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The FEBS Journal Feb 2020Hybrid cluster proteins (HCPs) are metalloproteins characterized by the presence of an iron-sulfur-oxygen cluster. These proteins occur in all three domains of life. In...
Hybrid cluster proteins (HCPs) are metalloproteins characterized by the presence of an iron-sulfur-oxygen cluster. These proteins occur in all three domains of life. In eukaryotes, HCPs have so far been found only in a few anaerobic parasites and photosynthetic microalgae. With respect to all species harboring an HCP, the green microalga Chlamydomonas reinhardtii stands out by the presence of four HCP genes. The study of the gene and protein structures as well as the phylogenetic analyses strongly support a model in which the HCP family in the alga has emerged from a single gene of alpha proteobacterial origin and then expanded by several rounds of duplications. The spectra and redox properties of HCP1 and HCP3, produced heterologously in Escherichia coli, were analyzed by electron paramagnetic resonance spectroscopy on redox-titrated samples. Both proteins contain a [4Fe-4S]-cluster as well as a [4Fe-2O-2S]-hybrid cluster with paramagnetic properties related to those of HCPs from Desulfovibrio species. Immunoblotting experiments combined with mass spectrometry-based proteomics showed that both nitrate and darkness contribute to the strong upregulation of the HCP levels in C. reinhardtii growing under oxic conditions. The link to the nitrate metabolism is discussed in the light of recent data on the potential role of HCP in S-nitrosylation in bacteria.
Topics: Algal Proteins; Binding Sites; Chlamydomonas reinhardtii; Cloning, Molecular; Desulfovibrio; Escherichia coli; Evolution, Molecular; Gene Expression; Genetic Vectors; Iron-Sulfur Proteins; Microalgae; Models, Molecular; Multigene Family; Nitrates; Photosynthesis; Phylogeny; Protein Binding; Protein Conformation, alpha-Helical; Protein Conformation, beta-Strand; Protein Interaction Domains and Motifs; Recombinant Proteins; Structural Homology, Protein
PubMed: 31361397
DOI: 10.1111/febs.15025 -
ACS Chemical Biology Jul 2022Metal-dependent formate dehydrogenases are important enzymes due to their activity of CO reduction to formate. The tungsten-containing FdhAB formate dehydrogenase from...
Metal-dependent formate dehydrogenases are important enzymes due to their activity of CO reduction to formate. The tungsten-containing FdhAB formate dehydrogenase from Hildenborough is a good example displaying high activity, simple composition, and a notable structural and catalytic robustness. Here, we report the first spectroscopic redox characterization of FdhAB metal centers by EPR. Titration with dithionite or formate leads to reduction of three [4Fe-4S] clusters, and full reduction requires Ti(III)-citrate. The redox potentials of the four [4Fe-4S] centers range between -250 and -530 mV. Two distinct W signals were detected, W and W, which differ in only the -value. This difference can be explained by small variations in the twist angle of the two pyranopterins, as determined through DFT calculations of model compounds. The redox potential of W was determined to be -370 mV when reduced by dithionite and -340 mV when reduced by formate. The crystal structure of dithionite-reduced FdhAB was determined at high resolution (1.5 Å), revealing the same structural alterations as reported for the formate-reduced structure. These results corroborate a stable six-ligand W coordination in the catalytic intermediate W state of FdhAB.
Topics: Catalysis; Desulfovibrio; Desulfovibrio vulgaris; Dithionite; Electron Spin Resonance Spectroscopy; Formate Dehydrogenases; Formates; Metals; Oxidation-Reduction
PubMed: 35766974
DOI: 10.1021/acschembio.2c00336 -
Frontiers in Microbiology 2022Microbial symbionts can influence a myriad of insect behavioral and physiological traits. However, how microbial communities may shape or be shaped by insect...
