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https://www.readbyqxmd.com/read/29329439/conserved-proteins-of-the-rna-interference-system-in-the-arbuscular-mycorrhizal-fungus-rhizoglomus-irregulare-provide-new-insight-into-the-evolutionary-history-of-glomeromycota
#1
Soon-Jae Lee, Mengxuan Kong, Paul Harrison, Mohamed Hijri
Horizontal gene transfer (HGT) is an important mechanism in the evolution of many living organisms particularly in Prokaryotes where genes are frequently dispersed between taxa. Although, HGT has been reported in Eukaryotes, its accumulative effect and its frequency has been questioned. Arbuscular mycorrhizal fungi (AMF) are an early diverged fungal lineage belonging to phylum Glomeromycota, whose phylogenetic position is still under debate. The history of AMF and land plant symbiosis dates back to at least 460 million years ago...
January 10, 2018: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29309647/transcriptional-interference-by-small-transcripts-in-proximal-promoter-regions
#2
Amit Pande, Jürgen Brosius, Izabela Makalowska, Wojciech Makalowski, Carsten A Raabe
Proximal promoter regions (PPR) are heavily transcribed yielding different types of small RNAs. The act of transcription within PPRs might regulate downstream gene expression via transcriptional interference (TI). For analysis, we investigated capped and polyadenylated small RNA transcripts within PPRs of human RefSeq genes in eight different cell lines. Transcripts of our datasets overlapped with experimentally determined transcription factor binding sites (TFBS). For TFBSs intersected by these small RNA transcripts, we established negative correlation of sRNA expression levels and transcription factor (TF) DNA binding affinities; suggesting that the transcripts acted via TI...
January 4, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29309640/a-fungal-argonaute-interferes-with-rna-interference
#3
Quyet Nguyen, Akihide Iritani, Shuhei Ohkita, Ba V Vu, Kana Yokoya, Ai Matsubara, Ken-Ichi Ikeda, Nobuhiro Suzuki, Hitoshi Nakayashiki
Small RNA (sRNA)-mediated gene silencing phenomena, exemplified by RNA interference (RNAi), require a unique class of proteins called Argonautes (AGOs). An AGO protein typically forms a protein-sRNA complex that contributes to gene silencing using the loaded sRNA as a specificity determinant. Here, we show that MoAGO3, one of the three AGO genes in the fungus Pyricularia oryzae (Magnaporthe oryzae) interferes with RNAi. Gene knockout (KO) studies revealed that MoAGO1 and MoAGO2 additively or redundantly played roles in hairpin RNA- and retrotransposon (MAGGY)-triggered RNAi while, surprisingly, the KO mutants of MoAGO3 (Δmoago3) showed elevated levels of gene silencing...
January 4, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29297355/identification-of-streptococcal-small-rnas-that-are-putative-targets-of-rnase-iii-through-bioinformatics-analysis-of-rna-sequencing-data
#4
Ethan C Rath, Stephanie Pitman, Kyu Hong Cho, Yongsheng Bai
BACKGROUND: Small noncoding regulatory RNAs (sRNAs) are post-transcriptional regulators, regulating mRNAs, proteins, and DNA in bacteria. One class of sRNAs, trans-acting sRNAs, are the most abundant sRNAs transcribed from the intergenic regions (IGRs) of the bacterial genome. In Streptococcus pyogenes, a common and potentially deadly pathogen, many sRNAs have been identified, but only a few have been studied. The goal of this study is to identify trans-acting sRNAs that can be substrates of RNase III...
December 28, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29287583/cold-responsive-mirnas-and-their-target-genes-in-the-wild-eggplant-species-solanum-aculeatissimum
#5
Xu Yang, Fei Liu, Yu Zhang, Lu Wang, Yu-Fu Cheng
BACKGROUND: Low temperature is an important abiotic stress in plant growth and development, especially for thermophilic plants. Eggplants are thermophilic vegetables, although the molecular mechanism of their response to cold stress remains to be elucidated. MicroRNAs (miRNAs) are a class of endogenous small non-coding RNAs that play an essential role during plant development and stress responses. Although the role of many plant miRNAs in facilitating chilling tolerance has been verified, little is known about the mechanisms of eggplant chilling tolerance...
December 29, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29262317/a-small-rna-pathway-mediates-allelic-dosage-in-endosperm
#6
Robert M Erdmann, Prasad R V Satyaki, Maja Klosinska, Mary Gehring
Balance between maternal and paternal genomes within the triploid endosperm is necessary for normal seed development. The majority of endosperm genes are expressed in a 2:1 maternal:paternal ratio, reflecting genomic DNA content. Here, we find that the 2:1 transcriptional ratio is, unexpectedly, actively regulated. In A. thaliana and A. lyrata, endosperm 24-nt small RNAs are reduced in transposable elements and enriched in genes compared with the embryo. We find an inverse relationship between the parent of origin of sRNAs and mRNAs, with genes more likely to be associated with maternally than paternally biased sRNAs...
