Crystal structure of the potassium-importing KdpFABC membrane complex

Bacterial cell volume regulation and the importance of cyclic di-AMP

SUMMARYNucleotide-derived second messengers are present in all domains of life. In prokaryotes, most of their functionality is associated with general lifestyle and metabolic adaptations, often in response to environmental fluctuations of physical parameters. In the last two decades, cyclic di-AMP has emerged as an important signaling nucleotide in many prokaryotic lineages, including Firmicutes, Actinobacteria, and Cyanobacteria. Its importance is highlighted by the fact that both the lack and overproduction of cyclic di-AMP affect viability of prokaryotes that utilize cyclic di-AMP, and that it generates a strong innate immune response in eukaryotes. In bacteria that produce the second messenger, most molecular targets of cyclic di-AMP are associated with cell volume control. Besides, other evidence links the second messenger to cell wall remodeling, DNA damage repair, sporulation, central metabolism, and the regulation of glycogen turnover. In this review, we take a biochemical, quantitative approach to address the main cellular processes that are directly regulated by cyclic di-AMP and show that these processes are very connected and require regulation of a similar set of proteins to which cyclic di-AMP binds. Altogether, we argue that cyclic di-AMP is a master regulator of cell volume and that other cellular processes can be connected with cyclic di-AMP through this core function. We further highlight important directions in which the cyclic di-AMP field has to develop to gain a full understanding of the cyclic di-AMP signaling network and why some processes are regulated, while others are not.

KdpD is a tandem serine histidine kinase that controls K+ pump KdpFABC transcriptionally and post-translationally

Two-component systems, consisting of a histidine kinase and a response regulator, serve signal transduction in bacteria, often regulating transcription in response to environmental stimuli. Here, we identify a tandem serine histidine kinase function for KdpD, previously described as a histidine kinase of the KdpDE two-component system, which controls production of the potassium pump KdpFABC. We show that KdpD additionally mediates an inhibitory serine phosphorylation of KdpFABC at high potassium levels, using not its C-terminal histidine kinase domain but an N-terminal atypical serine kinase domain. Sequence analysis of KdpDs from different species highlights that some KdpDs are much shorter than others. We show that, while Escherichia coli KdpD's atypical serine kinase domain responds directly to potassium levels, a shorter version from Deinococcus geothermalis is controlled by second messenger cyclic di-AMP. Our findings add to the growing functional diversity of sensor kinases while simultaneously expanding the framework for regulatory mechanisms in bacterial potassium homeostasis.

Enhancing coevolutionary signals in protein-protein interaction prediction through clade-wise alignment integration

Protein-protein interactions (PPIs) play essential roles in most biological processes. The binding interfaces between interacting proteins impose evolutionary constraints that have successfully been employed to predict PPIs from multiple sequence alignments (MSAs). To construct MSAs, critical choices have to be made: how to ensure the reliable identification of orthologs, and how to optimally balance the need for large alignments versus sufficient alignment quality. Here, we propose a divide-and-conquer strategy for MSA generation: instead of building a single, large alignment for each protein, multiple distinct alignments are constructed under distinct clades in the tree of life. Coevolutionary signals are searched separately within these clades, and are only subsequently integrated using machine learning techniques. We find that this strategy markedly improves overall prediction performance, concomitant with better alignment quality. Using the popular DCA algorithm to systematically search pairs of such alignments, a genome-wide all-against-all interaction scan in a bacterial genome is demonstrated. Given the recent successes of AlphaFold in predicting direct PPIs at atomic detail, a discover-and-refine approach is proposed: our method could provide a fast and accurate strategy for pre-screening the entire genome, submitting to AlphaFold only promising interaction candidates-thus reducing false positives as well as computation time.

Magnesium Transporter MgtA revealed as a Dimeric P-type ATPase

Magnesium (Mg2+) uptake systems are present in all domains of life given the vital role of this ion. Bacteria acquire Mg2+ via conserved Mg2+ channels and transporters. The transporters are required for growth when Mg2+ is limiting or during bacterial pathogenesis, but, despite their significance, there are no known structures for these transporters. Here we report the first structure of the Mg2+ transporter MgtA solved by single particle cryo-electron microscopy (cryo-EM). Using mild membrane extraction, we obtained high resolution structures of both a homodimeric form (2.9 Å), the first for a P-type ATPase, and a monomeric form (3.6 Å). Each monomer unit of MgtA displays a structural architecture that is similar to other P-type ATPases with a transmembrane domain and two soluble domains. The dimer interface consists of contacts between residues in adjacent soluble nucleotide binding and phosphotransfer regions of the haloacid dehalogenase (HAD) domain. We suggest oligomerization is a conserved structural feature of the diverse family of P-type ATPase transporters. The ATP binding site and conformational dynamics upon nucleotide binding to MgtA were characterized using a combination of cryo-EM, molecular dynamics simulations, hydrogen-deuterium exchange mass spectrometry, and mutagenesis. Our structure also revealed a Mg2+ ion in the transmembrane segments, which, when combined with sequence conservation and mutagenesis studies, allowed us to propose a model for Mg2+ transport across the lipid bilayer. Finally, our work revealed the N-terminal domain structure and cytoplasmic Mg2+ binding sites, which have implications for related P-type ATPases defective in human disease.

Phosphatase A1 accessory protein PlaS from Serratia marcescens controls cell membrane permeability, fluidity, hydrophobicity, and fatty acid composition in Escherichia coli BL21

Phospholipase A1 (PlaA) plays a pivotal role in diverse applications within the food and biochemical medical industries. Herein, we investigate the impact of the accessory protein encoded by plaS from Serratia marcescens on PlaA activity in Escherichia coli. Notably, PlaS demonstrates the ability to enhance PlaA activity while concurrently exhibiting inhibitory effects on the growth of E. coli BL21 (DE3). Our study revolves around probing the inhibitory action of PlaS on E. coli BL21 (DE3). PlaS exhibits a propensity to heighten both the permeability of outer and inner cell membranes, leading to concomitant reductions in membrane fluidity and surface hydrophobicity. This phenomenon is validated through scanning electron microscopy (SEM) analysis, which highlights PlaS's capacity to compromise membrane integrity. Moreover, through a comprehensive comparative transcriptomic sequencing approach, we identify four down-regulated genes (galM, ybhC, ldtC, and kdpB) alongside two up-regulated genes (rbsB and degP). These genes are intricately associated with processes such as cell membrane synthesis and modification, energy metabolism, and transmembrane transport. Our investigation unveils the intricate gene-level mechanisms underpinning PlaS-mediated growth inhibition and membrane disruption. Consequently, our findings serve as a significant reference for the elucidation of membrane protein mechanisms, shedding light on potential avenues for future exploration.

