A widened substrate selectivity filter of eukaryotic formate-nitrite transporters enables high-level lactate conductance

Microbial membrane transport proteins and their biotechnological applications

Because of the hydrophobic nature of the membrane lipid bilayer, the majority of the hydrophilic solutes require special transportation mechanisms for passing through the cell membrane. Integral membrane transport proteins (MTPs), which belong to the Major Intrinsic Protein Family, facilitate the transport of these solutes across cell membranes. MTPs including aquaporins and carrier proteins are transmembrane proteins spanning across the cell membrane. The easy handling of microorganisms enabled the discovery of a remarkable number of transport proteins specific to different substances. It has been realized that these transporters have very important roles in the survival of microorganisms, their pathogenesis, and antimicrobial resistance. Astonishing features related to the solute specificity of these proteins have led to the acceleration of the research on the discovery of their properties and the development of innovative products in which these unique properties are used or imitated. Studies on microbial MTPs range from the discovery and characterization of a novel transporter protein to the mining and screening of them in a large transporter library for particular functions, from simulations and modeling of specific transporters to the preparation of biomimetic synthetic materials for different purposes such as biosensors or filtration membranes. This review presents recent discoveries on microbial membrane transport proteins and focuses especially on formate nitrite transport proteins and aquaporins, and advances in their biotechnological applications.

Heterologous expression of formate dehydrogenase enables photoformatotrophy in the emerging model microalga, Picochlorum renovo

Rising global greenhouse gas emissions and the impacts of resultant climate change necessitate development and deployment of carbon capture and conversion technologies. Amongst the myriad of bio-based conversion approaches under evaluation, a formate bio-economy has recently been proposed, wherein CO2-derived formate serves as a substrate for concurrent carbon and energy delivery to microbial systems. To date, this approach has been explored in chemolithotrophic and heterotrophic organisms via native or engineered formatotrophy. However, utilization of this concept in phototrophic organisms has yet to be reported. Herein, we have taken the first steps to establish formate utilization in Picochlorum renovo, a recently characterized eukaryotic microalga with facile genetic tools and promising applied biotechnology traits. Plastidial heterologous expression of a formate dehydrogenase (FDH) enabled P. renovo growth on formate as a carbon and energy source. Further, FDH expression enhanced cultivation capacity on ambient CO2, underscoring the potential for bypass of conventional CO2 capture and concentration limitations. This work establishes a photoformatotrophic cultivation regime that leverages light energy-driven formate utilization. The resultant photosynthetic formate platform has widespread implications for applied phototrophic cultivation systems and the bio-economy at large.

Formate Metabolism in Shigella flexneri and Its Effect on HeLa Cells at Different Stages during the Infectious Process

Shigellosis caused by Shigella is one of the most important foodborne illnesses in global health, but little is known about the metabolic cross talk between this bacterial pathogen and its host cells during the different stages of the infection process. A detailed understanding of the metabolism can potentially lead to new drug targets remedying the pressing problem of antibiotic resistance. Here, we use stable isotope-resolved metabolomics as an unbiased and fast method to investigate how Shigella metabolizes 13C-glucose in three different environments: inside the host cells, adhering to the host cells, and alone in suspension. We find that especially formate metabolism by bacteria is sensitive to these different environments. The role of formate in pathogen metabolism is sparsely described in the literature compared to the roles of acetate and butyrate. However, its metabolic pathway is regarded as a potential drug target due to its production in microorganisms and its absence in humans. Our study provides new knowledge about the regulatory effect of formate. Bacterial metabolism of formate is pH dependent when studied alone in culture medium, whereas this effect is less pronounced when the bacteria adhere to the host cells. Once the bacteria are inside the host cells, we find that formate accumulation is reduced. Formate also affects the host cells resulting in a reduced infection rate. This was correlated to an increased immune response. Thus, intriguingly formate plays a double role in pathogenesis by increasing the virulence of Shigella and at the same time stimulating the immune response of the host. IMPORTANCE Bacterial infection is a pressing societal concern due to development of resistance toward known antibiotics. Central carbon metabolism has been suggested as a potential new target for drug development, but metabolic changes upon infection remain incompletely understood. Here, we used a cellular infection model to study how the bacterial pathogen Shigella adapts its metabolism depending on the environment starting from the extracellular medium until Shigella successfully invaded and proliferated inside host cells. The mixed-acid fermentation of Shigella was the major metabolic pathway during the infectious process, and the glucose-derived metabolite formate surprisingly played a divergent role in the pathogen and in the host cell. Our data show reduced infection rate when both host cells and bacteria were treated with formate, which correlated with an upregulated immune response in the host cells. The formate metabolism in Shigella thus potentially provides a route toward alternative treatment strategies for Shigella prevention.

