Evolution of P-type ATPases

The role of interplay between the plant plasma membrane H+-ATPase and its lipid environment

The mechanisms behind the regulation of plasma membrane (PM) P-type H+-ATPase in plant cells mediated by lipid-protein interactions and lateral heterogeneity of the plasma membrane are discussed. This review will focus on 1) the structural organization and mechanisms of the catalytic cycle of the enzyme, 2) phosphorylation as the primary mechanism of pump regulation; 3) the possible role of lateral heterogeneity of the plasma membrane in this process, as well as 4) the role of lipids in the H+-ATPase biosynthesis and its delivery to the plasma membrane. In addition, 5) the potential role of membrane lipids in the H+-ATPase co-localisation with secondary active transporters is speculated.

Effect of Cations on ATP Binding to the N-domain of Na+, K+-ATPase

The nucleotide-binding domain (N-domain) of the Na+, K+-ATPase (NKA) is physicochemically characterized by a high content of Glu and Asp residues, resulting in a low isoelectric point (pI = 5.0). Acidic proteins are known to interact with cations. The analysis in silico revealed potential cation interaction sites in the NKA N-domain structure. The interaction with cations was tested in vitro by using a recombinant NKA N-domain. The N-domain contains two Trp residues at the protein surface, as determined by acrylamide-mediated fluorescence quenching, that are useful for structural studies through fluorescence changes. Intrinsic fluorescence of the N-domain was decreased by the presence of cations (Na+, K+, Ca2+) indicating an effect on the protein structure. ATP binding also decreased the N-domain intrinsic fluorescence, which allowed nucleotide affinity determination. In the presence of cations, the N-domain affinity for ATP was increased. Molecular docking of fluorescein isothiocyanate (FITC) with the N-domain showed two binding modes with the isothiocyanate group located 5-6 Å close to Lys485 and Lys506 in the nucleotide-binding site. The presence of ATP prevented the FITC covalent labeling of the N-domain demonstrating the competitive behavior for the binding site. It is proposed that cations interact with the N-domain structure and thereby modulate nucleotide (ATP) affinity and possibly affecting NKA catalysis.

Fungal Plasma Membrane H+-ATPase: Structure, Mechanism, and Drug Discovery

The fungal plasma membrane H+-ATPase (Pma1) pumps protons out of the cell to maintain the transmembrane electrochemical gradient and membrane potential. As an essential P-type ATPase uniquely found in fungi and plants, Pma1 is an attractive antifungal drug target. Two recent Cryo-EM studies on Pma1 have revealed its hexameric architecture, autoinhibitory and activation mechanisms, and proton transport mechanism. These structures provide new perspectives for the development of antifungal drugs targeting Pma1. In this article, we review the history of Pma1 structure determination, the latest structural insights into Pma1, and drug discoveries targeting Pma1.

Deficiencies in cluster-2 ALA lipid flippases result in salicylic acid-dependent growth reductions

P4 ATPases (i.e., lipid flippases) are eukaryotic enzymes that transport lipids across membrane bilayers. In plants, P4 ATPases are named Aminophospholipid ATPases (ALAs) and are organized into five phylogenetic clusters. Here we generated an Arabidopsis mutant lacking all five cluster-2 ALAs (ala8/9/10/11/12), which is the most highly expressed ALA subgroup in vegetative tissues. Plants harboring the quintuple knockout (KO) show rosettes that are 2.2-fold smaller and display chlorotic lesions. A similar but less severe phenotype was observed in an ala10/11 double KO. The growth and lesion phenotypes of ala8/9/10/11/12 mutants were reversed by expressing a NahG transgene, which encodes an enzyme that degrades salicylic acid (SA). A role for SA in promoting the lesion phenotype was further supported by quantitative PCR assays showing increased mRNA abundance for an SA-biosynthesis gene ISOCHORISMATE SYNTHASE 1 (ICS1) and two SA-responsive genes PATHOGENESIS-RELATED GENE 1 (PR1) and PR2. Lesion phenotypes were also reversed by growing plants in liquid media containing either low calcium (~0.1 mM) or high nitrogen concentrations (~24 mM), which are conditions known to suppress SA-dependent autoimmunity. Yeast-based fluorescent lipid uptake assays revealed that ALA10 and ALA11 display overlapping substrate specificities, including the transport of LysoPC signaling lipids. Together, these results establish that the biochemical functions of ALA8-12 are at least partially overlapping, and that deficiencies in cluster-2 ALAs result in an SA-dependent autoimmunity phenotype that has not been observed for flippase mutants with deficiencies in other ALA clusters.

Deep learning driven de novo drug design based on gastric proton pump structures

Existing drugs often suffer in their effectiveness due to detrimental side effects, low binding affinity or pharmacokinetic problems. This may be overcome by the development of distinct compounds. Here, we exploit the rich structural basis of drug-bound gastric proton pump to develop compounds with strong inhibitory potency, employing a combinatorial approach utilizing deep generative models for de novo drug design with organic synthesis and cryo-EM structural analysis. Candidate compounds that satisfy pharmacophores defined in the drug-bound proton pump structures, were designed in silico utilizing our deep generative models, a workflow termed Deep Quartet. Several candidates were synthesized and screened according to their inhibition potencies in vitro, and their binding poses were in turn identified by cryo-EM. Structures reaching up to 2.10 Å resolution allowed us to evaluate and re-design compound structures, heralding the most potent compound in this study, DQ-18 (N-methyl-4-((2-(benzyloxy)-5-chlorobenzyl)oxy)benzylamine), which shows a Ki value of 47.6 nM. Further high-resolution cryo-EM analysis at 2.08 Å resolution unambiguously determined the DQ-18 binding pose. Our integrated approach offers a framework for structure-based de novo drug development based on the desired pharmacophores within the protein structure.

Anionic Phospholipids Stimulate the Proton Pumping Activity of the Plant Plasma Membrane P-Type H+-ATPase

The activity of membrane proteins depends strongly on the surrounding lipid environment. Here, we characterize the lipid stimulation of the plant plasma membrane H+-ATPase Arabidopsis thaliana H+-ATPase isoform 2 (AHA2) upon purification and reconstitution into liposomes of defined lipid compositions. We show that the proton pumping activity of AHA2 is stimulated by anionic phospholipids, especially by phosphatidylserine. This activation was independent of the cytoplasmic C-terminal regulatory domain of the pump. Molecular dynamics simulations revealed several preferential contact sites for anionic phospholipids in the transmembrane domain of AHA2. These contact sites are partially conserved in functionally different P-type ATPases from different organisms, suggesting a general regulation mechanism by the membrane lipid environment. Our findings highlight the fact that anionic lipids play an important role in the control of H+-ATPase activity.

The Na+,K+-ATPase and its stoichiometric ratio: some thermodynamic speculations

 Almost seventy years after its discovery, the sodium-potassium adenosine triphosphatase (the sodium pump) located in the cell plasma membrane remains a source of novel mechanistic and physiologic findings. A noteworthy feature of this enzyme/transporter is its robust stoichiometric ratio under physiological conditions: it sequentially counter-transports three sodium ions and two potassium ions against their electrochemical potential gradients per each hydrolyzed ATP molecule. Here we summarize some present knowledge about the sodium pump and its physiological roles, and speculate whether energetic constraints may have played a role in the evolutionary selection of its characteristic stoichiometric ratio.

Mini-review: Lipid flippases as putative targets for biotechnological crop improvement

An increasing world population and drastic changes in weather conditions are challenging agricultural production. To face these challenges and ensure sustainable food production in the future, crop plants need to be improved to withstand several different biotic and abiotic stresses. Commonly, breeders select varieties that can tolerate a specific type of stress and then cross these varieties to stack beneficial traits. This strategy is time-consuming and strictly dependent on the stacked traits been genetically unlinked. Here, we revise the role of plant lipid flippases of the P4 ATPase family in stress-related responses with a special focus on the pleiotropic nature of their functions and discuss their suitability as biotechnological targets for crop improvement.