High-throughput computational discovery of inhibitory protein fragments with AlphaFold

Peptides can bind to specific sites on larger proteins and thereby function as inhibitors and regulatory elements. Peptide fragments of larger proteins are particularly attractive for achieving these functions due to their inherent potential to form native-like binding interactions. Recently developed experimental approaches allow for high-throughput measurement of protein fragment inhibitory activity in living cells. However, it has thus far not been possible to predict de novo which of the many possible protein fragments bind their protein targets, let alone act as inhibitors. We have developed a computational method, FragFold, that employs AlphaFold to predict protein fragment binding to full-length protein targets in a high-throughput manner. Applying FragFold to thousands of fragments tiling across diverse proteins revealed peaks of predicted binding along each protein sequence. These predictions were compared with experimentally measured peaks of inhibitory activity in E. coli. We establish that our approach is a sensitive predictor of protein fragment function: Evaluating inhibitory fragments derived from known protein-protein interaction interfaces, we found 87% were predicted by FragFold to bind in a native-like mode. Across full protein sequences, 68% of FragFold-predicted binding peaks match experimentally measured inhibitory peaks. This is true even when the underlying inhibitory mechanism is unclear from existing structural data, and we find FragFold is able to predict novel binding modes for inhibitory fragments of unknown structure, explaining previous genetic and biochemical data for these fragments. The success rate of FragFold demonstrates that this computational approach should be broadly applicable for discovering inhibitory protein fragments across proteomes.

P-type ATPases: Many more enigmas left to solve

P-type ATPases constitute a large ancient super-family of primary active pumps that have diverse substrate specificities ranging from H+ to phospholipids. The significance of these enzymes in biology cannot be overstated. They are structurally related, and their catalytic cycles alternate between high- and low-affinity conformations that are induced by phosphorylation and dephosphorylation of a conserved aspartate residue. In the year 1988, all P-type sequences available by then were analyzed and five major families, P1 to P5, were identified. Since then, a large body of knowledge has accumulated concerning the structure, function, and physiological roles of members of these families, but only one additional family, P6 ATPases, has been identified. However, much is still left to be learned. For each family a few remaining enigmas are presented, with the intention that they will stimulate interest in continued research in the field. The review is by no way comprehensive and merely presents personal views with a focus on evolution.

The First Quarter Century of the Dense Alignment Surface Transmembrane Prediction Method

The dense alignment surface (DAS) transmembrane (TM) prediction method was first published more than 25 years ago. DAS was the one of the earliest tools to discriminate TM proteins from globular ones and to predict the sequence positions of TM helices in proteins with high accuracy from their amino acid sequence alone. The algorithmic improvements that followed in 2002 (DAS-TMfilter) made it one of the best performing tools among those relying on local sequence information for TM prediction. Since then, many more experimental data about membrane proteins (including thousands of 3D structures of membrane proteins) have accumulated but there has been no significant improvement concerning performance in the area of TM helix prediction tools. Here, we report a new implementation of the DAS-TMfilter prediction web server. We reevaluated the performance of the method using a five-times-larger, updated test dataset. We found that the method performs at essentially the same accuracy as the original even without any change to the parametrization of the program despite the much larger dataset. Thus, the approach captures the physico-chemistry of TM helices well, essentially solving this scientific problem.

The Potassium Efflux System Kef: Bacterial Protection against Toxic Electrophilic Compounds

Kef couples the potassium efflux with proton influx in gram-negative bacteria. The resulting acidification of the cytosol efficiently prevents the killing of the bacteria by reactive electrophilic compounds. While other degradation pathways for electrophiles exist, Kef is a short-term response that is crucial for survival. It requires tight regulation since its activation comes with the burden of disturbed homeostasis. Electrophiles, entering the cell, react spontaneously or catalytically with glutathione, which is present at high concentrations in the cytosol. The resulting glutathione conjugates bind to the cytosolic regulatory domain of Kef and trigger activation while the binding of glutathione keeps the system closed. Furthermore, nucleotides can bind to this domain for stabilization or inhibition. The binding of an additional ancillary subunit, called KefF or KefG, to the cytosolic domain is required for full activation. The regulatory domain is termed K⁺ transport-nucleotide binding (KTN) or regulator of potassium conductance (RCK) domain, and it is also found in potassium uptake systems or channels in other oligomeric arrangements. Bacterial RosB-like transporters and K⁺ efflux antiporters (KEA) of plants are homologs of Kef but fulfill different functions. In summary, Kef provides an interesting and well-studied example of a highly regulated bacterial transport system.

Osmotic stress responses and the biology of the second messenger c-di-AMP in Streptomyces

Streptomyces are prolific antibiotic producers that thrive in soil, where they encounter diverse environmental cues, including osmotic challenges caused by rainfall and drought. Despite their enormous value in the biotechnology sector, which often relies on ideal growth conditions, how Streptomyces react and adapt to osmotic stress is heavily understudied. This is likely due to their complex developmental biology and an exceptionally broad number of signal transduction systems. With this review, we provide an overview of Streptomyces' responses to osmotic stress signals and draw attention to open questions in this research area. We discuss putative osmolyte transport systems that are likely involved in ion balance control and osmoadaptation and the role of alternative sigma factors and two-component systems (TCS) in osmoregulation. Finally, we highlight the current view on the role of the second messenger c-di-AMP in cell differentiation and the osmotic stress responses with specific emphasis on the two models, S. coelicolor and S. venezuelae.

