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Renée J St-Onge, Marie A Elliot
Non-coding regulatory RNAs fine-tune gene expression post-transcriptionally. In the streptomycetes, rpfA - encoding a muralytic enzyme required for establishing and exiting dormancy - is flanked by non-coding regulatory RNA elements both upstream (riboswitch) and downstream [antisense small RNA (sRNA)]. In Streptomyces coelicolor, the upstream riboswitch decreases rpfA transcript abundance in response to the second messenger cyclic di-AMP, itself involved in cell wall metabolism and dormancy. There is, however, no obvious expression platform associated with this riboswitch and consequently, its mechanism of action is entirely unknown...
June 22, 2017: RNA Biology
Xiaoran Niu, Yu Sun, Ze Chen, Rugang Li, Chellappan Padmanabhan, Jishou Ruan, Jan F Kreuze, KaiShu Ling, ZhangJun Fei, Shan Gao
Small interfering RNA (siRNA) duplexes are short (usually 21 to 24 bp) double-stranded RNAs (dsRNAs) with several overhanging nucleotides at both 5'- and 3'-ends. It has been found that siRNA duplexes bind the RNA-induced silencing complex (RISC) and cleave the sense strands with endonucleases. In this study, for the first time, we detected siRNA duplexes induced by plant viruses on a large scale using next-generation sequencing (NGS) data. In addition, we used the detected 21 nucleotide (nt) siRNA duplexes with 2 nt overhangs to construct a dataset for future data mining...
June 16, 2017: Genes
Yingxiu Cao, Xiaofei Li, Feng Li, Hao Song
Extracellular electron transfer (EET) in Shewanella oneidensis MR-1, which is one of the most well-studied exoelectrogens, underlies many microbial electrocatalysis processes, including microbial fuel cells, microbial electrolysis cells, and microbial electrosynthesis. However, regulating the efficiency of EET remains challenging due to the lack of efficient genome regulation tools that regulate gene expression levels in S. oneidensis. Here, we systematically established a transcriptional regulation technology, i...
June 15, 2017: ACS Synthetic Biology
Xinwei Guo, Zeyang Ma, Zhonghui Zhang, Lailiang Cheng, Xiuren Zhang, Tianhong Li
Transition from vegetative to floral buds is a critical physiological change during flower induction that determines fruit productivity. Small non-coding RNAs (sRNAs) including microRNAs (miRNAs) and small interfering RNAs (siRNAs) are pivotal regulators of plant growth and development. Although the key role of sRNAs in flowering regulation has been well-described in Arabidopsis and some other annual plants, their relevance to vegetative-to-floral transition (hereafter, referred to floral transition) in perennial woody trees remains under defined...
2017: Frontiers in Plant Science
Amar Ghodasara, Christopher A Voigt
Balancing protein expression is critical when optimizing genetic systems. Typically, this requires library construction to vary the genetic parts controlling each gene, which can be expensive and time-consuming. Here, we develop sRNAs corresponding to 15nt 'target' sequences that can be inserted upstream of a gene. The targeted gene can be repressed from 1.6- to 87-fold by controlling sRNA expression using promoters of different strength. A pool is built where six sRNAs are placed under the control of 16 promoters that span a ∼103-fold range of strengths, yielding ∼107 combinations...
June 13, 2017: Nucleic Acids Research
Alberto Carbonell
ARGONAUTE (AGO) proteins function in small RNA (sRNA)-based RNA silencing pathways to regulate gene expression and control invading nucleic acids. In posttranscriptional RNA silencing pathways, plant AGOs associate with sRNAs to interact with highly sequence-complementary target RNAs. Once the AGO-sRNA-target RNA ternary complex is formed, target RNA is typically repressed through AGO-mediated cleavage or through other cleavage-independent mechanisms. The universe of sRNAs associating with diverse plant AGOs has been determined though AGO immunoprecipitation (IP) and high-throughput sequencing of co-immunoprecipitated sRNAs...
2017: Methods in Molecular Biology
Alberto Carbonell
ARGONAUTEs (AGOs) are the effector proteins in eukaryotic small RNA (sRNA)-based gene silencing pathways controlling gene expression and transposon activity. In plants, AGOs regulate key biological processes such as development, response to stress, genome structure and integrity, and pathogen defense. Canonical functions of plant AGO-sRNA complexes include the endonucleolytic cleavage or translational inhibition of target RNAs and the methylation of target DNAs. Here, I provide a brief update on the major features, molecular functions, and biological roles of plant AGOs...
