Articles in 2011

Restoration of p53 activity is a promising chemotherapeutic approach, and because of the high binding affinity between HAUSP, MDM2 and p53, blocking HAUSP activity should have the net effect of robust p53 stabilization. HAUSP is inhibited by belt-like binding of vIRF4 from Kaposi's sarcoma–associated herpesvirus. Two peptides derived from vIRF4 can additively inhibit HAUSP, leading to p53-dependent cell cycle arrest and xenograft tumor regression.

SRP-type GTPases deviate from other GTPases in that they are not activated by GTPase-activating proteins (GAPs). New studies show that the MinD-type protein YlxH activates the SRP-GTPase FlhF, which is involved in flagellar biosynthesis. The crystal structure of the Bacillus subtilis FlhF–effector complex reveals the mechanism of activation, the general concept of which may also apply to RNA-mediated activation of the SRP-GTPases Ffh and FtsY.

Co-transcriptional splicing has been seen in lower eukaryotes as well as for a few mammalian genes, but the extent to which it affects mammalian gene regulation has been unclear. RNA sequencing now shows that co-transcriptional splicing is widespread in human cells and particularly abundant in the human brain.

The mammalian mitochondrial transcription factor A (TFAM) is encoded in the nucleus and imported into mitochondria, where it functions as an activator of mtDNA transcription and packages mtDNA into DNA-protein aggregates called mitochondrial nucleoids. Two studies in this issue reveal that TFAM shapes mtDNA into a sharp U-turn, providing a molecular mechanism for its dual roles in the expression and maintenance of mtDNA.

The microRNA-induced silencing complex (miRISC) protein TNRC6 (also called GW182) uses dispersed tryptophan-containing repeats in unstructured regions to recruit the CCR4–NOT nuclease complex leading to mRNA deadenylation and inhibition of translation initiation according to new research.

The eukaryotic proteasome is composed of a regulatory particle and a core particle. Now protein cross-linking is used to map the contacts between regulatory particle and core particle subunits, revealing that some Rpt subunits engage with the core particle in a dynamic fashion that is regulated by nucleotide binding and hydrolysis.

The mitochondrial transcription factor Tfam has a role in organizing the mitochondrial genome, in addition to its transcriptional function. Structural studies of human Tfam in complex with a mitochondrial DNA promoter show that Tfam imposes a U-turn on the DNA similarly to the unrelated HU family of proteins, which play analogous architectural roles in organizing bacterial nucleoids.

The human mitochondrial transcription factor TFAM is essential for DNA packaging as well as transcription. X-ray analysis of TFAM in complex with a mitochondrial promoter reveals that TFAM induces a 180-degree bend in the DNA, which creates an optimal DNA arrangement for transcription initiation, while facilitating DNA compaction of the mitochondrial genome elsewhere.

During protein synthesis, mRNA and tRNAs are iteratively translocated by the ribosome, but which molecular event is rate limiting for translocation has been unknown. Kinetics analyses now reveal that disruption of the interactions between the A-site codon and the ribosome accelerates translocation, suggesting that mRNA release from the decoding center of the ribosome is the rate-limiting step.

Tubulin undergoes cycles of removal or addition of a C-terminal tyrosine residue to the C-terminus of α-tubulin within the α-β heterodimer. Crystal structures of tubulin tyrosine ligase (TTL), along with SAXS and functional analyses, reveal that TTL interacts with the C-terminal tail of α-tubulin and also with its longitudinal face, preventing incorporation of the α–β tubulin dimer into the microtubule lattice.

Dimerization, ligand-binding and co-confinement are all expected to contribute to erbB1 signaling, but the level of their contribution has not yet been fully appreciated. Two-color quantum-dot tracking in live cells now shows that ligand-binding (two ligands with two receptors) stabilizes erbB1 dimers, whereas actin networks influence dimer mobility and promote repeated encounters between erbB1 monomers.

TiaS catalyzes the transfer of agmatine onto the first position cytidine of the tRNAIle2 anticodon in archaea, ensuring proper translation of the matching codon. Now the crystal structures of the TiaS–tRNAIle2 complex with ATP, or with AMPCPP and agmatine, reveal a novel kinase domain and show how TiaS selects the correct tRNA while segregating the target cytidine until agmatine is bound.

Monoclonal antibody 2F5 recognizes the membrane proximal external region (MPER) in GP41 and has broad neutralization activity against HIV-1 strains. NMR, EPR and HDX/MS analyses now show that 2F5 extracts MPER from the membrane using a scoop-like movement.

Archaea use a tRNA^Ile with agmatine conjugated at the C34 position to decode the AUA codon. The enzyme that catalyzes this reaction, TiaS, has been previously identified, and it is now shown that it uses a novel kinase domain to hydrolyze ATP into AMP and pyrophosphate before phosphorylating itself and the tRNA on its way to conjugating the agmatine.

Eukaryotic initiation factor eIF2 binds initiator Met-tRNA_i^Met to the P site of the 40S ribosomal subunit. Hydroxyl radical probing analyses allowed mapping of the binding of eIF2 on the ribosome and on Met-tRNA_i^Met. Interestingly, despite having structural similarities to elongation factor EF-Tu, which delivers aminoacyl-tRNAs to the A site of 70S elongating ribosomes, eIF2 binds tRNA in a substantially different manner.

Organism-wide RNA interference (RNAi) is due to the movement of mobile RNA species throughout the organism. New genetic evidence shows that double-stranded RNA (dsRNA), which triggers RNAi, and at least one dsRNA intermediate produced during RNAi can act as or generate mobile silencing RNAs in Caenorhabditis elegans. Interestingly, single-stranded primary and amplified secondary siRNAs do not generate mobile silencing RNAs.