Two Trk/Ktr/HKT-type potassium transporters, TrkG and TrkH, perform distinct functions in Escherichia coli K-12

Escherichia coli K-12 possesses two versions of Trk/Ktr/HKT-type potassium ion (K⁺) transporters, TrkG and TrkH. The current paradigm is that TrkG and TrkH have largely identical characteristics, and little information is available regarding their functional differences. Here, we show using cation uptake experiments with K⁺ transporter knockout mutants that TrkG and TrkH have distinct ion transport activities and physiological roles. K⁺-transport by TrkG required Na⁺, whereas TrkH-mediated K⁺ uptake was not affected by Na⁺. An aspartic acid located five residues away from a critical glycine in the third pore-forming region might be involved in regulation of Na⁺-dependent activation of TrkG. In addition, we found that TrkG but not TrkH had Na⁺ uptake activity. Our analysis of K⁺ transport mutants revealed that TrkH supported cell growth more than TrkG; however, TrkG was able to complement loss of TrkH-mediated K⁺ uptake in E. coli. Furthermore, we determined that transcription of trkG in E. coli was downregulated but not completely silenced by the xenogeneic silencing factor H-NS (histone-like nucleoid structuring protein or heat-stable nucleoid-structuring protein). Taken together, the transport function of TrkG is clearly distinct from that of TrkH, and TrkG seems to have been accepted by E. coli during evolution as a K⁺ uptake system that coexists with TrkH.

Dimerisation of the Yeast K+ Translocation Protein Trk1 Depends on the K+ Concentration

In baker's yeast (Saccharomyces cerevisiae), Trk1, a member of the superfamily of K-transporters (SKT), is the main K⁺ uptake system under conditions when its concentration in the environment is low. Structurally, Trk1 is made up of four domains, each similar and homologous to a K-channel α subunit. Because most K-channels are proteins containing four channel-building α subunits, Trk1 could be functional as a monomer. However, related SKT proteins TrkH and KtrB were crystallised as dimers, and for Trk1, a tetrameric arrangement has been proposed based on molecular modelling. Here, based on Bimolecular Fluorescence Complementation experiments and single-molecule fluorescence microscopy combined with molecular modelling; we provide evidence that Trk1 can exist in the yeast plasma membrane as a monomer as well as a dimer. The association of monomers to dimers is regulated by the K⁺ concentration.

Mapping functional regions of essential bacterial proteins with dominant-negative protein fragments

Massively parallel measurements of dominant-negative inhibition by protein fragments have been used to map protein interaction sites and discover peptide inhibitors. However, the underlying principles governing fragment-based inhibition have thus far remained unclear. Here, we adapted a high-throughput inhibitory fragment assay for use in Escherichia coli, applying it to a set of 10 essential proteins. This approach yielded single amino acid resolution maps of inhibitory activity, with peaks localized to functionally important interaction sites, including oligomerization interfaces and folding contacts. Leveraging these data, we performed a systematic analysis to uncover principles of fragment-based inhibition. We determined a robust negative correlation between susceptibility to inhibition and cellular protein concentration, demonstrating that inhibitory fragments likely act primarily by titrating native protein interactions. We also characterized a series of trade-offs related to fragment length, showing that shorter peptides allow higher-resolution mapping but suffer from lower inhibitory activity. We employed an unsupervised statistical analysis to show that the inhibitory activities of protein fragments are largely driven not by generic properties such as charge, hydrophobicity, and secondary structure, but by the more specific characteristics of their bespoke macromolecular interactions. Overall, this work demonstrates fundamental characteristics of inhibitory protein fragment function and provides a foundation for understanding and controlling protein interactions in vivo.

The PTS Ntr -KdpDE-KdpFABC Pathway Contributes to Low Potassium Stress Adaptation and Competitive Nodulation of Sinorhizobium fredii

In all ecological niches, potassium is actively consumed by diverse prokaryotes and their interacting eukaryote hosts. It is only just emerging that potassium is a key player in host-pathogen interactions, and the role of potassium in mutualistic interactions remains largely unknown.

Small Proteins; Big Questions

In recent years, there has been increased appreciation that a whole category of proteins, small proteins of around 50 amino acids or fewer in length, has been missed by annotation as well as by genetic and biochemical assays. With the increased recognition that small proteins are stable within cells and have regulatory functions, there has been intensified study of these proteins. As a result, important questions about small proteins in bacteria and archaea are coming to the fore. Here, we give an overview of these questions, the initial answers, and the approaches needed to address these questions more fully. More detailed discussions of how small proteins can be identified by ribosome profiling and mass spectrometry approaches are provided by two accompanying reviews (N. Vazquez-Laslop, C. M. Sharma, A. S. Mankin, and A. R. Buskirk, J Bacteriol 204:e00294-21, 2022, https://doi.org/10.1128/JB.00294-21; C. H. Ahrens, J. T. Wade, M. M. Champion, and J. D. Langer, J Bacteriol 204:e00353-21, 2022, https://doi.org/10.1128/JB.00353-21). We are excited by the prospects of new insights and possible therapeutic approaches coming from this emerging field.

Bacterial Small Membrane Proteins: the Swiss Army Knife of Regulators at the Lipid Bilayer

Small membrane proteins represent a subset of recently discovered small proteins (≤100 amino acids), which are a ubiquitous class of emerging regulators underlying bacterial adaptation to environmental stressors. Until relatively recently, small open reading frames encoding these proteins were not designated genes in genome annotations. Therefore, our understanding of small protein biology was primarily limited to a few candidates associated with previously characterized larger partner proteins. Following the first systematic analyses of small proteins in Escherichia coli over a decade ago, numerous small proteins across different bacteria have been uncovered. An estimated one-third of these newly discovered proteins in E. coli are localized to the cell membrane, where they may interact with distinct groups of membrane proteins, such as signal receptors, transporters, and enzymes, and affect their activities. Recently, there has been considerable progress in functionally characterizing small membrane protein regulators aided by innovative tools adapted specifically to study small proteins. Our review covers prototypical proteins that modulate a broad range of cellular processes, such as transport, signal transduction, stress response, respiration, cell division, sporulation, and membrane stability. Thus, small membrane proteins represent a versatile group of physiology regulators at the membrane and the whole cell. Additionally, small membrane proteins have the potential for clinical applications, where some of the proteins may act as antibacterial agents themselves while others serve as alternative drug targets for the development of novel antimicrobials.

