Cluster Assembly Research Articles

TusA influences Fe-S cluster assembly and iron homeostasis in E. coli by reducing the translation efficiency of Fur.

All sulfur transfer pathways have generally a l-cysteine desulfurase as an initial sulfur-mobilizing enzyme in common, which serves as a sulfur donor for the biosynthesis of numerous sulfur-containing biomolecules in the cell. In Escherichia coli, the housekeeping l-cysteine desulfurase IscS has several interaction partners, which bind at different sites of the protein. So far, the interaction sites of IscU, Fdx, CyaY, and IscX involved in iron-sulfur (Fe-S) cluster assembly have been mapped, in addition to TusA, which is required for molybdenum cofactor biosynthesis and mnm5s2U34 tRNA modifications, and ThiI, which is involved in thiamine biosynthesis and s4U8 tRNA modifications. Previous studies predicted that the sulfur acceptor proteins bind to IscS one at a time. E. coli TusA has, however, been suggested to be involved in Fe-S cluster assembly, as fewer Fe-S clusters were detected in a ∆tusA mutant. The basis for this reduction in Fe-S cluster content is unknown. In this work, we investigated the role of TusA in iron-sulfur cluster assembly and iron homeostasis. We show that the absence of TusA reduces the translation of fur, thereby leading to pleiotropic cellular effects, which we dissect in detail in this study.IMPORTANCEIron-sulfur clusters are evolutionarily ancient prosthetic groups. The ferric uptake regulator plays a major role in controlling the expression of iron homeostasis genes in bacteria. We show that a ∆tusA mutant is impaired in the assembly of Fe-S clusters and accumulates iron. TusA, therefore, reduces fur mRNA translation leading to pleiotropic cellular effects.

Multi-scale investigation on staged deterioration mechanism of sliding-zone soils induced by reservoir fluctuations

Water level fluctuations in the reservoir deteriorate soils and rocks on the bank landslides by drying-wetting (D-W) cycles, which results in a significant decrease in mechanical properties. A comprehensive understanding of deterioration mechanism of sliding-zone soils is of great significance for interpreting the deformation behavior of landslides. However, quantitative investigation on the deterioration characteristics of soils considering the structural evolution under D-W cycles is still limited. Here, we carry out a series of laboratory tests to characterize the multi-scale deterioration of sliding-zone soils and reveal the mechanism of shear strength decay under D-W cycles. Firstly, we describe the micropores into five grades by scanning electron microscope and observe a critical change in porosity after the first three cycles. We categorize the mesoscale cracks into five classes using digital photography and observe a stepwise increase in crack area ratio. Secondly, we propose a shear strength decay model based on fractal theory which is verified by the results of consolidated undrained triaxial tests. Cohesion and friction angle of sliding-zone soils are found to show different decay patterns resulting from the staged evolution of structure. Then, structural deterioration processes including cementation destruction, pores expansion, aggregations decomposition, and clusters assembly are considered to occur to decay the shear strength differently. Finally, a three-stage deterioration mechanism associated with four structural deterioration processes is revealed, which helps to better interpret the intrinsic mechanism of shear strength decay. These findings provide the theoretical basis for the further accurate evaluation of reservoir landslides stability under water level fluctuations.

Characterization of the SUF FeS cluster synthesis machinery in the amitochondriate eukaryote Monocercomonoides exilis

