DNA binding shifts the redox potential of the transcription factor SoxR

Electrochemistry measurements on DNA-modified electrodes are used to probe the effects of binding to DNA on the redox potential of SoxR, a transcription factor that contains a [2Fe-2S] cluster and is activated through oxidation. A DNA-bound potential of +200 mV versus NHE (normal hydrogen electrode) is found for SoxR isolated from Escherichia coli and Pseudomonas aeruginosa. This potential value corresponds to a dramatic shift of +490 mV versus values found in the absence of DNA. Using Redmond red as a covalently bound redox reporter affixed above the SoxR binding site, we also see, associated with SoxR binding, an attenuation in the Redmond red signal compared with that for Redmond red attached below the SoxR binding site. This observation is consistent with a SoxR-binding-induced structural distortion in the DNA base stack that inhibits DNA-mediated charge transport to the Redmond red probe. The dramatic shift in potential for DNA-bound SoxR compared with the free form is thus reconciled based on a high-energy conformational change in the SoxR–DNA complex. The substantial positive shift in potential for DNA-bound SoxR furthermore indicates that, in the reducing intracellular environment, DNA-bound SoxR is primarily in the reduced form; the activation of DNA-bound SoxR would then be limited to strong oxidants, making SoxR an effective sensor for oxidative stress. These results more generally underscore the importance of using DNA electrochemistry to determine DNA-bound potentials for redox-sensitive transcription factors because such binding can dramatically affect this key protein property

Two Coregulated Efflux Transporters Modulate Intracellular Heme and Protoporphyrin IX Availability in Streptococcus agalactiae

Streptococcus agalactiae is a major neonatal pathogen whose infectious route involves septicemia. This pathogen does not synthesize heme, but scavenges it from blood to activate a respiration metabolism, which increases bacterial cell density and is required for full virulence. Factors that regulate heme pools in S. agalactiae are unknown. Here we report that one main strategy of heme and protoporphyrin IX (PPIX) homeostasis in S. agalactiae is based on a regulated system of efflux using two newly characterized operons, gbs1753 gbs1752 (called pefA pefB), and gbs1402 gbs1401 gbs1400 (called pefR pefC pefD), where pef stands for ‘porphyrin-regulated efflux’. In vitro and in vivo data show that PefR, a MarR-superfamily protein, is a repressor of both operons. Heme or PPIX both alleviate PefR-mediated repression. We show that bacteria inactivated for both Pef efflux systems display accrued sensitivity to these porphyrins, and give evidence that they accumulate intracellularly. The ΔpefR mutant, in which both pef operons are up-regulated, is defective for heme-dependent respiration, and attenuated for virulence. We conclude that this new efflux regulon controls intracellular heme and PPIX availability in S. agalactiae, and is needed for its capacity to undergo respiration metabolism, and to infect the host

NIBBS-Search for Fast and Accurate Prediction of Phenotype-Biased Metabolic Systems

Understanding of genotype-phenotype associations is important not only for furthering our knowledge on internal cellular processes, but also essential for providing the foundation necessary for genetic engineering of microorganisms for industrial use (e.g., production of bioenergy or biofuels). However, genotype-phenotype associations alone do not provide enough information to alter an organism's genome to either suppress or exhibit a phenotype. It is important to look at the phenotype-related genes in the context of the genome-scale network to understand how the genes interact with other genes in the organism. Identification of metabolic subsystems involved in the expression of the phenotype is one way of placing the phenotype-related genes in the context of the entire network. A metabolic system refers to a metabolic network subgraph; nodes are compounds and edges labels are the enzymes that catalyze the reaction. The metabolic subsystem could be part of a single metabolic pathway or span parts of multiple pathways. Arguably, comparative genome-scale metabolic network analysis is a promising strategy to identify these phenotype-related metabolic subsystems. Network Instance-Based Biased Subgraph Search (NIBBS) is a graph-theoretic method for genome-scale metabolic network comparative analysis that can identify metabolic systems that are statistically biased toward phenotype-expressing organismal networks. We set up experiments with target phenotypes like hydrogen production, TCA expression, and acid-tolerance. We show via extensive literature search that some of the resulting metabolic subsystems are indeed phenotype-related and formulate hypotheses for other systems in terms of their role in phenotype expression. NIBBS is also orders of magnitude faster than MULE, one of the most efficient maximal frequent subgraph mining algorithms that could be adjusted for this problem. Also, the set of phenotype-biased metabolic systems output by NIBBS comes very close to the set of phenotype-biased subgraphs output by an exact maximally-biased subgraph enumeration algorithm ( MBS-Enum ). The code (NIBBS and the module to visualize the identified subsystems) is available at http://freescience.org/cs/NIBBS

Fine Tuning of the Lactate and Diacetyl Production through Promoter Engineering in Lactococcus lactis

