Mg2+ homeostasis and transport in cyanobacteria - at the crossroads of bacterial and chloroplast Mg2+ import

Optimization of degradation conditions and analysis of degradation mechanism for nitrite by Bacillus aryabhattai 47

Excessive nitrite levels cause significant damage to aquaculture, making it crucial to explore green and reliable nitrite removal technologies. In this study, A Bacillus aryabhattai (designated as the strain 47) isolated from aquaculture wastewater was used as the experimental strain. The nitrite degradation conditions of the strain 47 were optimized, and the optimal conditions are: glucose was 12.74 g/L, fermented special soybean meal was 21.27 g/L, MgCl2 369 mg/L, pH 7.0, incubated at 30 °C with the inoculum size of 2 % and the rotation speed of 170 rpm. Under the optimal conditions, the nitrite concentration of the culture solution was 200 mg/L, and the nitrite removal rate reached 91.4 %. Meanwhile, the mechanism by which Mg2+ enhanced the nitrite degradation ability of the strain 47 was investigated by transcriptomics. An operon structure directed cellular trafficking of Mg2+, and then, the Mg2+-mediated catalytic reaction of multiple enzymes enhanced and improved cellular metabolic processes (e.g. the transport and metabolism of nitrite, central carbohydrate metabolism oxidative phosphorylation). At the same time, with the progress of cell metabolism, cells secreted a series of enzymes related to nitrite transport and metabolism to promote the metabolism of nitrite. And the process of the assimilated nitrate reduction pathway of nitrite degradation in the strain 47 was elaborated at the transcriptome level. This study provided a new insight into nitrite treatment mediated by microbial organisms.

The bacterial magnesium transporter MgtA reveals highly selective interaction with specific cardiolipin species

The bacterial magnesium transporter A (MgtA) is a specialized P-type ATPase important for Mg2+ import into the cytoplasm; disrupted magnesium homeostasis is linked to intrinsic ribosome instability and antibacterial resistance in Salmonella strains. Here, we show that MgtA has functional specificity for cardiolipin 18:1. Still, it reaches maximum activity only in combination with cardiolipin 16:0, equivalent to the major components of native cardiolipin found in E. coli membranes. Native mass spectrometry indicates the presence of two binding sites for cardiolipin, agreeing with the kinetic studies revealing that a cooperative relationship likely exists between the two cardiolipin variants. This is the first experimental evidence of cooperative effects between lipids of the same class, with only minor variations in their acyl chain composition, acting on a membrane protein. In summary, our results reveal that MgtA exhibits a highly complex interaction with one cardiolipin 18:1 and one cardiolipin 16:0, affecting protein activity and stability, contributing to our understanding of the particular interactions between lipid environment and membrane proteins. Further, a better understanding of Mg2+ homeostasis in bacteria, due to its role as a virulence regulator, will provide further insights into the regulation and mechanism of bacterial infections.

Understanding the Effect of Different Glucose Concentrations in the Oligotrophic Bacterium Bacillus subtilis BS-G1 through Transcriptomics Analysis

Glucose is an important carbon source for microbial growth, and its content in infertile soils is essential for the growth of bacteria. Since the mechanism of oligotrophic bacterium adaptation in barren soils is unclear, this research employed RNA-seq technology to examine the impact of glucose concentration on the oligotrophic bacterium B. subtilis BS-G1 in soil affected by desertification. A global transcriptome analysis (RNA-Seq) revealed that the significantly differentially expressed genes (DEGs) histidine metabolism, glutamate synthesis, the HIF-1 signaling pathway, sporulation, and the TCA cycle pathway of B. subtilis BS-G1 were significantly enriched with a 0.015 g/L glucose concentration (L group), compared to a 10 g/L glucose concentration (H group). The DEGs amino acid system, two-component system, metal ion transport, and nitrogen metabolism system of B. subtilis BS-G1 were significantly enriched in the 5 g/L glucose concentration (M group), compared with the H group. In addition, the present study identified the regulation pattern and key genes under a low-glucose environment (7 mRNAs and 16 sRNAs). This study primarily investigates the variances in the regulatory pathways of the oligotrophic B. subtilis BS-G1, which holds substantial importance in comprehending the mechanism underlying the limited sugar tolerance of oligotrophic bacteria.