Structural Analysis and Diversity of Calmodulin-Binding Domains in Membrane and Intracellular Ca2+-ATPases

The plasma membrane and autoinhibited Ca²⁺-ATPases contribute to the Ca²⁺ homeostasis in a wide variety of organisms. The enzymatic activity of these pumps is stimulated by calmodulin, which interacts with the target protein through the calmodulin-binding domain (CaMBD). Most information about this region is related to all calmodulin modulated proteins, which indicates general chemical properties and there is no established relation between Ca²⁺ pump sequences and taxonomic classification. Thus, the aim of this study was to perform an in silico analysis of the CaMBD from several Ca²⁺-ATPases, in order to determine their diversity and to detect specific patterns and amino acid selection in different species. Patterns related to potential and confirmed CaMBD were detected using sequences retrieved from the literature. The occurrence of these patterns was determined across 120 sequences from 17 taxonomical classes, which were analyzed by a phylogenetic tree to establish phylogenetic groups. Predicted physicochemical characteristics including hydropathy and net charge were calculated for each group of sequences. 22 Ca²⁺-ATPases sequences from animals, unicellular eukaryotes, and plants were retrieved from bioinformatic databases. These sequences allow us to establish the Patterns 1(GQILWVRGLTRLQTQ), 3(KNPSLEALQRW), and 4(SRWRRLQAEHVKK), which are present at the beginning of putative CaMBD of metazoan, parasites, and land plants. A pattern 2 (IRVVNAFR) was consistently found at the end of most analyzed sequences. The amino acid preference in the CaMBDs changed depending on the phylogenetic groups, with predominance of several aliphatic and charged residues, to confer amphiphilic properties. The results here displayed show a conserved mechanism to contribute to the Ca²⁺ homeostasis across evolution and may help to detect putative CaMBDs.

Phosphorylation of the plasma membrane H+-ATPase AHA2 by BAK1 is required for ABA-induced stomatal closure in Arabidopsis

Stomatal opening is largely promoted by light-activated plasma membrane-localized proton ATPases (PM H+-ATPases), while their closure is mainly modulated by abscisic acid (ABA) signaling during drought stress. It is unknown whether PM H+-ATPases participate in ABA-induced stomatal closure. We established that BRI1-ASSOCIATED RECEPTOR KINASE 1 (BAK1) interacts with, phosphorylates and activates the major PM Arabidopsis H+-ATPase isoform 2 (AHA2). Detached leaves from aha2-6 single mutant Arabidopsis thaliana plants lost as much water as bak1-4 single and aha2-6 bak1-4 double mutants, with all three mutants losing more water than the wild-type (Columbia-0 [Col-0]). In agreement with these observations, aha2-6, bak1-4, and aha2-6 bak1-4 mutants were less sensitive to ABA-induced stomatal closure than Col-0, whereas the aha2-6 mutation did not affect ABA-inhibited stomatal opening under light conditions. ABA-activated BAK1 phosphorylated AHA2 at Ser-944 in its C-terminus and activated AHA2, leading to rapid H+ efflux, cytoplasmic alkalinization, and reactive oxygen species (ROS) accumulation, to initiate ABA signal transduction and stomatal closure. The phosphorylation-mimicking mutation AHA2S944D driven by its own promoter could largely compensate for the defective phenotypes of water loss, cytoplasmic alkalinization, and ROS accumulation in both aha2-6 and bak1-4 mutants. Our results uncover a crucial role of AHA2 in cytoplasmic alkalinization and ABA-induced stomatal closure during the plant's response to drought stress.

Structural Basis for Binding of Potassium-Competitive Acid Blockers to the Gastric Proton Pump

As specific inhibitors of the gastric proton pump, responsible for gastric acidification, K⁺-competitive acid blockers (P-CABs) have recently been utilized in the clinical treatment of gastric acid-related diseases in Asia. However, as these compounds have been developed based on phenotypic screening, their detailed binding poses are unknown. We show crystal and cryo-EM structures of the gastric proton pump in complex with four different P-CABs, tegoprazan, soraprazan, PF-03716556 and revaprazan, at resolutions reaching 2.8 Å. The structures describe molecular details of their interactions and are supported by functional analyses of mutations and molecular dynamics simulations. We reveal that revaprazan has a novel binding mode in which its tetrahydroisoquinoline moiety binds deep in the cation transport conduit. The mechanism of action of these P-CABs can now be evaluated at the molecular level, which will facilitate the rational development and improvement of currently available P-CABs to provide better treatment of acid-related gastrointestinal diseases.

Structure and activation mechanism of the hexameric plasma membrane H+-ATPase

The S. cerevisiae plasma membrane H+-ATPase, Pma1, is a P3A-type ATPase and the primary protein component of the membrane compartment of Pma1 (MCP). Like other plasma membrane H+-ATPases, Pma1 assembles and functions as a hexamer, a property unique to this subfamily among the larger family of P-type ATPases. It has been unclear how Pma1 organizes the yeast membrane into MCP microdomains, or why it is that Pma1 needs to assemble into a hexamer to establish the membrane electrochemical proton gradient. Here we report a high-resolution cryo-EM study of native Pma1 hexamers embedded in endogenous lipids. Remarkably, we found that the Pma1 hexamer encircles a liquid-crystalline membrane domain composed of 57 ordered lipid molecules. The Pma1-encircled lipid patch structure likely serves as the building block of the MCP. At pH 7.4, the carboxyl-terminal regulatory α-helix binds to the phosphorylation domains of two neighboring Pma1 subunits, locking the hexamer in the autoinhibited state. The regulatory helix becomes disordered at lower pH, leading to activation of the Pma1 hexamer. The activation process is accompanied by a 6.7 Å downward shift and a 40° rotation of transmembrane helices 1 and 2 that line the proton translocation path. The conformational changes have enabled us to propose a detailed mechanism for ATP-hydrolysis-driven proton pumping across the plasma membrane. Our structures will facilitate the development of antifungal drugs that target this essential protein.

Structural basis of the P4B ATPase lipid flippase activity

P4 ATPases are lipid flippases that are phylogenetically grouped into P4A, P4B and P4C clades. The P4A ATPases are heterodimers composed of a catalytic α-subunit and accessory β-subunit, and the structures of several heterodimeric flippases have been reported. The S. cerevisiae Neo1 and its orthologs represent the P4B ATPases, which function as monomeric flippases without a β-subunit. It has been unclear whether monomeric flippases retain the architecture and transport mechanism of the dimeric flippases. Here we report the structure of a P4B ATPase, Neo1, in its E1-ATP, E2P-transition, and E2P states. The structure reveals a conserved architecture as well as highly similar functional intermediate states relative to dimeric flippases. Consistently, structure-guided mutagenesis of residues in the proposed substrate translocation path disrupted Neo1’s ability to establish membrane asymmetry. These observations indicate that evolutionarily distant P4 ATPases use a structurally conserved mechanism for substrate transport.

The P4 ATPase lipid flippases play a crucial role in membrane biogenesis. Here the authors report the structure of the monomeric P4B ATPase Neo1 in several states, clarifying the mechanism of substrate transport.

