Dynamic interactions of the HIV-1 Tat with nucleic acids are critical for Tat activity in reverse transcription

The HIV-1 transactivator of transcription (Tat) protein is thought to stimulate reverse transcription (RTion). The Tat protein and, more specifically, its (44–61) domain were recently shown to promote the annealing of complementary DNA sequences representing the HIV-1 transactivation response element TAR, named dTAR and cTAR, that plays a key role in RTion. Moreover, the kinetic mechanism of the basic Tat(44–61) peptide in this annealing further revealed that this peptide constitutes a representative nucleic acid annealer. To further understand the structure–activity relationships of this highly conserved domain, we investigated by electrophoresis and fluorescence approaches the binding and annealing properties of various Tat(44–61) mutants. Our data showed that the Tyr47 and basic residues of the Tat(44–61) domain were instrumental for binding to cTAR through stacking and electrostatic interactions, respectively, and promoting its annealing with dTAR. Furthermore, the annealing efficiency of the mutants clearly correlates with their ability to rapidly associate and dissociate the complementary oligonucleotides and to promote RTion. Thus, transient and dynamic nucleic acid interactions likely constitute a key mechanistic component of annealers and the role of Tat in the late steps of RTion. Finally, our data suggest that Lys50 and Lys51 acetylation regulates Tat activity in RTion.

Structural and functional role of INI1 and LEDGF in the HIV-1 preintegration complex

Integration of the HIV-1 cDNA into the human genome is catalyzed by the viral integrase (IN) protein. Several studies have shown the importance of cellular cofactors that interact with integrase and affect viral integration and infectivity. In this study, we produced a stable complex between HIV-1 integrase, viral U5 DNA, the cellular cofactor LEDGF/p75 and the integrase binding domain of INI1 (INI1-IBD), a subunit of the SWI/SNF chromatin remodeling factor. The stoichiometry of the IN/LEDGF/INI1-IBD/DNA complex components was found to be 4/2/2/2 by mass spectrometry and Fluorescence Correlation Spectroscopy. Functional assays showed that INI1-IBD inhibits the 3′ processing reaction but does not interfere with specific viral DNA binding. Integration assays demonstrate that INI1-IBD decreases the amount of integration events but inhibits by-product formation such as donor/donor or linear full site integration molecules. Cryo-electron microscopy locates INI1-IBD within the cellular DNA binding site of the IN/LEDGF complex, constraining the highly flexible integrase in a stable conformation. Taken together, our results suggest that INI1 could stabilize the PIC in the host cell, by maintaining integrase in a stable constrained conformation which prevents non-specific interactions and auto integration on the route to its integration site within nucleosomes, while LEDGF organizes and stabilizes an active integrase tetramer suitable for specific vDNA integration. Moreover, our results provide the basis for a novel type of integrase inhibitor (conformational inhibitor) representing a potential new strategy for use in human therapy.

Site-selective probing of cTAR destabilization highlights the necessary plasticity of the HIV-1 nucleocapsid protein to chaperone the first strand transfer

The HIV-1 nucleocapsid protein (NCp7) is a nucleic acid chaperone required during reverse transcription. During the first strand transfer, NCp7 is thought to destabilize cTAR, the (−)DNA copy of the TAR RNA hairpin, and subsequently direct the TAR/cTAR annealing through the zipping of their destabilized stem ends. To further characterize the destabilizing activity of NCp7, we locally probe the structure and dynamics of cTAR by steady-state and time resolved fluorescence spectroscopy. NC(11–55), a truncated NCp7 version corresponding to its zinc-finger domain, was found to bind all over the sequence and to preferentially destabilize the penultimate double-stranded segment in the lower part of the cTAR stem. This destabilization is achieved through zinc-finger–dependent binding of NC to the G₁₀ and G₅₀ residues. Sequence comparison further revealed that C•A mismatches close to the two G residues were critical for fine tuning the stability of the lower part of the cTAR stem and conferring to G₁₀ and G₅₀ the appropriate mobility and accessibility for specific recognition by NC. Our data also highlight the necessary plasticity of NCp7 to adapt to the sequence and structure variability of cTAR to chaperone its annealing with TAR through a specific pathway.

