Biochar from recovered cellulose as new admixture in constructed wetlands for micropollutant removal: A circular approach

This study aimed to evaluate the suitability of biochar produced by pyrolysis from recovered wastewater cellulose and activated biologically as an admixture in Constructed Wetlands (CWs) when applied as a post-treatment step to remove micropollutants (MPs) from municipal wastewater effluent. Two planted vertical flow mesocosm CWs with cellulose-based admixtures of different origins (plant residue and recovered toilet paper) were fed with a municipal wastewater effluent representative for rural catchments. The results showed an average MPs elimination of 89.1 % for the activated biochar produced from recovered cellulose when 15 relevant compounds are considered and a reduction of the risk from compounds cocktail below the maximum acceptable level having diclofenac, carbamazepine, PFOS, ciprofloxacin and clarithromycin as main risk drivers (Risk Quotient > 1). The implementation of a circular approach to reduce MPs was finally conducted for the Blies catchment (Saarland region in Germany) characterized by low population density and small, sensitive water bodies. This approach demonstrates the feasibility of combining cellulose recovery with a fine sieve in large wastewater treatment plants (WWTPs) and providing biochar produced from recovered cellulose as an admixture to small WWTP where CW is an affordable solution for MP mitigation.

Fate of glyphosate and its metabolite AminoMethylPhosponic acid (AMPA) from point source through wastewater sludge and advanced treatment

The fate of glyphosate and its metabolite AminoMethylPhosponic acid (AMPA) was followed at the catchment of the Sûre river, mainly characterized by small population density and small and medium-sized wastewater treatment plants (WWTPs). A high concentration of AMPA was found in water samples collected in inlet from different wastewater streams, the industry being the main contributor, while glyphosate resulted mainly in domestic origin. The two molecules were also monitored in the anaerobic digestion as in the supernatant produced after centrifugation (reject water). A total of 0.0713 and 2.24 g/d of glyphosate and AMPA respectively were regularly returned to the activated sludge tank (AST) indicating a 20% impact of the sludge management line on the global wastewater mass balance. Finally, the use of Constructed Wetlands (CWs) in Vertical Flow (VF) configuration was tested as a suitable technology to retain both glyphosate and AMPA (90 and up to 50% elimination respectively) and minimize their discharge into surface water.

Operation of a pilot-scale lipid accumulation technology employing parameters to select Microthrix parvicella for biodiesel production from wastewater

Wastewater treatment plants (WWTPs) may play a crucial role in shifting to a zero-emission future by becoming more sustainable and contributing to the circular economy (CE). Recovered lipids from urban sewage can serve as a raw material for biofuel production contributing to a waste reduction, mitigation of natural resources depletion and reinforcing security and energy independence. A novel, pilot-scale lipid accumulation technology (LAT) employing parameters to select M. parvicella for the biofuel/biodiesel production was implemented on a side stream of an urban WWTP. The LAT proved its concept as the average amount of extracted lipids accumulated in the bioreactors was three-fold higher when compared to the lipids existing in activated sludge. The average transesterification of extracted lipids to biodiesel resulted in a 1.6 % yield, meaning that from 1 kg of dried sludge, 16 g of biodiesel could be formed. The biodiesel produced complies with European standard specifications (EN14214).

Characterization of unconventional sand-based substrates for adsorption of micropollutants in nature-based systems