Gastric proton pump with two occluded K+ engineered with sodium pump-mimetic mutations

The gastric H⁺,K⁺-ATPase mediates electroneutral exchange of 1H⁺/1K⁺ per ATP hydrolysed across the membrane. Previous structural analysis of the K⁺-occluded E2-P transition state of H⁺,K⁺-ATPase showed a single bound K⁺ at cation-binding site II, in marked contrast to the two K⁺ ions occluded at sites I and II of the closely-related Na⁺,K⁺-ATPase which mediates electrogenic 3Na⁺/2K⁺ translocation across the membrane. The molecular basis of the different K⁺ stoichiometry between these K⁺-counter-transporting pumps is elusive. We show a series of crystal structures and a cryo-EM structure of H⁺,K⁺-ATPase mutants with changes in the vicinity of site I, based on the structure of the sodium pump. Our step-wise and tailored construction of the mutants finally gave a two-K⁺ bound H⁺,K⁺-ATPase, achieved by five mutations, including amino acids directly coordinating K⁺ (Lys791Ser, Glu820Asp), indirectly contributing to cation-binding site formation (Tyr340Asn, Glu936Val), and allosterically stabilizing K⁺-occluded conformation (Tyr799Trp). This quintuple mutant in the K⁺-occluded E2-P state unambiguously shows two separate densities at the cation-binding site in its 2.6 Å resolution cryo-EM structure. These results offer new insights into how two closely-related cation pumps specify the number of K⁺ accommodated at their cation-binding site.

The gastric H⁺,K⁺-ATPase is a proton pump that creates the acidic environment of the stomach lumen, maintaining high proton gradient across the gastric mucosa cell membrane. Here, structural analysis of rationally designed H⁺,K⁺-ATPase mutants provides insight into this and other P-type ATPases cation binding stoichiometry and mechanisms.

Yeast YPK9 deficiency results in shortened replicative lifespan and sensitivity to hydrogen peroxide

YPK9/YOR291W of Saccharomyces cerevisiae encodes a vacuolar membrane protein. Previous research has suggested that Ypk9p is similar to the yeast P5-type ATPase Spf1p and that it plays a role in the sequestration of heavy metals. In addition, bioinformatics analysis has suggested that Ypk9p is a homolog of human ATP13A2, which encodes a protein of the subfamily of P5 ATPases. However, no specific function of Ypk9p has been described to date. In this study, we found, for the first time, that YPK9 is involved in the oxidative stress response and modulation of the replicative lifespan (RLS). We found that YPK9 deficiency confers sensitivity to the oxidative stress inducer hydrogen peroxide accompanied by increased intracellular ROS levels, decreased mitochondrial membrane potential, abnormal mitochondrial function, and increased incidence of early apoptosis in budding yeast. More importantly, YPK9 deficiency can lead to a shortened RLS. In addition, we found that overexpression of the catalase-encoding gene CTA1 can reverse the phenotypic abnormalities of the ypk9Δ yeast strain. Collectively, these findings highlight the involvement of Ypk9p in the oxidative stress response and modulation of RLS.

Clinical significance of P-class pumps in cancer

P-class pumps are specific ion transporters involved in maintaining intracellular/extracellular ion homeostasis, gene transcription, and cell proliferation and migration in all eukaryotic cells. The present review aimed to evaluate the role of P-type pumps [Na⁺/K⁺ ATPase (NKA), H⁺/K⁺ ATPase (HKA) and Ca2⁺-ATPase] in cancer cells across three fronts, namely structure, function and genetic expression. It has been shown that administration of specific P-class pumps inhibitors can have different effects by: i) Altering pump function; ii) inhibiting cell proliferation; iii) inducing apoptosis; iv) modifying metabolic pathways; and v) induce sensitivity to chemotherapy and lead to antitumor effects. For example, the NKA β2 subunit can be downregulated by gemcitabine, resulting in increased apoptosis of cancer cells. The sarcoendoplasmic reticulum calcium ATPase can be inhibited by thapsigargin resulting in decreased prostate tumor volume, whereas the HKA α subunit can be affected by proton pump inhibitors in gastric cancer cell lines, inducing apoptosis. In conclusion, the present review highlighted the central role of P-class pumps and their possible use and role as anticancer cellular targets for novel therapeutic chemical agents.

The CATP-8/P5A-type ATPase functions in multiple pathways during neuronal patterning

The assembly of neuronal circuits involves the migrations of neurons from their place of birth to their final location in the nervous system, as well as the coordinated growth and patterning of axons and dendrites. In screens for genes required for patterning of the nervous system, we identified the catp-8/P5A-ATPase as an important regulator of neural patterning. P5A-ATPases are part of the P-type ATPases, a family of proteins known to serve a conserved function as transporters of ions, lipids and polyamines in unicellular eukaryotes, plants, and humans. While the function of many P-type ATPases is relatively well understood, the function of P5A-ATPases in metazoans remained elusive. We show here, that the Caenorhabditis elegans ortholog catp-8/P5A-ATPase is required for defined aspects of nervous system development. Specifically, the catp-8/P5A-ATPase serves functions in shaping the elaborately sculpted dendritic trees of somatosensory PVD neurons. Moreover, catp-8/P5A-ATPase is required for axonal guidance and repulsion at the midline, as well as embryonic and postembryonic neuronal migrations. Interestingly, not all axons at the midline require catp-8/P5A-ATPase, although the axons run in the same fascicles and navigate the same space. Similarly, not all neuronal migrations require catp-8/P5A-ATPase. A CATP-8/P5A-ATPase reporter is localized to the ER in most, if not all, tissues and catp-8/P5A-ATPase can function both cell-autonomously and non-autonomously to regulate neuronal development. Genetic analyses establish that catp-8/P5A-ATPase can function in multiple pathways, including the Menorin pathway, previously shown to control dendritic patterning in PVD, and Wnt signaling, which functions to control neuronal migrations. Lastly, we show that catp-8/P5A-ATPase is required for localizing select transmembrane proteins necessary for dendrite morphogenesis. Collectively, our studies suggest that catp-8/P5A-ATPase serves diverse, yet specific, roles in different genetic pathways and may be involved in the regulation or localization of transmembrane and secreted proteins to specific subcellular compartments.

Protecting P-type plasma membrane H+-ATPases from ROS

P-type ATPase are ubiquitous transport proteins across all kingdoms of life. These proteins share a common mechanism involving phosphorylation of an invariant aspartate to facilitate movement of substrates from protons to phospholipids across cellular membranes. In this issue of the Biochemical Journal, Welle et al. identify a conserved cysteine near the functionally critical aspartate of P-type plasma membrane H+-ATPases that protects the protein from reactive oxygen species.

Isolation and characterization of a halophilic Modicisalibacter sp. strain Wilcox from produced water

We report the isolation a halophilic bacterium that degrades both aromatic and aliphatic hydrocarbons as the sole sources of carbon at high salinity from produced water. Phylogenetic analysis of 16S rRNA-gene sequences shows the isolate is a close relative of Modicisalibacter tunisiensis isolated from an oil-field water in Tunisia. We designate our isolate as Modicisalibacter sp. strain Wilcox. Genome analysis of strain Wilcox revealed the presence of a repertoire of genes involved in the metabolism of aliphatic and aromatic hydrocarbons. Laboratory culture studies corroborated the predicted hydrocarbon degradation potential. The strain degraded benzene, toluene, ethylbenzene, and xylenes at salinities ranging from 0.016 to 4.0 M NaCl, with optimal degradation at 1 M NaCl. Also, the strain degraded phenol, benzoate, biphenyl and phenylacetate as the sole sources of carbon at 2.5 M NaCl. Among aliphatic compounds, the strain degraded n-decane and n-hexadecane as the sole sources of carbon at 2.5 M NaCl. Genome analysis also predicted the presence of many heavy metal resistance genes including genes for metal efflux pumps, transport proteins, and enzymatic detoxification. Overall, due to its ability to degrade many hydrocarbons and withstand high salt and heavy metals, strain Wilcox may prove useful for remediation of produced waters.

The transport mechanism of P4 ATPase lipid flippases

P4 ATPase lipid flippases are ATP-driven transporters that translocate specific lipids from the exoplasmic to the cytosolic leaflet of biological membranes, thus establishing a lipid gradient between the two leaflets that is essential for many cellular processes. While substrate specificity, subcellular and tissue-specific expression, and physiological functions have been assigned to a number of these transporters in several organisms, the mechanism of lipid transport has been a topic of intense debate in the field. The recent publication of a series of structural models based on X-ray crystallography and cryo-EM studies has provided the first glimpse into how P4 ATPases have adapted the transport mechanism used by the cation-pumping family members to accommodate a substrate that is at least an order of magnitude larger than cations.