Monocercomonoides exilis is the first known amitochondriate eukaryote. Loss of mitochondria in M.exilis ocurred after the replacement of the essential mitochondrial iron-sulfur cluster (ISC) assembly machinery by a unique, bacteria-derived, cytosolic SUF system. It has been hypothesized that the MeSuf pathway, in cooperation with proteins of the cytosolic iron-sulfur protein assembly (CIA) system, is responsible for the biogenesis of FeS clusters in M.exilis, yet biochemical evidence is pending. Here, we address the M.exilis MeSuf system and show that SUF genes, individually or in tandem, support the loading of iron-sulfur (FeS) clusters into the reporter protein IscR in Escherichia coli. The Suf proteins MeSufB, MeSufC, and MeSufDSU interact invivo with one another and with Suf proteins of E.coli. Invitro, the M.exilis Suf proteins form large complexes of varying composition and hence may function as a dynamic biosynthetic system in the protist. The putative FeS cluster scaffold MeSufB-MeSufC (MeSufBC) forms multiple oligomeric complexes, some of which bind FeS clusters and form selectively only in the presence of adenosine nucleotides. The multi-domain fusion protein MeSufDSU binds a PLP cofactor and can form higher-order complexes with MeSufB and MeSufC. Our work demonstrates the biochemical property of M. exilis Suf proteins to act as a functional FeS cluster assembly system and provides insights into the molecular mechanism of this unique eukaryotic SUF system.

Neural network-based control for the on-orbit assembly of heterogeneous spacecraft cluster based on Vicsek fractal

On-orbit assembly is a highly effective technique for building large space structures. This paper presents the dynamics and control of an on-orbit assembly of a large space structure based on a heterogenous spacecraft cluster comprising both rigid and flexible spacecraft. The topology of the large space structure is inspired by the Vicsek fractal. A distributed assembly strategy is proposed for the spacecraft team. Radial Basis Function neural networks (RBFNNs) are utilized to approximate the bounded uncertain terms in translational and attitude dynamics. To avoid collisions during the pre-assembly phase, a neural network (NN)-based controller with collision avoidance force is designed for relative position motion. During the assembly phase, only proportional-derivative (PD) law is employed for relative position control. In addition, an NN-based controller is designed for relative attitude control for both rigid and flexible spacecraft. To estimate the unmeasured flexible vibrations, modal coordinate observers are introduced for the flexible spacecraft. The stability of the closed-loop system is proved via Lyapunov functions. Moreover, numerical results are presented to validate the effectiveness of the proposed controllers and assembly strategy.

New Observational Recipes for Measuring Dynamical States of Galaxy Clusters

During cluster assembly, a cluster’s virialization process leaves behind signatures that can provide information on its dynamical state. However, no clear consensus yet exists on the best way to achieve this. Therefore, we attempt to derive improved recipes for classifying the dynamical states of clusters in observations using cosmological simulations. The cluster halo mass and their subhalos’ mass are used to 1014 M ⊙ h −1 and 1010 M ⊙ h −1 to calculate five independent dynamical state indicators. We experiment with recipes by combining two to four indicators for detecting specific merger stages, like recent and ancient mergers. These recipes are made by plotting merging clusters and a control sample of relaxed clusters in multiple-indicator parameter space, then applying a rotation matrix method to derive the best way to separate mergers from the control sample. The success of the recipe is quantified using the success rate and overlap percentage of the merger and control histograms along the newly rotated x-axis. This provides us with recipes using different numbers of combined indicators and for different merger stages. Among the recipes, the stellar mass gap and center offset are the first and second most dominant of the indicators, and using more indicators improves the effectiveness of the recipe. When applied to observations, our results show good agreement with literature values of cluster dynamical states.

Assembly of Homochiral Magneto-Optical Dy6 Triangular Clusters by Fixing Carbon Dioxide in the Air.

A new hydrazone Schiff base bridging ligand (H2LSchiff (E)-N'-((1-hydroxynaphthalen-2-yl)methylene)pyrazine-2-carbohydrazide) and L/D-proline were used to construct a pair of homochiral Dy6 cluster complexes, [Dy6(CO3)(L-Pro)6(LSchiff)4(HLSchiff)2]·5DMA·2H2O (L-1, L-HPro = L-proline; DMA = N,N-dimethylacetamide) and [Dy6(CO3)(D-Pro)6(LSchiff)4(HLSchiff)2]·5DMA·2H2O (D-1, D-HPro = D-proline), which show a novel triangular Dy6 topology. Notably, the fixation of CO2 in the air formed a carbonato central bridge, playing a key role in assembling L-1/D-1. Magnetic measurements revealed that L-1/D-1 displays intramolecular ferromagnetic coupling and magnetic relaxation behaviours. Furthermore, L-1/D-1 shows a distinct magneto-optical Faraday effect and has a second harmonic generation (SHG) response (1.0 × KDP) at room temperature. The results show that the immobilization of CO2 provides a novel pathway for homochiral multifunctional 4f cluster complexes.

