Articles in 2009

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 2009 Nobel Prize for Physiology or Medicine goes to telomerase researchers, the Lasker Award to nuclear reprogramming pioneers, and crystallographers are awarded the Chemistry Nobel once again.

Influenza virus binding to host cells and neutrophil trafficking to sites of inflammation are diverse aspects of biology mediated by receptor recognition of sialic acids that terminate glycans on cell surface glycoproteins and glycolipids. The first crystal structure of a mammalian sialyltransferase provides insights into the biosynthesis of the rich spectrum of sialic acid–containing glycans in the mammalian glycome.

A relatively simple but powerful method to measure RNA polymerase II transcription elongation as well as co-transcriptional RNA splicing rates at many genes in vivo is described in this issue. The results demonstrate a rather uniform, and high, elongation rate at large human genes and co-transcriptional pre-mRNA splicing of both U2- and U12-dependent primary transcripts.

A recent study has put together the three-dimensional structures of proteins involved in the central metabolism of one organism, providing insight into the evolution of metabolic networks.

How does a transcription factor select a specific DNA response element given the presence of degenerate sequences? To date, this question has largely been viewed from the standpoint of DNA sequence variability and transcription factor binding affinity under steady-state conditions. Here we propose that to address this problem, it is also necessary to account for fluctuating cellular conditions. These lead to dynamic changes in the ensemble of protein (and DNA) conformational states via allosteric effects.

Phage lysis requires the enzymatic degradation of the host cell wall by a phage-encoded lysin. Secretory endolysins are inactive at the membrane but active in the cytoplasm, and the signal-anchor-release (SAR) domain is shown to be essential for regulating its effects. The structure of coliphage 21 lysozyme explains how this endolysin is controlled.

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 poxvirus 2L protein binds tumor necrosis factor-α (TNFα). Structural data now indicate that 2L interacts with TNFα at a site overlapping with that for its receptor, arguing for the basis of inhibition of receptor interaction and TNFα-induced immune responses.

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.

Screening a library of artificial zinc fingers for transcriptional activators in mammalian cells can be laborious. Now a strategy is described that couples the screening to production of retroviral particles that will carry the positive clones, allowing iterative rounds of selection.