A chemical probe based on the PreQ
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
06 10 2021
06 10 2021
Historique:
received:
12
03
2021
accepted:
26
08
2021
entrez:
7
10
2021
pubmed:
8
10
2021
medline:
28
10
2021
Statut:
epublish
Résumé
The role of metabolite-responsive riboswitches in regulating gene expression in bacteria is well known and makes them useful systems for the study of RNA-small molecule interactions. Here, we study the PreQ
Identifiants
pubmed: 34615874
doi: 10.1038/s41467-021-25973-x
pii: 10.1038/s41467-021-25973-x
pmc: PMC8494917
doi:
Substances chimiques
7-(aminomethyl)-7-deazaguanine
0
Ligands
0
Pyrimidinones
0
Pyrroles
0
RNA, Bacterial
0
Riboswitch
0
Types de publication
Journal Article
Research Support, N.I.H., Intramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
5856Informations de copyright
© 2021. This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply.
Références
Breaker, R. R. Riboswitches and the RNA world. Cold Spring Harb. Perspect. Biol. 4, a003566 (2012).
Serganov, A. & Nudler, E. A decade of riboswitches. Cell 152, 17–24 (2013).
pubmed: 23332744
pmcid: 4215550
doi: 10.1016/j.cell.2012.12.024
Roth, A. & Breaker, R. R. The structural and functional diversity of metabolite-binding riboswitches. Annu. Rev. Biochem 78, 305–34 (2009).
pubmed: 19298181
pmcid: 5325118
doi: 10.1146/annurev.biochem.78.070507.135656
Howe, J. A. et al. Selective small-molecule inhibition of an RNA structural element. Nature 526, 672–7 (2015).
pubmed: 26416753
doi: 10.1038/nature15542
Warner, K. D. et al. Validating fragment-based drug discovery for biological RNAs: lead fragments bind and remodel the TPP riboswitch specifically. Chem. Biol. 21, 591–5 (2014).
pubmed: 24768306
pmcid: 4057041
doi: 10.1016/j.chembiol.2014.03.007
Blount, K. F., Wang, J. X., Lim, J., Sudarsan, N. & Breaker, R. R. Antibacterial lysine analogs that target lysine riboswitches. Nat. Chem. Biol. 3, 44–9 (2007).
pubmed: 17143270
doi: 10.1038/nchembio842
McCown, P. J., Liang, J. J., Weinberg, Z. & Breaker, R. R. Structural, functional, and taxonomic diversity of three preQ
pubmed: 25036777
pmcid: 4145258
doi: 10.1016/j.chembiol.2014.05.015
Roth, A. et al. A riboswitch selective for the queuosine precursor preQ
pubmed: 17384645
doi: 10.1038/nsmb1224
Batey, R. T. Riboswitches: still a lot of undiscovered country. RNA 21, 560–3 (2015).
pubmed: 25780138
pmcid: 4371280
doi: 10.1261/rna.050765.115
Wang, X. et al. Queuosine modification protects cognate tRNAs against ribonuclease cleavage. RNA 24, 1305–1313 (2018).
pubmed: 29970597
pmcid: 6140461
doi: 10.1261/rna.067033.118
Alexander, S. C., Busby, K. N., Cole, C. M., Zhou, C. Y. & Devaraj, N. K. Site-specific covalent labeling of RNA by enzymatic transglycosylation. J. Am. Chem. Soc. 137, 12756–9 (2015).
pubmed: 26393285
doi: 10.1021/jacs.5b07286
Zhang, D., Zhou, C. Y., Busby, K. N., Alexander, S. C. & Devaraj, N. K. Light-activated control of translation by enzymatic covalent mRNA labeling. Angew. Chem. Int. Ed. Engl. 57, 2822–2826 (2018).
pubmed: 29380476
pmcid: 6052764
doi: 10.1002/anie.201710917
Wu, M. C. et al. Rational re-engineering of a transcriptional silencing PreQ
pubmed: 26106809
doi: 10.1021/jacs.5b03405
Wilkinson, K. A., Merino, E. J. & Weeks, K. M. Selective 2’-hydroxyl acylation analyzed by primer extension (SHAPE): quantitative RNA structure analysis at single nucleotide resolution. Nat. Protoc. 1, 1610–6 (2006).
pubmed: 17406453
doi: 10.1038/nprot.2006.249
Tijerina, P., Mohr, S. & Russell, R. DMS footprinting of structured RNAs and RNA-protein complexes. Nat. Protoc. 2, 2608–23 (2007).
