Survival of Anaerobic Fe2+ Stress Requires the ClpXP Protease

Interactome Analysis of ClpX Reveals Its Regulatory Role in Metabolism and Photosynthesis in Cyanobacteria

Protein homeostasis is essential for cyanobacteria to maintain proper cellular function under adverse and fluctuating conditions. The AAA+ superfamily of proteolytic complexes in cyanobacteria plays a critical role in this process, including ClpXP, which comprises a hexameric ATPase ClpX and a tetradecameric peptidase ClpP. Despite the physiological effects of ClpX on growth and photosynthesis, its potential substrates and underlying mechanisms in cyanobacteria remain unknown. In this study, we employed a streptavidin-biotin affinity pull-down assay coupled with label-free proteome quantitation to analyze the interactome of ClpX in the model cyanobacterium Synechocystis sp. PCC 6803 (hereafter Synechocystis). We identified 503 proteins as potential ClpX-binding targets, many of which had novel interactions. These ClpX-binding targets were found to be involved in various biological processes, with particular enrichment in metabolic processes and photosynthesis. Using protein-protein docking, GST pull-down, and biolayer interferometry assays, we confirmed the direct association of ClpX with the photosynthetic proteins, ferredoxin-NADP+ oxidoreductase (FNR) and phycocyanin subunit (CpcA). Subsequent functional investigations revealed that ClpX participates in the maintenance of FNR homeostasis and functionality in Synechocystis grown under different light conditions. Overall, our study provides a comprehensive understanding of the extensive functions regulated by ClpX in cyanobacteria to maintain protein homeostasis and adapt to environmental challenges.

Metabolism of hydrogen peroxide by Lactobacillus plantarum NJAU-01: A proteomics study

This study aimed to investigate the time-course effect of Lactobacillus plantarum NJAU-01 in scavenging exogenous hydrogen peroxide (H₂O₂). The results showed that L. plantarum NJAU-01 at 10⁷ CFU/mL was able to eliminate a maximum of 4 mM H₂O₂ within a prolonged lag phase and resume to proliferate during the following culture. Redox state in the start-lag phase (0 h, without the addition of H₂O₂), indicated by glutathione and protein sulfhydryl, was impaired in the lag phase (3 h and 12 h) and then gradually recovered during subsequent growing stages (20 h and 30 h). By using sodium dodecyl sulfate-polyacrylamide gel electrophoresis and proteomics analysis, a total of 163 proteins such as PhoP family transcriptional regulator, glutamine synthetase, peptide methionine sulfoxide reductase, thioredoxin reductase, ribosomal proteins, acetolactate synthase, ATP binding subunit ClpX, phosphoglycerate kinase, UvrABC system protein A and UvrABC system protein B were identified as differential proteins across the entire growth phase. Those proteins were mainly involved in H₂O₂ sensing, protein synthesis, repairing proteins and DNA lesions, amino sugar and nucleotide sugar metabolism. Our data suggest that biomolecules of L. plantarum NJAU-01 are oxidized to passively consume H₂O₂ and are restored by the enhanced protein and/or gene repair systems.

Enhanced detoxification of Cr6+ by Shewanella oneidensis via adsorption on spherical and flower-like manganese ferrite nanostructures

