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https://www.readbyqxmd.com/read/28934467/the-important-conformational-plasticity-of-dsra-srna-for-adapting-multiple-target-regulation
#1
Pengzhi Wu, Xiaodan Liu, Lingna Yang, Yitong Sun, Qingguo Gong, Jihui Wu, Yunyu Shi
In bacteria, small non-coding RNAs (sRNAs) could function in gene regulations under variable stress responses. DsrA is an ∼90-nucleotide Hfq-dependent sRNA found in Escherichia coli. It regulates the translation and degradation of multiple mRNAs, such as rpoS, hns, mreB and rbsD mRNAs. However, its functional structure and particularly how it regulates multiple mRNAs remain obscure. Using NMR, we investigated the solution structures of the full-length and isolated stem-loops of DsrA. We first solved the NMR structure of the first stem-loop (SL1), and further studied the melting process of the SL1 induced by the base-pairing with the rpoS mRNA and the A-form duplex formation of the DsrA/rpoS complex...
September 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28928453/molecular-characterization-of-emaraviruses-associated-with-pigeonpea-sterility-mosaic-disease
#2
Surender Kumar, B L Subbarao, Vipin Hallan
Sterility Mosaic Disease (SMD) of pigeonpea (Cajanus cajan (L.) Millspaugh) is a complex disease due to various factors including the presence of a mixed infection. Comparison of dsRNA profile and small RNA (sRNA) deep sequencing analysis of samples from three locations revealed the presence of Pigeonpea sterility mosaic virus-I and II (PPSMV-I and II) from Chevella and only PPSMV-II from Bengaluru and Coimbatore. PPSMV-I genome consisted of four while PPSMV-II encompassed six RNAs. The two viruses have modest sequence homology between their corresponding RNA 1-4 encoding RdRp, glycoprotein precursor, nucleocapsid and movement proteins and the corresponding orthologs of other emaraviruses...
September 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28904860/regulation-of-neisseria-meningitidis-cytochrome-bc1-components-by-nrrf-a-fur-controlled-small-noncoding-rna
#3
Yvonne Pannekoek, Robert Huis In 't Veld, Kim Schipper, Sandra Bovenkerk, Gertjan Kramer, Dave Speijer, Arie van der Ende
NrrF is a small regulatory RNA of the human pathogen Neisseria meningitidis. NrrF was previously shown to repress succinate dehydrogenase (sdhCDAB) under control of the ferric uptake regulator (Fur). Here, we provide evidence that cytochrome bc1 , encoded by the polycistronic mRNA petABC, is a NrrF target as well. We demonstrated differential expression of cytochrome bc1 comparing wild-type meningococci and meningococci expressing NrrF when sufficient iron is available. Using a gfp-reporter system monitoring translational control and target recognition of sRNA in Escherichia coli, we show that interaction between NrrF and the 5' untranslated region of the petABC mRNA results in its repression...
September 2017: FEBS Open Bio
https://www.readbyqxmd.com/read/28900423/esre-a-yigp-locus-encoded-transcript-is-a-3-utr-srna-involved-in-the-respiratory-chain-of-e-coli
#4
Hui Xia, Xichen Yang, Qiongwei Tang, Jiang Ye, Haizhen Wu, Huizhan Zhang
The yigP locus is widely conserved among γ-proteobacteria. Mutation of the yigP locus impacts aerobic growth of Gram-negative bacteria. However, the underlying mechanism of how the yigP locus influences aerobic growth remains largely unknown. Here, we demonstrated that the yigP locus in Escherichia coli encodes two transcripts; the mRNA of ubiquinone biosynthesis protein, UbiJ, and the 3' untranslated region small regulatory RNA (sRNA), EsrE. EsrE is an independent transcript that is transcribed using an internal promoter of the yigP locus...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28894187/small-rnas-in-vancomycin-resistant-enterococcus-faecium-involved-in-daptomycin-response-and-resistance
#5
Clara Sinel, Yoann Augagneur, Mohamed Sassi, Julie Bronsard, Margherita Cacaci, François Guérin, Maurizio Sanguinetti, Pierrick Meignen, Vincent Cattoir, Brice Felden
Vancomycin-resistant Enterococcus faecium is a leading cause of hospital-acquired infections and outbreaks. Regulatory RNAs (sRNAs) are major players in adaptive responses, including antibiotic resistance. They were extensively studied in gram-negative bacteria, but less information is available for gram-positive pathogens. No sRNAs are described in E. faecium. We sought to identify a set of sRNAs expressed in vancomycin-resistant E. faecium Aus0004 strain to assess their roles in daptomycin response and resistance...