Extracellular Proteomic Profiling from the Erythrocytes Infected with Plasmodium Falciparum 3D7 Holds Promise for the Detection of Biomarkers.

Plasmodium falciparum (P. falciparum), which causes the most severe form of malaria, if left untreated, has 24h window in which it can cause severe illness and even death. The aim of this study was to create the most comprehensive and informative secretory-proteome possible by combining high-accuracy and high-sensitivity protein identification technology. In this study, we used Plasmodium falciparum 3D7 (Pf3D7) as the model parasite to develop a label-free quantification proteomic strategy with the main goal of identifying Pf3D7 proteins that are supposed to be secreted outside the infected erythrocytes in the spent media culture during the in-vitro study. The spent culture media supernatant was subjected to differential and ultra-centrifugation steps followed by total protein extraction, estimation, and in-solution digestion using trypsin, digested peptides were analyzed using Nano-LC coupled with ESI for MS/MS. MS/MS spectra were processed using Maxquant software (v2.1.4.0.). Non-infected erythrocytes incubated spent cultured media supernatant were considered as control. Out of discovered 38 proteins, proteins belonging to P. falciparum spp. were EGF-like protein (C0H544), Endoplasmic reticulum chaperone GRP170 (C0H5H0), Small GTP-binding protein sar1 (Q8I1S0), Erythrocyte membrane protein 1, PfEMP1 (Q8I639), aldehyde reductase (Q8ID61), Conserved Plasmodium proteins (Q8IEH3, Q8ILD1), Antigen 332, DBL-like protein (Q8IHN4), Fe-S cluster assembly protein (Q8II78), identified and chosen for further in-depth investigation. This study highlights the value of secretory Plasmodium proteins play crucial roles in various aspects of the disease progression and host-pathogen interactions which can serve as diagnostic markers for malaria infection.

Binding of IscU and TusA to different but competing sites of IscS influences the activity of IscS and directs sulfur to the respective biomolecular synthesis pathway.

All sulfur transfer pathways generally have in common an l-cysteine desulfurase as the initial sulfur-mobilizing enzyme, which serves as a sulfur donor for the biosynthesis of numerous sulfur-containing biomolecules in the cell. In Escherichia coli, the housekeeping l-cysteine desulfurase IscS functions as a hub for sulfur transfer through interactions with several partner proteins, which bind at different sites on IscS. So far, the interaction sites of IscU, Fdx, CyaY, and IscX involved in iron sulfur (Fe-S) cluster assembly, TusA, required for molybdenum cofactor biosynthesis and mnm5s2U34 transfer RNA (tRNA) modifications, and ThiI, involved in both the biosynthesis of thiamine and s4U8 tRNA modifications, have been mapped. Previous studies have suggested that IscS partner proteins bind only one at a time, with the exception of Fe-S cluster assembly, which involves the formation of a ternary complex involving IscS, IscU, and one of CyaY, Fdx, or IscX. Here, we show that the affinity of TusA for IscS is similar to but lower than that of IscU and that these proteins compete for binding to IscS. We show that heterocomplexes involving the IscS dimer and single IscU and TusA molecules are readily formed and that binding of both TusA and IscU to IscS affects its l-cysteine desulfurase activity. A model is proposed in which the delivery of sulfur to different sulfur-requiring pathways is controlled by sulfur acceptor protein levels, IscS-binding affinities, and acceptor protein-modulated IscS desulfurase activity.IMPORTANCEIron-sulfur clusters are evolutionarily ancient prosthetic groups. The housekeeping l-cysteine desulfurase IscS functions as a central core for sulfur transfer through interactions with several partner proteins, which bind at different sites on each IscS monomer with different affinities and partially overlapping binding sites. We show that heterocomplexes involving the IscS dimer and single IscU and TusA molecules at each site of the dimer are formed, thereby influencing the activity of IscS.