The focus of this study is the characterization of unconventional sand-based substrates used in our previous project EmiSûre, (Interreg Greater Region (German federal states Rhineland-Palatinate and Saarland, the Grand Duchy of Luxembourg, regions Wallonia and Lorraine from Belgium and France, respectively), 2017-2021). The project aimed to develop and test alternative, nature-based technologies for the elimination of micropollutants (MPs) from municipal wastewater. For the characterization, two approaches were chosen. In the first approach, adsorption kinetics with a single compound allowed a perception of the adsorption capacity of the studied substrates compared to conventional substrates (granular activated carbons). This knowledge was completed by the second approach: an implementation of the studied substrates in packed-bed columns, which treated a mixture of 27 MPs in tap water for 10 months. Additionally, all three substrates (bentonite sand, sand with 15% activated biochar and sand with 15% zeolite) were characterized for physical and chemical properties, and the microbial potential of the activated and non-activated biochar was examined. From the studies, it is clear that the sand with an admixture of activated biochar is the most efficient sorbent in terms of single compound adsorption in batch (dye) and adsorption of 27 MPs on packed-bed columns. In contrast to the two other substrates, it shows long-term stable removal efficiencies. In the packed-bed columns, 18 out of 27 compounds were removed on average with high efficiency (80-99%), which is impressive, if we consider the variety of the compounds examined (pharmaceuticals, herbicides, pesticides, etc.) and their removal in conventional treatments. Additionally, adsorption models were created for the experimental data of all compounds adsorbed on the substrate with an admixture of activated biochar resulting in the best fit with the combined Langmuir-Freundlich model. These satisfying results suggest the application of the sand-based substrate with an admixture of activated biochar for further research and possibly upscale installations with the aim to offer and prove a reasonable and efficient alternative for MPs elimination from municipal wastewater.

Assessing the impact of micropollutant mitigation measures using vertical flow constructed wetlands for municipal wastewater catchments in the greater region: a reference case for rural areas

The present research aims at giving an approach to the issue of surface water contamination due to micropollutants in rural areas. The catchment of the Sûre river was selected as a reference case for the Greater Region, characterized mainly by settlements with low population density, small water bodies and small- to medium-sized wastewater treatment plants (WWTPs). For these WWTPs, conventional technical solutions for micropollutant elimination are not suitable; therefore, an adapted mitigation strategy is needed to prevent the impact of micropollutants, especially during the dry season. As a suitable alternative to more intensive technologies, Constructed Wetlands (CW) in Vertical Flow (VF) configuration have been successfully tested over a 1-year period and the elimination rate of 27 micropollutants was quantified. Emission reduction by VF was then considered in a static mass balance model that calculates the longitudinal concentration profile for the entire river catchment. The EmiSûre approach, which focuses on river quality (concentrations of pollutants) instead of emitted loads, effectively allowed simulation of adopted measures a priori and resulted in efficient support for decision-makers with WWTP upgrade scenarios.

Behaviour of 27 selected emerging contaminants in vertical flow constructed wetlands as post-treatment for municipal wastewater

Six substrates (i.e. sand enriched with activated or non-activated biochar or zeolite in different ratios) were tested in Vertical Flow Constructed Wetlands (VFCWs) planted with Phragmites australis and Iris pseudacorus for the removal of 27 emerging contaminants from municipal wastewater. The laboratory investigation under controlled conditions (spiked constant concentrations in synthetic wastewater) lasted 357 days and proved VFCWs being able to provide excellent effluent quality in terms of both macro - and micropollutant elimination. Because overall removal efficiencies exceeded 90% in most of the cases, significant differences among the substrates were not detectable. For compounds with medium elimination (i.e. AMPA) the type of substrate seemed to play a strong role and the maximum amount of active ingredient adsorbed per amount of substrate has been quantified (i.e. 0.77 μg of AMPA per g of 30% biochar mixed with sand). Three of the most promising substrates from laboratory where thus selected to be tested under real conditions (fluctuation in concentration, variable temperature). As result, VFCWs with 15% activated biochar mixed with sand proved to be effective in the removal of 18 emerging contaminants and complying with national discharge standards for 4 selected compounds.

