Regulation and distinct physiological roles of manganese in bacteria

Compatibility of intracellular binding: Evolutionary design principles for metal sensors

In the common cellular space, hundreds of binding reactions occur reliably and simultaneously without disruptive mutual interference. The design principles that enable this remarkable compatibility have not yet been adequately elucidated. In order to delineate these principles, we consider the intracellular sensing of transition metals in bacteria-an integral part of cellular metal homeostasis. Protein cytosolic sensors typically interact with metals through three types of lateral chain residues, containing oxygen, nitrogen, or sulfur. The very existence of complete sets of mutually compatible sensors is a nontrivial problem solved by evolution, since each metal sensor has to bind to its cognate metal without being "mismetallated" by noncognate competitors. Here, based solely on theoretical considerations and limited information about binding constants for metal-amino acid interactions, we are able to predict possible "sensor compositions," i.e., the residues forming the binding sites. We find that complete transition-metal sensor sets are severely limited in their number by compatibility requirements, leaving only a handful of possible sensor compositions for each transition metal. Our theoretical results turn out to be broadly consistent with experimental data on known bacterial sensors. If applicable to other cytosolic binding interactions, the results generated by our approach imply that compatibility requirements may play a crucial role in the organization and functioning of intracellular processes.

Food, Health, and Environmental Impact of Lactic Acid Bacteria: The Superbacteria for Posterity

Lactic acid bacteria (LAB) are Gram-positive cocci or rods that do not produce spores or respire. Their primary function is to ferment carbohydrates and produce lactic acid. The two primary forms of LAB that are currently recognized are homofermentative and heterofermentative. This review discusses the evolutionary diversity and the biochemical and biophysical conditions required by LAB for their metabolism. Next, it concentrates on the applications of these bacteria in gut health, cancer prevention, and overall well-being and food systems. There are numerous uses for LAB, including the food and dairy sectors, as probiotics to improve human and animal gut-health, as anti-carcinogenic agents, and in food safety as biopreservatives, pathogen inhibitors, and reducers of anti-nutrients in foods. The group included many genera, including Aerococcus, Carnobacterium, Enterococcus, Lactobacillus, Lactococcus, Leuconostoc, Streptococcus, Tetragenococcus, Vagococcus, and Weissella. Numerous species of Lactobacillus and Bifidobacterium genera as well as other microbes have been suggested as probiotic strains, or live microorganisms added to meals to improve health. LAB can colonize the intestine and take part in the host's physiological processes. This review briefly highlights the role of these bacteria in food safety and security as well as aspects of regulation and consumer acceptance. Finally, the recent innovations in LAB fermentations and the limitations and challenges of the applications of LAB in the food industry are discussed. Notwithstanding recent developments, the study of LAB and their functional components is still an emerging topic of study that has not yet realized its full potential.

Heme and iron limitation in a GI-tract foundation species leads to a reshuffling of the metalloproteome and a shift toward manganese usage

The metal-binding complement of the cellular proteome (the metalloproteome) depends on metal availability in the cellular environment and drives cellular metabolism. Bacteroides thetaiotaomicron (Bacteroides theta) is a foundational species in the anaerobic gut microbiome and a heme auxotroph, though little is known about why it requires heme. We hypothesized that B. theta would overproduce heme-binding proteins in response to limitations in non-heme iron, and reciprocally, activate non-heme iron pathways when heme was growth limiting. Here we showed that heme and/or non-heme iron scarcity triggers a more holistic reorganization of its metallome and metalloproteome. Under non-heme iron limitation induced by an Fe(II)-specific chelator, manganese supplementation restored growth, suggesting manganese can partly compensate for non-heme iron. Metalloproteomic analyses using tandem HPLC-ICP-MS revealed significant changes in the distribution of zinc, manganese, and iron in response to varying iron or heme availability. These findings highlight the interplay between heme/non-heme iron and the metallome in bacterial growth regulation, and they underscore a role for manganese under iron scarcity.

SloR-SRE binding to the S. mutans mntH promoter is cooperative

Streptococcus mutans is a commensal member of the plaque microbiome. It is especially prevalent when dietary sugars are available for S. mutans fermentation, generating acid byproducts that lower plaque pH and foster tooth decay. S. mutans can survive in the transient conditions of the mouth, in part because it can regulate the uptake of manganese and iron during periods of feast when metal ions are available, and famine when they are limited. S. mutans depends on a 25kDa metalloregulatory protein, called SloR, to modulate the uptake of these cations across the bacterial cell surface. When bound to manganese, SloR binds to palindromic recognition elements in the promoter of the sloABC genes that encode the major manganese transporter in S. mutans. Reports in the literature describe MntH, an ancillary manganese transporter in S. mutans, that is also subject to SloR control. In the present study, we performed expression profiling experiments that reveal coordinate regulation of the sloABC and mntH genes at the level of transcription. In addition, we describe a role for the mntH gene product that is redundant with that of the sloABC-encoded metal ion uptake machinery. The results of DNA-binding studies support direct SloR binding to the mntH promoter region which, like that at the sloABC promoter, harbors three palindromic recognition elements to which SloR binds cooperatively to repress downstream transcription. These findings expand our understanding of the SloR metalloregulome and elucidate SloR-DNA binding that is essential for S. mutans metal ion homeostasis and fitness in the oral cavity.

IMPORTANCE

Dental caries disproportionately impacts low-income socioeconomic groups in the United States and abroad. Research that is focused on S. mutans, the primary causative agent of dental caries in humans, is significant to mitigation efforts aimed at alleviating or preventing dental caries. The SloR protein is a major regulator of the S. mutans metal ion uptake machinery encoded by the sloABC- and mntH genes. This SloR-mediated gene control is essential for maintaining intracellular metal ion homeostasis, and hence S. mutans fitness in the plaque microbiome. An improved understanding of the sloABC and mntH metal ion transporters and their regulation by SloR can guide rational drug design that, by targeting the SloR-DNA-binding interface, can alleviate or prevent S. mutans-induced disease.

Metals in Motion: Understanding Labile Metal Pools in Bacteria

Metal ions are essential for all life. In microbial cells, potassium (K+) is the most abundant cation and plays a key role in maintaining osmotic balance. Magnesium (Mg2+) is the dominant divalent cation and is required for nucleic acid structure and as an enzyme cofactor. Microbes typically require the transition metals manganese (Mn), iron (Fe), copper (Cu), and zinc (Zn), although the precise set of metal ions needed to sustain life is variable. Intracellular metal pools can be conceptualized as a chemically complex mixture of rapidly exchanging (labile) ions, complemented by those reservoirs that exchange slowly relative to cell metabolism (sequestered). Labile metal pools are buffered by transient interactions with anionic metabolites and macromolecules, with the ribosome playing a major role. Sequestered metal pools include many metalloproteins, cofactors, and storage depots, with some pools redeployed upon metal depletion. Here, I review the size, composition, and dynamics of intracellular metal pools and highlight the major gaps in understanding.

Membrane-embedded CdaA is required for efficient synthesis of second messenger cyclic di-AMP

Cyclic di-adenylate monophosphate (cyclic di-AMP) is an important second messenger in microorganisms. Cyclic di-AMP regulates bacterial cell volume and turgor via control of potassium and compatible solute transport but is also involved in many other processes, including the activation of the metazoan innate immune response to bacterial infections. We compare the activity of full-length membrane-embedded CdaA, the enzyme that synthesizes cyclic di-AMP, with the water-soluble catalytic domain CdaA-DAC. Purified CdaA from L. lactis was studied in the detergent-solubilized state, and in lipid nanodiscs and vesicles. We show that CdaA is tetrameric and the membrane-bound complex has more than 2-orders of magnitude higher activity than soluble CdaA-DAC. CdaA activity increases with pH but does not strongly depend on the salt or lipid content, factors that are crucial for the control of osmoregulatory transporters. Cryo-EM and in-silico structure prediction of CdaA show that the two DAC dimers engage in a head-to-head interaction, leading to cyclic-di-AMP formation. The inhibitor phosphoglucomutase prevents this active conformation. We observe dynamic flexibility between the catalytic and membrane domains, even in the presence of ATP or non-hydrolyzable substrate ApCpp. This is the first comprehensive functional and structural characterization of a full-length cyclic di-AMP-specific cyclase.