Mechanisms of Energy Transduction by Charge Translocating Membrane Proteins

Life relies on the constant exchange of different forms of energy, i.e., on energy transduction. Therefore, organisms have evolved in a way to be able to harvest the energy made available by external sources (such as light or chemical compounds) and convert these into biological useable energy forms, such as the transmembrane difference of electrochemical potential (Δμ̃). Membrane proteins contribute to the establishment of Δμ̃ by coupling exergonic catalytic reactions to the translocation of charges (electrons/ions) across the membrane. Irrespectively of the energy source and consequent type of reaction, all charge-translocating proteins follow two molecular coupling mechanisms: direct- or indirect-coupling, depending on whether the translocated charge is involved in the driving reaction. In this review, we explore these two coupling mechanisms by thoroughly examining the different types of charge-translocating membrane proteins. For each protein, we analyze the respective reaction thermodynamics, electron transfer/catalytic processes, charge-translocating pathways, and ion/substrate stoichiometries.

Highly exposed segment of the Spf1p P5A-ATPase near transmembrane M5 detected by limited proteolysis

The yeast Spf1p protein is a primary transporter that belongs to group 5 of the large family of P-ATPases. Loss of Spf1p function produces ER stress with alterations of metal ion and sterol homeostasis and protein folding, glycosylation and membrane insertion. The amino acid sequence of Spf1p shows the characteristic P-ATPase domains A, N, and P and the transmembrane segments M1-M10. In addition, Spf1p exhibits unique structures at its N-terminus (N-T region), including two putative additional transmembrane domains, and a large insertion connecting the P domain with transmembrane segment M5 (D region). Here we used limited proteolysis to examine the structure of Spf1p. A short exposure of Spf1p to trypsin or proteinase K resulted in the cleavage at the N and C terminal regions of the protein and abrogated the formation of the catalytic phosphoenzyme and the ATPase activity. In contrast, limited proteolysis of Spf1p with chymotrypsin generated a large N-terminal fragment containing most of the M4-M5 cytosolic loop, and a minor fragment containing the C-terminal region. If lipids were present during chymotryptic proteolysis, phosphoenzyme formation and ATPase activity were preserved. ATP slowed Spf1p proteolysis without detectable changes of the generated fragments. The analysis of the proteolytic peptides by mass spectrometry and Edman degradation indicated that the preferential chymotryptic site was localized near the cytosolic end of M5. The susceptibility to proteolysis suggests an unexpected exposure of this region of Spf1p that may be an intrinsic feature of P5A-ATPases.

Evolution of Plant Na+-P-Type ATPases: From Saline Environments to Land Colonization

Soil salinity is one of the major factors obstructing the growth and development of agricultural crops. Eukaryotes have two main transport systems involved in active Na⁺ removal: cation/H⁺ antiporters and Na⁺-P-type ATPases. Key transport proteins, Na⁺/K⁺-P-ATPases, are widely distributed among the different taxa families of pumps which are responsible for keeping cytosolic Na⁺ concentrations below toxic levels. Na⁺/K⁺-P-ATPases are considered to be absent in flowering plants. The data presented here are a complete inventory of P-type Na⁺/K⁺-P-ATPases in the major branches of the plant kingdom. We also attempt to elucidate the evolution of these important membrane pumps in plants in comparison with other organisms. We were able to observe the gradual replacement of the Na+-binding site to the Ca²⁺-binding site, starting with cyanobacteria and moving to modern land plants. Our results show that the α-subunit likely evolved from one common ancestor to bacteria, fungi, plants, and mammals, whereas the β-subunit did not evolve in green algae. In conclusion, our results strongly suggest the significant differences in the domain architecture and subunit composition of plant Na⁺/K⁺-P-ATPases depending on plant taxa and the salinity of the environment. The obtained data clarified and broadened the current views on the evolution of Na⁺/K⁺-P-ATPases. The results of this work would be helpful for further research on P-type ATPase functionality and physiological roles.

Transport mechanism of P4 ATPase phosphatidylcholine flippases

The P4 ATPases use ATP hydrolysis to transport large lipid substrates across lipid bilayers. The structures of the endosome- and Golgi-localized phosphatidylserine flippases—such as the yeast Drs2 and human ATP8A1—have recently been reported. However, a substrate-binding site on the cytosolic side has not been found, and the transport mechanisms of P4 ATPases with other substrates are unknown. Here, we report structures of the S. cerevisiae Dnf1–Lem3 and Dnf2–Lem3 complexes. We captured substrate phosphatidylcholine molecules on both the exoplasmic and cytosolic sides and found that they have similar structures. Unexpectedly, Lem3 contributes to substrate binding. The conformational transitions of these phosphatidylcholine transporters match those of the phosphatidylserine transporters, suggesting a conserved mechanism among P4 ATPases. Dnf1/Dnf2 have a unique P domain helix-turn-helix insertion that is important for function. Therefore, P4 ATPases may have retained an overall transport mechanism while evolving distinct features for different lipid substrates.

P-type Na+/K+ ATPases essential and nonessential for cellular homeostasis and insect pathogenicity of Beauveria bassiana

ENA1 and ENA2 are P-type IID/ENA Na+/K+-ATPases required for cellular homeostasis in yeasts but remain poorly understood in filamentous fungal insect pathogens. Here, we characterized seven genes encoding five ENA1/2 homologues (ENA1a-c and ENA2a/b) and two P-type IIC/NK Na+/K+-ATPases (NK1/2) in Beauveria bassiana, an insect-pathogenic fungus serving as a main source of fungal insecticides worldwide. Most of these genes were highly responsive to alkaline pH and Na+/K+ cues at transcription level. Cellular Na+, K+ and H+ homeostasis was disturbed only in the absence of ena1a or ena2b. The disturbed homeostasis featured acceleration of vacuolar acidification, elevation of cytosolic Na+/K+ level at pH 5.0 to 9.0, and stabilization of extracellular H+ level to initial pH 7.5 during a 5-day period of submerged incubation. Despite little defect in hyphal growth and asexual development, the Δena1a and Δena2b mutants were less tolerant to metal cations (Na+, K+, Li+, Zn2+, Mn2+ and Fe3+), cell wall perturbation, oxidation, non-cation hyperosmolarity and UVB irradiation, severely compromised in insect pathogenicity via normal cuticle infection, and attenuated in virulence via hemocoel injection. The deletion mutants of five other ENA and NK genes showed little change in vacuolar pH and all examined phenotypes. Therefore, only ENA1a and ENA2b evidently involved in both transmembrane and vacuolar activities are essential for cellular cation homeostasis, insect pathogenicity and multiple stress tolerance in B. bassiana. These findings provide a novel insight into ENA1a- and ENA2b-dependent vacuolar pH stability, cation-homeostatic process and fungal fitness to host insect and environment.

The SERCA residue Glu340 mediates interdomain communication that guides Ca2+ transport

We present a crystal structure, functional data, and molecular dynamics (MD) simulations of the sarco(endo)plasmic reticulum Ca²⁺-ATPase (SERCA) mutant E340A. The mutation slows Ca²⁺-binding kinetics, and the structural differences between wild type and E340A indicate that the mutation disrupts a central interdomain “communication hub” governing Ca²⁺ binding/dissociation. MD simulations reveal altered dynamics in regions mediating Ca²⁺ occlusion, a critical step in SERCA’s alternating access mechanism. The mutation stabilizes a more occluded state of the Ca²⁺ sites. The strict conservation of Glu340 among P-type ATPases is the result of its critical role in interdomain communication between the cytosolic headpiece and the transmembrane domain, ensuring a delicate balance between dynamics of ion binding, occlusion, and release—key steps in the transport process.