pubmed: 17948004
pmcid: 2701642
doi: 10.1038/nprot.2007.380
Kadina, A., Kietrys, A. M. & Kool, E. T. RNA cloaking by reversible acylation. Angew. Chem. Int. Ed. Engl. 57, 3059–3063 (2018).
pubmed: 29370460
pmcid: 5842138
doi: 10.1002/anie.201708696
Ayele, T. M., Loya, T., Valdez-Sinon, A. N., Bassell, G. J. & Heemstra, J. M. Imaging and Tracking mRNA in Live Mammalian Cells Via Fluorogenic Photoaffinity Labeling. (Cold Spring Harbor Laboratory, 2020).
Zhou, C. Y., Alexander, S. C. & Devaraj, N. K. Fluorescent turn-on probes for wash-free mRNA imaging. Chem. Sci. 8, 7169–7173 (2017).
pubmed: 29081948
pmcid: 5635419
doi: 10.1039/C7SC03150E
Wang, J., Schultz, P. G. & Johnson, K. A. Mechanistic studies of a small-molecule modulator of SMN2 splicing. Proc. Natl Acad. Sci. USA 115, E4604–E4612 (2018).
pubmed: 29712837
pmcid: 5960314
Mortison, J. D. et al. Tetracyclines modify translation by targeting key human rRNA substructures. Cell Chem. Biol. 25, 1506–1518.e13 (2018).
pubmed: 30318461
pmcid: 6309532
doi: 10.1016/j.chembiol.2018.09.010
Suresh, B. M. et al. A general fragment-based approach to identify and optimize bioactive ligands targeting RNA. Proc. Natl Acad. Sci. USA 117, 33197–33203 (2020).
pubmed: 33318191
pmcid: 7777249
doi: 10.1073/pnas.2012217117
Mukherjee, H. et al. PEARL-seq: a photoaffinity platform for the analysis of small molecule-RNA interactions. ACS Chem. Biol. 15, 2374–2381 (2020).
pubmed: 32804474
doi: 10.1021/acschembio.0c00357
Hargrove, A. E. Small molecule-RNA targeting: starting with the fundamentals. Chem. Commun. (Camb.) 56, 14744–14756 (2020).
doi: 10.1039/D0CC06796B
Connelly, C. M., Moon, M. H. & Schneekloth, J. S. The emerging role of RNA as a therapeutic target for small molecules. Cell Chem. Biol. 23, 1077–1090 (2016).
pubmed: 27593111
pmcid: 5064864
doi: 10.1016/j.chembiol.2016.05.021
Meyer, S. M. et al. Small molecule recognition of disease-relevant RNA structures. Chem. Soc. Rev. 49, 7167–7199 (2020).
pubmed: 32975549
doi: 10.1039/D0CS00560F
pmcid: 7717589
Baker, J. L. et al. Widespread genetic switches and toxicity resistance proteins for fluoride. Science 335, 233–235 (2012).
pubmed: 22194412
doi: 10.1126/science.1215063
Sarkar, B., Ishii, K. & Tahara, T. Microsecond folding of preQ
pubmed: 34013733
doi: 10.1021/jacs.1c01077
Klein, D. J., Edwards, T. E. & Ferré-D’Amaré, A. R. Cocrystal structure of a class I preQ
pubmed: 19234468
pmcid: 2657927
doi: 10.1038/nsmb.1563
Connelly, C. M. et al. Synthetic ligands for PreQ. Nat. Commun. 10, 1501 (2019).
pubmed: 30940810
pmcid: 6445138
doi: 10.1038/s41467-019-09493-3
Jenkins, J. L., Krucinska, J., McCarty, R. M., Bandarian, V. & Wedekind, J. E. Comparison of a preQ
pubmed: 21592962
pmcid: 3137038
doi: 10.1074/jbc.M111.230375
Schroeder, G. M. et al. Analysis of a preQ
pubmed: 32597951
pmcid: 7641330
doi: 10.1093/nar/gkaa546
Santner, T., Rieder, U., Kreutz, C. & Micura, R. Pseudoknot preorganization of the preQ
pubmed: 22775200
doi: 10.1021/ja3049964
Eichhorn, C. D., Kang, M. & Feigon, J. Structure and function of preQ. Biochim. Biophys. Acta 1839, 939–950 (2014).
