@article{gagnon_biswas_zhang_brown_wollenzien_mattos_maxwell_2012, title={Structurally Conserved Nop56/58 N-terminal Domain Facilitates Archaeal Box C/D Ribonucleoprotein-guided Methyltransferase Activity}, volume={287}, ISSN={["1083-351X"]}, DOI={10.1074/jbc.m111.323253}, abstractNote={Background: Box C/D RNPs direct site-specific 2′-O-methylation of rRNA. Results: The Nop56/58 and fibrillarin core proteins establish a very stable dimer with Nop56/58 contributing to methyltransferase activity. Conclusion: The Nop56/58 core protein plays a role not only in RNP assembly, but also methyltransferase activity. Significance: Our observations reveal a novel role for the Nop56/58 core protein in box C/D RNP function. Box C/D RNA-protein complexes (RNPs) guide the 2′-O-methylation of nucleotides in both archaeal and eukaryotic ribosomal RNAs. The archaeal box C/D and C′/D′ RNP subcomplexes are each assembled with three sRNP core proteins. The archaeal Nop56/58 core protein mediates crucial protein-protein interactions required for both sRNP assembly and the methyltransferase reaction by bridging the L7Ae and fibrillarin core proteins. The interaction of Methanocaldococcus jannaschii (Mj) Nop56/58 with the methyltransferase fibrillarin has been investigated using site-directed mutagenesis of specific amino acids in the N-terminal domain of Nop56/58 that interacts with fibrillarin. Extensive mutagenesis revealed an unusually strong Nop56/58-fibrillarin interaction. Only deletion of the NTD itself prevented dimerization with fibrillarin. The extreme stability of the Nop56/58-fibrillarin heterodimer was confirmed in both chemical and thermal denaturation analyses. However, mutations that did not affect Nop56/58 binding to fibrillarin or sRNP assembly nevertheless disrupted sRNP-guided nucleotide modification, revealing a role for Nop56/58 in methyltransferase activity. This conclusion was supported with the cross-linking of Nop56/58 to the target RNA substrate. The Mj Nop56/58 NTD was further characterized by solving its three-dimensional crystal structure to a resolution of 1.7 Å. Despite low primary sequence conservation among the archaeal Nop56/58 homologs, the overall structure of the archaeal NTD domain is very well conserved. In conclusion, the archaeal Nop56/58 NTD exhibits a conserved domain structure whose exceptionally stable interaction with fibrillarin plays a role in both RNP assembly and methyltransferase activity.}, number={23}, journal={JOURNAL OF BIOLOGICAL CHEMISTRY}, author={Gagnon, Keith T. and Biswas, Shyamasri and Zhang, Xinxin and Brown, Bernard A., II and Wollenzien, Paul and Mattos, Carla and Maxwell, E. Stuart}, year={2012}, month={Jun}, pages={19418–19428} }
 @article{bleichert_gagnon_brown_maxwell_leschziner_unger_baserga_2009, title={A Dimeric Structure for Archaeal Box C/D Small Ribonucleoproteins}, volume={325}, ISSN={["1095-9203"]}, DOI={10.1126/science.1176099}, abstractNote={Seeing Double
          
            A particular set of ubiquitous small (nucleolar) ribonucleoproteins are important for optimal ribosome function and protein synthesis.
            
              Bleichert
              et al.
            
            (p.
            1384
            ) used electron microscopy and single-particle analysis to investigate the structure of an archaeal version that contains the small RNA (sRNA) and all the associated core proteins. Unexpectedly, this ribonucleoprotein is a homodimer, formed of two sRNAs and four copies of each of the core proteins. This dimer is likely to be the enzymatically active form, as mutations disrupting di-sRNP formation inhibited activity.