Characterization of extracellular chitin deacetylase from Aneurinibacillus aneurinilyticus isolated from marine crustacean shell

Chitosan is a promising biopolymer with wide range of applications. It is the deacetylated product of chitin. Commercially, it is produced from chitin via a harsh thermochemical process that has several shortcomings and heterogenous deacetylation product. Chitin can be transformed into chitosan through enzymatic deacetylation using chitin deacetylase (CDA), enabling the production of chitosan with a specific degree of deacetylation. CDA is primarily extracted from fungi followed by bacteria and insects. The extraction of CDA from fungus is more complex, possess several health risks for human including skin lesions. Therefore, screening of potent bacterial CDA is the need of the hour. In this study, for the first time we have isolated a bacterial strain Aneurinibacillus aneurinilyticus from the rinsed water of marine crab shell, and it was found to be a potent CDA producer. The extracellular CDA from A. aneurinilyticus has been partially purified and the specific activity of the enzyme was found to be 569.73 U/ mg protein. SDS-PAGE profiling of the purified sample depicts two isomers of CDA with molecular weights of 27 kD and 45 kD. The pH and temperature optima of the purified CDA were found to be 7.4 and 37 °C, respectively. The partially purified enzyme has Km and Vmax values of 98.455 µM and 909.09 µmole/min, for non-chitinous substrate such as p-nitroacetanilide. For chitinous substrates like glycol chitin, N-acetyl glucosamine hexamer and colloidal chitin, the enzyme exhibited Km of 96.96, 111.75 and 127.86 µM, respectively, Vmax for these substrates were 23.31, 10.12 and 10.772 µmole/min, respectively. Metal ions like Mn and Mg considerably boost the production and activity of CDA, whereas Cd and Co strongly inhibit its activity. Insights from this study further substantiate that this enzyme follows Michaelis-Menten equation and has potential for industrial applications.

SloR-SRE binding to the S. mutans mntH promoter is cooperative

Streptococcus mutans is a commensal member of the plaque microbiome. It is especially prevalent when dietary sugars are available for S. mutans fermentation, generating acid byproducts that lower plaque pH and foster tooth decay. S. mutans can survive in the transient conditions of the mouth, in part because it can regulate the uptake of manganese and iron during periods of feast when metal ions are available, and famine when they are limiting. S. mutans depends on a 25kDa metalloregulatory protein, called SloR, to modulate uptake of these cations across the bacterial cell surface. When bound to manganese, SloR, binds to palindromic recognition elements in the promoter of the sloABC genes that encode the major manganese transporter in S. mutans. Reports in the literature describ MntH, an ancillary manganese transporter in S. mutans, that is also subject to SloR control. In the present study, we performed expression profiling experiments that reveal coordinate regulation of the sloABC and mntH genes at the level of transcription. In addition, we describe a role for the mntH gene product that is redundant with that of the sloABC-encoded metal ion uptake machinery. The results of DNA binding studies support direct SloR binding to the mntH promoter region which, like that at the sloABC promoter, harbors three palindromic recognition elements to which SloR binds cooperatively to repress downstream transcription. These findings expand our understanding of the SloR metalloregulome and elucidate SloR-DNA binding that is essential for S. mutans metal ion homeostasis and fitness in the oral cavity.

Study of excess manganese stress response highlights the central role of manganese exporter Mnx for holding manganese homeostasis in the cyanobacterium Synechocystis sp. PCC 6803

Cellular levels of the essential micronutrient manganese (Mn) need to be carefully balanced within narrow borders. In cyanobacteria, a sufficient Mn supply is critical for ensuring the function of the oxygen-evolving complex as the central part of the photosynthetic machinery. However, Mn accumulation is fatal for the cells. The reason for the observed cytotoxicity is unclear. To understand the causality behind Mn toxicity in cyanobacteria, we investigated the impact of excess Mn on physiology and global gene expression in the model organism Synechocystis sp. PCC 6803. We compared the response of the WT and the knock-out mutant in the Mn exporter (Mnx), ∆mnx, which is disabled in the export of surplus Mn and thus functions as a model for toxic Mn overaccumulation. While growth and pigment accumulation in ∆mnx were severely impaired 24 h after the addition of tenfold Mn, the WT was not affected and thus mounted an adequate transcriptional response. RNA-seq data analysis revealed that the Mn stress transcriptomes partly resembled an iron limitation transcriptome. However, the expression of iron limitation signature genes isiABDC was not affected by the Mn treatment, indicating that Mn excess is not accompanied by iron limitation in Synechocystis. We suggest that the ferric uptake regulator, Fur, gets partially mismetallated under Mn excess conditions and thus interferes with an iron-dependent transcriptional response. To encounter mismetallation and other Mn-dependent problems on a protein level, the cells invest in transcripts of ribosomes, proteases and chaperones. In the case of the ∆mnx mutant, the consequences of the disability to export excess Mn from the cytosol manifest in additionally impaired energy metabolism and oxidative stress transcriptomes with a fatal outcome. This study emphasizes the central importance of Mn homeostasis and the transporter Mnx's role in restoring and holding it.

Enhanced oxidation of Mn(II) and As(III) by aerobic granular sludge via ferrous citrate: Key roles of colloidal iron and extracellular superoxide radical

Microbial manganese (Mn) oxidation plays a crucial role in shaping the fate of various elements, including arsenic (As). However, this process faces challenges in wastewater environments due to its inherent inefficiency and instability. In our initial research, a serendipitous discovery occurred: the addition of citrate to Fe(II)-containing wastewater stimulated the oxidation of Mn(II) by aerobic granular sludge (AGS). Subsequent experiments in four sequencing batch reactors (SBRs) over a 67-day period confirmed this stimulatory effect. The presence of Fe(II)-citrate led to a remarkable twofold increase in the oxidation of Mn(II) and As(III). The removal efficiency improved from 21±4 % to 87±7 % for Mn(II) and from 77.1 ± 1.8 % to 93.6 ± 0.2 % for As(III). The verification experiments demonstrated that the simultaneous addition of manganese-oxidizing bacteria (MnOB) and Fe(II)-citrate is an effective strategy for enhancing the oxidation and removal of Mn(II) and As(III) by AGS. Through a combination of genomic analysis, cell-free filtrate incubation, and bacterial batch cultivations (including monitoring the time-course changes of 17 substances and 2 free radicals), we elucidated a novel Mn(II) oxidation pathway in Pseudomonas, along with its stimulation method and mechanism. First, bacteria rapidly degrade citrate possibly via the citrate-Mg2+:H+ symporter (CitMHS) and the tricarboxylic acid (TCA) cycle, resulting in the formation of colloidal Fe(II), colloidal Fe(III), and biogenic iron (hydr)oxides (FeOx). Then, colloidal Fe(II) and colloidal Fe(III) stimulated extracellular proteins to produce superoxide radicals (·O2-). These radicals were responsible for oxidizing Mn(II) into Mn(III), ultimately forming biogenic manganese oxides (MnOx). Finally, MnOx effectively oxidized As(III) to the less toxic As(V). This innovative approach for bacterial Mn(II) oxidation holds promise for treating Mn(II) and As(III) in water and wastewater. Furthermore, the mechanism by which colloidal iron stimulates extracellular proteins to produce ·O2-, thereby facilitating Mn(II) oxidation, may widely occur across various engineering and natural ecosystems.

Antimicrobial blue light inactivation of Pseudomonas aeruginosa: Unraveling the multifaceted impact of wavelength, growth stage, and medium composition

Pseudomonas aeruginosa, a notable pathogen frequently associated with hospital-acquired infections, displays diverse intrinsic and acquired antibiotic resistance mechanisms, posing a significant challenge in infection management. Antimicrobial blue light (aBL) has been demonstrated as a potential alternative for treating P. aeruginosa infections. In this study, we investigated the impact of blue light wavelength, bacterial growth stage, and growth medium composition on the efficacy of aBL. First, we compared the efficacy of light wavelengths 405 nm, 415 nm, and 470 nm in killing three multidrug resistant clinical strains of P. aeruginosa. The findings indicated considerably higher antibacterial efficacy for 405 nm and 415 nm wavelength compared to 470 nm. We then evaluated the impact of the bacterial growth stage on the efficacy of 405 nm light in killing P. aeruginosa using a reference strain PAO1 in exponential, transitional, or stationary phase. We found that bacteria in the exponential phase were the most susceptible to aBL, followed by the transitional phase, while those in the stationary phase exhibited the highest tolerance. Additionally, we quantified the production of reactive oxygen species (ROS) in bacteria using the 2',7'-dichlorofluorescein diacetate (DCFH-DA) probe and flow cytometry, and observed a positive correlation between aBL efficacy and ROS production. Finally, we determined the influence of growth medium on aBL efficacy. PAO1 was cultivated in brain heart infusion (BHI), Luria-Bertani (LB) broth or Casamino acids (CAA) medium, before being irradiated with aBL at 405 nm. The CAA-grown bacteria exhibited the highest sensitivity to aBL, followed by those grown in LB broth, and the BHI-grown bacteria demonstrated the lowest sensitivity. By incorporating FeCl3, MnCl2, ZnCl2, or the iron chelator 2,2'-bipyridine (BIP) into specific media, we discovered that aBL efficacy was affected by the iron levels in culture media.

