The Mrp system: a giant among monovalent cation/proton antiporters?

Association Analysis of the Genomic and Functional Characteristics of Halotolerant Glutamicibacter endophyticus J2-5-19 from the Rhizosphere of Suaeda salsa

Halotolerant plant growth-promoting bacteria (HT-PGPB) have attracted considerable attention for their significant potential in mitigating salt stress in crops. However, the current exploration and development of HT-PGPB remain insufficient to meet the increasing demands of agriculture. In this study, an HT-PGPB isolated from coastal saline-alkali soil in the Yellow River Delta was identified as Glutamicibacter endophyticus J2-5-19. The strain was capable of growing in media with up to 13% NaCl and producing proteases, siderophores, and the plant hormone IAA. Under 4‱ salt stress, inoculation with strain J2-5-19 significantly increased the wheat seed germination rate from 37.5% to 95%, enhanced the dry weight of maize seedlings by 41.92%, and notably improved the development of maize root systems. Moreover, this work presented the first whole-genome of Glutamicibacter endophyticus, revealing that G. endophyticus J2-5-19 resisted salt stress by expelling sodium ions and taking up potassium ions through Na+/H+ antiporters and potassium uptake proteins, while also accumulating compatible solutes such as betaine, proline, and trehalose. Additionally, the genome contained multiple key plant growth-promoting genes, including those involved in IAA biosynthesis, siderophore production, and GABA synthesis. The findings provide a theoretical foundation and microbial resources for the development of specialized microbial inoculants for saline-alkali soils.

Quantitative proteomics reveals oxygen-induced adaptations in Caldalkalibacillus thermarum TA2.A1 microaerobic chemostat cultures

The thermoalkaliphile Caldalkalibacillus thermarum possesses a highly branched respiratory chain. These primarily facilitate growth at a wide range of dissolved oxygen levels. The aim of this study was to investigate the regulation of C. thermarum respiratory chain. C. thermarum was cultivated in chemostat bioreactors with a range of oxygen levels (0.25% O2-4.2% O2). Proteomic analysis unexpectedly showed that both the type I and the type II NADH dehydrogenase present are constitutive. The two terminal oxidases detected were the cytochrome c:oxygen aa 3 oxidase, whose abundance was highest at 4.2% O2. The cytochrome c:oxygen ba 3 oxidase was more abundant at most other O2 levels, but its abundance started to decline below 0.42% O2. We expected this would result in the emergence of the cytochrome c:oxygen bb 3 complex or the menaquinol:oxygen bd complex, the other two terminal oxidases of C. thermarum; but neither was detected. Furthermore, the sodium-proton antiporter complex Mrp was downregulated under the lower oxygen levels. Normally, in alkaliphiles, this enzyme is considered crucial for sodium homeostasis. We propose that the existence of a sodium:acetate exporter decreases the requirement for Mrp under strong oxygen limitation.

Metagenomic assembled genomes indicated the potential application of hypersaline microbiome for plant growth promotion and stress alleviation in salinized soils

Climate change is causing unpredictable seasonal variations globally. Due to the continuously increasing earth's surface temperature, the rate of water evaporation is enhanced, conceiving a problem of soil salinization, especially in arid and semi-arid regions. The accumulation of salt degrades soil quality, impairs plant growth, and reduces agricultural yields. Salt-tolerant, plant-growth-promoting microorganisms may offer a solution, enhancing crop productivity and soil fertility in salinized areas. In the current study, genome-resolved metagenomic analysis has been performed to investigate the salt-tolerating and plant growth-promoting potential of two hypersaline ecosystems, Sambhar Lake and Drang Mine. The samples were co-assembled independently by Megahit, MetaSpades, and IDBA-UD tools. A total of 67 metagenomic assembled genomes (MAGs) were reconstructed following the binning process, including 15 from Megahit, 26 from MetaSpades, and 26 from IDBA_UD assembly tools. As compared to other assemblers, the MAGs obtained by MetaSpades were of superior quality, with a completeness range of 12.95%-96.56% and a contamination range of 0%-8.65%. The medium and high-quality MAGs from MetaSpades, upon functional annotation, revealed properties such as salt tolerance (91.3%), heavy metal tolerance (95.6%), exopolysaccharide (95.6%), and antioxidant (60.86%) biosynthesis. Several plant growth-promoting attributes, including phosphate solubilization and indole-3-acetic acid (IAA) production, were consistently identified across all obtained MAGs. Conversely, characteristics such as iron acquisition and potassium solubilization were observed in a substantial majority, specifically 91.3%, of the MAGs. The present study indicates that hypersaline microflora can be used as bio-fertilizing agents for agricultural practices in salinized areas by alleviating prevalent stresses.

IMPORTANCE

The strategic implementation of metagenomic assembled genomes (MAGs) in exploring the properties and harnessing microorganisms from ecosystems like hypersaline niches has transformative potential in agriculture. This approach promises to redefine our comprehension of microbial diversity and its ecosystem roles. Recovery and decoding of MAGs unlock genetic resources, enabling the development of new solutions for agricultural challenges. Enhanced understanding of these microbial communities can lead to more efficient nutrient cycling, pest control, and soil health maintenance. Consequently, traditional agricultural practices can be improved, resulting in increased yields, reduced environmental impacts, and heightened sustainability. MAGs offer a promising avenue for sustainable agriculture, bridging the gap between cutting-edge genomics and practical field applications.

Metagenomic analysis towards understanding the effects of ammonia on chain elongation process for medium chain fatty acids production

The production of medium chain fatty acids (MCFAs) through chain elongation (CE) from organic wastes/wastewater has attracted much attention, while the effects of a common inhibitor-ammonia has not been elucidated. The mechanism of ammonia affecting CE was studied by metagenomic. The lag phase duration of caproate production was increased, and the maximum caproate production rate was decreased by 43.4 % at 4 g-N/L, as compared to 0 g-N/L. And hydrochar (HC) alleviated the inhibition of ammonia at 4 g-N/L. Metagenomic analysis indicated that ammonia induced UBA4085 sp.FDU78 as the dominant microorganism, and metabolic reconstruction revealed its potential CE ability. Furthermore, ammonia inhibited the reverse β oxidation pathway and Acetyl-CoA production pathway. The tolerance of UBA4085 sp.FDU78 to ammonia was associated with the uptake of inorganic ions, energy conservation, and synthesis of osmoprotectants. The present study provided a deep-insight on the ammonia tolerance mechanism on the CE process.

Decoding Microbial Responses to Ammonia Shock Loads in Biogas Reactors through Metagenomics and Metatranscriptomics

The presence of elevated ammonia levels is widely recognized as a significant contributor to process inhibition in biogas production, posing a common challenge for biogas plant operators. The present study employed a combination of biochemical, genome-centric metagenomic and metatranscriptomic data to investigate the response of the biogas microbiome to two shock loads induced by single pulses of elevated ammonia concentrations (i.e., 1.5 g NH4+/LR and 5 g NH4+/LR). The analysis revealed a microbial community of high complexity consisting of 364 Metagenome Assembled Genomes (MAGs). The hydrogenotrophic pathway was the primary route for methane production during the entire experiment, confirming its efficiency even at high ammonia concentrations. Additionally, metatranscriptomic analysis uncovered a metabolic shift in the methanogens Methanothrix sp. MA6 and Methanosarcina flavescens MX5, which switched their metabolism from the acetoclastic to the CO2 reduction route during the second shock. Furthermore, multiple genes associated with mechanisms for maintaining osmotic balance in the cell were upregulated, emphasizing the critical role of osmoprotection in the rapid response to the presence of ammonia. Finally, this study offers insights into the transcriptional response of an anaerobic digestion community, specifically focusing on the mechanisms involved in recovering from ammonia-induced stress.

Genomic basis for the unique phenotype of the alkaliphilic purple nonsulfur bacterium Rhodobaca bogoriensis

Although several species of purple sulfur bacteria inhabit soda lakes, Rhodobaca bogoriensis is the first purple nonsulfur bacterium cultured from such highly alkaline environments. Rhodobaca bogoriensis strain LBB1T was isolated from Lake Bogoria, a soda lake in the African Rift Valley. The phenotype of Rhodobaca bogoriensis is unique among purple bacteria; the organism is alkaliphilic but not halophilic, produces carotenoids absent from other purple nonsulfur bacteria, and is unable to grow autotrophically or fix molecular nitrogen. Here we analyze the draft genome sequence of Rhodobaca bogoriensis to gain further insight into the biology of this extremophilic purple bacterium. The strain LBB1T genome consists of 3.91 Mbp with no plasmids. The genome sequence supports the defining characteristics of strain LBB1T, including its (1) production of a light-harvesting 1-reaction center (LH1-RC) complex but lack of a peripheral (LH2) complex, (2) ability to synthesize unusual carotenoids, (3) capacity for both phototrophic (anoxic/light) and chemotrophic (oxic/dark) energy metabolisms, (4) utilization of a wide variety of organic compounds (including acetate in the absence of a glyoxylate cycle), (5) ability to oxidize both sulfide and thiosulfate despite lacking the capacity for autotrophic growth, and (6) absence of a functional nitrogen-fixation system for diazotrophic growth. The assortment of properties in Rhodobaca bogoriensis has no precedent among phototrophic purple bacteria, and the results are discussed in relation to the organism's soda lake habitat and evolutionary history.

