Volume 16 Issue 10, October 2009

A functional proteomics study reveals that nuclear pore proteins are direct substrates for mitogen-activated protein (MAP) kinases, leading to a new mechanism for growth factor control of nuclear transport.

Trigger factor is a ribosome-associated chaperone that assists early folding steps of nascent proteins in bacteria. A new study presents the first crystal structure of Trigger factor in complex with a folded protein bound as substrate, challenges the current model for how Trigger factor interacts with substrates and suggests an unexpected role for Trigger factor in protein assembly and ribosome biogenesis.

Developmental expression of the microRNA let-7 is tightly regulated in many animals, and turnover has been linked to LIN-28 and uridylation in mammals. This regulation is now shown to be conserved in Caenorhabditis elegans, and PUP-2 is shown to be a uridylase that is specifically recruited to let-7 in a LIN-28–dependent manner.

The let-7 microRNA has been implicated in development and disease. Its expression must thus be tightly regulated, and previously uridylation and Lin28 were implicated in let-7 stability. Zcchc11 is now shown to be the uridylase that mediates pre–let-7 modification and regulates mature let-7 levels and activity in mouse embryonic stem cells.

An improved method for detecting proteins phosphorylated by the ERK kinase reveals multiple new in vitro ERK substrates, including three nucleoporin proteins. Nup50 is phosphorylated in FG repeats by ERK2 in vivo and in vitro, suggesting a new mechanism by which MAP kinase signaling controls nuclear translocation of proteins.

Rhesus macaque monkeys can inhibit retroviral replication via TRIMCyp, a variant of TRIM5a with an insertion of the cyclophilin A cDNA. Cyclophilin A binds to HIV-1 capsid, whereas TRIMCyp restricts HIV-2. How the change in specificity of this domain occurred is now revealed through biophysical and structural studies.

Transcription initiation involves recruitment of key factors to promoters. Yeast TATA-binding protein (TBP) turnover is now examined genome-wide and genes transcribed by the three RNA polymerases found to have distinct signatures. Further analyses suggest that TBP dynamics, rather than DNA sequence affinity per se, is key to gene expression.

Colicins are secreted bacterial toxins. To avoid killing the producer organism, each colicin is coexpressed with a high-affinity inhibitor, or immunity protein (Im). The evolution of Im-Colicin interfaces and the evolvability traits of protein-protein interactions are now examined using in vitro evolution and structural analyses.

The positions of nucleosomes can affect processes occurring on DNA. DNA curtains are now used to study nucleosome positioning in vitro. This allows assessment of sequence-related effects on positioning and indicates that the yeast factor Scm3 can overcome the aversion of nucleosomes to AT-rich sequences.

Escherichia coli YiiP, a member of the cation diffusion facilitator family, exports cytoplasmic zinc, maintaining cellular homeostasis. The high-resolution crystal structure of YiiP, combined with functional studies focused on its cytoplasmic C-terminal domain, suggest how it is able to allosterically modulate zinc transport.

F₁F_o ATP synthases produce ATP using proton- or sodium-motive force to drive ions through the membrane-embedded F_o complex, causing rotation of its c-ring rotor leading to ATP synthesis. The first high-resolution crystal structure of the c-ring from a proton-translocating F₁F_o-ATP synthase reveals the architecture of the proton-binding site and provides insight into the mechanism of proton transport.

Nucleosomes can be modified by replacing the core histones with variants, the most diverse of which is macroH2A. The localization of macroH2A variants in human male pluripotent cells indicates that this variant functions in repression of key developmental genes and is essential for zebrafish embryogenesis.

Increasing evidence indicates that membrane protein function can be affected by the surrounding membrane bilayer. A new study on voltage-gated potassium channels using tarantula toxins suggests that lipid interaction with the voltage sensor can influence channel function.

Some p53 mutations result in gain-of-function variants that can contribute to tumorigenesis. Three such mutants, R175H, R273H and R280K p53, are now shown to cooperate with transcription factor E2F1 to upregulate the expression of ID4, which in turn stabilizes the transcripts from pro-angiogenic factors IL-8 and GRO-α.

Alternative splicing increases genome coding potential and is affected by factors including the hnRNPs. The effect of altering splice site strength on splicing activity is now found to be antagonized by nearby hnRNP H binding sites. Other splicing factor sites may have similar effects and may thus have influenced splice form evolution.

Identifying physiological substrates of proteases still poses a challenge. An unbiased approach using the heterologous Escherichia coli proteome now identifies the structural and sequence determinants for caspase-3 substrates, revealing a kinetic threshold that can distinguish relevant substrates.

The maturation of tRNAs involves folding into their L shape and nucleotide modifications at several positions. Some modifying enzymes require an L-shaped substrate, and the crystal structure of methylase Trm5 in complex with AdoMet and tRNA now reveals how the substrate tertiary structure is sensed.