A binuclear metallohydrolase model for RelA/SpoT-Homolog (RSH) hydrolases

When challenged by starvation, bacterial organisms synthesize guanosine pentaphosphate and tetraphosphate, collectively denoted as (p)ppGpp, as second messengers to reprogram metabolism toward slower growth and enhanced stress tolerance. When starvation is alleviated, the RelA-SpoT Homolog (RSH) hydrolases downregulate (p)ppGpp, cleaving the 3'-diphosphate to produce GTP or GDP. Metazoan RSH hydrolases possess phosphatase activity responsible for converting cytoplasmic NADPH to NADH in mammalian cells. Inhibitor development for this family may therefore provide therapies to combat bacterial infection or metabolic dysregulation. Despite the availability of dozens of high-resolution structures, catalytic mechanisms of RSH hydrolases have remained poorly understood. All RSH hydrolases tightly bind a Mn2+ near its active center, which is believed sufficient for hydrolase activity. In contrast to this notion, we demonstrate, using the (p)ppGpp hydrolase SpoT from Acinetobacter baumannii, that a second divalent cation, presumably a Mg2+ under physiological conditions, is required for efficient catalysis. We also show that SpoT preferentially cleaves 3'-diphosphate over 3'-phosphate substrates, likely due to a key coordination between the β-phosphate and the second metal center. Metazoan RSH hydrolase replaces this β-phosphate with the side chain of an aspartate residue, thereby functioning as a phosphatase. We propose a binuclear metallohydrolase model where an invariant ED (Glu-Asp) diad, previously believed to activate the water nucleophile, instead coordinates to a Mg2+ center. The refined molecular and evolutionary blueprint of RSH hydrolases will provide a more reliable foundation for the development of small-molecule inhibitors of this important enzyme family.

Biological characteristics of manganese transporter MntP in Klebsiella pneumoniae

Klebsiella pneumoniae is an important opportunistic pathogen that causes a variety of infections. It is critical for bacteria to maintain metal homeostasis during infection. By using an isogenic mntP deletion mutant of K. pneumoniae strain NTUH-K2044, we found that MntP was a manganese efflux pump. Manganese increased the tolerance to oxidative stress, and oxidative stress could increase the intracellular manganese concentration. In oxidative stress, the mntP deletion mutant exhibited significantly higher sensitivity to manganese. Furthermore, iron could increase the tolerance of the mntP deletion mutant to manganese. Inductively coupled plasma mass spectrometry analysis revealed that the mntP deletion mutant had higher intracellular manganese and iron concentrations than wild-type and complementary strains. These findings suggested that iron could increase manganese tolerance in K. pneumoniae. This work elucidated the role of MntP in manganese detoxification and Mn/Fe homeostasis in K. pneumoniae.IMPORTANCEMetal homeostasis plays an important role during the process of bacterial infection. Herein, we revealed that MntP was involved in intracellular manganese homeostasis. Manganese promoted resistance to oxidative stress in Klebsiella pneumoniae. Furthermore, we demonstrated that the mntP deletion mutant exhibited significantly lower survival under manganese and H2O2 conditions. Oxidative stress increased the intracellular manganese content of the mntP deletion mutant. MntP played a critical role in maintaining intracellular manganese and iron concentrations. MntP contributed to manganese detoxification and Mn/Fe homeostasis in K. pneumoniae.

A riboswitch-controlled TerC family transporter Alx tunes intracellular manganese concentration in Escherichia coli at alkaline pH

Cells use transition metal ions as structural components of biomolecules and cofactors in enzymatic reactions, making transition metal ions integral cellular components. Organisms optimize metal ion concentration to meet cellular needs by regulating the expression of proteins that import and export that metal ion, often in a metal ion concentration-dependent manner. One such regulation mechanism is via riboswitches, which are 5'-untranslated regions of an mRNA that undergo conformational changes to promote or inhibit the expression of the downstream gene, commonly in response to a ligand. The yybP-ykoY family of bacterial riboswitches shares a conserved aptamer domain that binds manganese ions (Mn2+). In Escherichia coli, the yybP-ykoY riboswitch precedes and regulates the expression of two different genes: mntP, which based on genetic evidence encodes an Mn2+ exporter, and alx, which encodes a putative metal ion transporter whose cognate ligand is currently in question. The expression of alx is upregulated by both elevated concentrations of Mn2+ and alkaline pH. With metal ion measurements and gene expression studies, we demonstrate that the alkalinization of media increases the cytoplasmic manganese pool, which, in turn, enhances alx expression. The Alx-mediated Mn2+ export prevents the toxic buildup of the cellular manganese, with the export activity maximal at alkaline pH. We pinpoint a set of acidic residues in the predicted transmembrane segments of Alx that play a critical role in Mn2+ export. We propose that Alx-mediated Mn2+ export serves as a primary protective mechanism that fine tunes the cytoplasmic manganese content, especially during alkaline stress.IMPORTANCEBacteria use clever ways to tune gene expression upon encountering certain environmental stresses, such as alkaline pH in parts of the human gut and high concentration of a transition metal ion manganese. One way by which bacteria regulate the expression of their genes is through the 5'-untranslated regions of messenger RNA called riboswitches that bind ligands to turn expression of genes on/off. In this work, we have investigated the roles and regulation of alx and mntP, the two genes in Escherichia coli regulated by the yybP-ykoY  riboswitches, in alkaline pH and high concentration of Mn2+. This work highlights the intricate ways through which bacteria adapt to their surroundings, utilizing riboregulatory mechanisms to maintain Mn2+ levels amidst varying environmental factors.

Aquaporin Modulation by Cations, a Review

Aquaporins (AQPs) are transmembrane channels initially discovered for their role in water flux facilitation through biological membranes. Over the years, a much more complex and subtle picture of these channels appeared, highlighting many other solutes accommodated by AQPs and a dense regulatory network finely tuning cell membranes' water permeability. At the intersection between several transduction pathways (e.g., cell volume regulation, calcium signaling, potassium cycling, etc.), this wide and ancient protein family is considered an important therapeutic target for cancer treatment and many other pathophysiologies. However, a precise and isoform-specific modulation of these channels function is still challenging. Among the modulators of AQPs functions, cations have been shown to play a significant contribution, starting with mercury being historically associated with the inhibition of AQPs since their discovery. While the comprehension of AQPs modulation by cations has improved, a unifying molecular mechanism integrating all current knowledge is still lacking. In an effort to extract general trends, we reviewed all known modulations of AQPs by cations to capture a first glimpse of this regulatory network. We paid particular attention to the associated molecular mechanisms and pinpointed the residues involved in cation binding and in conformational changes tied up to the modulation of the channel function.

Manganese-dependent transcription regulation by MntR and PerR in Thermus thermophilus HB8

Bacteria contain conserved mechanisms to control the intracellular levels of metal ions. Metalloregulatory transcription factors bind metal cations and play a central role in regulating gene expression of metal transporters. Often, these transcription factors regulate transcription by binding to a specific DNA sequence in the promoter region of target genes. Understanding the preferred DNA-binding sequence for transcriptional regulators can help uncover novel gene targets and provide insight into the biological role of the transcription factor in the host organism. Here, we identify consensus DNA-binding sequences and subsequent transcription regulatory networks for two metalloregulators from the ferric uptake regulator (FUR) and diphtheria toxin repressor (DtxR) superfamilies in Thermus thermophilus HB8. By homology search, we classify the DtxR homolog as a manganese-specific, MntR (TtMntR), and the FUR homolog as a peroxide-sensing, PerR (TtPerR). Both transcription factors repress separate ZIP transporter genes in vivo, and TtPerR acts as a bifunctional transcription regulator by activating the expression of ferric and hemin transport systems. We show TtPerR and TtMntR bind DNA in the presence of manganese in vitro and in vivo; however, TtPerR is unable to bind DNA in the presence of iron, likely due to iron-mediated histidine oxidation. Unlike canonical PerR homologs, TtPerR does not appear to contribute to peroxide detoxification. Instead, the TtPerR regulon and DNA binding sequence are more reminiscent of Fur or Mur homologs. Collectively, these results highlight the similarities and differences between two metalloregulatory superfamilies and underscore the interplay of manganese and iron in transcription factor regulation.