Fenton reaction-assisted photodynamic inactivation of calcined melamine sponge against Salmonella and its application

Photodynamic inactivation (PDI) is an effective alternative to traditional antibiotics to broadly kill bacteria. This study aimed to develop a potent PDI system by coupling calcinated melamine sponges (CMSs) with the Fenton reaction. The results showed that CMS calcined at 350 ℃ was successfully carbonized with intact and porous structures, and it possessed excellent hydrophilicity and photothermal conversion performance. When Fe²⁺ was added and internalized, the Fenton reaction in which Fe²⁺ reacted with H₂O₂ in cells occurred to produce reactive oxygen species (ROS) (OH, OOH, etc.) and O₂, and notably, the O₂ molecules could serve as a raw material to absorb the photothermal energy of CMS to generate highly reactive ¹O₂. Under synergistic effects, CMS-350 coupled with Fe²⁺ potently inactivated > 6 Log CFU/mL (>99.9999%) of Salmonella under 201.6 J/cm² blue LED illumination by destroying Na⁺/K⁺-ATPase and Ca²⁺/Mg²⁺-ATPase, DNA synthesis-related enzymes, cell membranes, etc. Meanwhile, the composite photocatalyst was proven to be nontoxic and could inactivate Salmonella in various foods, including vegetables (Brassica chinensis L), eggs and fresh cucumber juice. As a result, CMS coupled with the Fenton reaction greatly improves the inactivation potency of PDI against harmful bacteria.

What do we know about osmoadaptation of Yersinia pestis?

The plague agent Yersinia pestis mainly spreads among mammalian hosts and their associated fleas. Production of a successful mammal-flea-mammal life cycle implies that Y. pestis senses and responds to distinct cues in both host and vector. Among these cues, osmolarity is a fundamental parameter. The plague bacillus lives in a tightly regulated environment in the mammalian host, while osmolarity fluctuates in the flea gut (300-550 mOsM). Here, we review the mechanisms that enable Y. pestis to perceive fluctuations in osmolarity, as well as genomic plasticity and physiological adaptation of the bacterium to this stress.

Structural mechanisms for gating and ion selectivity of the human polyamine transporter ATP13A2

Mutations in ATP13A2, also known as PARK9, cause a rare monogenic form of juvenile-onset Parkinson's disease named Kufor-Rakeb syndrome and other neurodegenerative diseases. ATP13A2 encodes a neuroprotective P5B P-type ATPase highly enriched in the brain that mediates selective import of spermine ions from lysosomes into the cytosol via an unknown mechanism. Here we present three structures of human ATP13A2 bound to an ATP analog or to spermine in the presence of phosphomimetics determined by cryoelectron microscopy. ATP13A2 autophosphorylation opens a lysosome luminal gate to reveal a narrow lumen access channel that holds a spermine ion in its entrance. ATP13A2's architecture suggests physical principles underlying selective polyamine transport and anticipates a "pump-channel" intermediate that could function as a counter-cation conduit to facilitate lysosome acidification. Our findings establish a firm foundation to understand ATP13A2 mutations associated with disease and bring us closer to realizing ATP13A2's potential in neuroprotective therapy.

Deciphering ion transport and ATPase coupling in the intersubunit tunnel of KdpFABC

KdpFABC, a high-affinity K⁺ pump, combines the ion channel KdpA and the P-type ATPase KdpB to secure survival at K⁺ limitation. Here, we apply a combination of cryo-EM, biochemical assays, and MD simulations to illuminate the mechanisms underlying transport and the coupling to ATP hydrolysis. We show that ions are transported via an intersubunit tunnel through KdpA and KdpB. At the subunit interface, the tunnel is constricted by a phenylalanine, which, by polarized cation-π stacking, controls K⁺ entry into the canonical substrate binding site (CBS) of KdpB. Within the CBS, ATPase coupling is mediated by the charge distribution between an aspartate and a lysine. Interestingly, individual elements of the ion translocation mechanism of KdpFABC identified here are conserved among a wide variety of P-type ATPases from different families. This leads us to the hypothesis that KdpB might represent an early descendant of a common ancestor of cation pumps.

Escherichia coli Small Proteome

Escherichia coli was one of the first species to have its genome sequenced and remains one of the best-characterized model organisms. Thus, it is perhaps surprising that recent studies have shown that a substantial number of genes have been overlooked. Genes encoding more than 140 small proteins, defined as those containing 50 or fewer amino acids, have been identified in E. coli in the past 10 years, and there is substantial evidence indicating that many more remain to be discovered. This review covers the methods that have been successful in identifying small proteins and the short open reading frames that encode them. The small proteins that have been functionally characterized to date in this model organism are also discussed. It is hoped that the review, along with the associated databases of known as well as predicted but undetected small proteins, will aid in and provide a roadmap for the continued identification and characterization of these proteins in E. coli as well as other bacteria.

Two newly identified Haematococcus strains efficiently accumulated radioactive cesium over higher astaxanthin production

In this study, we investigated the morphological, genomic and bioaccumulation characteristics of two isolated Haematococcus strains (namely Goyang and Sogang), which were newly discovered in South Korea. Morphological analysis revealed that the isolated strains were unicellular and bi-flagellated green microalgae that formed thickened walls at the palmelloid or red-cyst phase. Phylogenetic analysis of 18S rRNA and rbcL gDNA sequences demonstrated that both strains were taxonomically related to the genus Haematococcus. The two strains showed growth pattern that was similar to a typical Haematococcus strain, and accumulated astaxanthin within 48 h of exposure to intensive light. Both red-cyst cells effectively removed radioactive cesium to more than 50% within 48 h from low-level cesium-contaminated water of 5 Bq/ml concentration. The cesium-accumulation mechanism is largely associated with the replacement of cellular potassium in thick cell walls during biouptake, and the cesium-removal rate highly depends on the corresponding astaxanthin accumulation involving the potassium-transporting protein (P-type ATPase).

