A Bacillus subtilis secreted phosphodiesterase/alkaline phosphatase is the product of a Pho regulon gene, phoD

Plant communication with rhizosphere microbes can be revealed by understanding microbial functional gene composition

Understanding rhizosphere microbial ecology is necessary to reveal the interplay between plants and associated microbial communities. The significance of rhizosphere-microbial interactions in plant growth promotion, mediated by several key processes such as auxin synthesis, enhanced nutrient uptake, stress alleviation, disease resistance, etc., is unquestionable and well reported in numerous literature. Moreover, rhizosphere research has witnessed tremendous progress due to the integration of the metagenomics approach and further shift in our viewpoint from taxonomic to functional diversity over the past decades. The microbial functional genes corresponding to the beneficial functions provide a solid foundation for the successful establishment of positive plant-microbe interactions. The microbial functional gene composition in the rhizosphere can be regulated by several factors, e.g., the nutritional requirements of plants, soil chemistry, soil nutrient status, pathogen attack, abiotic stresses, etc. Knowing the pattern of functional gene composition in the rhizosphere can shed light on the dynamics of rhizosphere microbial ecology and the strength of cooperation between plants and associated microbes. This knowledge is crucial to realizing how microbial functions respond to unprecedented challenges which are obvious in the Anthropocene. Unraveling how microbes-mediated beneficial functions will change under the influence of several challenges, requires knowledge of the pattern and composition of functional genes corresponding to beneficial functions such as biogeochemical functions (nutrient cycle), plant growth promotion, stress mitigation, etc. Here, we focus on the molecular traits of plant growth-promoting functions delivered by a set of microbial functional genes that can be useful to the emerging field of rhizosphere functional ecology.

New insights in bacterial organophosphorus cycling: From human pathogens to environmental bacteria

In terrestrial and aquatic ecosystems, phosphorus (P) availability controls primary production, with consequences for climate regulation and global food security. Understanding the microbial controls on the global P cycle is a prerequisite for minimising our reliance on non-renewable phosphate rock reserves and reducing pollution associated with excessive P fertiliser use. This recognised importance has reinvigorated research into microbial P cycling, which was pioneered over 75 years ago through the study of human pathogenic bacteria-host interactions. Immobilised organic P represents a significant fraction of the total P pool. Hence, microbes have evolved a plethora of mechanisms to transform this fraction into labile inorganic phosphate, the building block for numerous biological molecules. The 'genomics era' has revealed an extraordinary diversity of organic P cycling genes exist in the environment and studies going 'back to the lab' are determining how this diversity relates to function. Through this integrated approach, many hitherto unknown genes and proteins that are involved in microbial P cycling have been discovered. Not only do these fundamental discoveries push the frontier of our knowledge, but several examples also provide exciting opportunities for biotechnology and present possible solutions for improving the sustainability of how we grow our food, both locally and globally. In this review, we provide a comprehensive overview of bacterial organic P cycling, covering studies on human pathogens and how this knowledge is informing new discoveries in environmental microbiology.

Comparative chemical genomics in Babesia species identifies the alkaline phosphatase PhoD as a determinant of antiparasitic resistance

Babesiosis is an emerging zoonosis and widely distributed veterinary infection caused by 100+ species of Babesia parasites. The diversity of Babesia parasites and the lack of specific drugs necessitate the discovery of broadly effective antibabesials. Here, we describe a comparative chemogenomics (CCG) pipeline for the identification of conserved targets. CCG relies on parallel in vitro evolution of resistance in independent populations of Babesia spp. (B. bovis and B. divergens). We identified a potent antibabesial, MMV019266, from the Malaria Box, and selected for resistance in two species of Babesia. After sequencing of multiple independently derived lines in the two species, we identified mutations in a membrane-bound metallodependent phosphatase (phoD). In both species, the mutations were found in the phoD-like phosphatase domain. Using reverse genetics, we validated that mutations in bdphoD confer resistance to MMV019266 in B. divergens. We have also demonstrated that BdPhoD localizes to the endomembrane system and partially with the apicoplast. Finally, conditional knockdown and constitutive overexpression of BdPhoD alter the sensitivity to MMV019266 in the parasite. Overexpression of BdPhoD results in increased sensitivity to the compound, while knockdown increases resistance, suggesting BdPhoD is a pro-susceptibility factor. Together, we have generated a robust pipeline for identification of resistance loci and identified BdPhoD as a resistance mechanism in Babesia species.

Comparative chemical genomics in Babesia species identifies the alkaline phosphatase phoD as a novel determinant of resistance

Babesiosis is an emerging zoonosis and widely distributed veterinary infection caused by 100+ species of Babesia parasites. The diversity of Babesia parasites, coupled with the lack of potent inhibitors necessitates the discovery of novel conserved druggable targets for the generation of broadly effective antibabesials. Here, we describe a comparative chemogenomics (CCG) pipeline for the identification of novel and conserved targets. CCG relies on parallel in vitro evolution of resistance in independent populations of evolutionarily-related Babesia spp. ( B. bovis and B. divergens ). We identified a potent antibabesial inhibitor from the Malaria Box, MMV019266. We were able to select for resistance to this compound in two species of Babesia, achieving 10-fold or greater resistance after ten weeks of intermittent selection. After sequencing of multiple independently derived lines in the two species, we identified mutations in a single conserved gene in both species: a membrane-bound metallodependent phosphatase (putatively named PhoD). In both species, the mutations were found in the phoD-like phosphatase domain, proximal to the predicted ligand binding site. Using reverse genetics, we validated that mutations in PhoD confer resistance to MMV019266. We have also demonstrated that PhoD localizes to the endomembrane system and partially with the apicoplast. Finally, conditional knockdown and constitutive overexpression of PhoD alter the sensitivity to MMV019266 in the parasite: overexpression of PhoD results in increased sensitivity to the compound, while knockdown increases resistance, suggesting PhoD is a resistance mechanism. Together, we have generated a robust pipeline for identification of resistance loci, and identified PhoD as a novel determinant of resistance in Babesia species.

Highlights

Use of two species for in vitro evolution identifies a high confidence locus associated with resistance Resistance mutation in phoD was validated using reverse genetics in B. divergens Perturbation of phoD using function genetics results in changes in the level of resistance to MMV019266Epitope tagging reveals localization to the ER/apicoplast, a conserved localization with a similar protein in diatoms Together, phoD is a novel resistance determinant in multiple Babesia spp .

Arbuscular mycorrhizal fungi enhance plant phosphorus uptake through stimulating hyphosphere soil microbiome functional profiles for phosphorus turnover

The extraradical hyphae of arbuscular mycorrhizal (AM) fungi are colonized by different bacteria in natural and agricultural systems, but the mechanisms by which AM fungi interact with the hyphosphere soil microbiome and influence soil organic phosphorus (P) mobilization remain unclear. We grew Medicago in two-compartment microcosms, inoculated with Rhizophagus irregularis, or not, in the root compartment and set up P treatments (without P, with P addition as KH₂ PO₄ or nonsoluble phytate) in the hyphal compartment. We studied the processes of soil P turnover and characterized the microbiome functional profiles for P turnover in the hyphosphere soil by metagenomic sequencing. Compared with the bulk soil, the hyphosphere soil of R. irregularis was inhabited by a specific bacterial community and their functional profiles for P turnover was stimulated. At the species level, the shift in hyphosphere soil microbiome was characterized by the recruitment of the genome bin2.39 harbouring both gcd and phoD genes and genome bin2.97 harbouring the phoD gene, which synergistically drove nonsoluble phytate mobilization in the hyphosphere soil. Our results suggest that AM fungi recruits a specific hyphosphere soil microbiome and stimulated their functional profiles for P turnover to enhance utilization of phytate.