An opportunistic pathogen under stress: how Group B Streptococcus responds to cytotoxic reactive species and conditions of metal ion imbalance to survive

Group B Streptococcus (GBS; also known as Streptococcus agalactiae) is an opportunistic bacterial pathogen that causes sepsis, meningitis, pneumonia, and skin and soft tissue infections in neonates and healthy or immunocompromised adults. GBS is well-adapted to survive in humans due to a plethora of virulence mechanisms that afford responses to support bacterial survival in dynamic host environments. These mechanisms and responses include counteraction of cell death from exposure to excess metal ions that can cause mismetallation and cytotoxicity, and strategies to combat molecules such as reactive oxygen and nitrogen species that are generated as part of innate host defence. Cytotoxicity from reactive molecules can stem from damage to proteins, DNA, and membrane lipids, potentially leading to bacterial cell death inside phagocytic cells or within extracellular spaces within the host. Deciphering the ways in which GBS responds to the stress of cytotoxic reactive molecules within the host will benefit the development of novel therapeutic and preventative strategies to manage the burden of GBS disease. This review summarizes knowledge of GBS carriage in humans and the mechanisms used by the bacteria to circumvent killing by these important elements of host immune defence: oxidative stress, nitrosative stress, and stress from metal ion intoxication/mismetallation.

Metalloproteome plasticity - a factor in bacterial pathogen adaptive responses?

Through homeostatic processes, bacterial cells maintain intracytoplasmic metal ions at concentrations which enable the 'correct' metal to be inserted into an enzyme, thereby ensuring function. However, fluctuations in intracytoplasmic metal ion concentrations mean that under different conditions certain enzymes may contain different metals at their active site. This perspective describes examples of such cases and suggests that metalloproteome plasticity may contribute to the dynamic adaptation of pathogens to stresses in the host environment.

Allosteric mechanism of MntR transcription factor from alkalophilic bacterium Halalkalibacterium halodurans

Bacterium Halalkalibacterium halodurans is an industrially important alkalophilic bacteria. It is recognized as a producer of enzymes such as β-galactosidase, xylanase, amylase and protease which are able to function at higher pH values and thus can be used in textile, food, paper industry and more. This bacterium, as any other bacterium, requires a sensitive mechanism for regulation of homeostasis of manganese ions (Mn2+) in order to survive. The key protein regulating this mechanism in H. halodurans is MntR - a transcriptional factor that binds to DNA and regulates the transcription of genes for proteins involved in manganese homeostasis. Long range all-atom molecular dynamics (MD) simulations, from 500 ns up to 1.25 µs, were used to study different forms of H. halodurans MntR in order to investigate the differences in the protein's structural and dynamical properties upon Mn2+ binding. Simulations revealed an allosteric mechanism which is activated by Mn2+ binding. The results of simulations show that Mn2+ binding alters the non-covalent interaction network of the protein structure which leads to a conformational change that primarily affects the positions of the DNA binding domains and, consequently, the DNA binding affinity of H. halodurans MntR. The key amino acid residues of the proposed mechanism were identified and their role in the proposed mechanism was computationally confirmed by MD simulations of in silico mutants.

The small protein MntS evolved from a signal peptide and acquired a novel function regulating manganese homeostasis in Escherichia coli

Small proteins (<50 amino acids) are emerging as ubiquitous and important regulators in organisms ranging from bacteria to humans, where they commonly bind to and regulate larger proteins during stress responses. However, fundamental aspects of small proteins, such as their molecular mechanism of action, downregulation after they are no longer needed, and their evolutionary provenance, are poorly understood. Here, we show that the MntS small protein involved in manganese (Mn) homeostasis binds and inhibits the MntP Mn transporter. Mn is crucial for bacterial survival in stressful environments but is toxic in excess. Thus, Mn transport is tightly controlled at multiple levels to maintain optimal Mn levels. The small protein MntS adds a new level of regulation for Mn transporters, beyond the known transcriptional and post-transcriptional control. We also found that MntS binds to itself in the presence of Mn, providing a possible mechanism of downregulating MntS activity to terminate its inhibition of MntP Mn export. MntS is homologous to the signal peptide of SitA, the periplasmic metal-binding subunit of a Mn importer. Remarkably, the homologous signal peptide regions can substitute for MntS, demonstrating a functional relationship between MntS and these signal peptides. Conserved gene neighborhoods support that MntS evolved from the signal peptide of an ancestral SitA protein, acquiring a life of its own with a distinct function in Mn homeostasis.

Hypoferremia of inflammation: Innate host defense against infections

Iron is an essential nutrient for microbes, plants and animals. Multicellular organisms have evolved multiple strategies to control invading microbes by restricting microbial access to iron. Hypoferremia of inflammation is a rapidly-acting organismal response that prevents the formation of iron species that would be readily accessible to microbes. This review takes an evolutionary perspective to explore the mechanisms and host defense function of hypoferremia of inflammation and its clinical implications.

Manganese transporters regulate the resumption of replication in hydrogen peroxide-stressed Escherichia coli

Following hydrogen peroxide treatment, ferrous iron (Fe2+) is oxidized to its ferric form (Fe3+), stripping it from and inactivating iron-containing proteins. Many mononuclear iron enzymes can be remetallated by manganese to restore function, while other enzymes specifically utilize manganese as a cofactor, having redundant activities that compensate for iron-depleted counterparts. DNA replication relies on one or more iron-dependent protein(s) as synthesis abates in the presence of hydrogen peroxide and requires manganese in the medium to resume. Here, we show that manganese transporters regulate the ability to resume replication following oxidative challenge in Escherichia coli. The absence of the primary manganese importer, MntH, impairs the ability to resume replication; whereas deleting the manganese exporter, MntP, or transporter regulator, MntR, dramatically increases the rate of recovery. Unregulated manganese import promoted recovery even in the absence of Fur, which maintains iron homeostasis. Similarly, replication was not restored in oxyR mutants, which cannot upregulate manganese import following hydrogen peroxide stress. Taken together, the results define a central role for manganese transport in restoring replication following oxidative stress.

Habitat-related variability in the morphological and taxonomic diversity of microbial communities in two Hungarian epigenic karst caves

The physical and chemical characteristics of the bedrock, along with the geological and hydrological conditions of karst caves may influence the taxonomic and functional diversity of prokaryotes. Most studies so far have focused on microbial communities of caves including only a few samples and have ignored the chemical heterogeneity of different habitat types such as sampling sites, dripping water, carbonate precipitates, cave walls, cave sediment and surface soils connected to the caves. The aim of the present study was to compare the morphology, the composition and physiology of the microbiota in caves with similar environmental parameters (temperature, host rock, elemental and mineral composition of speleothems) but located in different epigenic karst systems. Csodabogyós Cave and Baradla Cave (Hungary) were selected for the analysis of bacterial and archaeal communities using electron microscopy, amplicon sequencing, X-ray diffraction, and mass spectroscopic techniques. The microbial communities belonged to the phyla Pseudomonadota, Acidobacteriota, Nitrospirota and Nitrososphaerota, and they showed site-specific variation in composition and diversity. The results indicate that morphological and physiological adaptations provide survival for microorganisms according to the environment. In epigenic karst caves, prokaryotes are prone to increase their adsorption surface, cooperate in biofilms, and implement chemolithoautotrophic growth with different electron-donors and acceptors available in the microhabitats.

Bioprotection Potential of Lacticaseibacillus rhamnosus LRH01 and Lactiplantibacillus plantarum LP01 against Spoilage-Associated Penicillium Strains in Yoghurt

Penicillium spp. are considered a major spoilage fungus in dairy products. Due to the growing concerns over food safety issues and the demand for "clean label" food products from consumers, the use of lactic acid bacteria (LAB) as a bioprotective tool to control fungal spoilage of dairy products appears to be a promising alternative. Here, the antifungal activities of ten LAB cultures against five dairy-spoilage-associated Penicillium strains were studied in a model system, and the most potent bioprotective cultures were further tested in yoghurt. Lacticaseibacillus rhamnosus (L. rhamnosus) LRH01 and Lactiplantibacillus plantarum (L. plantarum) LP01 exhibited potent antifungal efficacy at low concentrations. The inhibitory effects of cell-containing fermentates (C-fermentates), cell-free fermentates (CF-fermentates), and volatiles produced by the two cultures were tested in a yoghurt serum medium. The C-fermentates showed antifungal effects, while the removal of cells from C-fermentates led to decreased antifungal activities. Volatiles alone displayed some antifungal efficiency, but less than the fermentates. In a yoghurt matrix, the specific effect of manganese depletion by the bioprotective cultures on mold growth was investigated. Here, the LAB cultures could completely suppress the growth of molds, while addition of manganese partially or fully restored the mold growth, demonstrating that manganese depletion played a key role in the antifungal activity of the tested LAB cultures in the yoghurt matrix. Both L. plantarum LP01 and L. rhamnosus LRH01 showed efficient antifungal activities in the yoghurt serum, while L. rhamnosus LRH01 exhibited the most potent inhibitory effects on Penicillium strains when added during the processing of the yoghurt with subsequent storage at 7 °C for 22 days. Our findings suggested that L. rhamnosus LRH01 could be a promising bioprotective culture for yoghurt biopreservation.