Comparison of ion selectivities of nitrite channel NirC and water channel aquaporin

nirC gene coding for the nitrite channel of E. coli K12 was cloned into the pET28a vector and expressed in E. coli BL21 cells. 28.5 kDa NirC monomer was purified from membrane components of E. coli. Selectivity of NirC for different ions including nitrite, nitrate, sulfate, formate, and acetate anions, and a divalent cation, magnesium, was compared with that of bacterial aquaporin from Halomonas elongata. Water and ion permeability values were determined by measuring the light scattering rates of proteoliposomes containing NirC and aquaporins during their water loss and gain. NirC shows a selective permeability to nitrite and is more resistant to the entry of other anions as compared to aquaporin. The single channel permeability of NirC for nitrite is about 10-fold that of a single aquaporin channel. Both aquaporin and NirC channel proteins were impermeable to MgCl₂ and (NH₄)₂SO₄ and their permeability to other tested ions was remarkably lower as compared to nitrite ions. The study also presents the 3D model and channel characteristics of NirC. The translocation channel of E. coli NirC is determined to be larger, and its length is shorter than aquaporin channels. Although the NirC channel throat is more hydrophobic than aquaporin, its water permeability is almost equal to that of aquaporin. The hydrophobic nature of the NirC channel might play an important role in the selective permeability of the channel for nitrite ions.

FocA and its central role in fine-tuning pH homeostasis of enterobacterial formate metabolism

During enterobacterial mixed-acid fermentation, formate is generated from pyruvate by the glycyl-radical enzyme pyruvate formate-lyase (PflB). In Escherichia coli, especially at low pH, formate is then disproportionated to CO₂ and H₂ by the cytoplasmically oriented, membrane-associated formate hydrogenlyase (FHL) complex. If electron acceptors are available, however, formate is oxidized by periplasmically oriented, respiratory formate dehydrogenases. Formate translocation across the cytoplasmic membrane is controlled by the formate channel, FocA, a member of the formate-nitrite transporter (FNT) family of homopentameric anion channels. This review highlights recent advances in our understanding of how FocA helps to maintain intracellular formate and pH homeostasis during fermentation. Efflux and influx of formate/formic acid are distinct processes performed by FocA and both are controlled through protein interaction between FocA's N-terminal domain with PflB. Formic acid efflux by FocA helps to maintain cytoplasmic pH balance during exponential-phase growth. Uptake of formate against the electrochemical gradient (inside negative) is energetically and mechanistically challenging for a fermenting bacterium unless coupled with proton/cation symport. Translocation of formate/formic acid into the cytoplasm necessitates an active FHL complex, whose synthesis also depends on formate. Thus, FocA, FHL and PflB function together to govern formate homeostasis. We explain how FocA achieves efflux of formic acid and propose mechanisms for pH-dependent uptake of formate both with and without proton symport. We propose that FocA displays both channel- and transporter-like behaviour. Whether this translocation behaviour is shared by other members of the FNT family is also discussed.

Mutational Widening of Constrictions in a Formate-Nitrite/H+ Transporter Enables Aquaporin-Like Water Permeability and Proton Conductance

The unrelated protein families of the microbial formate–nitrite transporters (FNTs) and aquaporins (AQP) likely adapted the same protein fold through convergent evolution. FNTs facilitate weak acid anion/H⁺ cotransport, whereas AQP water channels strictly exclude charged substrates including protons. The FNT channel–like transduction pathway bears two lipophilic constriction sites that sandwich a highly conserved histidine residue. Because of lacking experiments, the function of these constrictions is unclear, and the protonation status of the central histidine during substrate transport remains a matter of debate. Here, we introduced constriction-widening mutations into the prototypical FNT from Escherichia coli, FocA, and assayed formate/H⁺ transport properties, water/solute permeability, and proton conductance. We found that enlargement of these constrictions concomitantly decreased formate/formic acid transport. In contrast to wildtype FocA, the mutants were unable to make use of a transmembrane proton gradient as a driving force. A construct in which both constrictions were eliminated exhibited water permeability, similar to AQPs, although accompanied by a proton conductance. Our data indicate that the lipophilic constrictions mainly act as barriers to isolate the central histidine from the aqueous bulk preventing protonation via proton wires. These results are supportive of an FNT transport model in which the central histidine is uncharged, and weak acid substrate anion protonation occurs in the vestibule regions of the transporter before passing the constrictions.

