Volume 15 Issue 12, December 2008

Analysis of in vivo and in vitro interactions between chaperonins and the whole spectrum of potential cytoplasmic substrates helps answer the vexed question of substrate specificity in the TRiC system.

New work suggests that Prp8, a highly conserved protein in the heart of the spliceosome, both orients the substrate and participates in catalysis.

The N-end rule relates the in vivo half-life of a protein to the identity of its N-terminal residue. The N-end rule pathway, ubiquitin-dependent in eukaryotes, is also present in prokaryotes, which lack the ubiquitin system. An illuminating new study presents the crystal structure of a bacterial N-end rule recognition component in complex with a peptide containing a cognate degradation signal.

The tumor suppressor protein 53BP1 decorates DNA damage sites and is instrumental for nonhomologous end joining. Evidence that 53BP1 facilitates synapsis of DNA ends by modulating chromatin dynamics reveals a hitherto unanticipated strategy for joining distant ends.

A recent report shows that several 'poly-ADP-ribose-polymerases' may function exclusively as a family of endogenous mono-ADP-ribosyltransferases, providing a new, molecularly less complex and broadened cellular role for this elusive post-translational modification.

Oxidative stress can lead to cellular senescence, in a p53-dependent pathway. Bach1, a transcription factor that regulates the response to oxidative stress, is now shown to inhibit senescence induced by high oxygen concentrations or by Ras. Bach1 is recruited to a subset of p53 target genes and contributed to impeding p53 action by promoting histone deacetylation.

The interactome of eukaryotic chaperonin TRiC/CCT is identified through a genome-wide approach, revealing an enrichment in large, multidomain proteins, or components of multimeric complexes, rich in hydrophobic sequences and with high β-sheet propensity. Thus, TRiC substrates are slow-folding proteins with complex topology, which are likely to be more prone to aggregation.

Understanding the kinetics of gene expression involves accurate quantitation of gene expression. This is now undertaken by quantifying nascent-RNA levels and relating this indication of transcriptional activity to mRNA abundance in single yeast cells. Combining these measurements with computational modeling indicates that the tested yeast housekeeping genes are probably expressed through single initiation events, whereas a SAGA-transcribed gene shows behavior consistent with transcriptional bursting.

The ATP-dependent chromatin-remodeling complexes are involved in repositioning, evicting and restructuring nucleosomes. The EM reconstruction of the RSC remodeler in complex with a nucleosome gives structural insights into remodeling.

Emerging evidence suggests that ESCRT proteins, well characterized in their role in multivesicular body trafficking, contribute to various cellular processes including cytokinesis. Structural and functional analyses indicate that the ESCRT-III protein CHMP1B promotes the midbody localization of spastin, a microtubule-severing protein required for membrane abscission.

The replication of many retroviruses depends on interactions between the viral TAR RNA element and Tat as well as Cyclin T1, a component of the cellular transcriptional elongation complex. Structural insights into this ternary complex now suggest that the equine infectious anemia virus TAR is engaged by both proteins with Tat in a helical conformation and that binding depends on flipping out specific bases in the TAR loop region.

The IpaH family of Shigella virulence factors are E3 ubiquitin ligases that may target host proteins. Structural and functional characterization of IpaH1.4 and IpaH9.8 reveal a unique C-terminal catalytic domain that seems to have HECT-like E3 ligase activity. Together with an accompanying publication from Zhu et al., these data suggest that the IpaH proteins constitute a new category of ubiquitin ligases.

The IpaH proteins from Shigella show ubiquitin-ligase activity but lack obvious sequence similarity to HECT- or RING-type ubiquitin ligases. The crystal structure of IpaH3 reveals a two-domain protein with HECT-like catalytic activity mapped to a C-terminal domain of novel fold. These findings suggest that IpaH proteins represent a new family of ubiquitin ligases, a conclusion supported by results from a related study by Tyers et al.

Bag2 acts as a nucleotide-exchange factor for Hsp70 and also binds misfolded substrates. Now structural work reveals that Bag2 promotes nucleotide exchange via a mechanism distinct from other Hsp70 nucleotide-exchange factors, and mapping of the binding sites for client peptides suggests how Bag2 assists Hsp70 in processing misfolded proteins.

The MSL complex is involved in upregulation of genes on the Drosophila melanogaster male X chromosome during dosage compensation. Using mutagenesis, the MSL3 chromodomain is now shown to interact with methylated histone H3K36 and is implicated in the spreading of the dosage-compensation complex from its initial binding sites, defining a process of spreading by activation complexes analogous to that defined for silencing complexes.

F1 ATPase contains three catalytic β subunits that hydrolyze ATP, causing the central γ subunit to rotate. Now, using fluorescent tags, conformational changes in β and rotation of γ are observed simultaneously within the same complex, allowing the motions in β to be correlated with catalytic events and ultimately rotation.

Pirh2 is one of several ubiquitin ligases known to modify and negatively regulate p53. Solution studies reveal the structures of the three Pirh2 domains and indicate that the C-terminal domain of Pirh2 interacts with the p53 tetramerization domain. Additional data suggest that Pirh2 preferentially modifies the tetrameric, transcriptionally active form of p53 for proteasome-mediated degradation.

Muscleblind-like (MBNL) proteins have been implicated in alternative-splicing regulation during development, and altered levels of these proteins have been implicated in myotonic dystrophy. The structure of the MBNL1 zinc finger domains in complex with RNA indicates how the target sequence is recognized and suggests that an antiparallel arrangement of the zinc fingers causes a trajectory reversal in the pre-mRNA target. The potential role of such generated looped segments in alternative splicing is discussed.