Volume 19 Issue 12, December 2012

Two recent reports on the structures of cobalamin riboswitches uncover amazing details on how a ubiquitous riboswitch class selectively grips a large and ancient coenzyme, revealing that some variants in this class have evolved to detect a different metabolite target.

Exon junction complexes (EJCs) are deposited on mRNAs during splicing and are key regulators of the post-transcriptional fate of messenger ribonucleoprotein particles (mRNPs). Two recent papers reporting on the transcriptome-wide mapping of EJC-binding sites in human cells reveal an unexpected heterogeneity of EJC distribution on mRNAs and a tight network of EJC–SR protein interactions contributing to the formation of a higher-order, compacted mRNP structure.

Three structures were recently reported for tyrosyl DNA phosphodiesterase 2 (Tdp2), a protein that protects the metazoan genome from shredding following abortive topoisomerase activity. The physiological significance of these findings is discussed here.

A newly uncovered activity of a family of Polycomb-group proteins provides insight into the mechanisms by which active genes become repressed during the transition from pluripotency to restricted cell fates as stem cells undergo lineage specification.

Histone post-translational modifications (PTMs) can directly influence histone-DNA and histone-histone interactions, or they can be targeted by protein effectors, or histone readers. This Review outlines known readers of histone PTMs, details their mechanism of action and the functional significance of histone PTM recognition and discusses cross-talk between protein effectors and consequences of the combinatorial readout of PTMs.

Cryo-EM studies of the 60S ribosomal subunit reconstituted with biogenesis factor Arx1 and Rei1 and Jji1 suggest that, in addition to its role during pre-60S nuclear export, Arx1 shields the polypeptide tunnel-exit region and inhibits the premature association of nascent chain–processing factors, whereas Rei1 and Jjj1, which have been implicated in Arx1 recycling, may function in Arx1 release from the tunnel exit.

Preribosomal particles need to be exported from the nucleus, but their architecture and composition have been unknown. Cryo-EM analysis of pre-60S particles bound to the nuclear export factor Arx1 provides the first structural glance at the immature 60S particle, and the position of Arx1 near the exit tunnel suggests that it may restrict access of factors active during translation.

An early step in the autophagy process is the conjugation of the ubiquitin-like proteins (UBLs) Atg8 and Atg12 to their targets. Structural and functional experiments reveal how the autophagy E1 Atg7 uses a trans mechanism to catalyze the charging of the autophagy UBLs onto their respective carrier E2 proteins, Atg3 and Atg10.

The enzymes involved in autophagy-related UBL conjugation bear only passing resemblance to their counterparts in the better-known UBL conjugation pathways. New structural work provides insight into the mechanism by which the UBL proteins Atg8 and Atg12 are correctly charged by a single activating enzyme, Atg7, then transferred onto their cognate E2 proteins, Atg3 and Atg10, respectively.

Methylation of H3K27 by Polycomb repressive complex 2 (PRC2) is essential for gene regulation. A new study provides structural evidence for the recognition of di- and trimethylated H3K36 by the Tudor domain of PRC2 subunit Phf19 as well as functional data suggesting that recognition of di- or trimethylated Phf19–H3K36 is required for regulating PRC2 activity and for full repression of selected PRC2 targets in embryonic stem cells.

The human Polycomb-like protein PHF1 has been implicated in transcription-regulatory and DNA damage repair pathways. A new study demonstrates that the Tudor domain of PHF1 binds histone H3K36me3 with high specificity and affinity, that Tudor-H3K36me3 interaction inhibits Polycomb repressive complex 2-mediated H3K27 methylation and that PHF1 accumulates at DNA damage sites in a Tudor-dependent manner.

How Polycomb repressive complex 2 (PRC2) is recruited to active chromatin to mediate transcriptional silencing during lineage specification in metazoans has been unclear. New findings now show that PRC2 component PHF19, which associates with the H3K36me3 demethylase NO66, binds the active chromatin mark H3K36me3 through its Tudor domain, leading to PRC2-mediated H3K27 trimethylation, loss of H3K36me3 and transcriptional silencing.

The protein KSRP binds to precursors of let-7 miRNA and promotes their processing to the mature form. The molecular basis for KSRP's specificity for pre-let-7 is now examined by using NMR spectroscopy and biochemistry, which reveals that the third KH domain of KSRP recognizes a G-rich sequence in the pre-let-7 terminal loop in a noncanonical manner.