Structure memes: Intuitive visualization of sequence logo and subfamily logo information in a 3D protein-structural context

The number of available protein sequences covering virtually all known species is tremendous and ever growing due to the feasibility of the underlying nucleotide sequencing. The speed at which protein structures are being determined is increasing, and as a result of refined cryo-electron microscopy the proportion of solved membrane protein folds is expanding. Sequence data are used to illustrate evolution and to group proteins into families with various levels of subfamilies. Structure data of prototypical proteins provide insight into function brought about by an interplay of specific amino acid residues that are dispersed throughout the sequence. Visually combining rich sequence information with structure data in an intuitively comprehensible way would enhance the process of elucidating key protein aspects regarding evolution, sequence relations, and function. Here, a method is described that projects the information contained in sequence logos and subfamily logos onto protein structures. The amino acid composition at a site is encoded by a mix color in the red-yellow-blue space and the information content is presented by the radius of a sphere at the α-carbon position. The resulting display is termed "structure meme." The underlying sequence and atom coordinate data are retained in the file for simple retrieval on demand using a molecular structure visualization program. Structure memes are recognizable and convey extensive information in a human-discernable way that requires little training.

Pentafluoro-3-hydroxy-pent-2-en-1-ones Potently Inhibit FNT-Type Lactate Transporters from all Five Human-Pathogenic Plasmodium Species

The protozoan parasite Plasmodium falciparum causes the most severe and prevailing form of malaria in sub-Saharan Africa. Previously, we identified the plasmodial lactate transporter, PfFNT, a member of the microbial formate-nitrite transporter family, as a novel antimalarial drug target. With the pentafluoro-3-hydroxy-pent-2-en-1-ones, we discovered PfFNT inhibitors that potently kill P. falciparum parasites in vitro. Four additional human-pathogenic Plasmodium species require attention, that is, P. vivax, most prevalent outside of Africa, and the regional P. malariae, P. ovale and P. knowlesi. Herein, we show that the plasmodial FNT variants are highly similar in terms of protein sequence and functionality. The FNTs from all human-pathogenic plasmodia and the rodent malaria parasite were efficiently inhibited by pentafluoro-3-hydroxy-pent-2-en-1-ones. We further established a phenotypic yeast-based FNT inhibitor screen, and found very low compound cytotoxicity and monocarboxylate transporter 1 off-target activity on human cells, particularly of the most potent FNT inhibitor BH267.meta, allowing these compounds to proceed towards animal model malaria studies.

Aquaporins with lactate/lactic acid permeability at physiological pH conditions

The spectrum of putative and experimentally shown permeants of cellular water and solute channels of the ubiquitous aquaporin family is still increasing. Virtually all AQP substrates, e.g. water, glycerol, urea, hydrogen peroxide, or carbon dioxide, are permanently neutral small molecule compounds. Several reports, however, describe aquaporins that exhibit lactate permeability. Lactate in aqueous solution undergoes a pH-dependent protonation equilibrium with neutral lactic acid, which likely represents the actual substrate form passing the aquaporin channel. Certain aquaporins, however, appear to be better geared for lactate/lactic acid permeability even at low proton availability. Here, we discuss the structural properties of such aquaporins and compare them to the microbial protein family of the formate-nitrite (lactate) transporters that assume the aquaporin fold despite unrelated protein sequences.

Structural basis of transport and inhibition of the Plasmodium falciparum transporter PfFNT

The intra-erythrocyte stage of P. falciparum relies primarily on glycolysis to generate adenosine triphosphate (ATP) and the energy required to support growth and reproduction. Lactic acid, a metabolic byproduct of glycolysis, is potentially toxic as it lowers the pH inside the parasite. Plasmodium falciparum formate-nitrite transporter (PfFNT), a 34-kDa transmembrane protein, has been identified as a novel drug target as it exports lactate from inside the parasite to the surrounding parasitophorous vacuole within the erythrocyte cytosol. The structure and detailed molecular mechanism of this membrane protein are not yet available. Here we present structures of PfFNT in the absence and presence of the functional inhibitor MMV007839 at resolutions of 2.56 Å and 2.78 Å using single-particle cryo-electron microscopy. Genetic analysis and transport assay indicate that PfFNT is able to transfer lactate across the membrane. Combined, our data suggest a stepwise displacement mechanism for substrate transport. The PfFNT membrane protein is capable of picking up lactate ions from the parasite's cytosol, converting them to lactic acids and then exporting these acids into the extracellular space.

