Crystal structure of PhoU from Pseudomonas aeruginosa, a negative regulator of the Pho regulon

PhoU homologs from Staphylococcus aureus dimerization and protein interactions

PhoU proteins are negative regulators of the phosphate response, regulate virulence, and contribute to antibiotic resistance. Staphylococcus aureus has multiple genes encoding PhoU homologs that regulate persister formation and potentially virulence, but the molecular mechanisms of this regulation are not fully understood. We used a bacterial adenylate cyclase two-hybrid system to assess interactions between PhoU homologs and other proteins known to interact with PhoU from Escherichia coli. S. aureus PhoU (also referred to as PhoU1) interacted with PhoU itself; PitR (also referred to as PhoU2) interacted with PitR itself. We identified potential structural and dimerization models for S. aureus PhoU homologs. Dimerization was confirmed using size exclusion chromatography of purified proteins. These results highlight the complex nature of PhoU proteins. Further analysis may elucidate the potential mechanisms for regulating gene expression, persister formation, and virulence in S. aureus.IMPORTANCEPhoU proteins affect pathogenesis and persister formation in many bacterial species. This protein is essential for signaling environmental phosphate levels in Escherichia coli but is still not well characterized in many other pathogenic bacterial strains. This work identifies some similarities and key differences in Staphylococcus aureus PhoU homologs compared to E. coli PhoU, specifically, PhoU and PitR from S. aureus form homodimers but do not appear to interact with PhoR or phosphate transporter proteins.

Loss of LasR function leads to decreased repression of Pseudomonas aeruginosa PhoB activity at physiological phosphate concentrations

While the Pseudomonas aeruginosa LasR transcription factor plays a role in quorum sensing (QS) across phylogenetically-distinct lineages, isolates with loss-of-function mutations in lasR (LasR- strains) are commonly found in diverse settings including infections where they are associated with worse clinical outcomes. In LasR- strains, the transcription factor RhlR, which is controlled by LasR, can be alternately activated in low inorganic phosphate (Pi) concentrations via the two-component system PhoR-PhoB. Here, we demonstrate a new link between LasR and PhoB in which the absence of LasR increases PhoB activity at physiological Pi concentrations and raises the Pi concentration necessary for PhoB inhibition. PhoB activity was also less repressed by Pi in mutants lacking different QS regulators (RhlR and PqsR) and in mutants lacking genes required for the production of QS-regulated phenazines suggesting that decreased phenazine production was one reason for decreased PhoB repression by Pi in LasR- strains. In addition, the CbrA-CbrB two-component system, which is elevated in LasR- strains, was necessary for reduced PhoB repression by Pi and a Δcrc mutant, which lacks the CbrA-CbrB-controlled translational repressor, activated PhoB at higher Pi concentrations than the wild type. The ΔlasR mutant had a PhoB-dependent growth advantage in a medium with no added Pi and increased virulence-determinant gene expression in a medium with physiological Pi, in part through reactivation of QS. This work suggests PhoB activity may contribute to the virulence of LasR- P. aeruginosa and subsequent clinical outcomes.

Deletion of Rv2571c confers resistance to arylamide compounds in Mycobacterium tuberculosis

Tuberculosis, caused by Mycobacterium tuberculosis, is an urgent global health problem requiring new drugs, new drug targets and an increased understanding of antibiotic resistance. We have determined the mode of resistance to a series of arylamide compounds in M. tuberculosis We isolated M. tuberculosis resistant mutants to two arylamide compounds which are inhibitory to growth under host-relevant conditions (butyrate as a sole carbon source). Thirteen mutants were characterized, and all had mutations in Rv2571c; mutations included a premature stop codon and frameshifts as well as non-synonymous polymorphisms. We isolated a further ten strains with mutations in Rv2571c with resistance. Complementation with a wild-type copy of Rv2571c restored arylamide sensitivity. Over-expression of Rv2571c was toxic in both wild-type and mutant backgrounds. We constructed M. tuberculosis strains with an unmarked deletion of the entire Rv2571c gene by homologous recombination and confirmed that these were resistant to the arylamide series. Rv2571c is a member of the aromatic amino acid transport family and has a fusaric acid resistance domain which is associated with compound transport. Since loss or inactivation of Rv2571c leads to resistance, we propose that Rv2571c is involved in the import of arylamide compounds.

