Figure 4. In vitro mo5U forming activity of TrmR

Slides:

Advertisements

Similar presentations

Figure 1. Schematic of the corA leader mRNA

Advertisements

Figure 1. The flow chart illustrates the construction process of anti-CRISPRdb, and the information that users can obtain from anti-CRISPRdb. From: Anti-CRISPRdb:

Figure 1: Necrobiosis lipoidica: Yellow-brown skin lesions with indurated borders located on both lower legs. Figure 1: Necrobiosis lipoidica: Yellow-brown.

Figure 1. (A) The VEGF promoter PQS and scheme of G oxidation to OG, as well as (B) the proposed APE1-dependent pathway ... Figure 1. (A) The VEGF promoter.

Figure 1. Circular taxonomy tree based on the species that were sequenced in our study. Unless provided in the caption above, the following copyright applies.

Figure 1. An example of a thioviridamide-like molecule, thioalbamide, and inset, a proposed biochemical route to ... Figure 1. An example of a thioviridamide-like.

Figure 1. Overview of the workflow of NetworkAnalyst 3.0.

Figure 2. Status of rRNA methylations upon SAM depletion

Figure 1: Axial T2 W images of penis showed a well-defined septated area of 2 cm in the posterior aspect of ... Figure 1: Axial T2 W images.

Figure 1. Aminoacylation of 3′-NH2-tRNA catalyzed by flexizymes

FIGURE 1 Histological diagnoses divided into 8-year time frames (n = 1208). Unless provided in the caption above, the following copyright applies to the.

FIGURE 1 The effect of daprodustat on hemoglobin (Hgb) levels

FIGURE 2 Responses to the question: regarding vasoactive drugs, does your centre use the following frequently, rarely ... FIGURE 2 Responses to the question:

FIGURE 1 Maternal (A) urinary aldosterone; (B) plasma active renin; (C) urinary AGT concentrations; and (D) plasma AGT ... FIGURE 1 Maternal (A) urinary.

Figure 1. Ratios of observed to expected numbers of exon boundaries aligning to boundaries of domain and disorder ... Figure 1. Ratios of observed to expected.

Figure 1. autoMLST workflow depicting placement and de novo mode

Figure 1. Chemical structures of DNA and tc-DNA

Fig. 1 Mean change from baseline in ANC ± s. e

Point estimates with ... Point estimates with 95% CI. HR: hip replacement; KR: knee replacement. Unless provided in the caption above, the following copyright.

FIGURE 1 Participant flow diagram. Exercise Counseling Clinic (ECC).

Graph 1. The number of homicide cases per year discussing neuro-evidence. Unless provided in the caption above, the following copyright applies to the.

Figure 6. The DNA lyase activity of hNTHL1 contributes to the processing of lesions in nucleosomes, even in the ... Figure 6. The DNA lyase activity of.

Figure 1. Analysis of human TRIM5α protein with Blast-Search and PhyML+SMS ‘One click’ workflow. (A) NGPhylogeny.fr ... Figure 1. Analysis of human TRIM5α.

Figure 2. Natural history of chlamydia transmission, with arrows showing the transitions between health states. Figure 2. Natural history of chlamydia.

Figure 1 Nelson-Aalen estimates of the cumulative incidence rates for patients on versus off IST. ON = optic neuritis; ... Figure 1 Nelson-Aalen estimates.

FIGURE 1 Study consort diagram

Fig. 2 Case 2. Levels of serum creatinine and anti-GBM antibodies before and during treatment with cyclophosphamide, ... Fig. 2 Case 2. Levels of serum.

Figure 1. Illustration of DGR systems and their prediction using myDGR

Figure 1. The pipeline of Aggrescan3D 2.0 server.

FIGURE 1 Food groups consumed (mean, g/d) among US infants and young children by age group and tertile of mean ... FIGURE 1 Food groups consumed (mean,

Figure 1. EBOV VP35 has NTP-binding and NTPase activities

Figure 1. Prediction result for birch pollen allergen Bet v 1 (PDB: 1bv1), as obtained by comparison to the cherry ... Figure 1. Prediction result for.

Figure 1. Using Voronoi tessellation to define contacts

Figure 4. Levels of cerebrospinal fluid (CSF) immune and inflammatory markers in participants grouped by CSF human ... Figure 4. Levels of cerebrospinal.

Figure 1. Analysis of the AP lyase activity of BsuLigD

Figure 4. RLS spectra of (A) TMPipEOPP and (B) OMHEPzEOPP in the presence of different concentrations of KRAS. The RLS ... Figure 4. RLS spectra of (A)

Figure 1. PaintOmics 3 workflow diagram

Figure 1. Concept of poly(A) tail labeling for translation and localization analyses of reporter mRNAs. Azido-modified ... Figure 1. Concept of poly(A)

Figure 1. Schematic diagram of solar energy and coal-fired power generation system. Unless provided in the caption above, the following copyright applies.

Figure 1. Uncertainty reduction, value creation, and appropriation in two case studies. Unless provided in the caption above, the following copyright applies.