September 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28886174/development-of-hop-transcriptome-to-support-research-into-host-viroid-interactions
#6
Tine Pokorn, Sebastjan Radišek, Branka Javornik, Nataša Štajner, Jernej Jakše
Viroids, the smallest known pathogens, unable to encode any proteins, can cause severe diseases in their host plants. One of the proposed mechanisms of their pathogenicity includes silencing the host's genes via viroid-derived small RNAs, which are products of the host's immune response to the viroid's double stranded RNA. Humulus lupulus (hop) plants are hosts to several viroids; two of them, HLVd and CBCVd, are interesting models for studying host-viroid interactions, due to the symptomless infection of the former and severe stunting disease caused by the latter...
2017: PloS One
https://www.readbyqxmd.com/read/28885180/next-generation-sequencing-sheds-new-light-on-small-rnas-in-plant-reproductive-development
#7
Xiaobai Li
Reproductive development is a key step of the plant life cycles and indicates the start of a new life cycle. The reproductive organs including flower, fruit and seed, have diverse and complex structures, which is a syndrome in the evolution of angiosperms. The development of plant reproductive organs depends on the correct spatial and temporal expression of numerous genes acting in concert to form regulatory networks. Small non-coding RNAs (sRNAs) play a key role in the reproductive development through different modes of sequence-specific interaction with their targets...
September 8, 2017: Current Issues in Molecular Biology
https://www.readbyqxmd.com/read/28882222/role-of-the-trna-derived-small-rnas-in-cancer-new-potential-biomarkers-and-target-for-therapy
#8
Veronica Balatti, Yuri Pekarsky, Carlo M Croce
Noncoding RNAs are untranslated RNA molecules that can be divided into two main types: infrastructural, including transfer RNAs (tRNAs) and ribosomal RNAs (rRNAs), and regulatory, including long ncRNAs (lncRNAs) and small ncRNAs (sRNA). Among small ncRNA, the role of microRNAs (miRNAs) and Piwi-interacting RNAs (piRNAs) in cancer is well documented. Recently, other small ncRNAs have been described. In particular, tRNA-derived small RNAs (tsRNA) have been found to be frequently dysregulated in cancer. Since tsRNAs can be considered unique sequences and are able to bind both Argonaute proteins (like miRNAs) and Piwi proteins (like piRNAs), their dysregulation could play a critical role in cancer by interfering with gene expression regulation at different levels...
2017: Advances in Cancer Research
https://www.readbyqxmd.com/read/28878270/membrane-association-of-the-bacterial-riboregulator-hfq-and-functional-perspectives
#9
Antoine Malabirade, Javier Morgado-Brajones, Sylvain Trépout, Frank Wien, Ileana Marquez, Jérôme Seguin, Sergio Marco, Marisela Velez, Arluison Véronique
Hfq is a bacterial RNA binding protein that carries out several roles in genetic expression regulation, mainly at the post-transcriptional level. Previous studies have shown its importance in growth and virulence of bacteria. Here, we provide the direct observation of its ability to interact with membranes. This was established by co-sedimentation assay, cryo-transmission electron (cryo-TEM) and atomic force (AFM) microscopies. Furthermore, our results suggest a role for its C-terminus amyloidogenic domain in membrane disruption...
September 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28876208/deep-sequencing-uncovers-rice-long-sirnas-and-its-involvement-in-immunity-against-rhizoctonia-solani
#10
Dongdong Niu, Xin Zhang, Xiaoou Song, Zhihui Wang, Yanqiang Li, Lulu Qiao, Zhaoyun Wang, Junzhong Liu, Yiwen Deng, Zuhua He, Donglei Yang, Renyi Liu, Yangli Wang, Hongwei Zhao
Small RNA (sRNA) is a class of non-coding RNA that can silence the expression of target genes. In rice, the majority of characterized sRNAs are within the range of 21 to 24 nucleotide long, whose biogenesis and function are associated with a specific sets of components, such as Dicer-like (OsDCLs) and Argonaute proteins (OsAGOs). Rice sRNAs longer than 24 nt are occasionally reported, with biogenesis and functional mechanism uninvestigated, especially in a context of defense responses against pathogen infection...
September 6, 2017: Phytopathology
https://www.readbyqxmd.com/read/28874523/escherichia-coli-responds-to-environmental-changes-using-enolasic-degradosomes-and-stabilized-dicf-srna-to-alter-cellular-morphology
#11
Oleg N Murashko, Sue Lin-Chao
Escherichia coli RNase E is an essential enzyme that forms multicomponent ribonucleolytic complexes known as "RNA degradosomes." These complexes consist of four major components: RNase E, PNPase, RhlB RNA helicase, and enolase. However, the role of enolase in the RNase E/degradosome is not understood. Here, we report that presence of enolase in the RNase E/degradosome under anaerobic conditions regulates cell morphology, resulting in Ecoli MG1655 cell filamentation. Under anaerobic conditions, enolase bound to the RNase E/degradosome stabilizes the small RNA (sRNA) DicF, i...
