Research articles

Yeast possesses eight multisubunit vesicle tethering complexes, including TRAPPI and TRAPPII. The TRAPPII complex functions in the late Golgi and consists of all TRAPPI and three specific subunits. Purified native yeast TRAPPII is now characterized by single-particle electron microscopy, providing insights into the molecular basis for human pathologies resulting from defective TRAPP complex function.

The prokaryotic ubiquitin-like protein Pup is involved in the Mycobacterium tuberculosis proteasome pathway but is an intrinsically disordered protein, unlike eukaryotic Ub. Structural data now indicate that the Mycobacterium proteasomal ATPase (Mpa) binds Pup in an α-helical form, indicative of binding-induced folding of Pup upon reaching the proteasome in this system.

Understanding the genesis of histone may give functional insight and elucidate maintenance of post-translational histone modifications. Using biochemical purification and characterization from human cell fractions, the authors examine pre-deposition histone complexes, giving insight into processes from assembly through to nuclear import.

Nuclear HIV-1 mRNA export is mediated by cooperative Rev protein binding to the Rev response element (RRE) RNA, forming a complex recognized by the Crm1 host export factor. A structure of a Rev dimer now shows that the organization of Rev monomers within a dimer defines the RRE recognition interface, with the other side likely binding Crm1.

The crystal structure of the complex formed by the death domains from Fas and FADD at physiological pH is now solved, revealing a 5:5 complex that is supported by electron microscopy data. Along with mutagenesis and mass spectrometry analyses, the work provide insight into Fas mutations that cause autoimmune lymphoproliferative syndrome.

Electron cryo-microscopy images of actin filaments (F-actin) allow the visualization of different conformational states, which can be classified into different groups. Further analyses reveal the plasticity of the subdomain 2 region and suggest that missense mutations related to disease affect F-actin structural dynamics.

A complex substrate containing mobile double Holliday junctions is now used to show that yeast proteins Sgs1 (DNA helicase) and Top3 (topoisomerase) act together to dissolve the junctions and avoid crossing over; the protein Rmi1 stimulates this process.

Rad51 plays a central role in homologous recombination pathways. Now work with Xenopus laevis egg extracts shows that Rad51 prevents formation of DNA gaps at or behind replication forks, which are dependent on Mre11 nuclease activity.

The NoGo decay pathway involves the Dom34–Hbs1 complex and targets mRNAs that are stalled during translational elongation for cleavage. The structure of the Dom34–Hbs1 complex now reveals its structural similarity to release and elongation factor complexes. Upon binding Hbs1, Doom34 adopts a tRNA-like conformational change that suggests it would act to terminate translation.

Telomere shortening, senescence and aging are connected, but how the signal at shortening telomeres is transmitted to the cell more globally is unclear. H3 and H4 synthesis is now shown to be reduced as cell cultures age. This alters expression of Asf1, a histone chaperone, compromising the ability of aging cells to restore chromatin after replication and DNA. In this way localized effects at shortening telomeres can be propagated throughout the cell.

Tumor suppressor PALB2 is known to interact with BRCA1 and BRCA2, and to be required for the latter's localization to sites of DNA damage. Now PALB2 is shown to bind directly to DNA, to recombinase RAD51 and its accessory factor RAD51AP1. PALB2 also stimulates D loop formation by RAD51 in a synergistic manner with RAD51AP1.

Tumor suppressor PALB2 is known to interact with BRCA2 and promote homologous recombination in vivo. Now PALB2's activities have been studied, together with a BRCA2 chimeric protein, revealing that PALB2 binds D-loop structures, interacts directly with RAD51 and promotes strand invasion synergistically with BRCA2.

The 2009 pandemic flu influenza A H1N1 strain has caused great public health concern. Now the structure of H1N1 neuraminidase (NA) reveals that it lacks the characteristic additional cavity at its active site, known as the 150-cavity, found in all other known group 1 NAs.

Bacteriocins are toxins produced by bacteria to inhibit similar or related bacterial strains, and one such toxin, colicin E3, is known to target the ribosome by cleaving the 16S rRNA. The structure of the 70S ribosome in complex with the cytotoxic domain of colicin E3 now gives insight into the cleavage mechanism.

RecBCD is a bacterial complex that functions in repair of DNA breaks. The RecBC heterodimer has an ATPase motor (RecB) that translocates along ssDNA with a 3'->5' polarity. Now a second translocase activity is revealed in RecBC that moves the proteins along the opposite strand of a forked DNA at a similar rate.

Secretins are bacterial outer membrane proteins involved in different pathways for protein secretion or macromolecular complex assembly. Secretin can form a large oligomeric pore, whose opening needs to be carefully regulated. Now cryo-EM analysis of the Vibrio cholerae secretin GspD reveals a closed channel, with a constricted periplasmic vestibule, offering insight into the mechanism of GspD opening during protein secretion.

AZT is a nucleoside analog drug that inhibits HIV-1 reverse transcriptase (RT). The viral enzyme can acquire AZT resistance by mutations that enhance the rate of ATP-mediated excision of the incorporated AZT. Now structural work illustrates how the AZT resistance mutations create a high-affinity binding site for ATP and thus promote excision.

Ubr1 and Ubr2 are E3 ligases that target substrates by the N-end rule, and it is the UBR box that is needed for substrate recognition. The structures of the UBR boxes of human UBR1 and UBR2 show that they adopt a previously undescribed fold stabilized by zinc. One of the zinc-binding ligands is mutated in Johnson-Blizzard syndrome and leads to UBR box unfolding.

In the N-end rule pathway, the N-terminal residue of a protein is recognized by specific E3 ligases that promote its ubiquitination and proteasomal degradation. Now the structural basis for the recognition of N-terminal basic residues by the UBR box from yeast Ubr1 is solved. Together with functional analysis, the work reveals that the residue at position 2 of the substrate may influence the binding.

The C-terminal domain (CTD) of RNA polymerase II (Pol II) contains a number of repeats, phosphorylation of which influences RNA processing factor recruitment. Genome-wide CTD phosphorylation is now assessed and found not to be scaled to gene length. The kinases mediating these modifications are found not to alter Pol II distribution across a given gene uniformly, arguing that CTD phosphorylation is gene specific.