The sarco(endo)plasmic reticulum Ca²⁺-ATPase (SERCA) is a P-type ATPase that transports Ca²⁺ from the cytosol into the sarco(endo)plasmic reticulum (SR/ER) lumen, driven by ATP. This primary transport activity depends on tight coupling between movements of the transmembrane helices forming the two Ca²⁺-binding sites and the cytosolic headpiece mediating ATP hydrolysis. We have addressed the molecular basis for this intramolecular communication by analyzing the structure and functional properties of the SERCA mutant E340A. The mutated Glu340 residue is strictly conserved among the P-type ATPase family of membrane transporters and is located at a seemingly strategic position at the interface between the phosphorylation domain and the cytosolic ends of 5 of SERCA’s 10 transmembrane helices. The mutant displays a marked slowing of the Ca²⁺-binding kinetics, and its crystal structure in the presence of Ca²⁺ and ATP analog reveals a rotated headpiece, altered connectivity between the cytosolic domains, and an altered hydrogen bonding pattern around residue 340. Supported by molecular dynamics simulations, we conclude that the E340A mutation causes a stabilization of the Ca²⁺ sites in a more occluded state, hence displaying slowed dynamics. This finding underpins a crucial role of Glu340 in interdomain communication between the headpiece and the Ca²⁺-binding transmembrane region.

The Effect of Spring Water Geochemistry on Copper Proteins in Tengchong Hot Springs, China

Copper (Cu) is an essential trace metal cofactor for a variety of proteins; however, excess Cu is toxic to most organisms. Cu homeostasis is maintained by a complex machinery of Cu binding proteins that control the uptake, transport, sequestration, and efflux of Cu ions. Despite the importance of Cu binding proteins in electron transfer, substrate oxidation, superoxide dismutation, and denitrification, little information exists about microbial Cu utilization in extreme environments, where the geochemical conditions may affect Cu bioavailability. Using metagenomic data from 9 hot springs in Tengchong, China, which range in temperature from 42°C to 96°C and in pH from 2.3 to 9, the effects of pH, temperature, and spring geochemistry on the distribution of Cu binding domains of proteins and oxidoreductases were studied. Dissolved Cu and Cu binding domains were detected across all temperature and pH gradients. Cu binding domains of cytochrome c oxidase subunits, heavy-metal-associated domains, and nitrous oxide reductase were detected at all sites. DoxB, a quinol oxidase, and other quinol oxidase subunits were the dominant Cu binding oxidoreductase subunits present at low-pH and high-temperature sites, whereas cbb ₃-type cytochrome c oxidase subunits were dominant at high-pH and high-temperature sites. Additionally, aa ₃-type cytochrome c oxidase was more prominent than cbb ₃-type cytochrome c oxidase under circumneutral-pH conditions. This suggests that the type of cytochrome c oxidase pathway and the Cu proteins employed by microbes to carry out important functions such as energy acquisition and efflux of excess Cu are affected by the physicochemical conditions of the springs.IMPORTANCE Copper is present in a variety of proteins and is required to carry out essential functions by all organisms. However, in hot spring environments, copper availability may be limited due to the high temperatures and the wide range in pH. The significance of our research is in relating the physicochemical environment to the distribution of copper proteins across hot spring environments, which provides increased understanding of primary functions and adaptions in these environments.

Crystal structure of a human plasma membrane phospholipid flippase

ATP11C, a member of the P4-ATPase flippase, translocates phosphatidylserine from the outer to the inner plasma membrane leaflet, and maintains the asymmetric distribution of phosphatidylserine in the living cell. We present the crystal structures of a human plasma membrane flippase, ATP11C-CDC50A complex, in a stabilized E2P conformation. The structure revealed a deep longitudinal crevice along transmembrane helices continuing from the cell surface to the phospholipid occlusion site in the middle of the membrane. We observed that the extension of the crevice on the exoplasmic side is open, and the complex is therefore in an outward-open E2P state, similar to a recently reported cryo-EM structure of yeast flippase Drs2p-Cdc50p complex. We noted extra densities, most likely bound phosphatidylserines, in the crevice and in its extension to the extracellular side. One was close to the phosphatidylserine occlusion site as previously reported for the human ATP8A1-CDC50A complex, and the other in a cavity at the surface of the exoplasmic leaflet of the bilayer. Substitutions in either of the binding sites or along the path between them impaired specific ATPase and transport activities. These results provide evidence that the observed crevice is the conduit along that phosphatidylserine traverses from the outer leaflet to its occlusion site in the membrane and suggest that the exoplasmic cavity is important for phospholipid recognition. They also yield insights into how phosphatidylserine is incorporated from the outer leaflet of the plasma membrane into the transmembrane.

Genome-Wide Identification and Characterization of Apple P3A-Type ATPase Genes, with Implications for Alkaline Stress Responses

The P3A-type ATPases play crucial roles in various physiological processes via the generation of a transmembrane H+ gradient (∆pH). However, the P3A-type ATPase superfamily in apple remains relatively uncharacterized. In this study, 15 apple P3A-type ATPase genes were identified based on the new GDDH13 draft genome sequence. The exon-intron organization of these genes, the physical and chemical properties, and conserved motifs of the encoded enzymes were investigated. Analyses of the chromosome localization and ω values of the apple P3A-type ATPase genes revealed the duplicated genes were influenced by purifying selection pressure. Six clades and frequent old duplication events were detected. Moreover, the significance of differences in the evolutionary rates of the P3A-type ATPase genes were revealed. An expression analysis indicated that all of the P3A-type ATPase genes were specifically expressed in more than one tissue. The expression of one P3A-type ATPase gene (MD15G1108400) was significantly upregulated in response to alkaline stress. Furthermore, a subcellular localization assay indicated that MD15G1108400 is targeted to the plasma membrane. These results imply that MD15G1108400 may be involved in responses to alkaline stress. Our data provide insights into the molecular characteristics and evolutionary patterns of the apple P3A-type ATPase gene family and provide a theoretical foundation for future in-depth functional characterizations of P3A-type ATPase genes under alkaline conditions.

A single K+-binding site in the crystal structure of the gastric proton pump

The gastric proton pump (H⁺,K⁺-ATPase), a P-type ATPase responsible for gastric acidification, mediates electro-neutral exchange of H⁺ and K⁺ coupled with ATP hydrolysis, but with an as yet undetermined transport stoichiometry. Here we show crystal structures at a resolution of 2.5 Å of the pump in the E2-P transition state, in which the counter-transporting cation is occluded. We found a single K⁺ bound to the cation-binding site of the H⁺,K⁺-ATPase, indicating an exchange of 1H⁺/1K⁺ per hydrolysis of one ATP molecule. This fulfills the energy requirement for the generation of a six pH unit gradient across the membrane. The structural basis of K⁺ recognition is resolved and supported by molecular dynamics simulations, establishing how the H⁺,K⁺-ATPase overcomes the energetic challenge to generate an H⁺ gradient of more than a million-fold-one of the highest cation gradients known in mammalian tissue-across the membrane.

Mutations in ATP13A2 (PARK9) are associated with an amyotrophic lateral sclerosis-like phenotype, implicating this locus in further phenotypic expansion

BACKGROUND

Amyotrophic lateral sclerosis [1] is a genetically heterogeneous neurodegenerative disorder, characterized by late-onset degeneration of motor neurons leading to progressive limb and bulbar weakness, as well as of the respiratory muscles, which is the primary cause of disease fatality. To date, over 25 genes have been implicated as causative in ALS with C9orf72, SOD1, FUS, and TARDBP accounting for the majority of genetically positive cases.