Recombinant Actifensin and Defensin-d2 Induce Critical Changes in the Proteomes of Multidrug-Resistant Pseudomonas aeruginosa and Candida albicans

Drug-resistant strains of Pseudomonas aeruginosa and Candida albicans pose serious threats to human health because of their propensity to cause fatal infections. Defensin and defensin-like antimicrobial peptides (AMPs) are being explored as new lines of antimicrobials, due to their broad range of activity, low toxicity, and low pathogen resistance. Defensin-d2 and actifensin are AMPs from spinach and Actinomyces ruminicola, respectively, whose mechanisms of action are yet to be clearly elucidated. This study investigated the mechanisms of action of the recombinant AMPs through label-free quantitative proteomics. The data are available at PRIDE with accession number PXD034169. A total of 28 and 9 differentially expressed proteins (DEPs) were identified in the treated P. aeruginosa and C. albicans, respectively, with a 2-fold change threshold and P values of <0.05. Functional analysis revealed that the DEPs were involved in DNA replication and repair, translation, and membrane transport in P. aeruginosa, while they were related mainly to oxidative phosphorylation, RNA degradation, and energy metabolism in C. albicans. Protein-protein interactions showed that the DEPs formed linear or interdependent complexes with one another, indicative of functional interaction. Subcellular localization indicated that the majority of DEPs were cytoplasmic proteins in P. aeruginosa, while they were of nuclear or mitochondrial origin in C. albicans. These results show that recombinant defensin-d2 and actifensin can elicit complex multiple organism responses that cause cell death in P. aeruginosa and C. albicans. IMPORTANCE AMPs are considered essential alternatives to conventional antimicrobials because of their broad-spectrum efficacy and low potential for resistance by target cells. In this study, we established that the recombinant AMPs defensin-d2 and actifensin exert proteomic changes in P. aeruginosa and C. albicans within 1 h after treatment. We also found that the DEPs in peptide-treated P. aeruginosa are related to ion transport and homeostasis, molecular functions including nucleic and amino acid metabolism, and structural biogenesis and activity, while the DEPs in treated C. albicans are mainly involved in membrane synthesis and mitochondrial metabolism. Our results also highlight ATP synthase as a potential drug target for multidrug-resistant P. aeruginosa and C. albicans.

Membrane destabilization and pore formation induced by the Synechocystis IM30 protein

The inner membrane-associated protein of 30 kDa (IM30) is essential in chloroplasts and cyanobacteria. The spatio-temporal cellular localization of the protein appears to be highly dynamic and triggered by internal as well as external stimuli, mainly light intensity. The soluble fraction of the protein is localized in the cyanobacterial cytoplasm or the chloroplast stroma, respectively. Additionally, the protein attaches to the thylakoid membrane as well as to the chloroplast inner envelope or the cyanobacterial cytoplasmic membrane, respectively, especially under conditions of membrane stress. IM30 is involved in thylakoid membrane biogenesis and/or maintenance, where it either stabilizes membranes and/or triggers membrane-fusion processes. These apparently contradicting functions have to be tightly controlled and separated spatiotemporally in chloroplasts and cyanobacteria. IM30's fusogenic activity depends on Mg2+ binding to IM30; yet, it still is unclear how Mg2+-loaded IM30 interacts with membranes and promotes membrane fusion. Here, we show that the interaction of Mg2+ with IM30 results in increased binding of IM30 to native, as well as model, membranes. Via atomic force microscopy in liquid, IM30-induced bilayer defects were observed in solid-supported bilayers in the presence of Mg2+. These structures differ dramatically from the membrane-stabilizing carpet structures that were previously observed in the absence of Mg2+. Thus, Mg2+-induced alterations of the IM30 structure switch the IM30 activity from a membrane-stabilizing to a membrane-destabilizing function, a crucial step in membrane fusion.

Mg2+ -mediated autophagy-dependent polarization of macrophages mediates the osteogenesis of bone marrow stromal stem cells by interfering with macrophage-derived exosomes containing miR-381