Unraveling the Solvent Regulation in the Heteroatom-Doped Endohedral Gold Clusters: A Theoretical Study on the Electronic Properties and O2 Activation.

Liquid-phase synthesis of atomically precise nanoclusters has experienced rapid development recently, where polar solvents are indispensable in such a process. However, the regulation effect of solvents on the structural and electronic properties of different metal clusters and cluster assembly materials is still not well understood. Herein, a comprehensive density functional theory calculation has been performed to explore the solvation effect on heteroatom-doped endohedral gold clusters that always have remarkable stabilities and tunable electronic structures. The solvation free energy of the M@Au12 clusters (M = Cr, Mo, W, Co, Rh, Ir, Cu, Ag, and Au) was found to be related to the charge distribution of the central doped-atom M and the outer Au12 cage. Moreover, the aqueous solvent was observed to be able to increase the adsorption capacity of M@Au12 to O2 following the activation of O2 through the charge transfer from M@Au12 to O2, in which the transferred electrons occupy the π antibonding orbital of O2. In addition, the water solvent can also improve the hydrogenation reaction of O2 to form OOH over M@Au12, where the activation energy barrier for this process is very low with the participation of the solvent. Considering the importance of solvents in the liquid-phase synthesis of atomically precise clusters, these findings highlighted here could provide valuable theoretical guidance in potential applications of functional gold nanoclusters, especially in the liquid-phase cluster catalysis.

Unraveling the Intertwining Factors Underlying the Assembly of High-Nuclearity Heterometallic Clusters.

Two closely related yet distinctly different cationic clusters, [Dy52Ni44(HEIDA)36(OH)138(OAc)24(H2O)30]10+ (1) and [Dy112Ni76(HEIDA)44(EIDA)24(IDA)4(OH)268(OAc)48(H2O)44]4+ (2) (HEIDA=N-(2-hydroxyethyl)iminodiacetate), each featuring a multi-shell core of Platonic and Archimedean polyhedra, were obtained. Depending on the specific conditions used for the co-hydrolysis of Dy3+ and Ni2+, the product can be crystallized out as one particular type of cluster or as a mixture of 1 and 2. How the reaction process was affected by the amount of hydrolysis-facilitating base and/or by the reaction temperature and duration was investigated. It has been found that a reaction at a high temperature and/or for an extended period favors the formation of the compact and thermodynamically more stable 1, while a brief reaction with a large amount of the base is good for the kinetic product 2. By tuning these intertwining conditions, the reaction can be regulated toward a particular product.

Electronic Transport Properties of Molecular Clusters Sb4O6, P4Se3, and P4O6.

Inorganic molecular crystal (IMC) is a trending class of materials in which structural units comprise molecular cages or clusters bonded via van der Waal forces. The structure-property relationship in IMCs is less known due to the unusual assembly of molecular clusters in these materials. In this paper, the density functional theory-calculated electronic transport properties of the molecular clusters of antimony oxide (Sb4O6), phosphorus triselenide (P4Se3), and phosphorus trioxide (P4O6) are described in detail. The calculated values of highest occupied molecular orbital-lowest unoccupied molecular orbital gaps appeared as 5.487, 2.296, and 4.425 eV for Sb4O6, P4Se3, and P4O6, respectively. The work was carried out to explore the charge transport mechanism in IMCs in order to disclose their potential in practical applications. The calculations involved charge-transfer integral based on Marcus theory to compute the electronic coupling (V), reorganization energies (λ), and hopping rate (k) in the structures. The hopping rate for Sb4O6, P4Se3, and P4O6 is found as 8.49 × 10-12, 1.28 × 10-14, and 2.51 × 10-20 s-1, respectively. The transport properties of Sb4O6 are found better, which predicts the application of the relevant IMC for device grade applications. The findings of this study are important for future application of the IMCs in electronic and optoelectronic applications.

