SummaryPoly(ADP-ribose)polymerase 1 (PARP-1) is a key eukaryotic stress sensor that responds in seconds to DNA single-strand breaks (SSBs), the most frequent genomic damage. A burst of poly(ADP-ribose) synthesis initiates DNA damage response, whereas PARP-1 inhibition kills BRCA-deficient tumor cells selectively, providing the first anti-cancer therapy based on synthetic lethality. However, the mechanism underlying PARP-1’s function remained obscure; inherent dynamics of SSBs and PARP-1’s multi-domain architecture hindered structural studies. Here we reveal the structural basis of SSB detection and how multi-domain folding underlies the allosteric switch that determines PARP-1’s signaling response. Two flexibly linked N-terminal zinc fingers recognize the extreme deformability of SSBs and drive co-operative, stepwise self-assembly of remaining PARP-1 domains to control the activity of the C-terminal catalytic domain. Automodifcation in cis explains the subsequent release of monomeric PARP-1 from DNA, allowing repair and replication to proceed. Our results provide a molecular framework for understanding PARP inhibitor action and, more generally, allosteric control of dynamic, multi-domain proteins.

The anti-cancer drug target poly(ADP-ribose) polymerase 1 (PARP1) and its close homologue, PARP2, are early responders to DNA damage in human cells 1 , 2 . Upon binding to genomic lesions, these enzymes utilise NAD + to modify a plethora of proteins with mono- and poly(ADP-ribose) signals that are important for subsequent chromatin decompaction and repair factor recruitment 3 , 4 . These post-translational modification events are predominantly serine-linked and require HPF1, an accessory factor that is specific for DNA damage response and switches the amino-acid specificity of PARP1/2 from aspartate/glutamate to serine residues 5 – 10 . Here, we report a co-structure of HPF1 bound to the catalytic domain of PARP2 that, in combination with NMR and biochemical data, reveals a composite active site formed by residues from both PARP1/2 and HPF1. We further show that the assembly of this new catalytic centre is essential for DNA damage-induced protein ADP-ribosylation in human cells. In response to DNA damage and NAD + binding site occupancy, the HPF1-PARP1/2 interaction is enhanced via allosteric networks operating within PARP1/2, providing an additional level of regulation in DNA repair induction. As HPF1 forms a joint active site with PARP1/2, our data implicate HPF1 as an important determinant of the response to clinical PARP inhibitors.

Poly(ADP-ribose)polymerase-1 (PARP-1) is a highly abundant chromatin-associated enzyme present in all higher eukaryotic cell nuclei, where it plays key roles in the maintenance of genomic integrity, chromatin remodeling and transcriptional control. It binds to DNA single- and double-strand breaks through an N-terminal region containing two zinc fingers, F1 and F2, following which its C-terminal catalytic domain becomes activated via an unknown mechanism, causing formation and addition of polyadenosine-ribose (PAR) to acceptor proteins including PARP-1 itself. Here, we report a biophysical and structural characterization of the F1 and F2 fingers of human PARP-1, both as independent fragments and in the context of the 24-kDa DNA-binding domain (F1 + F2). We show that the fingers are structurally independent in the absence of DNA and share a highly similar structural fold and dynamics. The F1 + F2 fragment recognizes DNA single-strand breaks as a monomer and in a single orientation. Using a combination of NMR spectroscopy and other biophysical techniques, we show that recognition is primarily achieved by F2, which binds the DNA in an essentially identical manner whether present in isolation or in the two-finger fragment. F2 interacts much more strongly with nicked or gapped DNA ligands than does F1, and we present a mutational study that suggests origins of this difference. Our data suggest that different DNA lesions are recognized by the DNA-binding domain of PARP-1 in a highly similar conformation, helping to rationalize how the full-length protein participates in multiple steps of DNA single-strand breakage and base excision repair.

Accurate read-out of chromatin modifications is essential for eukaryotic life. Mutations in the gene encoding X-linked ATRX protein cause a mental-retardation syndrome, whereas wild-type ATRX protein targets pericentric and telomeric heterochromatin for deposition of the histone variant H3.3 by means of a largely unknown mechanism. Here we show that the ADD domain of ATRX, in which most syndrome-causing mutations occur, engages the N-terminal tail of histone H3 through two rigidly oriented binding pockets, one for unmodified Lys4 and the other for di- or trimethylated Lys9. In vivo experiments show this combinatorial readout is required for ATRX localization, with recruitment enhanced by a third interaction through heterochromatin protein-1 (HP1) that also recognizes trimethylated Lys9. The cooperation of ATRX ADD domain and HP1 in chromatin recruitment results in a tripartite interaction that may span neighboring nucleosomes and illustrates how the 'histone-code' is interpreted by a combination of multivalent effector-chromatin interactions.

Translation initiation factor eIF3 acts as the key orchestrator of the canonical initiation pathway in eukaryotes, yet its structure is greatly unexplored. We report the 2.2 Å resolution crystal structure of the complex between the yeast seven-bladed β-propeller eIF3i/TIF34 and a C-terminal α-helix of eIF3b/PRT1, which reveals universally conserved interactions. Mutating these interactions displays severe growth defects and eliminates association of eIF3i/TIF34 and strikingly also eIF3g/TIF35 with eIF3 and 40S subunits in vivo. Unexpectedly, 40S-association of the remaining eIF3 subcomplex and eIF5 is likewise destabilized resulting in formation of aberrant pre-initiation complexes (PICs) containing eIF2 and eIF1, which critically compromises scanning arrest on mRNA at its AUG start codon suggesting that the contacts between mRNA and ribosomal decoding site are impaired. Remarkably, overexpression of eIF3g/TIF35 suppresses the leaky scanning and growth defects most probably by preventing these aberrant PICs to form. Leaky scanning is also partially suppressed by eIF1, one of the key regulators of AUG recognition, and its mutant sui1G107R but the mechanism differs. We conclude that the C-terminus of eIF3b/PRT1 orchestrates co-operative recruitment of eIF3i/TIF34 and eIF3g/TIF35 to the 40S subunit for a stable and proper assembly of 48S pre-initiation complexes necessary for stringent AUG recognition on mRNAs.

