Articles in 2010

Secretion of strigolactone from plant roots mediates mutualistic fungal interactions but also facilitates parasitic plant invasion. A screen in Arabidopsis thaliana has identified compounds that perturb strigolactone levels and link this hormone to light signaling pathways in host plants.

The multiple lysines that can link ubiquitin chains have created challenges in studying these important biopolymers. The ribosomal incorporation of a protected lysine analog now allows the specific construction of native K6- and K29-linked diubiquitin chains, enabling structural analysis and deubiquitinase profiling.

Iron-sulfur clusters are essential components of many proteins and are assembled in a hierarchical pathway. Tah18 is a diflavin reductase that transfers electrons to the [2Fe-2S] cluster of Dre2 in an early step of iron-sulfur cluster biogenesis in the cytoplasm of eukaryotes.

Structure-specific flap endonuclease 1 (FEN1) is known to interact with multiple nuclear proteins involved in DNA metabolism. Arginine methylation in FEN1 blocks phosphorylation of a nearby serine and enhances FEN1 binding to PCNA, which serves to channel FEN1 toward DNA replication and repair pathways.

Polymerase exclusion of ribonucleotides during DNA replication is imperfect. New data indicate that DNA polymerase ϵ incorporates into DNA ribonucleotides that are repaired by an RNase H2–dependent process and that defective repair results in replicative stress and genome instability.

Although FPPS is a potential anti-cancer target, the high bone affinity of nitrogen-containing bisphosphonates, FPPS inhibitors used clinically to treat bone disease, has prevented their development as cancer therapeutics. Using fragment-based drug discovery, non-bisphosphonate inhibitors were discovered that bind in a previously undescribed allosteric pocket.

A chemical array screen identifies a small-molecule inhibitor of pirin that inhibits its interaction with the oncoprotein Bcl3 and decreases the expression of the tumor mobility protein SNAI2. As a result, the compound perturbs the migration of melanoma cells that have high pirin expression levels.

Biotin synthesis is known to include a pimelate intermediate, the construction of which is controversial. Genetic manipulations and chemical feeding now demonstrate that the two mystery enzymes in the process create and cleave a methyl ester that sends a biotin precursor into the fatty acid synthesis machinery.

Probing the biological location and function of transition metals has proven difficult. X-ray fluorescence microscopy in combination with an array of metal chelators now provides a way to interrogate zinc in maturing mouse oocytes, demonstrating a role for this metal in cell division.

Instability of (CTG)•(CAG) repeats in microsatellite DNA has been linked to numerous neurological diseases. Probing trinucleotide repeat structures using engineered zinc-finger nucleases provides evidence that DNA hairpins form in vivo and are linked to replication-dependent genomic instability.

Current methods to investigate glycosylation allow the identification of modification sites but provide limited additional information. A new strategy using polymers to label specific sugars now shows a huge variety in the occupancy of known glycosylation sites as well as unexpected interplay between post-translational modifications.

Proteins rely on a combination of intramolecular forces to form and stabilize their structures. A careful comparison of computational analysis and high-resolution crystal structures now indicates that the n→π* interaction merits inclusion in this group.

Evidence for the existence and importance of GPCR dimers and oligomers is mounting, but direct detection of these species has been challenging. The development of improved fluorescent ligands for time-resolved spectroscopy confirms their presence across GPCR families and in native tissue.

Proteomic analysis in dendritic cells identifies three palmitoylation sites within IFITM3, an innate immunity protein involved in inhibition of early replication of several viruses. Palmitoylation of IFITM3 regulates its clustering in membranes and is crucial for inhibition of influenza virus infection.

Small RNAs targeted to gene promoters are known regulators of transcription in mammalian cells. Antigene RNAs complementary to non-coding transcripts localized to the 3′ termini of genes are now shown to regulate transcription across long genomic sequences.

The lipocalin protein Scn-Ngal is known to bind iron-chelating siderophores, leading to inhibition of bacterial growth. New results reveal that Scn-Ngal, in the absence of bacterial infection, can form a complex with catechol that binds and transports iron in vivo.

Amide bonds are routinely formed in biological systems using carboxylic acids that have been activated at the expense of ATP. The biochemical characterization of a putative β-lactamase now reveals a new way to form amide bonds using stable methyl ester intermediates.

MCL-1 has emerged as a major oncogenic and chemoresistance factor. A screen of stapled peptide helices identified the MCL-1 BH3 domain as selectively inhibiting MCL-1 among the related anti-apoptotic Bcl-2 family members, providing insights into the molecular determinants of binding specificity and a new approach for sensitizing cancer cells to apoptosis.

The target of theonellamides, a family of bicyclic peptides with antifungal activity, has previously proven elusive. A combination of chemical-genomic profiling and biochemical and cellular analysis now reveals that these compounds target sterols to activate Rho1 signaling and induce membrane damage.

Chemical screening in C. elegans is limited by the relatively poor target accessibility of small molecules. A systematic survey of drug-like small molecule accumulation and metabolism in C. elegans was used to create a computational tool for preselecting compounds likely to effectively perturb worms.