Assembly of Copper Alkynyl Clusters into Dimensionally Diverse Coordinated Polymers Mediated by Pyridine Ligands.

Surface ligands play crucial roles in modifying the properties of metal nanoclusters and stabilizing atomically precise structures, and also serve as vital linkers for constructing cluster-based coordination polymers. In this study, we present the results of the solvothermal synthesis of eight novel copper alkynyl clusters incorporating pyridine ligands using a one-pot method. The resulting compounds underwent characterization through elemental analysis, Fourier transform infrared (FT-IR) spectroscopy, powder X-ray diffraction (PXRD), and single-crystal X-ray diffraction (SCXRD). Our observations revealed that distinct pyridine ligands with varying lengths and coordination sites exert significant influence on the structure and dimensionality of the clusters. The structural diversity of these clusters led to the formation of one-dimensional (1D), two-dimensional (2D), or dimer arrangements linked by seven pyridine bridging ligands. Remarkably, these complexes exhibited unique UV-vis absorption and photoluminescence properties, which were influenced by the specific bridging ligand and structural framework. Furthermore, density functional theory (DFT) calculations demonstrated the capability of the conjugated system in the pyridine ligand to impact the band gap of clusters. This study not only unveils the inherent structural diversity in coordination polymers based on copper alkynyl clusters but also offers valuable insights into harnessing ligand engineering for structural and property modulation.

The Fe-S cluster biosynthesis in Enterococcus faecium is essential for anaerobic growth and gastrointestinal colonization

ABSTRACT The facultative anaerobic Gram-positive bacterium Enterococcus faecium is a ubiquitous member of the human gut microbiota. However, it has gradually evolved into a pathogenic and multidrug resistant lineage that causes nosocomial infections. The establishment of high-level intestinal colonization by enterococci represents a critical step of infection. The majority of current research on Enterococcus has been conducted under aerobic conditions, while limited attention has been given to its physiological characteristics in anaerobic environments, which reflects its natural colonization niche in the gut. In this study, a high-density transposon mutant library containing 26,620 distinct insertion sites was constructed. Tn-seq analysis identified six genes that significantly contribute to growth under anaerobic conditions. Under anaerobic conditions, deletion of sufB (encoding Fe-S cluster assembly protein B) results in more extensive and significant impairments on carbohydrate metabolism compared to aerobic conditions. Consistently, the pathways involved in this utilization-restricted carbohydrates were mostly expressed at significantly lower levels in mutant compared to wild-type under anaerobic conditions. Moreover, deletion of sufB or pflA (encoding pyruvate formate lyase-activating protein A) led to failure of gastrointestinal colonization in mice. These findings contribute to our understanding of the mechanisms by which E. faecium maintains proliferation under anaerobic conditions and establishes colonization in the gut.

Nonlinear Optical Responses of Thin Nanowire Assemblies of Drum-Shaped Boron Clusters

Nonlinear Optical Responses of Thin Nanowire Assemblies of Drum-Shaped Boron Clusters

Toward mapping turbulence in the intra-cluster medium

Context. Future X-ray observatories with high spectral resolution and imaging capabilities will enable measurements and mappings of emission line shifts in the intracluster medium (ICM). Such direct measurements can serve as unique probes of turbulent motions in the ICM. Determining the level and scales of turbulence will improve our understanding of the galaxy cluster dynamical evolution and assembly, together with a more precise evaluation of the non thermal support pressure budget. This will allow for more accurate constraints to be placed on the masses of galaxy clusters, among other potential benefits. Aims. In this view, we implemented the methods presented in the previous instalments of our work to characterising the turbulence in the intra-cluster medium in a feasibility study with the X-ray Integral Field Unit (X-IFU) on board the future European X-ray observatory, Athena. Methods. From idealized mock observations of a toy model cluster, we reconstructed the second-order structure function built with the observed velocity field to constrain the turbulence. We carefully accounted for the various sources of errors to derive the most realistic and comprehensive error budget within the limits of our approach. With prior assumptions on the dissipation scale and power spectrum slope, we constrained the parameters of the turbulent power spectrum model through the use of Markov chain Monte Carlo (MCMC) sampling. Results. With a very long exposure time, a favourable configuration, and a prior assumption of the dissipation scale, we were able to retrieve the injection scale, velocity dispersion, and power spectrum slope, with 1σ uncertainties for better than ∼15% of the input values. We demonstrated the efficiency of our carefully set framework to constrain the turbulence in the ICM from high-resolution X-ray spectroscopic observations, paving the way for more in-depth investigation of the optimal required observing strategy within a more restrictive observational setup with the future Athena/X-IFU instrument.