Different mechanisms driving increasing abundance of microbial phosphorus cycling gene groups along an elevational gradient

Microbes play an integral role in forest soil phosphorus (P) cycling. However, the variation of microbial P-cycling functional genes and their controlling factors in forest soils is unclearly. We used metagenomics to investigate changes in the abundance of genes involved in P-starvation response regulation, P-uptake and transport, and P-solubilization and mineralization along the five elevational gradients. Our results showed the abundance of three P cycling gene groups increasing along the elevational gradient. Acidobacteria and Proteobacteria were the dominant microbial phyla determining the turnover of soil P-solubilization and immobilization. Along the elevational gradient, soil substrates are the major factor explaining variation in P-starvation response regulation genes. Soil environment is the main driver of P-uptake and transport and P-solubilization and mineralization genes. This study provided insights into the regulation of P-cycling from a microbial functional profile perspective, highlighting the importance of substrate and environmental factors for P-cycling genes in forest soils.

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P-cycling functional genes increased along the elevational gradient

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Acidobacteria and Proteobacteria are the key phyla for P cycle in forest soils

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Microbial functional gene groups for P-cycling were driven by different factors

Prospects for Using Phosphate-Solubilizing Microorganisms as Natural Fertilizers in Agriculture

Phosphates are known to be essential for plant growth and development, with phosphorus compounds being involved in various physiological and biochemical reactions. Phosphates are known as one of the most important factors limiting crop yields. The problem of phosphorus deficiency in the soil has traditionally been solved by applying phosphate fertilizers. However, chemical phosphate fertilizers are considered ineffective compared to the organic fertilizers manure and compost. Therefore, increasing the bioavailability of phosphates for plants is one of the primary goals of sustainable agriculture. Phosphate-solubilizing soil microorganisms can make soil-insoluble phosphate bioavailable for plants through solubilization and mineralization. These microorganisms are currently in the focus of interest due to their advantages, such as environmental friendliness, low cost, and high biological efficiency. In this regard, the solubilization of phosphates by soil microorganisms holds strong potential in research, and inoculation of soils or crops with phosphate-solubilizing bacteria is a promising strategy to improve plant phosphate uptake. In this review, we analyze all the species of phosphate-solubilizing bacteria described in the literature to date. We discuss key mechanisms of solubilization of mineral phosphates and mineralization of organic phosphate-containing compounds: organic acids secreted by bacteria for the mobilization of insoluble inorganic phosphates, and the enzymes hydrolyzing phosphorus-containing organic compounds. We demonstrate that phosphate-solubilizing microorganisms have enormous potency as biofertilizers since they increase phosphorus bioavailability for the plant, promote sustainable agriculture, improve soil fertility, and raise crop yields. The use of phosphate-solubilizing microbes is regarded as a new frontier in increasing plant productivity.

PCycDB: a comprehensive and accurate database for fast analysis of phosphorus cycling genes

BACKGROUND

Phosphorus (P) is one of the most essential macronutrients on the planet, and microorganisms (including bacteria and archaea) play a key role in P cycling in all living things and ecosystems. However, our comprehensive understanding of key P cycling genes (PCGs) and microorganisms (PCMs) as well as their ecological functions remains elusive even with the rapid advancement of metagenome sequencing technologies. One of major challenges is a lack of a comprehensive and accurately annotated P cycling functional gene database.

RESULTS

In this study, we constructed a well-curated P cycling database (PCycDB) covering 139 gene families and 10 P metabolic processes, including several previously ignored PCGs such as pafA encoding phosphate-insensitive phosphatase, ptxABCD (phosphite-related genes), and novel aepXVWPS genes for 2-aminoethylphosphonate transporters. We achieved an annotation accuracy, positive predictive value (PPV), sensitivity, specificity, and negative predictive value (NPV) of 99.8%, 96.1%, 99.9%, 99.8%, and 99.9%, respectively, for simulated gene datasets. Compared to other orthology databases, PCycDB is more accurate, more comprehensive, and faster to profile the PCGs. We used PCycDB to analyze P cycling microbial communities from representative natural and engineered environments and showed that PCycDB could apply to different environments.

CONCLUSIONS

We demonstrate that PCycDB is a powerful tool for advancing our understanding of microbially driven P cycling in the environment with high coverage, high accuracy, and rapid analysis of metagenome sequencing data. The PCycDB is available at https://github.com/ZengJiaxiong/Phosphorus-cycling-database . Video Abstract.

Comparative Genome Analysis Reveals Phylogenetic Identity of Bacillus velezensis HNA3 and Genomic Insights into Its Plant Growth Promotion and Biocontrol Effects

Bacillus velezensis HNA3, a potential plant growth promoter and biocontrol rhizobacterium, was isolated from plant rhizosphere soils in our previous work. Here, we sequenced the entire genome of the HNA3 strain and performed a comparative genome analysis. We found that HNA3 has a 3,929-kb chromosome with 46.5% GC content and 4,080 CDSs. We reclassified HNA3 as a Bacillus velezensis strain by core genome analysis between HNA3 and 74 previously defined Bacillus strains in the evolutionary tree. A comparative genomic analysis among Bacillus velezensis HNA3, Bacillus velezensis FZB42, Bacillus amyloliquefaciens DSM7, and Bacillus subtilis 168 showed that only HNA3 has one predicated secretory protein feruloyl esterase that catalyzes the hydrolysis of plant cell wall polysaccharides. The analysis of gene clusters revealed that whole biosynthetic gene clusters type Lanthipeptide was exclusively identified in HNA3 and might lead to the synthesis of new bioactive compounds. Twelve gene clusters were detected in HNA3 responsible for the synthesis of 14 secondary metabolites including Bacillaene, Fengycin, Bacillomycin D, Surfactin, Plipastatin, Mycosubtilin, Paenilarvins, Macrolactin, Difficidin, Amylocyclicin, Bacilysin, Iturin, Bacillibactin, Paenibactin, and others. HNA3 has 77 genes encoding for possible antifungal and antibacterial secreting carbohydrate active enzymes. It also contains genes involved in plant growth promotion, such as 11 putative indole acetic acid (IAA)-producing genes, spermidine and polyamine synthase genes, volatile compound producing genes, and multiple biofilm related genes. HNA3 also has 19 phosphatase genes involved in phosphorus solubilization. Our results provide insights into the genetic characteristics responsible for the bioactivities and potential application of HNA3 as plant growth-promoting strain in ecological agriculture.

IMPORTANCE This study is the primary initiative to identify Bacillus velezensis HNA3 whole genome sequence and reveal its genomic properties as an effective biocontrol agent against plant pathogens and a plant growth stimulator. HNA3 genetic profile can be used as a reference for future studies that can be applied as a highly effective biofertilizer and biofungicide inoculum to improve agriculture productivity. HNA3 reclassified in the phylogenetic tree which may be helpful for highly effective strain engineering and taxonomy. The genetic comparison among HNA3 and closely similar species B. velezensis FZB42, B. amyloliquefaciens DSM7, and B. subtilis 168 demonstrates some distinctive genetic properties of HNA3 and provides a basis for the genetic diversity of the Bacillus genus, which allows developing more effective eco-friendly resources for agriculture and separation of Bacillus velezensis as distinct species in the phylogenetic tree.

Metagenomic Analysis of Bacterial Communities in Agricultural Soils from Vietnam with Special Attention to Phosphate Solubilizing Bacteria

Bacterial communities can promote increased phosphorus (P) availability for plants and microbes in soil via various mechanisms of phosphate solubilization. The production of extracellular phosphatases releases available P through the hydrolysis of organic P. Examining the abundance and diversity of the bacterial community, including phosphate solubilizing bacteria in soil, may provide valuable information to overcome P scarcity in soil ecosystems. Here, the diversity and relative abundance of bacterial phyla and genera of six agricultural soil samples from Vietnam were analysed by next generation sequencing of the 16S rRNA gene. Phosphatase activities of each soil were compared with physico-chemical parameters and the abundance of the alkaline phosphatase gene phoD. We showed the dominance of Chloroflexi, Proteobacteria, Actinobacteria, Acidobacteria and Firmicutes. Total nitrogen positively correlated with phyla Proteobacteria, Acidobacteria, Firmicutes and Planctomycetes. The abundance of several genera of Proteobacteria showed positive relationship with the copy number of the phoD gene. The abundance of several taxa positively correlated with silt content, while a negative relationship of Proteobacteria was found with sand content. Our results demonstrated the clear influence of soil physico-chemical properties on the abundance of various bacterial taxa including those potentially involved in phosphate solubilization.