Removal of 27 micropollutants by selected wetland macrophytes in hydroponic conditions

In this work, the primary focus is given on a mixture of 27 micropollutants (pharmaceuticals, pesticides, herbicides, fungicides and others) and its removal from aqueous solution by phytoremediation. Phytoremediation belongs to technologies, which are contributing on removal of micropollutants from wastewater in constructed wetlands. Constructed wetlands can be used as an additional step for elimination of micropollutants from municipal medium-sized wastewater treatment plants. To our knowledge, such a broad variety of micropollutants was never targeted for removal by phytoremediation before. In this work, we carry out experiments with 3 emergent macrophytes: Phragmites australis, Iris pseudacorus and Lythrum salicaria in hydroponic conditions. The selected plants are exposed to mixture of micropollutants in concentrations 1-14 mg/l for a time period of 30 days. The highest affinity for phytoremediation is detected at groups of fluorosurfactants (removal rate up to 30%), beta-blockers (removal rate up to 50%) and antibiotics (removal rate up to 90%). The leading capability for micropollutant uptake is detected at Lythrum salicaria, where 25 out of 27 compounds are removed with more than 20% efficiency. The results demonstrate well usefulness of this technology e.g. in an additional treatment step, because the mentioned groups of micropollutants are removed with comparable or even higher effectivity, than it is in case of conventional wastewater treatment plants.

Search for Lepton Number and Flavor Violation in K^{+} and π^{0} Decays

Searches for the lepton number violating K^{+}→π^{-}μ^{+}e^{+} decay and the lepton flavor violating K^{+}→π^{+}μ^{-}e^{+} and π^{0}→μ^{-}e^{+} decays are reported using data collected by the NA62 experiment at CERN in 2017-2018. No evidence for these decays is found and upper limits of the branching ratios are obtained at 90% confidence level: B(K^{+}→π^{-}μ^{+}e^{+})<4.2×10^{-11}, B(K^{+}→π^{+}μ^{-}e^{+})<6.6×10^{-11} and B(π^{0}→μ^{-}e^{+})<3.2×10^{-10}. These results improve by 1 order of magnitude over previous results for these decay modes.

NA62 and NA48/2 results on search for Heavy Neutral Leptons

In this paper we present new results on upper limits for the search of Heavy Neutral Leptons (HNL) with data collected by NA48/2 (2003-2004), NA62-RK (2007) and NA62 (2015) CERN experiments. The data collected with different trigger configuration allow to search for both long and short living heavy neutrinos in the mass range below the kaon mass. In addition the status of the search for K+ → π+vv with the NA62 detector will be briefly presented.

Tracer tests and uncertainty propagation to design monitoring setups in view of pharmaceutical mass flow analyses in sewer systems

The development of a strategic approach to manage pollution of surface waters with pharmaceutical residues is in centre of interest in Europe. In this context a lack of reliable standard procedures for sampling and subsequent assessment of pharmaceutical mass flows in the water cycle has been identified. Authoritative assessment of relevant substance concentrations and flows is essential for environmental risk assessments and reliable efficiency analysis of measures to reduce or avoid emissions of drugs to water systems. Accordingly, a detailed preparation of monitoring campaigns including an accuracy check for the sampling configuration provides important information on the reliability of the gathered data. It finally supports data analysis and interpretation for evaluations of the efficiency of measures as well as for cost benefit assessments. The precision of mass flow balances is expected to be particularly weak when substances with high short-term variations and rare upstream emissions are considered. This is especially true for substance flow analysis in sewers close to source because of expectable highly dynamic flow conditions and emission patterns of pollutants. The case study presented here focusses on the verification of a monitoring campaign in a hospital sewer in Luxembourg. The results highlight the importance for a priori accuracy checks and provide a blueprint for well-designed monitoring campaigns of pharmaceutical trace pollutants on the one hand. On the other hand, the study provides evidence that the defined and applied continuous flow proportional sampling procedure enables a representative monitoring of short-term peak loads of the x-ray contrast media iobitridol close to source.

