Biochemical and genetic analysis of the Sox multienzyme complex in the purple sulfur bacterium <i>Allochromatium vinosum</i>

The best studied pathway of thiosulfate oxidation is the complete transformation to sulfate by a sox encoded periplasmic multienzyme complex. In the chemotroph Paracoccus pantotrophus Sox proteins are essential for thiosulfate and also for sulfide oxidation. Intermediates are not formed on the pathway to sulfate [1]. The purple sulfur bacterium Allochromatium vinosum oxidizes thiosulfate either to tetrathionate or to sulfate, dependent on pH. Intracellular sulfur globules occur as obligate intermediate of the latter pathway. Sequence analysis revealed the presence of five sox genes in two independent gene loci, soxBXA and soxYZ. The genes soxCD, encoding important proteins of the P. pantotrophus Sox complex, are not present in A. vinosum. Interposon mutagenesis of soxB and soxX in A. vinosum led to a complete inability of the cells to metabolize thiosulfate to sulfate while sulfide oxidation and tetrathionate formation remained uninhibited. Thiosulfate oxidation was also completely abolished in an in frame deletion mutant of soxY. Interestingly, this soxY mutation had further deleterious effects on sulfur compound oxidation: decomposition of sulfur globules formed during sulfide oxidation to sulfate was significantly slower and sulfite was excreted into the medium as an intermediate of this process. A. vinosum wild type is able to effectively use externally added sulfite as photosynthetic electron donor. Oxidation of external sulfite in the soxY mutant appeared greatly impaired, further demonstrating that the effects of a soxY mutation are not limited to thiosulfate oxidation. The observed phenotypes lead us to conclude that Sox proteins play a prominent role in A. vinosum. While SoxB and SoxXA are essential for thiosulfate oxidation, SoxY has an even more extensive function not only in thiosulfate oxidation but also in degradation of other sulfur compounds. In addition to the results obtained on a genetic basis, the work on protein level provided further proof for the actual presence of Sox proteins in A. vinosum. Three different proteins, encoded by the five sox genes present in A. vinosum, were purified from the organism. The first protein, SoxB, was isolated as a monomer. The second protein, SoxXA, was purified as a heterodimeric c-type cytochrome with both subunits containing a heme group. The third protein, the substrate binding molecule SoxYZ, was also present as a heterodimer in A. vinosum. [1] Friedrich, C.G. et al. (2001), Appl.Env.Microbiol.67: 2873-2882Biochemische und genetische Analyse des Sox-Multienzym-Komplexes in dem Schwefelpurpurbakterium Allochromatium vinosum Der am besten untersuchte Weg der Thiosulfat-Oxidation ist die komplette Umsetzung zum Sulfat durch einen sox-Gen codierten, periplasmatischen Multienzym-Komplex. Im chemotrophen Bakterium Paracoccus pantotrophus sind Sox-Proteine essentiell für die Oxidation von Thiosulfat und Sulfid. Auf dem Weg zum Sulfat werden keine Intermediate gebildet [1]. Das Schwefelpurpurbakterium Allochromatium vinosum oxidiert in Abhängigkeit vom pH-Wert Thiosulfat entweder zu Tetrathionat oder zu Sulfat. Als obligates Intermediat auf dem Weg zum Sulfat werden intrazellulär Schwefelkugeln gebildet. Eine Gensequenz-Analyse zeigte die Anwesenheit von fünf sox-Genen (soxBXA und soxYZ), lokalisiert an zwei unabhängigen Positionen im Genom. Die Gene soxCD, die ein essentielles Protein des Sox-Komplexes von P. pantotrophus codieren, sind in A. vinosum nicht vorhanden. Die Interposon-Mutagenese von soxB und soxX führte zu einer kompletten Hemmung der Oxidation von Thiosulfat zu Sulfat, während Sulfidoxidation und Tetrathionatbildung unbeeinflußt blieben. Auch in einer in frame-Deletionsmutante von soxY zeigte sich eine vollständige Inhibition der Thiosulfatoxidation. Die Ausschaltung von soxY hatte noch weitere negative Effekte auf die Oxidation von Schwefelverbindungen: Schwefelkugeln, die während der Sulfidoxidation gebildet wurden, konnten nur signifikant verlangsamt abgebaut werden. Zusätzlich wurde Sulfit, als Intermediat des Oxidationsweges zum Sulfat, in das Medium ausgeschieden. Der A. vinosum-Wildtyp kann extern zugegebenes Sulfit effektiv als photosynthetischen Elektronendonor nutzen. Die Oxidation von extern zugegebenem Sulfit in der soxY-Mutante dagegen war deutlich beeinträchtigt. Die Auswirkungen der soxY-Deletion sind daher nicht auf die Oxidation von Thiosulfat beschränkt. Die beobachteten Phänotypen ließen den Schluß zu, dass Sox-Proteine eine wichtige Rolle in A. vinosum spielen. Während SoxB und SoxXA essentiell für die Thiosulfatoxidation sind, hat SoxY eine weitreichendere Funktion sowohl bei der Oxidation von Thiosulfat als auch beim Abbau anderer Schwefelverbindungen. Zusätzlich zu den Ergebnissen auf genetischer Basis lieferte die Arbeit auf Proteinebene Beweise für die tatsächliche Anwesenheit der Sox-Proteine in A. vinosum. Es konnten drei verschiedene Proteine aus dem Organismus isoliert werden, die von den fünf identifizierten sox-Genen codiert werden. Das erste Protein, SoxB, wurde als Monomer aufgereinigt. Das zweite Protein, SoxXA, wurde als heterodimeres c-Typ-Cytochrom identifiziert, wobei jede Untereinheit Träger einer Hämgruppe ist. Das dritte Protein, identifiziert als Substratbindemolekül SoxYZ, konnte ebenfalls als Heterodimer aus A. vinosum isoliert werden. [1] Friedrich, C.G. et al. (2001), Appl.Env.Microbiol.67: 2873-288