The transferred translocases: An old wine in a new bottle

The role of translocases was underappreciated and was not included as a separate class in the enzyme commission until August 2018. The recent research interests in proteomics of orphan enzymes, ionomics, and metallomics along with high-throughput sequencing technologies generated overwhelming data and revamped this enzyme into a separate class. This offers a great opportunity to understand the role of new or orphan enzymes in general and specifically translocases. The enzymes belonging to translocases regulate/permeate the transfer of ions or molecules across the membranes. These enzyme entries were previously associated with other enzyme classes, which are now transferred to a new enzyme class 7 (EC 7). The entries that are reclassified are important to extend the enzyme list, and it is the need of the hour. Accordingly, there is an upgradation of entries of this class of enzymes in several databases. This review is a concise compilation of translocases with reference to the number of entries currently available in the databases. This review also focuses on function as well as dysfunction of translocases during normal and disordered states, respectively.

Structural basis for potassium transport in prokaryotes by KdpFABC

KdpFABC is an oligomeric K⁺ transport complex in prokaryotes that maintains ionic homeostasis under stress conditions. The complex comprises a channel-like subunit (KdpA) from the superfamily of K⁺ transporters and a pump-like subunit (KdpB) from the superfamily of P-type ATPases. Recent structural work has defined the architecture and generated contradictory hypotheses for the transport mechanism. Here, we use substrate analogs to stabilize four key intermediates in the reaction cycle and determine the corresponding structures by cryogenic electron microscopy. We find that KdpB undergoes conformational changes consistent with other representatives from the P-type superfamily, whereas KdpA, KdpC, and KdpF remain static. We observe a series of spherical densities that we assign as K⁺ or water and which define a pathway for K⁺ transport. This pathway runs through an intramembrane tunnel in KdpA and delivers ions to sites in the membrane domain of KdpB. Our structures suggest a mechanism where ATP hydrolysis is coupled to K⁺ transfer between alternative sites in KdpB, ultimately reaching a low-affinity site where a water-filled pathway allows release of K⁺ to the cytoplasm.

An Intracellular Pathway Controlled by the N-terminus of the Pump Subunit Inhibits the Bacterial KdpFABC Ion Pump in High K+ Conditions

The heterotetrameric bacterial KdpFABC transmembrane protein complex is an ion channel-pump hybrid that consumes ATP to import K⁺ against its transmembrane chemical potential gradient in low external K⁺ environments. The KdpB ion-pump subunit of KdpFABC is a P-type ATPase, and catalyses ATP hydrolysis. Under high external K⁺ conditions, K⁺ can diffuse into the cells through passive ion channels. KdpFABC must therefore be inhibited in high K⁺ conditions to conserve cellular ATP. Inhibition is thought to occur via unusual phosphorylation of residue Ser162 of the TGES motif of the cytoplasmic A domain. It is proposed that phosphorylation most likely traps KdpB in an inactive E1-P like conformation, but the molecular mechanism of phosphorylation-mediated inhibition remains unknown. Here, we employ molecular dynamics (MD) simulations of the dephosphorylated and phosphorylated versions of KdpFABC to demonstrate that phosphorylated KdpB is trapped in a conformation where the ion-binding site is hydrated by an intracellular pathway between transmembrane helices M1 and M2 which opens in response to the rearrangement of cytoplasmic domains resulting from phosphorylation. Cytoplasmic access of water to the ion-binding site is accompanied by a remarkable loss of secondary structure of the KdpB N-terminus and disruption of a key salt bridge between Glu87 in the A domain and Arg212 in the P domain. Our results provide the molecular basis of a unique mechanism of regulation amongst P-type ATPases, and suggest that the N-terminus has a significant role to play in the conformational cycle and regulation of KdpFABC.

Molecular Mechanisms for Bacterial Potassium Homeostasis

Potassium ion homeostasis is essential for bacterial survival, playing roles in osmoregulation, pH homeostasis, regulation of protein synthesis, enzyme activation, membrane potential adjustment and electrical signaling. To accomplish such diverse physiological tasks, it is not surprising that a single bacterium typically encodes several potassium uptake and release systems. To understand the role each individual protein fulfills and how these proteins work in concert, it is important to identify the molecular details of their function. One needs to understand whether the systems transport ions actively or passively, and what mechanisms or ligands lead to the activation or inactivation of individual systems. Combining mechanistic information with knowledge about the physiology under different stress situations, such as osmostress, pH stress or nutrient limitation, one can identify the task of each system and deduce how they are coordinated with each other. By reviewing the general principles of bacterial membrane physiology and describing the molecular architecture and function of several bacterial K⁺-transporting systems, we aim to provide a framework for microbiologists studying bacterial potassium homeostasis and the many K⁺-translocating systems that are still poorly understood.

The largely unexplored biology of small proteins in pro- and eukaryotes

The large abundance of small open reading frames (smORFs) in prokaryotic and eukaryotic genomes and the plethora of smORF-encoded small proteins became only apparent with the constant advancements in bioinformatic, genomic, proteomic, and biochemical tools. Small proteins are typically defined as proteins of < 50 amino acids in prokaryotes and of less than 100 amino acids in eukaryotes, and their importance for cell physiology and cellular adaptation is only beginning to emerge. In contrast to antimicrobial peptides, which are secreted by prokaryotic and eukaryotic cells for combatting pathogens and competitors, small proteins act within the producing cell mainly by stabilizing protein assemblies and by modifying the activity of larger proteins. Production of small proteins is frequently linked to stress conditions or environmental changes, and therefore, cells seem to use small proteins as intracellular modifiers for adjusting cell metabolism to different intra- and extracellular cues. However, the size of small proteins imposes a major challenge for the cellular machinery required for protein folding and intracellular trafficking and recent data indicate that small proteins can engage distinct trafficking pathways. In the current review, we describe the diversity of small proteins in prokaryotes and eukaryotes, highlight distinct and common features, and illustrate how they are handled by the protein trafficking machineries in prokaryotic and eukaryotic cells. Finally, we also discuss future topics of research on this fascinating but largely unexplored group of proteins.

