scholarly journals Global Analysis of Tomato Gene Expression During Potato spindle tuber viroid Infection Reveals a Complex Array of Changes Affecting Hormone Signaling

2012 ◽  
Vol 25 (4) ◽  
pp. 582-598 ◽  
Author(s):  
Robert A. Owens ◽  
Kimberly B. Tech ◽  
Jonathan Y. Shao ◽  
Teruo Sano ◽  
C. Jacyn Baker
Keyword(s):  
Gene Expression ◽  
Messenger Rna ◽  
Large Scale ◽  
Global Analysis ◽  
Potato Spindle Tuber Viroid ◽  
Circular Rna ◽  
Small Interfering Rnas ◽  
Viroid Infection ◽  
Disease Induction ◽  
Tomato Gene

Viroids like Potato spindle tuber viroid (PSTVd) are the smallest known agents of infectious disease—small, highly structured, circular RNA molecules that lack detectable messenger RNA activity, yet are able to replicate autonomously in susceptible plant species. To better understand the possible role of RNA silencing in disease induction, a combination of microarray analysis and large-scale RNA sequence analysis was used to compare changes in tomato gene expression and microRNA levels associated with PSTVd infection in two tomato cultivars plus a third transformed line expressing small PSTVd small interfering RNAs in the absence of viroid replication. Changes in messenger (m)RNA levels for the sensitive cultivar ‘Rutgers’ were extensive, involving more than half of the approximately 10,000 genes present on the array. Chloroplast biogenesis was down-regulated in both sensitive and tolerant cultivars, and effects on mRNAs encoding enzymes involved in the biosynthesis of gibberellin and other hormones were accompanied by numerous changes affecting their respective signaling pathways. In the dwarf cultivar ‘MicroTom’, a marked upregulation of genes involved in response to stress and other stimuli was observed only when exogenous brassinosteroid was applied to infected plants, thereby providing the first evidence for the involvement of brassinosteroid-mediated signaling in viroid disease induction.

scholarly journals Dynamic profiling of mRNA turnover reveals gene-specific and system-wide regulation of mRNA decay

2011 ◽  
Vol 22 (15) ◽  
pp. 2787-2795 ◽  
Author(s):  
Sarah E. Munchel ◽  
Ryan K. Shultzaberger ◽  
Naoki Takizawa ◽  
Karsten Weis
Keyword(s):  
Gene Expression ◽  
Large Scale ◽  
Mrna Decay ◽  
Global Analysis ◽  
Decay Rates ◽  
Mrna Turnover ◽  
Control Of Gene Expression ◽  
Mrna Stabilization ◽  
Highly Sensitive ◽  
Wide Range

RNA levels are determined by the rates of both transcription and decay, and a mechanistic understanding of the complex networks regulating gene expression requires methods that allow dynamic measurements of transcription and decay in living cells with minimal perturbation. Here, we describe a metabolic pulse-chase labeling protocol using 4-thiouracil combined with large-scale RNA sequencing to determine decay rates of all mRNAs in Saccharomyces cerevisiae. Profiling in various growth and stress conditions reveals that mRNA turnover is highly regulated both for specific groups of transcripts and at the system-wide level. For example, acute glucose starvation induces global mRNA stabilization but increases the degradation of all 132 detected ribosomal protein mRNAs. This effect is transient and can be mimicked by inhibiting the target-of-rapamycin kinase. Half-lives of mRNAs critical for galactose (GAL) metabolism are also highly sensitive to changes in carbon source. The fast reduction of GAL transcripts in glucose requires their dramatically enhanced turnover, highlighting the importance of mRNA decay in the control of gene expression. The approach described here provides a general platform for the global analysis of mRNA turnover and transcription and can be applied to dissect gene expression programs in a wide range of organisms and conditions.

scholarly journals mRNA destabilisation through CDS-targeting is the primary role of endogenous miRNA in the green alga Chlamydomonas

2016 ◽  
Author(s):  
Betty Y-W. Chung ◽  
Michael J. Deery ◽  
Arnoud J. Groen ◽  
Julie Howard ◽  
David Baulcombe
Keyword(s):  
Gene Expression ◽  
Green Alga ◽  
Messenger Rna ◽  
Global Analysis ◽  
Translational Efficiency ◽  
Primary Role ◽  
Regulate Gene Expression ◽  
Coding Regions ◽  
Unicellular Green Alga ◽  
Regulate Gene

AbstractMicroRNAs regulate gene expression as part of the RNA-induced silencing complex, where the sequence identity of the miRNA provides the specificity to the target messenger RNA, and the result is target repression. The mode of repression can be through target cleavage, RNA destabilization and/or decreased translational efficiency. Here, we provide a comprehensive global analysis of the evolutionarily distant unicellular green alga Chlamydomonas reinhardtii to quantify the effects of miRNA on protein synthesis and RNA abundance. We show that, similar to metazoan systems, miRNAs in Chlamydomonas regulate gene-expression primarily by destabilizing mRNAs. However, unlike metazoan miRNA where target site utilization localizes mainly to 3’UTRs, in Chlamydomonas utilized target sites lie predominantly within coding regions. These results demonstrate that destabilization of mRNA is the main evolutionarily conserved mode of action for miRNAs, but details of the mechanism diverge between plant and metazoan kingdoms.

