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PUF proteins are single-stranded RNA-binding proteins that contain multiple repeat elements, each of which contains a tripartite amino acid motif that dictates the identity of the targeted RNA base. Wickens and colleagues analyze the specificities of two dozen PUF proteins to create a palette of RNA specificities that can be used to design new proteins tailored to RNA targets. Cover image from Kasia75/iStock/Thinkstock. pp 732–738, News and Views p 653
Two sibling DNA polymerases synthesize most of the eukaryotic nuclear genome. A new study provides insights into the distinct protein interactions that deliver these replicases for asymmetric leading- and lagging-strand replication and reveals possible cross-talk between DNA replication and other cellular processes.
The development of new strategies to deplete maternal histone proteins in vivo and in vitro has led to the discovery of unexpected roles of histones in forming a functional nuclear envelope.
Classical PUF proteins bind to single-stranded RNA with sequence specificity that can be engineered by site-directed mutagenesis according to a simple RNA-recognition code. Now in-depth probing of the PUF RNA-recognition code enhances future design of PUF proteins and exposes hidden complexity in generating specificity.
Mechanisms of DNA damage repair within actively transcribed genes are poorly understood. Five new reports shed light on the contributions of chromatin to this process by uncovering roles for histone H3 Lys36 methylation, a post-translational modification previously linked to transcription elongation, in the control of DNA-damage signaling and double strand break repair.
Structural elucidation of the RNA aptamer 'Spinach' reveals that a new G-quadruplex structure forms the fluorophore-binding site that confers the ability of the RNA to function as a GFP mimic.
Eukaryotic DNA replication is carried out by two DNA polymerases, Pol ɛ and Pol δ. An in vitro–replication system reconstituted with purified yeast components identifies the factors that selectively recruit each polymerase for leading- or lagging-strand synthesis.
Roquin controls T-cell activity through interactions with mRNAs of stimulatory receptors. Structural and functional elucidation of its RNA-binding domain reveals how it interacts with constitutive decay elements in the 3' UTR of its targets to regulate their expression.
Roquin recognizes the CDE element in mRNAs to promote their decay. Crystal structures of human Roquin ROQ domain in complex with RNA reveals two distinct RNA-binding sites for stem-loop RNA and dsRNA.
Mammalian RPRD proteins bind the phosphorylated CTD of RNA pol II with different affinities. Structural elucidation and characterization of their CTD interaction domains reveal the basis of RPRD binding preferences and a role in directing CTD dephosphorylation.
Plk4 regulates centriole duplication. Two centrosomal scaffold proteins, Cep192 and Cep152, are shown to interact with Plk4 in a temporally and spatially regulated manner, and structural analyses reveal that these interactions are mutually exclusive.
MAP kinases recognize pathway-specific substrates via docking interactions. NMR analyses now reveal that docking interactions also stimulate ATP binding and phosphotransfer activity of p38α via an allosteric mechanism.
A screen identifies 15 genes that modulate CUG-repeat toxicity in C. elegans, including those encoding RNA-export and clearance factors. Toxic RNAs are recognized by the NMD pathway via their 3' UTR GC content.
Eukaryotic initiation factor 5b (eIF5B) is essential for translation initiation. Spahn and colleagues now report cryo-EM structures of the mammalian 80S initiation complex associated with eIF5B that redefine eIF5B as a tRNA reorientation factor.
Guettou et al. describe structural studies on a bacterial homolog of PepT1 and PepT2 peptide transporters—nutrient transporters responsible for all peptide transport across the plasma membrane—in complex with three di- or tripeptides. The data suggest how the transporter's broad peptide specificity is achieved.
A randomized RNA library is used to determine the specificities of RNA recognition by PUF repeats. The code is then used to design a protein that targets endogenous human cyclin B1 mRNA and activates its translation.