Comparative and integrative environmental assessment of advanced wastewater treatment processes based on an average removal of pharmaceuticals

Pharmaceuticals are normally barely removed by conventional wastewater treatments. Advanced technologies as a post-treatment, could prevent these pollutants reaching the environment and could be included in a centralized treatment plant or, alternatively, at the primary point source, e.g. hospitals. In this study, the environmental impacts of different options, as a function of several advanced treatments as well as the centralized/decentralized implementation options, have been evaluated using Life Cycle Assessment (LCA) methodology. In previous publications, the characterization of the toxicity of pharmaceuticals within LCA suffers from high uncertainties. In our study, LCA was therefore only used to quantify the generated impacts (electricity, chemicals, etc.) of different treatment scenarios. These impacts are then weighted by the average removal rate of pharmaceuticals using a new Eco-efficiency Indicator EFI. This new way of comparing the scenarios shows significant advantages of upgrading a centralized plant with ozonation as the post-treatment. The decentralized treatment option reveals no significant improvement on the avoided environmental impact, due to the comparatively small pollutant load coming from the hospital and the uncertainties in the average removal of the decentralized scenarios. When comparing the post-treatment technologies, UV radiation has a lower performance than both ozonation and activated carbon adsorption.

Elimination of pharmaceutical residues in biologically pre-treated hospital wastewater using advanced UV irradiation technology: a comparative assessment

UV irradiation technology as a membrane bioreactor (MBR) post-treatment was investigated and assessed. Both UV low pressure (LP) and medium pressure (MP) lamps were examined. The technology was installed in a pilot plant treating hospital wastewater to provide the study with adequate field data. The effect of the UV irradiation was enhanced with varying dosages of H2O2 to establish an advanced oxidation process (AOP). The efficiency of the pharmaceutical removal process was assessed by examining 14 micropollutants (antibiotics, analgesics, anticonvulsants, beta-blockers, cytostatics and X-ray contrast media) which are typically released by hospitals and detected with liquid chromatography coupled tandem mass spectrometry (LC-MS/MS). While the MBR treatment generally showed only a low degradation capacity for persistent pharmaceuticals, much better degradation was obtained by applying UV irradiation and H2O2 as AOP. The "conventional" cost-benefit analysis of the different technology options taking into account both electrical energy consumption and pharmaceutical removal efficiency, revealed clearly better performance of low pressure UV lamps as AOP. However, a holistic comparison between the different scenarios was carried out by evaluating their environmental impacts using the life cycle assessment (LCA) methodology. Decisive advantages were highlighted to include this approach in the decision making process.

Is it better to remove pharmaceuticals in decentralized or conventional wastewater treatment plants? A life cycle assessment comparison

After ingestion, pharmaceuticals are excreted unchanged or metabolized. They subsequently arrive in conventional wastewater treatment plants and are then released into the environment, often without undergoing any degradation. Conventional treatment plants can be upgraded with post treatment, alternatively the removal of pharmaceuticals could be achieved directly at point sources. In the European project PILLS, several solutions for decentralized treatment of pharmaceuticals at hospitals were investigated at both pilot plant and full scale, and were then compared to conventional and upgraded centralized treatment plants using Life Cycle Assessment (LCA). Within the scope of the study, pharmaceuticals were found to have a comparatively minor environmental impact. As a consequence, an additional post treatment does not provide significant benefits. In the comparison of post treatment technologies, ozonation and activated carbon performed better than UV. These results suffer however from high uncertainties due to the assessment models of the toxicity of pharmaceuticals in LCA. Our results should therefore be interpreted with caution. LCA is a holistic approach and does not cover effects or issues on a local level, which may be highly relevant. We should therefore apply the precautionary ALARA principle (As Low As Reasonably Achievable) and not conclude that the effect of pharmaceuticals is negligible in the environment.

Telomere-based neo-Darwinian selection of yeast clonal subpopulations

In Saccharomyces cerevisiae, imbalance of the genes coding for the heterochromatin components Sir3p and histone H4 (namely, overdosage of SIR3 and lack of one of the two genes coding for H4) causes modifications in telomere length and telomere sequence organization, favoring the insertion of Y' elements into a stably shortened (C1-3A)n repeat tract. We report here that the newly inserted Y' elements are unstable and are lost with high frequency, generating clonal subpopulations with short telomeres, as revealed by the analysis of a specific telomere (LIII) and of the overall population of telomeres. Moreover, the growth rates of the subpopulations with and without Y' elements on LIII are different, the Y'-less individuals reproducing 20% more slowly than individuals bearing Y' elements. When grown together with Y'-bearing individuals, the subpopulations with the normal LIII telomere (which are viable and genetically stable if grown alone) are rapidly competed out. Hence, genetic imbalance for the structural components of heterochromatin results in a complex and rapidly changing mixture of subpopulations in such cultures. Thus, in situations where subpopulations are allowed to compete, heterochromatin-based differential growth rates result in neo-Darwinian clonal selection.

