Research articles

The reconstitution of two fungal NRPSs provides the first biochemical evidence that these assembly lines use a condensation-like domain to complete the synthesis of cyclic natural products instead of the thioesterase domain used in bacterial species.

DNA damage products influence DNA replication but also may induce stalling or mutagenesis during transcription. A competitive transcription and adduct bypass assay provides a new approach for assessing the transcriptional effects of DNA lesions and links transcriptional arrest of several lesions to nucleotide excision repair pathways.

The plant hormone auxin affects many aspects of root development, including lateral root branching. A high-throughput screen in Arabidopsis thaliana has led to the identification of naxillin, a non-auxin chemical probe that enhances lateral root branching and has revealed an important role of the root cap in regulating this process.

Genetic code expansion by ribosomal incorporation of non-natural amino acids has provided a useful approach for site-specific protein modification. This approach has now been extended to the model organism Drosophila melanogaster, permitting the introduction of non-standard amino acids into proteins within specific cell and tissue types and across developmental stages.

Peroxidasin uses hypohalous acid oxidants to catalyze the formation of sulfilimine bonds in basement membranes.

Discovery of the native activity of the ~60,000 putative glycosyltransferases remains a substantial challenge. A high-throughput, label-free method drastically speeds this process, with assays of 85 enzymes, 24 acceptors and 7 donors returning functions for four new proteins.

Single-molecule imaging reveals that GPI-anchored proteins in the plasma membrane form homodimer rafts via ectodomain protein interactions. Raft-lipid interactions stabilize higher order oligomers, which trigger intracellular signaling upon ligand binding.

A study of three synthetases involved in streptothricin biosynthesis demonstrates roles for two A domains in activating lysine, with one A domain transferring lysine to a carrier T domain and the second directly catalyzing amide bond formation to form a growing lysine oligopeptide.

AWP28, an activity-based probe for caspase-1, reveals that caspase-1 is required to bypass apoptosis for pyroptotic cell death during bacterial infection of macrophages.

Application of a new thermal light scattering technique to quantitatively analyze nearly 150 mutants of the rhomboid intramembrane protease GlpG, coupled with thermodynamic measurements and protease assays, reveals how interactions throughout the molecule collaborate to support enzyme structure and function.

Bacterial siderophores are known to bind various metals in vitro but are generally thought of as iron chelators in vivo. MS now demonstrates that yersiniabactin binds copper in vivo, with yersiniabactin expression correlated to bacterial fitness.

AID/APOBEC deaminases, which convert cytosine bases to uracils in DNA and RNA, have recently been assigned a role in epigenetic regulation as components of DNA demethylation pathways. A systematic study shows that AID/APOBEC enzymes preferentially deaminate unmodified cytosine over its C5-modified forms, calling into question the plausibility of deaminase-mediated DNA demethylation pathways.

Hydrogen sulfide anion reacts with cellular electrophiles, including 8-nitro-cGMP, and sulfhydration products inhibit S-guanylation–dependent H-Ras activation in cardiac inflammatory injury models.

The chaperone FimC only selects unfolded, disulfide-intact pilus subunits and accelerates protein folding by lowering topological complexity, thereby ensuring quality control in pilus assembly.

Bacterial resistance is propagated in part by metallo-β-lactamases, which hydrolyze and inactivate β-lactam antibiotics. An unusual cysteine residue in the active site is now shown to be critical for retaining the second metal ion, and thus enzyme activity, at low zinc concentrations.

Different key residues mediate melanocortin-4 receptor activation via the agonist αMSH or constitutive activation via interaction of the transmembrane domain with the N-terminal domain, and these modes are further distinguishable by the different effects of the physiological antagonist.

Elongation factor P is a conserved translational regulatory protein that has an unusual post-translational modification, in which Lys34 forms an amide linkage to (R)-β-lysine. Further characterization reveals that Lys34 is also hydroxylated, drawing parallels to a functional modification of eukaryotic initiation factor 5A.

Phenylketonuria (PKU) is characterized by increased levels of phenylalanine in the blood and progressive mental retardation. Now, phenylalanine is shown to form toxic amyloid fibrils at high concentrations, which accumulate in the brains of PKU patients and mouse models.

Phage display reveals peptides that bind to the caspase-6 zymogen, inducing its tetramerization and specifically inhibiting its enzyme activity both in vitro and in neuronal cells.

Fluorinated, cell-permeable analogs of sialic acid and fucose are processed by monosaccharide salvage pathways to generate sialyl- and fucosyltransferase inhibitors intracellularly. These compounds serve as important new tools to dissect the role of glycan modifications within complex biological systems.