          }, number={5946}, journal={SCIENCE}, author={Bleichert, Franziska and Gagnon, Keith T. and Brown, Bernard A., II and Maxwell, E. Stuart and Leschziner, Andres E. and Unger, Vinzenz M. and Baserga, Susan J.}, year={2009}, month={Sep}, pages={1384–1387} }
 @article{gagnon_ju_goshe_maxwell_franzen_2009, title={A role for hydrophobicity in a DielsAlder reaction catalyzed by pyridyl-modified RNA}, volume={37}, ISSN={["1362-4962"]}, DOI={10.1093/nar/gkp177}, abstractNote={New classes of RNA enzymes or ribozymes have been obtained by in vitro evolution and selection of RNA molecules. Incorporation of modified nucleotides into the RNA sequence has been proposed to enhance function. DA22 is a modified RNA containing 5-(4-pyridylmethyl) carboxamide uridines, which has been selected for its ability to promote a Diels–Alder cycloaddition reaction. Here, we show that DA_TR96, the most active member of the DA22 RNA sequence family, which was selected with pyridyl-modified nucleotides, accelerates a cycloaddition reaction between anthracene and maleimide derivatives with high turnover. These widely used reactants were not used in the original selection for DA22 and yet here they provide the first demonstration of DA_TR96 as a true multiple-turnover catalyst. In addition, the absence of a structural or essential kinetic role for Cu2+, as initially postulated, and nonsequence-specific hydrophobic interactions with the anthracene substrate have led to a reevaluation of the pyridine modification's role. These findings broaden the catalytic repertoire of the DA22 family of pyridyl-modified RNAs and suggest a key role for the hydrophobic effect in the catalytic mechanism.}, number={9}, journal={NUCLEIC ACIDS RESEARCH}, author={Gagnon, Keith T. and Ju, Show-Yi and Goshe, Michael B. and Maxwell, E. Stuart and Franzen, Stefan}, year={2009}, month={May}, pages={3074–3082} }
 @article{gagnon_zhang_qu_biswas_suryadi_brown_maxwell_2010, title={Signature amino acids enable the archaeal L7Ae box C/D RNP core protein to recognize and bind the K-loop RNA motif}, volume={16}, ISSN={["1469-9001"]}, DOI={10.1261/rna.1692310}, abstractNote={The archaeal L7Ae and eukaryotic 15.5kD protein homologs are members of the L7Ae/15.5kD protein family that characteristically recognize K-turn motifs found in both archaeal and eukaryotic RNAs. In Archaea, the L7Ae protein uniquely binds the K-loop motif found in box C/D and H/ACA sRNAs, whereas the eukaryotic 15.5kD homolog is unable to recognize this variant K-turn RNA. Comparative sequence and structural analyses, coupled with amino acid replacement experiments, have demonstrated that five amino acids enable the archaeal L7Ae core protein to recognize and bind the K-loop motif. These signature residues are highly conserved in the archaeal L7Ae and eukaryotic 15.5kD homologs, but differ between the two domains of life. Interestingly, loss of K-loop binding by archaeal L7Ae does not disrupt C′/D′ RNP formation or RNA-guided nucleotide modification. L7Ae is still incorporated into the C′/D′ RNP despite its inability to bind the K-loop, thus indicating the importance of protein–protein interactions for RNP assembly and function. Finally, these five signature amino acids are distinct for each of the L7Ae/L30 family members, suggesting an evolutionary continuum of these RNA-binding proteins for recognition of the various K-turn motifs contained in their cognate RNAs.}, number={1}, journal={RNA}, author={Gagnon, Keith T. and Zhang, Xinxin and Qu, Guosheng and Biswas, Shyamasri and Suryadi, Jimmy and Brown, Bernard A., II and Maxwell, E. Stuart}, year={2010}, month={Jan}, pages={79–90} }
 @misc{gagnon_zhang_maxwell_2007, title={In vitro reconstitution and affinity purification of catalytically active archaeal box C/D sRNP complexes}, volume={425}, DOI={10.1016/s0076-6879(07)25012-8}, abstractNote={Archaeal box C/D RNAs guide the site‐specific 2′‐O‐methylation of target nucleotides in ribosomal RNAs and tRNAs. In vitro reconstitution of catalytically active box C/D RNPs by use of in vitro transcribed box C/D RNAs and recombinant core proteins provides model complexes for the study of box C/D RNP assembly, structure, and function. Described here are protocols for assembly of the archaeal box C/D RNP and assessment of its nucleotide modification activity. Also presented is a novel affinity purification scheme that uses differentially tagged core proteins and a sequential three‐step affinity selection protocol that yields fully assembled and catalytically active box C/D RNPs. This affinity selection protocol can provide highly purified complex in sufficient quantities not only for biochemical analyses but also for biophysical approaches such as cryoelectron microscopy and X‐ray crystallography.}, journal={RNA modification}, publisher={San Diego: Elsevier academic press inc}, author={Gagnon, K. and Zhang, X. X. and Maxwell, E. S.}, year={2007}, pages={263–282} }
