Research articles

Escherichia coli YiiP, a member of the cation diffusion facilitator family, exports cytoplasmic zinc, maintaining cellular homeostasis. The high-resolution crystal structure of YiiP, combined with functional studies focused on its cytoplasmic C-terminal domain, suggest how it is able to allosterically modulate zinc transport.

The positions of nucleosomes can affect processes occurring on DNA. DNA curtains are now used to study nucleosome positioning in vitro. This allows assessment of sequence-related effects on positioning and indicates that the yeast factor Scm3 can overcome the aversion of nucleosomes to AT-rich sequences.

Nucleosomes can be modified by replacing the core histones with variants, the most diverse of which is macroH2A. The localization of macroH2A variants in human male pluripotent cells indicates that this variant functions in repression of key developmental genes and is essential for zebrafish embryogenesis.

DNA polymerase δ (Pol δ) has a crucial role in eukaryotic replication. Now the crystal structure of the yeast DNA Pol δ catalytic subunit in complex with template primer and incoming nucleotide is presented at 2.0-Å resolution, providing insight into its high fidelity and a framework to understand the effects of mutations involved in tumorigenesis.

The let-7 microRNA has been implicated in development and disease. Its expression must thus be tightly regulated, and previously uridylation and Lin28 were implicated in let-7 stability. Zcchc11 is now shown to be the uridylase that mediates pre–let-7 modification and regulates mature let-7 levels and activity in mouse embryonic stem cells.

Developmental expression of the microRNA let-7 is tightly regulated in many animals, and turnover has been linked to LIN-28 and uridylation in mammals. This regulation is now shown to be conserved in Caenorhabditis elegans, and PUP-2 is shown to be a uridylase that is specifically recruited to let-7 in a LIN-28–dependent manner.

Nucleosomes can interfere with DNA binding by factors, but previous work showed that protein-binding sites on a single nucleosome are accessible. Dynamics in the context of higher-order chromatin structure are now examined, with compaction dynamics and DNA-binding site exposure on a centrally placed nucleosome in an array assessed.

Co-transcriptional splicing of pre-mRNAs has been proposed to involve exon tethering to the elongating RNA polymerase II. By inserting a fast-cleaving ribozyme in the nascent transcript, the linear integrity of the transcript is found to be key to splicing, arguing against tethering and for a pathway that clears such disrupted transcripts.

X family DNA polymerases can fill short DNA gaps by binding both the 5′ and 3′ ends of the gap. What happens to the template strand is now revealed in the crystal structure of human polymerase λ bound to a 2-nucleotide gap substrate. The template strand is scrunched, with the additional base in an extrahelical position going into an enzyme pocket.

Prions can adopt a transmissible β-sheet-rich conformation and also form strains with different structural and biological properties. Polymorphic crystal structures of peptides from prion- and other amyloid-forming proteins suggest the structural basis for prion strains, revealing two potential mechanisms: packing and segmental polymorphism.

Splicing and transcription have been argued to be coupled, but the mechanisms behind this are unclear. Published data sets examining nucleosome positioning are now analyzed and show that exons tend to have higher nucleosome occupancy than introns. This may indicate why metazoan exons are ∼150 nucleotides, similar to the length of DNA on a nucleosome.

miRNAs are loaded onto Argonautes (Agos) to guide silencing of targets, but duplex unwinding is required for targeting. Detection of Drosophila Ago1 complexes containing the duplexed or unwound miRNA now give insight into the basis for cleavage-independent unwinding of miRNA duplexes to generate a functional, mature complex.

Phosphorylation-dependent SUMOylation of MEF2A promotes postsynaptic dendrite differentiation. Analyses now reveal that a surface on the SUMO E2 UBC9 is responsible for integrating phosphorylation signal recognition and SUMOylation and suggests that regulation of some SUMO substrate recognition events may have evolved to use the E2 rather than an E3 ligase.

Chromatin influences transcription, but its effects on downstream processing have been less clear. Analyses of published high-throughput data examining nucleosomal positions in T cell and C. elegans genomes now indicates that intron-exon architecture is reflected in nucleosome occupancy.

Poly-ADP-ribosylation is a post-translational modification catalyzed by enzymes such as PARP1, which responds to metabolic and genotoxic stress. Now macrodomain-containing proteins are shown to rapidly move to PARP1 activation sites, and recruitment of the macrodomain-containing histone macroH2A1.1 results in local chromatin changes.

The anaphase promoting complex (APC) is a key cell-cycle regulator that has ubiquitin-ligase activity. The first structure of a complex formed between APC subunits, that of CDC26 and APC6, provides detailed structural information of APC components and suggests how CDC26 may stabilize APC6 and other complex subunits.

Platelets are anucleate elements in the cardiovascular system involved in clotting. Platelets are now found to contain microRNAs and the key cytoplasmic elements of a processing and effector pathway, suggesting that platelet mRNAs may be subjected to microRNA regulation.

The cap binding complex (CBC) interacts with mRNAs and snRNAs and accompanies them to the cytoplasm, where they are released and CBC is imported back into the nucleus by the importin complex. Multiple approaches are now combined to gain structural and functional insights into the regulation and coordination of these CBC interactions.

The tumor suppressor p53 activates the transcription of a number of genes under conditions of genotoxic stress. Some of these regulated promoters show p53 occupancy even under normal conditions. Now calcineurin-binding protein 1 (Cabin1) is shown to keep p53 inactive in these promoters.

Grb10 and Grb14 are adaptor proteins that inhibit insulin signaling through direct interactions with the insulin receptor kinase domain. Structural and functional studies now reveal that the tandem Ras-associating and pleckstrin-homology domains of these proteins are necessary for membrane recruitment and insulin receptor inhibition.