Research articles

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.

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 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.

Group II introns are retroelements that have invaded the genomes of many prokaryotes and eukaryotes. The structure of a self-spliced group IIC intron cocrystallized with ligated exons (the target substrate) reveals the metal ions that have a role in catalysis and the intron sequences that are important in exon recognition in group II introns.

Most known nucleotidyl-transfer enzymes use two metal ions for catalysis, but some enzymes use only one divalent cation in their active sites. A comparative analysis of previously available structural data reveals that the one-metal-ion enzymes use a similar mechanism to coordinate their single metal ion, which corresponds, functionally and structurally, to metal ion B in the two-metal-ion enzymes.

The tri-snRNP is the largest preassembled unit of the spliceosome, and its components are key to the splicing reaction. The overall structure and conformations of the yeast tri-snRNP are now analyzed by EM, and the general positions of some of its major protein components mapped.

The Ca²⁺ binding loops of the C₂A and C₂B domains of synaptotagmin-1 are known to be important in Ca²⁺-triggered neurotransmitter release. Biophysical and in vivo data now indicate that a basic patch on the opposite face of the C₂B domain has an equally crucial but Ca²⁺-independent role.

G9a is involved in gene silencing during early embryonic development, catalyzing the methylation of H3K9, which results in heterochromatinization, and also promoting methylation of DNA de novo. These two G9a activities are now dissected, and de novo DNA methylation is shown to occur via recruitment of Dnmt3a/3b and to be necessary and sufficient to prevent reprogramming.

The bacterial AAA+ ClpX unfolds substrates using the energy from ATP hydrolysis and delivers them to the associated protease ClpP. A loop with an aromatic-hydrophobic motif protrudes into the central pore of the ClpX hexamer and was known to be important for activity. Now mutational analysis using covalently linked subunits provides evidence that this loop actually grips the substrate and undergoes conformational changes to drive its translocation and unfolding.

The Fanconi anemia pathway is involved in the signaling of DNA damage. Several Fanconi anemia proteins have been identified, but how the pathway is actually activated was unclear. Now, work on chicken DT40 cells indicates that phosphorylation of FANCI at multiple sites triggers FANCD2 monoubiquitination and DNA-damage repair.

The voltage-sensor and RCK1 domains of BK channels act synergistically to sense electric and chemical signals. New data now indicate that the Mg²⁺-mediated interactions between these domains occurs between channel subunits, suggesting a structural arrangement that differs from other potassium channels.

The ATPase activity of AAA+ proteins is regulated by their interaction with ligands, but depending on the particular protein it can be stimulated or inhibited, and the mechanism for such control remained unclear. An analysis of previous structural data on various AAA+ proteins now reveals that a conserved glutamate residue adopts two conformations and and thus regulates the ATPase activity.

The effect of transcription factor affinity and accessibility on gene expression has been difficult to quantify and model. The contribution of both transcription factor binding affinity and nucleosomes to tuning and diversification of gene expression output is now quantitatively uncovered, and a model that can be applied to other eukaryotic gene expression systems generated.

The antiretroviral cytidine deaminase APOBEC3G inhibits HIV-1 replication, but the enzyme is targeted for degradation by HIV-1 Vif. Protein kinase A activity is known to be elevated in HIV-1–infected T cells. New data indicate that phosphorylation of APOBEC3G by protein kinase A renders the protein less susceptible to Vif-mediated degradation.

The Ink4a-Arf-Ink4b locus has a role in both senescence and tumorigenesis, and dysregulation can result in tumorigenesis. The Jhdm1b Jumonji family protein is now shown to be an H3K36 demethylase and is implicated in regulating cellular proliferation and senescence through p15^Ink4b.

The interferon regulatory factors (IRFs) are involved in the innate immune response and are activated by phosphorylation. The structure of a pseudophosphorylated IRF5 activation domain now reveals structural changes in the activated form that would turn an autoinhibitory region into a dimerization interface. In vivo analysis supports the relevance of such a dimer to transcriptional activation.

The spliceosome consists of five RNAs and more than 100 associated proteins. One of these, PRP8, is both one of the largest and most highly conserved spliceosomal proteins. Previous genetic and cross-linking data pointed to the importance of domain IV of PRP8 in spliceosome assembly and/or catalysis. Its structure has now been solved and found to contain an RNase H fold, suggestive of an RNA binding surface. The RNA binding data suggest that the PRP8 core recognizes, rather than a specific sequence, a structure resembling the four-helix junction proposed for the catalytically active U2/U6 snRNA interaction.

DcuS is a multidomain membrane sensor kinase important for Escherichia coli interactions with its environment. A new approach combining solution- and solid-state NMR with in silico modeling and mutagenesis has provided a three-dimensional model for most of this large membrane protein and suggests a mechanism for DcuS activation.