rna-seq
#11
Michele Bortolomeazzi, Enrico Gaffo, Stefania Bortoluzzi
Since the small RNA-sequencing (sRNA-seq) technology became available, it allowed the discovery of thousands new microRNAs (miRNAs) in humans and many other species, providing new data on these small RNAs (sRNAs) of high biological and translational relevance. MiRNA discovery has not yet reached saturation, even in the most studied model organisms, and many researchers are using sRNA-seq in studies with different aims in biomedicine, fundamental research and in applied animal sciences. We review several miRNA discovery and characterization software tools that implement different strategies, providing a useful guide for researchers to select the programs best suiting their study objectives and data...
November 6, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/29125938/new-aspects-of-rna-based-regulation-by-hfq-and-its-partner-srnas
#12
REVIEW
Kumari Kavita, Francois de Mets, Susan Gottesman
Hfq, an RNA chaperone, promotes the pairing of small RNAs (sRNAs) to target mRNAs, mediating post-transcriptional regulation of mRNA stability and translation. This regulation contributes to bacterial adaptation during stress and pathogenesis. Recent advances in sequencing techniques demonstrate the presence of sRNAs encoded not only in intergenic regions but also from the 3' and 5' UTRs of mRNAs, expanding sRNA regulatory networks. Additional layers of regulation by Hfq and its associated RNAs continue to be found...
November 7, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/29121117/correction-genome-wide-investigation-using-srna-seq-degradome-seq-and-transcriptome-seq-reveals-regulatory-networks-of-micrornas-and-their-target-genes-in-soybean-during-soybean-mosaic-virus-infection
#13
https://www.readbyqxmd.com/read/29120256/silent-but-deadly-is200-promotes-pathogenicity-in-salmonella-typhimurium
#14
Michael J Ellis, Lindsey A Carfrae, Craig R Macnair, Ryan S Trussler, Eric D Brown, David B Haniford
Bacterial transposons were long thought of as selfish mobile genetic elements that propagate at the expense of 'host' bacterium fitness. However, limited transposition can benefit the host organism by promoting DNA rearrangements and facilitating horizontal gene transfer. Here we discuss and provide context for our recently published work which reported the surprising finding that an otherwise dormant transposon, IS200, encodes a regulatory RNA in Salmonella Typhimurium. This previous work identified a trans-acting sRNA that is encoded in the 5'UTR of IS200 transposase mRNA (tnpA)...
November 9, 2017: RNA Biology
https://www.readbyqxmd.com/read/29105762/regulation-of-genome-wide-dna-methylation-by-mobile-small-rnas
#15
REVIEW
Muluneh Tamiru, Thomas J Hardcastle, Mathew G Lewsey
Contents I. II. III. IV. V. VI. VII. VIII. IX. References SUMMARY: RNA-directed DNA methylation (RdDM) at cytosine residues regulates gene expression, silences transposable elements and influences genome stability. The mechanisms responsible for RdDM are guided to target loci by small RNAs (sRNAs) that can move within plants cell to cell and long distance. Here we discuss recent advances in the understanding of interactions between mobile sRNAs and DNA methylation. We describe the mechanisms of sRNA movement, the differences between known classes of mobile sRNA-DNA methylation interactions and the limits of current knowledge...
November 6, 2017: New Phytologist
https://www.readbyqxmd.com/read/29099689/identification-of-novel-small-rnas-in-burkholderia-cenocepacia-kc-01-expressed-under-iron-limitation-and-oxidative-stress-conditions
#16
Suparna Ghosh, Chetna Dureja, Indu Khatri, Srikrishna Subramanian, Saumya Raychaudhuri, Sagarmoy Ghosh
Small RNA (sRNA)-mediated regulation of gene expression is a major tool to understand bacterial responses to environmental changes. In particular, pathogenic bacteria employ sRNAs to adapt to the host environment and establish infection. Members of the Burkholderia cepacia complex, normally present in soil microbiota, cause nosocomial lung infection especially in hospitalized cystic fibrosis patients. We sequenced the draft genome of Burkholderia cenocepacia KC-01, isolated from the coastal saline soil, and identified several potential sRNAs in silico...
November 3, 2017: Microbiology
https://www.readbyqxmd.com/read/29097088/small-rna-big-effect-control-of-flagellin-production
#17
Aleksandra A Miranda-CasoLuengo, Stefani C Kary, Marc Erhardt, Carsten Kröger
Many bacteria move in their environment using a remarkable, rotating nanomachine - the flagellum. In a recent publication, Choi et al. report a new addition to the group of flagellar regulators, a trans-acting small RNA (sRNA).
October 30, 2017: Trends in Microbiology
https://www.readbyqxmd.com/read/29096602/identification-and-expression-profiling-of-micrornas-involved-in-the-stigma-exsertion-under-high-temperature-stress-in-tomato
#18
Changtian Pan, Lei Ye, Yi Zheng, Yan Wang, Dandan Yang, Xue Liu, Lifei Chen, Youwei Zhang, Zhangjun Fei, Gang Lu
BACKGROUND: Autogamy in cultivated tomato varieties is a derived trait from wild type tomato plants, which are mostly allogamous. However, environmental stresses can cause morphological defects in tomato flowers and hinder autogamy. Under elevated temperatures, tomato plants usually exhibit the phenotype of stigma exsertion, with severely hindered self-pollination and fruit setting, whereas the inherent mechanism of stigma exsertion have been hitherto unknown. Numerous small RNAs (sRNAs) have been shown to play significant roles in plant development and stress responses, however, none of them have been studied with respect to stamen and pistil development under high-temperature conditions...
November 2, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29090851/bacillus-amyloliquefaciens-fzb42-repressed-plant-mir846-to-induce-systemic-resistance-via-jasmonic-acid-dependent-signaling-pathway
#19
Shanshan Xie, Haiyang Jiang, Ting Ding, Qianqian Xu, Wenbo Chai, Beijiu Cheng
Bacillus amyloliquefaciens FZB42 is a kind of plant-growth-promoting rhizobacteria (PGPR) that activates induced systemic resistance (ISR) in Arabidopsis. Blocking in cyclic lipopeptides and 2,3-butanediol synthesis of FZB42, which were proved to be involved in priming ISR, resulted in abolishment of plant defense responses. To further clarify the ISR activated by PGPR at miRNA level, sRNA libraries from Arabidopsis leaves after root-irrigated with FZB42, FZB42ΔsfpΔalsS and control were constructed and sequenced...
November 1, 2017: Molecular Plant Pathology
https://www.readbyqxmd.com/read/29079634/small-rna-mediated-regulation-of-dna-dosage-in-the-ciliate-oxytricha
#20
Jaspreet S Khurana, Derek Clay, Sandrine Moreira, Xing Wang, Laura F Landweber
Dicer-dependent small non-coding RNAs play important roles in gene regulation in a wide variety of organisms. Endogenous small interfering RNAs (siRNAs) are part of an ancient pathway of transposon control in plants and animals. The ciliate, Oxytricha trifallax, has approximately 16,000 gene-sized chromosomes in its somatic nucleus. Long non-coding RNAs establish high ploidy levels at the onset of sexual development, but the factors that regulate chromosome copy numbers during cell division and growth have been a mystery...
October 27, 2017: RNA
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