Microbial Key Players Involved in P Turnover Differ in Artificial Soil Mixtures Depending on Clay Mineral Composition

Nutrient turnover in soils is strongly driven by soil properties, including clay mineral composition. One main nutrient is phosphorus (P), which is known to be easily immobilized in soil. Therefore, the specific surface characteristics of clay minerals might substantially influence P availability in soil and thus the microbial strategies for accessing P pools. We used a metagenomic approach to analyze the microbial potential to access P after 842 days of incubation in artificial soils with a clay mineral composition of either non-expandable illite (IL) or expandable montmorillonite (MT), which differ in their surface characteristics like soil surface area and surface charge. Our data indicate that microorganisms of the two soils developed different strategies to overcome P depletion, resulting in similar total P concentrations. Genes predicted to encode inorganic pyrophosphatase (ppa), exopolyphosphatase (ppx), and the pstSCAB transport system were higher in MT, suggesting effective P uptake and the use of internal poly-P stores. Genes predicted to encode enzymes involved in organic P turnover like alkaline phosphatases (phoA, phoD) and glycerophosphoryl diester phosphodiesterase were detected in both soils in comparable numbers. In addition, P_o concentrations did not differ significantly. Most identified genes were assigned to microbial lineages generally abundant in agricultural fields, but some were assigned to lineages known to include oligotrophic specialists, such as Bacillaceae and Microchaetaceae.

Rhizobia as a Source of Plant Growth-Promoting Molecules: Potential Applications and Possible Operational Mechanisms

The symbiotic interaction between rhizobia and legumes that leads to nodule formation is a complex chemical conversation involving plant release of nod-gene inducing signal molecules and bacterial secretion of lipo-chito-oligossacharide nodulation factors. During this process, the rhizobia and their legume hosts can synthesize and release various phytohormones, such as IAA, lumichrome, riboflavin, lipo-chito-oligossacharide Nod factors, rhizobitoxine, gibberellins, jasmonates, brassinosteroids, ethylene, cytokinins and the enzyme 1-aminocyclopropane-1-carboxylate (ACC) deaminase that can directly or indirectly stimulate plant growth. Whereas these attributes may promote plant adaptation to various edapho-climatic stresses including the limitations in nutrient elements required for plant growth promotion, tapping their full potential requires understanding of the mechanisms involved in their action. In this regard, several N2-fixing rhizobia have been cited for plant growth promotion by solubilizing soil-bound P in the rhizosphere via the synthesis of gluconic acid under the control of pyrroloquinoline quinone (PQQ) genes, just as others are known for the synthesis and release of siderophores for enhanced Fe nutrition in plants, the chelation of heavy metals in the reclamation of contaminated soils, and as biocontrol agents against diseases. Some of these metabolites can enhance plant growth via the suppression of the deleterious effects of other antagonistic molecules, as exemplified by the reduction in the deleterious effect of ethylene by ACC deaminase synthesized by rhizobia. Although symbiotic rhizobia are capable of triggering biological outcomes with direct and indirect effects on plant mineral nutrition, insect pest and disease resistance, a greater understanding of the mechanisms involved remains a challenge in tapping the maximum benefits of the molecules involved. Rather than the effects of individual rhizobial or plant metabolites however, a deeper understanding of their synergistic interactions may be useful in alleviating the effects of multiple plant stress factors for increased growth and productivity.

Double trouble: Bacillus depends on a functional Tat machinery to avoid severe oxidative stress and starvation upon entry into a NaCl-depleted environment

The widely conserved twin-arginine translocases (Tat) allow the transport of fully folded cofactor-containing proteins across biological membranes. In doing so, these translocases serve different biological functions ranging from energy conversion to cell division. In the Gram-positive soil bacterium Bacillus subtilis, the Tat machinery is essential for effective growth in media lacking iron or NaCl. It was previously shown that this phenomenon relates to the Tat-dependent export of the heme-containing peroxidase EfeB, which converts Fe²⁺ to Fe³⁺ at the expense of hydrogen peroxide. However, the reasons why the majority of tat mutant bacteria perish upon dilution in NaCl-deprived medium and how, after several hours, a sub-population adapts to this condition was unknown. Here we show that, upon growth in the absence of NaCl, the bacteria face two major problems, namely severe oxidative stress at the membrane and starvation leading to death. The tat mutant cells can overcome these challenges if they are fed with arginine, which implies that severe arginine depletion is a major cause of death and resumed arginine synthesis permits their survival. Altogether, our findings show that the Tat system of B. subtilis is needed to preclude severe oxidative stress and starvation upon sudden drops in the environmental Na⁺ concentration as caused by flooding or rain.

Using a phenotype microarray and transcriptome analysis to elucidate multi-drug resistance regulated by the PhoR/PhoP two-component system in Bacillus subtilis strain NCD-2

The PhoRP two-component system (TCS), one of the most important signaling pathways in Bacillus subtilis, regulates cell physiological reactions mainly under phosphate starvation conditions. The mechanism by which PhoRP TCS regulates resistance towards antibiotics in B. subtilis strain NCD-2 was investigated in this study. Using phenotype microarray (PM) technology, the susceptibility of B. subtilis to 240 antimicrobial compounds was compared among the wild-type strain NCD-2, the phoR-null mutant (MR), and the phoP-null mutant (MP). Compared with the wild type, the MR mutant was more resistant to 13 antibiotics with different functions, and the MP mutant was more resistant to 14 antibiotics, of which 8 were 30S/50S ribosome-targeted. To investigate the molecular mechanisms involved in changing the level of antibiotic resistance, transcriptional analysis was performed to compare the differentially expressed genes among the wild-type strain and the MR and MP mutants. Compared with the wild-type strain, 294 genes were differentially expressed in the MR mutant, including 97 up-regulated genes and 197 down-regulated genes. Most of the differently expressed genes were associated with carbohydrate mechanism, amino acid mechanism, ABC-transporters and phosphotransferase systems. A total of 212 genes were differentially expressed in the MP mutant, including 10 up-regulated genes and 202 down-regulated genes, and most were associated with ribosome synthesis, amino acid metabolism, carbohydrate metabolism and ABC-transporters. The khtSTU operon (encoding the K⁺ efflux pump) that was up-regulated in the MP mutant was deleted by in-frame deletion in the MP mutant. The phoP and khtSTU operon double mutant MPK showed decreased antibiotic resistance to doxycycline, chlortetracycline, spiramycin, puromycin, and paromomycin when compared with the MP mutant. Thus, the results indicated that the khtSTU operon was responsible for the PhoP-mediated multiple antibiotic resistance.

Long-term nutrient inputs shift soil microbial functional profiles of phosphorus cycling in diverse agroecosystems

Microorganisms play an important role in soil phosphorus (P) cycling and regulation of P availability in agroecosystems. However, the responses of the functional and ecological traits of P-transformation microorganisms to long-term nutrient inputs are largely unknown. This study used metagenomics to investigate changes in the relative abundance of microbial P-transformation genes at four long-term experimental sites that received various inputs of N and P nutrients (up to 39 years). Long-term P input increased microbial P immobilization by decreasing the relative abundance of the P-starvation response gene (phoR) and increasing that of the low-affinity inorganic phosphate transporter gene (pit). This contrasts with previous findings that low-P conditions facilitate P immobilization in culturable microorganisms in short-term studies. In comparison, long-term nitrogen (N) input significantly decreased soil pH, and consequently decreased the relative abundances of total microbial P-solubilizing genes and the abundances of Actinobacteria, Gammaproteobacteria, and Alphaproteobacteria containing genes coding for alkaline phosphatase, and weakened the connection of relevant key genes. This challenges the concept that microbial P-solubilization capacity is mainly regulated by N:P stoichiometry. It is concluded that long-term N inputs decreased microbial P-solubilizing and mineralizing capacity while P inputs favored microbial immobilization via altering the microbial functional profiles, providing a novel insight into the regulation of P cycling in sustainable agroecosystems from a microbial perspective.