Alkaliphiles for comprehensive utilization of red mud (bauxite residue)-an alkaline waste from the alumina refinery

The mining industry has powered the human endeavor to make life more innovative, flexible, and comfortable. However, it has also led to concerns due to the increasing amount of mining and associated industrial waste. Special attention is highly desired for its proper management and safe disposal in the environment. The problem has only augmented with the increase in the mining costs because of the investments needed for ecological remediation after the mining operation. It is pertinent that the targeted technologies need to be developed to utilize mining and associated industrial waste as a secondary resource to ensure sustainable mining operations. Every perceived waste is a valuable resource that is needed to be utilized to create additional value. In this review, the case of alkaline bauxite residue (red mud)-alumina refinery waste has been discussed at length. The highlight of the proposed work is to understand the importance of alkaliphile-assisted biomining-a sustainable alternative to conventional metal recovery processes. Along with the recovery of metals, pH reduction of red mud is possible through biomining, which ultimately paves the way for its complete utilization. The unique adaptation strategies of alkaliphiles make them more suitable for biomining of red mud through bioleaching, biosorption, and bioaccumulation, which have been discussed here. Furthermore, we have focused on the potential of the indigenous microflora of red mud for metal recovery in addition to its neutralization. The study of indigenous alkaliphiles from red mud, including its isolation and propagation, is crucial for the industrial-scale application of alkaliphile-based technology and has been emphasized.

Ion transfer mechanisms in Mrp-type antiporters from high resolution cryoEM and molecular dynamics simulations

Multiple resistance and pH adaptation (Mrp) cation/proton antiporters are essential for growth of a variety of halophilic and alkaliphilic bacteria under stress conditions. Mrp-type antiporters are closely related to the membrane domain of respiratory complex I. We determined the structure of the Mrp antiporter from Bacillus pseudofirmus by electron cryo-microscopy at 2.2 Å resolution. The structure resolves more than 99% of the sidechains of the seven membrane subunits MrpA to MrpG plus 360 water molecules, including ~70 in putative ion translocation pathways. Molecular dynamics simulations based on the high-resolution structure revealed details of the antiport mechanism. We find that switching the position of a histidine residue between three hydrated pathways in the MrpA subunit is critical for proton transfer that drives gated trans-membrane sodium translocation. Several lines of evidence indicate that the same histidine-switch mechanism operates in respiratory complex I.

Disturbance-based management of ecosystem services and disservices in partial nitritation-anammox biofilms

The resistance and resilience provided by functional redundancy, a common feature of microbial communities, is not always advantageous. An example is nitrite oxidation in partial nitritation-anammox (PNA) reactors designed for nitrogen removal in wastewater treatment, where suppression of nitrite oxidizers like Nitrospira is sought. In these ecosystems, biofilms provide microhabitats with oxygen gradients, allowing the coexistence of aerobic and anaerobic bacteria. We designed a disturbance experiment where PNA biofilms, treating water from a high-rate activated sludge process, were constantly or intermittently exposed to anaerobic sidestream wastewater, which has been proposed to inhibit nitrite oxidizers. With increasing sidestream exposure we observed decreased abundance, alpha-diversity, functional versatility, and hence functional redundancy, among Nitrospira in the PNA biofilms, while the opposite patterns were observed for anammox bacteria within Brocadia. At the same time, species turnover was observed for aerobic ammonia-oxidizing Nitrosomonas populations. The different exposure regimens were associated with metagenomic assembled genomes of Nitrosomonas, Nitrospira, and Brocadia, encoding genes related to N-cycling, substrate usage, and osmotic stress response, possibly explaining the three different patterns by niche differentiation. These findings imply that disturbances can be used to manage the functional redundancy of biofilm microbiomes in a desirable direction, which should be considered when designing operational strategies for wastewater treatment.

Comprehensive Genome Analysis of Halolamina pelagica CDK2: Insights into Abiotic Stress Tolerance Genes

Halophilic archaeon Halolamina pelagica CDK2, showcasing plant growth-promoting properties and endurance towards harsh environmental conditions (high salinity, heavy metals, high temperature and UV radiation) was sequenced earlier. Pan-genome of Halolamina genus was created and investigated for strain-specific genes of CDK2, which might confer it with features helping it to withstand high abiotic stress. Pathways and subsystems in CDK2 were compared with other Halolamina strain CGHMS and analysed using KEGG and RAST. A genome-scale metabolic model was reconstructed from the genome of H. pelagica CDK2. Results implicated strain-specific genes like thermostable carboxypeptidase and DNA repair protein MutS which might protect the proteins and DNA from high temperature and UV denaturation respectively. A bifunctional trehalose synthase gene responsible for trehalose biosynthesis was also annotated specifying the need for low salt compatible solute strategy, the probable reason behind the ability of this haloarchaea to survive in a wide range of salt concentrations. A modified shikimate and mevalonate pathways were also identified in CDK2, along with many ABC transporters for metal uptakes like zinc and cobalt through pathway analysis. Probable employment of one multifunctional ABC transporter in place of two for similar metals (Nickel/cobalt and molybdenum/tungsten) might be employed as a strategy for energy conservation. The findings of the present study could be utilized for future research relating metabolic model for flux balance analysis and the genetic repertoire imparting resistance to harsh conditions can be transferred to crops for improving their tolerance to abiotic stresses.

Salt tolerance-based niche differentiation of soil ammonia oxidizers

Ammonia oxidizers are key players in the global nitrogen cycle, yet little is known about their ecological performances and adaptation strategies for growth in saline terrestrial ecosystems. This study combined ¹³C-DNA stable-isotope probing (SIP) microcosms with amplicon and shotgun sequencing to reveal the composition and genomic adaptations of active ammonia oxidizers in a saline-sodic (solonetz) soil with high salinity and pH (20.9 cmol_c exchangeable Na⁺ kg^-1 soil and pH 9.64). Both ammonia-oxidizing archaea (AOA) and bacteria (AOB) exhibited strong nitrification activities, although AOB performed most of the ammonia oxidation observed in the solonetz soil and in the farmland soil converted from solonetz soil. Members of the Nitrosococcus, which are more often associated with aquatic habitats, were identified as the dominant ammonia oxidizers in the solonetz soil with the first direct labeling evidence, while members of the Nitrosospira were the dominant ammonia oxidizers in the farmland soil, which had much lower salinity and pH. Metagenomic analysis of "Candidatus Nitrosococcus sp. Sol14", a new species within the Nitrosococcus lineage, revealed multiple genomic adaptations predicted to facilitate osmotic and pH homeostasis in this extreme habitat, including direct Na⁺ extrusion/H⁺ import and the ability to increase intracellular osmotic pressure by accumulating compatible solutes. Comparative genomic analysis revealed that variation in salt-tolerance mechanisms was the primary driver for the niche differentiation of ammonia oxidizers in saline-sodic soils. These results demonstrate how ammonia oxidizers can adapt to saline-sodic soil with excessive Na⁺ content and provide new insights on the nitrogen cycle in extreme terrestrial ecosystems.

Spiractinospora alimapuensis gen. nov., sp. nov., isolated from marine sediment of Valparaíso Bay (Chile) and proposal for reclassification of two species of the genus Nocardiopsis

An alkaliphilic actinobacterium, designated VN6-2T, was isolated from marine sediment collected from Valparaíso Bay, Chile. Strain VN6-2T formed yellowish-white branched substrate mycelium without fragmentation. Aerial mycelium was well developed, forming wavy or spiral spore chains. Strain VN6-2T exhibited a 16S rRNA gene sequence similarity of 93.9 % to Salinactinospora qingdaonensis CXB832T, 93.7 % to Murinocardiopsis flavida 14-Be-013T, and 93.7 % to Lipingzhangella halophila 14-Be-013T. Genome sequencing revealed a genome size of 5.9 Mb and an in silico G+C content of 69.3 mol%. Both of the phylogenetic analyses based on 16S rRNA gene sequences and the up-to-date bacterial core gene sequences revealed that strain VN6-2T formed a distinct monophyletic clade within the family Nocardiopsaceae . Chemotaxonomic assessment of strain VN6-2T showed that the major fatty acids were iso-C16 : 0, anteiso-C17 : 0 and 10-methyl-C18 : 0, and the predominant respiratory quinones were MK-9, MK-9(H2) and MK-9(H4). Whole-cell hydrolysates contained meso-diaminopimelic acid as the cell-wall diamino acid, and ribose and xylose as the diagnostic sugars. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, aminophospholipids, glycolipid and phospholipid. Based on the results of this polyphasic study, a novel genus, Spiractinospora gen. nov., is proposed within the family Nocardiopsaceae and the type species Spiractinospora alimapuensis gen. nov., sp. nov. The type strain is VN6-2T (CECT 30026T, CCUG 66258T). On the basis of the phylogenetic results herein, we also propose that Nocardiopsis arvandica and Nocardiopsis litoralis are later heterotypic synonyms of Nocardiopsis sinuspersici and Nocardiopsis kunsanensis , respectively, for which emended descriptions are given.

