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https://www.readbyqxmd.com/read/28167519/regulation-of-polyhydroxybutyrate-accumulation-in-sinorhizobium-meliloti-by-the-trans-encoded-small-rna-mmgr
#1
Antonio Lagares, Germán Ceizel Borella, Uwe Linne, Anke Becker, Claudio Valverde
Riboregulation has a major role in the fine-tuning of multiple bacterial processes. Among the RNA players, trans-encoded untranslated small RNAs (sRNAs) regulate complex metabolic networks by tuning expression from multiple target genes in response to numerous signals. In Sinorhizobium meliloti, over 400 sRNAs are expressed under different stimuli. The sRNA MmgR-standing for Makes more granules Regulator-has been of particular interest to us since its sequence and structure are highly conserved among the α-proteobacteria, and its expression is regulated by the amount and quality of the bacterium's available nitrogen source...
February 6, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28165059/combined-analysis-of-mrna-and-mirna-identifies-dehydration-and-salinity-responsive-key-molecular-players-in-citrus-roots
#2
Rangjin Xie, Jin Zhang, Yanyan Ma, Xiaoting Pan, Cuicui Dong, Shaoping Pang, Shaolan He, Lie Deng, Shilai Yi, Yongqiang Zheng, Qiang Lv
Citrus is one of the most economically important fruit crops around world. Drought and salinity stresses adversely affected its productivity and fruit quality. However, the genetic regulatory networks and signaling pathways involved in drought and salinity remain to be elucidated. With RNA-seq and sRNA-seq, an integrative analysis of miRNA and mRNA expression profiling and their regulatory networks were conducted using citrus roots subjected to dehydration and salt treatment. Differentially expressed (DE) mRNA and miRNA profiles were obtained according to fold change analysis and the relationships between miRNAs and target mRNAs were found to be coherent and incoherent in the regulatory networks...
February 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28164038/a-novel-mechanism-underlying-the-innate-immune-response-induction-upon-viral-dependent-replication-of-host-cell-mrna-a-mistake-of-srna-viruses-replicases
#3
REVIEW
Laura R Delgui, María I Colombo
Viruses are lifeless particles designed for setting virus-host interactome assuring a new generation of virions for dissemination. This interactome generates a pressure on host organisms evolving mechanisms to neutralize viral infection, which places the pressure back onto virus, a process known as virus-host cell co-evolution. Positive-single stranded RNA (+sRNA) viruses are an important group of viral agents illustrating this interesting phenomenon. During replication, their genomic +sRNA is employed as template for translation of viral proteins; among them the RNA-dependent RNA polymerase (RdRp) is responsible of viral genome replication originating double-strand RNA molecules (dsRNA) as intermediates, which accumulate representing a potent threat for cellular dsRNA receptors to initiate an antiviral response...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/28158242/de-novo-characterization-of-micrornas-in-oriental-fruit-moth-grapholita-molesta-and-selection-of-reference-genes-for-normalization-of-microrna-expression
#4
Xiu Wang, Yisong Li, Jing Zhang, Qingwen Zhang, Xiaoxia Liu, Zhen Li
MicroRNAs (miRNAs) are a group of endogenous non-coding small RNAs that have critical regulatory functions in almost all known biological processes at the post-transcriptional level in a variety of organisms. The oriental fruit moth Grapholita molesta is one of the most serious pests in orchards worldwide and threatens the production of Rosacea fruits. In this study, a de novo small RNA library constructed from mixed stages of G. molesta was sequenced through Illumina sequencing platform and a total of 536 mature miRNAs consisting of 291 conserved and 245 novel miRNAs were identified...