Key players in the regulation of iron homeostasis at the host-pathogen interface

Iron plays a crucial role in the biochemistry and development of nearly all living organisms. Iron starvation of pathogens during infection is a striking feature utilized by a host to quell infection. In mammals and some other animals, iron is essentially obtained from diet and recycled from erythrocytes. Free iron is cytotoxic and is readily available to invading pathogens. During infection, most pathogens utilize host iron for their survival. Therefore, to ensure limited free iron, the host's natural system denies this metal in a process termed nutritional immunity. In this fierce battle for iron, hosts win over some pathogens, but others have evolved mechanisms to overdrive the host barriers. Production of siderophores, heme iron thievery, and direct binding of transferrin and lactoferrin to bacterial receptors are some of the pathogens' successful strategies which are highlighted in this review. The intricate interplay between hosts and pathogens in iron alteration systems is crucial for understanding host defense mechanisms and pathogen virulence. This review aims to elucidate the current understanding of host and pathogen iron alteration systems and propose future research directions to enhance our knowledge in this field.

TerC proteins function during protein secretion to metalate exoenzymes

Cytosolic metalloenzymes acquire metals from buffered intracellular pools. How exported metalloenzymes are appropriately metalated is less clear. We provide evidence that TerC family proteins function in metalation of enzymes during export through the general secretion (Sec-dependent) pathway. Bacillus subtilis strains lacking MeeF(YceF) and MeeY(YkoY) have a reduced capacity for protein export and a greatly reduced level of manganese (Mn) in the secreted proteome. MeeF and MeeY copurify with proteins of the general secretory pathway, and in their absence the FtsH membrane protease is essential for viability. MeeF and MeeY are also required for efficient function of the Mn2+-dependent lipoteichoic acid synthase (LtaS), a membrane-localized enzyme with an extracytoplasmic active site. Thus, MeeF and MeeY, representative of the widely conserved TerC family of membrane transporters, function in the co-translocational metalation of Mn2+-dependent membrane and extracellular enzymes.

Glucose controls manganese homeostasis through transcription factors regulating known and newly identified manganese transporter genes in Bacillus subtilis

Mn2+ is an essential nutrient whose concentration is tightly controlled in bacteria. In Bacillus subtilis, the Mn2+-activated transcription factor MntR controls Mn2+ transporter genes. However, factors regulating intracellular Mn2+ concentration are incompletely understood. Here, we found that glucose addition induces an increase in intracellular Mn2+ concentration. We determined this upshift was mediated by glucose induction of the major Mn2+ importer gene mntH by the transcription factor AhrC, which is known to be involved in arginine metabolism and to be indirectly induced by glucose. In addition, we identified novel AhrC-regulated genes encoding the Mn2+ importer YcsG and the ABC-type exporter YknUV. We found the expression of these genes was also regulated by glucose and contributes to the glucose induction of Mn2+ concentrations. ycsG expression is regulated by MntR as well. Furthermore, we analyzed the interaction of AhrC and MntR with the promoter driving ycsG expression and examined the Mn2+-dependent induction of this promoter to identify the transcription factors responsible for the Mn2+ induction. RNA-Seq revealed that disruption of ahrC and mntR affected the expression of 502 and 478 genes, respectively (false discovery rate, <0.001, log2[fold change] ≥ |2|. The AhrC- and/or MntR-dependent expression of twenty promoters was confirmed by LacZ analysis, and AhrC or MntR binding to some of these promoters was observed via EMSA. The finding that glucose promotes an increase in intracellular Mn2+ levels without changes in extracellular Mn2+ concentrations is reasonable for the bacterium, as intracellular Mn2+ is required for enzymes and pathways mediating glucose metabolism.

Microbe-driven elemental cycling enables microbial adaptation to deep-sea ferromanganese nodule sediment fields

BACKGROUND

Ferromanganese nodule-bearing deep-sea sediments cover vast areas of the ocean floor, representing a distinctive habitat in the abyss. These sediments harbor unique conditions characterized by high iron concentration and low degradable nutrient levels, which pose challenges to the survival and growth of most microorganisms. While the microbial diversity in ferromanganese nodule-associated sediments has been surveyed several times, little is known about the functional capacities of the communities adapted to these unique habitats.

RESULTS

Seven sediment samples collected adjacent to ferromanganese nodules from the Clarion-Clipperton Fracture Zone (CCFZ) in the eastern Pacific Ocean were subjected to metagenomic analysis. As a result, 179 high-quality metagenome-assembled genomes (MAGs) were reconstructed and assigned to 21 bacterial phyla and 1 archaeal phylum, with 88.8% of the MAGs remaining unclassified at the species level. The main mechanisms of resistance to heavy metals for microorganisms in sediments included oxidation (Mn), reduction (Cr and Hg), efflux (Pb), synergy of reduction and efflux (As), and synergy of oxidation and efflux (Cu). Iron, which had the highest content among all metallic elements, may occur mainly as Fe(III) that potentially functioned as an electron acceptor. We found that microorganisms with a diverse array of CAZymes did not exhibit higher community abundance. Instead, microorganisms mainly obtained energy from oxidation of metal (e.g., Mn(II)) and sulfur compounds using oxygen or nitrate as an electron acceptor. Chemolithoautotrophic organisms (Thaumarchaeota and Nitrospirota phyla) were found to be potential manganese oxidizers. The functional profile analysis of the dominant microorganisms further indicated that utilization of inorganic nutrients by redox reactions (rather than organic nutrient metabolism) is a major adaptive strategy used by microorganisms to support their survival in the ferromanganese nodule sediments.

CONCLUSIONS

This study provides a comprehensive metagenomic analysis of microbes inhabiting metal-rich ferromanganese nodule sediments. Our results reveal extensive redundancy across taxa for pathways of metal resistance and transformation, the highly diverse mechanisms used by microbes to obtain nutrition, and their participation in various element cycles in these unique environments. Video Abstract.

Structures and coordination chemistry of transporters involved in manganese and iron homeostasis

A repertoire of transporters plays a crucial role in maintaining homeostasis of biologically essential transition metals, manganese, and iron, thus ensuring cell viability. Elucidating the structure and function of many of these transporters has provided substantial understanding into how these proteins help maintain the optimal cellular concentrations of these metals. In particular, recent high-resolution structures of several transporters bound to different metals enable an examination of how the coordination chemistry of metal ion-protein complexes can help us understand metal selectivity and specificity. In this review, we first provide a comprehensive list of both specific and broad-based transporters that contribute to cellular homeostasis of manganese (Mn2+) and iron (Fe2+ and Fe3+) in bacteria, plants, fungi, and animals. Furthermore, we explore the metal-binding sites of the available high-resolution metal-bound transporter structures (Nramps, ABC transporters, P-type ATPase) and provide a detailed analysis of their coordination spheres (ligands, bond lengths, bond angles, and overall geometry and coordination number). Combining this information with the measured binding affinity of the transporters towards different metals sheds light into the molecular basis of substrate selectivity and transport. Moreover, comparison of the transporters with some metal scavenging and storage proteins, which bind metal with high affinity, reveal how the coordination geometry and affinity trends reflect the biological role of individual proteins involved in the homeostasis of these essential transition metals.