Highly integrated adaptive mechanisms in Spiribacter halalkaliphilus, a bacterium abundant in Chinese soda-saline lakes

Soda-saline lakes are polyextreme environments inhabited by many haloalkaliphiles, including one of the most abundant Spiribacter species. However, its mechanisms of adaptation are not ecophysiologically characterized. Based on a large-scale cultivation strategy, we obtained a representative isolate of this Spiribacter species whose relative abundance was the highest (up to 15.63%) in a wide range of salinities in the soda-saline lakes in Inner Mongolia, China. This species is a chemoorganoheterotrophic haloalkaliphile. It has a small and streamlined genome and utilizes a wide variety of compatible solutes to resist osmotic pressure and multiple monovalent cation/proton antiporters for pH homeostasis. In addition to growth enhancement by light under microaerobic conditions, cell growth, organic substrate consumption and polyhydroxybutyrate biosynthesis were also improved by inorganic sulfide. Both quantitative RT-PCR and enzymatic assays verified that sulfide:quinone oxidoreductase was upregulated during this process. Metatranscriptomic analysis indicated that all genes related to environmental adaptation were transcribed in natural environments. Overall, this study has identified a novel abundant haloalkaliphile with multiple and highly integrated adaptive strategies and found that inorganic sulfide was able to improve the adaptation of a heterotroph to polyextreme environments.

pH Homeostasis and Sodium Ion Pumping by Multiple Resistance and pH Antiporters in Pyrococcus furiosus

Multiple Resistance and pH (Mrp) antiporters are seven-subunit complexes that couple transport of ions across the membrane in response to a proton motive force (PMF) and have various physiological roles, including sodium ion sensing and pH homeostasis. The hyperthermophilic archaeon Pyrococcus furiosus contains three copies of Mrp encoding genes in its genome. Two are found as integral components of two respiratory complexes, membrane bound hydrogenase (MBH) and the membrane bound sulfane sulfur reductase (MBS) that couple redox activity to sodium translocation, while the third copy is a stand-alone Mrp. Sequence alignments show that this Mrp does not contain an energy-input (PMF) module but contains all other predicted functional Mrp domains. The P. furiosus Mrp deletion strain exhibits no significant changes in optimal pH or sodium ion concentration for growth but is more sensitive to medium acidification during growth. Cell suspension hydrogen gas production assays using the deletion strain show that this Mrp uses sodium as the coupling ion. Mrp likely maintains cytoplasmic pH by exchanging protons inside the cell for extracellular sodium ions. Deletion of the MBH sodium-translocating module demonstrates that hydrogen gas production is uncoupled from ion pumping and provides insights into the evolution of this Mrp-containing respiratory complex.

Genetic and Biochemical Characterization of the Na+/H+ Antiporters of Pseudomonas aeruginosa

Pseudomonas aeruginosa has four Na⁺/H⁺ antiporters that interconvert and balance Na⁺ and H⁺ gradients across the membrane. These gradients are important for bioenergetics and ionic homeostasis. To understand these transporters, we constructed four strains, each of which has only one antiporter, i.e., NhaB, NhaP, NhaP2, and Mrp. We also constructed a quadruple deletion mutant that has no Na⁺/H⁺ antiporters. Although the antiporters of P. aeruginosa have been studied previously, the strains constructed here present the opportunity to characterize their kinetic properties in their native membranes and their roles in the physiology of P. aeruginosa. The strains expressing only NhaB or Mrp, the two electrogenic antiporters, were able to grow essentially like the wild-type strain across a range of Na⁺ concentrations and pH values. Strains with only NhaP or NhaP2, which are electroneutral, grew more poorly at increasing Na⁺ concentrations, especially at high pH values, with the strain expressing NhaP being more sensitive. The strain with no Na⁺/H⁺ antiporters was extremely sensitive to the Na⁺ concentration and showed essentially no Na⁺(Li⁺)/H⁺ antiporter activity, but it retained most K⁺/H⁺ antiporter activity of the wild-type strain at pH 7.5 and approximately one-half at pH 8.5. We also used the four strains that each express one of the four antiporters to characterize the kinetic properties of each transporter. Transcriptome sequencing analysis of the quadruple deletion strain showed widespread changes, including changes in pyocyanin synthesis, biofilm formation, and nitrate and glycerol metabolism. Thus, the strains constructed for this study will open a new door to understanding the physiological roles of these proteins and their activities in P. aeruginosa. IMPORTANCE Pseudomonas aeruginosa has four Na⁺/H⁺ antiporters that connect and interconvert its Na⁺ and H⁺ gradients. We have constructed four deletion mutants, each of which has only one of the four Na⁺/H⁺ antiporters. These strains made it possible to study the properties and physiological roles of each antiporter independently in its native membrane. Mrp and NhaB are each able to sustain growth over a wide range of pH values and Na⁺ concentrations, whereas the two electroneutral antiporters, NhaP and NhaP2, are most effective at low pH values. We also constructed a quadruple mutant lacking all four antiporters, in which the H⁺ and Na⁺ gradients are disconnected. This will make it possible to study the role of the two gradients independently.

Role of extremophiles and their extremozymes in biorefinery process of lignocellulose degradation

Technological advances in the field of life sciences have led to discovery of organisms that live in harsh environmental conditions referred to as extremophiles. These organisms have adapted themselves to thrive in extreme habitat giving these organisms an advantage over conventional mesophilic organisms in various industrial applications. Extremozymes produced by these extremophiles have high tolerance to inhospitable environmental conditions making them an ideal enzyme system for various industrial processes. A notable application of these extremophiles and extremozymes is their use in the degradation of recalcitrant lignocellulosic biomass and application in biorefineries. For maximum utilization of the trapped carbon source from this obstinate biomass, pretreatment is a necessary step that requires various physiochemical and enzymatic treatments. From search for novel extremophiles and extremozymes to development of various genetic and protein engineering techniques, investigation on extremozymes with enhanced stability and efficiency is been done. Since extremozymes are easily calibrated to work under such conditions, they have become an emerging topic in the research field of biofuel production. The review discusses the various extremozymes that play an important role in lignocellulose degradation along with recent studies on their molecular and genetic evolution for industrial application and production of biofuels and various value-added products.

Implication of cation-proton antiporters (CPA) in human health and diseases causing microorganisms

Cation and protons perform a substantial role in all the organism and its homeostasis within the cells are maintained by the cation-proton antiporters (CPAs). CPA is the huge family of the membrane transporter protein throughout the plant and animal kingdom including microorganism. In human, any malfunctioning of these proteins may lead to severe diseases like hypertension, heart diseases etc and CPAs are recently proposed to be responsible for the virulent property of various pathogens including Vibrio cholerae, Yersinia pestis etc. Human Sodium-Proton exchangers (Na⁺/H⁺ exchangers, NHEs) are crucial in ion homeostasis whereas Ec-NhaA, Na + -H + Antiporters maintain a balance of Na+ and proton in E. coli, regulating pH and cell volume within the cell. These Sodium-Proton antiporters are found to be responsible for the virulence in various pathogens causing human diseases. Understanding of these CPAs may assist investigators to target such human diseases, that further may lead to establishing the effective path for therapeutics or drug designing against associated human disease. Here we have compiled all such information on CPAs and provide a systematic approach to unravel the mechanism and role of antiporter proteins in a wide range of organisms. Being involved throughout all the species, this review on cation-proton antiporters may attract the attention of many investigators and concerned researchers and will be provided with the recent detailed information on the role of CPA in human health.

Expansion of the "Sodium World" through Evolutionary Time and Taxonomic Space

In 1986, Vladimir Skulachev and his colleagues coined the term "Sodium World" for the group of diverse organisms with sodium (Na)-based bioenergetics. Albeit only few such organisms had been discovered by that time, the authors insightfully noted that "the great taxonomic variety of organisms employing the Na-cycle points to the ubiquitous distribution of this novel type of membrane-linked energy transductions". Here we used tools of bioinformatics to follow expansion of the Sodium World through the evolutionary time and taxonomic space. We searched for those membrane protein families in prokaryotic genomes that correlate with the use of the Na-potential for ATP synthesis by different organisms. In addition to the known Na-translocators, we found a plethora of uncharacterized protein families; most of them show no homology with studied proteins. In addition, we traced the presence of Na-based energetics in many novel archaeal and bacterial clades, which were recently identified by metagenomic techniques. The data obtained support the view that the Na-based energetics preceded the proton-dependent energetics in evolution and prevailed during the first two billion years of the Earth history before the oxygenation of atmosphere. Hence, the full capacity of Na-based energetics in prokaryotes remains largely unexplored. The Sodium World expanded owing to the acquisition of new functions by Na-translocating systems. Specifically, most classes of G-protein-coupled receptors (GPCRs), which are targeted by almost half of the known drugs, appear to evolve from the Na-translocating microbial rhodopsins. Thereby the GPCRs of class A, with 700 representatives in human genome, retained the Na-binding site in the center of the transmembrane heptahelical bundle together with the capacity of Na-translocation. Mathematical modeling showed that the class A GPCRs could use the energy of transmembrane Na-potential for increasing both their sensitivity and selectivity. Thus, GPCRs, the largest protein family coded by human genome, stem from the Sodium World, which encourages exploration of other Na-dependent enzymes of eukaryotes.

