Volume 15 Issue 10, October 2008

The Argonaute-1 (Ago1) protein bound to small interfering RNAs (siRNAs) directs heterochromatin formation in fission yeast. A high-throughput sequencing approach reveals that the composition of the Ago1-bound siRNA population is sensitive to the noncanonical poly(A) polymerase Cid14, indicating that the RNA-interference and Cid14-TRAMP RNA-degradation pathways compete for substrates in fission yeast.

By recruiting the Dnmt1 DNA methyltransferase to hemimethylated DNA, the ubiquitin-like with PHD and ring finger domains 1 (UHRF1) protein plays an important part in DNA methylation. The structures of the SRA domain of UHRF1 in complex with hemimethylated DNA show that the methylated cytosine is flipped out of the DNA helix, as observed previously with DNA methyltransferases.

Mutation of Cid14, a key enzyme in the TRAMP RNA surveillance pathway, has previously been shown to decrease small interfering RNA production in Schizosaccharomyces pombe. Analysis of Argonaute-associated proteins now indicates that, in the absence of Cid14, RNAs usually processed by TRAMP now enter the small interfering RNA pathway, suggesting that the RNA surveillance pathway prevents abundant RNAs from entering the RNA interference pathway.

Viral fusion proteins are required for the fusion of viral and host membranes for all enveloped viruses. The structure of the Baculovirus postfusion form of glycoprotein gp64, a class III fusion protein, explains its ability to fuse with many different cell types, and structural comparisons suggest that all three classes of fusion proteins may be more closely related than previously thought.

DcuS is a multidomain membrane sensor kinase important for Escherichia coli interactions with its environment. A new approach combining solution- and solid-state NMR with in silico modeling and mutagenesis has provided a three-dimensional model for most of this large membrane protein and suggests a mechanism for DcuS activation.

SRp38, unlike other SR proteins, functions as a general splicing repressor when it is dephosphorylated. When phosphorylated it functions as a sequence-specific splicing activator and also affects the selection of mutually exclusive exons in the GluR-B pre-mRNA. Thus, SRp38 is a previously uncharacterized kind of splicing factor that can switch from a repressor to an activator and regulator of alternative splicing.

Rad51 is an essential protein with a central role in homologous recombination. An N-end rule degron Rad51 is now used in DT-40 cells to show that Rad51 is not required for DNA synthesis, but it is necessary to resolve RPA-bound DNA structures during G2.

APOBEC3G is a cytidine deaminase that can be incorporated into HIV-1 virions and process the viral genome upon cell infection, leading to viral hypermutation and inactivation. APOBEC3G's activities are counteracted by viral protein Vif. Using a sensitive enzymatic assay, low levels of APOBEC3G can be detected associated to Vif(+) virions. Furthermore, the authors show that APOBEC3G functions in a distributive manner and causes dispersed hypermutation via intersegmental transfer.

The binding of kinesin to microtubules promotes nucleotide exchange by the kinesin. Structural studies of the intermediate states of nucleotide exchange reveal the sequence of interactions and conformational changes that occur and the role of Mg²⁺ in the process, providing a testable model for microtubule-activated ADP release.

S-adenosyl-L-methionine is a methyl donor in many biological reactions and in bacteria regulates gene expression through binding to the SAM riboswitch. The structure of a third class of SAM riboswitches now indicates which features of SAM the riboswitches have converged on to distinguish it from the closely related S-adenosyl-L-homocysteine.

Glycine receptors (GlyR), part of the Cys-loop neurotransmitter receptor family, are Zn²⁺-modulated ion channels. Electrophysiological studies on GlyR mutants indicate that the hydrophobic cores of the channel's ligand binding domains are important for allosteric communication between the ligand-binding and Zn²⁺-inhibitory sites. The findings suggest a general activation mechanism for this receptor family.

Caspases are cysteine proteases that have a central role in triggering apoptosis; thus, it is essential to tightly control their activity. Now a caspase inhibitor has been identified in Caenorhabditis elegans: CSP-3 is a caspase homolog that associates with the CED-3 zymogen, inhibiting its autoactivation.

In vitro, pure tubulin assembles into B-lattice microtubules, in which lateral αα and ββ contacts between tubulin heterodimers predominate. Mal3, a homolog of the plus end–tracking protein EB1, is now shown to promote microtubule assembly into an A-lattice arrangement, forcing reconsideration of in vivo microtubule structure.

Substitution of the active site gatekeeper residue in the BCR-ABL oncoprotein and related kinases is a common mechanism of imanitib resistance but has also been observed in drug-naïve patients. New work suggests that this residue stabilizes a hydrophobic spine that links the N and C kinase lobes, promoting the active conformation, and that adverse mutations at the gatekeeper residue further stabilize the spine. Disruption of the spine would be an attractive new goal in drug development.

Kinesins are molecular motors that slide along microtubules. A quantum dot is now attached to a microtubule, allowing the visualization of its rotation as it is moved by kinesins. The rotational pitch provides information about the motor, revealing the low processivity of human mitotic kinesin Eg5.

Histone methylation has important consequences for chromatin activity. Now, histones with methyllysine analogs are used to reconstitute nucleosomes: the crystal structures show no global changes in nucleosomes with H3K79me2 and H4K20me3, but the latter modification enhances compaction of nucleosomal arrays.