scholarly journals Nuclear mRNA export requires specific FG nucleoporins for translocation through the nuclear pore complex

2007 ◽  
Vol 178 (7) ◽  
pp. 1121-1132 ◽  
Author(s):  
Laura J. Terry ◽  
Susan R. Wente
Keyword(s):  
Messenger Rna ◽  
Large Scale ◽  
Protein Import ◽  
Global Analysis ◽  
Mrna Export ◽  
Nuclear Pore ◽  
Nuclear Pore Complexes ◽  
Versus Protein ◽  
Transport Receptors ◽  
Pore Complexes

Trafficking of nucleic acids and large proteins through nuclear pore complexes (NPCs) requires interactions with NPC proteins that harbor FG (phenylalanine-glycine) repeat domains. Specialized transport receptors that recognize cargo and bind FG domains facilitate these interactions. Whether different transport receptors utilize preferential FG domains in intact NPCs is not fully resolved. In this study, we use a large-scale deletion strategy in Saccharomyces cerevisiae to generate a new set of more minimal pore (mmp) mutants that lack specific FG domains. A comparison of messenger RNA (mRNA) export versus protein import reveals unique subsets of mmp mutants with functional defects in specific transport receptors. Thus, multiple functionally independent NPC translocation routes exist for different transport receptors. Our global analysis of the FG domain requirements in mRNA export also finds a requirement for two NPC substructures—one on the nuclear NPC face and one in the NPC central core. These results pinpoint distinct steps in the mRNA export mechanism that regulate NPC translocation efficiency.

Life without RNAi: noncoding RNAs and their functions in Saccharomyces cerevisiaeThis paper is one of a selection of papers published in this Special Issue, entitled 30th Annual International Asilomar Chromatin and Chromosomes Conference, and has undergone the Journal’s usual peer review process.

2009 ◽  
Vol 87 (5) ◽  
pp. 767-779 ◽  
Author(s):  
Benjamin R. Harrison ◽  
Oya Yazgan ◽  
Jocelyn E. Krebs
Keyword(s):  
Gene Expression ◽  
Gene Regulation ◽  
Chromatin Structure ◽  
Messenger Rna ◽  
Peer Review Process ◽  
Regulation Of Gene Expression ◽  
Noncoding Rnas ◽  
Rna Degradation ◽  
Small Interfering Rnas ◽  
Ideal System

There are a number of well-characterized and fundamental roles for noncoding RNAs (ncRNAs) in gene regulation in all kingdoms of life. ncRNAs, such as ribosomal RNAs, transfer RNAs, small nuclear RNAs, small nucleolar RNAs, and small interfering RNAs, can serve catalytic and scaffolding functions in transcription, messenger RNA processing, translation, and RNA degradation. Recently, our understanding of gene expression has been dramatically challenged by the identification of large and diverse populations of novel ncRNAs in the eukaryotic genomes surveyed thus far. Studies carried out using the budding yeast Saccharomyces cerevisiae indicate that at least some coding genes are regulated by these novel ncRNAs. S. cerevisiae lacks RNA interference (RNAi) and, thus, provides an ideal system for studying the RNAi-independent mechanisms of ncRNA-based gene regulation. The current picture of gene regulation is one of great unknowns, in which the transcriptional environment surrounding a given locus may have as much to do with its regulation as its DNA sequence or local chromatin structure. Drawing on the recent research in S. cerevisiae and other organisms, this review will discuss the identification of ncRNAs, their origins and processing, and several models that incorporate ncRNAs into the regulation of gene expression and chromatin structure.

scholarly journals Engineering a Circular Riboregulator in Escherichia coli

2020 ◽  
Vol 2020 ◽  
pp. 1-9
Author(s):  
William Rostain ◽  
Shensi Shen ◽  
Teresa Cordero ◽  
Guillermo Rodrigo ◽  
Alfonso Jaramillo
Keyword(s):  
Gene Expression ◽  
Escherichia Coli ◽  
Messenger Rna ◽  
Noncoding Rna ◽  
Circular Rna ◽  
Circular Rnas ◽  
Fluorescent Reporter ◽  
Small Noncoding Rna ◽  
E Coli ◽  
Group I