 @article{garrett_andreyev_austin_ball_bandyopadhyay_becker_boston_boston_chakrawarthy_churchman_et al._2007, title={The TRIUMF nuclear structure program and TIGRESS}, volume={261}, ISSN={["1872-9584"]}, DOI={10.1016/j.nimb.2007.04.258}, abstractNote={The isotope separator and accelerator (ISAC) facility located at the TRIUMF laboratory in Vancouver, Canada, is one of the world’s most advanced isotope separator on-line-type radioactive ion beam facilities. An extensive γ-ray spectroscopy programme at ISAC is centred around two major research facilities: (i) the 8π γ-ray spectrometer for β-delayed γ-ray spectroscopy experiments with the low-energy beams from ISAC-I, and (ii) the next generation TRIUMF-ISAC gamma-ray escape suppressed spectrometer (TIGRESS) for in-beam experiments with the accelerated radioactive-ion beams. An overview of these facilities and recent results from the diverse programme of nuclear structure and fundamental interaction studies they support is presented.}, number={1-2}, journal={NUCLEAR INSTRUMENTS & METHODS IN PHYSICS RESEARCH SECTION B-BEAM INTERACTIONS WITH MATERIALS AND ATOMS}, author={Garrett, P. E. and Andreyev, A. and Austin, R. A. E. and Ball, G. C. and Bandyopadhyay, D. and Becker, J. A. and Boston, A. J. and Boston, H. C. and Chakrawarthy, R. S. and Churchman, R. and et al.}, year={2007}, month={Aug}, pages={1084–1088} }
 @article{gagnon_zhang_agris_maxwell_2006, title={Assembly of the archaeal box C/D sRNP can occur via alternative pathways and requires temperature-facilitated sRNA remodeling}, volume={362}, DOI={10.1016/j.jmb.2006.07.091}, abstractNote={Archaeal dual-guide box C/D small nucleolar RNA-like RNAs (sRNAs) bind three core proteins in sequential order at both terminal box C/D and internal C'/D' motifs to assemble two ribonuclear protein (RNP) complexes active in guiding nucleotide methylation. Experiments have investigated the process of box C/D sRNP assembly and the resultant changes in sRNA structure or "remodeling" as a consequence of sRNP core protein binding. Hierarchical assembly of the Methanocaldococcus jannaschii sR8 box C/D sRNP is a temperature-dependent process with binding of L7 and Nop56/58 core proteins to the sRNA requiring elevated temperature to facilitate necessary RNA structural dynamics. Circular dichroism (CD) spectroscopy and RNA thermal denaturation revealed an increased order and stability of sRNA folded structure as a result of L7 binding. Subsequent binding of the Nop56/58 and fibrillarin core proteins to the L7-sRNA complex further remodeled sRNA structure. Assessment of sR8 guide region accessibility using complementary RNA oligonucleotide probes revealed significant changes in guide region structure during sRNP assembly. A second dual-guide box C/D sRNA from M. jannaschii, sR6, also exhibited RNA remodeling during temperature-dependent sRNP assembly, although core protein binding was affected by sR6's distinct folded structure. Interestingly, the sR6 sRNP followed an alternative assembly pathway, with both guide regions being continuously exposed during sRNP assembly. Further experiments using sR8 mutants possessing alternative guide regions demonstrated that sRNA folded structure induced by specific guide sequences impacted the sRNP assembly pathway. Nevertheless, assembled sRNPs were active for sRNA-guided methylation independent of the pathway followed. Thus, RNA remodeling appears to be a common and requisite feature of archaeal dual-guide box C/D sRNP assembly and formation of the mature sRNP can follow different assembly pathways in generating catalytically active complexes.}, number={5}, journal={Journal of Molecular Biology}, author={Gagnon, K. T. and Zhang, X. X. and Agris, P. F. and Maxwell, E. S.}, year={2006}, pages={1025–1042} }