September 5, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28865341/small-rnas-in-major-foodborne-pathogens-from-novel-regulatory-activities-to-future-applications
#12
REVIEW
Mette Thorsing, Patrícia Teixeira Dos Santos, Birgitte Haahr Kallipolitis
Small regulatory RNAs (sRNAs) are involved in post-transcriptional control of important cellular processes and contribute to the success of a pathogen. Here, we use studies primarily selected from Salmonella enterica and Listeria monocytogenes to illustrate the current status of sRNA biology in important foodborne pathogens. We discuss how the regulatory activities of sRNAs can be affected by base pairing RNAs known as 'sponge RNAs', or by RNA-binding proteins, such as the newly discovered sRNA chaperone ProQ...
August 30, 2017: Current Opinion in Biotechnology
https://www.readbyqxmd.com/read/28861401/micropathogen-community-analysis-in-hyalomma-rufipes-via-high-throughput-sequencing-of-small-rnas
#13
Jin Luo, Min-Xuan Liu, Qiao-Yun Ren, Ze Chen, Zhan-Cheng Tian, Jia-Wei Hao, Feng Wu, Xiao-Cui Liu, Jian-Xun Luo, Hong Yin, Hui Wang, Guang-Yuan Liu
Ticks are important vectors in the transmission of a broad range of micropathogens to vertebrates, including humans. Because of the role of ticks in disease transmission, identifying and characterizing the micropathogen profiles of tick populations have become increasingly important. The objective of this study was to survey the micropathogens of Hyalomma rufipes ticks. Illumina HiSeq2000 technology was utilized to perform deep sequencing of small RNAs (sRNAs) extracted from field-collected H. rufipes ticks in Gansu Province, China...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/28852099/intermolecular-base-stacking-mediates-rna-rna-interaction-in-a-crystal-structure-of-the-rna-chaperone-hfq
#14
Eike C Schulz, Markus Seiler, Cecilia Zuliani, Franka Voigt, Vladimir Rybin, Vivian Pogenberg, Norbert Mücke, Matthias Wilmanns, Toby J Gibson, Orsolya Barabas
The RNA-chaperone Hfq catalyses the annealing of bacterial small RNAs (sRNAs) with target mRNAs to regulate gene expression in response to environmental stimuli. Hfq acts on a diverse set of sRNA-mRNA pairs using a variety of different molecular mechanisms. Here, we present an unusual crystal structure showing two Hfq-RNA complexes interacting via their bound RNA molecules. The structure contains two Hfq6:A18 RNA assemblies positioned face-to-face, with the RNA molecules turned towards each other and connected via interdigitating base stacking interactions at the center...
August 29, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28851971/a-broad-range-quorum-sensing-inhibitor-working-through-srna-inhibition
#15
Tim H Jakobsen, Anders N Warming, Rebecca M Vejborg, Joana A Moscoso, Marc Stegger, Frederik Lorenzen, Morten Rybtke, Jens B Andersen, Rico Petersen, Paal Skytt Andersen, Thomas E Nielsen, Tim Tolker-Nielsen, Alain Filloux, Hanne Ingmer, Michael Givskov
For the last decade, chemical control of bacterial virulence has received considerable attention. Ajoene, a sulfur-rich molecule from garlic has been shown to reduce expression of key quorum sensing regulated virulence factors in the opportunistic pathogen Pseudomonas aeruginosa. Here we show that the repressing effect of ajoene on quorum sensing occurs by inhibition of small regulatory RNAs (sRNA) in P. aeruginosa as well as in Staphylococcus aureus, another important human pathogen that employs quorum sensing to control virulence gene expression...
August 29, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28843192/systems-and-synthetic-biology-for-the-biotechnological-application-of-cyanobacteria
#16
REVIEW
Martin Hagemann, Wolfgang R Hess
Cyanobacteria are the only prokaryotes that perform oxygenic photosynthesis. Their evolutionary relation to plastids in eukaryotic phototrophs and their increasing utilization as green cell factories initiated the use of systems biology approaches early on. For select model strains, extensive 'omics' data sets have been generated, and genome-wide models have been elucidated. Moreover, the results obtained may be used for the optimization of cyanobacterial metabolism, which can direct the biotechnological production of biofuels or chemical feedstock...