Exploring the upper pH limits of nitrite oxidation: diversity, ecophysiology, and adaptive traits of haloalkalitolerant Nitrospira

Nitrite-oxidizing bacteria of the genus Nitrospira are key players of the biogeochemical nitrogen cycle. However, little is known about their occurrence and survival strategies in extreme pH environments. Here, we report on the discovery of physiologically versatile, haloalkalitolerant Nitrospira that drive nitrite oxidation at exceptionally high pH. Nitrospira distribution, diversity, and ecophysiology were studied in hypo- and subsaline (1.3-12.8 g salt/l), highly alkaline (pH 8.9-10.3) lakes by amplicon sequencing, metagenomics, and cultivation-based approaches. Surprisingly, not only were Nitrospira populations detected, but they were also considerably diverse with presence of members from  Nitrospira lineages I, II and IV. Furthermore, the ability of Nitrospira enrichment cultures to oxidize nitrite at neutral to highly alkaline pH of 10.5 was demonstrated. Metagenomic analysis of a newly enriched Nitrospira lineage IV species, "Candidatus Nitrospira alkalitolerans", revealed numerous adaptive features of this organism to its extreme environment. Among them were a sodium-dependent N-type ATPase and NADH:quinone oxidoreductase next to the proton-driven forms usually found in Nitrospira. Other functions aid in pH and cation homeostasis and osmotic stress defense. "Ca. Nitrospira alkalitolerans" also possesses group 2a and 3b [NiFe] hydrogenases, suggesting it can use hydrogen as alternative energy source. These results reveal how Nitrospira cope with strongly fluctuating pH and salinity conditions and expand our knowledge of nitrogen cycling in extreme habitats.

Structure of the Dietzia Mrp complex reveals molecular mechanism of this giant bacterial sodium proton pump

Multiple resistance and pH adaptation (Mrp) complexes are the most sophisticated known cation/proton exchangers and are essential for the survival of a vast variety of alkaliphilic and/or halophilic microorganisms. Moreover, this family of antiporters represents the ancestor of cation pumps in nearly all known redox-driven transporter complexes, including the complex I of the respiratory chain. For the Mrp complex, an experimental structure is lacking. We now report the structure of Mrp complex at 3.0-Å resolution solved using the single-particle cryo-EM method. The structure-inspired functional study of Mrp provides detailed information for further biophysical and biochemical investigation of the intriguingly pumping mechanism and physiological functions of this complex, as well as for exploring its potential as a therapeutic drug target.

Multiple resistance and pH adaptation (Mrp) complexes are sophisticated cation/proton exchangers found in a vast variety of alkaliphilic and/or halophilic microorganisms, and are critical for their survival in highly challenging environments. This family of antiporters is likely to represent the ancestor of cation pumps found in many redox-driven transporter complexes, including the complex I of the respiratory chain. Here, we present the three-dimensional structure of the Mrp complex from a Dietzia sp. strain solved at 3.0-Å resolution using the single-particle cryoelectron microscopy method. Our structure-based mutagenesis and functional analyses suggest that the substrate translocation pathways for the driving substance protons and the substrate sodium ions are separated in two modules and that symmetry-restrained conformational change underlies the functional cycle of the transporter. Our findings shed light on mechanisms of redox-driven primary active transporters, and explain how driving substances of different electric charges may drive similar transport processes.

Pan-genomic analysis reveals that the evolution of Dietzia species depends on their living habitats

The bacterial genus Dietzia is widely distributed in various environments. The genomes of 26 diverse strains of Dietzia, including almost all the type strains, were analysed in this study. This analysis revealed a lipid metabolism gene richness, which could explain the ability of Dietzia to live in oil related environments. The pan-genome consists of 83,976 genes assigned into 10,327 gene families, 792 of which are shared by all the genomes of Dietzia. Mathematical extrapolation of the data suggests that the Dietzia pan-genome is open. Both gene duplication and gene loss contributed to the open pan-genome, while horizontal gene transfer was limited. Dietzia strains primarily gained their diverse metabolic capacity through more ancient gene duplications. Phylogenetic analysis of Dietzia isolated from aquatic and terrestrial environments showed two distinct clades from the same ancestor. The genome sizes of Dietzia strains from aquatic environments were significantly larger than those from terrestrial environments, which was mainly due to the occurrence of more gene loss events during the evolutionary progress of the strains from terrestrial environments. The evolutionary history of Dietzia was tightly coupled to environmental conditions, and iron concentrations should be one of the key factors shaping the genomes of the Dietzia lineages.

Improved Salt Tolerance and Metabolomics Analysis of Synechococcus elongatus UTEX 2973 by Overexpressing Mrp Antiporters

The fast-growing cyanobacterium Synechococcus elongatus UTEX 2973 (Syn2973) is a promising candidate for photosynthetic microbial factory. Seawater utilization is necessary for large-scale cultivation of Syn2973 in the future. However, Syn2973 is sensitive to salt stress, making it necessary to improve its salt tolerance. In this study, 21 exogenous putative transporters were individually overexpressed in Syn2973 to evaluate their effects on salt tolerance. The results showed the overexpression of three Mrp antiporters significantly improved the salt tolerance of Syn2973. Notably, overexpressing the Mrp antiporter from Synechococcus sp. PCC 7002 improved cell growth by 57.7% under 0.4 M NaCl condition. In addition, the metabolomics and biomass composition analyses revealed the possible mechanisms against salt stress in both Syn2973 and the genetically engineered strain. The study provides important engineering strategies to improve salt tolerance of Syn2973 and is valuable for understanding mechanisms of salt tolerance in cyanobacteria.

Polar or Charged Residues Located in Four Highly Conserved Motifs Play a Vital Role in the Function or pH Response of a UPF0118 Family Na+(Li+)/H+ Antiporter

Functionally uncharacterized UPF0118 family has been re-designated as autoinducer-2 exporter (AI-2E) family since one of its members, Escherichia coli YdgG, was identified to function as an AI-2E. However, it's very likely that AI-2E family members may exhibit significantly distinct functions due to low identities between them. Recently, we identified one member of this family designated as UPF0118 to represent a novel class of Na⁺(Li⁺)/H⁺ antiporters. In this study, we presented that UPF0118, together with its homologs, should represent an independent group of AI-2E family, designated as Na⁺/H⁺ Antiporter Group. Notably, this group shows five highly conserved motifs designated as Motifs A to E, which are not detected in the majority of AI-2E family members. Functional analysis established that polar or charged residues located in Motif A to D play a vital role in Na⁺(Li⁺)/H⁺ antiport activity or pH response of UPF0118. However, three basic residues located in Motif E are not involved in the function of UPF0118, although the truncation of C terminus resulted in the non-expression of this transporter. Therefore, we propose that E₁₇₉-R₁₈₂-K₂₁₅-Q₂₁₇-D₂₅₁-R₂₉₂-R₂₉₃-E₂₉₆-K₂₉₈-S_{30 7} located in Motifs A to D can be used for signature functional motifs to recognize whether AI-2E family members function as Na⁺(Li⁺)/H⁺ antiporters. Current findings positively contribute to the knowledge of molecular mechanism of Na⁺, Li⁺ transporting and pH response of UPF0118, and the functional prediction of uncharacterized AI-2E family members.

Sodium antiporters of Pseudomonas aeruginosa in challenging conditions: effects on growth, biofilm formation, and swarming motility

BACKGROUND

Pseudomonas aeruginosa is a bacterial pathogen that can cause grave and sometimes chronic infections in patients with weakened immune systems and cystic fibrosis. It is expected that sodium/proton transporters in the cellular membrane are crucial for the organism's survival and growth under certain conditions, since many cellular processes rely on the maintenance of Na⁺ and H⁺ transmembrane gradients.

RESULTS

This study focused on the role of the primary and secondary proton and/or sodium pumps Mrp, Nuo, NhaB, NhaP, and NQR for growth, biofilm formation, and swarming motility in P. aeruginosa. Using mutants with gene deletions, we investigated the impact of each sodium pump's absence on the overall growth, biofilm formation, motility, and weak acid tolerance of the organism. We found that the absence of some, but not all, of the sodium pumps have a deleterious effect on the different phenotypes of P. aeruginosa.

CONCLUSION

The absence of the Mrp sodium/proton antiporter was clearly important in the organism's ability to survive and function in environments of higher pH and sodium concentrations, while the absence of Complex I, which is encoded by the nuo genes, had some consistent impact on the organism's growth regardless of the pH and sodium concentration of the environment.