MPM motifs of the yeast SKT protein Trk1 can assemble to form a functional K+-translocation system

The yeast Trk1 polypeptide, like other members of the Superfamily of K Transporters (SKT proteins) consists of four Membrane-Pore-Membrane motifs (MPMs A-D) each of which is homologous to a single K-channel subunit. SKT proteins are thought to have evolved from ancestral K-channels via two gene duplications and thus single MPMs might be able to assemble when located on different polypeptides. To test this hypothesis experimentally we generated a set of partial gene deletions to create alleles encoding one, two, or three MPMs, and analysed the cellular localisation and interactions of these Trk1 fragments using GFP tags and Bimolecular Fluorescence Complementation (BiFC). The function of these partial Trk1 proteins either alone or in combinations was assessed by expressing the encoding genes in a K⁺-uptake deficient strain lacking also the K-channel Tok1 (trk1,trk2,tok1Δ) and (i) analysing their ability to promote growth in low [K⁺] media and (ii) by ion flux measurements using "microelectrode based ion flux estimation" (MIFE). We found that proteins containing only one or two MPM motifs can interact with each other and assemble with a polypeptide consisting of the rest of the Trk system to form a functional K⁺-translocation system.

iTRAQ-based quantitative proteomic analysis of synergistic antibacterial mechanism of phenyllactic acid and lactic acid against Bacillus cereus

Phenyllactic acid (PLA) as a phenolic acid by lactic acid (LA) bacteria shows enhanced antibacterial activity when coexisting with LA, while the antibacterial mechanism of PLA combined with LA was unknown. Hence, the antibacterial mechanism of PLA and LA was investigated against Bacillus cereus. Flow cytometry and TEM analysis demonstrated that single PLA and LA disrupted the membrane integrity and the morphology, while combined PLA and LA synergistically enhanced the damage. iTRAQ-based proteomic analysis suggested that PLA down-regulated kdpB and inhibited K⁺ transport, disturbed the function of ribosome and expression of competence genes; LA down-regulated periplasmic phosphorus-binding proteins and inhibited phosphorus transport, disturbed the function of ribosome, TCA cycle, as well as purine and pyrimidine metabolism; and combined PLA and LA inhibited K⁺ and phosphorus transport, and influenced the synthesis of purine and pyrimidine metabolism. The investigation could provide some insights into the application of PLA in food preservation.

Serine phosphorylation regulates the P-type potassium pump KdpFABC

KdpFABC is an ATP-dependent K⁺ pump that ensures bacterial survival in K⁺-deficient environments. Whereas transcriptional activation of kdpFABC expression is well studied, a mechanism for down-regulation when K⁺ levels are restored has not been described. Here, we show that KdpFABC is inhibited when cells return to a K⁺-rich environment. The mechanism of inhibition involves phosphorylation of Ser162 on KdpB, which can be reversed in vitro by treatment with serine phosphatase. Mutating Ser162 to Alanine produces constitutive activity, whereas the phosphomimetic Ser162Asp mutation inactivates the pump. Analyses of the transport cycle show that serine phosphorylation abolishes the K⁺-dependence of ATP hydrolysis and blocks the catalytic cycle after formation of the aspartyl phosphate intermediate (E1~P). This regulatory mechanism is unique amongst P-type pumps and this study furthers our understanding of how bacteria control potassium homeostasis to maintain cell volume and osmotic potential.

The KdpFABC complex - K+ transport against all odds

In bacteria, K⁺ is used to maintain cell volume and osmotic potential. Homeostasis normally involves a network of constitutively expressed transport systems, but in K⁺ deficient environments, the KdpFABC complex uses ATP to pump K⁺ into the cell. This complex appears to be a hybrid of two types of transporters, with KdpA descending from the superfamily of K⁺ transporters and KdpB belonging to the superfamily of P-type ATPases. Studies of enzymatic activity documented a catalytic cycle with hallmarks of classical P-type ATPases and studies of ion transport indicated that K⁺ import into the cytosol occurred in the second half of this cycle in conjunction with hydrolysis of an aspartyl phosphate intermediate. Atomic structures of the KdpFABC complex from X-ray crystallography and cryo-EM have recently revealed conformations before and after formation of this aspartyl phosphate that appear to contradict the functional studies. Specifically, structural comparisons with the archetypal P-type ATPase, SERCA, suggest that K⁺ transport occurs in the first half of the cycle, accompanying formation of the aspartyl phosphate. Further controversy has arisen regarding the path by which K⁺ crosses the membrane. The X-ray structure supports the conventional view that KdpA provides the conduit, whereas cryo-EM structures suggest that K⁺ moves from KdpA through a long, intramembrane tunnel to reach canonical ion binding sites in KdpB from which they are released to the cytosol. This review discusses evidence supporting these contradictory models and identifies key experiments needed to resolve discrepancies and produce a unified model for this fascinating mechanistic hybrid.

Evolution of Predicted Acid Resistance Mechanisms in the Extremely Acidophilic Leptospirillum Genus

Organisms that thrive in extremely acidic environments (≤pH 3.5) are of widespread importance in industrial applications, environmental issues, and evolutionary studies. Leptospirillum spp. constitute the only extremely acidophilic microbes in the phylogenetically deep-rooted bacterial phylum Nitrospirae. Leptospirilli are Gram-negative, obligatory chemolithoautotrophic, aerobic, ferrous iron oxidizers. This paper predicts genes that Leptospirilli use to survive at low pH and infers their evolutionary trajectory. Phylogenetic and other bioinformatic approaches suggest that these genes can be classified into (i) "first line of defense", involved in the prevention of the entry of protons into the cell, and (ii) neutralization or expulsion of protons that enter the cell. The first line of defense includes potassium transporters, predicted to form an inside positive membrane potential, spermidines, hopanoids, and Slps (starvation-inducible outer membrane proteins). The "second line of defense" includes proton pumps and enzymes that consume protons. Maximum parsimony, clustering methods, and gene alignments are used to infer the evolutionary trajectory that potentially enabled the ancestral Leptospirillum to transition from a postulated circum-neutral pH environment to an extremely acidic one. The hypothesized trajectory includes gene gains/loss events driven extensively by horizontal gene transfer, gene duplications, gene mutations, and genomic rearrangements.

