Articles in 2010

Telomere shortening, senescence and aging are connected, but how the signal at shortening telomeres is transmitted to the cell more globally is unclear. H3 and H4 synthesis is now shown to be reduced as cell cultures age. This alters expression of Asf1, a histone chaperone, compromising the ability of aging cells to restore chromatin after replication and DNA. In this way localized effects at shortening telomeres can be propagated throughout the cell.

Tumor suppressor PALB2 is known to interact with BRCA1 and BRCA2, and to be required for the latter's localization to sites of DNA damage. Now PALB2 is shown to bind directly to DNA, to recombinase RAD51 and its accessory factor RAD51AP1. PALB2 also stimulates D loop formation by RAD51 in a synergistic manner with RAD51AP1.

Tumor suppressor PALB2 is known to interact with BRCA2 and promote homologous recombination in vivo. Now PALB2's activities have been studied, together with a BRCA2 chimeric protein, revealing that PALB2 binds D-loop structures, interacts directly with RAD51 and promotes strand invasion synergistically with BRCA2.

Bacteriocins are toxins produced by bacteria to inhibit similar or related bacterial strains, and one such toxin, colicin E3, is known to target the ribosome by cleaving the 16S rRNA. The structure of the 70S ribosome in complex with the cytotoxic domain of colicin E3 now gives insight into the cleavage mechanism.

RecBCD is a bacterial complex that functions in repair of DNA breaks. The RecBC heterodimer has an ATPase motor (RecB) that translocates along ssDNA with a 3'->5' polarity. Now a second translocase activity is revealed in RecBC that moves the proteins along the opposite strand of a forked DNA at a similar rate.

Secretins are bacterial outer membrane proteins involved in different pathways for protein secretion or macromolecular complex assembly. Secretin can form a large oligomeric pore, whose opening needs to be carefully regulated. Now cryo-EM analysis of the Vibrio cholerae secretin GspD reveals a closed channel, with a constricted periplasmic vestibule, offering insight into the mechanism of GspD opening during protein secretion.

AZT is a nucleoside analog drug that inhibits HIV-1 reverse transcriptase (RT). The viral enzyme can acquire AZT resistance by mutations that enhance the rate of ATP-mediated excision of the incorporated AZT. Now structural work illustrates how the AZT resistance mutations create a high-affinity binding site for ATP and thus promote excision.

Ubr1 and Ubr2 are E3 ligases that target substrates by the N-end rule, and it is the UBR box that is needed for substrate recognition. The structures of the UBR boxes of human UBR1 and UBR2 show that they adopt a previously undescribed fold stabilized by zinc. One of the zinc-binding ligands is mutated in Johnson-Blizzard syndrome and leads to UBR box unfolding.

In the N-end rule pathway, the N-terminal residue of a protein is recognized by specific E3 ligases that promote its ubiquitination and proteasomal degradation. Now the structural basis for the recognition of N-terminal basic residues by the UBR box from yeast Ubr1 is solved. Together with functional analysis, the work reveals that the residue at position 2 of the substrate may influence the binding.

The co-transcriptional processing of RNA depends on the precisely timed recruitment of different factors to the elongating transcript, which depends on the phosphorylation state of the C-terminal domain (CTD) of RNA polymerase II. Varani and coworkers show that two transcription termination factors, Rtt103 and Pcf1, bind specifically and cooperatively to Ser2-phosphorylated CTD. This provides a way to ensure that proper polyadenylation occurs only where Ser2 phosphorylation density is highest.

SpoT has a key role in the bacterial starvation response. Now the metazoan ortholog of SpoT, Mesh1, has been identified, and the structure reveals a conserved active site that can catalyze ppGpp hydrolysis. The Drosophila Mesh1 deletion mutant has impaired starvation resistance, and microarray analysis gives further insight into the starvation response.

The structure of the small heat shock protein αB-crystallin, associated with multiple sclerosis and Alzheimer's disease, has eluded biologists for years. Small angle X-ray scattering and solid-state NMR reveal a curved dimer that modulates substrate interactions upon a change in pH.

How changes in chromatin can modulate the repair pathway of DNA double-strand breaks is now investigated. The work shows that histone deacetylases HDAC1 and HDAC2 are recruited to sites of DNA damage, where they mediate the removal of H3K56 acetyl marks, and their activity is important for repair via non-homologous end-joining.

AID is a DNA cytidine deaminase with a central role in the generation of antibody diversity. AID initiates class switch recombination by modifying DNA within the switch (S) regions in the IgH locus. Now AID is shown to be targeted to the S regions by interaction with adaptor proteins 14-3-3, which in turn bind directly to the DNA motif 5'AGCT.

The synthetic ABA agonist pyrabactin helped identify the PYR/PYL family of ABA receptors. Now the selectivity of pyrabactin toward specific members of this family is explained using genetic, chemical and structural approaches. Subtle differences in the binding pockets of the receptors lead to productive or nonproductive conformations upon pyrabactin binding.

The fourteen members of the PYR/PYL family are receptors for the plant hormone abscisic acid (ABA). Now structural and functional work using the synthetic ligand pyrabactin, which inhibits seed germination, reveal that the PYL/PYR receptors respond differently to pyrabactin, elucidate the mechanisms for selective activation or inhibition of ABA receptors and allow the design of novel agonists.

The function of GenX, an aminoacyl-tRNA synthetase paralog in Escherichia coli, is now probed by structural and functional analyses. The work shows that GenX mediates the lysylation of translation elongation factor EF-P, and this activity is essential for cell growth.

PTB is a repressive splicing regulator. The effect of PTB knockdown in HeLa cells is now examined, indicating that similar to other recently examined factors, PTB variably affects splicing in a predictable fashion depending on where its binding site is relative to the target exon.

Dcp2 mediated decapping of mRNAs is a key step in 5'-3' transcript decay. Using NMR-based analysis, it is now shown that the cap is recognized by two distinct regions in the regulatory and catalytic domains of Dcp2. This argues that cap recognition involves these regions coming together, in a step promoted by the regulatory factor Dcp1, thus leading to catalysis.

The FUSE regulatory system, consisting of FBP binding the FUSE DNA element and recruiting the FIR repressor, acts as a transcriptional on/off switch that promotes a peak of c-myc expression over the course of a cell cycle. FIR recruitment and its interaction with FBP is now examined, providing a basis for precise c-myc transcriptional regulation.