RESULTS

We identified two patients of Italian and French ancestry with a clinical diagnosis of juvenile-onset ALS who were mutation-negative in any of the known ALS causative genes. Starting with the index case, a consanguineous family of Italian origin, we performed whole-exome sequencing and identified candidate pathogenic mutations in 35 genes, 27 of which were homozygous. We next parsed all candidates against a cohort of 3641 ALS cases; only ATP13A2 was found to harbor recessive changes, in a patient with juvenile-onset ALS, similar to the index case. In vivo complementation of ATP13A2 using a zebrafish surrogate model that focused on the assessment of motor neuron morphology and cerebellar integrity confirmed the role of this gene in central and peripheral nervous system maintenance and corroborated the damaging direction of effect of the change detected in the index case of this study.

CONCLUSIONS

We here expand the phenotypic spectrum associated with genetic variants in ATP13A2 that previously comprised Kufor-Rakeb syndrome, spastic paraplegia 78, and neuronal ceroid lipofuscinosis type 12 (CLN12), to also include juvenile-onset ALS, as supported by both genetic and functional data. Our findings highlight the importance of establishing a complete genetic profile towards obtaining an accurate clinical diagnosis.

Thermodynamic first law efficiency of membrane proteins

Proteins are nature's biomolecular machines. Proteins, such as transporters, pumps and motors, have complex function/operating-machinery/mechanisms, comparable to the macro-scaled machines that we encounter in our daily life. These proteins, as it is for their macro-scaled counterparts, convert (part of) other/various forms of energy into work. In this study, we are performing the first law analysis on a set of proteins, including the dopamine transporter, glycine transporters I and II, glutamate transporter, sodium-potassium pump and Ca²⁺ ATPase. Each of these proteins operates on a thermodynamic/mechanic cycle to perform their function. In each of these cycles, they receive energy from a source, convert part of this energy into work and reject the remaining part of the energy to the environment. Conservation of energy principle was applied to the thermodynamic/mechanic cycle of each protein, and thermodynamic first law efficiency was evaluated for each cycle, which shows how much of the energy input per cycle was converted into useful work. Interestingly, calculations based on experimental data indicate that proteins can operate under a range of efficiencies, which vary based on the extracellular and intracellular ion and substrate concentrations. The lowest observed first law efficiency was 50%, which is a very high value if compared to the efficiency of the macro-scaled heat engines we encounter in our daily lives.Communicated by Ramaswamy H. Sarma.

The Vacuolar Ca2+ ATPase Pump Pmc1p Is Required for Candida albicans Pathogenesis

Maintenance of Ca²⁺ homeostasis is important for fungal cells to respond to a multitude of stresses, as well as antifungal treatment, and for virulence in animal models. Here, we demonstrate that a P-type ATPase, Pmc1p, is required for Candida albicans to respond to a variety of stresses, affects azole susceptibility, and is required to sustain tissue invasive hyphal growth and to cause disease in a mouse model of disseminated infection. Defining the mechanisms responsible for maintaining proper Ca²⁺ homeostasis in this important human pathogen can ultimately provide opportunities to devise new chemotherapeutic interventions that dysregulate intracellular signaling and induce Ca²⁺ toxicity.

Calcium is a critically important secondary messenger of intracellular signal transduction in eukaryotes but must be maintained at low levels in the cytoplasm of resting cells to avoid toxicity. This is achieved by several pumps that actively transport excess cytoplasmic Ca²⁺ out of the cell across the plasma membrane and into other intracellular compartments. In fungi, the vacuole serves as the major storage site for excess Ca²⁺, with two systems actively transporting cytoplasmic calcium ions into the vacuole. The H⁺/Ca²⁺ exchanger, Vcx1p, harnesses the proton-motive force across the vacuolar membrane (generated by the V-ATPase) to drive Ca²⁺ transport, while the P-type ATPase Pmc1p uses ATP hydrolysis to translocate Ca²⁺ into the vacuole. Ca²⁺-dependent signaling is required for the prevalent human fungal pathogen Candida albicans to endure exposure to the azole antifungals and to cause disease within the mammalian host. The purpose of this study was to determine if the Pmc1p or Vcx1p Ca²⁺ pumps are required for C. albicans pathogenicity and if these pumps impact antifungal resistance. Our results indicate that Pmc1p is required by C. albicans to transition from yeast to hyphal growth, to form biofilms in vitro, and to cause disease in a mouse model of disseminated infection. Moreover, loss of Pmc1p function appears to enhance C. albicans azole tolerance in a temperature-dependent manner.

IMPORTANCE Maintenance of Ca²⁺ homeostasis is important for fungal cells to respond to a multitude of stresses, as well as antifungal treatment, and for virulence in animal models. Here, we demonstrate that a P-type ATPase, Pmc1p, is required for Candida albicans to respond to a variety of stresses, affects azole susceptibility, and is required to sustain tissue invasive hyphal growth and to cause disease in a mouse model of disseminated infection. Defining the mechanisms responsible for maintaining proper Ca²⁺ homeostasis in this important human pathogen can ultimately provide opportunities to devise new chemotherapeutic interventions that dysregulate intracellular signaling and induce Ca²⁺ toxicity.

Genomic Comparison of the P-ATPase Gene Family in Four Cotton Species and Their Expression Patterns in Gossypium hirsutum

Plant P-type H⁺-ATPase (P-ATPase) is a membrane protein existing in the plasma membrane that plays an important role in the transmembrane transport of plant cells. To understand the variety and quantity of P-ATPase proteins in different cotton species, we combined four databases from two diploid cotton species (Gossypium raimondii and G. arboreum) and two tetraploid cotton species (G. hirsutum and G. barbadense) to screen the P-ATPase gene family and resolved the evolutionary relationships between the former cotton species. We identified 53, 51, 99 and 98 P-ATPase genes from G. arboretum, G. raimondii, G. barbadense and G. hirsutum, respectively. The structural and phylogenetic analyses revealed that the gene structure was consistent between P-ATPase genes, with a close evolutionary relationship. The expression analysis of P-ATPase genes showed that many P-ATPase genes were highly expressed in various tissues and at different fiber developmental stages in G. hirsutum, suggesting that they have potential functions during growth and fiber development in cotton.

Parkinson disease related ATP13A2 evolved early in animal evolution

Several human P5-type transport ATPases are implicated in neurological disorders, but little is known about their physiological function and properties. Here, we investigated the relationship between the five mammalian P5 isoforms ATP13A1-5 in a comparative study. We demonstrated that ATP13A1-4 isoforms undergo autophosphorylation, which is a hallmark P-type ATPase property that is required for substrate transport. A phylogenetic analysis of P5 sequences revealed that ATP13A1 represents clade P5A, which is highly conserved between fungi and animals with one member in each investigated species. The ATP13A2-5 isoforms belong to clade P5B and diversified from one isoform in fungi and primitive animals to a maximum of four in mammals by successive gene duplication events in vertebrate evolution. We revealed that ATP13A1 localizes in the endoplasmic reticulum (ER) and experimentally demonstrate that ATP13A1 likely contains 12 transmembrane helices. Conversely, ATP13A2-5 isoforms reside in overlapping compartments of the endosomal system and likely contain 10 transmembrane helices, similar to what was demonstrated earlier for ATP13A2. ATP13A1 complemented a deletion of the yeast P5A ATPase SPF1, while none of ATP13A2-5 could complement either the loss of SPF1 or that of the single P5B ATPase YPK9 in yeast. Thus, ATP13A1 carries out a basic ER function similar to its yeast counterpart Spf1p that plays a role in ER related processes like protein folding and processing. ATP13A2-5 isoforms diversified in mammals and are expressed in the endosomal system where they may have evolved novel complementary or partially redundant functions. While most P5-type ATPases are widely expressed, some P5B-type ATPases (ATP13A4 and ATP13A5) display a more limited tissue distribution in the brain and epithelial glandular cells, where they may exert specialized functions. At least some P5B isoforms are of vital importance for the nervous system, since ATP13A2 and ATP13A4 are linked to respectively Parkinson disease and autism spectrum disorders.