Imbalance in dosage of the genes for the heterochromatin components Sir3p and histone H4 results in changes in the length and sequence organization of yeast telomeres

Telomeric heterochromatin plays an essential role in telomere function, including the regulation of telomere length. We observe that in Saccharomyces cerevisiae an imbalance in the dosage of genes for two protein components of heterochromatin (namely Sir3p and histone H4) causes modifications in telomere length and telomere sequence organization. The effects of Sir3p/H4 imbalance were analyzed in yeast strains in which the wild-type SIR3 gene (normally a single-copy gene) was either absent or present in 20-30 copies, and both histone H4 genes (HHF1 and HHF2) were present or HHF1 was deleted, thus covering a wide range of viable gene-dosage combinations. Modifications of telomeres and of subtelomeric regions were identified by analyzing both the overall telomere population and by focusing on two single telomeric regions: the left telomere of chromosome III (LIII) and the right telomere of chromosome XI (RXI). The modifications induced by alteration of the Sir3p/H4 ratio consist of a reduction in the length and an increase in the instability of the terminal block of (C(1-3)A)n repeats and in susceptibility to insertion of Y' elements into this repeat element. Restoration of the wild-type gene ratio (by removal of the extra copies of SIR3 or by complementation with the missing second copy of HHF) restored the original telomere organization, both with respect to the length of the (C(1-3)A)n repeat stretch and the absence of Y' elements. This behavior shows that the stability of the wild-type sequence organization requires maintenance of the normal structure of telomeric heterochromatin.

Heterochromatin organization of a natural yeast telomere. Recruitment of Sir3p through interaction with histone H4 N terminus is required for the establishment of repressive structures

The chromatin organization of eukaryotic telomeres is essential for telomeric function and is currently receiving great attention. In yeast, the structural organization of telomeres involves a complex interplay of telomeric proteins that results in the formation of heterochromatin. This telomeric heterochromatin involves homotypic and heterotypic protein interactions that have been summarized in a general model. Recent analyses have focused on the study of the structural complexity at yeast telomeres to the level of specific nucleosomes and of the distribution of protein complexes in a natural telomeric region (LIII). In this report, we further analyze the structural complexity of LIII and the implication of this structure on telomeric silencing. It is shown that the establishment of repressive heterochromatin structures at LIII requires the recruitment of Sir3p through interaction with the N terminus of histone H4. The establishment of such structures does not require acetylation of any of four lysines located in the H4 N terminus (lysines 5, 8, 12, and 16).

Heterochromatin organization of a natural yeast telomere. Changes of nucleosome distribution driven by the absence of Sir3p

We have defined the in vivo heterochromatin structure of the left telomere of Saccharomyces cerevisiae chromosome III (LIII). Analysis of heterochromatin of a single telomere was so far lacking, due to the difficulties intrinsic to the highly repetitive nature of telomeric sequences. In LIII, the terminal (C1-3A)n repetitive sequences are followed by a complete X element and by the single copy Ty5-1 retrotransposon. Both the telosome and the X element exhibit overall resistance to micrococcal nuclease digestion reflecting their tight chromatin structure organization. The X element contains protein complexes and irregularly distributed but well localized nucleosomes. In contrast, a regular array of phased nucleosomes is associated with the promoter region of Ty5-1 and with the more centromere-proximal sequences. The lack of a structural component of yeast telomeres, the SIR3 protein, does not alter the overall tight organization of the X element but causes a nucleosome rearrangement within the promoter region of Ty5-1 and releases Ty5-1 silencing. Thus, Sir3p links the modification of the heterochromatin structure with loss of transcriptional silencing.