#1546 Mitochondrial oxidative phosphorylation in human proximal tubular epithelial cells is impaired by iron deficiency

Abstract Background and Aims We recently reported that iron deficiency may precede decline in renal function in patients with diabetes who had normal renal function at baseline but had a subsequent annual rate of eGFR decline of 3.3% or more (J Diabetes Investig. 2023;14:874-882.). Mitochondria contain many mitochondrial respiratory chain (MRC) enzymes that require iron as an active center, and consequently iron deficiency is known to impair mitochondrial function. Since the proximal tubular epithelial cells (PTECs) of the kidney are the cells with the greatest number of mitochondria in the body, we investigated whether iron deficiency impairs the mitochondrial capacity of the PTECs. Method Human cultured PTECs were analyzed in ‘control group’, ‘iron-deficient group ‘(co-cultured with deferiprone (DFP), an iron chelator), and ‘rescue group’ (co-cultured with DFP and FeCl3 which saturates the chelating ability of DFP), each with n ≥ 4 (MRC activities n = 4-5, others n ≥ 5). All analyses were performed after 24 hours of incubation. Values are shown as averages ± SEM. Results A Seahorse Extracellular Flux Analyzer showed that the basal oxygen consumption rates (OCRs) of control, iron-deficiency and rescue groups were 30.5 ± 1.2 pmol/min, 11.5 ± 0.7 pmol/min, and 31.1 ± 1.2 pmol/min, respectively, which revealed that basal OCRs of PTECs significantly decreased in the iron-deficient group. In addition, the analyzer also revealed that the activities of MRC for complexes I, II, and III, which have iron-sulfur clusters as their active centers, were significantly decreased in citrate synthase ratio to 77.6 ± 6.2%, 75.1 ± 6.4%, and 72.8 ± 9.3% of the control group, respectively, while complex IV was not significantly different at 84.9% of the control group. These reductions in MRC activities were not observed in the rescue group. Western blotting results also revealed that complex I, II, and III subunit proteins, NDUF9, SDHA, and UQCR2, were significantly reduced in the iron-deficient group (reduced to 38 ± 5.8%, 87 ± 8.8%, and 55 ± 5.7% of the control group, respectively). On the other hand, lactate concentrations in the culture medium of control group, iron-deficient group and rescue group were 1.73 ± 0.13 mmol, 3.01 ± 0.15 mmol and 1.61 ± 0.12 mmol, which revealed that glycolytic system was increased in the iron-deficient group, presumably to compensate for decreased oxidative phosphorylation. In response to intracellular iron deficiency, the iron regulatory protein 2 (IRP2) was shown in Western blotting to be unchanged in the rescue group (123 ± 4.0% of the control group), but increased in the iron-deficient group (170 ± 20% of the control group). The qRT-PCR analyses showed that mRNA expression of iron-sulfur cluster assembly enzyme (ISCU) was significantly decreased in the iron-deficiency group compared with the control group (41.8%), but not in the rescue group (95.1%), which is presumed that IRP2 suppressed ISCU expression, as has been proved previously. These results should indicate that iron deficiency suppressed iron utilization in the mitochondria of PTECs. The number of viable PTECs in the iron-deficient group after 24 hours was 1.99 ± 0.09 × 10^5 cells/well, which was significantly lower than that of the control (3.15 ± 0.15 × 10^5 cells/well) and rescue (2.68 ± 0.18 × 10^5 cells/well) groups. On the other hand, the number of dead PTECs was 0.042 ± 0.019 × 10^5 cells in the iron-deficient group, which was not significantly different from the control (0.023 ± 0.005 × 10^5 cells) and the rescue (0.020 ± 0.011 × 10^5 cells) groups. These data suggest that cell growth should be suppressed by iron deficiency. Conclusion Mitochondrial oxidative phosphorylation through the MRC was impaired by iron deficiency in PTECs. This impairment of mitochondrial capacity in PTECs may lead to PTECs dysfunction, potentially inducing renal damage such as cell death and interstitial injury. Further analysis of the effects of this mitochondrial dysfunction on ATP production capacity and reactive oxygen species production is needed.