August 23, 2017: Current Opinion in Biotechnology
https://www.readbyqxmd.com/read/28839112/an-ago2-associated-capped-transcriptional-start-site-small-rna-suppressing-adenovirus-dna-replication
#17
Wael Kamel, Göran Akusjärvi
Here we show that the adenovirus major late promoter produces a 31-nucleotide transcriptional start site small RNA (MLP-TSS-sRNA) that retains the 7-methylguanosine (m7G)-cap and is incorporated onto Ago2-containing RNA-induced silencing complexes (RISC) in human adenovirus-37 infected cells. RNA polymerase II CLIP (UV-cross linking immunoprecipitation) experiments suggest that the MLP-TSS-sRNA is produced by promoter proximal stalling/termination of RNA polymerase II transcription at the site of the small RNA 3'end...
August 24, 2017: RNA
https://www.readbyqxmd.com/read/28830349/prediction-of-bacterial-small-rnas-in-the-rsma-csra-and-toxt-pathways-a-machine-learning-approach
#18
Carl Tony Fakhry, Prajna Kulkarni, Ping Chen, Rahul Kulkarni, Kourosh Zarringhalam
BACKGROUND: Small RNAs (sRNAs) constitute an important class of post-transcriptional regulators that control critical cellular processes in bacteria. Recent research using high-throughput transcriptomic approaches has led to a dramatic increase in the discovery of bacterial sRNAs. However, it is generally believed that the currently identified sRNAs constitute a limited subset of the bacterial sRNA repertoire. In several cases, sRNAs belonging to a specific class are already known and the challenge is to identify additional sRNAs belonging to the same class...
August 22, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28830343/divergence-of-functional-effects-among-bacterial-srna-paralogs
#19
I-Chen Kimberly Chen, Gregory J Velicer, Yuen-Tsu Nicco Yu
BACKGROUND: Non-coding small RNAs (sRNAs) regulate a variety of important biological processes across all life domains, including bacteria. However, little is known about the functional evolution of sRNAs in bacteria, which might occur via changes in sRNA structure and/or stability or changes in interactions between sRNAs and their associated regulatory networks, including target mRNAs. The sRNA Pxr functions as a developmental gatekeeper in the model cooperative bacterium Myxococcus xanthus...
August 22, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28829439/an-integrated-expression-atlas-of-mirnas-and-their-promoters-in-human-and-mouse
#20
Derek de Rie, Imad Abugessaisa, Tanvir Alam, Erik Arner, Peter Arner, Haitham Ashoor, Gaby Åström, Magda Babina, Nicolas Bertin, A Maxwell Burroughs, Ailsa J Carlisle, Carsten O Daub, Michael Detmar, Ruslan Deviatiiarov, Alexandre Fort, Claudia Gebhard, Daniel Goldowitz, Sven Guhl, Thomas J Ha, Jayson Harshbarger, Akira Hasegawa, Kosuke Hashimoto, Meenhard Herlyn, Peter Heutink, Kelly J Hitchens, Chung Chau Hon, Edward Huang, Yuri Ishizu, Chieko Kai, Takeya Kasukawa, Peter Klinken, Timo Lassmann, Charles-Henri Lecellier, Weonju Lee, Marina Lizio, Vsevolod Makeev, Anthony Mathelier, Yulia A Medvedeva, Niklas Mejhert, Christopher J Mungall, Shohei Noma, Mitsuhiro Ohshima, Mariko Okada-Hatakeyama, Helena Persson, Patrizia Rizzu, Filip Roudnicky, Pål Sætrom, Hiroki Sato, Jessica Severin, Jay W Shin, Rolf K Swoboda, Hiroshi Tarui, Hiroo Toyoda, Kristoffer Vitting-Seerup, Louise Winteringham, Yoko Yamaguchi, Kayoko Yasuzawa, Misako Yoneda, Noriko Yumoto, Susan Zabierowski, Peter G Zhang, Christine A Wells, Kim M Summers, Hideya Kawaji, Albin Sandelin, Michael Rehli, Yoshihide Hayashizaki, Piero Carninci, Alistair R R Forrest, Michiel J L de Hoon
MicroRNAs (miRNAs) are short non-coding RNAs with key roles in cellular regulation. As part of the fifth edition of the Functional Annotation of Mammalian Genome (FANTOM5) project, we created an integrated expression atlas of miRNAs and their promoters by deep-sequencing 492 short RNA (sRNA) libraries, with matching Cap Analysis Gene Expression (CAGE) data, from 396 human and 47 mouse RNA samples. Promoters were identified for 1,357 human and 804 mouse miRNAs and showed strong sequence conservation between species...
September 2017: Nature Biotechnology
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