@article{tran_zhang_lackey_maxwell_2005, title={Conserved spacing between the box C/D and C '/D ' RNPs of the archaeal box C/D sRNP complex is required for efficient 2 '-O-methylation of target RNAs}, volume={11}, ISSN={["1469-9001"]}, DOI={10.1261/rna.7223405}, abstractNote={RNA-guided nucleotide modification complexes direct the post-transcriptional nucleotide modification of both archaeal and eukaryotic RNAs. We have previously demonstrated that efficient 2′-O-methylation activity guided by an in vitro reconstituted archaeal box C/D sRNP requires juxtaposed box C/D and C′/D′ RNP complexes. In these experiments, we investigate the importance of spatially positioning the box C/D and C′/D′ RNPs within the sRNP complex for nucleotide modification. Initial sequence analysis of 245 archaeal box C/D sRNAs from both Eukyarchaeota and Crenarchaeota kingdoms revealed highly conserved spacing between the box C/D and C′/D′ RNA motifs. Distances between boxes C to D′ and C′ to D (D′ and D spacers, respectively) exhibit highly constrained lengths of 12 nucleotides (nt). Methanocaldococcus jannaschii sR8 sRNA, a model box C/D sRNA with D and D′ spacers of 12 nt, was mutated to alter the distance between the two RNA motifs. sRNAs with longer or shorter spacer regions could still form sRNPs by associating with box C/D core proteins, L7, Nop56/58, and fibrillarin, comparable to wild-type sR8. However, these reconstituted box C/D sRNP complexes were severely deficient in methylation activity. Alteration of the D and D′ spacer lengths disrupted the guided methylation activity of both the box C/D and C′/D′ RNP complexes. When only one spacer region was altered, methylation activity of the corresponding RNP was lost. Collectively, these results demonstrate the importance of box C/D and C′/D′ RNP positioning for preservation of critical inter-RNP interactions required for efficient box C/D sRNP-guided nucleotide methylation.}, number={3}, journal={RNA}, author={Tran, E and Zhang, XX and Lackey, L and Maxwell, ES}, year={2005}, month={Mar}, pages={285–293} }
 @article{suryadi_tran_maxwell_brown_2005, title={The crystal structure of the Methanocaldococcus jannaschii multifunctional L7Ae RNA-binding protein reveals an induced-fit interaction with the box C/D RNAs}, volume={44}, ISSN={["0006-2960"]}, DOI={10.1021/bi050568q}, abstractNote={Archaeal ribosomal protein L7Ae is a multifunctional RNA-binding protein that recognizes the K-turn motif in ribosomal, box H/ACA, and box C/D sRNAs. The crystal structure of Methanocaldococcus jannaschii L7Ae has been determined to 1.45 A, and L7Ae's amino acid composition, evolutionary conservation, functional characteristics, and structural details have been analyzed. Comparison of the L7Ae structure to those of a number of related proteins with diverse functions has revealed significant structural homology which suggests that this protein fold is an ancient RNA-binding motif. Notably, the free M. jannaschii L7Ae structure is essentially identical to that with RNA bound, suggesting that RNA binding occurs through an induced-fit interaction. Circular dichroism experiments show that box C/D and C'/D' RNA motifs undergo conformational changes when magnesium or the L7Ae protein is added, corroborating the induced-fit model for L7Ae-box C/D RNA interactions.}, number={28}, journal={BIOCHEMISTRY}, author={Suryadi, J and Tran, EJ and Maxwell, ES and Brown, BA}, year={2005}, month={Jul}, pages={9657–9672} }
 @article{tran_brown_maxwell_2004, title={Evolutionary origins of the RNA-guided nucleotide-modification complexes: from the primitive translation apparatus?}, volume={29}, ISSN={0968-0004}, url={http://dx.doi.org/10.1016/j.tibs.2004.05.001}, DOI={10.1016/j.tibs.2004.05.001}, abstractNote={Eukarya and Archaea possess scores of RNA-guided nucleotide-modification complexes that target specific ribonucleotides for 2′-O-methylation or pseudouridylation. Recent characterization of these RNA-modification machines has yielded striking results with implications for their evolutionary origins: the two main classes of nucleotide-modification complex in Archaea share a common ribonucleoprotein (RNP) core element that has evolved from a progenitor RNP. The fact that this common RNP element is also found in ribosomes suggests that the origin of the progenitor RNP lies in the primitive translation apparatus. Thus, the trans-acting, RNA-guided nucleotide-modification complexes of the modern RNP world seem to have evolved from cis-acting RNA or RNP elements contained in the primitive translation apparatus during the transition from the ancient RNA world to the modern RNP world.}, number={7}, journal={Trends in Biochemical Sciences}, publisher={Elsevier BV}, author={Tran, Elizabeth and Brown, James and Maxwell, E.Stuart}, year={2004}, month={Jul}, pages={343–350} }