Immune cell infiltration and prognostic index in cervical cancer: insights from metabolism-related differential genes.

Cervical cancer remains a significant gynecologic malignancy in both China and the United States, posing a substantial threat to women's lives and health due to its high morbidity and mortality rates. Altered energy metabolism and dysregulated mitochondrial function play crucial roles in the development, growth, metastasis, and recurrence of malignant tumors. In this study, we aimed to predict prognosis and assess efficacy of anti-tumor therapy in cervical cancer patients based on differential genes associated with mitochondrial metabolism. Transcriptomic data and clinical profiles of cervical cancer patients were retrieved from the TCGA and GEO databases. Differential gene-related cellular pathways were identified through GO, KEGG, and GSEA analyses. Prognostic indices were constructed using LASSO regression analysis. Immune cell infiltration was assessed using CIBERSORT and ssGSEA, and the correlation between immune checkpoint inhibitor genes and differential genes was examined. Tumor mutation load (TMB) and its association with prognostic indices were analyzed using nucleotide variant data from the TCGA database. Patient response to immunotherapy and sensitivity to antitumor drugs were determined using the TIDE algorithm and the oncoPredic algorithm, respectively. A prognostic index based on metabolism-related differential genes was developed to predict the clinical outcome of cervical cancer patients, enabling their classification into two distinct subtypes. The prognostic index emerged as an independent risk factor for unfavorable prognosis. The high-index group exhibited a significantly worse overall prognosis, along with elevated tumor mutation burden (TMB), increased immune cell infiltration, and lower TIDE scores, indicating a potential benefit from immunotherapy. Conversely, the low-index group demonstrated increased sensitivity to metabolism-related antitumor agents, specifically multikinase inhibitors. The aim of this study was to develop a prognostic index based on differential genes associated with mitochondrial metabolism, which could be used to predict cervical cancer patients' prognoses. When combined with TIDE and TMB analyses, this prognostic index offers insights into the immune cell infiltration landscape, as well as the potential efficacy of immunotherapy and targeted therapy. Our analysis suggests that the Iron-Sulfur Cluster Assembly Enzyme (ISCU) gene holds promise as a biomarker for cervical cancer immunotherapy.

Requirements for the biogenesis of [2Fe-2S] proteins in the human and yeast cytosol

The biogenesis of iron-sulfur (Fe/S) proteins entails the synthesis and trafficking of Fe/S clusters, followed by their insertion into target apoproteins. In eukaryotes, the multiple steps of biogenesis are accomplished by complex protein machineries in both mitochondria and cytosol. The underlying biochemical pathways have been elucidated over the past decades, yet the mechanisms of cytosolic [2Fe-2S] protein assembly have remained ill-defined. Similarly, the precise site of glutathione (GSH) requirement in cytosolic and nuclear Fe/S protein biogenesis is unclear, as is the molecular role of the GSH-dependent cytosolic monothiol glutaredoxins (cGrxs). Here, we investigated these questions in human and yeast cells by various in vivo approaches. [2Fe-2S] cluster assembly of cytosolic target apoproteins required the mitochondrial ISC machinery, the mitochondrial transporter Atm1/ABCB7 and GSH, yet occurred independently of both the CIA system and cGrxs. This mechanism was strikingly different from the ISC-, Atm1/ABCB7-, GSH-, and CIA-dependent assembly of cytosolic-nuclear [4Fe-4S] proteins. One notable exception to this cytosolic [2Fe-2S] protein maturation pathway defined here was yeast Apd1 which used the CIA system via binding to the CIA targeting complex through its C-terminal tryptophan. cGrxs, although attributed as [2Fe-2S] cluster chaperones or trafficking proteins, were not essential in vivo for delivering [2Fe-2S] clusters to either CIA components or target apoproteins. Finally, the most critical GSH requirement was assigned to Atm1-dependent export, i.e. a step before GSH-dependent cGrxs function. Our findings extend the general model of eukaryotic Fe/S protein biogenesis by adding the molecular requirements for cytosolic [2Fe-2S] protein maturation.