A Novel Alkaline Phosphatase/Phosphodiesterase, CamPhoD, from Marine Bacterium Cobetia amphilecti KMM 296

A novel extracellular alkaline phosphatase/phosphodiesterase from the structural protein family PhoD that encoded by the genome sequence of the marine bacterium Cobetia amphilecti KMM 296 (CamPhoD) has been expressed in Escherichia coli cells. The calculated molecular weight, the number of amino acids, and the isoelectric point (pI) of the mature protein’s subunit are equal to 54832.98 Da, 492, and 5.08, respectively. The salt-tolerant, bimetal-dependent enzyme CamPhoD has a molecular weight of approximately 110 kDa in its native state. CamPhoD is activated by Co²⁺, Mg²⁺, Ca²⁺, or Fe³⁺ at a concentration of 2 mM and exhibits maximum activity in the presence of both Co²⁺ and Fe³⁺ ions in the incubation medium at pH 9.2. The exogenous ions, such as Zn²⁺, Cu²⁺, and Mn²⁺, as well as chelating agents EDTA and EGTA, do not have an appreciable effect on the CamPhoD activity. The temperature optimum for the CamPhoD activity is 45 °C. The enzyme catalyzes the cleavage of phosphate mono- and diester bonds in nucleotides, releasing inorganic phosphorus from p-nitrophenyl phosphate (pNPP) and guanosine 5′-triphosphate (GTP), as determined by the Chen method, with rate approximately 150- and 250-fold higher than those of bis-pNPP and 5′-pNP-TMP, respectively. The Michaelis–Menten constant (K_m), V_max, and efficiency (k_cat/K_m) of CamPhoD were 4.2 mM, 0.203 mM/min, and 7988.6 S⁻¹/mM; and 6.71 mM, 0.023 mM/min, and 1133.0 S⁻¹/mM for pNPP and bis-pNPP as the chromogenic substrates, respectively. Among the 3D structures currently available, in this study we found only the low identical structure of the Bacillus subtilis enzyme as a homologous template for modeling CamPhoD, with a new architecture of the phosphatase active site containing Fe³⁺ and two Ca²⁺ ions. It is evident that the marine bacterial phosphatase/phosphidiesterase CamPhoD is a new structural member of the PhoD family.

Regulatory rewiring through global gene regulations by PhoB and alarmone (p)ppGpp under various stress conditions

The phosphorus availability in soil ranged from <0.01 to 1 ppm and found limiting for the utilization by plants. Hence, phosphate solubilizing bacteria (PSB) proficiently fulfill the phosphorus requirement of plants in an eco-friendly manner. The PSB encounter dynamic and challenging environmental conditions viz., high temperature, osmotic, acid, and climatic changes often hamper their activity and proficiency. The modern trend is shifting from isolation of the PSB to their genetic potentials and genome annotation not only for their better performance in the field trials but also to study their ability to cope up with stresses. In order to withstand environmental stress, bacteria need to restructure its metabolic network to ensure its survival. Pi starving condition response regulator (PhoB) and the mediator of stringent stress response alarmone (p)ppGpp known to regulate the global regulatory network of bacteria to provide balanced physiology under various stress condition. The current review discusses the global regulation and crosstalk of genes involved in phosphorus homeostasis, solubilization, and various stress response to fine tune the bacterial physiology. The knowledge of these network crosstalk help bacteria to respond efficiently to the challenging environmental parameters, and their physiological plasticity lead us to develop proficient long-lasting consortia for plant growth promotion.

Genomic Insights Into Plant-Growth-Promoting Potentialities of the Genus Frankia

This study was designed to determine the plant growth promoting (PGP) potential of members of the genus Frankia. To this end, the genomes of 21 representative strains were examined for genes associated directly or indirectly with plant growth. All of the Frankia genomes contained genes that encoded for products associated with the biosynthesis of auxins [indole-3-glycerol phosphate synthases, anthranilate phosphoribosyltransferases (trpD), anthranilate synthases, and aminases (trpA and B)], cytokinins (11 well-conserved genes within the predicted biosynthetic gene cluster), siderophores, and nitrogenases (nif operon except for atypical Frankia) as well as genes that modulate the effects of biotic and abiotic environmental stress (e.g., alkyl hydroperoxide reductases, aquaporin Z, heat shock proteins). In contrast, other genes were associated with strains assigned to one or more of four host-specific clusters. The genes encoding for phosphate solubilization (e.g., low-affinity inorganic phosphate transporters) and lytic enzymes (e.g., cellulases) were found in Frankia cluster 1 genomes, while other genes were found only in cluster 3 genomes (e.g., alkaline phosphatases, extracellular endoglucanases, pectate lyases) or cluster 4 and subcluster 1c genomes (e.g., NAD(P) transhydrogenase genes). Genes encoding for chitinases were found only in the genomes of the type strains of Frankia casuarinae, F. inefficax, F. irregularis, and F. saprophytica. In short, these in silico genome analyses provide an insight into the PGP abilities of Frankia strains of known taxonomic provenance. This is the first study designed to establish the underlying genetic basis of cytokinin production in Frankia strains. Also, the discovery of additional genes in the biosynthetic gene cluster involved in cytokinin production opens up the prospect that Frankia may have novel molecular mechanisms for cytokinin biosynthesis.

Activation of the PhoPR-Mediated Response to Phosphate Limitation Is Regulated by Wall Teichoic Acid Metabolism in Bacillus subtilis

Phosphorous is essential for cell viability. To ensure an adequate supply under phosphate limiting conditions, bacteria induce a cohort of enzymes to scavenge for phosphate, and a high affinity transporter for its uptake into the cell. This response is controlled by a two-component signal transduction system named PhoBR in Escherichia coli and PhoPR in Bacillus subtilis. PhoR is a sensor kinase whose activity is responsive to phosphate availability. Under phosphate limiting conditions, PhoR exists in kinase mode that phosphorylates its cognate response regulator (PhoB, PhoP). When activated, PhoB∼P/PhoP∼P execute changes in gene expression that adapt cells to the phosphate limited state. Under phosphate replete conditions, PhoR exists in phosphatase mode that maintains PhoB/PhoP in an inactive, non-phosphorylated state. The mechanism by which phosphate availability is sensed and how it controls the balance between PhoR kinase and phosphatase activities has been studied in E. coli and B. subtilis. Two different mechanisms have emerged. In the most common mechanism, PhoR activity is responsive to phosphate transport through a PstSCAB/PhoU signaling complex that relays the conformational status of the transporter to PhoR. In the second mechanism currently confined to B. subtilis, PhoR activity is responsive to wall teichoic acid metabolism whereby biosynthetic intermediates can promote or inhibit PhoR autokinase activity. Variations of both mechanisms are found that allow each bacterial species to adapt to phosphate availability in their particular environmental niche.

Secreted Phosphatase and Deoxyribonuclease Are Required by Pseudomonas aeruginosa To Defend against Neutrophil Extracellular Traps

Neutrophil extracellular traps (NETs) are produced by neutrophils as an innate immune defense mechanism to trap and kill microbial pathogens. NETs are comprised of ejected chromatin that forms a lattice structure enmeshed with numerous antimicrobial proteins. In addition to forming the structural backbone of NETs, extracellular DNA (eDNA) has membrane-disrupting antimicrobial activity that contributes to NET killing. Many pathogens produce secreted extracellular DNases to evade the antimicrobial activity of NETs. Pseudomonas aeruginosa encodes an operon of two secreted enzymes, a predicted alkaline phosphatase and a DNase. The DNase (eddB) degrades eDNA to use as a nutrient source. Here we report that both eDNA and NETs are potent inducers of this DNase-phosphatase operon. Furthermore, the secreted DNase contributes to degrading NET DNA and defends P. aeruginosa against NET-mediated killing. We demonstrate that EddA has both alkaline phosphatase and phosphodiesterase (PDase) activities and also protects against the antimicrobial activity of NETs. Although the phosphatase does not cause DNA degradation similar to that of the DNase, its protective function is likely a result of removing the cation-chelating phosphates from the eDNA phosphodiester backbone. Therefore, both the DNase and PDase contribute to defense against NET killing of P. aeruginosa, highlighting the role of DNA-manipulating enzymes in targeting the eDNA in neutrophil extracellular traps.

