News & Views in 2013

Faithful bypass of replication forks encountering obstructive DNA lesions is essential to prevent fork collapse and cell death. PrimPol is a new human primase and translesion polymerase that is able to bypass fork-blocking UV-induced lesions and to restart replication by origin-independent repriming.

Mediator of DNA-damage checkpoint 1 (MDC1) has a central role in repair of DNA double-strand breaks (DSBs) by both homologous recombination and nonhomologous end joining, and its function is regulated by post-translational phosphorylation, ubiquitylation and SUMOylation. In this issue, a new study by Watanabe et al. reveals that methylation of MDC1 is also critical for its function in DSB repair and specifically affects repair through BRCA1-dependent homologous recombination.

An unresolved question in mammalian epigenetic regulation is how ubiquitously expressed chromatin-modifying complexes such as Polycomb group complex 2 (PRC2) find their specific target sites across an intricate choreography of localization events in time and space. Two recent studies now provide critical new insights into an intriguing genome-wide role for RNA in PRC2 regulation.

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.

BamA proteins are essential for the biogenesis of β-barrel outer-membrane proteins, but how BamA-assisted folding and outer-membrane insertion occur is not clear. X-ray crystal structures of three bacterial BamA orthologs now show a lateral gate in the BamA barrel that provides tantalizing clues regarding the biogenesis of outer-membrane proteins.

Sodium-coupled glutamate transporters regulate excitatory signaling in the brain. A new crystal structure shows how the substrate induces changes in the binding pocket of an archaeal transporter homolog, providing new insights into the mechanism of transport.

Translation initiation in eukaryotes is a complex and highly regulated process during which several initiation factors cooperate to recruit an initiator tRNA to the small ribosomal subunit, where the mRNA is scanned for an AUG start codon. Two recent reports provide new structural insights into this process and reveal key functions of initiation factors 1 (eIF1) and 1A (eIF1A) in start-codon selection in atomic detail.

High-throughput RNA sequencing has unveiled the existence of a large number of noncoding antisense RNAs derived from bidirectional promoters; unlike sense transcripts, these RNAs are often unstable. Two recent reports investigate why downstream transcription is productive, whereas upstream transcripts are prone to degradation, revealing that an asymmetric distribution of polyadenylation signals and U1 snRNP–binding sites surrounding transcription start sites control the outcome of bidirectional transcription.

Translocation is an essential step of protein synthesis in which the large tRNA₂–mRNA complex inside the ribosome moves from the A and P sites to the P and E sites, respectively, bringing a new mRNA codon into the decoding center. This process is catalyzed by the elongation factor EF-G–GTP (eEF2 in eukaryotes) and is the least understood stage of peptide elongation. Four new reports describe the crystal structures of translocation intermediates, illustrating important details of the translocation reaction.

Mitochondria contain multisubunit translocases to import preproteins from the cytosol. The presequence translocase of the inner membrane operates in a voltage-gated manner, but how a preprotein-conducting channel responds to the membrane potential was unknown. A new study identifies a voltage-coupled conformational change in a transmembrane segment of the Tim23 import channel, representing a major step toward understanding the molecular basis of a voltage-gated protein translocase.

The binding of stromal interaction molecule 1 (STIM1) to ORAI calcium channels is critical for store-operated calcium entry (SOCE), a calcium influx pathway conserved among nearly all vertebrate cells. Although many major steps of this pathway are well understood, crucial details regarding the mechanism of STIM1 activation remain unclear. A study in this issue provides important new insights into the conformational changes that occur during STIM1 activation.

The detailed mechanism by which the molecular motors kinesin and myosin travel along their respective protein tracks as they generate force during motile processes is still poorly understood. In a recent breakthrough, a crystal structure of kinesin in complex with tubulin illuminates the atomic-level details of a motor-track interaction, answering many questions yet leaving a number of mysteries unresolved.

A shield of glycans coats the viral-envelope proteins of HIV. Recent work shows how broadly neutralizing antibodies can recognize this shield despite structural variation in these 'self' carbohydrate structures.

Multiple Argonaute proteins are implicated in gene silencing by RNA interference (RNAi), but only one is known to be an endonuclease that can cleave target mRNAs. Chimeric Argonaute proteins now reveal an unexpected mechanism by which mutations distal to the catalytic center can unmask intrinsic catalytic activity, results hinting at structurally mediated regulation.

The anaphase-promoting complex/cyclosome (APC/C) is restricted by metazoan protein early mitotic inhibitor 1 (EMI1), a natural, potent inhibitor. New findings suggest that the multimodal inhibitory mechanisms of EMI1 control APC/C-dependent ubiquitylation.

Whether centromere-specific CENP-A–containing nucleosomes comprise one molecule each of CENP-A and histones H4, H2A and H2B (forming a tetramer or hemisome) or two molecules of all four histones (forming an octamer) has been controversial. Three new studies now address this controversy using complementary in vitro and in vivo approaches.

At last, structures have been solved for different conformational states, facing in and facing out, for the same transporter protein of the major facilitator superfamily. The structural basis of alternating substrate access for binding and translocation can now be properly visualized.

Eukaryotic mRNAs containing nonsense codons are degraded by nonsense-mediated mRNA decay (NMD). In humans, NMD was proposed to act exclusively on newly synthesized mRNA during a 'pioneer round' of translation, when mRNA is associated with the nuclear cap-binding complex (CBC). Two reports now challenge this view, revealing that NMD is independent of whether CBC or the cytoplasmic cap-binding protein (eIF4E) promotes translation and can occur later in an mRNA's life.

Two structural variants of the RNaseH-like domain of the highly conserved spliceosomal protein Prp8 are correlated with Prp8 mutants that stabilize either the first- or second-step active sites of the spliceosome.