A new parametrization of the Stillinger-Weber potential for an improved description of defects and plasticity of silicon

A new parametrization of the widely used Stillinger-Weber potential is proposed for silicon, allowing for an improved modelling of defects and plasticity-related properties. The performance of the new potential is compared to the original version, as well as to another parametrization (Vink et al 2001 J. Non-Cryst. Solids, 282 248), in the case of several situations: point defects and dislocation core stability, threshold displacement energies, bulk shear, generalized stacking fault energy surfaces, fracture, melting temperature, amorphous structure, and crystalline phase stability. A significant improvement is obtained in the case of dislocation cores, bulk behaviour under high shear stress, the amorphous structure, and computation of threshold displacement energies, while most of the features of the original version (elastic constants, point defects) are retained. However, despite a slight improvement, a complex process like fracture remains difficult to model.

Is preoperative embolization a prerequisite for spinal metastases surgical management?

BACKGROUND

Preoperative embolization decreases the intraoperative risk of hemorrhage in spinal decompression surgery of hypervascular metastases such as renal cell carcinoma. There is no consensus concerning embolization in other metastases. The purpose of this study was to compare the intraoperative amount of blood loss in embolized versus non-embolized patients, seeking for differences depending on the primary tumor and the extent of surgery.

PATIENTS AND METHODS

Ninety-three patients, average age 60.5 years, were operated. The origins of metastases were: 28 breast cancer (30.1%), 19 pulmonary carcinoma (20.4%), 16 renal cell carcinoma (17.2%), 30 other cancers (32.3%). Surgical procedures were: 52 thoracolumbar laminectomies with instrumentation, 29 thoracolumbar corpectomies or vertebrectomies, 12 cervical corpectomies. A preoperative microsphere embolization was performed in 35 patients. Blood loss was evaluated by: blood volume in surgical aspiration devices, number of transfused packed red blood cells units and hemoglobin variation during surgery.

RESULTS

Renal metastases were systematically embolized. In the breast group, there was no significant difference (P>0.05) in blood loss between embolization versus non-embolization. In the pulmonary group and in other metastases, no difference was found either. The extent of surgery (corpectomy/vertebrectomy versus thoracolumbar instrumentation and cervical corpectomy) increased bleeding: breast 1775ml versus 778ml and 600ml respectively (P=0.048), pulmonary 2500ml versus 430ml and 180ml (P=0.020), renal 3346ml versus 1175ml and 780ml (P=0.036) and others 1550ml versus 474ml and 400ml (P=0.020).

CONCLUSIONS

Embolization decreases the risk of hemorrhage in highly vascularized metastases such as renal cell carcinoma. A benefit of embolization was not found for metastases of breast or pulmonary tumors. As far as other metastases, thyroid carcinoma should be analyzed on a greater cohort. The extent of surgery remains an important risk factor for intraoperative bleeding. A preoperative angiogram should be carried out in all types of metastases prior to a thoracolumbar corpectomy or vertebrectomy to perform an embolization if the tumor is hypervascular.

LEVEL OF EVIDENCE

Level IV, retrospective study.

Comparative nucleic acid chaperone properties of the nucleocapsid protein NCp7 and Tat protein of HIV-1

RNA chaperones are proteins able to rearrange nucleic acid structures towards their most stable conformations. In retroviruses, the reverse transcription of the viral RNA requires multiple and complex nucleic acid rearrangements that need to be chaperoned. HIV-1 has evolved different viral-encoded proteins with chaperone activity, notably Tat and the well described nucleocapsid protein NCp7. We propose here an overview of the recent reports that examine and compare the nucleic acid chaperone properties of Tat and NCp7 during reverse transcription to illustrate the variety of mechanisms of action of the nucleic acid chaperone proteins.