The small protein MntS evolved from a signal peptide and acquired a novel function regulating manganese homeostasis in Escherichia coli

Small proteins (< 50 amino acids) are emerging as ubiquitous and important regulators in organisms ranging from bacteria to humans, where they commonly bind to and regulate larger proteins during stress responses. However, fundamental aspects of small proteins, such as their molecular mechanism of action, downregulation after they are no longer needed, and their evolutionary provenance are poorly understood. Here we show that the MntS small protein involved in manganese (Mn) homeostasis binds and inhibits the MntP Mn transporter. Mn is crucial for bacterial survival in stressful environments, but is toxic in excess. Thus, Mn transport is tightly controlled at multiple levels to maintain optimal Mn levels. The small protein MntS adds a new level of regulation for Mn transporters, beyond the known transcriptional and post-transcriptional control. We also found that MntS binds to itself in the presence of Mn, providing a possible mechanism of downregulating MntS activity to terminate its inhibition of MntP Mn export. MntS is homologous to the signal peptide of SitA, the periplasmic metal-binding subunit of a Mn importer. Remarkably, the homologous signal peptide regions can substitute for MntS, demonstrating a functional relationship between MntS and these signal peptides. Conserved gene-neighborhoods support that MntS evolved from an ancestral SitA, acquiring a life of its own with a distinct function in Mn homeostasis.

Significance

This study demonstrates that the MntS small protein binds and inhibits the MntP Mn exporter, adding another layer to the complex regulation of Mn homeostasis. MntS also interacts with itself in cells with Mn, which could prevent it from regulating MntP. We propose that MntS and other small proteins might sense environmental signals and shut off their own regulation via binding to ligands (e.g., metals) or other proteins. We also provide evidence that MntS evolved from the signal peptide region of the Mn importer, SitA. Homologous SitA signal peptides can recapitulate MntS activities, showing that they have a second function beyond protein secretion. Overall, we establish that small proteins can emerge and develop novel functionalities from gene remnants.

TerC Proteins Function During Protein Secretion to Metalate Exoenzymes

Cytosolic metalloenzymes acquire metals from buffered intracellular pools. How exported metalloenzymes are appropriately metalated is less clear. We provide evidence that TerC family proteins function in metalation of enzymes during export through the general secretion (Sec-dependent) pathway. Bacillus subtilis strains lacking MeeF(YceF) and MeeY(YkoY) have a reduced capacity for protein export and a greatly reduced level of manganese (Mn) in the secreted proteome. MeeF and MeeY copurify with proteins of the general secretory pathway, and in their absence the FtsH membrane protease is essential for viability. MeeF and MeeY are also required for efficient function of the Mn2+-dependent lipoteichoic acid synthase (LtaS), a membrane-localized enzyme with an extracytoplasmic active site. Thus, MeeF and MeeY, representative of the widely conserved TerC family of membrane transporters, function in the co-translocational metalation of Mn2+-dependent membrane and extracellular enzymes.

Manganese uptake mediated by the NRAMP-type transporter MntH is required for acid tolerance in Listeria monocytogenes

Listeria monocytogenes is a foodborne pathogen that is characterized by its ability to withstand mild stresses (i.e. cold, acid, salt) often encountered in food products or food processing environments. In the previous phenotypic and genotypic characterization of a collection of L. monocytogenes strains, we have identified one strain 1381, originally obtained from EURL-lm, as acid sensitive (reduced survival at pH 2.3) and extremely acid intolerant (no growth at pH 4.9, which supports the growth of most strains). In this study, we investigated the cause of acid intolerance in strain 1381 by isolating and sequencing reversion mutants that were capable of growth at low pH (pH 4.8) to a similar extent as another strain (1380) from the same MLST clonal complex (CC2). Whole genome sequencing showed that a truncation in mntH, which encodes a homologue of an NRAMP (Natural Resistance-Associated Macrophage Protein) type Mn²⁺ transporter, is responsible for the acid intolerance phenotype observed in strain 1381. However, the mntH truncation alone was not sufficient to explain the acid sensitivity of strain 1381 at lethal pH values as strain 1381R1 (a mntH⁺ revertant) exhibited similar acid survival to its parental strain at pH 2.3. Further growth experiments demonstrated that Mn²⁺ (but not Fe²⁺, Zn²⁺, Cu²⁺, Ca²⁺, or Mg²⁺) supplementation fully rescues the growth of strain 1381 under low pH conditions, suggesting that a Mn²⁺ limitation is the likely cause of growth arrest in the mntH^- background. Consistent with the important role of Mn²⁺ in the acid stress response was the finding that mntH and mntB (both encoding Mn²⁺ transporters) had higher transcription levels following exposure to mild acid stress (pH 5). Taken together, these results provide evidence that MntH-mediated Mn²⁺ uptake is essential for the growth of L. monocytogenes under low pH conditions. Moreover, since strain 1381 was recommended for conducting food challenge studies by the European Union Reference Laboratory, the use of this strain in evaluating the growth of L. monocytogenes in low pH environments where Mn²⁺ is scarce should be reconsidered. Furthermore, since it is unknown when strain 1381 acquired the mntH frameshift mutation, the ability of the strains used for challenge studies to grow under food-related stresses needs to be routinely validated.

TerC Proteins Function During Protein Secretion to Metalate Exoenzymes

Cytosolic metalloenzymes acquire metals from buffered intracellular pools. How exported metalloenzymes are appropriately metalated is less clear. We provide evidence that TerC family proteins function in metalation of enzymes during export through the general secretion (Sec-dependent) pathway. Bacillus subtilis strains lacking MeeF(YceF) and MeeY(YkoY) have a reduced capacity for protein export and a greatly reduced level of manganese (Mn) in the secreted proteome. MeeF and MeeY copurify with proteins of the general secretory pathway, and in their absence the FtsH membrane protease is essential for viability. MeeF and MeeY are also required for efficient function of the Mn 2+ -dependent lipoteichoic acid synthase (LtaS), a membrane-localized enzyme with an extracytoplasmic active site. Thus, MeeF and MeeY, representative of the widely conserved TerC family of membrane transporters, function in the co-translocational metalation of Mn 2+ -dependent membrane and extracellular enzymes.

Manganese Transporter Proteins in Salmonella enterica serovar Typhimurium

The metal cofactors are essential for the function of many enzymes. The host restricts the metal acquisition of pathogens for their immunity and the pathogens have evolved many ways to obtain metal ions for their survival and growth. Salmonella enterica serovar Typhimurium also needs several metal cofactors for its survival, and manganese has been found to contribute to Salmonella pathogenesis. Manganese helps Salmonella withstand oxidative and nitrosative stresses. In addition, manganese affects glycolysis and the reductive TCA, which leads to the inhibition of energetic and biosynthetic metabolism. Therefore, manganese homeostasis is crucial for full virulence of Salmonella. Here, we summarize the current information about three importers and two exporters of manganese that have been identified in Salmonella. MntH, SitABCD, and ZupT have been shown to participate in manganese uptake. mntH and sitABCD are upregulated by low manganese concentration, oxidative stress, and host NRAMP1 level. mntH also contains a Mn²⁺-dependent riboswitch in its 5' UTR. Regulation of zupT expression requires further investigation. MntP and YiiP have been identified as manganese efflux proteins. mntP is transcriptionally activated by MntR at high manganese levels and repressed its activity by MntS at low manganese levels. Regulation of yiiP requires further analysis, but it has been shown that yiiP expression is not dependent on MntS. Besides these five transporters, there might be additional transporters that need to be identified.

Why is manganese so valuable to bacterial pathogens?

Apart from oxygenic photosynthesis, the extent of manganese utilization in bacteria varies from species to species and also appears to depend on external conditions. This observation is in striking contrast to iron, which is similar to manganese but essential for the vast majority of bacteria. To adequately explain the role of manganese in pathogens, we first present in this review that the accumulation of molecular oxygen in the Earth's atmosphere was a key event that linked manganese utilization to iron utilization and put pressure on the use of manganese in general. We devote a large part of our contribution to explanation of how molecular oxygen interferes with iron so that it enhances oxidative stress in cells, and how bacteria have learned to control the concentration of free iron in the cytosol. The functioning of iron in the presence of molecular oxygen serves as a springboard for a fundamental understanding of why manganese is so valued by bacterial pathogens. The bulk of this review addresses how manganese can replace iron in enzymes. Redox-active enzymes must cope with the higher redox potential of manganese compared to iron. Therefore, specific manganese-dependent isoenzymes have evolved that either lower the redox potential of the bound metal or use a stronger oxidant. In contrast, redox-inactive enzymes can exchange the metal directly within the individual active site, so no isoenzymes are required. It appears that in the physiological context, only redox-inactive mononuclear or dinuclear enzymes are capable of replacing iron with manganese within the same active site. In both cases, cytosolic conditions play an important role in the selection of the metal used. In conclusion, we summarize both well-characterized and less-studied mechanisms of the tug-of-war for manganese between host and pathogen.

