Volume 16 Issue 11, November 2009

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.

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.

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.

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.

Despite the importance of small RNA–mediated silencing, no structural information exists for complexes of known function. Using single-particle EM, the structure of the minimal functional unit for RNAi in humans (AGO2, Dicer and TRBP) is now presented.

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.

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.

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.

Studying protein interactions at membranes is a technical challenge. A quantitative approach to measuring the interaction between the apoptotic proteins tBid and Bcl using fluorescence correlation spectroscopy reveals that membranes have an active role in modulating BCL2 protein interactions.

Sialic acid is the most abundant terminal monosaccharide on mammalian cell surface glycoconjugates. The crystal structures of a mammalian sialyltransferase, that of porcine ST3Gal-I, in the apo form and bound to analogues of the donor and acceptor substrate are now described, providing insights into the catalytic mechanism and for inhibitor design.

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.

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.

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.