Stem-loops direct precise processing of 3′ UTR-derived small RNA MicL

Mapping Intimacies ◽

10.1101/341578 ◽

2018 ◽

Author(s):

Taylor B Updegrove ◽

Andrew B Kouse ◽

Katarzyna J Bandyra ◽

Gisela Storz

Keyword(s):

Small Rna ◽

Cleavage Site ◽

Differential Sensitivity ◽

Rnase E ◽

Small Regulatory Rnas ◽

Regulatory Rnas ◽

Derivatives Of

AbstractIncreasing numbers of 3′UTR-derived small, regulatory RNAs (sRNAs) are being discovered in bacteria, most generated by cleavage from longer transcripts. The enzyme required for these cleavages has been reported to be RNase E, the major endoribonuclease in enterica bacteria. Previous studies investigating RNase E have come to a range of different conclusions regarding the determinants for RNase E processing. To understand the sequence and structure determinants for the precise processing of the 3′ UTR-derived sRNAs, we examined the cleavage of multiple mutant and chimeric derivatives of the 3′ UTR-derived MicL sRNA in vivo and in vitro. Our results revealed that tandem stem-loops 3′ to the cleavage site define optimal, correctly-positioned cleavage of MicL and likely other similar sRNAs. Moreover, our assays of MicL, ArcZ and CpxQ showed that sRNAs exhibit differential sensitivity to RNase E, likely a consequence of a hierarchy of sRNA features recognized by the endonuclease.

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The Etiological Agent of Lyme Disease, Borrelia burgdorferi, Appears To Contain Only a Few Small RNA Molecules

Journal of Bacteriology ◽

10.1128/jb.186.24.8472-8477.2004 ◽

2004 ◽

Vol 186 (24) ◽

pp. 8472-8477 ◽

Cited By ~ 22

Author(s):

Yngve Östberg ◽

Ignas Bunikis ◽

Sven Bergström ◽

Jörgen Johansson

Keyword(s):

Borrelia Burgdorferi ◽

Small Rna ◽

Rna Binding ◽

Rna Binding Protein ◽

Rnase E ◽

Regulatory Pathways ◽

Rna Molecules ◽

Small Regulatory Rnas ◽

Regulatory Rnas

ABSTRACT Small regulatory RNAs (sRNAs) have recently been shown to be the main controllers of several regulatory pathways. The function of sRNAs depends in many cases on the RNA-binding protein Hfq, especially for sRNAs with an antisense function. In this study, the genome of Borrelia burgdorferi was subjected to different searches for sRNAs, including direct homology and comparative genomics searches and ortholog- and annotation-based search strategies. Two new sRNAs were found, one of which showed complementarity to the rpoS region, which it possibly controls by an antisense mechanism. The role of the other sRNA is unknown, although observed complementarities against particular mRNA sequences suggest an antisense mechanism. We suggest that the low level of sRNAs observed in B. burgdorferi is at least partly due to the presumed lack of both functional Hfq protein and RNase E activity.

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Derivatives of Deoxypodophyllotoxin Induce Apoptosis Through Bcl-2/Bax Proteins Expression

Anti-Cancer Agents in Medicinal Chemistry ◽

10.2174/1871520620999200730160952 ◽

2020 ◽

Vol 20 ◽

Author(s):

Ya-Nan Li ◽

Ni Ning ◽

Lei Song ◽

Yun Geng ◽

Jun-Ting Fan ◽

...

Keyword(s):

Annexin V ◽

Mtt Method ◽

Anthriscus Sylvestris ◽

Anti Tumor Activity ◽

Derivatives Of ◽

Toxicity In Vitro ◽

Ht 29 ◽

Mcf 7

Background: Deoxypodophyllotoxin, isolated from theTraditional Chinese Medicine Anthriscus sylvestris, is well-known because of its significant antitumor activity with strong toxicity in vitro and in vivo. Objective: In this article, we synthesized a series of deoxypodophyllotoxin derivatives, and evaluated their antitumor effectiveness.Methods:The anti tumor activity of deoxypodophyllotoxin derivatives was investigated by the MTT method. Apoptosis percentage was measured by flow cytometer analysis using Annexin-V-FITC. Results: The derivatives revealed obvious cytotoxicity in the MTT assay by decreasing the number of late cancer cells. The decrease of Bcl-2/Bax could be observed in MCF-7, HepG2, HT-29 andMG-63 using Annexin V-FITC. The ratio of Bcl-2/Bax in the administration group was decreased, which was determined by the ELISA kit. Conclusion: The derivatives of deoxypodophyllotoxin could induce apoptosis in tumor cell lines by influencing Bcl-2/Bax.