Maximizing the safe removal of hexavalent chromium (Cr6+) from waste streams is an increasing demand due to the environmental, economic and health benefits. The integrated adsorption and bio-reduction method can be applied for the elimination of the highly toxic Cr6+ and its detoxification. This work describes a synthetic method for achieving the best chemical composition of spherical and flower-like manganese ferrite (MnxFe3-xO4) nanostructures (NS) for Cr6+ adsorption. We selected NS with the highest adsorption performance to study its efficiency in the extracellular reduction of Cr6+ into a trivalent state (Cr3+) by Shewanella oneidensis (S. oneidensis) MR-1. MnxFe3-xO4 NS were prepared by a polyol solvothermal synthesis process. They were characterised by powder X-ray diffraction (XRD), transmission electron microscopy (TEM), X-ray photoelectron spectrometry (XPS), dynamic light scattering (DLS) and Fourier transform-infrared (FTIR) spectroscopy. The elemental composition of MnxFe3-xO4 was evaluated by inductively coupled plasma atomic emission spectroscopy. Our results reveal that the oxidation state of the manganese precursor significantly affects the Cr6+ adsorption efficiency of MnxFe3-xO4 NS. The best adsorption capacity for Cr6+ is 16.8 ± 1.6 mg Cr6+/g by the spherical Mn0.22+Fe2.83+O4 nanoparticles at pH 7, which is 1.4 times higher than that of Mn0.8Fe2.2O4 nanoflowers. This was attributed to the relative excess of divalent manganese in Mn0.22+Fe2.83+O4 based on our XPS analysis. The lethal concentration of Cr6+ for S. oneidensis MR-1 was 60 mg L-1 (determined by flow cytometry). The addition of Mn0.22+Fe2.83+O4 nanoparticles to S. oneidensis MR-1 enhanced the bio-reduction of Cr6+ 2.66 times compared to the presence of the bacteria alone. This work provides a cost-effective method for the removal of Cr6+ with a minimum amount of sludge production.

Mixed heavy metal stress induces global iron starvation response

Multiple heavy metal contamination is an increasingly common global problem. Heavy metals have the potential to disrupt microbially mediated biogeochemical cycling. However, systems-level studies on the effects of combinations of heavy metals on bacteria are lacking. For this study, we focused on the Oak Ridge Reservation (ORR; Oak Ridge, TN, USA) subsurface which is contaminated with several heavy metals and high concentrations of nitrate. Using a native Bacillus cereus isolate that represents a dominant species at this site, we assessed the combined impact of eight metal contaminants, all at site-relevant concentrations, on cell processes through an integrated multi-omics approach that included discovery proteomics, targeted metabolomics, and targeted gene-expression profiling. The combination of eight metals impacted cell physiology in a manner that could not have been predicted from summing phenotypic responses to the individual metals. Exposure to the metal mixture elicited a global iron starvation response not observed during individual metal exposures. This disruption of iron homeostasis resulted in decreased activity of the iron-cofactor-containing nitrate and nitrite reductases, both of which are important in biological nitrate removal at the site. We propose that the combinatorial effects of simultaneous exposure to multiple heavy metals is an underappreciated yet significant form of cell stress in the environment with the potential to disrupt global nutrient cycles and to impede bioremediation efforts at mixed waste sites. Our work underscores the need to shift from single- to multi-metal studies for assessing and predicting the impacts of complex contaminants on microbial systems.

Proteomic analysis of the regulatory networks of ClpX in a model cyanobacterium Synechocystis sp. PCC 6803

Protein homeostasis is tightly regulated by protein quality control systems such as chaperones and proteases. In cyanobacteria, the ClpXP proteolytic complex is regarded as a representative proteolytic system and consists of a hexameric ATPase ClpX and a tetradecameric peptidase ClpP. However, the functions and molecular mechanisms of ClpX in cyanobacteria remain unclear. This study aimed to decipher the unique contributions and regulatory networks of ClpX in the model cyanobacterium Synechocystis sp. PCC 6803 (hereafter Synechocystis). We showed that the interruption of clpX led to slower growth, decreased high light tolerance, and impaired photosynthetic cyclic electron transfer. A quantitative proteomic strategy was employed to globally identify ClpX-regulated proteins in Synechocystis cells. In total, we identified 172 differentially expressed proteins (DEPs) upon the interruption of clpX. Functional analysis revealed that these DEPs are involved in diverse biological processes, including glycolysis, nitrogen assimilation, photosynthetic electron transport, ATP-binding cassette (ABC) transporters, and two-component signal transduction. The expression of 24 DEPs was confirmed by parallel reaction monitoring (PRM) analysis. In particular, many hypothetical or unknown proteins were found to be regulated by ClpX, providing new candidates for future functional studies on ClpX. Together, our study provides a comprehensive ClpX-regulated protein network, and the results serve as an important resource for understanding protein quality control systems in cyanobacteria.

