Articles in 2009

Fatty acid synthase is composed by several catalytic domains that work in sequence, with reaction intermediates being transferred between them. Single-particle EM analysis of different catalytic mutants of rat FAS imaged in the presence of substrates reveals the domains' movements during the reaction cycle.

Small RNAs are involved in the regulation of gene expression. During a hunt for microRNAs in the simple chordate Ciona intestinalis, a distinct class of small RNAs, offset from the microRNA expressed from a given hairpin, have been defined. These offset small RNAs are expressed in relative abundance in C. intestinalis and are also detected at specific developmental stages. Although their function is unclear, these results suggest that microRNA processing has distinct properties in this simple organism.

Nucleic acid polymerases catalyze nucleotidyl transfer reactions with two proton-transfer events, deprotonation of the 3′-hydroxyl nucleophile and protonation of the pyrophosphate leaving group. Functional analyses now show that the proton donor for the latter transfer is an active-site residue.

The Dsl1p tethering complex is crucial for Golgi-to-ER retrograde trafficking of vesicles in yeast. The crystal structures of two out of three Dsl1p complex components reveal similarity to exocyst and COG complex components, which act in tethering vesicles to the plasma membrane and Golgi, respectively, suggesting a conserved tethering strategy at several eukaryotic membranes.

Expanded CGG repeats cause chromosomal fragility and hereditary neurological disorders in humans. These repeats adopt unusual structures that block DNA replication in vitro and in unicellular organisms. Mirkin and co-workers asked whether the same holds true in mammalian cells. They find that CGG repeats stall replication forks in a length-dependent, but orientation-independent, manner and do not seem to trigger an intra–S phase checkpoint response. They suggest that fragile sites arise because the cell cycle continues before replication is complete and the under-replicated areas would convert into constrictions and/or double-stranded breaks.

DNA packaging into nucleosomes presents a barrier to many motor proteins, including the transcriptional machinery. By unzipping DNA in single nucleosomes, a detailed map at near base pair resolution of histone-DNA interactions is now provided, suggesting that interaction with the two DNA strands is decoupled and that unraveling past the dyad axis of the nucleosome, as might occur when a motor protein passes through, is sufficient to displace histones.

Using CLIP-seq technology, the genome-wide binding sites of the FOX2 splicing regulator in human embryonic stem cells (hESCs) are now identified. Further work based on FOX2 depletion uncovers the underlying logic of FOX2-mediated regulation of alternative splicing and finds that such compromised hESCs undergo rapid cell death.

Endonuclease V can initiate the repair of deaminated purine bases by recognizing them and hydrolyzing the second phosphodiester bond on their 3′ side. Now the crystal structures of endonuclease V in complex with its substrate and its product reveal a wedge motif acting as a minor groove–damage sensor and a pocket to recognize the lesion; the enzyme remains tightly bound to the 5′ phosphate product, perhaps to hand it over to downstream repair factors.

Triple expansions underlie a number of human disorders. Triplet repeat instability in yeast mutants for the Srs2 and Sgs1 helicases indicate that recombination underlies instability in such a genetic background. Further analysis of replication intermediates indicates that Srs2 is likely to be involved in replication fork reversal within repetitive sequences, a process involved in preventing repeat instability and fragility.

Sortilin is a neuronal receptor involved in sorting and signal transduction. The crystal structure of the mature Sortilin ectodomain bound to one of its ligands, neurotensin, reveals a binding tunnel formed by the Sortilin β-propeller domain. Combined with binding and mutagenesis studies, the findings suggest that Sortilin substrates compete for access to the tunnel so that only one ligand binds at a time.

Myosins have roles in many biological processes that go beyond muscle contraction and vesicle transport, including furrowing during cytokinesis, signal transduction and RNA polymerase I–dependent transcription. Studying these various complex processes will require the use of isoform-specific small molecules that alter motor activity. The marine natural product pentabromopseudilin is now shown to act as an allosteric effector of myosin function and potent inhibitor of vertebrate myosin-5a–dependent motor activity.

As we enter 2009 and celebrate the anniversaries associated with the birth of Darwin and publication of The Origin of Species, it's worth asking why there isn't greater public awareness of the increasing molecular evidence relevant to evolution and what can be done to address this.

Biochemical studies on the spliceosomal helicase Brr2 reveal that it is activated by Prp8, the master regulator of the splicing cycle. Substitutions in Prp8 that cause retinal degeneration in humans block activation of Brr2, providing insight into the molecular pathology of retinitis pigmentosa.

Endonucleases have generally not been considered among the major factors in well-studied mRNA-decay and quality-control pathways in mammals and yeast. However, two important players in these pathways, the exosome and SMG6, have now been shown to contain functionally significant endonucleolytic activities.

The formation of heterochromatin involves spreading of repressor proteins along large chromosomal domains. A new study reveals that the concept of spreading also holds true for establishing domains of active chromatin. More specifically, spreading of the Drosophila melanogaster male-specific lethal (MSL) activator complex, which is required for dosage compensation on the X chromosome, involves interaction between the MSL3 chromodomain and histone H3 methylated at lysine 36.

Alternative splicing is typically thought to be controlled by RNA binding proteins that modulate the activity of the spliceosome. A new study not only demonstrates that alternative splicing can be regulated without the involvement of auxiliary splicing factors, but also provides mechanistic insight into how this can occur.

Hsp90s, molecular chaperones critically involved in many essential cellular processes, were the focus of a recent international conference held in Seeon, Germany. The scope of the conference ranged from structural and mechanistic insights all the way to medical applications.