Volume 17 Issue 7, July 2010

The innate immune system relies on a series of specific receptors that recognize RNAs that might come from viruses. The structure of the C terminal domain of one such receptor, RIG-I, in complex with 5'ppp-dsRNA, now indicates the basis of recognition of the observable 5'pp-RNA, through interactions that are shown to be needed for tight binding and a cellular response to this trigger.

Type three secretion systems consist of a multisubunit protein complex that crosses the bacterial membranes and an extracellular needle-shaped structure. New data show that the needle protomer partially refolds from alpha-helix into beta-strand conformation to extend the needle from the distal end. The closely related flagellar system also grows at the tip, but it is not known whether protomer refolding is required for its assembly.

Using single molecule fluorescence resonance energy transfer it is now possible to follow the intersubunit conformation of the ribosome, in real time, as it moves from one codon to the next. The translating ribosome cycles between the locked state, where tRNA selection and peptide bond formation take place, and the unlocked state that facilitates translocation to the next codon. These experiments reveal the mechanism of antibiotic action and demonstrate the processivity of the ribosome as it elongates.

Retinoic acid receptor (RAR) can repress gene expression in the absence of ligand. The crystal structure of RARα LBD bound to a fragment of the corepressor NCoR and an inverse agonist now reveals the basis for such activity: a region that is helical in the agonist-bound state adopts a β-strand conformation and forms a β-sheet with the corepressor.

The ligand binding domain of nuclear receptor Rev-Erbα recruits corepressor NCoR to regulate target gene expression. Here the crystal structure of Rev-Erbα LBD in complex with a peptide from NCoR ID1 reveals formation of an anti-parallel β-sheet and also shows the corepressor a-helix in a registry different from those previously described in such complexes.

The HIV-1 Tat protein relieves a block to transcription elongation by recruiting positive transcription elongation factor b (P-TEFb) to an RNA element (TAR) on the viral mRNA, but why the HIV-1 promoter was inactive was unclear. Now it is shown that Tat binds to P-TEFb in its inactive 7SK snRNP form, and this complex is recruited to the HIV-1 promoter before transcription initiation, in a TAR-independent manner. The inhibitory 7SK snRNP complex is displaced once transcription begins, resulting in P-TEFb activation.

LeuT is a bacterial sodium/leucine symporter, related to human neurotransmitters targeted by antidepressant drugs. Now spin labeling and EPR analysis on the dynamics in the extracellular vestibule of LeuT reveal the conformational changes caused by Na⁺ and Leu binding that drive the transport cycle.

Single particle cryo-electron microscopy reconstructions of marine podovirus particles, together with cryo-electron tomography studies during the host infection process, have revealed structural features that suggest a mechanism whereby, upon binding to the Prochlorococcus host cell, the tail fibers induce a cascade of structural alterations of the portal vertex complex that triggers release of its genome.

Prokaryotic DegP functions as an ATPase-independent protease chaperone complex that is activated by oligomerization. Site-directed mutagenesis, combined with refolding and oligomerization studies of chemically denatured DegP, shows how substrates trigger the conversion of the resting conformation into the active conformation.

HtrA proteases can switch between active and inactive states to adjust their enzymatic activity to the needs of the cell. Structural and biochemical studies of bacterial DegP show that peptide binding to the PDZ domain of DegP induces the conversion of resting hexameric DegP into active higher-order DegP complexes. A specific protease loop in the 12- and 24-meric DegP particles senses the relocated PDZ domain, inducing conformational changes that ultimately result in protease activation.

How heterogeneous nuclear ribonucleoprotein (RNP) F regulates alternative splicing is unclear. Solution structures of three quasi RNA recognition motifs (qRRMs) bound to G-tract RNA now reveal an unusual binding mode, confirmed by mutagenesis and isothermal titration calorimetry analysis. Binding and splicing assays suggest that hnRNP F prevents RNA structure formation.

Evidence has indicated that non-coding RNAs are involved in gene repression by Polycomb complexes. MOV10, a putative RNA helicase, is now found to be associated with a human Polycomb protein and linked to Polycomb-mediated repression of the INK4a tumor suppressor, suggesting a role for RNA helicase activity in the silencing mechanism.

Hv1 voltage-gated proton channels lack a canonical pore domain and selectivity filter, suggesting the mechanism of permeation differs from other cation channels. Mutagenesis with conductance measurements coupled with molecular dynamics simulations now indicate that Hv1 has an internal water wire mediating selective H⁺ transport.

ARF proteins play key roles in the budding and maturation of eukaryotic transport vesicles. The high-resolution NMR structure of full-length yeast Arf1-GTP anchored to a membrane mimic reveals a flexible linker between the myristoylated N-terminal helix and the GTPase domain, which would facilitate interaction with multiple partners.

Herpesviruses contain two conserved fusion machinery components, gB and the gH–gL complex. The crystal structure of the gH ectodomain bound to gL from herpes simplex virus 2 forms an unusually tight complex that does not resemble any known fusogen. Instead, it is proposed that gH–gL may activate the fusogenic potential of gB by binding it directly.

The crystal structure of human DNA pol beta with DNA template and an incoming 8-oxo-dGTP forming a mutagenic pair with template base A is now presented, revealing the structural constraints within the polymerase active site that result in this mutagenic incorporation.

mTERF is a mitochondrial protein involved in transcription and replication pausing. The crystal structure of human mTERF bound to DNA now reveals the presence of nine repeats that form a left-handed solenoid, named the Zurdo domain.

Accessibility may play a key regulatory role affecting factors that bind to or target DNA. Using accessibility to DNA methyltransferases, the genome-wide profile of DNA accessibility in Drosophila melanogaster is presented and analyzed, indicating correlations with PcG repression, H4K16 acetylation and replication initiation.

A quantitative genetic interaction map, or E-MAP, of ∼400 genes involved in plasma membrane biology, in combination with triplet genetic motif analysis, has led to the identification of a new component of the eisosome, Eis1, links the poorly characterized EMP70 gene to endocytic and eisosome functions, and uncovers a link between Rom2—a GDP/GTP exchange factor for Rho1 and Rho2—and the regulation of sphingolipid metabolism.

Even though heterogeneous nuclear ribonucleoprotein C (hnRNP C) is among the most abundant proteins in the nucleus, its role in splicing has remained unresolved. Data obtained using a newly developed individual-nucleotide UV crosslinking and immunoprecipitation (iCLIP) technique, integrated with alternative splicing profiles, indicate how the position of hnRNP particles determines their effect on inclusion of alternative exons.