Volume 20 Issue 11, November 2013

RNA interference (RNAi) is a powerful mechanism to fight viral infections in plants and invertebrates. Two recent reports provide new, compelling evidence for a functional role for antiviral RNAi in mammals.

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.

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.

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.

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.

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 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.

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.

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.

The outer-membrane protein TamA is involved in autotransporter biogenesis in Escherichia coli. The crystal structure of TamA, determined to 2.3 Å, reveals a 16-strand β-barrel that is closed by a lid on its extracellular face. A weakened lateral wall in the barrel suggests the presence of a gate for substrate exit to the lipid bilayer.

It has been challenging to label endogenous genomic sequences in living cells, and this has limited attempts to study the dynamics of nuclear architecture in genome function. In a newly developed methodology, transcription activator–like effectors (TALEs) were used to label endogenous repetitive genomic sequences to visualize nuclear positioning and chromatin dynamics in cultured mouse cells and embryos.

Analysis of data from The Cancer Genome Atlas generates a pan-cancer network of 143 recurrent miRNA-target relationships. The identified miRNAs were frequently regulated by genetic and epigenetic alterations in cancer. The work also reveals that some miRNAs might coordinately regulate cancer pathways, such as miR-29 regulation of TET1 and TDG mRNAs, encoding components from the active DNA demethylation pathway.

The accurate and thorough genome-wide detection of A-to-I editing has proven technically challenging. Using a combination of computational prediction and experimental validation, the authors report ~3,500 high-probability editing sites with sufficient accuracy to reveal the global patterns underlying biological functions of RNA editing in adult male Drosophila melanogaster.