7 research outputs found
The Effects of Ultraviolet Radiation on Nucleoside Modifications in RNA
Ultraviolet
radiation (UVR) is a known genotoxic agent. Although
its effects on DNA have been well-documented, its impact on RNA and
RNA modifications is less studied. By using <i>Escherichia coli</i> tRNA (tRNA) as a model system, we identify the UVA (370 nm) susceptible
chemical groups and bonds in a large variety of modified nucleosides.
We use liquid chromatography tandem mass spectrometry to identify
specific nucleoside photoproducts under <i>in vitro</i> and <i>in vivo</i> conditions, which were then verified by employing
stable-isotope labeled tRNAs. These studies suggest that the -amino
or -oxy groups of modified nucleosides, in addition to sulfur, are
labile in the oxidative environment generated by UVA exposure. Further,
these studies document a range of RNA photoproducts and post-transcriptional
modifications that arise because of UVR-induced cellular stress
Directed Evolution of Heterologous tRNAs Leads to Reduced Dependence on Post-transcriptional Modifications
Heterologous tRNA:aminoacyl tRNA
synthetase pairs are often employed
for noncanonical amino acid incorporation in the quest for an expanded
genetic code. In this work, we investigated one possible mechanism
by which directed evolution can improve orthogonal behavior for a
suite of <i>Methanocaldococcus jannaschii</i> (<i>Mj</i>) tRNA<sup>Tyr</sup>-derived amber suppressor tRNAs. Northern blotting
demonstrated that reduced expression of heterologous tRNA variants
correlated with improved orthogonality. We suspected that reduced
expression likely minimized nonorthogonal interactions with host cell
machinery. Despite the known abundance of post-transcriptional modifications
in tRNAs across all domains of life, few studies have investigated
how host enzymes may affect behavior of heterologous tRNAs. Therefore,
we measured tRNA orthogonality using a fluorescent reporter assay
in several modification-deficient strains, demonstrating that heterologous
tRNAs with high expression are strongly affected by some native <i>E.Β coli</i> RNA-modifying enzymes, whereas low abundance
evolved heterologous tRNAs are less affected by these same enzymes.
We employed mass spectrometry to map ms<sup>2</sup>i<sup>6</sup>A37
and Ξ¨39 in the anticodon arm of two high abundance tRNAs (Nap1
and tRNA<sup>Opt</sup><sub>CUA</sub>), which provides (to our knowledge)
the first direct evidence that MiaA and TruA post-transcriptionally
modify evolved heterologous amber suppressor tRNAs. Changes in total
tRNA modification profiles were observed by mass spectrometry in cells
hosting these and other evolved suppressor tRNAs, suggesting that
the demonstrated interactions with host enzymes might disturb native
tRNA modification networks. Together, these results suggest that heterologous
tRNAs engineered for specialized amber suppression can evolve highly
efficient suppression capacity within the native post-transcriptional
modification landscape of host RNA processing machinery
Normalized expression data for the NASC Arabidopsis biotic stress series (Additional file ) were extracted and plotted as shown
The legends indicate the correspondence between the plots and the respective Arabidopsis gene identification designation. The numerical key for each array experiment is given along the X-axis. While the full list of the agents can be found in Additional file , here is a brief list: 1β16, control and infection; 17β22, control and infection; 23β36, control and elicitors treatment; 37β52, dark and different light treatment.<p><b>Copyright information:</b></p><p>Taken from "Arabidopsis mRNA polyadenylation machinery: comprehensive analysis of protein-protein interactions and gene expression profiling"</p><p>http://www.biomedcentral.com/1471-2164/9/220</p><p>BMC Genomics 2008;9():220-220.</p><p>Published online 14 May 2008</p><p>PMCID:PMC2391170.</p><p></p
Normalized expression data for the NASC Arabidopsis developmental series (Additional file ) were extracted and plotted as shown
The set of genes listed in Table 1 were split into three groups; the grouping was done according to historical views of the polyadenylation complex. Thus, genes encoding CPSF and CSTF subunits are shown in the top panel, PAPS and PABN genes in the middle, and the remaining genes in the lower panel. This grouping also applies for the plots shown in Figures 3β5. The legends indicate the correspondence between the plots and the respective Arabidopsis gene identification designation. The numerical key for each array experiment is given along the X-axis. The full list of the keys can be found in the Additional file . Here is a brief description of these samples, including wt and some mutants: 1β7, root 7β21 days; 8β10, stem 7β21 days; 11β27, leaf 7β35 days; 28β38, whole plant 7β23 days; 39β49, shoot apex 7β21 days; 50β71, flowers and floral organs 21+ day; 72β79, 8 week seeds and siliques. The arrows point to the positions for mature pollen.<p><b>Copyright information:</b></p><p>Taken from "Arabidopsis mRNA polyadenylation machinery: comprehensive analysis of protein-protein interactions and gene expression profiling"</p><p>http://www.biomedcentral.com/1471-2164/9/220</p><p>BMC Genomics 2008;9():220-220.</p><p>Published online 14 May 2008</p><p>PMCID:PMC2391170.</p><p></p
Normalized expression data for the NASC Arabidopsis chemical/hormone series (Additional file ) were extracted and plotted as shown
The legends indicate the correspondence between the plots and the respective Arabidopsis gene identification designation. The numerical key for each array experiment is given along the X-axis, and the detail can be found in Additional file . The single arrows indicate the position for cycloheximide; double arrows for GA mutants; empty arrows for imbibition and ABA treatment.<p><b>Copyright information:</b></p><p>Taken from "Arabidopsis mRNA polyadenylation machinery: comprehensive analysis of protein-protein interactions and gene expression profiling"</p><p>http://www.biomedcentral.com/1471-2164/9/220</p><p>BMC Genomics 2008;9():220-220.</p><p>Published online 14 May 2008</p><p>PMCID:PMC2391170.</p><p></p
The values for each gene in the array analysis of mature pollen were plotted as shown
<p><b>Copyright information:</b></p><p>Taken from "Arabidopsis mRNA polyadenylation machinery: comprehensive analysis of protein-protein interactions and gene expression profiling"</p><p>http://www.biomedcentral.com/1471-2164/9/220</p><p>BMC Genomics 2008;9():220-220.</p><p>Published online 14 May 2008</p><p>PMCID:PMC2391170.</p><p></p
Normalized expression data for the NASC Arabidopsis abiotic stress series (Additional file ) were extracted and plotted as shown
The legends indicate the correspondence between the plots and the respective Arabidopsis gene identification designation. The numerical key for each array experiment is given along the X-axis and the detail can be found in Additional file . Here is a brief list of the stress treatments: 1β18, control; 19β30, cold; 31β42, osmotic; 43β54, salt; 55β68, drought; 69β80, genotoxic; 81β92, oxidative; 93β106, UV-B; 107β120, wound; 121β136, heat; 137β141, cell culture control; 142β149, cell culture + heat.<p><b>Copyright information:</b></p><p>Taken from "Arabidopsis mRNA polyadenylation machinery: comprehensive analysis of protein-protein interactions and gene expression profiling"</p><p>http://www.biomedcentral.com/1471-2164/9/220</p><p>BMC Genomics 2008;9():220-220.</p><p>Published online 14 May 2008</p><p>PMCID:PMC2391170.</p><p></p