Articles in 2009

Some bacteria have the remarkable ability to switch from a free-swimming, planktonic phase to coexistence in a complex biofilm. In this issue of NSMB, the structures of the ligand-bound c-di-GMP riboswitch give insight into some of the molecular processes linked to lifestyle changes but also suggest a potential avenue for applications that begs exploration.

Chromosome end protection is accomplished by telomeres. How cells cope with spontaneously unprotected telomeres while avoiding cell cycle arrest or cell death is a fascinating question.

Flu viruses package essential functions into a small integral membrane protein known as M2. Such small membrane proteins represent major challenges for structural biology. A new study presented in this issue details the structure and functions of the influenza B M2 protein through the use of functional domain–specific solution NMR spectroscopy.

Ubiquitin chains have critical roles in activating the NF-κB pathway and mediating immune responses. Recent structural work on distinct ubiquitin chains in complexes with selective ubiquitin-binding domains provides an explanation for directionality and specificity in the NF-κB pathway.

Argonaute family members are effectors in small RNA-mediated silencing. In vitro analysis of the four human Argonautes demonstrates that AGO1 and AGO2 mediate multiple rounds of microRNA strand dissociation, mediate siRNA passenger-strand cleavage activity, and indicate distinct mechanisms from mRNA endonuclease activity.

How potassium channels select intracellular K⁺ over Na⁺ and Li⁺ is investigated, using experimental and theoretical approaches. The results indicate that selectivity is not due to higher affinity for K⁺ binding, but rather to an energy barrier blocking Na⁺ and Li⁺ entry in the presence of K⁺.

The TAK1 kinase binds K63-linked ubiquitin specifically via its TAB2 subunit. The structure of the TAB2 NZF domain in complex with K63-linked ubiquitins now indicates that this domain interacts with neighboring ubiquitins through distinct sites, explaining the basis of specific recognition.

Telomeric DNA is protected by the shelterin complex, whose disruption triggers DNA-damage responses, checkpoint activation and chromosomal fusions. Now analysis of human cell lines reveals a spontaneously occurring intermediate state in which the DNA-damage response is activated at the telomeres without cell cycle arrest or chromosomal fusions, and with TRF2 playing a central role in determining such a state.

On specific DNA sequences in vitro, a nucleosome is a polar barrier to RNA polymerase II (Pol II). Further analyses of the sequences underlying this barrier effect now indicate the formation of a loop that would preserve the position of the nucleosome on the DNA, while allowing passage of Pol II.

Pre-mRNA splicing is catalyzed by the spliceosome in a two-step reaction. Both catalytic steps have now been reconstituted using purified, defined components. This system identifies a role for Cwc25 in the first step of splicing and allows future detailed mechanistic analyses of splicing.

De novo methylation of DNA can affect the function of underlying genes and transposons in plants. Using a genetic screen, two factors required for de novo demethylation in Arabidopsis thaliana are identified and analyzed.

Condensins are protein complexes essential for eukaryotic mitosis and whose chromosome association is regulated by phosphorylation and dephosphorylation events. Now protein phosphatase PP2A is important for association of condensin II to mitotic chromosomes, but its catalytic activity is not required.

H2A.Z is implicated in genome stability across species. Acetylation of this histone variant in S. pombe is now found to be involved in maintaining condensed chromosomes during mitosis, with premature dissociation of condensin occurring in its absence.

The bacterial transcriptional termination factor Rho is a hexameric helicase that tracks along RNA and dissociates DNA-RNA hybrids. Here the activity of Rho is examined using nucleotide analog interference mapping, revealing that the helicase takes large, 7-nt steps, triggered by contacts with 2′OH in the tracked RNA substrate.

Inward-rectifier K⁺ channels respond to voltage via blockage by intracellular polyamines. How these blockers work is not entirely clear. Now a crystal structure of the cytoplasmic portion of Kir3.1 reveals five ion sites, and functional analyses indicate these ions are displaced by spermine binding.

The eukaryotic group II chaperonin TRiC can block polyQ tract aggregation, present in proteins such as Htt. Here the TRiC-Htt interaction is examined using in vitro and in vivo experiments, revealing that TRiC does not physically block the polyQ tract, but rather sequesters a short N-terminal sequence that promotes the amyloidogenic conformation.

The GEMM riboswitch is conserved in diverse bacteria and recognizes the second messenger c-di-GMP which mediates many processes, such as the transition between sedentary and motile behavior. The structure of the GEMM riboswitch with ligand now elucidates ligand recognition and specificity.