RNAs of different shapes and sizes, natural or synthetic, can regulate gene expression in prokaryotes and eukaryotes. Circular RNAs have recently appeared to be more widespread than previously thought, but their role in prokaryotes remains elusive. Here, by inserting a riboregulatory sequence within a group I permuted intron-exon ribozyme, we created a small noncoding RNA that self-splices to produce a circular riboregulator in Escherichia coli. We showed that the resulting riboregulator can trans-activate gene expression by interacting with a cis-repressed messenger RNA. We characterized the system with a fluorescent reporter and with an antibiotic resistance marker, and we modeled this novel posttranscriptional mechanism. This first reported example of a circular RNA regulating gene expression in E. coli adds to an increasing repertoire of RNA synthetic biology parts, and it highlights that topological molecules can play a role in the case of prokaryotic regulation.

scholarly journals Characterization of a Tomato Protein Kinase Gene Induced by Infection by Potato spindle tuber viroid

2000 ◽  
Vol 13 (9) ◽  
pp. 903-910 ◽  
Author(s):  
Rosemarie W. Hammond ◽  
Yan Zhao
Keyword(s):  
Protein Kinase ◽  
Protein Kinases ◽  
Catalytic Domain ◽  
Potato Spindle Tuber Viroid ◽  
Circular Rna ◽  
Sequence Motifs ◽  
Kinase Gene ◽  
Viroid Infection ◽  
Protein Kinase Gene

Viroids—covalently closed, circular RNA molecules in the size range of 250 to 450 nucleotides—are the smallest known infectious agents and cause a number of diseases of crop plants. Viroids do not encode proteins and replicate within the nucleus without a helper virus. In many cases, viroid infection results in symptoms of stunting, epinasty, and vein clearing. In our study of the molecular basis of the response of tomato cv. Rutgers to infection by Potato spindle tuber viroid (PSTVd), we have identified a specific protein kinase gene, pkv, that is transcriptionally activated in plants infected with either the intermediate or severe strain of PSTVd, at a lower level in plants inoculated with a mild strain, and not detectable in mock-inoculated plants. A full-length copy of the gene encoding the 55-kDa PKV (protein kinase viroid)-induced protein has been isolated and sequence analysis revealed significant homologies to cyclic nucleotide-dependent protein kinases. Although the sequence motifs in the catalytic domain suggest that it is a serine/threonine protein kinase, the recombinant PKV protein autophosphorylates in vitro on serine and tyrosine residues, suggesting that it is a putative member of the class of dual-specificity protein kinases.

scholarly journals Histological, immunohistochemical and mRNA gene expression responses in coeliac disease patients challenged with gluten using PAXgene fixed paraffin-embedded duodenal biopsies

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Juha Taavela ◽  
Keijo Viiri ◽  
Alina Popp ◽  
Mikko Oittinen ◽  
Valeriia Dotsenko ◽  
...  
Keyword(s):  
Gene Expression ◽  
Coeliac Disease ◽  
Mrna Expression ◽  
Messenger Rna ◽  
Large Scale ◽  
Rna Extraction ◽  
Unmet Need ◽  
Γδ T Cells ◽  
Specific Gene ◽  
Small Intestinal Mucosa

Abstract Background There is an unmet need for novel treatments, such as drugs or vaccines, adjunctive to or replacing a burdensome life-long gluten-free diet for coeliac disease. The gold standard for successful treatment is a healed small intestinal mucosa, and therefore, the outcome measures in proof-of-concept studies should be based on evaluation of small intestine biopsies. We here evaluated morphometric, immunohistochemical and messenger RNA (mRNA) expression changes in coeliac disease patients challenged with gluten using PAXgene fixed paraffin-embedded biopsies. Methods Fifteen coeliac disease patients were challenged with 4 g of gluten per day for 10 weeks and 24 non-coeliac patients served as disease controls. A wide array of histological and immunohistochemical staining and mRNA-based gene expression tests (RT-qPCR and RNAseq) were carried out. Results Digital quantitative villous height: crypt depth ratio (VH: CrD) measurements revealed significant duodenal mucosal deterioration in all coeliac disease patients on gluten challenge. In contrast, the Marsh-Oberhuber class worsened in only 80% of coeliac patients. Measuring the intraepithelial CD3+ T-lymphocyte and lamina propria CD138+ plasma cell densities simultaneously proved to be a meaningful new measure of inflammation. Stainings for γδ T cells and IgA deposits, where previously frozen samples have been needed, were successful in PAXgene fixed paraffin-embedded samples. Messenger RNA extraction from the same paraffin-embedded biopsy block was successful and allowed large-scale qRT-PCR and RNAseq analyses for gene expression. Molecular morphometry, using the mRNA expression ratio of villous epithelium-specific gene APOA4 to crypt proliferation gene Ki67, showed a similar significant distinction between paired baseline and post-gluten challenge biopsies as quantitative histomorphometry. Conclusion Rigorous digitally measured histologic and molecular markers suitable for gluten challenge studies can be obtained from a single paraffin-embedded biopsy specimen. Molecular morphometry seems to be a promising new tool that can be used in situations where assessing duodenal mucosal health is of paramount importance. In addition, the diagnostically valuable IgA deposits were now stained in paraffin-embedded specimens making them more accessible in routine clinics.

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