 @article{sanjay_singh_gurha_tran_maxwell_gupta_2004, title={Sequential 2 '-O-methylation of archaeal pre-tRNA(Trp) nucleotides is guided by the intron-encoded but trans-acting box c/D ribonucleoprotein of pre-tRNA}, volume={279}, ISSN={["1083-351X"]}, DOI={10.1074/jbc.M408868200}, abstractNote={Haloferax volcanii pre-tRNATrp processing requires box C/D ribonucleoprotein (RNP)-guided 2′-O-methylation of nucleotides C34 and U39 followed by intron excision. Positioning of the box C/D guide RNA within the intron of this pre-tRNA led to the assumption that nucleotide methylation is guided by the cis-positioned box C/D RNPs. We have now investigated the mechanism of 2′-O-methylation for the H. volcanii pre-tRNATrp in vitro by assembling methylation-competent box C/D RNPs on both the pre-tRNA and the excised intron (both linear and circular forms) using Methanocaldococcus jannaschii box C/D RNP core proteins. With both kinetic studies and single nucleotide substitutions of target and guide nucleotides, we now demonstrate that pre-tRNA methylation is guided in trans by the intron-encoded box C/D RNPs positioned in either another pre-tRNATrp or in the excised intron. Methylation by in vitro assembled RNPs prefers but does not absolutely require Watson-Crick pairing between the guide and target nucleotides. We also demonstrate for the first time that methylation of two nucleotides guided by a single box C/D RNA is sequential, that is, box C′/D′ RNP-guided U39 methylation first requires box C/D RNP-guided methylation of C34. Methylation of the two nucleotides of exogenous pre-tRNATrp added to an H. volcanii cell extract also occurs sequentially and is also accomplished in trans using RNPs that pre-exist in the extract. Thus, this trans mechanism is analogous to eukaryal pre-rRNA 2′-O-methylation guided by intron-encoded but trans-acting box C/D small nucleolar RNPs. This trans mechanism could explain the observed accumulation of the excised H. volcanii pre-tRNATrp intron in vivo. A trans mechanism would also eliminate the obligatory refolding of the pre-tRNA that would be required to carry out two cis-methylation reactions before pre-tRNA splicing.}, number={46}, journal={JOURNAL OF BIOLOGICAL CHEMISTRY}, author={Sanjay, KS and Singh, SK and Gurha, P and Tran, EJ and Maxwell, ES and Gupta, R}, year={2004}, month={Nov}, pages={47661–47671} }
 @article{tran_zhang_maxwell_2003, title={Efficient RNA 2 '-O-methylation requires juxtaposed and symmetrically assembled archaeal box C/D and C '/D ' RNPs}, volume={22}, ISSN={["0261-4189"]}, DOI={10.1093/emboj/cdg368}, abstractNote={Box C/D ribonucleoprotein (RNP) complexes direct the nucleotide‐specific 2′‐O‐methylation of ribonucleotide sugars in target RNAs. In vitro assembly of an archaeal box C/D sRNP using recombinant core proteins L7, Nop56/58 and fibrillarin has yielded an RNA:protein enzyme that guides methylation from both the terminal box C/D core and internal C′/D′ RNP complexes. Reconstitution of sRNP complexes containing only box C/D or C′/D′ motifs has demonstrated that the terminal box C/D RNP is the minimal methylation‐competent particle. However, efficient ribonucleotide 2′‐O‐methylation requires that both the box C/D and C′/D′ RNPs function within the full‐length sRNA molecule. In contrast to the eukaryotic snoRNP complex, where the core proteins are distributed asymmetrically on the box C/D and C′/D′ motifs, all three archaeal core proteins bind both motifs symmetrically. This difference in core protein distribution is a result of altered RNA‐binding capabilities of the archaeal and eukaryotic core protein homologs. Thus, evolution of the box C/D nucleotide modification complex has resulted in structurally distinct archaeal and eukaryotic RNP particles.}, number={15}, journal={EMBO JOURNAL}, author={Tran, EJ and Zhang, XX and Maxwell, ES}, year={2003}, month={Aug}, pages={3930–3940} }
 @article{kuhn_tran_maxwell_2002, title={Archaeal ribosomal protein L7 is a functional homolog of the eukaryotic 15.5kD/Snu13p snoRNP core protein}, volume={30}, DOI={10.1093/nar/30.4.931}, abstractNote={Recent investigations have identified homologs of eukaryotic box C/D small nucleolar RNAs (snoRNAs) in Archaea termed sRNAs. Archaeal homologs of the box C/D snoRNP core proteins fibrillarin and Nop56/58 have also been identified but a homolog for the eukaryotic 15.5kD snoRNP protein has not been described. Our sequence analysis of archaeal genomes reveals that the highly conserved ribosomal protein L7 exhibits extensive homology with the eukaryotic 15.5kD protein. Protein binding studies demonstrate that recombinant Methanoccocus jannaschii L7 protein binds the box C/D snoRNA core motif with the same specificity and affinity as the eukaryotic 15.5kD protein. Identical to the eukaryotic 15.5kD core protein, archaeal L7 requires a correctly folded box C/D core motif and intact boxes C and D. Mutational analysis demonstrates that critical features of the box C/D core motif essential for 15.5kD binding are also required for L7 interaction. These include stem I which juxtaposes boxes C and D, as well as the sheared G:A pairs and protruded pyrimidine nucleotide of the asymmetric bulge region. The demonstrated presence of L7Ae in the Haloarcula marismortui 50S ribosomal subunit, taken with our demonstration of the ability of L7 to bind to the box C/D snoRNA core motif, indicates that this protein serves a dual role in Archaea. L7 functioning as both an sRNP core protein and a ribosomal protein could potentially regulate and coordinate sRNP assembly with ribosome biogenesis.}, number={4}, journal={Nucleic Acids Research}, author={Kuhn, J. F. and Tran, E. J. and Maxwell, E. S.}, year={2002}, pages={931–941} }