Isolation and characterization of "Arabidopsis" mutants with altered homologous recombination levels : a new function for an INO80 SWI/SNF ATPase

Homologous recombination (HR) in eukaryotic organisms serves a dual role in providing genetic flexibility by creating novel sequence assortments upon meiosis and in maintaining genome integrity through DNA repair in somatic tissues. HR represents an alternative pathway to non-homologous end-joining (NHEJ) for the repair of double-strand breaks (DSB). The repair by NHEJ may not preserve the integrity of the genetic information whereas the HR pathway is more faithful. The choice of a pathway to repair DSBs is thus crucial for genome integrity and evolution, especially in plants where the germline is only determined late during development. Very little is known on what influences the choice of the pathway taken, but chromatin structure at the site of a lesion likely will play a major role in the recruitment of repair enzymes and thereby the choice of repair pathway. As a consequence, various proteins that are not part of the core of the recombination machinery may directly participate in the regulation of HR. At the time this work was initiated, no plant gene involved in the HR pathway or its regulation was characterized yet. As plants are powerful genetic tools especially for screening, we decided on designing and conducting a genetic screen to identify plant genes involved in HR. Here I describe a genetic screen in Arabidopsis thaliana for mutants with altered somatic recombination levels and the characterization of the resulting mutant candidates. For the screen, I used a stably integrated luciferase based intrachromosomal HR substrate and a T-DNA construct designed for activation tagging as a mutagenic agent. Out of 19520 individual transformants tested, 37 exhibited an altered HR phenotype. Nine of them were sterile and/or exhibited important developmental or growth phenotypes that precluded the formation of progeny seeds, which is more than the average number of sterile plants expected. However, in most cases the altered recombination phenotype was lost in the offspring. To characterize the mutations, I cloned all the T-DNA insertion sites by plasmid rescue and determined the potential target genes. I discuss the genes likely to be responsible of the observed phenotype. Here I report the thorough analysis of a mutant in the Arabidopsis INO80 ortholog of the SWI/SNF ATPase family, which shows a reduced frequency of HR. In contrast, sensitivity to genotoxic agents and efficiency of T-DNA integration remain unaffected. This suggests that INO80 is a positive regulator of HR, while not affecting other repair pathways. Further, transcriptionaly silent TSI loci are not reactivated in absence of INO80, suggesting that Arabidopsis INO80 function is independent of transcriptional silencing. Using whole genome expression studies by microarray profiling I show evidence that INO80 regulates a small subset of Arabidopsis genes, suggesting a dual role for INO80 in transcription and repair by HR. Moreover, the recombination-promoting function of INO80 is not likely to involve general transcriptional regulation, and the transcriptional regulation of repair related genes is unaffected in the mutant. This is the first report of INO80 function in a higher eukaryote. Mononucleosome binding studies support the suggestion that INO80 positively regulates HR through modification of chromatin structure at sites of DNA repair by HR. Finally, I provide evidence for the existence and/or connectivity of INO80 with other INO80 complex partners in Arabidopsis

Reversible Top1 cleavage complexes are stabilized strand-specifically at the ribosomal replication fork barrier and contribute to ribosomal DNA stability

Various topological constraints at the ribosomal DNA (rDNA) locus impose an extra challenge for transcription and DNA replication, generating constant torsional DNA stress. The topoisomerase Top1 is known to release such torsion by single-strand nicking and re-ligation in a process involving transient covalent Top1 cleavage complexes (Top1cc) with the nicked DNA. Here we show that Top1ccs, despite their usually transient nature, are specifically targeted to and stabilized at the ribosomal replication fork barrier (rRFB) of budding yeast, establishing a link with previously reported Top1 controlled nicks. Using ectopically engineered rRFBs, we establish that the rRFB sequence itself is sufficient for induction of DNA strand-specific and replication-independent Top1ccs. These Top1ccs accumulate only in the presence of Fob1 and Tof2, they are reversible as they are not subject to repair by Tdp1- or Mus81-dependent processes, and their presence correlates with Top1 provided rDNA stability. Notably, the targeted formation of these Top1ccs accounts for the previously reported broken replication forks at the rRFB. These findings implicate a novel and physiologically regulated mode of Top1 action, suggesting a mechanism by which Top1 is recruited to the rRFB and stabilized in a reversible Top1cc configuration to preserve the integrity of the rDN

