Articles in 2008

Channel gating in tetrameric cation channels occurs as structural transitions that involve straightening and bending of inner helices at a conserved glycine residue. Structural representatives of these closed and opened states have come from crystal structure of KcsA and MthK, respectively. The structure of NaK in the open state, when combined with a previously determined structure of NaK in the closed state, allows the detailed analysis of channel gating within the same channel.

The negatively coupled movement of the activation and inactivation gates of Kv channels regulates ion flow across membranes in response to changes in membrane potential. Although they share a common pore design, the K_2P leak channels are open at all potentials and are believed to act only through a slow inactivation gate. New data reveal that, similarly to the Kv channels, leak channels possess a constitutively open lower activation gate. Positive coupling between the two gates ensure constant leak currents across the membrane.

Although a number of DExD/H-box family RNA-dependent ATPases are required in the spliceosome, their regulation is unclear. The Brr2-dependent unwinding of U4/U6 snRNAs, a key step in splicing, is now shown to be promoted in a purified system by the C-terminal region of Prp8, an enigmatic spliceosome component associated with a dominant form of retinitis pigmentosa.

Ion selectivity is as important to ion channel function as channel gating. Much of what is currently known about selectivity comes from structural studies of K⁺-selective channels. Detailed structural analysis of the ion binding sites in the NaK pore provides a first look at the geometry and ionic selectivity in a Na⁺-permeable channel and may provide a basis for understanding permeation through nonselective cation channels.

The transcription factor and tumor suppressor p53 is central to many stress responses and is the target of multiple regulators. The regulatory subunit of PI3 kinase, p85α and CDC42 are now both found to be targets of the miR-29 microRNAs. As p85α and CDC42 are repressors of p53, these miRNAs indirectly activate p53 and thus apoptosis.

Nucleosome stability can influence gene expression and is regulated by nucleosome-positioning sequences, histone chaperones, remodeling complexes, post-translational modifications and histone variants. Now, histone H3 tail clipping has been added to the list. Kouzarides and co-workers have identified a serine endopeptidase in yeast that cleaves H3 after Ala21 and shows a preference for H3 tails with repressive modifications. In vivo, this occurs at the promoters of induced genes and precedes histone eviction when genes become fully active.

Nonsense-mediated decay (NMD) is an mRNA surveillance process that targets transcripts containing a premature stop codon for degradation. Evidence now suggests that mammalian NMD involves an endonucleolytic cleavage that is mediated by human SMG6.

The exosome is a large complex with cellular functions including exoribonucleolytic mRNA degradation and processing of a number of RNAs including small nuclear RNAs, small nucleolar RNAs and ribosomal RNAs. The yeast exosome is now shown to possess an unexpected endoribonucleolytic activity, and the essential Csl4 subunit is shown to contain a domain involved in mRNA decay. This suggests that particular domains in the complex have specialized roles.

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.

PKR responds to viral infection and shuts down translation through phosphorylation of eIF2α. PKR is found to have rapidly evolved in comparison to other kinases targeting the same substrate across a broad range of vertebrate lineages. Some positively selected residues are found to confer resistance to poxviral inhibitors that mimic substrate. In addition, substituting a single residue in mouse PKR with the corresponding residue under positive selection in human PKR renders mouse PKR more resistant to K3L and vice versa, providing evidence for species-specific selection driven by beneficial mutations.

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.

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.

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 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.

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.

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.

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.

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.