2017: PloS One
https://www.readbyqxmd.com/read/28154810/genome-wide-transcriptional-start-site-mapping-and-srna-identification-in-the-pathogen-leptospira-interrogans
#5
Anna Zhukova, Luis Guilherme Fernandes, Perrine Hugon, Christopher J Pappas, Odile Sismeiro, Jean-Yves Coppée, Christophe Becavin, Christophe Malabat, Azad Eshghi, Jun-Jie Zhang, Frank X Yang, Mathieu Picardeau
Leptospira are emerging zoonotic pathogens transmitted from animals to humans typically through contaminated environmental sources of water and soil. Regulatory pathways of pathogenic Leptospira spp. underlying the adaptive response to different hosts and environmental conditions remains elusive. In this study, we provide the first global Transcriptional Start Site (TSS) map of a Leptospira species. RNA was obtained from the pathogen Leptospira interrogans grown at 30°C (optimal in vitro temperature) and 37°C (host temperature) and selectively enriched for 5' ends of native transcripts...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/28146558/genome-wide-exonic-small-interference-rna-mediated-gene-silencing-regulates-sexual-reproduction-in-the-homothallic-fungus-fusarium-graminearum
#6
Hokyoung Son, Ae Ran Park, Jae Yun Lim, Chanseok Shin, Yin-Won Lee
Various ascomycete fungi possess sex-specific molecular mechanisms, such as repeat-induced point mutations, meiotic silencing by unpaired DNA, and unusual adenosine-to-inosine RNA editing, for genome defense or gene regulation. Using a combined analysis of functional genetics and deep sequencing of small noncoding RNA (sRNA), mRNA, and the degradome, we found that the sex-specifically induced exonic small interference RNA (ex-siRNA)-mediated RNA interference (RNAi) mechanism has an important role in fine-tuning the transcriptome during ascospore formation in the head blight fungus Fusarium graminearum...
February 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28134784/sibling%C3%A2-srna%C3%A2-ryfa1%C3%A2-influences%C3%A2-shigella%C3%A2-dysenteriae-pathogenesis
#7
Megan E Fris, William H Broach, Sarah E Klim, Peter W Coschigano, Ronan K Carroll, Clayton C Caswell, Erin R Murphy
Small regulatory RNAs (sRNAs) of Shigella dysenteriae and other pathogens are vital for the regulation of virulence-associated genes and processes. Here, we characterize RyfA1, one member of a sibling pair of sRNAs produced by S. dysenteriae. Unlike its nearly identical sibling molecule, RyfA2, predicted to be encoded almost exclusively by non-pathogenic species, the presence of a gene encoding RyfA1, or a RyfA1-like molecule, is strongly correlated with virulence in a variety of enteropathogens. In S. dysenteriae, the overproduction of RyfA1 negatively impacts the virulence-associated process of cell-to-cell spread as well as the expression of ompC, a gene encoding a major outer membrane protein important for the pathogenesis of Shigella...
January 26, 2017: Genes
https://www.readbyqxmd.com/read/28131377/identification-of-otpr-regulated-srnas-in-brucella-melitensis-expressed-under-acidic-stress-and-their-roles-in-pathogenesis-and-metabolism
#8
Udayakumar S Vishnu, Jagadesan Sankarasubramanian, Paramasamy Gunasekaran, Jeyaprakash Rajendhran
Small RNAs (sRNAs) are the small regulatory molecules that regulate various biological processes in bacteria. Though the functions of sRNAs are well documented, very little information is available on the sRNAs of Brucella spp. The otpR is the response regulator of a two-component regulatory system, which plays a significant role in Brucella virulence. In this study, we identified the sRNAs expressed in B. melitensis 16M and its otpR mutant under acidic stress from the RNAseq dataset. We identified 94 trans-encoded and 948 cis-encoded sRNAs in B...
February 2017: Comparative Immunology, Microbiology and Infectious Diseases
https://www.readbyqxmd.com/read/28130298/global-transcriptional-responses-to-osmotic-oxidative-and-imipenem-stress-conditions-in-pseudomonas-putida
#9
Klara Bojanovič, Isotta D'Arrigo, Katherine S Long
: Bacteria cope with and adapt to stress by modulating gene expression in response to specific environmental cues. In this study the transcriptional response of Pseudomonas putida KT2440 to osmotic, oxidative, and imipenem stress conditions at two time points was investigated via identification of differentially expressed mRNAs and sRNAs. A total of 440 small RNA transcripts were detected, where 10% correspond to previously annotated sRNAs, 40% to novel intergenic transcripts and 50% to novel transcripts antisense to annotated genes...
January 27, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28119418/nucleoid-and-cytoplasmic-localization-of-small-rnas-in-escherichia-coli
#10
Huanjie Sheng, Weston T Stauffer, Razika Hussein, Chris Lin, Han N Lim
Bacterial small RNAs (sRNAs) regulate protein production by binding to mRNAs and altering their translation and degradation. sRNAs are smaller than most mRNAs but larger than many proteins. Therefore it is uncertain whether sRNAs can enter the nucleoid to target nascent mRNAs. Here, we investigate the intracellular localization of sRNAs transcribed from plasmids in Escherichia coli using RNA fluorescent in-situ hybridization. We found that sRNAs (GlmZ, OxyS, RyhB and SgrS) have equal preference for the nucleoid and cytoplasm, and no preferential localization at the cell membrane...