52-kDa Ro/SSA epitopes preferentially recognized by antibodies from mothers of children with neonatal lupus and congenital heart block

Neonatal lupus erythematosus is a rare disorder caused by the transplacental passage of maternal autoantibodies. The 52-kDa Ro/SSA antigen (Ro52) ribonucleoprotein represents an antigenic target strongly associated with the autoimmune response in mothers whose children have neonatal lupus and cardiac conduction disturbances, mainly congenital heart block. The objective of this study was to identify putative Ro52/60-kDa Ro/SSA antigen (Ro60) epitopes associated with neonatal lupus and congenital heart block. The reactivity of IgG antibodies present in the sera from mothers with systemic lupus erythematosus and Sjögren's syndrome and in the sera from asymptomatic mothers (a longitudinal study of 192 samples from 66 subjects) was investigated by ELISA using Ro52, Ro60 and 48-kDa La/SSB antigen proteins, as well as 45 synthetic peptides, 13–24 residues long, of Ro52/Ro60 proteins. One to 19 samples collected before, during and after pregnancy were available for each mother. Forty-three disease controls selected randomly and normal sera were tested in parallel. Although no differences were found between Sjögren's syndrome and asymptomatic mothers of group I, who had at least one infant with neonatal lupus, and of group II, who had healthy babies only, significant differences were observed between lupus mothers from both groups. In the former group of lupus mothers, a significantly higher frequency of antibodies to Ro52 peptides 107–122 and 277–292 was observed. Between 18 and 30 weeks of gestation, the period of risk, there was clearly an elevated level of antibodies reacting with Ro52 peptides 1–13, 277–292 and 365–382. Antibodies to Ro52 peptide 365–382 have been shown previously to cross-react with residues 165–185 of the heart 5-HT(4 )serotoninergic receptor, and might be pathologically important. The level of these Ro52 antibody subsets decreased at the end of pregnancy and after delivery. IgG antibodies to Ro52 peptides 1–13, 107–122, 277–292 and 365–382 may therefore represent important biomarkers to predict a complication in pregnant lupus women with Ro52 antibodies

Trojan Horse Siderophore Conjugates Induce Pseudomonas aeruginosa Suicide and Qualify the TonB Protein as a Novel Antibiotic Target

Rising infection rates with multidrug-resistant pathogens calls for antibiotics with novel modes of action. Herein, we identify the inner membrane protein TonB, a motor of active uptake in Gram-negative bacteria, as a novel target in antimicrobial therapy. The interaction of the TonB box of outer membrane transporters with TonB is crucial for the internalization of essential metabolites. We designed TonB box peptides and coupled them with synthetic siderophores in order to facilitate their uptake into bacteria in up to 32 synthetic steps. Three conjugates repressed the growth of Pseudomonas aeruginosa cells unable to produce their own siderophores, with minimal inhibitory concentrations between 0.1 and 0.5 μM. The transporters mediating uptake of these compounds were identified as PfeA and PirA. The study illustrates a variant of cellular suicide where a transporter imports its own inhibitor and demonstrates that artificial siderophores can import cargo with molecular weights up to 4 kDa