2017: Methods in Molecular Biology
Teppei Morita, Ryo Nishino, Hiroji Aiba
Many Rho-independent transcription terminators of the genes encoding bacterial Hfq-binding sRNAs possess a set of 7 or more T residues at the 3' end (Otaka et al. 2011; Ishikawa et al. 2012). Here, we have studied the role of terminator hairpin in biogenesis of sRNAs focusing on SgrS and RyhB in Esherichia coli. We constructed variant sRNA genes in which the GC-rich inverted repeat sequences are extended to stabilize the terminator hairpins. We demonstrate that the extension of the hairpin stem leads to generation of heterogeneous transcripts in which the polyU tail is shortened...
June 12, 2017: RNA
Rong Fu, Mi Zhang, Yinchuan Zhao, Xuechuan He, Chenyun Ding, Shuangkuai Wang, Yan Feng, Xianliang Song, Ping Li, Baohua Wang
To identify the known and novel microRNAs (miRNAs) and their targets that are involved in the response and adaptation of maize (Zea mays) to salt stress, miRNAs and their targets were identified by a combined analysis of the deep sequencing of small RNAs (sRNA) and degradome libraries. The identities were confirmed by a quantitative expression analysis with over 100 million raw reads of sRNA and degradome sequences. A total of 1040 previously known miRNAs were identified from four maize libraries, with 762 and 726 miRNAs derived from leaves and roots, respectively, and 448 miRNAs that were common between the leaves and roots...
2017: Frontiers in Plant Science
Fangli Wu, Yue Chen, Xing Tian, Xiaole Zhu, Weibo Jin
Phased small interfering RNAs (phasiRNAs) are encoded by a novel class of genes known as phasiRNA producing (PHAS) genes. These genes play important regulatory roles by targeting protein coding transcripts in plant species. In this study, 91 regions were identified as potential PHAS loci in tomato, with additional evidence that seven of them can be triggered by five miRNAs. Among the identified loci, 51 were located in genic regions, and the remaining 40 were located in intergenic regions. The transient overexpression of PHAS15 and PHAS26 demonstrated that phasiRNAs predicted by PhaseTank were indeed generated from their respective PHAS loci...
June 8, 2017: Scientific Reports
Robert A G Huis In 't Veld, Gertjan Kramer, Arie van der Ende, Dave Speijer, Yvonne Pannekoek
The conserved RNA-binding protein, Hfq, has multiple regulatory roles within the prokaryotic cell, including promoting stable duplex formation between small RNAs and mRNAs, and thus hfq deletion mutants have pleiotropic phenotypes. Previous proteome and transcriptome studies of Neisseria meningitidis have generated limited insight into differential gene expression due to Hfq loss. In this study, reversed-phase liquid chromatography combined with data-independent alternate scanning mass spectrometry (LC-MS(E)) was utilized for rapid high-resolution quantitative proteomic analysis to further elucidate the differentially expressed proteome of a meningococcal hfq deletion mutant...
June 2017: FEBS Open Bio
Ming Wang, Nicholas Thomas, Hailing Jin
​Small RNA (sRNA) induces RNA interference (RNAi) in almost all eukaryotes. While sRNAs can move within an organism, they can also move between interacting organisms to induce gene silencing, a phenomenon called 'cross-kingdom RNAi'. Some sRNAs from pathogens or pests move into host cells and suppress host immunity in both plants and animals; whereas some host sRNAs travel into pathogen/pest cells to inhibit their virulence. Moreover, uptake of exogenous RNAs from the environment was recently discovered in certain fungal pathogens, which makes it possible to suppress fungal diseases by directly applying pathogen-targeting RNAs on crops and post-harvest products...
May 29, 2017: Current Opinion in Plant Biology
Shan Shan Liu, Wen Hui Zhu, Qing Hui Zhi, Jia Liu, Yan Wang, Huan Cai Lin
Streptococcus mutans (S. mutans) is the major pathogen contributing to dental caries. Sucrose is an important carbohydrate source for S. mutans and is crucial for dental caries. Small RNAs (sRNAs) are key post-transcriptional regulators of stress adaptation and virulence in bacteria. Here, for the first time, we created three replicate RNA libraries exposed to either 1 or 5% sucrose. The expression levels of sRNAs and target genes (gtfB, gtfC, and spaP) related to virulence were assessed. In addition, some phenotypic traits were evaluated...
May 31, 2017: Applied Microbiology and Biotechnology
Selin Özkan, Irina Mohorianu, Ping Xu, Tamas Dalmay, Robert H A Coutts
BACKGROUND: Mycoviruses are viruses that naturally infect and replicate in fungi. Aspergillus fumigatus, an opportunistic pathogen causing fungal lung diseases in humans and animals, was recently shown to harbour several different types of mycoviruses. A well-characterised defence against virus infection is RNA silencing. The A. fumigatus genome encodes essential components of the RNA silencing machinery, including Dicer, Argonaute and RNA-dependent RNA polymerase (RdRP) homologues. Active silencing of double-stranded (ds)RNA and the generation of small RNAs (sRNAs) has been shown for several mycoviruses and it is anticipated that a similar mechanism will be activated in A...