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Extensive Analysis of miRNA Trimming and Tailing Indicates that AGO1 Has a Complex Role in miRNA Turnover

Plants ◽

10.3390/plants10020267 ◽

2021 ◽

Vol 10 (2) ◽

pp. 267

Author(s):

Axel J. Giudicatti ◽

Ariel H. Tomassi ◽

Pablo A. Manavella ◽

Agustin L. Arce

Keyword(s):

Small Rna ◽

Stress Responses ◽

Cellular Localization ◽

Mirna Biogenesis ◽

Small Rna Sequencing ◽

Sequencing Data ◽

Extensive Analysis ◽

Small Regulatory Rnas ◽

Regulatory Rnas ◽

Argonaute 1

MicroRNAs are small regulatory RNAs involved in several processes in plants ranging from development and stress responses to defense against pathogens. In order to accomplish their molecular functions, miRNAs are methylated and loaded into one ARGONAUTE (AGO) protein, commonly known as AGO1, to stabilize and protect the molecule and to assemble a functional RNA-induced silencing complex (RISC). A specific machinery controls miRNA turnover to ensure the silencing release of targeted-genes in given circumstances. The trimming and tailing of miRNAs are fundamental modifications related to their turnover and, hence, to their action. In order to gain a better understanding of these modifications, we analyzed Arabidopsis thaliana small RNA sequencing data from a diversity of mutants, related to miRNA biogenesis, action, and turnover, and from different cellular fractions and immunoprecipitations. Besides confirming the effects of known players in these pathways, we found increased trimming and tailing in miRNA biogenesis mutants. More importantly, our analysis allowed us to reveal the importance of ARGONAUTE 1 (AGO1) loading, slicing activity, and cellular localization in trimming and tailing of miRNAs.

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Synthesis, in vitro and in vivo antitumor activity of symmetrical bis-Schiff base derivatives of isatin

European Journal of Medicinal Chemistry ◽

10.1016/j.ejmech.2013.04.040 ◽

2014 ◽

Vol 74 ◽

pp. 742-750 ◽

Cited By ~ 57

Author(s):

Chengyuan Liang ◽

Juan Xia ◽

Dong Lei ◽

Xiang Li ◽

Qizheng Yao ◽

...

Keyword(s):

Schiff Base ◽

Antitumor Activity ◽

Schiff Base Derivatives ◽

In Vivo Antitumor Activity ◽

Derivatives Of

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Synthesis, characterization and in vitro and in vivo anticancer activity of Pt(iv) derivatives of [Pt(1S,2S-DACH)(5,6-dimethyl-1,10-phenanthroline)]

Dalton Transactions ◽

10.1039/c7dt01054k ◽

2017 ◽

Vol 46 (21) ◽

pp. 7005-7019 ◽

Cited By ~ 25

Author(s):

Benjamin W. J. Harper ◽

Emanuele Petruzzella ◽

Roman Sirota ◽

Fernanda Fabiola Faccioli ◽

Janice R. Aldrich-Wright ◽

...

Keyword(s):

Anticancer Activity ◽

Biological Evaluation ◽

Synthesis And Biological Evaluation ◽

Derivatives Of

Synthesis and biological evaluation in vitro and in vivo of functionalized Pt(iv) derivatives of Pt56MeSS.