Integrin α5β1 plays a critical role in resistance to temozolomide by interfering with the p53 pathway in high-grade glioma

Integrins play a role in the resistance of advanced cancers to radiotherapy and chemotherapy. In this study, we show that high expression of the α5 integrin subunit compromises temozolomide-induced tumor suppressor p53 activity in human glioblastoma cells. We found that depletion of the α5 integrin subunit increased p53 activity and temozolomide sensitivity. However, when cells were treated with the p53 activator nutlin-3a, the protective effect of α5 integrin on p53 activation and cell survival was lost. In a functional p53 background, nutlin-3a downregulated the α5 integrin subunit, thereby increasing the cytotoxic effect of temozolomide. Clinically, α5β1 integrin expression was associated with a more aggressive phenotype in brain tumors, and high α5 integrin gene expression was associated with decreased survival of patients with high-grade glioma. Taken together, our findings indicate that negative cross-talk between α5β1 integrin and p53 supports glioma resistance to temozolomide, providing preclinical proof-of-concept that α5β1 integrin represents a therapeutic target for high-grade brain tumors. Direct activation of p53 may remain a therapeutic option in the subset of patients with high-grade gliomas that express both functional p53 and a high level of α5β1 integrin.

Involvement of the TGFβ pathway in the regulation of α5 β1 integrins by caveolin-1 in human glioblastoma

Caveolin-1 plays a crucial role in the development of cancer and its progression. We previously reported that glioblastoma cells expressing low levels of caveolin-1 exerted a more aggressive phenotype than cells expressing high levels. Such phenotype was due to the induction of α(5) β(1) integrin subsequent to the depletion of caveolin-1. Caveolin-1 was identified as a transcriptional repressor of α(5) β(1) integrin. The current study was designed to identify in vitro, the molecular mechanisms by which caveolin-1 controls α(5) β(1) integrin expression and to determine if a negative correlation between caveolin-1 and α(5) β(1) integrins also exists in biopsies and xenografted human brain tumors. We showed that depletion of caveolin-1 lead to the activation of the TGFβ/TGFβRI/Smad2 pathway which in turn induced the expression of α(5) β(1) integrins. We showed that cells expressing the lowest levels of caveolin-1 but the highest levels of α(5) β(1) integrins and TGFβRI were the most sensitive to a α(5) β(1) integrin antagonist and a TGFβRI inhibitor. Screening human glioma biopsies and human glioblastoma xenografts, we isolated subgroups with either low levels of caveolin-1 but high levels of α(5) β(1) integrin and TGFβRI or high levels of caveolin-1 but low levels of α(5) β(1) integrin and TGFβRI. In conclusion, caveolin-1 controls α(5) β(1) integrin expression through the TGFβ/TGFβRI/Smad2 pathway. The status of caveolin-1/α(5) β(1) integrins/TGFβRI might be a useful marker of the tumor evolution/prognosis as well as a predictor of anti-TGFβ or anti-α(5) β(1) integrin therapies.

Structural determinants of TAR RNA-DNA annealing in the absence and presence of HIV-1 nucleocapsid protein

Annealing of the TAR RNA hairpin to the cTAR DNA hairpin is required for the minus-strand transfer step of HIV-1 reverse transcription. HIV-1 nucleocapsid protein (NC) plays a crucial role by facilitating annealing of the complementary hairpins. To gain insight into the mechanism of NC-mediated TAR RNA–DNA annealing, we used structural probes (nucleases and potassium permanganate), gel retardation assays, fluorescence anisotropy and cTAR mutants under conditions allowing strand transfer. In the absence of NC, cTAR DNA-TAR RNA annealing depends on nucleation through the apical loops. We show that the annealing intermediate of the kissing pathway is a loop–loop kissing complex involving six base-pairs and that the apical stems are not destabilized by this loop–loop interaction. Our data support a dynamic structure of the cTAR hairpin in the absence of NC, involving equilibrium between both the closed conformation and the partially open ‘Y’ conformation. This study is the first to show that the apical and internal loops of cTAR are weak and strong binding sites for NC, respectively. NC slightly destabilizes the lower stem that is adjacent to the internal loop and shifts the equilibrium toward the ‘Y’ conformation exhibiting at least 12 unpaired nucleotides in its lower part.