January 23, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28110777/streptococcus-suis-small-rna-rss04-contributes-to-the-induction-of-meningitis-by-regulating-capsule-synthesis-and-by-inducing-biofilm-formation-in-a-mouse-infection-model
#11
Genhui Xiao, Huanyu Tang, Shouming Zhang, Haiyan Ren, Jiao Dai, Liying Lai, Chengping Lu, Huochun Yao, Hongjie Fan, Zongfu Wu
Streptococcus suis (SS) is an important pathogen for pigs, and it is also considered as a zoonotic agent for humans. Meningitis is one of the most common features of the infection caused by SS, but little is known about the mechanisms of SS meningitis. Recent studies have revealed that small RNAs (sRNAs) have emerged as key regulators of the virulence in several bacteria. In the previous study, we reported that SS sRNA rss04 was up-regulated in pig cerebrospinal fluid and contributes to SS virulence in a zebrafish infection model...
February 2017: Veterinary Microbiology
https://www.readbyqxmd.com/read/28074027/a-unique-cis-encoded-small-noncoding-rna-is-regulating-legionella-pneumophila-hfq-expression-in-a-life-cycle-dependent-manner
#12
Giulia Oliva, Tobias Sahr, Monica Rolando, Maike Knoth, Carmen Buchrieser
: Legionella pneumophila is an environmental bacterium that parasitizes protozoa, but it may also infect humans, thereby causing a severe pneumonia called Legionnaires' disease. To cycle between the environment and a eukaryotic host, L. pneumophila is regulating the expression of virulence factors in a life cycle-dependent manner: replicating bacteria do not express virulence factors, whereas transmissive bacteria are highly motile and infective. Here we show that Hfq is an important regulator in this network...
January 10, 2017: MBio
https://www.readbyqxmd.com/read/28067500/retargeting-a-dual-acting-srna-for-multiple-mrna-transcript-regulation
#13
Ashwin Lahiry, Samuel D Stimple, David W Wood, Richard A Lease
Multitargeting small regulatory RNAs (sRNAs) represent a potentially useful tool for metabolic engineering applications. Natural multitargeting sRNAs govern bacterial gene expression by binding to the translation initiation regions of protein-coding mRNAs through base pairing. We designed an Escherichia coli based genetic system to create and assay dual-acting retargeted-sRNA variants. The variants can be assayed for coordinate translational regulation of two alternate mRNA leaders fused to independent reporter genes...
January 24, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28056764/temperature-dependent-srna-transcriptome-of-the-lyme-disease-spirochete
#14
Niko Popitsch, Ivana Bilusic, Philipp Rescheneder, Renée Schroeder, Meghan Lybecker
BACKGROUND: Transmission of Borrelia burgdorferi from its tick vector to a vertebrate host requires extensive reprogramming of gene expression. Small regulatory RNAs (sRNA) have emerged in the last decade as important regulators of bacterial gene expression. Despite the widespread observation of sRNA-mediated gene regulation, only one sRNA has been characterized in the Lyme disease spirochete B. burgdorferi. We employed an sRNA-specific deep-sequencing approach to identify the small RNA transcriptome of B...
January 5, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28046132/transcriptome-wide-discovery-of-pasrs-promoter-associated-small-rnas-and-tasrs-terminus-associated-small-rnas-in-arabidopsis-thaliana
#15
Xiaoxia Ma, Ning Han, Chaogang Shao, Yijun Meng
Hints from animals point to the existence of two novel small RNA (sRNA) species surrounding the transcription start sites (TSSs) and the termini of the genes, respectively. In this study, we performed a comprehensive search for the two sRNA species named promoter-associated sRNAs (PASRs) and terminus-associated sRNAs (TASRs) in Arabidopsis. By using sRNA sequencing data from wild type plants and several mutants related to the sRNA biogenesis, Argonaute (AGO) 1- and AGO4-associated sRNA sequencing data, double-stranded RNA sequencing (dsRNA-seq) data, and DNA methylation profiling data, the biogenesis and action pathways of the PASRs and the TASRs were investigated...