Chromatin structure of the Saccharomyces cerevisiae DNA topoisomerase I promoter in different growth phases

We have determined the chromatin organization of the Saccharomyces cerevisiae DNA topoisomerase I promoter. Three nucleosomal core particles have been mapped at nucleotide level over the promoter region, encompassing the presumptive TATA sequence and the two RNA initiation sites; the most upstream nucleosome particle forms on to a 29 bp-long poly(dA-dT) element. This simple organization remains constant throughout both the logarithmic and the linear phase of growth, with the exception of an increased accessibility to micrococcal nuclease of the nucleosome covering the TATA box and the RNA initiation sites during the diauxic shift (the switching from the fermentative to the respiratory metabolism) in parallel with an increase of the DNA topoisomerase I mRNA. In addition, a strong disorganization of the bulk chromatin structure in the late stationary phase is also reported.

Effects of DNA topology in the interaction with histone octamers and DNA topoisomerase I

Several simple proteins and complex protein systems exist which do not recognize a defined sequence but--rather--a specific DNA conformation. We describe experiments and principles for two of these systems: nucleosomes and eukaryotic DNA topoisomerase I. Evidences are summarized that describe the effects of negative DNA supercoiling on nucleosome formation and the influence of DNA intrinsic curvature on their localization. The function of the DNA rotational information in nucleosome positioning and in the selection of multiple alternative positions on the same helical phase are described. This function suggests a novel genetic regulatory mechanism, based on nucleosome mobility and on the correlation between in vitro and in vivo positions. We observe that the same rules that determine the in vitro localization apply to the in vivo nucleosome positioning, as determined by a technique that relies on the use of nystatin and on the import of active enzymes in living yeast cells. The sensitivity of DNA topoisomerase I to the topological condition of the DNA substrate is reviewed and discussed taking into account recent experiments that describe the effect of the DNA tridimensional context on the reaction. These topics are discussed in the following order: (i) Proteins that look for a consensus DNA conformation; (ii) Nucleosomes; (iii) Negative supercoiling and nucleosomes; (iv) DNA curvature/bending and nucleosomes; (v) Multiple positioning; (vi) Multiple nucleosomes offer a contribution to the solution of the linking number paradox; (vii) Rotational versus translational information; (viii) A regulatory mechanism; (ix) DNA topoisomerase I; (x) DNA topoisomerase I and DNA supercoiling: a regulation by topological feedback; (xi) DNA topoisomerase I and DNA curvature; (xii) The in-and-out problem in the accessibility of DNA information; (xiii) The integrating function of the free energy of supercoiling.

Conformational information in DNA: its role in the interaction with DNA topoisomerase I and nucleosomes

Information in DNA is not limited to sequence information. Both local and global conformational parameters are pivotal to the interaction with a number of relevant proteins. The function of the major components of the transcription machinery (RNA polymerase II, DNA topoisomerase I, nucleosomes, the TATA-binding factor) is dependent on the topological status of the substrate DNA molecule. The topological requirements and the conformational consensus that dictate the rules for localization of nucleosomes and define the active sites for DNA topoisomerase I have been established; the reaction of DNA topoisomerase I is regulated by a topological feedback mechanism. The integrating function of the free energy of supercoiling in the transcription process and the regulatory role of DNA topoisomerase I are discussed.

In vivo analysis of chromatin following nystatin-mediated import of active enzymes into Saccharomyces cerevisiae

In vivo DNA-protein interactions are usually studied at the molecular level using DNA-degrading agents of low molecular weight. In order to be useful, macromolecular probes of chromatin structure, such as enzymes must first cross the cell membrane. In this paper we describe the introduction and evaluation of macromolecules with enzymatic activity into yeast spheroplasts treated with the polyene antibiotic nystatin. We report the low resolution analysis of chromatin structure in the promoter region of the Saccharomyces cerevisiae gene encoding DNA topoisomerase I by this technique using micrococcal nuclease and restriction enzymes.

