Articles in 2012

The exoribonuclease Eri1 binds the stem-loop of histone mRNAs, but the functional significance of this interaction has been unclear. New studies now indicate that 3A oligouridylation of histone mRNAs enables the Lsm1–7 complex to bind the oligo(U) tail and to interact with Eri1, whose catalytic activity degrades the double-stranded stem-loop structure.

The ATG12~ATG5 conjugate promotes the transfer of the ubiquitin-like protein LC3 to phosphatidylethanolamine (PE), a modification required for autophagosome formation. Structural and biochemical analyses reveal the determinants for ATG12~ATG5 binding to ATG16 and the E3 ligase ATG3, and indicate how the conjugate stimulates PE–LC3 formation.

The eukaryotic ribosome-associated complex (RAC) chaperone is poorly understood. Structural analyses now provide insight into the catalytic inactivity and possible functions of the Ssz1 subunit and reveal that RAC interacts with the ribosome via the Zuo1 subunit. RAC crouches over the ribosomal exit tunnel, where its conformation may be controlled by the ribosomal expansion segment ES27.

Previous work has implied that the ATPase domain of ISWI chromatin remodelers cooperates with a DNA-binding accessory domain to achieve remodeling. Quantitative biochemical analyses now reveal that the ATPase domain exists in two conformations and that DNA binding induces the catalytically active conformation. The ATPase domain has an intrinsic ability to bind and remodel nucleosomes, which suggests that it acts autonomously.

Measles virus hemagglutinin (MVH) can bind to different cell surface receptors in the human host. CD46, the first identified MVH receptor, is used mainly by vaccine strains, whereas clinical strains can use SLAM on macrophages and dendritic cells and nectin-4 on epithelial cells. The crystal structure of MVH in complex with the outermost ectodomain of nectin-4 is now presented, revealing a potential target site for drug development.

Histone chaperone RbAp48 interacts with histones H3–H4 and delivers them to a second histone chaperone, ASF1, to be assembled into new nucleosomes. These interactions are now investigated, revealing that RbAp48 binds H3–H4 heterodimers (but not tetramers) and causes conformational changes in their core fold. Moreover, an allosteric mechanism facilitates exchange of H3–H4 between RbAp48 and ASF1.

Post-translational modifications are one way in which GTPase functions can be regulated. Monoubiquitination of Lys147 of Ras has been shown to promote tumorigenesis. New data now indicate that this modification promotes Ras activation by impairing GTP hydrolysis catalyzed by GTPase-activating proteins.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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 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.