The cellular world according to Hsp90

An international conference focusing on the Hsp90 molecular chaperone was recently held in Seeon, Germany. The program provided a current synopsis on a wide array of topics, including structural insights, roles in established and novel cellular pathways and disease implications.     

The PARP superfamily

Poly(ADP-ribosyl)ation is an immediate DNA-damage-dependent post-translational modification of histones and other nuclear proteins that contributes to the survival of injured proliferating cells. Poly(ADP-ribose) polymerases (PARPs) now constitute a large family of 18 proteins, encoded by different genes and displaying a conserved catalytic domain in which PARP-1 (113 kDa), the founding member, and PARP-2 (62 kDa) are so far the sole enzymes whose catalytic activity has been shown to be immediately stimulated by DNA strand breaks. A large repertoire of sequences encoding novel PARPs now extends considerably the field of poly(ADP-ribosyl)ation reactions to various aspects of the cell biology including cell proliferation and cell death. Some of these new members interact with each other, share common partners and common subcellular localizations suggesting possible fine tuning in the regulation of this post-translational modification of proteins. This review summarizes our present knowledge of this emerging superfamily, which might ultimately improve pharmacological strategies to enhance both antitumor efficacy and the treatment of a number of inflammatory and neurodegenerative disorders. A provisional nomenclature is proposed.     

The ways of PARP

Two papers in this issue of Cell describe two roles of poly(ADP-ribose) polymerase (PARP) in modulating chromatin structure: as a structural component replacing linker histone (Kim et al., 2004) and as a constituent of a corepressor complex poised to dismiss repression upon receipt of an activating signal (Ju et al., 2004).     

The world according to Arp: regulation of actin nucleation by the Arp2/3 complex.

The coordination of cell shape change and locomotion requires that actin polymerization at the cell cortex be tightly controlled in response to both intracellular and extracellular cues. The Arp2/3 complex - an actin filament nucleating and organizing factor - appears to be a central player in the cellular control of actin assembly. Recently, a molecular pathway leading from key signalling molecules to actin filament nucleation by the Arp2/3 complex has been discovered. In this pathway, the GTPase Cdc42 acts in concert with WASP family proteins to activate the Arp2/3 complex. These findings have led to a more complete picture of the mechanism of actin filament generation and organization during cell motility.     

Noncoding RNAs link PARP1 to heterochromatin

Comment on: Guetg C et al. Mol Cell 2012; 45:790-800.     

The Basques according to polymorphic Alu insertions

Polymorphic Alu insertions provide a set of DNA markers of interest in human population genetics. Approximately 1000-2000 of these insertions have not reached fixation within the human genome. Each one of these polymorphic loci most probably resulted from a unique insertional event, and therefore all individuals possessing the insertion are related by descent not just state. In addition, the direction of mutational change is toward the gain of the Alu element at a particular locus. Therefore, the improved knowledge of both the ancestral state and the direction of mutational change greatly facilitates the analysis of population relationships. As a result, Alu insertion polymorphisms represent a significant tool for population genetic studies. In this study, polymorphic Alu insertions have been employed to ascertain phylogenetic relationships among Basque groups and worldwide populations. The Basques are considered to be a geographic isolate with a unique language and customs. They may be direct descendants of Cro-Magnon enclaves from the upper Paleolithic (38,000 to 10,000 years). The Basques are distributed among narrow valleys in northeastern Spain with little migration between them until recently. This characteristic may have had an effect on allelic frequency distributions. With the aim of studying this possible effect, we have analyzed six autosomal polymorphic Alu loci from four different sites within the Spanish Basque region in order to ascertain any genetic heterogeneity among the Basques. The results are consistent with a lack of homogeneity among these four autochthonous Basque groups.     