Silver Cluster Assembled Materials: A Model-Driven Perspective on Recent Progress, with a Spotlight on Ag12 Cluster Assembly.

The exploration of individual nanoclusters is rapidly advancing, despite stability concerns. To address this challenge, the assembly of cluster nodes through linker molecules has been successfully implemented. However, the linking of the cluster nodes itself introduces a multitude of possibilities, especially when additional factors come into play. While this method proves effective in enhancing material stability, the specific reasons behind its success remain elusive. In our laboratory, we have undertaken extensive studies on Ag cluster-assembled materials. So, here our goal is to establish a model system that allows for the discernment of various factors, eliminating unnecessary complexities during the linking approach. So, we hope that the systematic discourse presented in here will contribute significantly to future endeavors, helping to set clear priorities, and provide solutions to concerns that arise when working with a model system.

The interplay between electron transport chain function and iron regulatory factors influences melanin formation in Cryptococcus neoformans.

Mitochondrial functions are critical for the ability of the fungal pathogen Cryptococcus neoformans to cause disease. However, mechanistic connections between key functions such as the mitochondrial electron transport chain (ETC) and virulence factor elaboration have yet to be thoroughly characterized. Here, we observed that inhibition of ETC complex III suppressed melanin formation, a major virulence factor. This inhibition was partially overcome by defects in Cir1 or HapX, two transcription factors that regulate iron acquisition and use. In this regard, loss of Cir1 derepresses the expression of laccase genes as a potential mechanism to restore melanin, while HapX may condition melanin formation by controlling oxidative stress. We hypothesize that ETC dysfunction alters redox homeostasis to influence melanin formation. Consistent with this idea, inhibition of growth by hydrogen peroxide was exacerbated in the presence of the melanin substrate L-DOPA. In addition, loss of the mitochondrial chaperone Mrj1, which influences the activity of ETC complex III and reduces ROS accumulation, also partially overcame antimycin A inhibition of melanin. The phenotypic impact of mitochondrial dysfunction was consistent with RNA-Seq analyses of WT cells treated with antimycin A or L-DOPA, or cells lacking Cir1 that revealed influences on transcripts encoding mitochondrial functions (e.g., ETC components and proteins for Fe-S cluster assembly). Overall, these findings reveal mitochondria-nuclear communication via ROS and iron regulators to control virulence factor production in C. neoformans.IMPORTANCEThere is a growing appreciation of the importance of mitochondrial functions and iron homeostasis in the ability of fungal pathogens to sense the vertebrate host environment and cause disease. Many mitochondrial functions such as heme and iron-sulfur cluster biosynthesis, and the electron transport chain (ETC), are dependent on iron. Connections between factors that regulate iron homeostasis and mitochondrial activities are known in model yeasts and are emerging for fungal pathogens. In this study, we identified connections between iron regulatory transcription factors (e.g., Cir1 and HapX) and the activity of complex III of the ETC that influence the formation of melanin, a key virulence factor in the pathogenic fungus Cryptococcus neoformans. This fungus causes meningoencephalitis in immunocompromised people and is a major threat to the HIV/AIDS population. Thus, understanding how mitochondrial functions influence virulence may support new therapeutic approaches to combat diseases caused by C. neoformans and other fungi.