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Synthesis of two classes of small RNA species in vivo and in vitro

Biochemistry ◽

10.1021/bi00639a029 ◽

1977 ◽

Vol 16 (20) ◽

pp. 4520-4525 ◽

Cited By ~ 76

Author(s):

Gary Zieve ◽

Bernd Joachim Benecke ◽

Sheldon Penman

Keyword(s):

Small Rna ◽

Small Rna Species

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xMD-miRNA-seq to generate near in vivo miRNA expression estimates in colon epithelial cells

10.1101/333658 ◽

2018 ◽

Author(s):

Avi Z. Rosenberg ◽

Carrie Wright ◽

Karen Fox-Talbot ◽

Anandita Rajpurohit ◽

Courtney Williams ◽

...

Keyword(s):

Epithelial Cells ◽

Small Rna ◽

Mirna Expression ◽

Low Cost ◽

Expression Patterns ◽

Small Rna Sequencing ◽

Rna Seq ◽

Cell Type

AbstractAccurate, RNA-seq based, microRNA (miRNA) expression estimates from primary cells have recently been described. However, this in vitro data is mainly obtained from cell culture, which is known to alter cell maturity/differentiation status, significantly changing miRNA levels. What is needed is a robust method to obtain in vivo miRNA expression values directly from cells. We introduce expression microdissection miRNA small RNA sequencing (xMD-miRNA-seq), a method to isolate cells directly from formalin fixed paraffin-embedded (FFPE) tissues. xMD-miRNA-seq is a low-cost, high-throughput, immunohistochemistry-based method to capture any cell type of interest. As a proof-of-concept, we isolated colon epithelial cells from two specimens and performed low-input small RNA-seq. We generated up to 600,000 miRNA reads from the samples. Isolated epithelial cells, had abundant epithelial-enriched miRNA expression (miR-192; miR-194; miR-200b; miR-200c; miR-215; miR-375) and overall similar miRNA expression patterns to other epithelial cell populations (colonic enteroids and flow-isolated colon epithelium). xMD-derived epithelial cells were generally not contaminated by other adjacent cells of the colon as noted by t-SNE analysis. xMD-miRNA-seq allows for simple, economical, and efficient identification of cell-specific miRNA expression estimates. Further development will enhance rapid identification of cell-specific miRNA expression estimates in health and disease for nearly any cell type using archival FFPE material.

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Maturation of UTR-Derived sRNAs Is Modulated during Adaptation to Different Growth Conditions

International Journal of Molecular Sciences ◽

10.3390/ijms222212260 ◽

2021 ◽

Vol 22 (22) ◽

pp. 12260

Author(s):

Daniel-Timon Spanka ◽

Gabriele Klug

Keyword(s):

Growth Conditions ◽

Global Scale ◽

Rnase E ◽

Bacterial Gene ◽

Ribonuclease E ◽

Mrna Targets ◽

Small Regulatory Rnas ◽

The Stability ◽

Ngs Data

Small regulatory RNAs play a major role in bacterial gene regulation by binding their target mRNAs, which mostly influences the stability or translation of the target. Expression levels of sRNAs are often regulated by their own promoters, but recent reports have highlighted the presence and importance of sRNAs that are derived from mRNA 3′ untranslated regions (UTRs). In this study, we investigated the maturation of 5′ and 3′ UTR-derived sRNAs on a global scale in the facultative phototrophic alphaproteobacterium Rhodobacter sphaeroides. Including some already known UTR-derived sRNAs like UpsM or CcsR1-4, 14 sRNAs are predicted to be located in 5′ UTRs and 16 in 3′ UTRs. The involvement of different ribonucleases during maturation was predicted by a differential RNA 5′/3′ end analysis based on RNA next generation sequencing (NGS) data from the respective deletion strains. The results were validated in vivo and underline the importance of polynucleotide phosphorylase (PNPase) and ribonuclease E (RNase E) during processing and maturation. The abundances of some UTR-derived sRNAs changed when cultures were exposed to external stress conditions, such as oxidative stress and also during different growth phases. Promoter fusions revealed that this effect cannot be solely attributed to an altered transcription rate. Moreover, the RNase E dependent cleavage of several UTR-derived sRNAs varied significantly during the early stationary phase and under iron depletion conditions. We conclude that an alteration of ribonucleolytic processing influences the levels of UTR-derived sRNAs, and may thus indirectly affect their mRNA targets.

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