In Vitro and in Silico Evidence of Phosphatase Diversity in the Biomineralizing Bacterium Ramlibacter tataouinensis

Microbial phosphatase activity can trigger the precipitation of metal-phosphate minerals, a process called phosphatogenesis with global geochemical and environmental implications. An increasing diversity of phosphatases expressed by diverse microorganisms has been evidenced in various environments. However, it is challenging to link the functional properties of genomic repertoires of phosphatases with the phosphatogenesis capabilities of microorganisms. Here, we studied the betaproteobacterium Ramlibacter tataouinensis (Rta), known to biomineralize Ca-phosphates in the environment and the laboratory. We investigated the functional repertoire of this biomineralization process at the cell, genome and molecular level. Based on a mineralization assay, Rta is shown to hydrolyse the phosphoester bonds of a wide range of organic P molecules. Accordingly, its genome has an unusually high diversity of phosphatases: five genes belonging to two non-homologous families, phoD and phoX, were detected. These genes showed diverse predicted cis-regulatory elements. Moreover, they encoded proteins with diverse structural properties according to molecular models. Heterologously expressed PhoD and PhoX in Escherichia coli had different profiles of substrate hydrolysis. As evidenced for Rta cells, recombinant E. coli cells induced the precipitation of Ca-phosphate mineral phases, identified as poorly crystalline hydroxyapatite. The phosphatase genomic repertoire of Rta (containing phosphatases of both the PhoD and PhoX families) was previously evidenced as prevalent in marine oligotrophic environments. Interestingly, the Tataouine sand from which Rta was isolated showed similar P-depleted, but Ca-rich conditions. Overall, the diversity of phosphatases in Rta allows the hydrolysis of a broad range of organic P substrates and therefore the release of orthophosphates (inorganic phosphate) under diverse trophic conditions. Since the release of orthophosphates is key to the achievement of high saturation levels with respect to hydroxyapatite and the induction of phosphatogenesis, Rta appears as a particularly efficient driver of this process as shown experimentally.

A qPCR method to quantify bioavailable phosphorus using indigenous aquatic species

BACKGROUND

Bioavailable phosphorus (BAP) represents the sum of phosphorus that is readily available for algae growth and is useful to indicate the severity of eutrophication in aquatic environments.

RESULTS

Here, a quantitative real-time PCR (qPCR)-based bioassay was developed to quantify BAP using the indigenous cyanobacterium species Anabaena sp. of Lake Tai, a large and shallow eutrophic lake in the Yangtze Valley, China. Primers were designed to quantify the gene expression of alkaline phosphatase (phoA/phoA-like) and phosphate transporter (pst1) genes of Anabaena. The specificity and efficiency of the primer sets were evaluated by gel electrophoresis and real-time PCR. The results showed that the primers developed here could successfully be used to measure BAP in the water. The linear range of BAP measurements by the pst1 gene after 2 h incubation was 0.125-2.00 mg/L. Then, the qPCR-based bioassay was applied to analyze water samples from Tai Lake, which had BAP levels in the range of 0.239-0.459 mg/L.

CONCLUSIONS

The qPCR-based bioassay represents a promising biomonitoring tool that can quantify phosphorus bioavailability in aquatic environments.

The 'known' genetic potential for microbial communities to degrade organic phosphorus is reduced in low-pH soils

In soil, bioavailable inorganic orthophosphate is found at low concentrations and thus limits biological growth. To overcome this phosphorus scarcity, plants and bacteria secrete numerous enzymes, namely acid and alkaline phosphatases, which cleave orthophosphate from various organic phosphorus substrates. Using profile hidden Markov modeling approaches, we investigated the abundance of various non specific phosphatases, both acid and alkaline, in metagenomes retrieved from soils with contrasting pH regimes. This analysis uncovered a marked reduction in the abundance and diversity of various alkaline phosphatases in low-pH soils that was not counterbalanced by an increase in acid phosphatases. Furthermore, it was also discovered that only half of the bacterial strains from different phyla deposited in the Integrated Microbial Genomes database harbor alkaline phosphatases. Taken together, our data suggests that these 'phosphatase lacking' isolates likely increase in low-pH soils and future research should ascertain how these bacteria overcome phosphorus scarcity.

Identification of Two Phosphate Starvation-induced Wall Teichoic Acid Hydrolases Provides First Insights into the Degradative Pathway of a Key Bacterial Cell Wall Component

The cell wall of most Gram-positive bacteria contains equal amounts of peptidoglycan and the phosphate-rich glycopolymer wall teichoic acid (WTA). During phosphate-limited growth of the Gram-positive model organism Bacillus subtilis 168, WTA is lost from the cell wall in a response mediated by the PhoPR two-component system, which regulates genes involved in phosphate conservation and acquisition. It has been thought that WTA provides a phosphate source to sustain growth during starvation conditions; however, WTA degradative pathways have not been described for this or any condition of bacterial growth. Here, we uncover roles for the Bacillus subtilis PhoP regulon genes glpQ and phoD as encoding secreted phosphodiesterases that function in WTA metabolism during phosphate starvation. Unlike the parent 168 strain, ΔglpQ or ΔphoD mutants retained WTA and ceased growth upon phosphate limitation. Characterization of GlpQ and PhoD enzymatic activities, in addition to X-ray crystal structures of GlpQ, revealed distinct mechanisms of WTA depolymerization for the two enzymes; GlpQ catalyzes exolytic cleavage of individual monomer units, and PhoD catalyzes endo-hydrolysis at nonspecific sites throughout the polymer. The combination of these activities appears requisite for the utilization of WTA as a phosphate reserve. Phenotypic characterization of the ΔglpQ and ΔphoD mutants revealed altered cell morphologies and effects on autolytic activity and antibiotic susceptibilities that, unexpectedly, also occurred in phosphate-replete conditions. Our findings offer novel insight into the B. subtilis phosphate starvation response and implicate WTA hydrolase activity as a determinant of functional properties of the Gram-positive cell envelope.

Novel oligonucleotide primers reveal a high diversity of microbes which drive phosphorous turnover in soil

Phosphorus (P) is of central importance for cellular life but likewise a limiting macronutrient in numerous environments. Certainly microorganisms have proven their ability to increase the phosphorus bioavailability by mineralization of organic-P and solubilization of inorganic-P. On the other hand they efficiently take up P and compete with other biota for phosphorus. However the actual microbial community that is associated to the turnover of this crucial macronutrient in different ecosystems remains largely anonymous especially taking effects of seasonality and spatial heterogeneity into account. In this study seven oligonucleotide primers are presented which target genes coding for microbial acid and alkaline phosphatases (phoN, phoD), phytases (appA), phosphonatases (phnX) as well as the quinoprotein glucose dehydrogenase (gcd) and different P transporters (pitA, pstS). Illumina amplicon sequencing of soil genomic DNA underlined the high rate of primer specificity towards the respective target gene which usually ranged between 98% and 100% (phoN: 87%). As expected the primers amplified genes from a broad diversity of distinct microorganisms. Using DNA from a beech dominated forest soil, the highest microbial diversity was detected for the alkaline phosphatase (phoD) gene which was amplified from 15 distinct phyla respectively 81 families. Noteworthy the primers also allowed amplification of phoD from 6 fungal orders. The genes coding for acid phosphatase (phoN) and the quinoprotein glucose dehydrogenase (gcd) were amplified from 20 respectively 17 different microbial orders. In comparison the phytase and phosphonatase (appA, phnX) primers covered 13 bacterial orders from 2 different phyla respectively. Although the amplified microbial diversity was apparently limited both primers reliably detected all orders that contributed to the P turnover in the investigated soil as revealed by a previous metagenomic approach. Genes that code for microbial P transporter (pitA, pstS) were amplified from 13 respectively 9 distinct microbial orders. Accordingly the introduced primers represent a valuable tool for further analysis of the microbial community involved in the turnover of phosphorus in soils but most likely also in other environments.