pubmed: 24798077
pmcid: 4177978
doi: 10.1016/j.bbagrm.2014.04.019
Dutta, D. & Wedekind, J. E. Nucleobase mutants of a bacterial preQ. J. Biol. Chem. 295, 2555–2567 (2020).
pubmed: 31659117
doi: 10.1074/jbc.RA119.010755
McCown, P. J., Corbino, K. A., Stav, S., Sherlock, M. E. & Breaker, R. R. Riboswitch diversity and distribution. RNA 23, 995–1011 (2017).
pubmed: 28396576
pmcid: 5473149
doi: 10.1261/rna.061234.117
Guan, L. & Disney, M. D. Covalent small-molecule-RNA complex formation enables cellular profiling of small-molecule-RNA interactions. Angew. Chem. Int. Ed. Engl. 52, 10010–3 (2013).
pubmed: 23913698
doi: 10.1002/anie.201301639
Behm-Ansmant, I., Helm, M. & Motorin, Y. Use of specific chemical reagents for detection of modified nucleotides in RNA. J. Nucleic Acids 2011, 1–17 (2011).
doi: 10.4061/2011/408053
Neuner, E., Frener, M., Lusser, A. & Micura, R. Superior cellular activities of azido- over amino-functionalized ligands for engineered preQ
pubmed: 30332908
pmcid: 6284575
doi: 10.1080/15476286.2018.1534526
Li, Z. et al. Design and synthesis of minimalist terminal alkyne-containing diazirine photo-crosslinkers and their incorporation into kinase inhibitors for cell- and tissue-based proteome profiling. Angew. Chem. Int. Ed. 52, 8551–8556 (2013).
doi: 10.1002/anie.201300683
Gao, J., Mfuh, A., Amako, Y. & Woo, C. M. Small molecule interactome mapping by photoaffinity labeling reveals binding site hotspots for the NSAIDs. J. Am. Chem. Soc. 140, 4259–4268 (2018).
pubmed: 29543447
doi: 10.1021/jacs.7b11639
Brunner, J., Senn, H. & Richards, F. M. 3-Trifluoromethyl-3-phenyldiazirine. A new carbene generating group for photolabeling reagents. J. Biol. Chem. 255, 3313–8 (1980).
pubmed: 7364745
doi: 10.1016/S0021-9258(19)85701-0
Dubinsky, L., Krom, B. P. & Meijler, M. M. Diazirine based photoaffinity labeling. Bioorg. Med. Chem. 20, 554–70 (2012).
pubmed: 21778062
doi: 10.1016/j.bmc.2011.06.066
Artsimovitch, I. & Henkin, T. M. In vitro approaches to analysis of transcription termination. Methods 47, 37–43 (2009).
pubmed: 18948199
doi: 10.1016/j.ymeth.2008.10.006
Williams, A. S. & Marzluff, W. F. The sequence of the stem and flanking sequences at the 3′end of histone mRNA are critical determinants for the binding of the stem-loop binding protein. Nucleic Acids Res. 23, 654–662 (1995).
pubmed: 7899087
pmcid: 306734
doi: 10.1093/nar/23.4.654
Dávila López, M. & Samuelsson, T. Early evolution of histone mRNA 3’ end processing. RNA 14, 1–10 (2008).
pubmed: 17998288
pmcid: 2151031
doi: 10.1261/rna.782308
Maida, Y. et al. An RNA-dependent RNA polymerase formed by TERT and the RMRP RNA. Nature 461, 230–235 (2009).
pubmed: 19701182
pmcid: 2755635
doi: 10.1038/nature08283
Su, Z. et al. Discovery of a biomarker and lead small molecules to target r(GGGGCC)-associated defects in c9FTD/ALS. Neuron 84, 239 (2014).
pubmed: 28898625
doi: 10.1016/j.neuron.2014.09.019
Chee, G. L., Yalowich, J. C., Bodner, A., Wu, X. & Hasinoff, B. B. A diazirine-based photoaffinity etoposide probe for labeling topoisomerase II. Bioorg. Med. Chem. 18, 830–8 (2010).
pubmed: 20006518
doi: 10.1016/j.bmc.2009.11.048
West, A. et al. Labeling preferences of diazirines with protein biomolecules. J. Am. Chem. Soc. 143, 6691–6700 (2020).