Hippocampal dysgenesis and variable neuropsychiatric phenotypes in patients with Bardet-Biedl syndrome underline complex CNS impact of primary cilia

The Bardet-Biedl syndrome (BBS) is a rare ciliopathy clinically defined by the association of retinitis pigmentosa, polydactyly, obesity, kidney disease and cognitive impairment. The cognitive functioning, behavioral phenotype, prevalence of psychiatric diseases and memory performances of a cohort of 34 patients with BBS were evaluated and a systemic brain magnetic resonance imaging (MRI) was performed. The patients' cognitive functioning was of marked variable efficiency ranging from normal to disabling performances. Neuropsychological disorders such as slow thought process, attention difficulties and obsessive-compulsive traits were observed. Our main finding was hippocampal dysgenesis, diagnosed by MRI, found in 42.31% of the patients in this cohort. Moreover, we show that BBS proteins are expressed in the human hippocampus and in the human brain in the normal subject. Recent literature in the murine model shows that hippocampal neurogenesis, in particular in the adult mouse, requires an intact primary cilia. These results encourage us to further investigate the possible role of BBS proteins in the hippocampus and related central nervous system structures.

Specific implications of the HIV-1 nucleocapsid zinc fingers in the annealing of the primer binding site complementary sequences during the obligatory plus strand transfer

Synthesis of the HIV-1 viral DNA by reverse transcriptase involves two obligatory strand transfer reactions. The second strand transfer corresponds to the annealing of the (−) and (+) DNA copies of the primer binding site (PBS) sequence which is chaperoned by the nucleocapsid protein (NCp7). NCp7 modifies the (+)/(−)PBS annealing mechanism by activating a loop–loop kissing pathway that is negligible without NCp7. To characterize in depth the dynamics of the loop in the NCp7/PBS nucleoprotein complexes, we investigated the time-resolved fluorescence parameters of a (−)PBS derivative containing the fluorescent nucleoside analogue 2-aminopurine at positions 6, 8 or 10. The NCp7-directed switch of (+)/(−)PBS annealing towards the loop pathway was associated to a drastic restriction of the local DNA dynamics, indicating that NCp7 can ‘freeze’ PBS conformations competent for annealing via the loops. Moreover, the modifications of the PBS loop structure and dynamics that govern the annealing reaction were found strictly dependent on the integrity of the zinc finger hydrophobic platform. Our data suggest that the two NCp7 zinc fingers are required to ensure the specificity and fidelity of the second strand transfer, further underlining the pivotal role played by NCp7 to control the faithful synthesis of viral HIV-1 DNA.

Biophysical studies of the nucleic acid chaperone properties of the HIV-1 nucleocapsid protein

The nucleocapsid protein NCp7 of HIV-1 possesses nucleic acid chaperone properties that are thought to be crucial throughout the viral life cycle. These properties promote the rearrangement of nucleic acids into their most thermodynamically stable conformations. These NCp7 properties involve two components, namely nucleic acid destabilization and activation of the annealing of complementary sequences. Biophysical techniques have been found extremely powerful to decipher the molecular mechanisms underlying these two components. We propose here an overview of the recent reports that examine the nucleic acid chaperone properties of NCp7 by these techniques.