Phosphorus depletion in forest soils shapes bacterial communities towards phosphorus recycling systems

Phosphorus (P) is an important macronutrient for all biota on earth but similarly a finite resource. Microorganisms play on both sides of the fence as they effectively mineralize organic and solubilize precipitated forms of soil phosphorus but conversely also take up and immobilize P. Therefore, we analysed the role of microbes in two beech forest soils with high and low P content by direct sequencing of metagenomic deoxyribonucleic acid. For inorganic P solubilization, a significantly higher microbial potential was detected in the P-rich soil. This trait especially referred to Candidatus Solibacter usiatus, likewise one of the dominating species in the data sets. A higher microbial potential for efficient phosphate uptake systems (pstSCAB) was detected in the P-depleted soil. Genes involved in P starvation response regulation (phoB, phoR) were prevalent in both soils. This underlines the importance of effective phosphate (Pho) regulon control for microorganisms to use alternative P sources during phosphate limitation. Predicted genes were primarily harboured by Rhizobiales, Actinomycetales and Acidobacteriales.

Twin-Arginine Protein Translocation

Twin-arginine protein translocation systems (Tat) translocate fully folded and co-factor-containing proteins across biological membranes. In this review, we focus on the Tat pathway of Gram-positive bacteria. The minimal Tat pathway is composed of two components, namely a TatA and TatC pair, which are often complemented with additional TatA-like proteins. We provide overviews of our current understanding of Tat pathway composition and mechanistic aspects related to Tat-dependent cargo protein translocation. This includes Tat pathway flexibility, requirements for the correct folding and incorporation of co-factors in cargo proteins and the functions of known cargo proteins. Tat pathways of several Gram-positive bacteria are discussed in detail, with emphasis on the Tat pathway of Bacillus subtilis. We discuss both shared and unique features of the different Gram-positive bacterial Tat pathways. Lastly, we highlight topics for future research on Tat, including the development of this protein transport pathway for the biotechnological secretion of high-value proteins and its potential applicability as an antimicrobial drug target in pathogens.

Genome wide in silico analysis of Plasmodium falciparum phosphatome

BACKGROUND

Eukaryotic cellular machineries are intricately regulated by several molecular mechanisms involving transcriptional control, post-translational control and post-translational modifications of proteins (PTMs). Reversible protein phosphorylation/dephosphorylation process, which involves kinases as well as phosphatases, represents an important regulatory mechanism for diverse pathways and systems in all organisms including human malaria parasite, Plasmodium falciparum. Earlier analysis on P. falciparum protein-phosphatome revealed presence of 34 phosphatases in Plasmodium genome. Recently, we re-analysed P. falciparum phosphatome aimed at identifying parasite specific phosphatases.

RESULTS

Plasmodium database (PlasmoDB 9.2) search, combined with PFAM and CDD searches, revealed 67 candidate phosphatases in P. falciparum. While this number is far less than the number of phosphatases present in Homo sapiens, it is almost the same as in other Plasmodium species. These Plasmodium phosphatase proteins were classified into 13 super families based on NCBI CDD search. Analysis of proteins expression profiles of the 67 phosphatases revealed that 44 phosphatases are expressed in both schizont as well as gametocytes stages. Fourteen phosphatases are common in schizont, ring and trophozoite stages, four phosphatases are restricted to gametocytes, whereas another three restricted to schizont stage. The phylogenetic trees for each of the known phosphatase super families reveal a considerable phylogenetic closeness amongst apicomplexan organisms and a considerable phylogenetic distance with other eukaryotic model organisms included in the study. The GO assignments and predicted interaction partners of the parasite phosphatases indicate its important role in diverse cellular processes.

CONCLUSION

In the study presented here, we reviewed the P. falciparum phosphatome to show presence of 67 candidate phosphatases in P. falciparum genomes/proteomes. Intriguingly, amongst these phosphatases, we could identify six Plasmodium specific phosphatases and 33 putative phosphatases that do not have human orthologs, thereby suggesting that these phosphatases have the potential to be explored as novel antimalarial drug targets.

Crystal structure of the Bacillus subtilis phosphodiesterase PhoD reveals an iron and calcium-containing active site

The PhoD family of extra-cytoplasmic phosphodiesterases are among the most commonly occurring bacterial phosphatases. The exemplars for this family are the PhoD protein of Bacillus subtilis and the phospholipase D of Streptomyces chromofuscus. We present the crystal structure of B. subtilis PhoD. PhoD is most closely related to purple acid phosphatases (PAPs) with both types of enzyme containing a tyrosinate-ligated Fe³⁺ ion. However, the PhoD active site diverges from that found in PAPs and uses two Ca²⁺ ions instead of the single extra Fe²⁺, Mn²⁺, or Zn²⁺ ion present in PAPs. The PhoD crystals contain a phosphate molecule that coordinates all three active site metal ions and that is proposed to represent a product complex. A C-terminal helix lies over the active site and controls access to the catalytic center. The structure of PhoD defines a new phosphatase active site architecture based on Fe³⁺ and Ca²⁺ ions.

The Tat system of Gram-positive bacteria

The twin-arginine protein translocation (Tat) system has a unique ability to translocate folded and co-factor-containing proteins across lipid bilayers. The Tat pathway is present in bacteria, archaea and in the thylakoid membranes of chloroplasts and, depending on the organism and environmental conditions, it can be deemed important for cell survival, virulence or bioproduction. This review provides an overview of the current understanding of the Tat system with specific focus on Gram-positive bacteria. The 'universal minimal Tat system' is composed of a TatA and a TatC protein. However, this pathway is more commonly composed of two TatA-like proteins and one TatC protein. Often the TatA-like proteins have diverged to have two different functions and, in this case, the second TatA-like protein is usually referred to as TatB. The correct folding and/or incorporation of co-factors are requirements for translocation, and the known quality control mechanisms are examined in this review. A number of examples of crosstalk between the Tat system and other protein transport systems, such as the Sec-YidC translocon and signal peptidases or sheddases are also discussed. Further, an overview of specific Gram-positive bacterial Tat systems found in monoderm and diderm species is detailed. Altogether, this review highlights the unique features of Gram-positive bacterial Tat systems and pinpoints key questions that remain to be addressed in future research. This article is part of a Special Issue entitled: Protein trafficking and secretion in bacteria. Guest Editors: Anastassios Economou and Ross Dalbey.

Identification and characterization of an extracellular alkaline phosphatase in the marine diatom Phaeodactylum tricornutum

In phosphorus-deficient conditions, Phaeodactylum tricornutum releases an alkaline phosphatase (PtAPase) to the medium that is readily detectable by activity staining. Nucleic acid and amino acid sequence of this alkaline phosphatase (APase) was identified by performing proteomic analysis and database searches. Sequence alignment suggests that PtAPase belongs to the PhoA family, and it possesses key residues at the Escherichia coli PhoA active site. Quantitative PCR results indicate that the induction of APase mRNA transcription is very sensitive to phosphorus availability and population growth. The molecular mass of native PtAPase (148 kDa) determined by gel filtration chromatography indicates that PtAPase, like most PhoA, is homodimeric. Zn and Mg ions are essential cofactors for most PhoA enzymes; however, PtAPase activity did not require Zn ions. In fact, 5 mM Zn²⁺, Mo²⁺, Co²⁺, Cd²⁺, or Cu²⁺ inhibited its enzymatic activity, whereas 5 mM Mn²⁺, Mg²⁺, or Ca²⁺ enhanced its enzymatic activity. The responses of PtAPase to divalent metal ions were different from those of most PhoAs, but were similar to the PhoA in a marine bacterium, Cobetia marina. Phylogenetic analysis shows that homologs of PhoA are also present in other diatom species, and that they clustered in a unique branch away from other PhoA members. PtAPase may represent a novel class of PhoA that helps diatoms to survive in the ocean. Quantification of the PtAPase mRNA may help monitor the physiological condition of diatoms in natural environments and artificial bioreactors.