May 30, 2017: BMC Genomics
Shunmugiah V Ramesh, Sarah Williams, Madhu Kappagantu, Neena Mitter, Hanu R Pappu
RNA silencing mechanism functions as a major defense against invading viruses. The caveat in the RNA silencing mechanism is that the effector small interfering RNAs (siRNAs) act on any RNA transcripts with sequence complementarity irrespective of target's origin. A subset of highly expressed viral small interfering RNAs (vsiRNAs) derived from the tomato spotted wilt virus (TSWV; Tospovirus: Bunyaviridae) genome was analyzed for their propensity to downregulate the tomato transcriptome. A total of 11898 putative target sites on tomato transcripts were found to exhibit a propensity for down regulation by TSWV-derived vsiRNAs...
May 22, 2017: Virus Research
Luis A de Haro, Analía D Dumón, María F Mattio, Evangelina Beatriz Argüello Caro, Gabriela Llauger, Diego Zavallo, Hervé Blanc, Vanesa C Mongelli, Graciela Truol, María-Carla Saleh, Sebastián Asurmendi, Mariana Del Vas
Plant reoviruses are able to multiply in gramineae plants and delphacid vectors encountering different defense strategies with unique features. This study aims to comparatively assess alterations of small RNA (sRNA) populations in both hosts upon virus infection. For this purpose, we characterized the sRNA profiles of wheat and planthopper vectors infected by Mal de Río Cuarto virus (MRCV, Fijivirus, Reoviridae) and quantified virus genome segments by quantitative reverse transcription PCR We provide evidence that plant and insect silencing machineries differentially recognize the viral genome, thus giving rise to distinct profiles of virus-derived small interfering RNAs (vsiRNAs)...
2017: Frontiers in Plant Science
Mor Nitzan, Rotem Rehani, Hanah Margalit
Small RNAs (sRNAs) are central regulators of gene expression in bacteria, controlling target genes posttranscriptionally by base pairing with their mRNAs. sRNAs are involved in many cellular processes and have unique regulatory characteristics. In this review, we discuss the properties of regulation by sRNAs and how it differs from and combines with transcriptional regulation. We describe the global characteristics of the sRNA-target networks in bacteria using graph-theoretic approaches and review the local integration of sRNAs in mixed regulatory circuits, including feed-forward loops and their combinations, feedback loops, and circuits made of an sRNA and another regulator, both derived from the same transcript...
May 22, 2017: Annual Review of Biophysics
Petra Dersch, Muna A Khan, Sabrina Mühlen, Boris Görke
The emergence of antibiotic resistance mechanisms among bacterial pathogens increases the demand for novel treatment strategies. Lately, the contribution of non-coding RNAs to antibiotic resistance and their potential value as drug targets became evident. RNA attenuator elements in mRNA leader regions couple expression of resistance genes to the presence of the cognate antibiotic. Trans-encoded small RNAs (sRNAs) modulate antibiotic tolerance by base-pairing with mRNAs encoding functions important for resistance such as metabolic enzymes, drug efflux pumps, or transport proteins...
2017: Frontiers in Microbiology
Katherine García, Cristian Yáñez, Nicolás Plaza, Francisca Peña, Pedro Sepúlveda, Diliana Pérez-Reytor, Romilio T Espejo
BACKGROUND: Vibrio parahaemolyticus is an autochthonous marine bacterial species comprising strains able to grow in broth containing bile salts at 37 °C, a condition seldom found in the ocean. However, this condition is used for isolation in the laboratory because it is considered a necessary property for pathogenesis. In this context, revealing how gene expression enables V. parahaemolyticus to adapt to this particular condition -common to almost all V. parahaemolyticus isolates- will improve our understanding of the biology of this important pathogen...
May 19, 2017: BMC Microbiology
Jinbu Jia, Wenqin Lu, Chengcheng Zhong, Ran Zhou, Junjie Xu, Wei Liu, Xiuhong Gou, Qinhu Wang, Junliang Yin, Cheng Xu, Weixing Shan
Small RNAs (sRNAs) are important non-coding RNA regulators, playing key roles in developmental regulation, transposon suppression, environmental response, host-pathogen interaction and other diverse biological processes. However, their roles in oomycetes are poorly understood. Here, we performed sRNA sequencing and RNA sequencing of Phytophthora parasitica at stages of vegetative growth and infection of Arabidopsis roots to examine diversity and function of sRNAs in P. parasitica, a model hemibiotrophic oomycete plant pathogen...
2017: Frontiers in Microbiology
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