Phenotypic characterization and comparative genome analysis of two strains of thermophilic, anaerobic, cellulolytic-xylanolytic bacterium Herbivorax saccincola

The genome sequences of thermophilic, anaerobic, and cellulolytic-xylanolytic bacterium Herbivorax saccincola strains A7 and GGR1 have recently been determined. Although both strains belong to the same species, A7 is alkaliphilic, non-endospore-forming, and ammonium-assimilating, whereas GGR1 is neutrophilic, endospore-forming, and weak-ammonium-assimilating. To better understand the phenotypic diversity among H. saccincola strains, the genome sequences of A7 and GGR1 were compared. A7 contained three additional genes showing similarity to an alkaline stress-associated ABC-transporter but lacked four endospore formation-associated genes, AUG58543 and AUG58618 (encoding SpoVT), AUG57258 (encoding SpoVS), and AUG58614 (encoding YdhD), all of which were present in GGR1. In addition, A7 contained key ammonia assimilation genes PQQ67145 and PQQ66619, encoding ornithine cyclodeaminase and arginase, respectively, which were absent in GGR1. There was no difference in the number and types of cellulosomal-scaffolding proteins and glycosyl hydrolases between the two strains. However, cellulase and xylanase enzymes from A7 demonstrated greater activity and stability at an alkaline pH compared with those from GGR1, and amino acid substitutions were identified in 11 glycosyl hydrolases from A7. This characterization though comparative genomic analysis provides useful information for understanding the genetic basis of the phenotypic differences between H. saccincola strains isolated from distinct areas and environments.

Whole-Genome Analysis of Halomonas sp. Soap Lake #7 Reveals It Possesses Putative Mrp Antiporter Operon Groups 1 and 2

The genus Halomonas possesses bacteria that are halophilic or halotolerant and exhibit a wide range of pH tolerance. The genome of Halomonas sp. Soap Lake #7 was sequenced to provide a better understanding of the mechanisms for salt and pH tolerance in this genus. The bacterium’s genome was found to possess two complete multiple resistance and pH antiporter systems, Group 1 and Group 2. This is the first report of both multiple resistance and pH antiporter Groups 1 and 2 in the genome of a haloalkaliphilic bacterium.

Occurrence and Function of the Na+-Translocating NADH:Quinone Oxidoreductase in Prevotella spp

Strictly anaerobic Prevotella spp. are characterized by their vast metabolic potential. As members of the Prevotellaceae family, they represent the most abundant organisms in the rumen and are typically found in monogastrics such as pigs and humans. Within their largely anoxic habitats, these bacteria are considered to rely primarily on fermentation for energy conservation. A recent study of the rumen microbiome identified multiple subunits of the Na⁺-translocating NADH:quinone oxidoreductase (NQR) belonging to different Prevotella spp. Commonly, the NQR is associated with biochemical energy generation by respiration. The existence of this Na⁺ pump in Prevotella spp. may indicate an important role for electrochemical Na⁺ gradients in their anaerobic metabolism. However, detailed information about the potential activity of the NQR in Prevotella spp. is not available. Here, the presence of a functioning NQR in the strictly anaerobic model organism P. bryantii B₁4 was verified by conducting mass spectrometric, biochemical, and kinetic experiments. Our findings propose that P. bryantii B₁4 and other Prevotella spp. retrieved from the rumen operate a respiratory NQR together with a fumarate reductase which suggests that these ruminal bacteria utilize a sodium motive force generated during respiratory NADH:fumarate oxidoreduction.

Potassium resistance of halotolerant and alkaliphilic Halomonas sp. Y2 by a Na+-induced K+ extrusion mechanism

In most halophiles, K⁺ generally acts as a major osmotic solute for osmotic adjustment and pH homeostasis. However, strains also need to extrude excessive intracellular K⁺ to avoid its toxicity. In the halotolerant and alkaliphilic Halomonas sp. Y2, an Na⁺-induced K⁺ extrusion process was observed when the cells were confronted with high extracellular K⁺ pressure and supplementation by millimolar Na⁺ ions. Among three mechanosensitive channels (KefA) and two K⁺/H⁺ antiporters founded in the genome of the strain, ke1 displayed around 3-5-fold upregulation to ion stress at pH 8.0, while much higher upregulation of Ha-mrp was observed at pH 10.0. Compared to the growth of wild-type Halomonas sp. Y2, deletion of these genes from the strain resulted in different growth phenotypes in response to the osmotic pressure of potassium. In combination with the transcriptional response of these genes, we proposed that the KefA channel of Ke1 is the main contributor to the K⁺-extrusion process under weak alkalinity, while the Mrp system plays critical roles in alleviating K⁺ contents at high pH. The combination of these strategies allows Halomonas sp. Y2 to grow over a range of extracellular pH and ion concentrations, and thus protect cells under high osmotic stress conditions.

Phenotypic and Genomic Properties of a Novel Deep-Lineage Haloalkaliphilic Member of the Phylum Balneolaeota From Soda Lakes Possessing Na+-Translocating Proteorhodopsin

Stable development of a heterotrophic bacterial satellite with a peculiar cell morphology has been observed in several enrichment cultures of haloalkaliphilic benthic filamentous cyanobacteria from a hypersaline soda lake in Kulunda Steppe (Altai, Russia). The organism was isolated in pure culture (strain Omega) using sonicated cyanobacterial cells as substrate and it was identified as a deep phylogenetic lineage within the recently proposed phylum Balneolaeota. It is an obligately aerobic heterotroph utilizing proteins and peptides for growth. The cell morphology significantly varied from semicircles to long filaments depending on the growth conditions. The cultures are red-orange colored due to a presence of carotenoids. The isolate is an obligate alkaliphile with a pH range for growth from 8.5 to 10.5 (optimum at 9.5-10) and moderately salt-tolerant with a range from 0.3 to 3 M total Na+ (optimum at 1 M). The genome analysis of strain Omega demonstrated a presence of gene, encoding a proteorhodopsin forming a separate branch in the sodium-translocating proteorhodopsin family. Experiments with washed cells of Omega confirmed light-dependent sodium export. A possible physiological role of the sodium proteorhodopsin in strain Omega is discussed. Phylogenomic analysis demostrated that strain Omega forms an deep, independent branch of a new genus and family level within a recently established phylum Balneolaeota.

Vibrio natriegens as Host for Expression of Multisubunit Membrane Protein Complexes

Escherichia coli is a convenient host for the expression of proteins, but the heterologous production of large membrane protein complexes often is hampered by the lack of specific accessory genes required for membrane insertion or cofactor assembly. In this study we introduce the non-pathogenic and fast-growing Vibrio natriegens as a suitable expression host for membrane-bound proteins from Vibrio cholerae. We achieved production of the primary Na⁺ pump, the NADH:quinone oxidoreductase (NQR), from V. cholerae in an active state, as indicated by increased overall NADH:quinone oxidoreduction activity of membranes from the transformed V. natriegens, and the sensitivity toward Ag⁺, a specific inhibitor of the NQR. Complete assembly of V. cholerae NQR expressed in V. natriegens was demonstrated by BN PAGE followed by activity staining. The secondary transport system Mrp from V. cholerae, another membrane-bound multisubunit complex, was also produced in V. natriegens in a functional state, as demonstrated by in vivo Li⁺ transport. V. natriegens is a promising expression host for the production of membrane protein complexes from Gram-negative pathogens.

The complete genome sequence of Rhodobaca barguzinensis alga05 (DSM 19920) documents its adaptation for life in soda lakes

Soda lakes, with their high salinity and high pH, pose a very challenging environment for life. Microorganisms living in these harsh conditions have had to adapt their physiology and gene inventory. Therefore, we analyzed the complete genome of the haloalkaliphilic photoheterotrophic bacterium Rhodobaca barguzinensis strain alga05. It consists of a 3,899,419 bp circular chromosome with 3624 predicted coding sequences. In contrast to most of Rhodobacterales, this strain lacks any extrachromosomal elements. To identify the genes responsible for adaptation to high pH, we compared the gene inventory in the alga05 genome with genomes of 17 reference strains belonging to order Rhodobacterales. We found that all haloalkaliphilic strains contain the mrpB gene coding for the B subunit of the MRP Na⁺/H⁺ antiporter, while this gene is absent in all non-alkaliphilic strains, which indicates its importance for adaptation to high pH. Further analysis showed that alga05 requires organic carbon sources for growth, but it also contains genes encoding the ethylmalonyl-CoA pathway for CO₂ fixation. Remarkable is the genetic potential to utilize organophosphorus compounds as a source of phosphorus. In summary, its genetic inventory indicates a large flexibility of the alga05 metabolism, which is advantageous in rapidly changing environmental conditions in soda lakes.