Magnesium ion (Mg²⁺ ) has received increased attention due to the roles it plays in promoting osteogenesis and preventing inflammation. This study was designed to investigate the mechanism by which Mg²⁺ influences the osteoblastic differentiation of bone marrow stromal stem cells (BMSCs). The polarization of Mø (macrophages) was measured after treatment with Mg²⁺ . Meanwhile, autophagy in Mø was measured by detecting LC3B expression. Mø-derived exosomes were isolated and cocultured with BMSCs; after which, osteogenic differentiation was evaluated by Alizarin Red staining and detection of alkaline phosphatase (ALP). Our results showed that Mg²⁺ could induce autophagy in macrophages and modulate the M1/M2 polarization of macrophages. Mg²⁺ -mediated macrophages could facilitate the osteogenic differentiation of BMSCs by regulating autophagy, and this facilitation by Mg²⁺ -mediated macrophages was closely related to macrophage-derived exosomes, and especially exosomes containing miR-381. However, miR-381 in macrophages did not influence autophagy or the polarization of Mg²⁺ -mediated macrophages. Furthermore, macrophage-derived exosomes containing miR-381 mainly determined the osteogenic differentiation of BMSCs. Mg²⁺ -mediated macrophages were shown to promote the osteogenic differentiation of BMSCs via autophagy through reducing miR-381 in macrophage-derived exosomes. In conclusion, our results suggest Mg²⁺ -mediated macrophage-derived exosomes containing miR-381 as novel vehicles for promoting the osteogenic differentiation of BMSCs.

Diurnal metabolic control in cyanobacteria requires perception of second messenger signaling molecule c-di-AMP by the carbon control protein SbtB

Because of their photosynthesis-dependent lifestyle, cyanobacteria evolved sophisticated regulatory mechanisms to adapt to oscillating day-night metabolic changes. How they coordinate the metabolic switch between autotrophic and glycogen-catabolic metabolism in light and darkness is poorly understood. Recently, c-di-AMP has been implicated in diurnal regulation, but its mode of action remains elusive. To unravel the signaling functions of c-di-AMP in cyanobacteria, we isolated c-di-AMP receptor proteins. Thereby, the carbon-sensor protein SbtB was identified as a major c-di-AMP receptor, which we confirmed biochemically and by x-ray crystallography. In search for the c-di-AMP signaling function of SbtB, we found that both SbtB and c-di-AMP cyclase–deficient mutants showed reduced diurnal growth and that c-di-AMP–bound SbtB interacts specifically with the glycogen-branching enzyme GlgB. Accordingly, both mutants displayed impaired glycogen synthesis during the day and impaired nighttime survival. Thus, the pivotal role of c-di-AMP in day-night acclimation can be attributed to SbtB-mediated regulation of glycogen metabolism.

Current knowledge and recent advances in understanding metabolism of the model cyanobacterium Synechocystis sp. PCC 6803

Cyanobacteria are key organisms in the global ecosystem, useful models for studying metabolic and physiological processes conserved in photosynthetic organisms, and potential renewable platforms for production of chemicals. Characterizing cyanobacterial metabolism and physiology is key to understanding their role in the environment and unlocking their potential for biotechnology applications. Many aspects of cyanobacterial biology differ from heterotrophic bacteria. For example, most cyanobacteria incorporate a series of internal thylakoid membranes where both oxygenic photosynthesis and respiration occur, while CO2 fixation takes place in specialized compartments termed carboxysomes. In this review, we provide a comprehensive summary of our knowledge on cyanobacterial physiology and the pathways in Synechocystis sp. PCC 6803 (Synechocystis) involved in biosynthesis of sugar-based metabolites, amino acids, nucleotides, lipids, cofactors, vitamins, isoprenoids, pigments and cell wall components, in addition to the proteins involved in metabolite transport. While some pathways are conserved between model cyanobacteria, such as Synechocystis, and model heterotrophic bacteria like Escherichia coli, many enzymes and/or pathways involved in the biosynthesis of key metabolites in cyanobacteria have not been completely characterized. These include pathways required for biosynthesis of chorismate and membrane lipids, nucleotides, several amino acids, vitamins and cofactors, and isoprenoids such as plastoquinone, carotenoids, and tocopherols. Moreover, our understanding of photorespiration, lipopolysaccharide assembly and transport, and degradation of lipids, sucrose, most vitamins and amino acids, and haem, is incomplete. We discuss tools that may aid our understanding of cyanobacterial metabolism, notably CyanoSource, a barcoded library of targeted Synechocystis mutants, which will significantly accelerate characterization of individual proteins.