Resolving the contributions of the membrane-bound and periplasmic nitrate reductase systems to nitric oxide and nitrous oxide production in Salmonella enterica serovar Typhimurium

The production of cytotoxic nitric oxide (NO) and conversion into the neuropharmacological agent and potent greenhouse gas nitrous oxide (N2O) is linked with anoxic nitrate catabolism by Salmonella enterica serovar Typhimurium. Salmonella can synthesize two types of nitrate reductase: a membrane-bound form (Nar) and a periplasmic form (Nap). Nitrate catabolism was studied under nitrate-rich and nitrate-limited conditions in chemostat cultures following transition from oxic to anoxic conditions. Intracellular NO production was reported qualitatively by assessing transcription of the NO-regulated genes encoding flavohaemoglobin (Hmp), flavorubredoxin (NorV) and hybrid cluster protein (Hcp). A more quantitative analysis of the extent of NO formation was gained by measuring production of N2O, the end-product of anoxic NO-detoxification. Under nitrate-rich conditions, the nar, nap, hmp, norV and hcp genes were all induced following transition from the oxic to anoxic state, and 20% of nitrate consumed in steady-state was released as N2O when nitrite had accumulated to millimolar levels. The kinetics of nitrate consumption, nitrite accumulation and N2O production were similar to those of wild-type in nitrate-sufficient cultures of a nap mutant. In contrast, in a narG mutant, the steady-state rate of N2O production was ~30-fold lower than that of the wild-type. Under nitrate-limited conditions, nap, but not nar, was up-regulated following transition from oxic to anoxic metabolism and very little N2O production was observed. Thus a combination of nitrate-sufficiency, nitrite accumulation and an active Nar-type nitrate reductase leads to NO and thence N2O production, and this can account for up to 20% of the nitrate catabolized

SARS-CoV-2 susceptibility and COVID-19 disease severity are associated with genetic variants affecting gene expression in a variety of tissues

Variability in SARS-CoV-2 susceptibility and COVID-19 disease severity between individuals is partly due to genetic factors. Here, we identify 4 genomic loci with suggestive associations for SARS-CoV-2 susceptibility and 19 for COVID-19 disease severity. Four of these 23 loci likely have an ethnicity-specific component. Genome-wide association study (GWAS) signals in 11 loci colocalize with expression quantitative trait loci (eQTLs) associated with the expression of 20 genes in 62 tissues/cell types (range: 1:43 tissues/gene), including lung, brain, heart, muscle, and skin as well as the digestive system and immune system. We perform genetic fine mapping to compute 99% credible SNP sets, which identify 10 GWAS loci that have eight or fewer SNPs in the credible set, including three loci with one single likely causal SNP. Our study suggests that the diverse symptoms and disease severity of COVID-19 observed between individuals is associated with variants across the genome, affecting gene expression levels in a wide variety of tissue types

A first update on mapping the human genetic architecture of COVID-19

peer reviewe

Low cost and state of the art methods to measure nitrous oxide emissions

This letter provides an overview of the available measurement techniques for nitrous oxide (N2O) flux measurement. It is presented to aid the choice of the most appropriate methods for different situations. Nitrous oxide is a very potent greenhouse gas; the effect of 1 kg of N2O is estimated to be equivalent to 300 kg of CO2. Emissions of N2O from the soil have a larger uncertainty compared to other greenhouse gases. Important reasons for this are low atmospheric concentration levels and enormous spatial and temporal variability. Traditionally such small increases are measured by chambers and analyzed by gas chromatography. Spatial and temporal resolution is poor, but costs are low. To detect emissions at the field scale and high temporal resolution, differences at tens of ppt levels need to be resolved. Reliable instruments are now available to measure N2O by a range of micrometeorological methods, but at high financial cost. Although chambers are effective in identifying processes and treatment effects and mitigation, the future lies with the more versatile high frequency and high sensitivity sensors

Multi-laboratory compilation of atmospheric carbon dioxide data for the period 1957-2020 [Dataset]

This product is constructed using the Observation Package (ObsPack) framework [Masarie et al., 2014; www.earth-syst-sci-data.net/6/375/2014/]. The framework is designed to bring together atmospheric greenhouse gas (GHG) observations from a variety of sampling platforms, prepare them with specific applications in mind, and package and distribute them in a self-consistent and well-documented product. ObsPack products are intended to support GHG budget studies and represent a new generation of cooperative value-added GHG data products. This product includes 524 atmospheric carbon dioxide datasets derived from observations made by 63 laboratories from 21 countries. Data for the period 1957-2020 (where available) are included

COVID-19 Host Genetics Initiative. A first update on mapping the human genetic architecture of COVID-19

The COVID-19 pandemic continues to pose a major public health threat, especially in countries with low vaccination rates. To better understand the biological underpinnings of SARS-CoV-2 infection and COVID-19 severity, we formed the COVID-19 Host Genetics Initiative1. Here we present a genome-wide association study meta-analysis of up to 125,584 cases and over 2.5 million control individuals across 60 studies from 25 countries, adding 11 genome-wide significant loci compared with those previously identified2. Genes at new loci, including SFTPD, MUC5B and ACE2, reveal compelling insights regarding disease susceptibility and severity.</p