Structure of an Ancient Respiratory System

Hydrogen gas-evolving membrane-bound hydrogenase (MBH) and quinone-reducing complex I are homologous respiratory complexes with a common ancestor, but a structural basis for their evolutionary relationship is lacking. Here, we report the cryo-EM structure of a 14-subunit MBH from the hyperthermophile Pyrococcus furiosus. MBH contains a membrane-anchored hydrogenase module that is highly similar structurally to the quinone-binding Q-module of complex I while its membrane-embedded ion-translocation module can be divided into a H⁺- and a Na⁺-translocating unit. The H⁺-translocating unit is rotated 180° in-membrane with respect to its counterpart in complex I, leading to distinctive architectures for the two respiratory systems despite their largely conserved proton-pumping mechanisms. The Na⁺-translocating unit, absent in complex I, resembles that found in the Mrp H⁺/Na⁺ antiporter and enables hydrogen gas evolution by MBH to establish a Na⁺ gradient for ATP synthesis near 100°C. MBH also provides insights into Mrp structure and evolution of MBH-based respiratory enzymes.

The Lysine 299 Residue Endows the Multisubunit Mrp1 Antiporter with Dominant Roles in Na+ Resistance and pH Homeostasis in Corynebacterium glutamicum

Corynebacterium glutamicum is generally regarded as a moderately salt- and alkali-tolerant industrial organism. However, relatively little is known about the molecular mechanisms underlying these specific adaptations. Here, we found that the Mrp1 antiporter played crucial roles in conferring both environmental Na⁺ resistance and alkali tolerance whereas the Mrp2 antiporter was necessary in coping with high-KCl stress at alkaline pH. Furthermore, the Δmrp1 Δmrp2 double mutant showed the most-severe growth retardation and failed to grow under high-salt or alkaline conditions. Consistent with growth properties, the Na⁺/H⁺ antiporters of C. glutamicum were differentially expressed in response to specific salt or alkaline stress, and an alkaline stimulus particularly induced transcript levels of the Mrp-type antiporters. When the major Mrp1 antiporter was overwhelmed, C. glutamicum might employ alternative coordinate strategies to regulate antiport activities. Site-directed mutagenesis demonstrated that several conserved residues were required for optimal Na⁺ resistance, such as Mrp1A K²⁹⁹, Mrp1C I⁷⁶, Mrp1A H²³⁰, and Mrp1D E¹³⁶ Moreover, the chromosomal replacement of lysine 299 in the Mrp1A subunit resulted in a higher intracellular Na⁺ level and a more alkaline intracellular pH value, thereby causing a remarkable growth attenuation. Homology modeling of the Mrp1 subcomplex suggested two possible ion translocation pathways, and lysine 299 might exert its effect by affecting the stability and flexibility of the cytoplasm-facing channel in the Mrp1A subunit. Overall, these findings will provide new clues to the understanding of salt-alkali adaptation during C. glutamicum stress acclimatization.IMPORTANCE The capacity to adapt to harsh environments is crucial for bacterial survival and product yields, including industrially useful Corynebacterium glutamicum Although C. glutamicum exhibits a marked resistance to salt-alkaline stress, the possible mechanism for these adaptations is still unclear. Here, we present the physiological functions and expression patterns of C. glutamicum putative Na⁺/H⁺ antiporters and conserved residues of Mrp1 subunits, which respond to different salt and alkaline stresses. We found that the Mrp-type antiporters, particularly the Mrp1 antiporter, played a predominant role in maintaining intracellular nontoxic Na⁺ levels and alkaline pH homeostasis. Loss of the major Mrp1 antiporter had a profound effect on gene expression of other antiporters under salt or alkaline conditions. The lysine 299 residue may play its essential roles in conferring salt and alkaline tolerance by affecting the ion translocation channel of the Mrp1A subunit. These findings will contribute to a better understanding of Na⁺/H⁺ antiporters in sodium antiport and pH regulation.

Compatible Solute Synthesis and Import by the Moderate Halophile Spiribacter salinus: Physiology and Genomics

Members of the genus Spiribacter are found worldwide and are abundant in ecosystems possessing intermediate salinities between seawater and saturated salt concentrations. Spiribacter salinus M19-40 is the type species of this genus and its first cultivated representative. In the habitats of S. salinus M19-40, high salinity is a key determinant for growth and we therefore focused on the cellular adjustment strategy to this persistent environmental challenge. We coupled these experimental studies to the in silico mining of the genome sequence of this moderate halophile with respect to systems allowing this bacterium to control its potassium and sodium pools, and its ability to import and synthesize compatible solutes. S. salinus M19-40 produces enhanced levels of the compatible solute ectoine, both under optimal and growth-challenging salt concentrations, but the genes encoding the corresponding biosynthetic enzymes are not organized in a canonical ectABC operon. Instead, they are scrambled (ectAC; ectB) and are physically separated from each other on the S. salinus M19-40 genome. Genomes of many phylogenetically related bacteria also exhibit a non-canonical organization of the ect genes. S. salinus M19-40 also synthesizes trehalose, but this compatible solute seems to make only a minor contribution to the cytoplasmic solute pool under osmotic stress conditions. However, its cellular levels increase substantially in stationary phase cells grown under optimal salt concentrations. In silico genome mining revealed that S. salinus M19-40 possesses different types of uptake systems for compatible solutes. Among the set of compatible solutes tested in an osmostress protection growth assay, glycine betaine and arsenobetaine were the most effective. Transport studies with radiolabeled glycine betaine showed that S. salinus M19-40 increases the pool size of this osmolyte in a fashion that is sensitively tied to the prevalent salinity of the growth medium. It was amassed in salt-stressed cells in unmodified form and suppressed the synthesis of ectoine. In conclusion, the data presented here allow us to derive a genome-scale picture of the cellular adjustment strategy of a species that represents an environmentally abundant group of ecophysiologically important halophilic microorganisms.

Roles of Staphylococcus aureus Mnh1 and Mnh2 Antiporters in Salt Tolerance, Alkali Tolerance, and Pathogenesis

Staphylococcus aureus has three types of cation/proton antiporters. The type 3 family includes two multisubunit Na⁺/H⁺ (Mnh) antiporters, Mnh1 and Mnh2. These antiporters are clusters of seven hydrophobic membrane-bound protein subunits. Mnh antiporters play important roles in maintaining cytoplasmic pH in prokaryotes, enabling their survival under extreme environmental stress. In this study, we investigated the physiological roles and catalytic properties of Mnh1 and Mnh2 in S. aureus. Both Mnh1 and Mnh2 were cloned separately into a pGEM3Z+ vector in the antiporter-deficient KNabc Escherichia coli strain. The catalytic properties of the antiporters were measured in everted (inside out) vesicles. The Mnh1 antiporter exhibited a significant exchange of Na⁺/H⁺ cations at pH 7.5. Mnh2 showed a significant exchange of both Na⁺/H⁺ and K⁺/H⁺ cations, especially at pH 8.5. Under elevated salt conditions, deletion of the mnhA1 gene resulted in a significant reduction in the growth rate of S. aureus in the range of pH 7.5 to 9. Deletion of mnhA2 had similar effects but mainly in the range of pH 8.5 to 9.5. Double deletion of mnhA1 and mnhA2 led to a severe reduction in the S. aureus growth rate mainly at pH values above 8.5. The effects of functional losses of both antiporters in S. aureus were also assessed via their support of virulence in a mouse in vivo infection model. Deletion of the mnhA1 gene led to a major loss of S. aureus virulence in mice, while deletion of mnh2 led to no change in virulence.

IMPORTANCE This study focuses on the catalytic properties and physiological roles of Mnh1 and Mnh2 cation/proton antiporters in S. aureus and their contributions under different stress conditions. The Mnh1 antiporter was found to have catalytic activity for Na⁺/H⁺ antiport, and it plays a significant role in maintaining halotolerance at pH 7.5 while the Mnh2 antiporter has catalytic antiporter activities for Na⁺/H⁺ and K⁺/H⁺ that have roles in both osmotolerance and halotolerance in S. aureus. Study of S. aureus with a single deletion of either mnhA1 or mnhA2 was assessed in an infection model of mice. The result shows that mnhA1, but not mnhA2, plays a major role in S. aureus virulence.

Comparative genomic analysis of Brevibacterium strains: insights into key genetic determinants involved in adaptation to the cheese habitat

Background

Brevibacterium strains are widely used for the manufacturing of surface-ripened cheeses, contributing to the breakdown of lipids and proteins and producing volatile sulfur compounds and red-orange pigments. The objective of the present study was to perform comparative genomic analyses in order to better understand the mechanisms involved in their ability to grow on the cheese surface and the differences between the strains.

Results

The genomes of 23 Brevibacterium strains, including twelve strains isolated from cheeses, were compared for their gene repertoire involved in salt tolerance, iron acquisition, bacteriocin production and the ability to use the energy compounds present in cheeses. All or almost all the genomes encode the enzymes involved in ethanol, acetate, lactate, 4-aminobutyrate and glycerol catabolism, and in the synthesis of the osmoprotectants ectoine, glycine-betaine and trehalose. Most of the genomes contain two contiguous genes encoding extracellular proteases, one of which was previously characterized for its activity on caseins. Genes encoding a secreted triacylglycerol lipase or involved in the catabolism of galactose and D-galactonate or in the synthesis of a hydroxamate-type siderophore are present in part of the genomes. Numerous Fe³⁺/siderophore ABC transport components are present, part of them resulting from horizontal gene transfers. Two cheese-associated strains have also acquired catecholate-type siderophore biosynthesis gene clusters by horizontal gene transfer. Predicted bacteriocin biosynthesis genes are present in most of the strains, and one of the corresponding gene clusters is located in a probable conjugative transposon that was only found in cheese-associated strains.