Microbial symbionts can influence a myriad of insect behavioral and physiological traits. However, how microbial communities may shape or be shaped by insect interactions with plants and neighboring species remains underexplored. The fig-fig wasp mutualism system offers a unique model to study the roles of microbiome in the interactions between the plants and co-habiting insects because a confined fig environment is shared by two fig wasp species, the pollinator wasp ( and ) and the cheater wasp ( sp1 and sp2). Here, we performed whole genome resequencing (WGS) on 48 individual fig wasps ( spp.) from Yunnan, China, to reveal the phylogenetic relationship and genetic divergence between pollinator and congeneric cheater wasps associated with the trees. We then extracted metagenomic sequences to explore the compositions, network structures, and functional capabilities of microbial communities associated with these wasps. We found that the cheaters and pollinators from the same fig species are sister species, which are highly genetically divergent. Fig wasps harbor diverse but stable microbial communities. Fig species dominate over the fig wasp genotype in shaping the bacterial and fungal communities. Variation in microbial communities may be partially explained by the filtering effect from fig and phylogeny of fig wasps. It is worth noting that cheaters have similar microbial communities to their sister pollinators, which may allow cheaters to coexist and gain resources from the same fig species. In terms of metabolic capabilities, some bacteria such as and are candidates involved in the nutritional uptake of fig wasps. Our results provide novel insights into how microbiome community and metabolic functions may couple with the fig-wasp mutualistic systems.
PubMed: 36466640
DOI: 10.3389/fmicb.2022.1009919 -
Frontiers in Microbiology 2023Colorectal cancer (CRC) commonly arises in individuals with premalignant colon lesions known as polyps, with both conditions being influenced by gut microbiota....
Colorectal cancer (CRC) commonly arises in individuals with premalignant colon lesions known as polyps, with both conditions being influenced by gut microbiota. Host-related factors and inherent characteristics of polyps and tumors may contribute to microbiome variability, potentially acting as confounding factors in the discovery of taxonomic biomarkers for both conditions. In this study we employed shotgun metagenomics to analyze the taxonomic diversity of bacteria present in fecal samples of 90 clinical subjects (comprising 30 CRC patients, 30 with polyps and 30 controls). Our findings revealed a decrease in taxonomic richness among individuals with polyps and CRC, with significant dissimilarities observed among the study groups. We identified significant alterations in the abundance of specific taxa associated with polyps (Streptococcaceae, , and ) and CRC (Lactobacillales, Clostridiaceae, , SFB, , and ). Clostridiaceae exhibited significantly lower abundance in the early stages of CRC. Additionally, our study revealed a positive co-occurrence among underrepresented genera in CRC, while demonstrating a negative co-occurrence between and , suggesting potential antagonistic relationships. Moreover, we observed variations in taxonomic richness and/or abundance within the polyp and CRC bacteriome linked to polyp size, tumor stage, dyslipidemia, diabetes with metformin use, sex, age, and family history of CRC. These findings provide potential new biomarkers to enhance early CRC diagnosis while also demonstrating how intrinsic host factors contribute to establishing a heterogeneous microbiome in patients with CRC and polyps.
PubMed: 38293554
DOI: 10.3389/fmicb.2023.1292490 -
BMC Genomics Nov 2015The σ(54) subunit controls a unique class of promoters in bacteria. Such promoters, without exception, require enhancer binding proteins (EBPs) for transcription...
BACKGROUND
The σ(54) subunit controls a unique class of promoters in bacteria. Such promoters, without exception, require enhancer binding proteins (EBPs) for transcription initiation. Desulfovibrio vulgaris Hildenborough, a model bacterium for sulfate reduction studies, has a high number of EBPs, more than most sequenced bacteria. The cellular processes regulated by many of these EBPs remain unknown.
RESULTS
To characterize the σ(54)-dependent regulome of D. vulgaris Hildenborough, we identified EBP binding motifs and regulated genes by a combination of computational and experimental techniques. These predictions were supported by our reconstruction of σ(54)-dependent promoters by comparative genomics. We reassessed and refined the results of earlier studies on regulation in D. vulgaris Hildenborough and consolidated them with our new findings. It allowed us to reconstruct the σ(54) regulome in D. vulgaris Hildenborough. This regulome includes 36 regulons that consist of 201 coding genes and 4 non-coding RNAs, and is involved in nitrogen, carbon and energy metabolism, regulation, transmembrane transport and various extracellular functions. To the best of our knowledge, this is the first report of direct regulation of alanine dehydrogenase, pyruvate metabolism genes and type III secretion system by σ(54)-dependent regulators.
