Volume 21 Issue 4, April 2014

Protein homeostasis is essential for cellular function, organismal growth and viability. Damaged and aggregated proteins are turned over by two major proteolytic routes of the cellular quality-control pathways: the ubiquitin-proteasome system and autophagy. For both these pathways, ubiquitination provides the recognition signal for substrate selection. This Commentary discusses how ubiquitin-dependent proteolytic pathways are coordinated with stress- and aging-induced signals.

The past decade has witnessed an explosion in the identification of ubiquitin-ligase complexes as the missing receptors for important small-molecule hormones regulating plant growth and development. These breakthroughs were initiated by genetic approaches, with structural analysis providing mechanistic insights into how hormone perception and signaling are coupled to protein ubiquitination. Although there are still many unknowns, plants have imparted valuable lessons about the pharmacology of ubiquitin modification.

The immune system must operate in an effective, precise and safe manner to defend against diverse pathogens while avoiding attacking the body itself and commensal bacteria. Inflammatory pathways mediated by NOD-like, Toll-like, RIG-I–like and tumor-necrosis-factor receptor families are tightly regulated by ubiquitination, especially by Lys63-linked and linear polyubiquitin chains. Here we discuss the human ubiquitin-mediated inflammatory signaling system, emphasizing the interactions and activities whose coordination ensures timely, accurate regulation of inflammatory responses.

Ubiquitin E3 ligases catalyze the final step of the ubiquitination cascade, promoting the transfer of ubiquitin from the E2 to the substrate target. Recent structural and biochemical studies have given insights in the catalytic mechanisms of all three E3 ligase classes, as discussed in this Review.

Ubiquitin and ubiquitin-like (UBL) modifications occur primarily on lysine residues of target proteins to stimulate downstream signals. This Review discusses current knowledge of lysine specificity in ubiquitin and UBL targeting, with particular focus on the systems in which a detailed mechanism of modification and downstream signaling has been validated biochemically.

DNA metabolism is regulated by the ubiquitin and SUMO modifications, but DNA also influences whether and when these modifications occur. This Review describes the mutual interactions between DNA, ubiquitin and SUMO that occur in DNA-associated processes.

The endoplasmic reticulum–associated degradation (ERAD) pathway maintains protein homeostasis in the ER by retrotranslocating unwanted proteins to the cytosol for proteasomal degradation. This Review discusses the integral role of the ubiquitin system in ERAD, highlighting how the two pathways intertwine to facilitate transport across the ER membrane.

Whereas the proteasome degrades individual proteins modified with ubiquitin chains, autophagy degrades many proteins and organelles en masse. A pair of ubiquitin-like proteins (UBLs), Atg8 and Atg12, regulate autophagy-mediated degradation in a manner completely distinct from that of ubiquitin in the proteasome pathway, as discussed in this Review.

Structures of the deubiquitinating enzyme Rpn11 of the proteasomal 19S regulatory particle reveal its role in hydrolyzing the proximal ubiquitin from a protein that is about to be degraded.

Microhomology-mediated end joining (MMEJ) is a mechanism of DNA double-strand-break repair that creates deletions and promotes other types of genome instability. New in vivo and in vitro analyses demonstrate that the heterotrimeric replication protein A (RPA) complex prevents spontaneous annealing of microhomologies, thereby preventing genome-destabilizing MMEJ.

Housekeeping σ factors are initiation factors for the bacterial RNA polymerase at most promoters, whereas alternative σs direct focused responses to specific environmental conditions. Structural and functional analysis of an alternative σ complexed with its cognate −10 motif elucidates the mechanism for initiation of strand opening, highlighting two critical properties: why alternative σs, compared to housekeeping σs, recognize so few promoters and how their promoter-recognition strategy was diversified during evolution.

Structural and functional analysis reveal the resting state of the voltage-gated proton channel Hv1. Comparison with structures of voltage-sensing domains from other systems, captured in the activated state, will aid in understanding the mechanism of voltage sensing.

RNAi pathways inhibit gene expression at the transcriptional and post-transcriptional level. Genome-wide analyses of nascent RNA transcripts in nematodes now suggest that the CSR-1 RNAi pathway helps maintain the directionality of active transcription and propagate the distinction between transcriptionally active and silent genomic regions.

DNA double-strand breaks (DSBs) may be repaired either by homologous recombination (HR) or nonhomologous end joining (NHEJ) pathways. A new high-resolution mapping study of DSBs in human cells shows that trimethylated histone H3 K36, a marker of active chromatin, targets RAD51 to DSBs within transcribed regions to promote preferential HR-mediated repair at transcriptionally active loci.

Thymic stromal lymphopoietin (TSLP) is a cytokine critical for the development of chronic inflammatory disorders including asthma and atopic dermatitis. The structure of the ternary complex formed by TSLP and its coreceptors TSLPR and the interleukin-7 receptor reveal how TSLP is able to organize receptor-receptor contacts to facilitate intracellular signaling.

Integrins are promising targets in the treatment of conditions that range from cancer to acute coronary syndromes. However, the partial agonism exhibited by RGD ligand–based drugs can result in life-threatening complications. A new study provides the structural basis for pure antagonism by a high-affinity integrin ligand and suggests a path to the design of safer integrin inhibitors.

A new study reports the first structure of a retrotransposon reverse transcriptase in complex with its cognate polypurine tract RNA-DNA hybrid. In contrast to its retroviral counterparts, Ty3 reverse transcriptase forms an asymmetric homodimer that forms in the presence of substrate, with its RNase H and DNA polymerase activities likely contributed by separate subunits.

IgE molecules associate with the FcɛRIα receptor in an acutely bent conformation where the Cɛ2 domains fold over the Cɛ3-Cɛ4 domains. A new study demonstrates that IgE can exist in an extended conformation with a Cɛ2 domain capable of flipping from side to side, suggesting a level of structural flexibility that could functionally impact allergen recognition.

Resection of DNA double strand–break ends generates single strands that can spontaneously anneal to undergo mutagenic microhomology-mediated end joining (MMEJ). A combination of genetic and biophysical assays now shows that replication protein A (RPA) thwarts strand annealing by binding to the resected ends to promote Rad51 filament assembly and error-free repair by homologous recombination.

IRSp53 is a BAR-domain protein under the control of Rho family GTPases and has crucial roles in processes such as cell motility and tumor invasiveness. In a new study, IRSp53 is shown to be autoinhibited and is synergistically activated by the combinatorial action of Cdc42 and the tumor-promoting factor Eps8.

Human endogenous retrovirus subfamily H (HERVH) is a class of transposable elements expressed preferentially in human embryonic stem cells (hESCs). A new study now shows that the long terminal repeats of HERVH function as enhancers and that HERVH is a nuclear long noncoding RNA required to maintain hESC identity.

Ubiquitin and ubiquitin-like proteins are protein modifiers that play key roles in a variety of cellular processes. This Focus highlights the recent major breakthroughs in understanding how these modifications are regulated and targeted to protein substrates. Recent insights in the role of ubiquitin-like proteins in autophagy, DNA targeting and ER-associated degradation will also be covered. Produced with support from Takeda.