Conclusions

Brevibacterium strains show differences in their gene repertoire potentially involved in the ability to grow on the cheese surface. Part of these differences can be explained by different phylogenetic positions or by horizontal gene transfer events. Some of the distinguishing features concern biotic interactions with other strains such as the secretion of proteases and triacylglycerol lipases, and competition for iron or bacteriocin production. In the future, it would be interesting to take the properties deduced from genomic analyses into account in order to improve the screening and selection of Brevibacterium strains, and their association with other ripening culture components.

Electronic supplementary material

The online version of this article (10.1186/s12864-017-4322-1) contains supplementary material, which is available to authorized users.

Mrp Antiporters Have Important Roles in Diverse Bacteria and Archaea

Mrp (Multiple resistance and pH) antiporter was identified as a gene complementing an alkaline-sensitive mutant strain of alkaliphilic Bacillus halodurans C-125 in 1990. At that time, there was no example of a multi-subunit type Na⁺/H⁺ antiporter comprising six or seven hydrophobic proteins, and it was newly designated as the monovalent cation: proton antiporter-3 (CPA3) family in the classification of transporters. The Mrp antiporter is broadly distributed among bacteria and archaea, not only in alkaliphiles. Generally, all Mrp subunits, mrpA–G, are required for enzymatic activity. Two exceptions are Mrp from the archaea Methanosarcina acetivorans and the eubacteria Natranaerobius thermophilus, which are reported to sustain Na⁺/H⁺ antiport activity with the MrpA subunit alone. Two large subunits of the Mrp antiporter, MrpA and MrpD, are homologous to membrane-embedded subunits of the respiratory chain complex I, NuoL, NuoM, and NuoN, and the small subunit MrpC has homology with NuoK. The functions of the Mrp antiporter include sodium tolerance and pH homeostasis in an alkaline environment, nitrogen fixation in Schizolobium meliloti, bile salt tolerance in Bacillus subtilis and Vibrio cholerae, arsenic oxidation in Agrobacterium tumefaciens, pathogenesis in Pseudomonas aeruginosa and Staphylococcus aureus, and the conversion of energy involved in metabolism and hydrogen production in archaea. In addition, some Mrp antiporters transport K⁺ and Ca²⁺ instead of Na⁺, depending on the environmental conditions. Recently, the molecular structure of the respiratory chain complex I has been elucidated by others, and details of the mechanism by which it transports protons are being clarified. Based on this, several hypotheses concerning the substrate transport mechanism in the Mrp antiporter have been proposed. The MrpA and MrpD subunits, which are homologous to the proton transport subunit of complex I, are involved in the transport of protons and their coupling cations. Herein, we outline other recent findings on the Mrp antiporter.

COGNAT: a web server for comparative analysis of genomic neighborhoods

Background

In prokaryotic genomes, functionally coupled genes can be organized in conserved gene clusters enabling their coordinated regulation. Such clusters could contain one or several operons, which are groups of co-transcribed genes. Those genes that evolved from a common ancestral gene by speciation (i.e. orthologs) are expected to have similar genomic neighborhoods in different organisms, whereas those copies of the gene that are responsible for dissimilar functions (i.e. paralogs) could be found in dissimilar genomic contexts. Comparative analysis of genomic neighborhoods facilitates the prediction of co-regulated genes and helps to discern different functions in large protein families.

Aim

We intended, building on the attribution of gene sequences to the clusters of orthologous groups of proteins (COGs), to provide a method for visualization and comparative analysis of genomic neighborhoods of evolutionary related genes, as well as a respective web server.

Results

Here we introduce the COmparative Gene Neighborhoods Analysis Tool (COGNAT), a web server for comparative analysis of genomic neighborhoods. The tool is based on the COG database, as well as the Pfam protein families database. As an example, we show the utility of COGNAT in identifying a new type of membrane protein complex that is formed by paralog(s) of one of the membrane subunits of the NADH:quinone oxidoreductase of type 1 (COG1009) and a cytoplasmic protein of unknown function (COG3002).

Reviewers

This article was reviewed by Drs. Igor Zhulin, Uri Gophna and Igor Rogozin.

Electronic supplementary material

The online version of this article (10.1186/s13062-017-0196-z) contains supplementary material, which is available to authorized users.

Guardians in a stressful world: the Opu family of compatible solute transporters from Bacillus subtilis

The development of a semi-permeable cytoplasmic membrane was a key event in the evolution of microbial proto-cells. As a result, changes in the external osmolarity will inevitably trigger water fluxes along the osmotic gradient. The ensuing osmotic stress has consequences for the magnitude of turgor and will negatively impact cell growth and integrity. No microorganism can actively pump water across the cytoplasmic membrane; hence, microorganisms have to actively adjust the osmotic potential of their cytoplasm to scale and direct water fluxes in order to prevent dehydration or rupture. They will accumulate ions and physiologically compliant organic osmolytes, the compatible solutes, when they face hyperosmotic conditions to retain cell water, and they rapidly expel these compounds through the transient opening of mechanosensitive channels to curb water efflux when exposed to hypo-osmotic circumstances. Here, we provide an overview on the salient features of the osmostress response systems of the ubiquitously distributed bacterium Bacillus subtilis with a special emphasis on the transport systems and channels mediating regulation of cellular hydration and turgor under fluctuating osmotic conditions. The uptake of osmostress protectants via the Opu family of transporters, systems of central importance for the management of osmotic stress by B. subtilis, will be particularly highlighted.

Phylogenomic Analysis of Type 1 NADH:Quinone Oxidoreductase

We performed phylogenomic analysis of the catalytic core of NADH:quinone oxidoreductases of type 1 (NDH-1). Analysis of phylogenetic trees, as constructed for the core subunits of NDH-1, revealed fundamental differences in their topologies. In the case of four putatively homologous ion-carrying membrane subunits, the trees for the NuoH and NuoN subunits contained separate archaeal clades, whereas subunits NuoL and NuoM were characterized by multiple archaeal clades spread among bacterial branches. Large, separate clades, which united sequences belonging to different archaeal subdomains, were also found for cytoplasmic subunits NuoD and NuoB, homologous to the large and small subunits of nickel-iron hydrogenases. A smaller such clade was also shown for subunit NuoC. Based on these data, we suggest that the ancestral NDH-1 complex could be present already at the stage of the Last Universal Cellular Ancestor (LUCA). Ancestral forms of membrane subunits NuoN and NuoH and cytoplasmic subunits NuoD, NuoB, and, perhaps NuoC, may have formed a membrane complex that operated as an ion-translocating membrane hydrogenase. After the complex attained the ability to reduce membrane quinones, gene duplications could yield the subunits NuoL and NuoM, which enabled translocation of additional ions.

Functional Role of MrpA in the MrpABCDEFG Na+/H+ Antiporter Complex from the Archaeon Methanosarcina acetivorans

The multisubunit cation/proton antiporter 3 family, also called Mrp, is widely distributed in all three phylogenetic domains (Eukarya, Bacteria, and Archaea). Investigations have focused on Mrp complexes from the domain Bacteria to the exclusion of Archaea, with a consensus emerging that all seven subunits are required for Na⁺/H⁺ antiport activity. The MrpA subunit from the MrpABCDEFG Na⁺/H⁺ antiporter complex of the archaeon Methanosarcina acetivorans was produced in antiporter-deficient Escherichia coli strains EP432 and KNabc and biochemically characterized to determine the role of MrpA in the complex. Both strains containing MrpA grew in the presence of up to 500 mM NaCl and pH values up to 11.0 with no added NaCl. Everted vesicles from the strains containing MrpA were able to generate a NADH-dependent pH gradient (ΔpH), which was abated by the addition of monovalent cations. The apparent K_m values for Na⁺ and Li⁺ were similar and ranged from 31 to 63 mM, whereas activity was too low to determine the apparent K_m for K⁺ Optimum activity was obtained between pH 7.0 and 8.0. Homology molecular modeling identified two half-closed symmetry-related ion translocation channels that are linked, forming a continuous path from the cytoplasm to the periplasm, analogous to the NuoL subunit of complex I. Bioinformatics analyses revealed genes encoding homologs of MrpABCDEFG in metabolically diverse methane-producing species. Overall, the results advance the biochemical, evolutionary, and physiological understanding of Mrp complexes that extends to the domain Archaea IMPORTANCE: The work is the first reported characterization of an Mrp complex from the domain Archaea, specifically methanogens, for which Mrp is important for acetotrophic growth. The results show that the MrpA subunit is essential for antiport activity and, importantly, that not all seven subunits are required, which challenges current dogma for Mrp complexes from the domain Bacteria A mechanism is proposed in which an MrpAD subcomplex catalyzes Na⁺/H⁺ antiport independent of an MrpBCEFG subcomplex, although the activity of the former is modulated by the latter. Properties of MrpA strengthen proposals that the Mrp complex is of ancient origin and that subunits were recruited to evolve the ancestral complex I. Finally, bioinformatics analyses indicate that Mrp complexes function in diverse methanogenic pathways.