Nano zero-valent iron: A pH buffer, electron donor and activator for chain elongation

Chain elongation produce medium chain carboxylates, which are important precursors to many pharmaceuticals, antimicrobials and biofuels. Results in the presented investigations show that the supply of nano zero-valent iron (NZVI) can enhance caproate production. The highest caproate concentration achieved amounted to 27.2 mmol/L when 5 g/L NZVI were added, which was about 100% higher than the control. The study also showed increase of ethanol oxidation and decrease of butyrate and butanol with NZVI addition. Mechanism study showed NZVI can stimulate caproate production by preventing pH to fall below 5.4 through displacement reaction. Electron balance analysis displayed that NZVI provides extra electron by promoting ethanol oxidation and its dissolution. H₂ was the potential electron shuttle between NZVI and chain elongators; High throughput sequencing showed function of NZVI on reshaping of microbial communities, especially enriching Oscillibacter Marseille-P3260, a kind of chain elongator and Corynebacterium which possesses fatty acid biosynthesis and iron utilization.

Progress and prospect of single-molecular ClpX ATPase researching system-a mini-review

ClpXP in Escherichia coli is a proteasome degrading protein substrates. It consists of one hexamer of ATPase (ClpX) and two heptamers of peptidase (ClpP). The ClpX binds ATP and translocates the substrate protein into the ClpP chamber by binding and hydrolysis of ATP. At single molecular level, ClpX harnesses cycles of power stroke (dwell and burst) to unfold the substrates, then releases the ADP and Pi. Based on the construction and function of ClpXP, especially the recent progress on how ClpX unfold protein substrates, in this mini-review, a currently proposed single ClpX molecular model system detected by optical tweezers, and its prospective for the elucidation of the mechanism of force generation of ClpX in its power stroke and the subunit interaction with each other, were discussed in detail.

HbtR, a Heterofunctional Homolog of the Virulence Regulator TcpP, Facilitates the Transition between Symbiotic and Planktonic Lifestyles in Vibrio fischeri

The bioluminescent bacterium Vibrio fischeri forms a mutually beneficial symbiosis with the Hawaiian bobtail squid, Euprymna scolopes, in which the bacteria, housed inside a specialized light organ, produce light used by the squid in its nocturnal activities. Upon hatching, E. scolopes juveniles acquire V. fischeri from the seawater through a complex process that requires, among other factors, chemotaxis by the bacteria along a gradient of N-acetylated sugars into the crypts of the light organ, the niche in which the bacteria reside. Once inside the light organ, V. fischeri transitions into a symbiotic, sessile state in which the quorum-signaling regulator LitR induces luminescence. In this work we show that expression of litR and luminescence are repressed by a homolog of the Vibrio cholerae virulence factor TcpP, which we have named HbtR. Further, we demonstrate that LitR represses genes involved in motility and chemotaxis into the light organ and activates genes required for exopolysaccharide production.IMPORTANCE TcpP homologs are widespread throughout the Vibrio genus; however, the only protein in this family described thus far is a V. cholerae virulence regulator. Here, we show that HbtR, the TcpP homolog in V. fischeri, has both a biological role and regulatory pathway completely unlike those in V. cholerae Through its repression of the quorum-signaling regulator LitR, HbtR affects the expression of genes important for colonization of the E. scolopes light organ. While LitR becomes activated within the crypts and upregulates luminescence and exopolysaccharide genes and downregulates chemotaxis and motility genes, it appears that HbtR, upon expulsion of V. fischeri cells into seawater, reverses this process to aid the switch from a symbiotic to a planktonic state. The possible importance of HbtR to the survival of V. fischeri outside its animal host may have broader implications for the ways in which bacteria transition between often vastly different environmental niches.