Iron overload impact on P-ATPases

Iron is a chemical element that is active in the fundamental physiological processes for human life, but its burden can be toxic to the body, mainly because of the stimulation of membrane lipid peroxidation. For this reason, the action of iron on many ATPases has been studied, especially on P-ATPases, such as the Na⁺,K⁺-ATPase and the Ca²⁺-ATPase. On the Fe²⁺-ATPase activity, the free iron acts as an activator, decreasing the intracellular Fe²⁺ and playing a protection role for the cell. On the Ca²⁺-ATPase activity, the iron overload decreases the enzyme activity, raising the cytoplasmic Ca²⁺ and decreasing the sarco/endoplasmic reticulum and the Golgi apparatus Ca²⁺ concentrations, which could promote an enzyme oxidation, nitration, and fragmentation. However, the iron overload effect on the Na⁺,K⁺-ATPase may change according to the tissue expressions. On the renal cells, as well as on the brain and the heart, iron promotes an enzyme inactivation, whereas its effect on the erythrocytes seems to be the opposite, directly stimulating the ATPase activity, or stimulating it by signaling pathways involving ROS and PKC. Modulations in the ATPase activity may impair the ionic transportation, which is essential for cell viability maintenance, inducing irreversible damage to the cell homeostasis. Here, we will discuss about the iron overload effect on the P-ATPases, such as the Na⁺,K⁺-ATPase, the Ca²⁺-ATPase, and the Fe²⁺-ATPase.

Differential Roles for Six P-Type Calcium ATPases in Sustaining Intracellular Ca2+ Homeostasis, Asexual Cycle and Environmental Fitness of Beauveria bassiana

A global insight into the roles of multiple P-type calcium ATPase (CA) pumps in sustaining the life of a filamentous fungal pathogen is lacking. Here we elucidated the functions of five CA pumps (Eca1, Spf1 and PmcA/B/C) following previous characterization of Pmr1 in Beauveria bassiana, a fungal insect pathogen. The fungal CA pumps interacted at transcriptional level, at which singular deletions of five CA genes depressed eca1 expression by 76–98% and deletion of spf1 resulted in drastic upregulation of four CA genes by 36–50-fold. Intracellular Ca²⁺ concentration increased differentially in most deletion mutants exposed to the stresses of Ca²⁺, EDTA chelator, and/or endoplasmic reticulum and calcineurin inhibitors, accompanied with their changed sensitivities to not only the mentioned agents but also Fe²⁺, Cu²⁺ and Zn²⁺. Liquid culture acidification was delayed in the Δspf1, Δpmr1 and ΔpmcA mutants, coinciding well with altered levels of their extracellular lactic and oxalic acids. Moreover, all deletion mutants showed differential defects in conidial germination, vegetative growth, conidiation capacity, antioxidant activity, cell wall integrity, conidial UV-B resistance and/or virulence. Our results provide the first global insight into differential roles for six CA pumps in sustaining intracellular Ca²⁺ level, asexual cycle and environmental fitness of B. bassiana.

ALA6, a P4-type ATPase, Is Involved in Heat Stress Responses in Arabidopsis thaliana

Maintaining lipid membrane integrity is an essential aspect of plant tolerance to high temperature. P₄-type ATPases are responsible for flipping and stabilizing asymmetric phospholipids in membrane systems, though their functions in stress tolerance are not entirely clear. Aminophospholipid ATPase6 (ALA6) is a member of the P₄-type ATPase family, which has 12 members in Arabidopsis thaliana. Here, we show that a loss-of-function mutant of ALA6 (ala6) exhibits clear sensitivity to heat stress, including both basal and acquired thermotolerance treatments. Overexpression of ALA6 improves seedling resistance to heat stress, while mutated ALA6 transgenic plants, in which the conserved functional site of the ALA family has a point mutation, are still susceptible to heat stress like ala6 loss-of-function mutant. In addition, ala6 displays higher ion-leakage during heat treatment, suggesting that the lipid flippase activity of ALA6 plays a vital role in heat stress responses. Transcriptome analysis reveals differences in gene expression between ala6 and wild-type plants with or without heat stress. The differentially expressed genes are involved primarily in the physiological processes of stress response, cellular compartment maintenance, macromolecule stability and energy production. Our results suggest that ALA6 is crucial for the stability of membrane when plants suffer from high temperature stress.

Bacterial Cu(+)-ATPases: models for molecular structure-function studies

The early discovery of the human Cu(+)-ATPases and their link to Menkes and Wilson's diseases brought attention to the unique role of these transporters in copper homeostasis. The characterization of bacterial Cu(+)-ATPases has significantly furthered our understanding of the structure, selectivity and transport mechanism of these enzymes, as well as their interplay with other elements of Cu(+) distribution networks. This review focuses on the structural-functional insights that have emerged from studies of bacterial Cu(+)-ATPases at the molecular level and how these observations have contributed to drawing up a comprehensive picture of cellular copper homeostasis.

Directed evolution of a sphingomyelin flippase reveals mechanism of substrate backbone discrimination by a P4-ATPase

Phospholipid flippases in the type IV P-type ATPase (P4-ATPases) family establish membrane asymmetry and play critical roles in vesicular transport, cell polarity, signal transduction, and neurologic development. All characterized P4-ATPases flip glycerophospholipids across the bilayer to the cytosolic leaflet of the membrane, but how these enzymes distinguish glycerophospholipids from sphingolipids is not known. We used a directed evolution approach to examine the molecular mechanisms through which P4-ATPases discriminate substrate backbone. A mutagenesis screen in the yeast Saccharomyces cerevisiae has identified several gain-of-function mutations in the P4-ATPase Dnf1 that facilitate the transport of a novel lipid substrate, sphingomyelin. We found that a highly conserved asparagine (N220) in the first transmembrane segment is a key enforcer of glycerophospholipid selection, and specific substitutions at this site allow transport of sphingomyelin.

Copper homeostasis in Mycobacterium tuberculosis

Copper (Cu) is a trace element essential for the growth and development of almost all organisms, including bacteria. However, Cu overload in most systems is toxic. Studies show Cu accumulates in macrophage phagosomes infected with bacteria, suggesting Cu provides an innate immune mechanism to combat invading pathogens. To counteract the host-supplied Cu, increasing evidence suggests that bacteria have evolved Cu resistance mechanisms to facilitate their pathogenesis. In particular, Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis, has evolved multiple pathways to respond to Cu. Here, we summarize what is currently known about Cu homeostasis in Mtb and discuss potential sources of Cu encountered by this and other pathogens in a mammalian host.

Inhibition of the Formation of the Spf1p Phosphoenzyme by Ca2

P5-ATPases are important for processes associated with the endosomal-lysosomal system of eukaryotic cells. In humans, the loss of function of P5-ATPases causes neurodegeneration. In the yeastSaccharomyces cerevisiae, deletion of P5-ATPase Spf1p gives rise to endoplasmic reticulum stress. The reaction cycle of P5-ATPases is poorly characterized. Here, we showed that the formation of the Spf1p catalytic phosphoenzyme was fast in a reaction medium containing ATP, Mg(2+), and EGTA. Low concentrations of Ca(2+)in the phosphorylation medium decreased the rate of phosphorylation and the maximal level of phosphoenzyme. Neither Mn(2+)nor Mg(2+)had an inhibitory effect on the formation of the phosphoenzyme similar to that of Ca(2+) TheKmfor ATP in the phosphorylation reaction was ∼1 μmand did not significantly change in the presence of Ca(2+) Half-maximal phosphorylation was attained at 8 μmMg(2+), but higher concentrations partially protected from Ca(2+)inhibition. In conditions similar to those used for phosphorylation, Ca(2+)had a small effect accelerating dephosphorylation and minimally affected ATPase activity, suggesting that the formation of the phosphoenzyme was not the limiting step of the ATP hydrolytic cycle.

