Volume 17 Issue 8, August 2010

A detailed quantitative model of signaling by IRE1 sheds light on the mechanism of its activation by endoplasmic reticulum stress and addresses a long-standing controversy in the field.

To cope with the life-threatening crisis of a DNA interstrand cross-link (ICL), human cells must invoke the Fanconi anemia (FA) DNA repair pathway. The FA pathway is a multistep repair process, requiring multiple nucleolytic incisions and translesion DNA synthesis. Recent work from four laboratories has identified a novel FA-associated nuclease, FAN1, that binds directly to monoubiquitinated FANCD2, resolving a decade-long puzzle regarding the function of this FANCD2 modification.

The HIV-1 Tat protein promotes viral transcription elongation by recruiting P-TEFb to RNA element TAR on the viral mRNA. Recent work from D'Orso and Frankel uncovers unexpected aspects of this process.

In order to get to their target sites, nearly all DNA binding proteins need to use some form of facilitated diffusion—for example, hopping, jumping, sliding and/or intersegmental transfer. Doing so can be made more difficult when nucleosomes are in their way. But is that really the case? Green and coworkers examine two different mismatch repair proteins using single-molecule microscopy and chromatin curtains and find that one can readily bypass the nucleosome by hopping over it while the other slides along until it is stopped in its tracks by the nucleosome. These types of studies can be used to distinguish between these different types of facilitated diffusion along chromatin.

Ubiquitin can form different polymeric chains, either linear or using each of its seven lysine residues. The best studied are Lys48 and Lys63 chains, but Lys11 chains have been shown to be abundant in yeast. Now a procedure to obtain large amounts of Lys11 chains is described, allowing the structural characterization of this linkage and the identification of a Lys11-specific deubiquitinase, Cezanne.

The Xist noncoding RNA is a key component in silencing of one X chromosome in female mammalian cells as part of the process of dosage compensation. Now a previously described repeat element in Xist, the A-repeat, is shown to bind the splicing factor ASF/SF2, and it is further shown that normal Xist processing may be involved in stochastically determining which X is inactivated.

The V3 crown region of HIV-1 gp120 is involved in binding to co-receptors CCR5 and CXCR4, and show high sequence variability. Structural work with cross-clade neutralizing antibodies in complex with V3 peptides now reveals conserved structural elements in this variable region, which are minimally affected by sequence variation.

Using expression of GFP-tagged SR proteins from stable transgenes, SRp20 and SRp75-associated mRNAs have now been identified, indicating that these factors interact with distinct functional transcripts that change upon neural differentiation.

DesT is a bacterial transcription factor that regulates targets which are in turn involved in controlling the unsaturated:saturated fatty acid ratio available for membrane lipid biosynthesis. The structures of DesT bound to various fatty acids now indicates the conformational changes involved in altering DNA binding site affinity, providing a structural basis for responding to changes in the ratio of unsaturated:saturated fatty acids.

In yeast, transcription of tRNA genes can act as replication fork barriers and lead to chromosome breakage, although the exact mechanism is not clear. Schultz and coworkers now show that checkpoint proteins specialized for signaling replication stress repress tRNA gene transcription during normal cell proliferation and in genotoxin-treated cells. Based on these findings they suggest that the fork-pausing activity of tRNA genes is regulated by the checkpoint system that has evolved to control replication.

Mdm2 negatively regulates tumor suppressor p53 via binding to the transactivation and the DNA-binding domains of p53. Now work reveals a novel interaction between the N-terminal domain of Mdm2 and the extreme C-terminal region of p53, a region that bears the sites of many post-translational modifications that inhibit the Mdm2-p53 interaction.

Tripeptidyl peptidase II is an eukaryotic serine protease that forms huge, spindle-shaped homopolymeric complexes, whose building block is an enzymatically inactive dimer. Now a combination of cryo-EM and crystal structure analysis of Drosophila TPPII allows a view on dimer organization and polymer architecture assembly, as well as insight into the mechanism of activation.

In some organisms, miRNA-mediated regulation leads to RNA-dependent RNA polymerase based amplification, involving generation of secondary siRNAs that target the same transcript, but why this happens for some miRNAs and not others has been unclear. It is now shown that Arabidopsis miRNAs that trigger this amplified response tend to be 22 nt rather than 21 nt in length, and that generation of 22 nt miRNAs this length seems to depend on the foldback structure of the precursor.

Bacterial pathogens can modify host cell proteins and interfere with their function. For example, bacterial enzymes can adenylylate Rho GTPases, inhibiting their interaction with downstream effectors. Now the crystal structure of the Fic domain from Histophilus somni adenylyltransferase IbpA in complex with target Cdc42 reveals the basis for their tight interaction and for Cdc42 modification.

let-7a, a miRNA involved in differentiation, was known to be regulated by Lin-28. Now work reveals another factor that could control let-7a levels in vivo: hnRNP A1 binds to unprocessed pri-let-7a and inhibits its processing by Drosha. The inhibitory effect of hnRNP A1 is further shown to occur via antagonizing the binding of KSRP to pri-let-7a, which is known to promote biogenesis.

Multi-ion pores produce a lower conduction rate when faced with a mixture of two conducting ions than with either single one, in what is called the anomalous mole fraction effect. Now high-resolution structures of the bacterial K⁺ channel MthK pore, together with functional studies, reveal that K⁺ occupancy of specific sites in the selectivity filter can block the passage of Na⁺ ions.

Previously, the molecular chaperone Hsp90 has been shown to copurify with RISC (RNA-induced silencing complex), involved in small RNA-mediated silencing. It is now shown that Hsp90 is needed for AGO2 to be loaded with a siRNA duplex by the RISC-loading complex suggesting a model where it is involved in modifying AGO2 conformation.

The MSL complex is conserved and in Drosophila melanogaster is involved in spreading of gene activation on the male X chromosome. Structural and functional analyses of the MSL3 chromodomain now indicate that DNA binding promotes methylated histone tail binding, suggesting coordinated binding that is here proposed to promote cross-nucleosome interaction in an array.

Recently described tiny RNAs (tiRNAs) are derived from sequences immediately downstream of transcriptional start sites. Here a second class of nuclear ∼17–18 nucleotide small RNAs is described and found to map to the splice donor site of internal exons.