Articles in 2013

Pentatricopeptide repeat (PPR) proteins are involved in different RNA processes, but how they recognize their target RNAs has been unclear. Now crystal structures of plant PPR protein–THA8 in complex with RNA, along with functional analyses, reveal an asymmetric THA8 dimer with RNA bound at the dimeric interface.

Using 13 intermediate-translocation-state models derived from X-ray and cryo-EM structures of Escherichia coli ribosomes to guide large-scale molecular dynamics simulations, a new study now models the path taken by tRNAs during spontaneous translocation to uncover the mechanisms that facilitate tRNA movement through the ribosome.

Through its association with Cdk–cyclin complexes, Cks has been implicated in the multisite phosphorylation of numerous cell cycle–regulatory proteins. A structural analysis of Cks1 bound to a target phosphopeptide, combined with binding-specificity studies, now reveals a Cks-binding consensus sequence and how Cks1 confers phosphodependent substrate specificity to Cdk1.

HIV-1 Env glycoprotein binds receptors on the host cells, triggering a conformational change from a closed to an open state. Now single-particle cryo-EM analysis of a soluble, trimeric Env construct reveals the structure of the closed state at ∼6-Å resolution. The structure features three gp41 helices at the center of the trimer, thus indicating that HIV-1 and influenza viruses use similar mechanisms to enter the cell.

Bacterial multidrug efflux transporters (MATEs) couple drug export to Na⁺ or H⁺ influx. A new crystal structure of the H⁺-coupled DinF transporter from Bacillus halodurans reveals differences in the substrate-binding sites and transport mechanisms of DinF and NorM MATE homologs.

Polycomb repressive complex 2 (PRC2) acts as an epigenetic repressor by depositing repressive H3K27me3 marks, but how it is regulated and directed to specific genes remains unknown. PRC2 is now found to bind at low levels to many gene promoters, including active ones devoid of H3K27me3, and the EZH2 catalytic subunit binds directly to nascent transcripts.

A new bacterial toxin from pathogen Photorhabdus asymbiotica is now described. The toxin contains a domain with glycosyltransferase activity that modifies a tyrosine residue of Rho GTPases in the host cell, inhibiting Rho activation and interaction with downstream effectors. The second domain is a glutamine deamidase that blocks GTP hydrolysis by Ga_q/11 and Ga_i proteins.

The dNTPase SAMHD1 inhibits infection by HIV-1 and other retroviruses. In the presence of dGTP, the enzyme forms tetramers and becomes active, a process that is now elucidated by structural, biochemical and cellular analyses of human SAMHD1. Binding of dGTP to four allosteric sites promotes tetramerization and induces a conformational change in the substrate-binding pocket to activate the enzyme.

The Ccr4–Not complex is involved in several aspects of gene expression, including mRNA decay, translational repression and transcription. Structural, biochemical and functional analyses of the Not module, comprising the C-terminal regions of Not1, Not2 and Not5, suggest that it forms a platform for protein and nucleic acid interactions that are important for Ccr4–Not's many functions.

The CCR4–NOT deadenylase complex has a crucial role in post-transcriptional mRNA regulation, catalyzing the removal of mRNA poly(A) tails and consequently repressing translation and promoting mRNA degradation. The crystal structure of the human NOT module, formed by the CNOT1, CNOT2 and CNOT3 C-terminal regions, now provides a structural framework for understanding its assembly and functions.

Mitochondrial DNA is transcribed by a single-subunit RNA polymerase (mtRNAP) that is distantly related to the RNAP of bacteriophage T7. Together with biochemical data, the crystal structure of the mtRNAP elongation complex with DNA template and RNA transcript elucidates the elongation mechanism of mtRNAP and reveals striking differences as compared with the T7 transcription system.

Analysis of primary protein sequences and tertiary structures has yielded important insights into the evolution of protein function, but little is known about the evolution of functional mechanisms and protein dynamics. An integrated approach including structural biology, mutagenesis, bioinformatics analyses and cell biology has now uncovered evolutionary aspects of the motions present in the dihydrofolate reductase enzyme family.

Skp is a bacterial chaperone that prevents aggregation of outer membrane proteins as they traverse the periplasmic space. The conformation and dynamics of Skp in complex with two OMPs are now examined by NMR spectroscopy. The analyses reveal that Skp provides a scaffold for its substrates, which in turn populate a dynamic conformational ensemble.

Polycomb repressive complex 2 (PRC2) is a histone methyltransferase required for epigenetic silencing during development and cancer, and it can be recruited to chromatin by long noncoding RNAs. In vitro binding studies and comparative analysis of genome-wide in vivo data now suggest a model for the maintenance of the repressed chromatin state by PRC2, directed by PRC2's promiscuous binding to nascent RNA transcripts.

mRNAs have been shown to cross-talk with other mRNAs by serving as competing endogenous RNAs that 'sponge up' microRNAs. A report now claims a new, physiologically significant function for mRNAs that cross-talk through partially complementary Alu elements in the 3′ untranslated region. The Staufen1-mediated mRNA pathway targets both mRNAs in the duplex, provided that they are translated.

4C (chromosome conformation capture on chip) analyses using the clock-controlled Dbp gene as bait reveal the existence of circadian long-range interactions in mouse embryonic fibroblasts. The Dbp circadian interactome is dependent on a functional circadian clock and contains a number of clock-related DNA elements.

p38α MAP kinase is activated by autophosphorylation, which is promoted by the protein TAB1 during myocardial ischemia and other stresses. Now cellular, biochemical and biophysical approaches reveal that TAB1 binds p38α's C-terminal kinase lobe and induces rearrangements within the activation segment that allow autophosphorylation in cis.

Noncoding telomere repeat–containing RNA (TERRA) expressed from chromosome ends can form RNA-DNA hybrids at telomeres, but how this influences telomere length is unclear. Now, TERRA RNA-DNA hybrids are shown to promote telomere recombination and delay senescence in cells lacking telomerase, establishing a function for TERRA in telomere-length maintenance.

The cancer-associated D2723H mutation causes mislocalization of BRCA2 to the cytoplasm. New work shows that this mutation disrupts the interaction of BRCA2 with DSS1, unmasking a BRCA2 nuclear export signal within the DSS1 binding domain. This impairs nuclear retention of BRCA2 and, consequently, RAD51, suggesting that the intracellular localization of these factors may control their function in maintaining genome integrity.

In the eukaryotic 26S proteasome, a heterohexameric AAA+ complex unfolds substrates prior to degradation. The yeast unfoldase subunits have now been expressed in bacteria and reconstituted into active proteasomes in vitro. Mutations of catalytic and structural motifs in each individual subunits reveal that they play distinct roles in substrate processing, peptidase binding and gate opening.