The histone variant H3.3 is deposited onto pericentric and telomeric heterochromatin by the histone chaperone DAXX. How DAXX selectively recognizes H3.3 over the canonical H3.1 is now revealed by the crystal structure of DAXX in complex with H3.3–H4, along with biochemical and cellular analyses.

Semaphorin-plexin cell-cell signaling is important in tissue development, with roles in axon guidance, immunity and cancer. The structure of the complex formed between semaphorin-3, plexin-A and their co-receptor neuropilin, combined with mutagenesis, reveals how neuropilin contributes to stabilizing the signaling complex.

VAMP7 is a SNARE protein involved in the fusion of endosomes and lysosomes with various cellular membranes. The longin domain of VAMP7 forms autoinhibitory interactions that prevent VAMP7 SNARE assembly. New structural and functional data reveal how the regulatory protein Varp, a known VAMP7 binding partner, kinetically inhibits SNARE complex formation.

Gram-negative bacteria use heme import systems to sequester heme from their environment. The structure of the ABC transporter HmuUV, the heme importer from Yersinia pestis, in the nucleotide-free, apo state was determined, revealing an outward-facing conformation for the transporter.

Rio2 is an atypical protein kinase required for pre-40S subunit maturation. The crystal structure of eukaryotic Rio2 with bound ATP and Mg²⁺ reveals an unusual phosphoaspartate intermediate typically observed in P-type ATPases. Rio2 has in vitro ATPase activity, and its catalytic activity stimulates its own dissociation from the ribosome, which is required for pre-40S maturation.

The removal of the mRNA 5′ cap structure by the decapping enzyme DCP2 leads to rapid 5′→3′ mRNA degradation by XRN1, suggesting that the two processes are coordinated. Biochemical and structural analyses now reveal a molecular basis for this coupling by showing that XRN1 directly interacts with the decapping activators EDC4 and DCP1 in human and Drosophila melanogaster cells, respectively.

Ribosomes that synthesize membrane proteins are targeted to the protein-conducting channel in the membrane via the signal recognition particle (SRP) pathway. Kinetic analyses now demonstrate that SRP scans ribosomes while undergoing dynamic fluctuations until it encounters a nascent peptide in the exit tunnel and binds the hydrophobic signal-anchor sequence, which stabilizes SRP and switches it into targeting mode.

In the E. coli Hsp100/Hsp70 system, the M domain of ClpB is essential for ClpB cooperation with DnaK and DnaJ and for protein disaggregation, but its function was largely unknown. New biochemical and biophysical data now indicate that the M domain acts as a molecular toggle that reversibly interacts with the AAA-1 domain of ClpB to regulate ATP hydrolysis and protein disaggregation activities. Also in this issue, Seyffer et al. show how DnaK interactions with M domain further enhance ClpB activity.

DnaK targets protein aggregates to ClpB. New data show that DnaK also activates ClpB in a species-specific manner through direct interactions with the M domain of ClpB, stabilizing a derepressed state that increases the ATP hydrolysis and protein disaggregation activities of the chaperone. Also in this issue, Oguchi et al. show how the M domain of ClpB acts as a reversible toggle to regulate these activities.

Vacuolar-type ATPases (V-type ATPases) are large integral membrane protein complexes. Their activity acidifies intracellular compartments, and they are regulated by the dissociation of the complex's V1 and VO regions. The cryo-EM reconstruction of the yeast V-type ATPase suggests how structural rearrangements triggered by dissociation of V1 leads to inhibition of activity.

Tyrosyl-DNA phosphodiesterase 2 (Tdp2) processes DNA termini with a 5′-phosphotyrosyl–linked topoisomerase II adduct, such as those stabilized by chemotherapeutic drugs anthracyclines and etoposides, by direct reversal of the 5′-phosphotyrosyl linkage. Now crystal structures of mouse Tdp2–DNA complexes, along with mutagenesis and functional analyses, reveal how Tdp2 recognizes and reverses such adduction.

DNA-repair enzyme Tdp2 hydrolyzes the 5'-phosphotyrosine bond formed by topoisomerases and is associated with resistance to anticancer drugs that trap such complexes. The crystal structures of zebrafish Tdp2 bound to DNA offer insight into substrate recognition. In addition, the crystal structure of nematode Tdp2 suggests a potential mechanism for autoregulation.