Fergus, C., Barnes, D., Alqasem, M. A. & Kelly, V. P. The queuine micronutrient: charting a course from microbe to man. Nutrients 7, 2897–929 (2015).
pubmed: 25884661
pmcid: 4425180
doi: 10.3390/nu7042897
Vinayak, M. & Pathak, C. Queuosine modification of tRNA: its divergent role in cellular machinery. Biosci. Rep. 30, 135–48 (2009).
pubmed: 19925456
doi: 10.1042/BSR20090057
Tuorto, F. et al. Queuosine‐modified tRNAs confer nutritional control of protein translation. EMBO J. 37, e99777 (2018).
pubmed: 30093495
pmcid: 6138434
doi: 10.15252/embj.201899777
Xu, D. et al. PreQ0 base, an unusual metabolite with anti-cancer activity from Streptomyces qinglanensis 172205. Anticancer Agents Med. Chem. 15, 285–90 (2015).
pubmed: 25353335
doi: 10.2174/1871520614666141027144653
Zhang, J. et al. tRNA Queuosine modification enzyme modulates the growth and microbiome recruitment to breast tumors. Cancers (Basel) 12, 628 (2020).
Artandi, S. E. & Depinho, R. A. Telomeres and telomerase in cancer. Carcinogenesis 31, 9–18 (2010).
pubmed: 19887512
doi: 10.1093/carcin/bgp268
Baena-Del Valle, J. A. et al. MYC drives overexpression of telomerase RNA (hTR/TERC) in prostate cancer. J. Pathol. 244, 11–24 (2018).
pubmed: 28888037
doi: 10.1002/path.4980
Cherkaoui Jaouad, I. et al. Novel mutation and structural RNA analysis of the noncoding RNase MRP gene in cartilage-hair hypoplasia. Mol. Syndromol. 6, 77–82 (2015).
pubmed: 26279652
pmcid: 4521058
doi: 10.1159/000430970
Zhang, Q., Kim, N.-K. & Feigon, J. Architecture of human telomerase RNA. Proc. Natl Acad. Sci. USA 108, 20325–20332 (2011).
pubmed: 21844345
pmcid: 3251123
doi: 10.1073/pnas.1100279108
Jafri, M. A., Ansari, S. A., Alqahtani, M. H. & Shay, J. W. Roles of telomeres and telomerase in cancer, and advances in telomerase-targeted therapies. Genome Med. 8, 69 (2016).
Klepper, F., Polborn, K. & Carell, T. Robust synthesis and crystal-structure analysis of 7-cyano-7-deazaguanine (PreQ
doi: 10.1002/hlca.200590201
Walzthoeni, T. et al. xTract: software for characterizing conformational changes of protein complexes by quantitative cross-linking mass spectrometry. Nat. Methods 12, 1185–1190 (2015).
pubmed: 26501516
pmcid: 4927332
doi: 10.1038/nmeth.3631
Fantoni, N. Z., El-Sagheer, A. H. & Brown, T. A Hitchhiker’s guide to click-chemistry with nucleic acids. Chem. Rev. 121, 7122–7154 (2021).
Hirata, K. et al. ZOO: an automatic data-collection system for high-throughput structure analysis in protein microcrystallography. Acta Crystallogr D. Struct. Biol. 75, 138–150 (2019).
pubmed: 30821703
pmcid: 6400253
doi: 10.1107/S2059798318017795
Yamashita, K., Hirata, K. & Yamamoto, M. KAMO: towards automated data processing for microcrystals. Acta Crystallogr D. Struct. Biol. 74, 441–449 (2018).
pubmed: 29717715
pmcid: 5930351
doi: 10.1107/S2059798318004576
Kabsch, W. XDS. Acta Crystallogr D. Biol. Crystallogr 66, 125–32 (2010).
pubmed: 20124692
pmcid: 2815665
doi: 10.1107/S0907444909047337
McCoy, A. J. et al. Phaser crystallographic software. J. Appl. Crystallogr. 40, 658–674 (2007).
pubmed: 19461840
pmcid: 2483472
doi: 10.1107/S0021889807021206
Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D. Biol. Crystallogr. 66, 213–21 (2010).
pubmed: 20124702
pmcid: 2815670
doi: 10.1107/S0907444909052925
Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D. Biol. Crystallogr. 60, 2126–32 (2004).
pubmed: 15572765
doi: 10.1107/S0907444904019158
Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–9 (2012).
pubmed: 22388286
pmcid: 3322381
doi: 10.1038/nmeth.1923
Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).
pubmed: 25516281
pmcid: 4302049
doi: 10.1186/s13059-014-0550-8
Livak, K. J. & Schmittgen, T. D. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods 25, 402–8 (2001).
pubmed: 11846609
doi: 10.1006/meth.2001.1262