Figure 1. (A) Architecture of Doc2Hpo. (B) Interactive user interface

Figure 1. MERMAID web server interface (Start page, Parameter page): MERMAID provides two ways to submit a protein ... Figure 1. MERMAID web server interface.

Figure 1. Yvis platform overview

Figure 1. The framework of NetGO with seven steps

Figure 1. Workflow of the HawkDock server that is divided into three major steps: (i) input of unbound or bound protein ... Figure 1. Workflow of the HawkDock.

Figure 1 Patient disposition

Figure 1. Workflow of the analysis to estimate the number of true human miRNAs. Samples containing NGS data were ... Figure 1. Workflow of the analysis.

Fig. 1. —Synteny analysis of melon chromosome 1 (brown) and cucumber chromosome 7 (green) based on melon-cucumber ... Fig. 1. —Synteny analysis of melon.

Figure 1. Trial profile. (A) Part A and (B) part B

Figure 4. MTase JHP1050 inactivation causes phenotypic effects that vary between strains: growth, viability and ... Figure 4. MTase JHP1050 inactivation.

Figure 1. Scheme of a phosphorothioated-terminal hairpin formation and self-priming extension (PS-THSP) for selection ... Figure 1. Scheme of a phosphorothioated-terminal.

Figure 1. 3C analysis of HEM3, BLM10, and SEN1 genes in rpb4Δ and isogenic wild type cells. (A) Schematic ... Figure 1. 3C analysis of HEM3, BLM10, and.

Figure 1 Genetic results. No case had more than one diagnostic result

Figure 1. CSB does not affect the recruitment of OGG1 to oxidative DNA damage. (A) Representative stills of time-lapse ... Figure 1. CSB does not affect.

Figure 1. (A) Baseline contrast-enhanced CT scan of melanoma patient presenting with metastases in the liver and lymph ... Figure 1. (A) Baseline contrast-enhanced.

Figure 1. Prevalence of parasitic infection and anemia among the children. Unless provided in the caption above, the following copyright applies to the.

Fig. 1. —OR gene tree including 2,973 genes from seven ants, honeybee, and jewel wasp. The tree was reconstructed ... Fig. 1. —OR gene tree including 2,973.

Figure 1. DNA-guided RNA cleavage activity

Figure 6. Protein-protein interactions

Figure 1. Optimization of the variant calling algorithm, ADIScan1, by tangential conversion of read depth ratios ... Figure 1. Optimization of the variant.

Figure 1. GWAS Catalog associations for coronary artery disease plotted across all chromosomes. Associations added ... Figure 1. GWAS Catalog associations.

Figure 1 The workflow of CAR development from a hybridoma

Figure 1. Crystal structures of Rim1

Source:Zimnisky (2014). Source:Zimnisky (2014).

Figure 1 Mechanisms of mitral regurgitation.

Fig. 1. —GO categories enriched in gene families showing high or low omega (dN/dS) values for Pneumocystis jirovecii. ... Fig. 1. —GO categories enriched.

Figure 1. Removal of the 2B subdomain activates Rep monomer unwinding

Figure 5. The endonucleolytic product from PfuPCNA/MR activity is displaced from dsDNA. Results from real-time ... Figure 5. The endonucleolytic product.

Figure 1. (A) Overview of ENPD including data source, data processing and features. Transcriptomes from TSA, genomes ... Figure 1. (A) Overview of ENPD.

Figure 1. Hepatitis C screening and diagnostic algorithm at the MSF clinic, Karachi, Pakistan, March 2016–September ... Figure 1. Hepatitis C screening.

Presentation transcript:

Figure 4. In vitro mo5U forming activity of TrmR Figure 4. In vitro mo5U forming activity of TrmR. (A) On the left, HPLC analysis of TrmR directed the ... Figure 4. In vitro mo<sup>5</sup>U forming activity of TrmR. (A) On the left, HPLC analysis of TrmR directed the formation of mo<sup>5</sup>U (solid line) versus control which contains no TrmR (dashed line). The peak corresponding mo<sup>5</sup>U eluted from the C-18 column at 8.6 min which has been confirmed by spiking with an authentic compound (right panel). (B) The assay sample was analyzed by LC-MS/MS in positive mode, where the peak corresponding to mo<sup>5</sup>U ([C<sub>10</sub>H<sub>15</sub>N<sub>2</sub>O<sub>7</sub>]<sup>+</sup>, calculated m/z = 275.088) was selected (left) and the subsequent fragmentation by ESI was confirmed as detection of 5-methoxyuracil ([C<sub>5</sub>H<sub>7</sub>N<sub>2</sub>O<sub>3</sub>]<sup>+</sup>, calculated m/z = 143.046) in MS/MS (right). Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com Nucleic Acids Res, Volume 46, Issue 17, 30 June 2018, Pages 9160–9169, https://doi.org/10.1093/nar/gky592 The content of this slide may be subject to copyright: please see the slide notes for details.