Site-specific characterization of HIV-1 nucleocapsid protein binding to oligonucleotides with two binding sites

The nucleocapsid protein (NC) of HIV-1 is a highly conserved protein essential for the virus life cycle that constitutes an attractive target for new antiviral agents. Most NC functions rely on its binding to the HIV-1 genomic RNA and its DNA copies that contain multiple and possibly interdependent binding sites. Therefore, a detailed understanding of NC binding requires a site-specific experimental approach. We have recently shown that 2-aminopurine (2Ap), a fluorescent adenine analogue, can site-selectively probe the binding of NC. Here, we introduced 2Ap at various positions of model single-stranded dodecanucleotides containing two TG motifs which constitute putative specific binding sites. Steady-state and time-resolved fluorescence experiments indicated that NC binding strongly increased the fluorescence quantum yield of 2AP by reducing the dynamic quenching of 2Ap by its close neighbors and slowing the picosecond to nanosecond conformational fluctuations of the oligonucleotides. The dodecanucleotides were found to bind two NC molecules at physiological salt concentrations, confirming the preferential binding of NC to TG motifs and an occluded binding site size for NC of five to six bases. Using the NC-induced changes in 2Ap fluorescence, we determined the microscopic affinity constants of the individual binding sites and showed that affinities can significantly differ from one site to another within the same dodecanucleotide, depending on the position of the TG dinucleotide and the nature of its close neighbors. Moreover, our data suggest that binding of NC even to close binding sites shows no strong cooperativity.

Investigation of the interaction between hydrogen and screw dislocation in silicon by first-principles calculations

The stability of atomic and molecular hydrogen in the vicinity of a screw dislocation in silicon has been investigated using first-principles calculations. The lowest energy configurations are obtained for H atoms located in the dislocation core, suggesting that the segregation of hydrogen is favoured in the dislocation core. It is found that a spontaneous dissociation of H(2) could occur in the dislocation core. Finally, the variation of the interaction energy between hydrogen and the dislocation core as a function of the separation distance has been calculated. There is no sizeable interaction variation for H(2). However, in the case of a single H, an inverse law has been obtained, which can be explained by the anisotropic stress field generated by the insertion of H in the silicon lattice.

Glissile dislocations with transient cores in silicon

We report an unexpected characteristic of dislocation cores in silicon. Using first-principles calculations, we show that all of the stable core configurations for a nondissociated 60 degrees dislocation are sessile. The only glissile configuration, previously obtained by nucleation from surfaces, surprisingly corresponds to an unstable core. As a result, the 60 degrees dislocation motion is solely driven by stress, with no thermal activation. We predict that this original feature could be relevant in situations for which large stresses occur, such as mechanical deformation at room temperature. Our work also suggests that postmortem observations of stable dislocations could be misleading and that mobile unstable dislocation cores should be taken into account in theoretical investigations.

HIV-1 nucleocapsid traps reverse transcriptase on nucleic acid substrates

Conversion of the genomic RNA of human immunodeficiency virus (HIV) into full-length viral DNA is a complex multistep reaction catalyzed by the reverse transcriptase (RT). Numerous studies have shown that the viral nucleocapsid (NC) protein has a vital impact on various steps during reverse transcription, which is crucial for virus infection. However, the exact molecular details are poorly defined. Here, we analyzed the effect of NC on RT-catalyzed single-turnover, single-nucleotide incorporation using different nucleic acid substrates. In the presence of NC, we observed an increase in the amplitude of primer extension of up to 3-fold, whereas the transient rate of nucleotide incorporation ( k pol) dropped by up to 50-fold. To unravel the underlying molecular mechanism, we carefully analyzed the effect of NC on RT-nucleic acid substrate dissociation. The studies revealed that NC considerably enhances the stability of RT-substrate complexes by reducing the observed dissociation rate constants, which more than compensates for the observed drop in k pol. In conclusion, our data strongly support the concept that NC not only indirectly assists the reverse transcription process by its nucleic acid chaperoning activity but also positively affects the RT-catalyzed nucleotide incorporation reaction by increasing polymerase processivity presumably via a physical interaction of the two viral proteins.