A DNA conformational alteration induced by a neighboring oligopurine tract on GAATTA enables nicking by EcoRI

The pseudo EcoRI site GAATTA in the U3 region of the long terminal repeat of human immunodeficiency virus, which is flanked by a 26-base pair oligopurine tract, is readily nicked by either EcoRI or RsrI. The strand-specific nick occurs predominantly between the G and A residues and is independent of negative supercoiling. Other GAATTA sites surrounded by random (non-oligopurine) sequences are not nicked by these restriction endonucleases. However, other types and lengths of oligopurine tracts are effective in inducing the nicking in neighboring GAATTA sites. Hence, we propose that the flanking oligopurine tracts induce an altered DNA conformation on the GAATTA target site which may be similar to the transition state induced by EcoRI when binding to its canonical recognition site. Gel retardation analyses on restriction fragments containing the oligopurine-GAATTA-oligopurine sequences suggest the presence of helical axis distortions which are consistent with this interpretation.

Linkage reduction allows reconstitution of nucleosomes on DNA microdomains

We have established an experimental system for reconstitution of an individual nucleosome on a closed DNA microdomain (operationally defined as a DNA domain of a size so small as to be unable to establish titratable superhelical turns). The microdomain (185 base-pairs (bp), composed of 128 bp encompassing the central part of the Saccharomyces cerevisiae ADH II promoter plus 57 bp of a polylinker) was obtained by ligation under conditions that produced three circularized forms characterized by different linkage numbers. These linkomers were tested for nucleosome reconstitution with S. cerevisiae histones. It was observed that only microcircles with linkage reduction (delta Lk = 1 or 2) could form a nucleosome, as defined by protection of a 145(+/- 2) bp DNA fragment from micrococcal nuclease, relaxed forms (open or closed circles) could not.

DNA conformational variations in the in vitro torsionally strained Ig kappa light chain gene localize on consensus sequences

We have analyzed the localization and the dependence upon superhelical density of the DNA sites which modify their conformation under torsional strain in a mouse Ig L kappa gene. The conformational variations occur on DNA sites which have been defined as protein interaction sites and consensus sequence motifs: the 5'-upstream regulatory decanucleotides, the TATA sequence, the consensus heptanucleotides of the J recombinational sequences.

The intrinsic topological information of the wild-type and of up-promoter mutations of the Saccharomyces cerevisiae alcohol dehydrogenase II regulatory region

A 569-base pair fragment encompassing the upstream regulatory region, the RNA initiation sites, and the initial part of the coding region of the Saccharomyces cerevisiae alcohol dehydrogenase II gene has been analyzed for the presence of sites which undergo conformational modification under torsional stress. Fine mapping of P1 and S1 endonuclease-sensitive sites was obtained on single topoisomers produced by in vitro ligation. It was shown that the upstream activator sequence, the TATA sequence, a region directly upstream to the RNA initiation sites, and several positions in the first segment of the transcribed region change conformation as a function of the applied torsional stress in a precisely coordinate fashion. The superhelical density optima for this coordinate modifications have been determined. Analysis of the conformational changes of the promoter sequence in several naturally occurring (Young, E. T., Williamson, V. M., Taguchi, A., Smith, M., Sledziewski, L., Russel, D., Osterman, J., Denis, C., Cox, D., and Beier, D., (1982) in Genetic Engineering of Microorganisms for Chemicals (Hollander, A., De Moss, R. D., Kaplan, S., Konisky, J., Savage, D., and Wolle, R. S., eds) pp. 335-361, Plenum Publishing Corp., New York) up-promoter constitutive mutants was performed. This analysis has shown that the conformation of functionally relevant sites changes as a function of sequence mutations that have taken place elsewhere; this shows that the conformational behavior of the whole promoter region is linked and suggests transmission in cis of topological effects in RNA polymerase II promoters.