2017: PloS One
https://www.readbyqxmd.com/read/28030576/functional-and-structural-analysis-of-a-highly-expressed-yersinia-pestis-small-rna-following-infection-of-cultured-macrophages
#16
Nan Li, Scott P Hennelly, Chris J Stubben, Sofiya Micheva-Viteva, Bin Hu, Yulin Shou, Momchilo Vuyisich, Chang-Shung Tung, Patrick S Chain, Karissa Y Sanbonmatsu, Elizabeth Hong-Geller
Non-coding small RNAs (sRNAs) are found in practically all bacterial genomes and play important roles in regulating gene expression to impact bacterial metabolism, growth, and virulence. We performed transcriptomics analysis to identify sRNAs that are differentially expressed in Yersinia pestis that invaded the human macrophage cell line THP-1, compared to pathogens that remained extracellular in the presence of host. Using ultra high-throughput sequencing, we identified 37 novel and 143 previously known sRNAs in Y...
2016: PloS One
https://www.readbyqxmd.com/read/28026103/artificial-micrornas-and-synthetic-trans-acting-small-interfering-rnas-interfere-with-viroid-infection
#17
Alberto Carbonell, José-Antonio Daròs
Artificial microRNAs (amiRNAs) and synthetic trans-acting small interfering RNAs (syn-tasiRNAs) are two classes of artificial small RNAs (sRNAs) engineered to silence endogenous transcripts as well as viral RNAs in plants. Here, we explore the possibility of using amiRNAs and syn-tasiRNAs to specifically interfere with infections by viroids, small (250-400 nt) non-coding circular RNAs with compact secondary structure infecting a wide range of plant species. The combined use of recent high-throughput methods for artificial sRNA construct generation and of the Potato spindle tuber viroid (PSTVd)/Nicotiana benthamiana pathosystem allowed for the simple and time-effective screening of multiple artificial sRNAs targeting sites distributed along PSTVd RNAs of (+) or (-) polarity...
December 27, 2016: Molecular Plant Pathology
https://www.readbyqxmd.com/read/28025711/differential-expression-of-mirnas-and-associated-gene-targets-in-grapevine-leafroll-associated-virus-3-infected-plants
#18
Rachelle Bester, Johan T Burger, Hans J Maree
MicroRNAs (miRNAs) are a class of endogenous small non-coding RNAs (sRNA) that play an essential role in the regulation of target mRNAs expressed during plant development and in response to stress. MicroRNA expression profiling has helped to identify miRNAs that regulate a range of processes, including the plant's defence response to pathogens. In this study, differential miRNA expression in own-rooted Vitis vinifera cv. Cabernet Sauvignon plants infected with grapevine leafroll-associated virus 3 was investigated with microarrays and next-generation sequencing (NGS) of sRNA and mRNA...
December 26, 2016: Archives of Virology
https://www.readbyqxmd.com/read/28018366/identification-of-mirnas-affecting-the-establishment-of-brassica-alboglabra-seedling
#19
Rongfang Guo, Yanping Deng, Zhongkai Huang, Xiaodong Chen, Xu XuHan, Zhongxiong Lai
MicroRNAs (miRNAs) are important for plant development including seed formation, dormancy, and germination, as well as seedling establishment. The Brassica vegetable seedling establishment stage influences the development of high quality seedlings, but also affects the nutrient content of sprouts. Chinese kale (Brassica alboglabra) seedlings at different growth stages were used to construct two small-RNA (sRNA) libraries. We comprehensively analyzed the miRNAs in 2- and 9-day-old seedlings. An average of 11,722,490 clean reads were generated after removing low-quality reads and adapter contaminants...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28005055/gril-seq-provides-a-method-for-identifying-direct-targets-of-bacterial-small-regulatory-rna-by-in-vivo-proximity-ligation
#20
Kook Han, Brian Tjaden, Stephen Lory
The first step in the post-transcriptional regulatory function of most bacterial small non-coding RNAs (sRNAs) is base pairing with partially complementary sequences of targeted transcripts. We present a simple method for identifying sRNA targets in vivo and defining processing sites of the regulated transcripts. The technique, referred to as global small non-coding RNA target identification by ligation and sequencing (GRIL-seq), is based on preferential ligation of sRNAs to the ends of base-paired targets in bacteria co-expressing T4 RNA ligase, followed by sequencing to identify the chimaeras...
December 22, 2016: Nature Microbiology
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