Effects of chromosomal deletion of the operon encoding the multiple resistance and pH-related antiporter in Vibrio cholerae

To examine the possible physiological significance of Mrp, a multi-subunit cation/proton antiporter from Vibrio cholerae, a chromosomal deletion Δmrp of V. cholerae was constructed and characterized. The resulting mutant showed a consistent early growth defect in LB broth that became more evident at elevated pH of the growth medium and increasing Na+ or K+ loads. After 24 h incubation, these differences disappeared likely due to the concerted effort of other cation pumps in the mrp mutant. Phenotype MicroArray analyses revealed an unexpected systematic defect in nitrogen utilization in the Δmrp mutant that was complemented by using the mrpA'-F operon on an arabinose-inducible expression vector. Deletion of the mrp operon also led to hypermotility, observable on LB and M9 semi-solid agar. Surprisingly, Δmrp mutation resulted in wild-type biofilm formation in M9 despite a growth defect but the reverse was true in LB. Furthermore, the Δmrp strain exhibited higher susceptibility to amphiphilic anions. These pleiotropic phenotypes of the Δmrp mutant demonstrate how the chemiosmotic activity of Mrp contributes to the survival potential of V. cholerae despite the presence of an extended battery of cation/proton antiporters of varying ion selectivity and pH profile operating in the same membrane.

Alkaline Response of a Halotolerant Alkaliphilic Halomonas Strain and Functional Diversity of Its Na+(K+)/H+ Antiporters

Halomonas sp. Y2 is a halotolerant alkaliphilic strain from Na⁺-rich pulp mill wastewater with high alkalinity (pH >11.0). Transcriptome analysis of this isolate revealed this strain may use various transport systems for pH homeostasis. In particular, the genes encoding four putative Na⁺/H⁺ antiporters were differentially expressed upon acidic or alkaline conditions. Further evidence, from heterologous expression and mutant studies, suggested that Halomonas sp. Y2 employs its Na⁺/H⁺ antiporters in a labor division way to deal with saline and alkaline environments. Ha-NhaD2 displayed robust Na⁺(Li⁺) resistance and high transport activities in Escherichia coli; a ΔHa-nhaD2 mutant exhibited growth inhibition at high Na⁺(Li⁺) concentrations at pH values of 6.2, 8.0, and 10.0, suggesting its physiological role in osmotic homeostasis. In contrast, Ha-NhaD1 showed much weaker activities in ion exporting and pH homeostasis. Ha-Mrp displayed a combination of properties similar to those of Mrp transporters from some Bacillus alkaliphiles and neutrophiles. This conferred obvious Na⁺(Li⁺, K⁺) resistance in E. coli-deficient strains, as those ion transport spectra of some neutrophil Mrp antiporters. Conversely, similar to the Bacillus alkaliphiles, Ha-Mrp showed central roles in the pH homeostasis of Halomonas sp. Y2. An Ha-mrp-disrupted mutant was seriously inhibited by high concentrations of Na⁺(Li⁺, K⁺) but only under alkaline conditions. Ha-NhaP was determined to be a K⁺/H⁺ antiporter and shown to confer strong K⁺ resistance both at acidic and alkaline stresses.

Differences in the phenotypic effects of mutations in homologous MrpA and MrpD subunits of the multi-subunit Mrp-type Na+/H+ antiporter

Mrp antiporters are the sole antiporters in the Cation/Proton Antiporter 3 family of transporter databases because of their unusual structural complexity, 6-7 hydrophobic proteins that function as a hetero-oligomeric complex. The two largest and homologous subunits, MrpA and MrpD, are essential for antiport activity and have direct roles in ion transport. They also show striking homology with proton-conducting, membrane-embedded Nuo subunits of respiratory chain complex I of bacteria, e.g., Escherichia coli. MrpA has the closest homology to the complex I NuoL subunit and MrpD has the closest homology to the complex I NuoM and N subunits. Here, introduction of mutations in MrpD, in residues that are also present in MrpA, led to defects in antiport function and/or complex formation. No significant phenotypes were detected in strains with mutations in corresponding residues of MrpA, but site-directed changes in the C-terminal region of MrpA had profound effects, showing that the MrpA C-terminal region has indispensable roles in antiport function. The results are consistent with a divergence in adaptations that support the roles of MrpA and MrpD in secondary antiport, as compared to later adaptations supporting homologs in primary proton pumping by the respiratory chain complex I.

Novel Metal Cation Resistance Systems from Mutant Fitness Analysis of Denitrifying Pseudomonas stutzeri

Metal ion transport systems have been studied extensively, but the specificity of a given transporter is often unclear from amino acid sequence data alone. In this study, predicted Cu(2+) and Zn(2+) resistance systems in Pseudomonas stutzeri strain RCH2 are compared with those experimentally implicated in Cu(2+) and Zn(2+) resistance, as determined by using a DNA-barcoded transposon mutant library. Mutant fitness data obtained under denitrifying conditions are combined with regulon predictions to yield a much more comprehensive picture of Cu(2+) and Zn(2+) resistance in strain RCH2. The results not only considerably expand what is known about well-established metal ion exporters (CzcCBA, CzcD, and CusCBA) and their accessory proteins (CzcI and CusF), they also reveal that isolates with mutations in some predicted Cu(2+) resistance systems do not show decreased fitness relative to the wild type when exposed to Cu(2+) In addition, new genes are identified that have no known connection to Zn(2+) (corB, corC, Psest_3226, Psest_3322, and Psest_0618) or Cu(2+) resistance (Mrp antiporter subunit gene, Psest_2850, and Psest_0584) but are crucial for resistance to these metal cations. Growth of individual deletion mutants lacking corB, corC, Psest_3226, or Psest_3322 confirmed the observed Zn-dependent phenotypes. Notably, to our knowledge, this is the first time a bacterial homolog of TMEM165, a human gene responsible for a congenital glycosylation disorder, has been deleted and the resulting strain characterized. Finally, the fitness values indicate Cu(2+)- and Zn(2+)-based inhibition of nitrite reductase and interference with molybdenum cofactor biosynthesis for nitrate reductase. These results extend the current understanding of Cu(2+) and Zn(2+) efflux and resistance and their effects on denitrifying metabolism.

IMPORTANCE

In this study, genome-wide mutant fitness data in P. stutzeri RCH2 combined with regulon predictions identify several proteins of unknown function that are involved in resisting zinc and copper toxicity. For zinc, these include a member of the UPF0016 protein family that was previously implicated in Ca(2+)/H(+) antiport and a human congenital glycosylation disorder, CorB and CorC, which were previously linked to Mg(2+) transport, and Psest_3322 and Psest_0618, two proteins with no characterized homologs. Experiments using mutants lacking Psest_3226, Psest_3322, corB, corC, or czcI verified their proposed functions, which will enable future studies of these little-characterized zinc resistance determinants. Likewise, Psest_2850, annotated as an ion antiporter subunit, and the conserved hypothetical protein Psest_0584 are implicated in copper resistance. Physiological connections between previous studies and phenotypes presented here are discussed. Functional and mechanistic understanding of transport proteins improves the understanding of systems in which members of the same protein family, including those in humans, can have different functions.

Functional Differentiation of Antiporter-Like Polypeptides in Complex I; a Site-Directed Mutagenesis Study of Residues Conserved in MrpA and NuoL but Not in MrpD, NuoM, and NuoN

It has long been known that the three largest subunits in the membrane domain (NuoL, NuoM and NuoN) of complex I are homologous to each other, as well as to two subunits (MrpA and MrpD) from a Na+/H+ antiporter, Mrp. MrpA and NuoL are more similar to each other and the same is true for MrpD and NuoN. This suggests a functional differentiation which was proven experimentally in a deletion strain model system, where NuoL could restore the loss of MrpA, but not that of MrpD and vice versa. The simplest explanation for these observations was that the MrpA and MrpD proteins are not antiporters, but rather single subunit ion channels that together form an antiporter. In this work our focus was on a set of amino acid residues in helix VIII, which are only conserved in NuoL and MrpA (but not in any of the other antiporter-like subunits.) and to compare their effect on the function of these two proteins. By combining complementation studies in B. subtilis and 23Na-NMR, response of mutants to high sodium levels were tested. All of the mutants were able to cope with high salt levels; however, all but one mutation (M258I/M225I) showed differences in the efficiency of cell growth and sodium efflux. Our findings showed that, although very similar in sequence, NuoL and MrpA seem to differ on the functional level. Nonetheless the studied mutations gave rise to interesting phenotypes which are of interest in complex I research.