Volume 18 Issue 8, August 2011

The RING protein RBX-1 is implicated in both NEDDylation and ubiquitylation reactions. In this issue, new structural analysis reveals how conformational flexibility of the RBX-1 linker allows for a marked reorientation of the CUL1–RBX1 complex to facilitate transfer of NEDD8 or ubiquitin by closing the gap between the E2 catalytic site and the substrate.

Alterations in DNA and histone modifications are known to occur during development and in disease. The changes that occur during TGF-β–triggered epithelial-to-mesenchymal transition are now examined on a global scale. DNA methylation remained relatively stable, but major changes in histone modifications, dependent on the histone demethylase Lsd1, were observed, particularly in large, organized heterochromatic Lys9-methylated regions.

Rubisco plays a central role in photosynthetic carbon fixation. Form I Rubisco is composed of eight large (RbcL) and eight small (RbcS) subunits. The assembly of the RbcL octamer requires dedicated chaperone RbcX. Now the crystal structure of the RbcL core bound to RbcX reveals how the latter assists assembly of the octamer, and has implications for the role of RbcS.

Using purified chromatin rings, what defines a promoter is now explored. Exposure of purified templates to the RSC ATP-dependent remodeling complex leads to Translocation of promoter rather than open reading frame nucleosomes. Together with analysis of the effect of histone deacetylase on this process, this argues that nucleosomes define promoter-specificity.

WIF-1 inhibits Wnt signaling by binding Wnt ligands. Structural and biochemical analysis of WIF-1 shows the EGF-like domains wrapping back to contact the ligand-binding WD domain, which also binds a phospholipid near the interaction site for Wnt ligands. The tail of EGF-like domains also harbors a proteoglycan binding site, indicating that all domains of WIF-1 contribute to the regulation of Wnt signaling in vivo.

The condensin complex contributes to the compaction of eukaryotic chromosomes during mitosis and meiosis. How condensin organizes and compacts chromatin is now investigated by the introduction of specific cleavage sites into yeast condensin subunits. The results indicate that condensin forms a ring-like structure that encircles DNA.

A previously uncharacterized member of the I-BAR subfamily of BAR-domain proteins, Pinkbar, is expressed in epithelial cells, where it stabilizes planar membrane sheets. Structural, biochemical and mutagenesis analyses suggest a molecular mechanism for this novel membrane-deforming activity.

Plasmodium parasites use Duffy-binding proteins (DBPs) to invade erythrocyte precursor cells via binding to host protein DARC. Now this interaction is examined by structural and functional work on Plasmodium vivax DBP, revealing that it binds to DARC as a dimer and providing insights into host protective responses and immune evasion by the parasite.

Previous models of γ-tubulin ring complex (γTuRC) assembly implied that γ-tubulin complex proteins (GCPs) 4–6 serve as a scaffold for arranging multiple γ-tubulin small complexes (γTuSCs) into large γTuRCs. The crystal structure of human GCP4 represents a prototype for all GCPs and can be precisely positioned within γTuSC, providing a new framework for understanding γTuRC formation.

Cdc13 forms a complex with Stn1-Ten1 that caps budding yeast telomeres; Cdc13 also recruits the telomerase complex. Indeed, Cdk1 phosphorylates Cdc13 and this favors the Cdc13- Est1p, at the expense of Cdc13 association with Stn1, which inhibits telomerase action at telomeres. Now a second, independent mechanism to control Cdc13-Stn1 interaction is revealed: sumoylation of Cdc13 promotes its interaction with Stn1 and prevents telomerase activity.

Structural studies of complexin bound to a mimetic of a prefusion SNARE complex provide insight into how complexin 'clamps' SNARE complex assembly, thereby inhibiting membrane fusion. While the central helix of complexin is anchored to a SNARE complex, its accessory helix extends away and bridges to a second SNARE complex, generating a zigzag array incompatible with fusion.

Comparison of the prefusion and postfusion structures of complexin associated with SNAREs reveals a conformational switch in complexin, which is triggered by the zippering of three key Asp residues in the “switch” region of v-SNAREs into t-SNAREs. This causes complexin to move its accessory helix, thereby releasing the clamped state. This switch is triggered when the calcium sensor synaptotagmin binds calcium ions.

The SNARE-binding protein complexin (CPX) can both facilitate and inhibit membrane fusion, which has been puzzling. Using the Surface Forces Apparatus (SFA) system to obtain distance and interaction measurements of SNARE complexes assembling between bilayers demonstrates that CPX stabilizes an intermediate energetic state in which the SNAREpins are half-zippered, explaining activation and inhibition as the dual consequences of this single mechanism of action.

RING E3 ligases mediate transfer of ubiquitin-like proteins from an E2 ligase to a substrate, but how this occurs is a long-standing mystery. Docking E2-RING structures onto a new crystal structure of the C-terminal domain of the E3-RING CUL1 in complex with the RBX1 RING protein now shows how a conformational change in RBX1 allows for the transfer by closing a gap between CUL1 and the E2.

The location of DNA breakpoints associated with somatic copy-number alterations in cancer genomes is analyzed, revealing an enrichment of sequences with propensity to adopt G-quadruplex conformation, often near transcription start sites, and a correlation with hypomethylation. The analysis indicates that G4 formation contributes to cancer genome instability.

Based on genome wide localization of initiating RNA polymerase II, general transcription factors and epigenetic marks in mouse thymocytes, transcription initiation platforms (TIPs) are evidenced, both at promoters and enhancers, as features able to promote tissue-specific expression.