December 19, 2017: Cell Reports
https://www.readbyqxmd.com/read/29220494/soapnuke-a-mapreduce-acceleration-supported-software-for-integrated-quality-control-and-preprocessing-of-high-throughput-sequencing-data
#7
Yuxin Chen, Yongsheng Chen, Chunmei Shi, Zhibo Huang, Yong Zhang, Shengkang Li, Yan Li, Jia Ye, Chang Yu, Zhuo Li, Xiuqing Zhang, Jian Wang, Huanming Yang, Lin Fang, Qiang Chen
Quality Control (QC) and preprocessing are essential steps for sequencing data analysis to ensure the accuracy of results. However, existing tools cannot provide a satisfying solution with integrated comprehensive functions, proper architectures and highly-scalable acceleration. In this article, we demonstrate SOAPnuke as a tool with abundant functions for a "QC-Preprocess-QC" workflow and MapReduce acceleration framework. Four modules with different preprocessing functions are designed for processing datasets from genomic, small RNA (sRNA), Digital Gene Expression (DGE) and metagenomic experiments respectively...
December 4, 2017: GigaScience
https://www.readbyqxmd.com/read/29218039/the-anaerobically-induced-srna-paii-affects-denitrification-in-pseudomonas-aeruginosa-pa14
#8
Muralidhar Tata, Fabian Amman, Vinay Pawar, Michael T Wolfinger, Siegfried Weiss, Susanne Häussler, Udo Bläsi
Pseudomonas aeruginosa is an opportunistic pathogen that can thrive by anaerobic respiration in the lungs of cystic fibrosis patients using nitrate as terminal electron acceptor. Here, we report the identification and characterization of the small RNA PaiI in the P. aeruginosa strain 14 (PA14). PaiI is anaerobically induced in the presence of nitrate and depends on the two-component system NarXL. Our studies revealed that PaiI is required for efficient denitrification affecting the conversion of nitrite to nitric oxide...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29215635/mapping-the-small-rna-interactome-in-bacteria-using-ril-seq
#9
Sahar Melamed, Raya Faigenbaum-Romm, Asaf Peer, Niv Reiss, Omer Shechter, Amir Bar, Yael Altuvia, Liron Argaman, Hanah Margalit
Small RNAs (sRNAs) are major post-transcriptional regulators of gene expression in bacteria. To enable transcriptome-wide mapping of bacterial sRNA-target pairs, we developed RIL-seq (RNA interaction by ligation and sequencing). RIL-seq is an experimental-computational methodology for capturing sRNA-target interactions in vivo that takes advantage of the mutual binding of the sRNA and target RNA molecules to the RNA chaperone protein Hfq. The experimental part of the protocol involves co-immunoprecipitation of Hfq and bound RNAs, ligation of RNAs, library preparation and sequencing...
January 2018: Nature Protocols
https://www.readbyqxmd.com/read/29215024/identification-of-srna-mediated-responses-to-nutrient-depletion-in-burkholderia-pseudomallei
#10
Hirzahida Mohd-Padil, Nadzirah Damiri, Suhaila Sulaiman, Shiao-Fei Chai, Sheila Nathan, Mohd Firdaus-Raih
The Burkholderia genus includes many species that are known to survive in diverse environmental conditions including low nutrient environments. One species, Burkholderia pseudomallei is a versatile pathogen that can survive in a wide range of hosts and environmental conditions. In this study, we investigated how a nutrient depleted growth environment evokes sRNA mediated responses by B. pseudomallei. Computationally predicted B. pseudomallei D286 sRNAs were mapped to RNA-sequencing data for cultures grown under two conditions: (1) BHIB as a nutrient rich media reference environment and (2) M9 media as a nutrient depleted stress environment...
December 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29214973/expression-of-the-small-regulatory-rna-gene-mmgr-is-regulated-negatively-by-ania-and-positively-by-ntrc-in-sinorhizobium-meliloti-2011
#11
Germán Ceizel Borella, Antonio Lagares, Claudio Valverde
In the N2-fixing symbiont of alfalfa root nodules, Sinorhizobium meliloti 2011, the mmgR gene encodes a 77 nt small untranslated RNA (sRNA) that negatively regulates the accumulation of polyhydroxybutyrate (PHB) when the bacterium is grown under conditions of surplus carbon (C) in relation to nitrogen (N). We previously showed that the expression of mmgR is primarily controlled at the transcriptional level and that it depends on the cellular N status, although the regulatory mechanism and the factors involved were unknown...