An alkaline phosphatase/phosphodiesterase, PhoD, induced by salt stress and secreted out of the cells of Aphanothece halophytica, a halotolerant cyanobacterium

Alkaline phosphatases (APases) are important enzymes in organophosphate utilization. Three prokaryotic APase gene families, PhoA, PhoX, and PhoD, are known; however, their functional characterization in cyanobacteria largely remains to be clarified. In this study, we cloned the phoD gene from a halotolerant cyanobacterium, Aphanothece halophytica (phoD(Ap)). The deduced protein, PhoD(Ap), contains Tat consensus motifs and a peptidase cleavage site at the N terminus. The PhoD(Ap) enzyme was activated by Ca(2+) and exhibited APase and phosphodiesterase (APDase) activities. Subcellular localization experiments revealed the secretion and processing of PhoD(Ap) in a transformed cyanobacterium. Expression of the phoD(Ap) gene in A. halophytica cells was upregulated not only by phosphorus (P) starvation but also under salt stress conditions. Our results suggest that A. halophytica cells possess a PhoD that participates in the assimilation of P under salinity stress.

Ecological genomics of marine picocyanobacteria

Marine picocyanobacteria of the genera Prochlorococcus and Synechococcus numerically dominate the picophytoplankton of the world ocean, making a key contribution to global primary production. Prochlorococcus was isolated around 20 years ago and is probably the most abundant photosynthetic organism on Earth. The genus comprises specific ecotypes which are phylogenetically distinct and differ markedly in their photophysiology, allowing growth over a broad range of light and nutrient conditions within the 45 degrees N to 40 degrees S latitudinal belt that they occupy. Synechococcus and Prochlorococcus are closely related, together forming a discrete picophytoplankton clade, but are distinguishable by their possession of dissimilar light-harvesting apparatuses and differences in cell size and elemental composition. Synechococcus strains have a ubiquitous oceanic distribution compared to that of Prochlorococcus strains and are characterized by phylogenetically discrete lineages with a wide range of pigmentation. In this review, we put our current knowledge of marine picocyanobacterial genomics into an environmental context and present previously unpublished genomic information arising from extensive genomic comparisons in order to provide insights into the adaptations of these marine microbes to their environment and how they are reflected at the genomic level.

Genetic and biochemical properties of an alkaline phosphatase PhoX family protein found in many bacteria

We report on the biochemical, phylogenetic and genetic regulation of PhoX, the major alkaline phosphatase protein from the soil bacterium Sinorhizobium meliloti. The protein is shown to be a member of a recently identified family of PhoX alkaline phosphatase proteins that is distinct from the well-characterized PhoA family. The mature S. meliloti PhoX protein is located in the periplasm and lacks a 76-amino-acid N-terminal Tat signal peptide. Its phosphatase activity was stimulated by Ca(+2) and was optimal at pH 9-11. Except for phytic acid and phosphatidic acid, the enzyme was active against a wide range of phosphorylated substrates (77 nucleotides, phosphorylated carbohydrates and amino acids) and thus exhibited low substrate specificity for C-O-P bonds. No C-P bond substrate was dephosphorylated while the protein was active with two of six phosphoramidate substrates (N-P bond) tested. Sinorhizobium meliloti phoX was induced when cells were starved for phosphorous and the induction was dependent on the PhoB-regulatory protein. We demonstrate by in vitro analysis that PhoB protein binds to two tandem 22 nt PhoB binding sites located 64-21 nt upstream from the phoX transcription start site. Analysis of 95 PhoX orthologues from diverse bacteria revealed two distinct phylogenetic groups of PhoX proteins. The two groups differed in having a conserved glycine (PhoX-I) or asparagine (PhoX-II) next to their putative catalytic Ca(+2) binding site. Analysis of the phoX promoter regions from many of these bacteria also revealed the presence of PhoB binding sites. Alkaline phosphatase proteins of either the PhoX or PhoA family (but rarely both) are found in many bacteria, thus it appears that these are functionally equivalent.

Microbial iron management mechanisms in extremely acidic environments: comparative genomics evidence for diversity and versatility

BACKGROUND

Iron is an essential nutrient but can be toxic at high intracellular concentrations and organisms have evolved tightly regulated mechanisms for iron uptake and homeostasis. Information on iron management mechanisms is available for organisms living at circumneutral pH. However, very little is known about how acidophilic bacteria, especially those used for industrial copper bioleaching, cope with environmental iron loads that can be 1018 times the concentration found in pH neutral environments. This study was motivated by the need to fill this lacuna in knowledge. An understanding of how microorganisms thrive in acidic ecosystems with high iron loads requires a comprehensive investigation of the strategies to acquire iron and to coordinate this acquisition with utilization, storage and oxidation of iron through metal responsive regulation. In silico prediction of iron management genes and Fur regulation was carried out for three Acidithiobacilli: Acidithiobacillus ferrooxidans (iron and sulfur oxidizer) A. thiooxidans and A. caldus (sulfur oxidizers) that can live between pH 1 and pH 5 and for three strict iron oxidizers of the Leptospirillum genus that live at pH 1 or below.

RESULTS

Acidithiobacilli have predicted FeoB-like Fe(II) and Nramp-like Fe(II)-Mn(II) transporters. They also have 14 different TonB dependent ferri-siderophore transporters of diverse siderophore affinity, although they do not produce classical siderophores. Instead they have predicted novel mechanisms for dicitrate synthesis and possibly also for phosphate-chelation mediated iron uptake. It is hypothesized that the unexpectedly large number and diversity of Fe(III)-uptake systems confers versatility to this group of acidophiles, especially in higher pH environments (pH 4-5) where soluble iron may not be abundant. In contrast, Leptospirilla have only a FtrI-Fet3P-like permease and three TonB dependent ferri-dicitrate siderophore systems. This paucity of iron uptake systems could reflect their obligatory occupation of extremely low pH environments where high concentrations of soluble iron may always be available and were oxidized sulfur species might not compromise iron speciation dynamics. Presence of bacterioferritin in the Acidithiobacilli, polyphosphate accumulation functions and variants of FieF-like diffusion facilitators in both Acidithiobacilli and Leptospirilla, indicate that they may remove or store iron under conditions of variable availability. In addition, the Fe(II)-oxidizing capacity of both A. ferrooxidans and Leptospirilla could itself be a way to evade iron stress imposed by readily available Fe(II) ions at low pH. Fur regulatory sites have been predicted for a number of gene clusters including iron related and non-iron related functions in both the Acidithiobacilli and Leptospirilla, laying the foundation for the future discovery of iron regulated and iron-phosphate coordinated regulatory control circuits.

CONCLUSION

In silico analyses of the genomes of acidophilic bacteria are beginning to tease apart the mechanisms that mediate iron uptake and homeostasis in low pH environments. Initial models pinpoint significant differences in abundance and diversity of iron management mechanisms between Leptospirilla and Acidithiobacilli, and begin to reveal how these two groups respond to iron cycling and iron fluctuations in naturally acidic environments and in industrial operations. Niche partitions and ecological successions between acidophilic microorganisms may be partially explained by these observed differences. Models derived from these analyses pave the way for improved hypothesis testing and well directed experimental investigation. In addition, aspects of these models should challenge investigators to evaluate alternative iron management strategies in non-acidophilic model organisms.

The two-component system PhoPR of Clostridium acetobutylicum is involved in phosphate-dependent gene regulation

The phoPR gene locus of Clostridium acetobutylicum ATCC 824 comprises two genes, phoP and phoR. Deduced proteins are predicted to represent a response regulator and sensor kinase of a phosphate-dependent two-component regulatory system. We analyzed the expression patterns of phoPR in P(i)-limited chemostat cultures and in response to P(i) pulses. A basic transcription level under high-phosphate conditions was shown, and a significant increase in mRNA transcript levels was found when external P(i) concentrations dropped below 0.3 mM. In two-dimensional gel electrophoresis experiments, a 2.5-fold increase in PhoP was observed under P(i)-limiting growth conditions compared to growth with an excess of P(i). At least three different transcription start points for phoP were determined by primer extension analyses. Proteins PhoP and an N-terminally truncated *PhoR were individually expressed heterologously in Escherichia coli and purified. Autophosphorylation of *PhoR and phosphorylation of PhoP were shown in vitro. Electromobility shift assays proved that there was a specific binding of PhoP to the promoter region of the phosphate-regulated pst operon of C. acetobutylicum.