The chromatin-associated protein ATRX was originally identified because mutations in the ATRX gene cause a severe form of syndromal X-linked mental retardation associated with ␣-thalassemia. Half of all of the disease-associated missense mutations cluster in a cysteine-rich region in the N terminus of ATRX. This region was named the ATRX-DNMT3-DNMT3L (ADD) domain, based on sequence homology with a family of DNA methyltransferases. Here, we report the solution structure of the ADD domain of ATRX, which consists of an N-terminal GATA-like zinc finger, a plant homeodomain finger, and a long C-terminal ␣-helix that pack together to form a single globular domain. Interestingly, the ␣-helix of the GATA-like finger is exposed and highly basic, suggesting a DNA-binding function for ATRX. The disease-causing mutations fall into two groups: the majority affect buried residues and hence affect the structural integrity of the ADD domain; another group affects a cluster of surface residues, and these are likely to perturb a potential protein interaction site. The effects of individual point mutations on the folding state and stability of the ADD domain correlate well with the levels of mutant ATRX protein in patients, providing insights into the molecular pathophysiology of ATR-X syndrome.ATR-X syndrome ͉ NMR structure ͉ zinc finger A TRX was identified when the gene encoding this protein was shown to be mutated in a form of X-linked mental retardation (ATR-X syndrome) in young males (1, 2). Furthermore, null mutations in mice are lethal at the embryonic stage of development (3). Because ATRX mutations reduce ␣-globin synthesis, causing ␣-thalassemia, it seems likely that ATRX normally plays a role in the regulation of globin gene expression (2, 4). The complexity of the disease also suggests that ATRX could be involved in the regulation of other as yet unidentified genes. ATRX is a large (2,492 residue; Ϸ280 kDa) nuclear protein predominantly localized to heterochromatin and nuclear PML bodies (5, 6). It contains two highly conserved domains, and missense mutations that give rise to ATR-X syndrome fall within these. At the C terminus is a helicase/ATPase domain, which characterizes ATRX as a member of the SNF2 (SWI/SNF) family of chromatin-associated proteins. Experimental evidence shows that ATRX acts as a DNA-dependent ATPase and as a DNA translocase, and it confers modest chromatin-remodeling activity in vitro (6). Thus, it seems likely that ATRX exerts its function by targeting chromatin.Of the missense mutations identified in the ATRX gene, 50% are located in the N terminus of the ATRX protein, which represents just 4% of the coding sequence (Fig. 1a) (7). This region is highly cysteine-rich and contains two different types of zinc-finger motif. It was first noticed that a region of the sequence shares homology with the plant homeodomain (PHD)-type zinc fingers (8). Mutations in other PHD-containing proteins (WSTF and AIRE) are also associated with human disease (9, 10). PHD fingers are found in nuclear proteins, and a...

Ratiometric fluorescence detection attracts much attention because of its decreased environmental influence and easy-to-differentiate color and intensity change. Herein, a guest-encapsulation metal-organic framework (MOF), Ru@MIL-NH, is prepared with 2-aminoterephthalic acid, AlCl, and Ru(bpy) by a simple one-pot method for ratiometric fluorescence sensing of water in organic solvents. The rational selection of the excitation wavelength provides dual emission at 465 and 615 nm from Ru@MIL-NH under a single excitation of 300 nm. High sensitivity, low detection limit (0.02% v/v), wide response range (0-100%), and fast response (less than 1 min) are obtained for ratiometric fluorescence sensing of water under single excitation with Ru@MIL-NH as the probe. Moreover, the result of water content is independent of the concentration of Ru@MIL-NH as the merit of ratiometric fluorescence detection. The response mechanism reveals that the protonation of the nitrogen atom of the MIL-NH, the π-conjugation system, and the stable fluorescence of Ru(bpy) achieve the ratiometric fluorescence. The analysis of real spirit samples confirms the proposed method. A test strip is prepared with Ru@MIL-NH for convenient use. We believe that such turn-on ratiometric host-guest MOFs and the rational selection of excitation wavelength will offer guidance for ratiometric fluorescence detection with wide applications.

SummaryPolyadenylation regulation and efficient nuclear export of mature mRNPs both require the polyadenosine-RNA-binding protein, Nab2, which contains seven CCCH Zn fingers. We describe here the solution structure of fingers 5-7, which are necessary and sufficient for high-affinity polyadenosine-RNA binding, and identify key residues involved. These Zn fingers form a single structural unit. Structural coherence is lost in the RNA-binding compromised Nab2-C437S mutant, which also suppresses the rat8-2 allele of RNA helicase Dbp5. Structure-guided Nab2 variants indicate that dbp5(rat8-2) suppression is more closely linked to hyperadenylation and suppression of mutant alleles of the nuclear RNA export adaptor, Yra1, than to affinity for polyadenosine-RNA. These results indicate that, in addition to modulating polyA tail length, Nab2 has an unanticipated function associated with generating export-competent mRNPs, and that changes within fingers 5-7 lead to suboptimal assembly of mRNP export complexes that are more easily disassembled by Dbp5 upon reaching the cytoplasm.