The PARP inhibitor PJ34 causes a PARP1-independent, p21 dependent mitotic arrest

Poly(ADP)-ribose polymerase (PARP) inhibitors modify the enzymatic activity of PARP1/2. When certain PARP inhibitors are used either alone or in combination with DNA damage agents they may cause a G2/M mitotic arrest and/or apoptosis in a susceptible genetic context. PARP1 interacts with the cell cycle checkpoint proteins Ataxia Telangectasia Mutated (ATM) and ATM and Rad3-related (ATR) and therefore may influence growth arrest cascades. The PARP inhibitor PJ34 causes a mitotic arrest by an unknown mechanism in certain cell lines, therefore we asked whether PJ34 conditionally activated the checkpoint pathways and which downstream targets were necessary for mitotic arrest. We found that PJ34 produced a concentration dependent G2/M mitotic arrest and differentially affected cell survival in cells with diverse genetic backgrounds. p53 was activated and phosphorylated at Serine15 followed by p21 gene activation through both p53-dependent and -independent pathways. The mitotic arrest was caffeine sensitive and UCN01 insensitive and did not absolutely require p53, ATM or Chk1, while p21 was necessary for maintaining the growth arrest. Significantly, by using stable knockdown cell lines, we found that neither PARP1 nor PARP2 was required for any of these effects produced by PJ34. These results raise questions and cautions for evaluating PARP inhibitor effectiveness, suggesting whether effects should be considered not only on PARP's diverse ADP-ribosylation independent protein interactions but also on homologous proteins that may be producing either overlapping or distinct effect.     

Risk of adverse outcomes among infants of immigrant women according to birth-weight curves tailored to maternal world region of origin

Background:Infants of immigrant women in Western nations generally have lower birth weights than infants of native-born women. Whether this difference is physiologic or pathological is unclear. We determined whether the use of birth-weight curves tailored to maternal world region of origin would discriminate adverse neonatal and obstetric outcomes more accurately than a single birth-weight curve based on infants of Canadian-born women.Methods:We performed a retrospective cohort study of in-hospital singleton live births (328 387 to immigrant women, 761 260 to nonimmigrant women) in Ontario between 2002 and 2012 using population health services data linked to the national immigration database. We classified infants as small for gestational age (< 10th percentile) or large for gestational age (≥ 90th percentile) using both Canadian and world region–specific birth-weight curves and compared associations with adverse neonatal and obstetric outcomes.Results:Compared with world region–specific birth-weight curves, the Canadian curve classified 20 431 (6.2%) additional newborns of immigrant women as small for gestational age, of whom 15 467 (75.7%) were of East or South Asian descent. The odds of neonatal death were lower among small-for-gestational-age infants of immigrant women than among those of nonimmigrant women based on the Canadian birth-weight curve (adjusted odds ratio [OR] 0.83, 95% confidence interval [CI] 0.72–0.95), but higher when small for gestational age was defined by the world region–specific curves (adjusted OR 1.24, 95% CI 1.08–1.42). Conversely, the odds of some adverse outcomes were lower among large-for-gestational-age infants of immigrant women than among those of nonimmigrant women based on world region–specific birth-weight curves, but were similar based on the Canadian curve.Interpretation:World region–specific birth-weight curves seemed to be more appropriate than a single Canadian population-based curve for assessing the risk of adverse neonatal and obstetric outcomes among small- and large-for-gestational-age infants born to immigrant women, especially those from the East and South Asian regions.In many Western nations, an increasing proportion of births are to immigrant women, many from world regions where low birth weight and infant death are more frequent.^1–3 The birth-weight distribution of infants born to immigrant mothers in Canada and the United Kingdom is shifted toward lower birth-weight values than that of infants born to native-born women.^4,5 Accordingly, use of a conventional population-based birth-weight chart may not be appropriate for all immigrant groups, potentially leading to an overestimation of infants as small for gestational age (birth weight < 10th percentile) and an underestimation of infants as large for gestational age (birth weight ≥ 90th percentile). The question remains whether these differences reflect a physiologic or a pathological process.Potentially misclassifying the physiologically small, but healthy, newborn as small for gestational age may lead to unnecessary interventions and undue parental stress.⁶ To date, comparisons between a single population-based standard and customized standards, including ones that are based on ethnicity, have focused on small-for-gestational-age infants, but less attention has been paid to the potential under-classification of large infants.^7–9 Overlooking a fetus or infant who would be considered large for gestational age according to the birth-weight distribution in his mother’s country of origin, but not according to the higher cut-off of a birth-weight curve for infants of Canadian-born women, may fail to identify a higher risk of birth trauma or obstetric complications, such as perineal laceration, shoulder dystocia and postpartum hemorrhage.^10–12To date, there is no consensus regarding the minimal set of maternal characteristics that improves detection of adverse outcomes through the use of customized charts.^13–17 So far, the single characteristic that has been shown to influence the size of newborns in this way is maternal country of birth.¹⁸We conducted a study to determine whether use of world region–specific birth-weight curves would be more accurate than use of a single birth-weight curve based on infants of Canadian-born women in predicting adverse neonatal and obstetric outcomes known to be associated with small for gestational age and large for gestational age among infants born to immigrant women in Canada.     