Nitrogen Sources and Iron Availability Affect Pigment Biosynthesis and Nutrient Consumption in Anabaena sp. UTEX 2576

Anabaena sp. UTEX 2576 metabolizes multiple nitrogen (N) sources and is deemed a biotechnological platform for chemical production. Cyanobacteria have been identified as prolific producers of biofertilizers, biopolymers, biofuels, and other bioactive compounds. Here, we analyze the effect of different N-sources and Fe availability on the bioproduction of phycobiliproteins and β-carotene. We characterize nutrient demand in modified BG11 media, including data on CO₂ fixation rates, N-source consumption, and mineral utilization (e.g., phosphorus (P), and 11 metallic elements). Results suggest that non-diazotrophic cultures grow up to 60% faster than diazotrophic cells, resulting in 20% higher CO₂-fixation rates. While the production of β-carotene was maximum in medium with NaNO₃, Fe starvation increased the cellular abundance of C-phycocyanin and allophycocyanin by at least 22%. Compared to cells metabolizing NaNO₃ and N₂, cultures adapted to urea media increased their P, calcium and manganese demands by at least 72%, 97% and 76%, respectively. Variations on pigmentation and nutrient uptake were attributed to changes in phycocyanobilin biosynthesis, light-induced oxidation of carotenoids, and urea-promoted peroxidation. This work presents insights into developing optimal Anabaena culture for efficient operations of bioproduction and wastewater bioremediation with cyanobacteria.

Comparative Genomics of the Transport Proteins of Ten Lactobacillus Strains

The genus Lactobacillus includes species that may inhabit different anatomical locations in the human body, but the greatest percentage of its species are inhabitants of the gut. Lactobacilli are well known for their probiotic characteristics, although some species may become pathogenic and exert negative effects on human health. The transportome of an organism consists of the sum of the transport proteins encoded within its genome, and studies on the transportome help in the understanding of the various physiological processes taking place in the cell. In this communication we analyze the transport proteins and predict probable substrate specificities of ten Lactobacillus strains. Six of these strains (L. brevis, L. bulgaricus, L. crispatus, L. gasseri, L. reuteri, and L. ruminis) are currently believed to be only probiotic (OP). The remaining four strains (L. acidophilus, L. paracasei, L. planatarum, and L. rhamnosus) can play dual roles, being both probiotic and pathogenic (PAP). The characteristics of the transport systems found in these bacteria were compared with strains (E. coli, Salmonella, and Bacteroides) from our previous studies. Overall, the ten lactobacilli contain high numbers of amino acid transporters, but the PAP strains contain higher number of sugar, amino acid and peptide transporters as well as drug exporters than their OP counterparts. Moreover, some of the OP strains contain pore-forming toxins and drug exporters similar to those of the PAP strains, thus indicative of yet unrecognized pathogenic potential. The transportomes of the lactobacilli seem to be finely tuned according to the extracellular and probiotic lifestyles of these organisms. Taken together, the results of this study help to reveal the physiological and pathogenic potential of common prokaryotic residents in the human body.

Proton Leakage Is Sensed by IM30 and Activates IM30-Triggered Membrane Fusion

The inner membrane-associated protein of 30 kDa (IM30) is crucial for the development and maintenance of the thylakoid membrane system in chloroplasts and cyanobacteria. While its exact physiological function still is under debate, it has recently been suggested that IM30 has (at least) a dual function, and the protein is involved in stabilization of the thylakoid membrane as well as in Mg2+-dependent membrane fusion. IM30 binds to negatively charged membrane lipids, preferentially at stressed membrane regions where protons potentially leak out from the thylakoid lumen into the chloroplast stroma or the cyanobacterial cytoplasm, respectively. Here we show in vitro that IM30 membrane binding, as well as membrane fusion, is strongly increased in acidic environments. This enhanced activity involves a rearrangement of the protein structure. We suggest that this acid-induced transition is part of a mechanism that allows IM30 to (i) sense sites of proton leakage at the thylakoid membrane, to (ii) preferentially bind there, and to (iii) seal leaky membrane regions via membrane fusion processes.

Functional Implications of Multiple IM30 Oligomeric States

The inner membrane-associated protein of 30 kDa (IM30), also known as the vesicle-inducing protein in plastids 1 (Vipp1), is essential for photo-autotrophic growth of cyanobacteria, algae and higher plants. While its exact function still remains largely elusive, it is commonly accepted that IM30 is crucially involved in thylakoid membrane biogenesis, stabilization and/or maintenance. A characteristic feature of IM30 is its intrinsic propensity to form large homo-oligomeric protein complexes. 15 years ago, it has been reported that these supercomplexes have a ring-shaped structure. However, the in vivo significance of these ring structures is not finally resolved yet and the formation of more complex assemblies has been reported. We here present and discuss research on IM30 conducted within the past 25 years with a special emphasis on the question of why we potentially need IM30 supercomplexes in vivo.