Mechanisms of toxicity by and resistance to ferrous iron in anaerobic systems

Iron is an essential element for nearly all life on Earth, primarily for its value as a redox active cofactor. Iron exists predominantly in two biologically relevant redox states: ferric iron, the oxidized state (Fe³⁺), and ferrous iron, the reduced state (Fe²⁺). Fe²⁺ is well known to facilitate electron transfer reactions that can lead to the generation of reactive oxygen species. Less is known about why iron is toxic to cells in the absence of oxygen, yet this phenomenon is critically important for our understanding of life on early Earth and in iron-rich ecosystems today. In this brief review, we will highlight our current understanding of anaerobic Fe²⁺ toxicity, focusing on molecular mechanistic studies in several model systems.

Periplanetasin-4, a novel antimicrobial peptide from the cockroach, inhibits communications between mitochondria and vacuoles

Communications between various organelle–organelles play an essential role in cell survival. The cross-talk between mitochondria and vacuoles comes up with the vital roles of the intercompartmental process. In this study, we found a couple of cell death features, membrane damage, and apoptosis using antimicrobial peptide from American Cockroach. Periplanetasin-4 (LRHKVYGYCVLGP-NH2) is a 13-mer peptide derived from Periplaneta americana and exhibits phosphatidylserine exposure and caspase activation without DNA fragmentation. Apoptotic features without DNA damage provide evidence that this peptide did not interact with DNA directly and exhibited dysfunction of mitochondria and vacuoles. Superoxide radicals were generated from mitochondria and converted to hydrogen peroxide. Despite the enhancement of catalase and total glutathione contents, oxidative damage disrupted intracellular contents. Periplanetasin-4 induced cell death associated with the production of superoxide radicals, calcium uptake in mitochondria and disorder of vacuoles, such as increased permeability and alkalization. While calcium movement from vacuoles to the mitochondria occurred, the cross-talk with these organelles proceeded and the inherent functionality was impaired. To sum up, periplanetasin-4 stimulates superoxide signal along with undermining the mitochondrial functions and interfering in communication with vacuoles.

MgtE Homolog FicI Acts as a Secondary Ferrous Iron Importer in Shewanella oneidensis Strain MR-1

The transport of metals into and out of cells is necessary for the maintenance of appropriate intracellular concentrations. Metals are needed for incorporation into metalloproteins but become toxic at higher concentrations. Many metal transport proteins have been discovered in bacteria, including the Mg2+ transporter E (MgtE) family of passive Mg2+/Co2+ cation-selective channels. Low sequence identity exists between members of the MgtE family, indicating that substrate specificity may differ among MgtE transporters. Under anoxic conditions, dissimilatory metal-reducing bacteria, such as Shewanella and Geobacter species, are exposed to high levels of soluble metals, including Fe2+ and Mn2+ Here we characterize SO_3966, which encodes an MgtE homolog in Shewanella oneidensis that we name FicI (ferrous iron and cobalt importer) based on its role in maintaining metal homeostasis. A SO_3966 deletion mutant exhibits enhanced growth over that of the wild type under conditions with high Fe2+ or Co2+ concentrations but exhibits wild-type Mg2+ transport and retention phenotypes. Conversely, deletion of feoB, which encodes an energy-dependent Fe2+ importer, causes a growth defect under conditions of low Fe2+ concentrations but not high Fe2+ concentrations. We propose that FicI represents a secondary, less energy-dependent mechanism for iron uptake by S. oneidensis under high Fe2+ concentrations.IMPORTANCEShewanella oneidensis MR-1 is a target of microbial engineering for potential uses in biotechnology and the bioremediation of heavy-metal-contaminated environments. A full understanding of the ways in which S. oneidensis interacts with metals, including the means by which it transports metal ions, is important for optimal genetic engineering of this and other organisms for biotechnology purposes such as biosorption. The MgtE family of metal importers has been described previously as Mg2+ and Co2+ transporters. This work broadens that designation with the discovery of an MgtE homolog in S. oneidensis that imports Fe2+ but not Mg2+ The research presented here also expands our knowledge of the means by which microorganisms have adapted to take up essential nutrients such as iron under various conditions.