Transmembrane Facilitation of Lactate/H+ Instead of Lactic Acid Is Not a Question of Semantics but of Cell Viability

Transmembrane transport of monocarboxylates is conferred by structurally diverse membrane proteins. Here, we describe the pH dependence of lactic acid/lactate facilitation of an aquaporin (AQP9), a monocarboxylate transporter (MCT1, SLC16A1), and a formate–nitrite transporter (plasmodium falciparum FNT, PfFNT) in the equilibrium transport state. FNTs exhibit a channel-like structure mimicking the aquaporin-fold, yet act as secondary active transporters. We used radiolabeled lactate to monitor uptake via yeast-expressed AQP9, MCT1, and PfFNT for long enough time periods to reach the equilibrium state in which import and export rates are balanced. We confirmed that AQP9 behaved perfectly equilibrative for lactic acid, i.e., the neutral lactic acid molecule enters and passes the channel. MCT1, in turn, actively used the transmembrane proton gradient and acted as a lactate/H⁺ co-transporter. PfFNT behaved highly similar to the MCT in terms of transport properties, although it does not adhere to the classical alternating access transporter model. Instead, the FNT appears to use the proton gradient to neutralize the lactate anion in the protein’s vestibule to generate lactic acid in a place that traverses the central hydrophobic transport path. In conclusion, we propose to include FNT-type proteins into a more generalized, function-based transporter definition.

Is the E. coli Homolog of the Formate/Nitrite Transporter Family an Anion Channel? A Computational Study

Formate/nitrite transporters (FNTs) selectively transport monovalent anions and are found in prokaryotes and lower eukaryotes. They play a significant role in bacterial growth and act against the defense mechanism of infected hosts. Because FNTs do not occur in higher animals, they are attractive drug targets for many bacterial diseases. Phylogenetic analysis revealed that they can be classified into eight subgroups, two of which belong to the uncharacterized YfdC-α and YfdC-β groups. Experimentally determined structures of FNTs belonging to different phylogenetic groups adopt the unique aquaporin-like hourglass helical fold. We considered the formate channel from Vibrio cholerae, the hydrosulphide channel from Clostridium difficile, and the uncharacterized channel from Escherichia coli (EcYfdC) to investigate the mechanism of transport and selectivity. Using equilibrium molecular dynamics and umbrella sampling studies, we determined temporal channel radius profiles, permeation events, and potential of mean force profiles of different substrates with the conserved central histidine residue in protonated or neutral form. Unlike the formate channel from V. cholerae and the hydrosulphide channel from C. difficile, molecular dynamics studies showed that the formate substrate was unable to enter the vestibule region of EcYfdC. Absence of a conserved basic residue and presence of acidic residues in the vestibule regions, conserved only in YfdC-α, were found to be responsible for high energy barriers for the anions to enter EcYfdC. Potential of mean force profiles generated for ammonia and ammonium ion revealed that EcYfdC can transport neutral solutes and could possibly be involved in the transport of cations analogous to the mechanism proposed for ammonium transporters. Although YfdC members belong to the FNT family, our studies strongly suggest that EcYfdC is not an anion channel. Absence or presence of specific charged residues at particular positions makes EcYfdC selective for neutral or possibly cationic substrates. Further experimental studies are needed to get a definitive answer to the question of the substrate selectivity of EcYfdC. This provides an example of membrane proteins from the same family transporting substrates of different chemical nature.

Cell-Free and Yeast-Based Production of the Malarial Lactate Transporter, PfFNT, Delivers Comparable Yield and Protein Quality

Cell-free protein production is an attractive alternative to cell-based expression. Rapid results, small-volume reactions, irrelevance of protein toxicity, flexibility, and openness of the system are strong points in favor of the cell-free system. However, the in vitro situation lacks the cellular quality control machinery comprising e.g., the translocon for inserting membrane proteins into lipid bilayers, and chaperon-assisted protein degradation pathways. Here, we compare yield and protein quality of the lactate transporter, PfFNT, from malaria parasites when produced in Pichia pastoris yeast, or in an Escherichia coli S30-extract-based cell-free system. Besides solubilization and correct folding, PfFNT requires oligomerization into homopentamers. We assessed PfFNT folding/oligomerization and function by transmission electron microscopy imaging, transport assays, and binding of small-molecule inhibitors. For the latter, we used chromatography of the PfFNT-inhibitor complex with dual-wavelength detection, and biolayer interferometry. Our data show, that PfFNT possesses an intrinsic capability for assuming the correct fold, oligomerization pattern, and functionality during in vitro translation. This competence depended on the detergent present in the cell-free reaction. The choice of detergent further affected purification and inhibitor binding. In conclusion, in the presence of a suitable detergent, cell-free systems are very well capable of producing high quality membrane proteins.