PARP inhibitors trap PARP2 and alter the mode of recruitment of PARP2 at DNA damage sites

Dual-inhibitors of PARP1 and PARP2 are promising anti-cancer drugs. In addition to blocking PARP1&2 enzymatic activity, PARP inhibitors also extend the lifetime of DNA damage-induced PARP1&2 foci, termed trapping. Trapping is important for the therapeutic effects of PARP inhibitors. Using live-cell imaging, we found that PARP inhibitors cause persistent PARP2 foci by switching the mode of PARP2 recruitment from a predominantly PARP1- and PAR-dependent rapid exchange to a WGR domain-mediated stalling of PARP2 on DNA. Specifically, PARP1-deletion markedly reduces but does not abolish PARP2 foci. The residual PARP2 foci in PARP1-deficient cells are DNA-dependent and abrogated by the R140A mutation in the WGR domain. Yet, PARP2-R140A forms normal foci in PARP1-proficient cells. In PARP1-deficient cells, PARP inhibitors - niraparib, talazoparib, and, to a lesser extent, olaparib - enhance PARP2 foci by preventing PARP2 exchange. This trapping of PARP2 is independent of auto-PARylation and is abolished by the R140A mutation in the WGR domain and the H415A mutation in the catalytic domain. Taken together, we found that PARP inhibitors trap PARP2 by physically stalling PARP2 on DNA via the WGR-DNA interaction while suppressing the PARP1- and PAR-dependent rapid exchange of PARP2.     

The road from The Microbial world to Microbe.

The year 2007 commemorates the 50th anniversary of the publication of The Microbial World, the seminal microbiology textbook that shattered the microbiology world and whose first edition was coauthored by Roger Y. Stanier, Michael Doudoroff and Edward A. Adelberg. The year 2007 marks also twenty-five years of Stanier's passing away. The Spanish Society for Microbiology (SEM) with the support of Fundación Ramón Areces has organized a Symposium, in the frame of the 21st national congress of the SEM (Seville, 17-20 September 2007), to commemorate those anniversaries, and has invited us (Schaechter, Ingraham and Neidhardt) to contribute to this celebration.     

Poly(ADP-ribose) polymerases in double-strand break repair: Focus on PARP1, PARP2 and PARP3

Poly(ADP-ribosyl)ation (PARylation) is a post-translational modification of proteins catalysed by Poly(ADP-ribose) polymerases (PARP). A wealth of recent advances in the biochemical and functional characterization of the DNA-dependent PARP family members have highlighted their key contribution in the DNA damage response network, the best characterized being the role of PARP1 and PARP2 in the resolution of single-strand breaks as part of the BER/SSBR process. How PARylation contributes to the repair of double-strand breaks is less well defined but has become recently the subject of significant research in the field. The aim of this review is to provide an overview of the current knowledge concerning the role of the DNA-activated PARP1, PARP2 and PARP3 in cellular response to double-strand breaks (DSB). In addition, we outline the biological significance of these properties in response to programmed DNA lesions formed during physiological processes such as antibody repertoire assembly and diversification.