The elements of life: A biocentric tour of the periodic table

Living systems are built from a small subset of the atomic elements, including the bulk macronutrients (C,H,N,O,P,S) and ions (Mg,K,Na,Ca) together with a small but variable set of trace elements (micronutrients). Here, we provide a global survey of how chemical elements contribute to life. We define five classes of elements: those that are (i) essential for all life, (ii) essential for many organisms in all three domains of life, (iii) essential or beneficial for many organisms in at least one domain, (iv) beneficial to at least some species, and (v) of no known beneficial use. The ability of cells to sustain life when individual elements are absent or limiting relies on complex physiological and evolutionary mechanisms (elemental economy). This survey of elemental use across the tree of life is encapsulated in a web-based, interactive periodic table that summarizes the roles chemical elements in biology and highlights corresponding mechanisms of elemental economy.

Manganese Pollution and Its Remediation: A Review of Biological Removal and Promising Combination Strategies

Manganese (Mn), as a cofactor of multiple enzymes, exhibits great significance to the human body, plants and animals. It is also a critical raw material and alloying element. However, extensive employment for industrial purposes leads to its excessive emission into the environment and turns into a significant threat to the ecosystem and public health. This review firstly introduces the essentiality, toxicity and regulation of Mn. Several traditional physicochemical methods and their problems are briefly discussed as well. Biological remediation, especially microorganism-mediated strategies, is a potential alternative for remediating Mn-polluted environments in a cost-efficient and eco-friendly manner. Among them, microbially induced carbonate precipitation (MICP), biosorption, bioaccumulation, bio-oxidation are discussed in detail, including their mechanisms, pivotal influencing factors along with strengths and limitations. In order to promote bioremediation efficiency, the combination of different techniques is preferable, and their research progress is also summarized. Finally, we propose the future directions of Mn bioremediation by microbes. Conclusively, this review provides a scientific basis for the microbial remediation performance for Mn pollution and guides the development of a comprehensive competent strategy towards practical Mn remediation.

Nramp: Deprive and conquer?

Solute carriers 11 (Slc11) evolved from bacterial permease (MntH) to eukaryotic antibacterial defense (Nramp) while continuously mediating proton (H⁺)-dependent manganese (Mn²⁺) import. Also, Nramp horizontal gene transfer (HGT) toward bacteria led to mntH polyphyly. Prior demonstration that evolutionary rate-shifts distinguishing Slc11 from outgroup carriers dictate catalytic specificity suggested that resolving Slc11 family tree may provide a function-aware phylogenetic framework. Hence, MntH C (MC) subgroups resulted from HGTs of prototype Nramp (pNs) parologs while archetype Nramp (aNs) correlated with phagocytosis. PHI-Blast based taxonomic profiling confirmed MntH B phylogroup is confined to anaerobic bacteria vs. MntH A (MA)’s broad distribution; suggested niche-related spread of MC subgroups; established that MA-variant MH, which carries ‘eukaryotic signature’ marks, predominates in archaea. Slc11 phylogeny shows MH is sister to Nramp. Site-specific analysis of Slc11 charge network known to interact with the protonmotive force demonstrates sequential rate-shifts that recapitulate Slc11 evolution. 3D mapping of similarly coevolved sites across Slc11 hydrophobic core revealed successive targeting of discrete areas. The data imply that pN HGT could advantage recipient bacteria for H⁺-dependent Mn²⁺ acquisition and Alphafold 3D models suggest conformational divergence among MC subgroups. It is proposed that Slc11 originated as a bacterial stress resistance function allowing Mn²⁺-dependent persistence in conditions adverse for growth, and that archaeal MH could contribute to eukaryogenesis as a Mn²⁺ sequestering defense perhaps favoring intracellular growth-competent bacteria.

ZccE is a Novel P-type ATPase That Protects Streptococcus mutans Against Zinc Intoxication

Zinc is a trace metal that is essential to all forms of life, but that becomes toxic at high concentrations. Because it has both antimicrobial and anti-inflammatory properties and low toxicity to mammalian cells, zinc has been used as a therapeutic agent for centuries to treat a variety of infectious and non-infectious conditions. While the usefulness of zinc-based therapies in caries prevention is controversial, zinc is incorporated into toothpaste and mouthwash formulations to prevent gingivitis and halitosis. Despite this widespread use of zinc in oral healthcare, the mechanisms that allow Streptococcus mutans, a keystone pathogen in dental caries and prevalent etiological agent of infective endocarditis, to overcome zinc toxicity are largely unknown. Here, we discovered that S. mutans is inherently more tolerant to high zinc stress than all other species of streptococci tested, including commensal streptococci associated with oral health. Using a transcriptome approach, we uncovered several potential strategies utilized by S. mutans to overcome zinc toxicity. Among them, we identified a previously uncharacterized P-type ATPase transporter and cognate transcriptional regulator, which we named ZccE and ZccR respectively, as responsible for the remarkable high zinc tolerance of S. mutans. In addition to zinc, we found that ZccE, which was found to be unique to S. mutans strains, mediates tolerance to at least three additional metal ions, namely cadmium, cobalt, and copper. Loss of the ability to maintain zinc homeostasis when exposed to high zinc stress severely disturbed zinc:manganese ratios, leading to heightened peroxide sensitivity that was alleviated by manganese supplementation. Finally, we showed that the ability of the ΔzccE strain to stably colonize the rat tooth surface after topical zinc treatment was significantly impaired, providing proof of concept that ZccE and ZccR are suitable targets for the development of antimicrobial therapies specifically tailored to kill S. mutans.

Dental caries is an overlooked infectious disease affecting more than 50% of the adult population. While several bacteria that reside in dental plaque have been associated with caries development and progression, Streptococcus mutans is deemed a keystone caries pathogen due to its capacity to modify the dental plaque environment in a way that is conducive with disease development. Zinc is an essential trace metal to life but toxic when encountered at high concentrations, to the point that it has been used as an antimicrobial for centuries. Despite the widespread use of zinc in oral healthcare products, little is known about the mechanisms utilized by oral bacteria to overcome its toxic effects. In this study, we discovered that S. mutans can tolerate exposure to much higher levels of zinc than closely related streptococcal species, including species that antagonize S. mutans and are associated with oral health. In this study, we identified a new metal transporter, named ZccE, as directly responsible for the inherently high zinc tolerance of S. mutans. Because ZccE is not present in other bacteria, our findings provide a new target for the development of a zinc-based therapy specifically tailored to kill S. mutans.

Metal Homeostasis in Pathogenic Streptococci

Streptococcus spp. are an important genus of Gram-positive bacteria, many of which are opportunistic pathogens that are capable of causing invasive disease in a wide range of populations. Metals, especially transition metal ions, are an essential nutrient for all organisms. Therefore, to survive across dynamic host environments, Streptococci have evolved complex systems to withstand metal stress and maintain metal homeostasis, especially during colonization and infection. There are many different types of transport systems that are used by bacteria to import or export metals that can be highly specific or promiscuous. Focusing on the most well studied transition metals of zinc, manganese, iron, nickel, and copper, this review aims to summarize the current knowledge of metal homeostasis in pathogenic Streptococci, and their role in virulence.

Calcium Determines Lactiplantibacillus plantarum Intraspecies Competitive Fitness

The importance of individual nutrients for microbial strain robustness and coexistence in habitats containing different members of the same species is not well understood. To address this for Lactiplantibacillus plantarum in food fermentations, we performed comparative genomics and examined the nutritive requirements and competitive fitness for L. plantarum strains B1.1 and B1.3 isolated from a single sample of teff injera fermentation batter. Compared to B1.1 and other L. plantarum strains, B1.3 has a smaller genome, limited biosynthetic capacities, and large mobilome. Despite these differences, B1.3 was equally competitive with B1.1 in a suspension of teff flour. In commercially sourced, nutrient-replete MRS (cMRS) medium, strain B1.3 reached 3-fold-higher numbers than B1.1 within 2 days of passage. Because B1.3 growth and competitive fitness were poor in mMRS medium (here called mMRS), a modified MRS medium lacking beef extract, we used mMRS to identify nutrients needed for robust B1.3 growth. No improvement was observed when mMRS was supplemented with nucleotides, amino acids, vitamins, or monovalent metals. Remarkably, the addition of divalent metal salts increased the growth rate and cell yields of B1.3 in mMRS. Metal requirements were confirmed by inductively coupled plasma mass spectrometry, showing that total B1.3 intracellular metal concentrations were significantly (up to 2.7-fold) reduced compared to B1.1. Supplemental CaCl₂ conferred the greatest effect, resulting in equal growth between B1.1 and B1.3 over five successive passages in mMRS. Moreover, calcium supplementation reversed a B1.3 strain-specific, stationary-phase, flocculation phenotype. These findings show how L. plantarum calcium requirements affect competitive fitness at the strain level.