Lactococcus lactis is a well-studied bacterium widely used in dairy fermentation and capable of producing metabolites with organoleptic and nutritional characteristics. For fine tuning of the distribution of glycolytic flux at the pyruvate branch from lactate to diacetyl and balancing the production of the two metabolites under aerobic conditions, a constitutive promoter library was constructed by randomizing the promoter sequence of the H2O-forming NADH oxidase gene in L. lactis. The library consisted of 30 promoters covering a wide range of activities from 7,000 to 380,000 relative fluorescence units using a green fluorescent protein as reporter. Eleven typical promoters of the library were selected for the constitutive expression of the H2O-forming NADH oxidase gene in L. lactis, and the NADH oxidase activity increased from 9.43 to 58.17-fold of the wild-type strain in small steps of activity change under aerobic conditions. Meanwhile, the lactate yield decreased from 21.15±0.08 mM to 9.94±0.07 mM, and the corresponding diacetyl production increased from 1.07±0.03 mM to 4.16±0.06 mM with the intracellular NADH/NAD+ ratios varying from 0.711±0.005 to 0.383±0.003. The results indicated that the reduced pyruvate to lactate flux was rerouted to the diacetyl with an almost linear flux variation via altered NADH/NAD+ ratios. Therefore, we provided a novel strategy to precisely control the pyruvate distribution for fine tuning of the lactate and diacetyl production through promoter engineering in L. lactis. Interestingly, the increased H2O-forming NADH oxidase activity led to 76.95% lower H2O2 concentration in the recombinant strain than that of the wild-type strain after 24 h of aerated cultivation. The viable cells were significantly elevated by four orders of magnitude within 28 days of storage at 4°C, suggesting that the increased enzyme activity could eliminate H2O2 accumulation and prolong cell survival

Soil measurements during HAPEX-Sahel intensive observation period

This article describes measurements made at each site and for each vegetation cover as part of the soils program for the HAPEX-Sahel regional scale experiment. The measurements were based on an initial sampling scheme and included profile soil water content, surface soil water content, soil water potential, infiltration rates, additional measurements on core samples, and grain size analysis. The measurements were used to categorize the state of the surface and profile soil water regimes during the experiment and to derive functional relationships for the soil water characteristic curve, unsaturated hydraulic conductivity function, and infiltration function. Sample results for different supersites and different vegetation covers are presented showing soil water profiles and total soil water storage on days corresponding to the experimental ‘Golden Days’. Sample results are also presented for spatial and temporal distribution of surface moisture content and infiltration tests. The results demonstrate that the major experimental objective of monitoring the supersites during the most rapid vegetative growth stage with the largest change of the surface energy balance following the rainy season was very nearly achieved. Separation of the effects of probable root activity and drainage of the soil profile is possible. The potential for localized advection between the bare soil and vegetation strips of the tiger bush sites is demonstrate

The Pierre Auger Observatory Open Data

The Pierre Auger Collaboration has embraced the concept of open access to their research data since its foundation, with the aim of giving access to the widest possible community. A gradual process of release began as early as 2007 when 1% of the cosmic-ray data was made public, along with 100% of the space-weather information. In February 2021, a portal was released containing 10% of cosmic-ray data collected from 2004 to 2018, during Phase I of the Observatory. The Portal included detailed documentation about the detection and reconstruction procedures, analysis codes that can be easily used and modified and, additionally, visualization tools. Since then the Portal has been updated and extended. In 2023, a catalog of the 100 highest-energy cosmic-ray events examined in depth has been included. A specific section dedicated to educational use has been developed with the expectation that these data will be explored by a wide and diverse community including professional and citizen-scientists, and used for educational and outreach initiatives. This paper describes the context, the spirit and the technical implementation of the release of data by the largest cosmic-ray detector ever built, and anticipates its future developments.Comment: 19 pages, 8 figure

Radio Measurements of the Depth of Air-Shower Maximum at the Pierre Auger Observatory

The Auger Engineering Radio Array (AERA), part of the Pierre Auger Observatory, is currently the largest array of radio antenna stations deployed for the detection of cosmic rays, spanning an area of $17$ km$^2$ with 153 radio stations. It detects the radio emission of extensive air showers produced by cosmic rays in the $30-80$ MHz band. Here, we report the AERA measurements of the depth of the shower maximum ($X_\text{max}$), a probe for mass composition, at cosmic-ray energies between $10^{17.5}$ to $10^{18.8}$ eV, which show agreement with earlier measurements with the fluorescence technique at the Pierre Auger Observatory. We show advancements in the method for radio $X_\text{max}$ reconstruction by comparison to dedicated sets of CORSIKA/CoREAS air-shower simulations, including steps of reconstruction-bias identification and correction, which is of particular importance for irregular or sparse radio arrays. Using the largest set of radio air-shower measurements to date, we show the radio $X_\text{max}$ resolution as a function of energy, reaching a resolution better than $15$ g cm$^{-2}$ at the highest energies, demonstrating that radio $X_\text{max}$ measurements are competitive with the established high-precision fluorescence technique. In addition, we developed a procedure for performing an extensive data-driven study of systematic uncertainties, including the effects of acceptance bias, reconstruction bias, and the investigation of possible residual biases. These results have been cross-checked with air showers measured independently with both the radio and fluorescence techniques, a setup unique to the Pierre Auger Observatory.Comment: Submitted to Phys. Rev.

Demonstrating Agreement between Radio and Fluorescence Measurements of the Depth of Maximum of Extensive Air Showers at the Pierre Auger Observatory

We show, for the first time, radio measurements of the depth of shower maximum ($X_\text{max}$) of air showers induced by cosmic rays that are compared to measurements of the established fluorescence method at the same location. Using measurements at the Pierre Auger Observatory we show full compatibility between our radio and the previously published fluorescence data set, and between a subset of air showers observed simultaneously with both radio and fluorescence techniques, a measurement setup unique to the Pierre Auger Observatory. Furthermore, we show radio $X_\text{max}$ resolution as a function of energy and demonstrate the ability to make competitive high-resolution $X_\text{max}$ measurements with even a sparse radio array. With this, we show that the radio technique is capable of cosmic-ray mass composition studies, both at Auger and at other experiments.Comment: Submitted to Phys. Rev. Let