Figure 3. Biosynthesis of mo5U by yrrM (or trmR) Figure 3. Biosynthesis of mo5U by yrrM (or trmR). Presence of mo5U in total RNA extracted from ... Figure 3. Biosynthesis of mo<sup>5</sup>U by yrrM (or trmR). Presence of mo<sup>5</sup>U in total RNA extracted from Bacillus subtilis and the single knockout mutants was examined by triple-quadruple (QqQ) mass spectrometry in positive ion mode. Multiple reaction monitoring of mo<sup>5</sup>U is quantified by tracing the fragmentation of 5-methoxyuracil (mass-to-charge ratio 143.046), and an exemplary chromatogram of the parent strain is displayed (left), whereas no equivalent transition was observed in the sample prepared from ΔyrrM, or ΔtrmR. Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com Nucleic Acids Res, Volume 46, Issue 17, 30 June 2018, Pages 9160–9169, https://doi.org/10.1093/nar/gky592 The content of this slide may be subject to copyright: please see the slide notes for details.

Figure 2. Proposed biosynthetic pathways for the synthesis of cmo5U and mo5U. (A) In ... Figure 2. Proposed biosynthetic pathways for the synthesis of cmo<sup>5</sup>U and mo<sup>5</sup>U. (A) In Gram-negative bacteria, Cx-SAM is synthesized from SAM and prephenate by CmoA. Subsequently, CmoB directs carboxymethyltransferation at the 5-hydroxyl group of ho<sup>5</sup>U<sub>34</sub>, which is generated by an unknown pathway. (B) TrmR transfers the methyl group from SAM onto ho<sup>5</sup>U<sub>34</sub> of equivalent isoacceptors in Gram-positives. B denotes a general base. Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com Nucleic Acids Res, Volume 46, Issue 17, 30 June 2018, Pages 9160–9169, https://doi.org/10.1093/nar/gky592 The content of this slide may be subject to copyright: please see the slide notes for details.

Figure 1. Examples of the wobble uridine modification at C5 Figure 1. Examples of the wobble uridine modification at C5. Chemical structures of modified uridine at the wobble ... Figure 1. Examples of the wobble uridine modification at C5. Chemical structures of modified uridine at the wobble position (U<sub>34</sub>) is shown with (A) alkylation or (B) O-alkylation at C5 of pyrimidine. 5-methyluridine (m<sup>5</sup>U), 5-taurinomethyluridine (τm<sup>5</sup>U), 5-carboxymethylaminomethyluridine (cmnm<sup>5</sup>U), 5-hydroxyuridine (ho<sup>5</sup>U), 5-methoxyuridine (mo<sup>5</sup>U), 5-carboxymethyluridine (cmo<sup>5</sup>U), 5-carboxymethoxyuridine (mcmo<sup>5</sup>U). Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com Nucleic Acids Res, Volume 46, Issue 17, 30 June 2018, Pages 9160–9169, https://doi.org/10.1093/nar/gky592 The content of this slide may be subject to copyright: please see the slide notes for details.

Figure 5. Overall structures of TrmR Figure 5. Overall structures of TrmR. The ribbon presentation of the crystal structure of (A) RNA-free TrmR (navy) with ... Figure 5. Overall structures of TrmR. The ribbon presentation of the crystal structure of (A) RNA-free TrmR (navy) with SAH (gray stick) and magnesium ion (sphere, magenta), and (B) TrmR (green) bound to tRNA<sup>ASL</sup> (red stick) with SAM (gray stick). (C) Overlaid structures of RNA-free TrmR (blue) and TrmR:tRNA<sup>ASL</sup> (green and red). (D) Ionic/hydrogen bond interactions between ASL tRNA and a set of basic residues of TrmR in the crystal structure of TrmR–ASL<sup>Ala</sup> complex. The ASL is shown with their carbon atoms colored gray, nitrogen atoms colored blue, oxygen atoms colored red and phosphorous atoms colored orange. Hydrogen bond is indicated by dashed lines. Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com Nucleic Acids Res, Volume 46, Issue 17, 30 June 2018, Pages 9160–9169, https://doi.org/10.1093/nar/gky592 The content of this slide may be subject to copyright: please see the slide notes for details.

Figure 6. Ligand/metal binding by TrmR Figure 6. Ligand/metal binding by TrmR. (A) Close-up view of SAM-binding site in the crystal structure of ... Figure 6. Ligand/metal binding by TrmR. (A) Close-up view of SAM-binding site in the crystal structure of Bacillus subtilis. SAM is shown in dark gray. TrmR amino acid residues that interact with SAM are shown in green. Hydrogen bonds are shown as dashed lines. (B) TrmR model colored according to the distribution of electrostatic potential, from red (−5 kT) to blue (5 kT). The SAM-binding pocket is largely negatively charged. (C) Coordination of magnesium ion in RNA-free TrmR structure, where the metal ion (magenta) is coordinated by six ligands; i.e. Asp-133, Asp-159 and Asn-160 residues and three ordered water molecules. (D) An absence of magnesium ion in TrmR:tRNA<sup>ASL</sup> structure. Note Asn160 is in two rotameric states. Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com Nucleic Acids Res, Volume 46, Issue 17, 30 June 2018, Pages 9160–9169, https://doi.org/10.1093/nar/gky592 The content of this slide may be subject to copyright: please see the slide notes for details.