CONCLUSIONS
The σ(54)-dependent regulome is an important component of transcriptional regulatory network in D. vulgaris Hildenborough and related free-living Deltaproteobacteria. Our study provides a representative collection of σ(54)-dependent regulons that can be used for regulation prediction in Deltaproteobacteria and other taxa.
Topics: Bacterial Proteins; Binding Sites; Cluster Analysis; DNA-Binding Proteins; Desulfovibrio vulgaris; Enhancer Elements, Genetic; Gene Expression Regulation, Bacterial; Nucleotide Motifs; Phylogeny; Position-Specific Scoring Matrices; Promoter Regions, Genetic; Protein Binding; Sigma Factor; Transcription Factors; Type III Secretion Systems
PubMed: 26555820
DOI: 10.1186/s12864-015-2176-y -
Gut Microbes Dec 2023Methanogens, reductive acetogens and sulfate-reducing bacteria play an important role in disposing of hydrogen in gut ecosystems. However, how they interact with each...
Methanogens, reductive acetogens and sulfate-reducing bacteria play an important role in disposing of hydrogen in gut ecosystems. However, how they interact with each other remains largely unknown. This study cocultured (reductive acetogen), (sulfate reducer) and (methanogen). Results revealed that these three species coexisted and did not compete for hydrogen in the early phase of incubations. Sulfate reduction was not affected by and . inhibited the growth of and after 10 h incubations, and the inhibition on was associated with increased sulfide concentration. Remarkably, growth lag phase was shortened by coculturing with and . Formate was rapidly used by under high acetate concentration. Overall, these findings indicated that the interactions of the hydrogenotrophic microbes are condition-dependent, suggesting their interactions may vary in gut ecosystems.
Topics: Methanobrevibacter; Ecosystem; Gastrointestinal Microbiome; Hydrogen; Sulfates
PubMed: 37753963
DOI: 10.1080/19490976.2023.2261784 -
Frontiers in Pharmacology 2022Tuo-Min-Ding-Chuan decoction (TMDCT) is a Traditional Chinese Medicine (TCM) formula consisting of twelve herbs that can relieve the symptoms and treat allergic asthma....
Tuo-Min-Ding-Chuan decoction (TMDCT) is a Traditional Chinese Medicine (TCM) formula consisting of twelve herbs that can relieve the symptoms and treat allergic asthma. Yet, the underlying mechanism of action is still unclear. In this study, we investigated the effect of TMDCT in regulating Treg/Th17 cells immune balance and explored potential metabolic and gut biomarkers associated with Treg and Th17 cells in eosinophilic asthma mice treated by TMDCT. We found that TMDCT increases Treg cells percentage and decreases Th17 cells percentage in the ovalbumin (OVA) -induced eosinophilic asthma mice model. Furthermore, Imidazoleacetic acid, dL-glutamine, L-pyroglutamic acid, 2-deoxy-d-glucose were preliminary identified as biomarkers in plasma metabolites treated by TMDCT, meanwhile genus , genus and genus were preliminary identified as gut microbiota biomarkers after TMDCT treatment. These results provide an experimental foundation for the treatment of allergic asthma with Chinese herbal compounds.
PubMed: 35211018
DOI: 10.3389/fphar.2022.819728 -
Nature Jun 2022Cellular iron homeostasis is vital and maintained through tight regulation of iron import, efflux, storage and detoxification. The most common modes of iron storage use...