Formate-nitrite transporters carrying nonprotonatable amide amino acids instead of a central histidine maintain pH-dependent transport

Microbial formate-nitrite transporter-type proteins (FNT) exhibit dual transport functionality. At neutral pH, electrogenic anion currents are detectable, whereas upon acidification transport of the neutral, protonated monoacid predominates. Physiologically, FNT-mediated proton co-transport is vital when monocarboxylic acid products of the energy metabolism, such as l-lactate, are released from the cell. Accordingly, Plasmodium falciparum malaria parasites can be killed by small-molecule inhibitors of PfFNT. Two opposing hypotheses on the site of substrate protonation are plausible. The proton relay mechanism postulates proton transfer from a highly conserved histidine centrally positioned in the transport path. The dielectric slide mechanism assumes decreasing acidity of substrates entering the lipophilic vestibules and protonation via the bulk water. Here, we defined the transport mechanism of the FNT from the amoebiasis parasite Entamoeba histolytica, EhFNT, and also show that BtFdhC from Bacillus thuringiensis is a functional formate transporter. Both FNTs carry a nonprotonatable amide amino acid, asparagine or glutamine, respectively, at the central histidine position. Despite having a nonprotonatable residue, EhFNT displayed the same substrate selectivity for larger monocarboxylates including l-lactate, a low substrate affinity as is typical for FNTs, and, strikingly, proton motive force-dependent transport as observed for PfFNT harboring a central histidine. These results argue against a proton relay mechanism, indicating that substrate protonation must occur outside of the central histidine region, most likely in the vestibules. Furthermore, EhFNT is the sole annotated FNT in the Entamoeba genome suggesting that it could be a putative new drug target with similar utility as that of the malarial PfFNT.

The intracellular parasite Toxoplasma gondii harbors three druggable FNT-type formate and l-lactate transporters in the plasma membrane

Toxoplasma gondii is a globally prevalent parasitic protist. It is well-known for its ability to infect almost all nucleated vertebrate cells, which is reflected by its unique metabolic architecture. Its fast-growing tachyzoite stage catabolizes glucose via glycolysis to yield l-lactate as a major by-product that must be exported from the cell to prevent toxicity; the underlying mechanism remains to be elucidated, however. Herein, we report three formate-nitrite transporter (FNT)-type monocarboxylate/proton symporters located in the plasma membrane of the T. gondii tachyzoite stage. We observed that all three proteins transport both l-lactate and formate in a pH-dependent manner and are inhibited by 2-hydroxy-chromanones (a class of small synthetic molecules). We also show that these compounds pharmacologically inhibit T. gondii growth. Using a chemical biology approach, we identified the critical residues in the substrate-selectivity region of the parasite transporters that determine differential specificity and sensitivity toward both substrates and inhibitors. Our findings further indicate that substrate specificity in FNT family proteins from T. gondii has evolved such that a functional repurposing of prokaryotic-type transporters helps fulfill a critical metabolic role in a clinically important parasitic protist. In summary, we have identified and characterized the lactate transporters of T. gondii and have shown that compounds blocking the FNTs in this parasite can inhibit its growth, suggesting that these transporters could have utility as potential drug targets.

Targeting Channels and Transporters in Protozoan Parasite Infections

Infectious diseases caused by pathogenic protozoa are among the most significant causes of death in humans. Therapeutic options are scarce and massively challenged by the emergence of resistant parasite strains. Many of the current anti-parasite drugs target soluble enzymes, generate unspecific oxidative stress, or act by an unresolved mechanism within the parasite. In recent years, collections of drug-like compounds derived from large-scale phenotypic screenings, such as the malaria or pathogen box, have been made available to researchers free of charge boosting the identification of novel promising targets. Remarkably, several of the compound hits have been found to inhibit membrane proteins at the periphery of the parasites, i.e., channels and transporters for ions and metabolites. In this review, we will focus on the progress made on targeting channels and transporters at different levels and the potential for use against infections with apicomplexan parasites mainly Plasmodium spp. (malaria) and Toxoplasma gondii (toxoplasmosis), with kinetoplastids Trypanosoma brucei (sleeping sickness), Trypanosoma cruzi (Chagas disease), and Leishmania ssp. (leishmaniasis), and the amoeba Entamoeba histolytica (amoebiasis).

Introduction to the Special Issue on Malaria

This minireview series highlights recent developments in malaria research. The reviews cover diverse topics, from conventional antimalarial therapies and the strategies used to circumvent the emergence of drug resistance, to the latest approaches for the discovery and validation of new druggable targets and for the development of effective antimalarial vaccines.