IMPORTANCE Ecological theory states that the struggle for existence is stronger between closely related species. Contrary to this assertion, fermented foods frequently sustain conspecific individuals, in spite of their high levels of phylogenetic relatedness. Therefore, we investigated two isolates of Lactiplantibacillus plantarum, B1.1 and B1.3, randomly selected from a single batch of teff injera batter. These strains spanned the known genomic and phenotypic range of the L. plantarum species, and in laboratory culture medium used for strain screening, B1.3 exhibited poor growth and was outcompeted by the more robust strain B1.1. Nonetheless, B1.1 and B1.3 were equally competitive in teff flour. This result shows how L. plantarum has adapted for coexistence in that environment. The capacity for the single macronutrient calcium to restore B1.3 competitive fitness in laboratory culture medium suggests that L. plantarum intraspecies diversity found in food systems is fine-tuned to nutrient requirements at the strain level.

Regulation of Bacterial Manganese Homeostasis and Usage During Stress Responses and Pathogenesis

Manganese (Mn) plays a multifaceted role in the survival of pathogenic and symbiotic bacteria in eukaryotic hosts, and it is also important for free-living bacteria to grow in stressful environments. Previous research has uncovered components of the bacterial Mn homeostasis systems that control intracellular Mn levels, many of which are important for virulence. Multiple studies have also identified proteins that use Mn once it is inside the cell, including Mn-specific enzymes and enzymes transiently loaded with Mn for protection during oxidative stress. Emerging evidence continues to reveal proteins involved in maintaining Mn homeostasis, as well as enzymes that can bind Mn. For some of these enzymes, Mn serves as an essential cofactor. For other enzymes, mismetallation with Mn can lead to inactivation or poor activity. Some enzymes may even potentially be regulated by differential metallation with Mn or zinc (Zn). This review focuses on new developments in regulatory mechanisms that affect Mn homeostasis and usage, additional players in Mn import that increase bacterial survival during pathogenesis, and the interplay between Mn and other metals during Mn-responsive physiological processes. Lastly, we highlight lessons learned from fundamental research that are now being applied to bacterial interactions within larger microbial communities or eukaryotic hosts.

Manganese Utilization in Salmonella Pathogenesis: Beyond the Canonical Antioxidant Response

The metal ion manganese (Mn²⁺) is equally coveted by hosts and bacterial pathogens. The host restricts Mn²⁺ in the gastrointestinal tract and Salmonella-containing vacuoles, as part of a process generally known as nutritional immunity. Salmonella enterica serovar Typhimurium counteract Mn²⁺ limitation using a plethora of metal importers, whose expression is under elaborate transcriptional and posttranscriptional control. Mn²⁺ serves as cofactor for a variety of enzymes involved in antioxidant defense or central metabolism. Because of its thermodynamic stability and low reactivity, bacterial pathogens may favor Mn²⁺-cofactored metalloenzymes during periods of oxidative stress. This divalent metal catalyzes metabolic flow through lower glycolysis, reductive tricarboxylic acid and the pentose phosphate pathway, thereby providing energetic, redox and biosynthetic outputs associated with the resistance of Salmonella to reactive oxygen species generated in the respiratory burst of professional phagocytic cells. Combined, the oxyradical-detoxifying properties of Mn²⁺ together with the ability of this divalent metal cation to support central metabolism help Salmonella colonize the mammalian gut and establish systemic infections.

Managing Manganese: The Role of Manganese Homeostasis in Streptococcal Pathogenesis

Pathogenic streptococci require manganese for survival in the host. In response to invading pathogens, the host recruits nutritional immune effectors at infection sites to withhold manganese from the pathogens and control bacterial growth. The manganese scarcity impairs several streptococcal processes including oxidative stress defenses, de novo DNA synthesis, bacterial survival, and virulence. Emerging evidence suggests that pathogens also encounter manganese toxicity during infection and manganese excess impacts streptococcal virulence by manganese mismetallation of non-cognate molecular targets involved in bacterial antioxidant defenses and cell division. To counter host-imposed manganese stress, the streptococcal species employ a sophisticated sensory system that tightly coordinates manganese stress-specific molecular strategies to negate host induced manganese stress and proliferate in the host. Here we review the molecular details of host-streptococcal interactions in the battle for manganese during infection and the significance of streptococcal effectors involved to bacterial pathophysiology.

Carbon Metabolism of a Soilborne Mn(II)-Oxidizing Escherichia coli Isolate Implicated as a Pronounced Modulator of Bacterial Mn Oxidation

Mn(II)-oxidizing microorganisms are generally considered the primary driving forces in the biological formation of Mn oxides. However, the mechanistic elucidation of the actuation and regulation of Mn oxidation in soilborne bacteria remains elusive. Here, we performed joint multiple gene-knockout analyses and comparative morphological and physiological determinations to characterize the influence of carbon metabolism on the Mn oxide deposit amount (MnODA) and the Mn oxide formation of a soilborne bacterium, Escherichia coli MB266. Different carbon source substances exhibited significantly varied effects on the MnODA of MB266. A total of 16 carbon metabolism-related genes with significant variant expression levels under Mn supplementation conditions were knocked out in the MB266 genome accordingly, but only little effect on the MnODA of each mutant strain was accounted for. However, a simultaneous four-gene-knockout mutant (namely, MB801) showed an overall remarkable MnODA reduction and an initially delayed Mn oxide formation compared with the wild-type MB266. The assays using scanning/transmission electron microscopy verified that MB801 exhibited not only a delayed Mn-oxide aggregate processing, but also relatively smaller microspherical agglomerations, and presented flocculent deposit Mn oxides compared with normal fibrous and crystalline Mn oxides formed by MB266. Moreover, the Mn oxide aggregate formation was highly related to the intracellular ROS level. Thus, this study demonstrates that carbon metabolism acts as a pronounced modulator of MnODA in MB266, which will provide new insights into the occurrence of Mn oxidation and Mn oxide formation by soilborne bacteria in habitats where Mn(II) naturally occurs.

Stable high-oxidation-state complex in situ Mn(V)-Mn(III) transition to achieve highly efficient cervical cancer therapy

Designing metal complexes to target the vulnerable redox balance in cancer cells is a promising strategy to realize successful cancer therapy. The synthesized stable nitridomanganese(V) complex Mn^V(N) (salen) not only reacts with GSH to achieve in situ Mn(V)-Mn(III) transformation to down-regulate the antioxidant system, but also catalyzes H₂O₂ to higher oxidation capacity ROS to up-regulate the intracellular oxidative level, finally resulting in cancer cell death.

Manganese Stress Adaptation Mechanisms of Bacillus safensis Strain ST7 From Mine Soil

The mechanism of bacterial adaption to manganese-polluted environments was explored using 50 manganese-tolerant strains of bacteria isolated from soil of the largest manganese mine in China. Efficiency of manganese removal by the isolated strains was investigated using atomic absorption spectrophotometry. Bacillus safensis strain ST7 was the most effective manganese-oxidizing bacteria among the tested isolates, achieving up to 82% removal at a Mn(II) concentration of 2,200 mg/L. Bacteria-mediated manganese oxide precipitates and high motility were observed, and the growth of strain ST7 was inhibited while its biofilm formation was promoted by the presence of Mn(II). In addition, strain ST7 could grow in the presence of high concentrations of Al(III), Cr(VI), and Fe(III). Genome-wide analysis of the gene expression profile of strain ST7 using the RNA-seq method revealed that 2,580 genes were differently expressed under Mn(II) exposure, and there were more downregulated genes (n = 2,021) than upregulated genes (n = 559) induced by Mn stress. KAAS analysis indicated that these differently expressed genes were mainly enriched in material metabolisms, cellular processes, organism systems, and genetic and environmental information processing pathways. A total of twenty-six genes from the transcriptome of strain ST7 were involved in lignocellulosic degradation. Furthermore, after 15 genes were knocked out by homologous recombination technology, it was observed that the transporters, multicopper oxidase, and proteins involved in sporulation and flagellogenesis contributed to the removal of Mn(II) in strain ST7. In summary, B. safensis ST7 adapted to Mn exposure by changing its metabolism, upregulating cation transporters, inhibiting sporulation and flagellogenesis, and activating an alternative stress-related sigB pathway. This bacterial strain could potentially be used to restore soil polluted by multiple heavy metals and is a candidate to support the consolidated bioprocessing community.