Volume 20 Issue 2, February 2013

Self-assembly of the COPII coat proteins Sec13 and Sec31 creates a spherical cage that drives vesicle formation from the endoplasmic reticulum. A multipronged approach now provides a convincing pseudoatomic model of the assembled cage that sharpens our understanding of the architecture, contact sites and flexibility of this remarkable structure.

Direct time-resolved single-molecule observations of promoter search by Escherichia coli RNA polymerase indicate no evidence of facilitated diffusion, according to a new report.

A biochemical approach is used to understand how the ULK1 complex integrates signals from ATG proteins during autophagy. The interaction between ULK1-associated protein FIP200 and ATG16L1 of the ATG5 complex is revealed. This interaction is important for autophagy induced by amino acid starvation but not by glucose deprivation.

Studies of the hepatitis C virus internal ribosome entry site (IRES) mechanism have focused on how IRES assembles an 80S ribosome at the start codon. Structural and functional analyses demonstrate that mutations of an IRES domain that docks in the 40S subunit's decoding groove cause conformational changes and that the mutated domain decreases IRES activity by inhibiting ribosome translocation and, thereby, translation elongation.

In order to locate the voltage-dependent gate in the MthK potassium channel, intracellular quaternary ammonium blockers are used for electrophysiology and crystallographic analyses. The data conclusively show that the inactivation gate is located at the selectivity filter and not at the cytoplasmic bundle crossing entrance.

The COPII cage, formed by Sec13 and Sec31, organizes other proteins into a lattice on the endoplasmic-reticulum membrane and is involved in transporting cargo from the endoplasmic reticulum to the Golgi apparatus. A combination of cryo-EM and H/D-exchange MS analyses leads to a 12-Å-resolution model of the COPII cage, yielding insight into its architecture and assembly.

The transcription machinery must locate specific promoter sequences among a vast excess of nonspecific DNA. Real-time single-molecule experiments with E. coli RNA polymerase, combined with theoretical calculations, suggest that facilitated diffusion does not contribute to promoter targeting at physiologically relevant protein concentrations but that instead the promoter search is dominated by three-dimensional diffusion.

Histone deacetylase 3 (HDAC3) has low enzymatic activity in vitro unless associated with the nuclear receptor corepressors NCOR1 and SMRT through the deacetylase activation domain (DAD). Mice lacking functional DADs in both NCOR1 and SMRT are born and reach adulthood but lack HDAC3 activity, whereas mice lacking HDAC3 are embryonic lethal, which suggests an essential deacetylase-independent function of HDAC3.

The protein α-catenin has an essential role in stabilizing cell-cell junctions, and it is involved in multiple interactions with other cytoskeleton proteins. The crystal structure of nearly full-length human α-catenin now reveals a handshake-like dimer with the two monomers in distinct conformations. This dimer asymmetry is important for F-actin binding and for interactions with activated vinculin.

In budding yeast, EcoI acetylates cohesin to establish sister chromatid cohesion in S phase. EcoI is subsequently modified by the ubiquitin E3 ligase SCF-Cdc4 and rapidly degraded. New work shows how sequential phosphorylation by three independent kinases generates a binding site for SCF-Cdc4 to promote EcoI degradation, thereby coupling EcoI activity, and thus sister chromatid cohesion, to the cell cycle.

The MSL complex acts on chromatin to and is required for X-chromosome dosage compensation. Chromatin-interacting protein MS (ChIP-MS) is now used to identify proteins and histone modifications interacting with the MSL complex, leading to the identification of CG4747. Functional analysis indicates that this protein is involved in targeting MSL to H3K36me3-containing chromatin.

GltPh is a homotrimeric Na+-coupled aspartate transporter that belongs to the glutamate transporter family. The conformational changes that occur during GltPh transport are now directly observed using EPR spectroscopy, revealing that the transporting domains sample multiple states, regardless of the presence of substrate or ions.

The sodium and aspartate symporter Glt_Ph mediates transport by alternating between outward-facing and inward-facing states. These conformational changes are now probed using double electron-electron resonance (DEER) spectroscopy. The data show that Glt_Ph samples both states with similar probabilities, and that each protomer in the Glt_Ph homotrimer behaves independently of the others.

The ISWI chromatin remodelers interact with extranucleosomal DNA to mediate nucleosome positioning. A new study now shows that the conserved SLIDE domain in the Isw2 subunit, which binds linker DNA, facilitates unidirectional linker DNA movement into nucleosomes. These findings suggest that the SLIDE domain functions in conjunction with the ATPase domain to mobilize nucleosomes.

Crystal structures of HIV-1 reverse transcriptase (RT) bound to an RNA/DNA hybrid (without any cross-linking) and in the presence of non-nucleotide RT inhibitors (NNRTIs) nevirapine and efavirenz are now reported. The structures show the RNA/DNA hybrid in a previously unseen conformation with ready access to the RNase-H active site of RT.

Rare or nonoptimal codons that cause ribosomes to pause have been suggested to be important determinants of cotranslational folding. A revised translational efficiency scale, which considers tRNA abundance as well as codon usage and codon-tRNA interaction, now suggests a correlation between optimal or nonoptimal codon usage and secondary structure of the nascent polypeptide.