Membrane Protein Solubilization and Quality Control: An Example of a Primary Active Transporter

When purifying a membrane protein, finding a detergent for solubilization is one of the first steps to master. Ideally, only little time is invested to identify the best-suited detergent, which on the one hand would solubilize large amounts of the target protein but on the other hand would sustain the protein's activity. Here we describe the solubilization screen and subsequent activity assay we have optimized for the bacterial P-type ATPase KdpFABC. In just 2 days, more than 70 detergents were tested for their solubilization potential. Afterwards, a smaller selection of the successful detergents was assayed for their ability to retain the activity of the membrane protein complex.

TrkA undergoes a tetramer-to-dimer conversion to open TrkH which enables changes in membrane potential

TrkH is a bacterial ion channel implicated in K⁺ uptake and pH regulation. TrkH assembles with its regulatory protein, TrkA, which closes the channel when bound to ADP and opens it when bound to ATP. However, it is unknown how nucleotides control the gating of TrkH through TrkA. Here we report the structures of the TrkH-TrkA complex in the presence of ADP or ATP. TrkA forms a tetrameric ring when bound to ADP and constrains TrkH to a closed conformation. The TrkA ring splits into two TrkA dimers in the presence of ATP and releases the constraints on TrkH, resulting in an open channel conformation. Functional studies show that both the tetramer-to-dimer conversion of TrkA and the loss of constraints on TrkH are required for channel gating. In addition, deletion of TrkA in Escherichia coli depolarizes the cell, suggesting that the TrkH-TrkA complex couples changes in intracellular nucleotides to membrane potential.

The potassium transporter KdpA affects persister formation by regulating ATP levels in Mycobacterium marinum

Mycobacterial persistence mechanisms remain to be fully characterized. Screening a transposon insertion library of Mycobacterium marinum identified kdpA, whose inactivation reduced the fraction of persisters after exposure to rifampicin. kdpA encodes a transmembrane protein that is part of the Kdp-ATPase, an ATP-dependent high-affinity potassium (K⁺) transport system. We found that kdpA is induced under low K⁺ conditions and is required for pH homeostasis and growth in media with low concentrations of K⁺. The inactivation of the Kdp system in a kdpA insertion mutant caused hyperpolarization of the cross-membrane potential, increased proton motive force (PMF) and elevated levels of intracellular ATP. The KdpA mutant phenotype could be complemented with a functional kdpA gene or supplementation with high K⁺ concentrations. Taken together, our results suggest that the Kdp system is required for ATP homeostasis and persister formation. The results also confirm that ATP-mediated regulation of persister formation is a general mechanism in bacteria, and suggest that K⁺ transporters could play a role in the regulation of ATP levels and persistence. These findings could have implications for the development of new drugs that could either target persisters or reduce their presence.

Multipathway Antibacterial Mechanism of a Nanoparticle-Supported Artemisinin Promoted by Nitrogen Plasma Treatment

Artemisinin has excellent antimalarial, antiparasitic, and antibacterial activities; however, the poor water solubility of artemisinin crystal limits their application in antibiosis. Herein, artemisinin crystal was first composited with silica nanoparticles (SNPs) to form an artemisinin@silica nanoparticle (A@SNP). After treating with nitrogen plasma, the aqueous solubility of plasma-treated A@SNP (A@SNP-p) approaches 42.26%, which is possibly attributed to the exposure of hydrophilic groups such as -OH groups on the SNPs during the plasma process. Compared with the pristine A@SNP, the antibacterial activity of A@SNP-p against both Gram-positive and Gram-negative strains is further enhanced, and its bactericidal rate against both strains exceeded 6 log CFU/mL (>99.9999%), which is contributed by the increased water solubility of the A@SNP-p. A possible multipathway antibacterial mechanism of A@SNP was proposed and preliminarily proved by the changes of intracellular materials of bacteria and the inhibition of bacterial metabolism processes, including the HMP pathway in Gram-negative strain and EMP pathway in Gram-positive strain, after treating with A@SNP-p. These findings from the present work will provide a new view for fabricating artemisinin-based materials as antibiotics.

Multiscale Simulations of Biological Membranes: The Challenge To Understand Biological Phenomena in a Living Substance

Biological membranes are tricky to investigate. They are complex in terms of molecular composition and structure, functional over a wide range of time scales, and characterized by nonequilibrium conditions. Because of all of these features, simulations are a great technique to study biomembrane behavior. A significant part of the functional processes in biological membranes takes place at the molecular level; thus computer simulations are the method of choice to explore how their properties emerge from specific molecular features and how the interplay among the numerous molecules gives rise to function over spatial and time scales larger than the molecular ones. In this review, we focus on this broad theme. We discuss the current state-of-the-art of biomembrane simulations that, until now, have largely focused on a rather narrow picture of the complexity of the membranes. Given this, we also discuss the challenges that we should unravel in the foreseeable future. Numerous features such as the actin-cytoskeleton network, the glycocalyx network, and nonequilibrium transport under ATP-driven conditions have so far received very little attention; however, the potential of simulations to solve them would be exceptionally high. A major milestone for this research would be that one day we could say that computer simulations genuinely research biological membranes, not just lipid bilayers.

Plants fighting back: to transport or not to transport, this is a structural question

Membrane-embedded transport proteins are fundamental to life; their co-ordinated action controls the movement and distribution of solutes into, around and out of cells for signalling, metabolism, nutrition, stress tolerance and development. Here we outline two case studies of transport systems that plants use to tolerate soil elemental toxicity, demonstrating how iterative studies of protein structure and function result in unparalleled insights into transport mechanics. Further, we propose that integrative platforms of biological, biochemical and biophysical tools can provide quantitative data on substrate specificity and transport rates, which are important in understanding transporter evolution and their roles in cell biology and whole plant physiology. Such knowledge equips biotechnologists and breeders with the power to deliver improvements in crop yields in sub-optimal soils.