The nuclear receptor transcriptional coregulator RIP140

The nuclear receptor superfamily comprises ligand-regulated transcription factors that control various developmental and physiological pathways. These receptors share a common modular structure and regulate gene expression through the recruitment of a large set of coregulatory proteins. These transcription cofactors regulate, either positively or negatively, chromatin structure and transcription initiation. One of the first proteins to be identified as a hormone-recruited cofactor was RIP140. Despite its recruitment by agonist-liganded receptors, RIP140 exhibits a strong transcriptional repressive activity which involves several inhibitory domains and different effectors. Interestingly, the RIP140 gene, located on chromosome 21 in humans, is finely regulated at the transcriptional level by various nuclear receptors. In addition, the protein undergoes several post-translational modifications which control its repressive activity. Finally, experiments performed in mice devoid of the RIP140 gene indicate that this transcriptional cofactor is essential for female fertility and energy homeostasis. RIP140 therefore appears to be an important modulator of nuclear receptor activity which could play major roles in physiological processes and hormone-dependent diseases

β6-Integrin Serves as a Potential Serum Marker for Diagnosis and Prognosis of Pancreatic Adenocarcinoma

INTRODUCTION Despite enormous efforts during the past decades, pancreatic adenocarcinoma (PAC) remains one of the most deleterious cancer entities. A useful biomarker for early detection or prognosis of PAC does not yet exist. The goal of our study was the characterization of β6-integrin (ITGB6) as a novel serum tumor marker for refined diagnosis and prognosis of PAC. Serum ITGB6 levels were analyzed in 3 independent PAC cohorts consisting of retrospectively and prospectively collected serum and/or (metastatic) PAC tissue specimens. METHODS Using 2 independent cohorts, we measured serum ITGB6 concentrations in 10 chronic pancreatitis patients, 10 controls, as well as in 27 (cohort 1) and 24 (cohort 2) patients with PAC, respectively. In these patients, we investigated whether ITGB6 serum levels correlate with known clinical and prognostic markers for PAC and whether they might differ between patients with PAC or benign inflammatory diseases of the pancreas. RESULTS We found that elevated serum ITGB6 levels (≥0.100 ng/mL) in patients suffering from metastasizing PAC presented an unfavorable prognostic outcome. By correlating the ITGB6 tissue expression in primary and metastatic PAC with clinical parameters, we found that positive ITGB6 expression in the tumor tissue is linked to increased serum ITGB6 levels in nonmetastatic PAC and correlates with carbohydrate antigen 19-9 and clinical outcome. DISCUSSION Our findings suggest that ITGB6 might serve as a novel serum biomarker for early diagnosis and prognosis of PAC. Given the limited specificity and sensitivity of currently used carbohydrate antigen 19-9-based assays, ITGB6 may have the potential to improve the diagnostic accuracy for PAC

Re‐evaluation of stannous chloride (E 512) as food additive

The Panel on Food Additives and Nutrient Sources added to Food (ANS) provides a scientific opinion re‐evaluating the safety of stannous chloride and stannous chloride dihydrate (E 512) as food additives. The Panel considered that adequate exposure and toxicity data were available. Stannous chloride is only permitted as food additives in one food category and no reply on the actual use level of stannous chloride (E 512) as a food additive and on its concentration in food was provided by any interested party. According to the Mintel's Global New Products Database (GNPD), stannous chloride was not labelled on any products in the EU nor in Norway. The regulatory maximum level exposure assessment scenario is based on the maximum permitted levels (MPLs) for stannous chloride (E 512), which is 25 mg Sn/kg. The mean exposure to stannous chloride (E 512) from its use as a food additive was below 1.3 μg Sn/kg body weight (bw) per day for all age groups. The 95th percentile of exposure to stannous chloride (E 512) ranged from 0.0 μg Sn/kg bw per day in all groups to 11.2 μg Sn/kg bw per day in adults. Absorption of stannous chloride from the gastrointestinal tract is low there is no concern with respect to carcinogenicity and genotoxicity. Gastrointestinal irritation was reported in humans after ingestion of a bolus dose of 40 mg Sn. The Panel concluded that stannous chloride (E 512) is of no safety concern in this current authorised use and use levels