Cellular iron homeostasis is vital and maintained through tight regulation of iron import, efflux, storage and detoxification. The most common modes of iron storage use proteinaceous compartments, such as ferritins and related proteins. Although lipid-bounded iron compartments have also been described, the basis for their formation and function remains unknown. Here we focus on one such compartment, herein named the 'ferrosome', that was previously observed in the anaerobic bacterium Desulfovibrio magneticus. Using a proteomic approach, we identify three ferrosome-associated (Fez) proteins that are responsible for forming ferrosomes in D. magneticus. Fez proteins are encoded in a putative operon and include FezB, a P-ATPase found in phylogenetically and metabolically diverse species of bacteria and archaea. We show that two other bacterial species, Rhodopseudomonas palustris and Shewanella putrefaciens, make ferrosomes through the action of their six-gene fez operon. Additionally, we find that fez operons are sufficient for ferrosome formation in foreign hosts. Using S. putrefaciens as a model, we show that ferrosomes probably have a role in the anaerobic adaptation to iron starvation. Overall, this work establishes ferrosomes as a new class of iron storage organelles and sets the stage for studying their formation and structure in diverse microorganisms.
Topics: Bacterial Proteins; Desulfovibrio; Ferric Compounds; Gram-Negative Bacteria; Multigene Family; Organelles; Phylogeny; Proteomics; Rhodopseudomonas; Shewanella putrefaciens
PubMed: 35585231
DOI: 10.1038/s41586-022-04741-x -
International Journal of Molecular... Mar 2023Gut microbes are closely associated with disease onset and improvement. However, the effects of gut microbes on the occurrence, prevention, and treatment of benign...
Gut microbes are closely associated with disease onset and improvement. However, the effects of gut microbes on the occurrence, prevention, and treatment of benign prostatic hyperplasia (BPH) are still unclear. We investigated the alteration of gut microbiota with implications for the diagnosis, prevention, and treatment of BPH and identified correlations among various indicators, including hormone indicators, apoptosis markers in BPH, and finasteride treatment models. BPH induction altered the abundance of , , , , , , and genera, which are related to BPH indicators. Among these, the altered abundance of and was associated with the promotion and inhibition of prostate apoptosis, respectively. Finasteride treatment altered the abundance of , , , , , and genera, which are related to BPH indicators. Among these, altered abundances of and were associated with the promotion and inhibition of prostate apoptosis, respectively. In addition, the abundances of and were normalized after finasteride treatment. In conclusion, the association between apoptosis and altered abundances of and , among other gut microbes, suggests their potential utility in the diagnosis, prevention, and treatment of BPH.
Topics: Male; Humans; Finasteride; Prostatic Hyperplasia; Gastrointestinal Microbiome; Prostate; Apoptosis
PubMed: 36982979
DOI: 10.3390/ijms24065904 -
Frontiers in Physiology 2021The effect of resistance training on gut microbiota composition has not been explored, despite the evidence about endurance exercise. The aim of this study was to...
The effect of resistance training on gut microbiota composition has not been explored, despite the evidence about endurance exercise. The aim of this study was to compare the effect of resistance and endurance training on gut microbiota composition in mice. Cecal samples were collected from 26 C57BL/6N mice, divided into three groups: sedentary (CTL), endurance training on a treadmill (END), and resistance training on a vertical ladder (RES). After 2 weeks of adaption, mice were trained for 4 weeks, 5 days/week. Maximal endurance and resistance capacity test were performed before and after training. Genomic DNA was extracted and 16S Ribosomal RNA sequenced for metagenomics analysis. The percentages for each phylum, class, order, family, or genus/species were obtained using an open-source bioinformatics pipeline. END showed higher diversity and evenness. Significant differences among groups in microbiota composition were only observed at genera and species level. END showed a significantly higher relative abundance of and sp., while and where higher for RES. Trained mice showed significantly lower relative abundance of and higher of the genus compared to CTL. We explored the relationship between relative taxa abundance and maximal endurance and resistance capacities after the training period. and families were negatively associated with endurance performance, while several taxa, including family, genus, and , were positively correlated. About resistance performance, sp. was negatively correlated, while showed a positive correlation. Resistance and endurance training differentially modify gut microbiota composition in mice, under a high-controlled environment. Interestingly, taxa associated with anti- and proinflammatory responses presented the same pattern after both models of exercise. Furthermore, the abundance of several taxa was differently related to maximal endurance or resistance performance, most of them did not respond to training.
PubMed: 35002754
DOI: 10.3389/fphys.2021.748854