The magnesium transporter A is activated by cardiolipin and is highly sensitive to free magnesium in vitro

The magnesium transporter A (MgtA) is a specialized P-type ATPase, believed to import Mg²⁺ into the cytoplasm. In Salmonella typhimurium and Escherichia coli, the virulence determining two-component system PhoQ/PhoP regulates the transcription of mgtA gene by sensing Mg²⁺ concentrations in the periplasm. However, the factors that affect MgtA function are not known. This study demonstrates, for the first time, that MgtA is highly dependent on anionic phospholipids and in particular, cardiolipin. Colocalization studies confirm that MgtA is found in the cardiolipin lipid domains in the membrane. The head group of cardiolipin plays major role in activation of MgtA suggesting that cardiolipin may act as a Mg²⁺ chaperone for MgtA. We further show that MgtA is highly sensitive to free Mg²⁺ (Mg²⁺_free) levels in the solution. MgtA is activated when the Mg²⁺_free concentration is reduced below 10 μM and is strongly inhibited above 1 mM, indicating that Mg²⁺_free acts as product inhibitor. Combined, our findings conclude that MgtA may act as a sensor as well as a transporter of Mg²⁺.

DOI:http://dx.doi.org/10.7554/eLife.11407.001

Magnesium is an essential element for living cells, meaning that organisms from bacteria to humans need magnesium to survive. All cells are surrounded by a membrane made of fatty molecules called lipids, which is also embedded with proteins. Magnesium, like other metal ions, is transported inside cells across the cell’s membrane by specific membrane proteins.

A species of gut bacteria called E. coli has two separate magnesium transport systems: one that works at high concentrations of magnesium and one at lower concentrations. The latter system involves a membrane protein called magnesium transporter A (or MgtA for short), which works like a molecular pump. However, it was not known exactly how this transporter was affected by magnesium nor how sensitive it was to this divalent metal ion. It was also unclear whether MgtA worked alone in the bacterial membrane or if it worked in conjunction with other molecules.

Now Subramani et al. have managed to show that MgtA can sense magnesium ions down to micromolar concentrations, which is the equivalent to a pinch (1 gram) of magnesium salt in 10,000 liters of water. The experiments also showed that this detection system depended on a specific lipid molecule in the membrane called cardiolipin. MgtA and cardiolipin were found together in the membrane of living E. coli suggesting that the two do indeed work together.

The discovery that a membrane transporter that pumps ions needs cardiolipin to work suggests that cells could indirectly control the movement of ions by changing the levels of specific lipids in their membranes. Subramani et al. now hope to use techniques, such as X-ray crystallography, to visualize how magnesium and cardiolipin bind to MtgA and explore how the three molecules work together as a complete system. Information about these interactions could in the future help researchers understand how these bacteria try to protect themself in the hostile environment in the human gut or cells of the immune systems. Further studies of this system could be used to develop biological sensors for magnesium or to design antibiotics that interfere with the magnesium transporter to treat bacterial infections.

DOI:http://dx.doi.org/10.7554/eLife.11407.002

P4-ATPases as Phospholipid Flippases-Structure, Function, and Enigmas

P4-ATPases comprise a family of P-type ATPases that actively transport or flip phospholipids across cell membranes. This generates and maintains membrane lipid asymmetry, a property essential for a wide variety of cellular processes such as vesicle budding and trafficking, cell signaling, blood coagulation, apoptosis, bile and cholesterol homeostasis, and neuronal cell survival. Some P4-ATPases transport phosphatidylserine and phosphatidylethanolamine across the plasma membrane or intracellular membranes whereas other P4-ATPases are specific for phosphatidylcholine. The importance of P4-ATPases is highlighted by the finding that genetic defects in two P4-ATPases ATP8A2 and ATP8B1 are associated with severe human disorders. Recent studies have provided insight into how P4-ATPases translocate phospholipids across membranes. P4-ATPases form a phosphorylated intermediate at the aspartate of the P-type ATPase signature sequence, and dephosphorylation is activated by the lipid substrate being flipped from the exoplasmic to the cytoplasmic leaflet similar to the activation of dephosphorylation of Na(+)/K(+)-ATPase by exoplasmic K(+). How the phospholipid is translocated can be understood in terms of a peripheral hydrophobic gate pathway between transmembrane helices M1, M3, M4, and M6. This pathway, which partially overlaps with the suggested pathway for migration of Ca(2+) in the opposite direction in the Ca(2+)-ATPase, is wider than the latter, thereby accommodating the phospholipid head group. The head group is propelled along against its concentration gradient with the hydrocarbon chains projecting out into the lipid phase by movement of an isoleucine located at the position corresponding to an ion binding glutamate in the Ca(2+)- and Na(+)/K(+)-ATPases. Hence, the P4-ATPase mechanism is quite similar to the mechanism of these ion pumps, where the glutamate translocates the ions by moving like a pump rod. The accessory subunit CDC50 may be located in close association with the exoplasmic entrance of the suggested pathway, and possibly promotes the binding of the lipid substrate. This review focuses on properties of mammalian and yeast P4-ATPases for which most mechanistic insight is available. However, the structure, function and enigmas associated with mammalian and yeast P4-ATPases most likely extend to P4-ATPases of plants and other organisms.

Calcium-ATPases: Gene disorders and dysregulation in cancer

Ca(2+)-ATPases belonging to the superfamily of P-type pumps play an important role in maintaining low, nanomolar cytoplasmic Ca(2+) levels at rest and priming organellar stores, including the endoplasmic reticulum, Golgi, and secretory vesicles with high levels of Ca(2+) for a wide range of signaling functions. In this review, we introduce the distinct subtypes of Ca(2+)-ATPases and their isoforms and splice variants and provide an overview of their specific cellular roles as they relate to genetic disorders and cancer, with a particular emphasis on recent findings on the secretory pathway Ca(2+)-ATPases (SPCA). Mutations in human ATP2A2, ATP2C1 genes, encoding housekeeping isoforms of the endoplasmic reticulum (SERCA2) and secretory pathway (SPCA1) pumps, respectively, confer autosomal dominant disorders of the skin, whereas mutations in other isoforms underlie various muscular, neurological, or developmental disorders. Emerging evidence points to an important function of dysregulated Ca(2+)-ATPase expression in cancers of the colon, lung, and breast where they may serve as markers of differentiation or novel targets for therapeutic intervention. We review the mechanisms underlying the link between calcium homeostasis and cancer and discuss the potential clinical relevance of these observations. This article is part of a Special Issue entitled: Calcium and Cell Fate. Guest Editors: Jacques Haiech, Claus Heizmann, Joachim Krebs, Thierry Capiod and Olivier Mignen.

A P4-ATPase gene GbPATP of cotton confers chilling tolerance in plants

Members of the P4 subfamily of P-type ATPases are implicated in generating lipid asymmetry between the two lipid leaflets of the plasma membrane in Arabidopsis and are important for resistance to low temperatures, but the function of P4-ATPases in cotton remains unclear. In this study, we found using quantitative reverse transcription-PCR analysis that the expression of the P4-ATPase gene GbPATP in cotton was induced at low temperatures. In addition, GbPATP-silenced cotton plants were more sensitive to low temperatures and exhibited greater malondialdehyde (MDA) content and lower catalase (CAT) activity than the control plants. GbPATP transgenic tobacco plants showed better chilling tolerance, had a lower MDA content and had higher CAT activity than wild-type plants under low-temperature treatment. The green fluorescent protein (GFP)-GbPATP fusion protein was found to be localized to the cell plasma membrane. Collectively, the results suggest that GbPATP functions as a P4-ATPase and plays an important role in improving chilling tolerance in plant.