The box C/D sRNP dimeric architecture is conserved across domain Archaea.

Box C/D small (nucleolar) ribonucleoproteins [s(no)RNPs] catalyze RNA-guided 2'-O-ribose methylation in two of the three domains of life. Recent structural studies have led to a controversy over whether box C/D sRNPs functionally assemble as monomeric or dimeric macromolecules. The archaeal box C/D sRNP from Methanococcus jannaschii (Mj) has been shown by glycerol gradient sedimentation, gel filtration chromatography, native gel analysis, and single-particle electron microscopy (EM) to adopt a di-sRNP architecture, containing four copies of each box C/D core protein and two copies of the Mj sR8 sRNA. Subsequently, investigators used a two-stranded artificial guide sRNA, CD45, to assemble a box C/D sRNP from Sulfolobus solfataricus with a short RNA methylation substrate, yielding a crystal structure of a mono-sRNP. To more closely examine box C/D sRNP architecture, we investigate the role of the omnipresent sRNA loop as a structural determinant of sRNP assembly. We show through sRNA mutagenesis, native gel electrophoresis, and single-particle EM that a di-sRNP is the near exclusive architecture obtained when reconstituting box C/D sRNPs with natural or artificial sRNAs containing an internal loop. Our results span three distantly related archaeal species--Sulfolobus solfataricus, Pyrococcus abyssi, and Archaeoglobus fulgidus--indicating that the di-sRNP architecture is broadly conserved across the entire archaeal domain.

Medium effects on the direct cis-trans photoisomerization of 1,4-diphenyl-1,3-butadiene in solution.

Quantum yields for the photoisomerization of trans,trans-1,4-diphenyl-1,3-butadiene (tt-DPB), determined in benzene, cyclohexane, methylcyclohexane, hexane, and perfluorohexane, confirm the low values reported earlier for benzene and cyclohexane and reveal even lower values in the last two solvents. In contrast to trans-stilbene (t-St), fluorescence and torsional relaxation leading to photoisomerization do not account exclusively for S(1)tt-DPB decay. Competing radiationless singlet excited-state decay pathways exist in tt-DPB, which do not lead to photoisomerization and may not involve large-amplitude torsional motions. Our results invalidate analyses of tt-DPB fluorescence quantum yields and lifetimes that assign all radiationless decay to the isomerization channel. Gas-phase chromatography analysis of tt-DPB photoisomerization in hexane shows the reaction to be concentration-independent and reveals, for the first time, a significant, two-bond photoisomerization pathway, φ(tt→tc) = 0.092 and φ(tt→cc) = 0.020. The dominant one-bond-twist (OBT) process is accompanied by a bicycle pedal (BP) process that accounts for almost 20% of tt-DPB photoisomerization. The OBT tt-DPB photoisomerization quantum yield is largest in benzene (Bz) and smallest in perfluorohexane (PFH). Contrary to expectations, reduction in medium friction in PFH is accompanied by a decrease in φ(tt→tc). The 1(1)B(u)/2(1)A(g) order and energy gap appear to control the contribution of torsional relaxation to radiationless decay. Lowering the 1(1)B(u) energy as in Bz favors photoisomerization. Reversal of the 1(1)B(u)/2(1)A(g) order in PFH is accompanied by short τ(f) and small φ(f) and φ(tt→tc) values that suggest the presence of competing 2(1)A(g) → 1(1)Ag relaxation paths that are unproductive with respect to photoisomerization. We conclude that the Birks extension to diphenylpolyenes of the Orlandi-Siebrand cis-trans photoisomerization mechanism is not valid. Photoisomerization appears to occur in the 1(I)B(u) state, and we argue that this applies to t-St as well.

The small subunit processome in ribosome biogenesis­progress and prospects.

The small subunit (SSU) processome is a 2.2-MDa ribonucleoprotein complex involved in the processing, assembly, and maturation of the SSU of eukaryotic ribosomes. The identities of many of the factors involved in SSU biogenesis have been elucidated over the past 40 years. However, as our understanding increases, so do the number of questions about the nature of this complicated process. Cataloging the components is the first step toward understanding the molecular workings of a system. This review will focus on how identifying components of ribosome biogenesis has led to the knowledge of how these factors, protein and RNA alike, associate with one another into subcomplexes, with a concentration on the small ribosomal subunit. We will also explore how this knowledge of subcomplex assembly has informed our understanding of the workings of the ribosome synthesis system as a whole.

Protein-RNA contacts at crystal packing surfaces.

The crystal packing surfaces comprising protein-RNA interactions were analyzed for 50 RNA-protein crystal structures in the Protein Data Bank database. Protein-RNA crystal contacts, which represent nonspecific protein-RNA interfaces, were investigated for their amino acid propensities, hydrogen bond patterns, and backbone and side chain interactions. When compared to biologically relevant interactions, the protein-RNA crystal contacts exhibit similarities as well as differences with respect to the principles of protein-RNA interactions. Similar to what was observed at cognate protein-RNA interfaces, positively charged amino acids have high propensities at noncognate protein-RNA interfaces and preferentially form hydrogen bonds with RNA phosphate groups. In contrast, nonpolar residues are less frequently associated with noncognate interactions. These results highlight the important roles of both electrostatic and hydrogen bonding interactions, facilitated by positively charged amino acids, in mediating both specific and nonspecific protein-RNA interactions.

Crystal structure of a Cbf5-Nop10-Gar1 complex and implications in RNA-guided pseudouridylation and dyskeratosis congenita.

H/ACA RNA-protein complexes, comprised of four proteins and an H/ACA guide RNA, modify ribosomal and small nuclear RNAs. The H/ACA proteins are also essential components of telomerase in mammals. Cbf5 is the H/ACA protein that catalyzes isomerization of uridine to pseudouridine in target RNAs. Mutations in human Cbf5 (dyskerin) lead to dyskeratosis congenita. Here, we describe the 2.1 A crystal structure of a specific complex of three archaeal H/ACA proteins, Cbf5, Nop10, and Gar1. Cbf5 displays structural properties that are unique among known pseudouridine synthases and are consistent with its distinct function in RNA-guided pseudouridylation. We also describe the previously unknown structures of both Nop10 and Gar1 and the structural basis for their essential roles in pseudouridylation. By using information from related structures, we have modeled the entire ribonucleoprotein complex including both guide and substrate RNAs. We have also identified a dyskeratosis congenita mutation cluster site within a modeled dyskerin structure.