Cys303 in the histidine kinase PhoR is crucial for the phosphotransfer reaction in the PhoPR two-component system in Bacillus subtilis

The PhoPR two-component system activates or represses Pho regulon genes to overcome a phosphate deficiency. The Pho signal transduction network is comprised of three two-component systems, PhoPR, ResDE, and Spo0A. Activated PhoP is required for expression of ResDE from the resA promoter, while ResD is essential for 80% of Pho induction, establishing a positive feedback loop between these two-component systems to amplify the signal received by the Pho system. The role of ResD in the Pho response is via production of terminal oxidases. Reduced quinones inhibit PhoR autophosphorylation in vitro, and it was proposed that the expression of terminal oxidases leads to oxidation of the quinone pool, thereby relieving the inhibition. We show here that the reducing environment generated by dithiothreitol (DTT) in vivo inhibited Pho induction in a PhoR-dependent manner, which is in agreement with our previous in vitro data. A strain containing a PhoR variant, PhoR(C303A), exhibited reduced Pho induction and remained sensitive to inhibition by DTT, suggesting that the mechanisms for Pho reduction via PhoR(C303A) and DTT are different. PhoR and PhoR(C303A) were similar with regard to cellular concentration, limited proteolysis patterns, rate of autophosphorylation, stability of PhoR approximately P, and inhibition of autophosphorylation by DTT. Phosphotransfer between PhoR approximately P or PhoR(C303A) approximately P and PhoP occurred rapidly; most label from PhoR approximately P was transferred to PhoP, but only 10% of the label from PhoR(C303A) approximately P was associated with PhoP, while 90% was released as inorganic phosphate. No difference in PhoP approximately P or PhoR autophosphatase activity was observed between PhoR and PhoR(C303A) that would explain the release of inorganic phosphate. Our data are consistent with a role for PhoR(C303) in PhoR activity via stabilization of the phosphoryl-protein intermediate(s) during phosphotransfer from PhoR approximately P to PhoP, which is stabilization that is required for efficient production of PhoP approximately P.

Dual role of the PhoP approximately P response regulator: Bacillus amyloliquefaciens FZB45 phytase gene transcription is directed by positive and negative interactions with the phyC promoter

Several Bacillus strains secrete phytase, an enzyme catalyzing dephosphorylation of myo-inositol hexakisphosphate (phytate). We identified the phyC (phytase) gene from environmental Bacillus amyloliquefaciens FZB45 as a member of the phosphate starvation-inducible PhoPR regulon. In vivo and in vitro assays revealed that PhoP approximately P is essential for phyC transcription. The transcriptional start site was identified downstream of a sigmaA-like promoter region located 27 bp upstream of the probable translation ATG start codon. Inspection of the phyC promoter sequence revealed an unusual structure. The -35 and -10 regions are separated by a window of 21 bp. A pair of tandemly repeated PhoP TT(T/A/C)ACA binding boxes was located within and upstream of the -35 consensus promoter region. A single PhoP box was found within the -10 consensus promoter region. DNase I footprinting experiments performed with isolated PhoP confirmed that PhoP approximately P binds at two sites overlapping with the phyC -35 and -10 consensus promoter region. While binding of dimeric PhoP approximately P at -35 is essential for activation of the phyC promoter, binding of PhoP approximately P at -10 suppresses promoter activity. A sixfold enhancement of phyC gene expression was registered after T:G substitution of nucleotide -13 (mutant MUT13), which eliminates PhoP binding at the single PhoP box without impairing the -10 consensus sequence. Moreover, MUT13 also expressed phyC during phosphate-replete growth, suggesting that the repressing effect due to binding of PhoP approximately P at -10 was abolished. A model is presented in which transcription initiation of phyC is positively and negatively affected by the actual concentration of the PhoP approximately P response regulator.

The phosphate-starvation response of Bacillus licheniformis

The phosphate-starvation stimulon of Bacillus licheniformis was analyzed at the transcriptional and translational level. The comparison of the transcriptome and the proteome demonstrated that this specific starvation response of B. licheniformis is partially similar to that of B. subtilis. However, it is also shown that B. licheniformis has evolved its own strategies to cope with this nutrient limitation. By means of the secretome analysis the phytase was identified as the most abundant protein under phosphate-starvation conditions. Data of this study indicate that, unlike in B. subtilis, phosphate starvation in B. licheniformis does not induce the SigmaB-dependent general stress response.

Conservation of the Pho regulon in Pseudomonas fluorescens Pf0-1

The Pho regulon integrates the sensing of environmental inorganic phosphate (Pi) availability with coregulation of gene expression, mediating an adaptive response to Pi limitation. Many aspects of the Pho regulon have been addressed in studies of Escherichia coli; however, it is unclear how transferable this knowledge is to other bacterial systems. Here, we report work to discern the conservation of the Pho regulon in Pseudomonas fluorescens Pf0-1. We demonstrate by mutational studies that PhoB/PhoR and the Pst system have conserved functions in the regulation of Pi-induced phosphatase activities, as well as expression of other Pi-regulated genes. A genetic screen was carried out to isolate factors that affect Pho-regulated phosphatase activity. We identified the Pho-regulated phosphatases PhoX and PhoD and present evidence that these enzymes are exported via the Tat system. The phoX and phoD genes were shown to be members of the Pho regulon by reverse transcription-PCR, as well as by functional assessment of putative PhoB binding sites (Pho boxes). Our data also suggested that at least one other non-Tat-secreted Pho-regulated phosphatase exists. From the genetic screen, numerous siderophore mutants that displayed severe defects in Pho-activated phosphatase activity were isolated. Subsequently, iron was shown to be important for modulating the activity of Pho-regulated phosphatases, but it does not regulate this activity at the level of transcription. We also identify and demonstrate a novel role in siderophore production and Pho-regulated phosphatase activity for ApaH, the hydrolase for the nucleotide-signaling molecule AppppA. Finally, numerous mutations in multiple cellular pathways were recovered that may be required for maximal induction of the Pho regulon under Pi-limiting conditions.

Transcriptional studies and regulatory interactions between the phoR-phoP operon and the phoU, mtpA, and ppk genes of Streptomyces lividans TK24

The PhoR/PhoP two-component system of Streptomyces lividans was previously shown to allow the growth of the bacteria at low Pi concentrations and to negatively control antibiotic production. The present study focuses on the transcriptional analysis of phoR and phoP, along with the phoU and mtpA genes that are transcribed divergently from the phoRP operon in S. lividans. The effect of phoR, phoP, phoU, and ppk mutations on transcription of these genes was examined under phosphate-replete and phosphate-limited conditions. We demonstrated that phoR and phoP were cotranscribed as a leaderless bicistronic transcript cleaved at discrete sites toward the 3' end of phoR. In addition, phoP could also be transcribed alone from a promoter located at the 3' end of phoR. The phoU and mtpA genes, predicted to encode metal binding proteins, were shown to be transcribed as monocistronic transcripts. The expression of phoR-phoP, phoP, and phoU was found to be induced under conditions of Pi limitation in S. lividans TK24. This induction, requiring both PhoR and PhoP, was significantly weaker in the phoU mutant but much stronger in the ppk mutant than in the parental strain. The expression of mtpA was also shown to be up-regulated when Pi was limiting but independently of PhoR/PhoP. The induction of mtpA expression was much stronger in the phoU mutant strain than in the other strains. This study revealed interesting regulatory interactions between the different genes and allowed us to propose putative roles for PhoU and MtpA in the adaptation to phosphate scarcity.