Molecular functions of small regulatory noncoding RNA

Huang, Yong; Zhang, Jiliang; Yu, Xue; Xu, Ting; Wang, Zhan Bin; Cheng, Xiang

doi:10.1134/s0006297913030024

Cited by 45 publications

(37 citation statements)

References 116 publications

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“…In eukaryotes, mi/si/piRNAs typically bind to the 3′-UTRs of their target mRNAs, leading to translational inhibition and/or degradation of the mRNAs (reviewed in ref. 80). In both domains, a number of computational approaches have been established that allow a genome-wide in silico search for putative targets of a specific sRNA 81 - 83 .…”

Section: Targets Of Archaeal Srnasmentioning

confidence: 99%

Small regulatory RNAs in Archaea

et al. 2014

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Small regulatory RNAs (sRNAs) are universally distributed in all three domains of life, Archaea, Bacteria, and Eukaryotes. In bacteria, sRNAs typically function by binding near the translation start site of their target mRNAs and thereby inhibit or activate translation. In eukaryotes, miRNAs and siRNAs typically bind to the 3′-untranslated region (3′-UTR) of their target mRNAs and influence translation efficiency and/or mRNA stability. In archaea, sRNAs have been identified in all species investigated using bioinformatic approaches, RNomics, and RNA-Seq. Their size can vary significantly between less than 50 to more than 500 nucleotides. Differential expression of sRNA genes has been studied using northern blot analysis, microarrays, and RNA-Seq. In addition, biological functions have been unraveled by genetic approaches, i.e., by characterization of designed mutants. As in bacteria, it was revealed that archaeal sRNAs are involved in many biological processes, including metabolic regulation, adaptation to extreme conditions, stress responses, and even in regulation of morphology and cellular behavior. Recently, the first target mRNAs were identified in archaea, including one sRNA that binds to the 5′-region of two mRNAs in Methanosarcina mazei Gö1 and a few sRNAs that bind to 3′-UTRs in Sulfolobus solfataricus, three Pyrobaculum species, and Haloferax volcanii, indicating that archaeal sRNAs appear to be able to target both the 5′-UTR or the 3′-UTRs of their respective target mRNAs. In addition, archaea contain tRNA-derived fragments (tRFs), and one tRF has been identified as a major ribosome-binding sRNA in H. volcanii, which downregulates translation in response to stress. Besides regulatory sRNAs, archaea contain further classes of sRNAs, e.g., CRISPR RNAs (crRNAs) and snoRNAs.

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Section: Targets Of Archaeal Srnasmentioning

confidence: 99%

Small regulatory RNAs in Archaea

et al. 2014

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“…This view has changed dramatically during the last decade and today it is clear that sRNAs are widespread in all three domains of life and have in fact been found in every species that has been tested [1]–[6]. The numbers of known sRNAs, their biological functions, and the different mechanisms of action that are uncovered, increase steadily.…”

Section: Introductionmentioning

confidence: 99%

Generation and Phenotyping of a Collection of sRNA Gene Deletion Mutants of the Haloarchaeon Haloferax volcanii

et al. 2014

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The haloarchaeon Haloferax volcanii was shown to contain 145 intergenic and 45 antisense sRNAs. In a comprehensive approach to unravel various biological roles of haloarchaeal sRNAs in vivo, 27 sRNA genes were selected and deletion mutants were generated. The phenotypes of these mutants were compared to that of the parent strain under ten different conditions, i.e. growth on four different carbon sources, growth at three different salt concentrations, and application of four different stress conditions. In addition, cell morphologies in exponential and stationary phase were observed. Furthermore, swarming of 17 mutants was analyzed. 24 of the 27 mutants exhibited a difference from the parent strain under at least one condition, revealing that haloarchaeal sRNAs are involved in metabolic regulation, growth under extreme conditions, regulation of morphology and behavior, and stress adaptation. Notably, 7 deletion mutants showed a gain of function phenotype, which has not yet been described for any other prokaryotic sRNA gene deletion mutant. Comparison of the transcriptomes of one sRNA gene deletion mutant and the parent strain led to the identification of differentially expressed genes. Genes for flagellins and chemotaxis were up-regulated in the mutant, in accordance with its gain of function swarming phenotype. While the deletion mutant analysis underscored that haloarchaeal sRNAs are involved in many biological functions, the degree of conservation is extremely low. Only 3 of the 27 genes are conserved in more than 10 haloarchaeal species. 22 of the 27 genes are confined to H. volcanii, indicating a fast evolution of haloarchaeal sRNA genes.

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“…Non-coding RNA species play very significant role in regulation of the protein synthesis via various mechanisms (Huang et al 2013). These regulating non-coding RNA (ncRNA) species include small RNAs (Bonnet et al 2006) and large non-coding RNA (Rinn and Chang 2012).…”

Section: Discovery Of Small and Long Non-coding Rna Speciesmentioning

confidence: 99%

Renaissance in phytomedicines: promising implications of NGS technologies

Sharma

Shrivastava

2016

Planta

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Medicinal plant research is growing significantly in faith to discover new and more biologically compatible phytomedicines. Deposition of huge genome/trancriptome sequence data assisted by NGS technologies has revealed the new possibilities for producing upgraded bioactive molecules in medicinal plants. Growing interest of investors and consumers in the herbal drugs raises the need for extensive research to open the facts and details of every inch of life canvas of medicinal plants to produce improved quality of phytomedicines. As in agriculture crops, knowledge emergence from medicinal plant's genome/transcriptome, can be used to assure their amended quality and these improved varieties are then transported to the fields for cultivation. Genome studies generate huge sequence data which can be exploited further for obtaining information regarding genes/gene clusters involved in biosynthesis as well as regulation. This can be achieved rapidly at a very large scale with NGS platforms. Identification of new RNA molecules has become possible, which can lead to the discovery of novel compounds. Sequence information can be combined with advanced phytochemical and bioinformatics tools to discover functional herbal drugs. Qualitative and quantitative analysis of small RNA species put a light on the regulatory aspect of biosynthetic pathways for phytomedicines. Inter or intra genomic as well as transcriptomic interactive processes for biosynthetic pathways can be elucidated in depth. Quality management of herbal material will also become rapid and high throughput. Enrichment of sequence information will be used to engineer the plants to get more efficient phytopharmaceuticals. The present review comprises of role of NGS technologies to boost genomic studies of pharmaceutically important plants and further, applications of sequence information aiming to produce enriched phytomedicines. Emerging knowledge from the medicinal plants genome/transcriptome can give birth to deep understanding of the processes responsible for biosynthesis of medicinally important compounds.

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Molecular functions of small regulatory noncoding RNA

Cited by 45 publications

References 116 publications

Small regulatory RNAs in Archaea

Small regulatory RNAs in Archaea

Generation and Phenotyping of a Collection of sRNA Gene Deletion Mutants of the Haloarchaeon Haloferax volcanii

Renaissance in phytomedicines: promising implications of NGS technologies

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