Cryo-EM structures of KdpFABC suggest a K+ transport mechanism via two inter-subunit half-channels

P-type ATPases ubiquitously pump cations across biological membranes to maintain vital ion gradients. Among those, the chimeric K⁺ uptake system KdpFABC is unique. While ATP hydrolysis is accomplished by the P-type ATPase subunit KdpB, K⁺ has been assumed to be transported by the channel-like subunit KdpA. A first crystal structure uncovered its overall topology, suggesting such a spatial separation of energizing and transporting units. Here, we report two cryo-EM structures of the 157 kDa, asymmetric KdpFABC complex at 3.7 Å and 4.0 Å resolution in an E1 and an E2 state, respectively. Unexpectedly, the structures suggest a translocation pathway through two half-channels along KdpA and KdpB, uniting the alternating-access mechanism of actively pumping P-type ATPases with the high affinity and selectivity of K⁺ channels. This way, KdpFABC would function as a true chimeric complex, synergizing the best features of otherwise separately evolved transport mechanisms.

Transcriptomic dissection of Bradyrhizobium sp. strain ORS285 in symbiosis with Aeschynomene spp. inducing different bacteroid morphotypes with contrasted symbiotic efficiency

To circumvent the paucity of nitrogen sources in the soil legume plants establish a symbiotic interaction with nitrogen-fixing soil bacteria called rhizobia. During symbiosis, the plants form root organs called nodules, where bacteria are housed intracellularly and become active nitrogen fixers known as bacteroids. Depending on their host plant, bacteroids can adopt different morphotypes, being either unmodified (U), elongated (E) or spherical (S). E- and S-type bacteroids undergo a terminal differentiation leading to irreversible morphological changes and DNA endoreduplication. Previous studies suggest that differentiated bacteroids display an increased symbiotic efficiency (E > U and S > U). In this study, we used a combination of Aeschynomene species inducing E- or S-type bacteroids in symbiosis with Bradyrhizobium sp. ORS285 to show that S-type bacteroids present a better symbiotic efficiency than E-type bacteroids. We performed a transcriptomic analysis on E- and S-type bacteroids formed by Aeschynomene afraspera and Aeschynomene indica nodules and identified the bacterial functions activated in bacteroids and specific to each bacteroid type. Extending the expression analysis in E- and S-type bacteroids in other Aeschynomene species by qRT-PCR on selected genes from the transcriptome analysis narrowed down the set of bacteroid morphotype-specific genes. Functional analysis of a selected subset of 31 bacteroid-induced or morphotype-specific genes revealed no symbiotic phenotypes in the mutants. This highlights the robustness of the symbiotic program but could also indicate that the bacterial response to the plant environment is partially anticipatory or even maladaptive. Our analysis confirms the correlation between differentiation and efficiency of the bacteroids and provides a framework for the identification of bacterial functions that affect the efficiency of bacteroids.© 2018 Society for Applied Microbiology and John Wiley & Sons Ltd.

Investigation of amino acid specificity in the CydX small protein shows sequence plasticity at the functional level

Small proteins are a new and expanding area of research. Many characterized small proteins are composed of a single hydrophobic α-helix, and the functional requirements of their limited amino acid sequence are not well understood. One hydrophobic small protein, CydX, has been shown to be a component of the cytochrome bd oxidase complex in Escherichia coli, and is required for enzyme function. To investigate small protein sequence specificity, an alanine scanning mutagenesis on the small protein CydX was conducted using mutant alleles expressed from the E. coli chromosome at the wild-type locus. The resulting mutant strains were assayed for CydX function. No single amino acid was required to maintain wild-type resistance to β-mercaptoethanol. However, substitutions of 10-amino acid blocks indicated that the N-terminus of the protein was required for wild-type CydX activity. A series of double mutants showed that multiple mutations at the N-terminus led to β-mercaptoethanol sensitivity in vivo. Triple mutants showed both in vivo and in vitro phenotypes. Together, these data provide evidence suggesting a high level of functional plasticity in CydX, in which multiple amino acids may work cooperatively to facilitate CydX function.

Structural variations in wheat HKT1;5 underpin differences in Na+ transport capacity

An important trait associated with the salt tolerance of wheat is the exclusion of sodium ions (Na+) from the shoot. We have previously shown that the sodium transporters TmHKT1;5-A and TaHKT1;5-D, from Triticum monoccocum (Tm) and Triticum aestivum (Ta), are encoded by genes underlying the major shoot Na+-exclusion loci Nax1 and Kna1, respectively. Here, using heterologous expression, we show that the affinity (K m) for the Na+ transport of TmHKT1;5-A, at 2.66 mM, is higher than that of TaHKT1;5-D at 7.50 mM. Through 3D structural modelling, we identify residues D471/a gap and D474/G473 that contribute to this property. We identify four additional mutations in amino acid residues that inhibit the transport activity of TmHKT1;5-A, which are predicted to be the result of an occlusion of the pore. We propose that the underlying transport properties of TmHKT1;5-A and TaHKT1;5-D contribute to their unique ability to improve Na+ exclusion in wheat that leads to an improved salinity tolerance in the field.

ChannelsDB: database of biomacromolecular tunnels and pores

ChannelsDB (http://ncbr.muni.cz/ChannelsDB) is a database providing information about the positions, geometry and physicochemical properties of channels (pores and tunnels) found within biomacromolecular structures deposited in the Protein Data Bank. Channels were deposited from two sources; from literature using manual deposition and from a software tool automatically detecting tunnels leading to the enzymatic active sites and selected cofactors, and transmembrane pores. The database stores information about geometrical features (e.g. length and radius profile along a channel) and physicochemical properties involving polarity, hydrophobicity, hydropathy, charge and mutability. The stored data are interlinked with available UniProt annotation data mapping known mutation effects to channel-lining residues. All structures with channels are displayed in a clear interactive manner, further facilitating data manipulation and interpretation. As such, ChannelsDB provides an invaluable resource for research related to deciphering the biological function of biomacromolecular channels.