December 7, 2017: Microbiology
https://www.readbyqxmd.com/read/29211829/small-rna-repertoires-and-their-intraspecies-variation-in-aggregatibacter-actinomycetemcomitans
#12
Yuichi Oogai, Yasuhiro Gotoh, Yoshitoshi Ogura, Miki Kawada-Matsuo, Tetsuya Hayashi, Hitoshi Komatsuzawa
Aggregatibacter actinomycetemcomitans is a major periodontal pathogen that has several virulence factors such as leukotoxin and cytolethal distending toxin. Although the genes responsible for virulence have been identified, little is known about their regulatory mechanisms. Small RNA (sRNA) has been recognized as an important factor for gene regulation. To identify new regulatory mechanisms via sRNA in A. actinomycetemcomitans HK1651, we performed a systematic search for sRNAs by RNA-seq and identified 90 intergenic region sRNAs and 30 antisense sRNAs...
December 2, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/29211019/dual-regulation-of-the-small-rna-micc-and-the-quiescent-porin-ompn-in-response-to-antibiotic-stress-in-escherichia-coli
#13
Sushovan Dam, Jean-Marie Pagès, Muriel Masi
Antibiotic resistant Gram-negative bacteria are a serious threat for public health. The permeation of antibiotics through their outer membrane is largely dependent on porin, changes in which cause reduced drug uptake and efficacy. Escherichia coli produces two major porins, OmpF and OmpC. MicF and MicC are small non-coding RNAs (sRNAs) that modulate the expression of OmpF and OmpC, respectively. In this work, we investigated factors that lead to increased production of MicC. micC promoter region was fused to lacZ, and the reporter plasmid was transformed into E...
December 6, 2017: Antibiotics
https://www.readbyqxmd.com/read/29197696/small-rna-differential-expression-and-regulation-in-tuxpe%C3%A3-o-maize-embryogenic-callus-induction-and-establishment
#14
Naholi D Alejandri-Ramírez, Elva C Chávez-Hernández, Jose L Contreras-Guerra, Jose L Reyes, Tzvetanka D Dinkova
Somatic embryogenesis represents an alternative developmental process used to achieve genetic transformation and to approach key questions in maize development. It is known that embryogenic callus induction and plant regeneration are accompanied by microRNA expression changes. However, small RNA (sRNA) populations have not been explored during the proliferative callus subculture establishment and their impact on maintaining the dedifferentiated status and embryogenic potential is far from being completely understood...
November 30, 2017: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/29196849/the-phenotypic-and-molecular-assessment-of-the-non-conserved-arabidopsis-microrna163-s-adenosyl-methyltransferase-regulatory-module-during-biotic-stress
#15
Celso Gaspar Litholdo, Andrew Leigh Eamens, Peter Michael Waterhouse
In plants, microRNAs (miRNAs) have evolved in parallel to the protein-coding genes that they target for expression regulation, and miRNA-directed gene expression regulation is central to almost every cellular process. MicroRNA, miR163, is unique to the Arabidopsis genus and is processed into a 24-nucleotide (nt) mature small regulatory RNA (sRNA) from a single precursor transcript transcribed from a single locus, the MIR163 gene. The MIR163 locus is a result of a recent inverted duplication event of one of the five closely related S-ADENOSYL-METHYLTRANSFERASE genes that the mature miR163 sRNA targets for expression regulation...
December 1, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/29194362/the-small-regulatory-rna-spot42-inhibits-indole-biosynthesis-to-negatively-regulate-the-locus-of-enterocyte-effacement-of-enteropathogenic-escherichia-coli
#16
Shantanu Bhatt, Valerie Jenkins, Elisabeth Mason, Sarah Muche
The locus of enterocyte effacement is necessary for enteropathogenic Escherichia coli (EPEC) to form attaching and effacing (A/E) lesions. A/E lesions are characterized by intimate bacterial adherence to intestinal cells and destruction of microvilli, which leads to diarrhea. Therefore, studies interrogating the regulation of the locus of enterocyte effacement (LEE) are critical for understanding the molecular epidemiology of EPEC infections and developing interventional strategies. Hitherto, most studies have centered on protein-based regulators, whereas the role of small regulatory RNAs remains underappreciated...
December 1, 2017: Microorganisms
https://www.readbyqxmd.com/read/29159897/identification-and-characterization-of-two-variants-of-the-hfq-srna-chaperone-in-the-fish-pathogen-piscirickettsia-salmonis
#17
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
#18
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
#19
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
#20
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
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