Research articles

On specific DNA sequences in vitro, a nucleosome is a polar barrier to RNA polymerase II (Pol II). Further analyses of the sequences underlying this barrier effect now indicate the formation of a loop that would preserve the position of the nucleosome on the DNA, while allowing passage of Pol II.

Pre-mRNA splicing is catalyzed by the spliceosome in a two-step reaction. Both catalytic steps have now been reconstituted using purified, defined components. This system identifies a role for Cwc25 in the first step of splicing and allows future detailed mechanistic analyses of splicing.

Condensins are protein complexes essential for eukaryotic mitosis and whose chromosome association is regulated by phosphorylation and dephosphorylation events. Now protein phosphatase PP2A is important for association of condensin II to mitotic chromosomes, but its catalytic activity is not required.

H2A.Z is implicated in genome stability across species. Acetylation of this histone variant in S. pombe is now found to be involved in maintaining condensed chromosomes during mitosis, with premature dissociation of condensin occurring in its absence.

The bacterial transcriptional termination factor Rho is a hexameric helicase that tracks along RNA and dissociates DNA-RNA hybrids. Here the activity of Rho is examined using nucleotide analog interference mapping, revealing that the helicase takes large, 7-nt steps, triggered by contacts with 2′OH in the tracked RNA substrate.

Inward-rectifier K⁺ channels respond to voltage via blockage by intracellular polyamines. How these blockers work is not entirely clear. Now a crystal structure of the cytoplasmic portion of Kir3.1 reveals five ion sites, and functional analyses indicate these ions are displaced by spermine binding.

The eukaryotic group II chaperonin TRiC can block polyQ tract aggregation, present in proteins such as Htt. Here the TRiC-Htt interaction is examined using in vitro and in vivo experiments, revealing that TRiC does not physically block the polyQ tract, but rather sequesters a short N-terminal sequence that promotes the amyloidogenic conformation.

The GEMM riboswitch is conserved in diverse bacteria and recognizes the second messenger c-di-GMP which mediates many processes, such as the transition between sedentary and motile behavior. The structure of the GEMM riboswitch with ligand now elucidates ligand recognition and specificity.

The crucial ion-binding events that drive H⁺/Cl⁻ exchange in the bacterial transporter CLC-ec1 are now probed by isothermal calorimetry and detergent-solubilized proteins. The results indicate that transport via CLC channels have an inherent directionality, rather than being driven by an electrochemical gradient.

Some proteins move along DNA, searching for a specific target. Now these proteins are shown to follow a helical path, i.e., they rotate while sliding, hence maintaining a specific orientation to the DNA helix. This is accomplished by tracking single molecules of labeled human oxoguanine DNA glycosylase 1, alone or bound to a bulky streptavidin moiety, and calculating their diffusion constants.

c-di-GMP is a bacterial second messenger implicated in processes such as biofilm formation and switches between motile and sedentary lifestyles. The structure of the c-di-GMP–binding GEMM riboswitch is now presented with ligand and the large conformational changes between ligand-bound and unbound forms analyzed by small-angle X-ray scattering.

Influenza B virus is responsible for about half of all the seasonal flu cases. The integral protein BM2 oligomerizes and forms a pH-activated proton channel that is essential for viral entry into host cells. The solution structures of the membrane-embedded chain domain and the C-terminal cytoplasmic domain reveal significant differences from the AM2 protein of influenza A virus and explain antiviral drug resistance.

PYL-PYR proteins were recently described as receptors for the plant hormone abscisic acid (ABA) and as inhibitors of the phosphatases ABI1 and ABI2 in the presence of ABA. The crystal structures of PYL2 in its apo and ABA-bound forms and of the ternary complex PYL1–ABA–ABI1 have now been solved, providing insight into ABA sensing and signaling.

The U2–U6 snRNA complex is argued to adopt different conformations during splicing. Using single-molecule FRET, the dynamics of an RNA representing U2–U6 are now probed and related to splicing steps through probing of mutations previously linked to this process.

Remodeling complexes can affect DNA transactions by altering chromatin, thus affecting accessibility of DNA. The INO80 remodeling complex has previously been implicated in replication and analyses now argue that it specifically acts through the DNA damage tolerance pathways that resolve recombination intermediates at impeded replication forks.

The nuclear pore complex (NPC) is key to nucleocytoplasmic transport and is based on a stable scaffold involving multiple heptameric Y complexes. The structure of the Nup84–Nup145C–Sec13 component of the Y complex now indicates that the Nup84–Nup145C and Sec31 homotypic interface in the COPII lattice are analogous, suggesting a lattice NPC model.

The SARS coronavirus protein nsp1 can suppress host gene expression at a post-transcriptional level, with previous work showing a reduction in mRNA abundance. Now a direct effect on protein synthesis is revealed, as nsp1 modifies transcripts and also inactivates the 40S ribosomal subunit.

Hsp90 is a molecular chaperone essential for the maintenance of cellular homeostasis. Now multiple approaches are used to study the deleterious effects of mutations in β-strand 8 of the N domain of Hsp90 and the role of the charged linker between N and M domains in mediating such effects.

miRNAs can repress transcripts through decay. Mammalian miRNA-mediated deadenylation is now shown to involve both the Pan2–Pan3 and the Ccr4–Caf1 deadenylases. Such deadenylation can be triggered by tethered Ago or TNRC6 and is followed by decapping of the reporter.

Rates of in vivo transcription have proven hard to pin down, especially across long mammalian genes that can contain lengthy introns. Using DRB inhibition followed by release, the rates of transcription of multiple human genes are now measured and splicing rates of both U2- and U12-dependent introns are assessed.