Prediction of the Iron–Sulfur Binding Sites in Proteins Using the Highly Accurate Three-Dimensional Models Calculated by AlphaFold and RoseTTAFold

AlphaFold and RoseTTAFold are deep learning-based approaches that predict the structure of proteins from their amino acid sequences. Remarkable success has recently been achieved in the prediction accuracy of not only the fold of the target protein but also the position of its amino acid side chains. In this article, I question the accuracy of these methods to predict iron–sulfur binding sites. I analyze three-dimensional models calculated by AlphaFold and RoseTTAFold of Fe–S–dependent enzymes, for which no structure of a homologous protein has been solved experimentally. In all cases, the amino acids that presumably coordinate the cluster were gathered together and facing each other, which led to a quite accurate model of the Fe–S cluster binding site. Yet, cysteine candidates were often involved in intramolecular disulfide bonds, and the number and identity of the protein amino acids that should ligate the cluster were not always clear. The experimental structure determination of the protein with its Fe–S cluster and in complex with substrate/inhibitor/product is still needed to unambiguously visualize the coordination state of the cluster and understand the conformational changes occurring during catalysis.

Disentangling the genetic basis of rhizosphere microbiome assembly in tomato

Microbiomes play a pivotal role in plant growth and health, but the genetic factors involved in microbiome assembly remain largely elusive. Here, 16S amplicon and metagenomic features of the rhizosphere microbiome were mapped as quantitative traits of a recombinant inbred line population of a cross between wild and domesticated tomato. Gene content analysis of prioritized tomato QTLs suggested a genetic basis for differential recruitment of various rhizobacterial lineages, including a Streptomyces-associated 6.31-Mbp region harboring tomato domestication sweeps and encoding, among others, the iron regulator FIT and the aquaporin SlTIP2.3. Within metagenome-assembled genomes of the rhizobacterial lineages Streptomyces and Cellvibrio, we identified microbial genes involved in metabolism of plant polysaccharides, iron, sulfur, trehalose, and vitamins, whose genetic variation associated with either modern or wild tomato QTLs. Integrating 'microbiomics' and quantitative plant genetics pinpointed putative plant and reciprocal microbial traits underlying microbiome assembly, thereby providing the first step towards plant-microbiome breeding programs.

The monofunctional CO dehydrogenase CooS is essential for growth of Thermoanaerobacter kivui on carbon monoxide

Thermoanaerobacter kivui is a thermophilic acetogen that can grow on carbon monoxide as sole carbon and energy source. To identify the gene(s) involved in CO oxidation, the genome sequence was analyzed. Two genes potentially encoding CO dehydrogenases were identified. One, cooS, potentially encodes a monofunctional CO dehydrogenase, whereas another, acsA, potentially encodes the CODH component of the CODH/ACS complex. Both genes were cloned, a His-tag encoding sequence was added, and the proteins were produced from a plasmid in T. kivui. His-AcsA copurified by affinity chromatography with AcsB, the acetyl-CoA synthase of the CO dehydrogenase/acetyl CoA synthase complex. His-CooS copurified with CooF1, a small iron-sulfur center containing protein likely involved in electron transport. Both protein complexes had CO:ferredoxin oxidoreductase as well as CO:methyl viologen oxidoreductase activity, but the activity of CooSF1 was 15-times and 231-times lower, respectively. To underline the importance of CooS, the gene was deleted in the CO-adapted strain. Interestingly, the ∆cooS deletion mutant did not grow on CO anymore. These experiments clearly demonstrated that CooS is essential for growth of T. kivui on CO. This is in line with the hypothesis that CooS is the CO-oxidizing enzyme in cells growing on CO.

Can Bottom Sediments Be a Prospective Fertilizing Material? A Chemical Composition Analysis for Potential Reuse in Agriculture

Every year, huge amounts of bottom sediments are extracted worldwide, which need to be disposed. The recycling of bottom sediments for soil fertilization is in line with the long-promoted circular economy policy and enables the use of micro and macronutrients accumulated in sediments for soil fertilization. When considering potential agricultural reuse of the dredge sediments, the first necessary step should be to analyze whether the heavy metal content meets the obligatory criteria. Then, the contents of valuable elements required for plant growth and their ratios should be assessed. In this study, the content of nitrogen, organic carbon, phosphorus, and potassium was tested and iron, sulfur, calcium, and magnesium were also analyzed along vertical profiles of sediments extracted from four urban retention tanks in Gdańsk (Poland). The sediments were indicated to have a low content of nutrients (Ntot 0.01–0.52%, Corg 0.1–8.4%, P2O5 0.00–0.65%, K 0.0–1.0%), while being quite rich in Fe and S (0.2–3.3%, 0.0–2.5%, respectively). The C/N ratio changed in the range of 17.4–28.4, which proved good nitrogen availability for plants. The mean values of the Fe/P ratio were above 2.0, which confirms that phosphorus in the sediments would be available to the plants in the form of iron phosphate. To summarize, the bottom sediments from municipal retention reservoirs are not a perfect material for soil fertilization, but they are a free waste material which, when enriched with little cost, can be a good fertilizer. Future research should focus on cultivation experiments with the use of sediments enriched with N, P, Corg.

A complete biomimetic iron-sulfur cubane redox series

Synthetic iron-sulfur cubanes are essential models for biological cofactors in the more complex enzymatic environments. However, a complete series of [Fe4S4]n complexes spanning all biorelevant oxidation states (n = 0-3+) has never been prepared. Here, we demonstrate that the use of a bulky arylthiolate ligand promoting the encapsulation of alkali-metal cations in the vicinity of the cubane enables the synthesis of such a series. Characterization by EPR, 57Fe Mössbauer spectroscopy, UV-Vis electronic absorption and variable-temperature X-ray diffraction analysis reveals key trends for the Fe4S4 core’s geometry as well as for the Mössbauer isomer shift, which both correlate systematically with oxidation state. Furthermore, we confirm the S=4 electronic ground state of the most reduced member, [Fe4S4]0, in agreement with that proposed for the all-ferrous cubanes in Nature.