Control of the phoBR Regulon in Escherichia coli

Phosphorus is required for many biological molecules and essential functions, including DNA replication, transcription of RNA, protein translation, posttranslational modifications, and numerous facets of metabolism. In order to maintain the proper level of phosphate for these processes, many bacteria adapt to changes in environmental phosphate levels. The mechanisms for sensing phosphate levels and adapting to changes have been extensively studied for multiple organisms. The phosphate response of Escherichia coli alters the expression of numerous genes, many of which are involved in the acquisition and scavenging of phosphate more efficiently. This review shares findings on the mechanisms by which E. coli cells sense and respond to changes in environmental inorganic phosphate concentrations by reviewing the genes and proteins that regulate this response. The PhoR/PhoB two-component signal transduction system is central to this process and works in association with the high-affinity phosphate transporter encoded by the pstSCAB genes and the PhoU protein. Multiple models to explain how this process is regulated are discussed.

The Role of Iron in the P-Acquisition Mechanisms of the Unicellular N2-Fixing Cyanobacteria Halothece sp., Found in Association With the Mediterranean Seagrass Posidonia oceanica

Posidonia oceanica, an endemic seagrass of the Mediterranean Sea harbors a high diversity of N₂-fixing prokaryotes. One of these is Halothece sp., a unicellular N₂-fixing cyanobacteria detected through nifH analysis from the epiphytes of P. oceanica. The most related strain in culture is Halothece sp. PCC 7418 and this was used as the test organism in this study. In the Mediterranean Sea, phosphorus (P) and iron (Fe) can be the major limiting nutrients for N₂ fixation. However, information about the mechanisms of P-acquisition and the role of metals (i.e., Fe) in these processes for N₂-fixing bacteria is scarce. From our genomic analyses of the test organism and other phylogenetically related N₂-fixing strains, Halothece sp. PCC 7418 is one of the strains with the greatest number of gene copies (eight copies) of alkaline phosphatases (APases). Our structural analysis of PhoD (alkaline phosphatase type D) and PhoU (phosphate acquisition regulator) of Halothece sp. PCC 7418 showed the connection among metals (Ca²⁺ and Fe³⁺), and the P-acquisition mechanisms. Here, we measured the rates of alkaline phosphatase activity (APA) through MUF-P hydrolysis under different combinations of concentrations of inorganic P (PO43−) and Fe in experiments under N₂-fixing (low NO3− availability) and non-N₂ fixing (high NO3− availability) conditions. Our results showed that APA rates were enhanced by the increase in Fe availability under low levels of PO43−, especially under N₂-fixing conditions. Moreover, the increased PO43−-uptake was reflected in the increased of the P-cellular content of the cells under N₂ fixation conditions. We also found a positive significant relationship between cellular P and cellular Fe content of the cells (r² = 0.71, p < 0.05). Our results also indicated that Fe-uptake in Halothece sp. PCC 7418 was P and Fe-dependent. This study gives first insights of P-acquisition mechanisms in the N₂-fixing cyanobacteria (Halothece sp.) found in P. oceanica and highlights the role of Fe in these processes.

Roles of Phosphorus Sources in Microbial Community Assembly for the Removal of Organic Matters and Ammonia in Activated Sludge

Various phosphorus sources are utilized by microbes in WWTPs, eventually affecting microbial assembly and functions. This study identified the effects of phosphorus source on microbial communities and functions in the activated sludge. By cultivation with 59 phosphorus sources, including inorganic phosphates (IP), nucleoside-monophosphates (NMP), cyclic-nucleoside-monophosphates (cNMP), and other organophosphates (OP), we evaluated the change in removal efficiencies of total organic carbon (TOC) and ammonia, microbial biomass, alkaline phosphatase (AKP) activity, microbial community structure, and AKP-associated genes. TOC and ammonia removal efficiency was highest in IP (64.8%) and cNMP (52.3%) treatments. Microbial community structure changed significantly across phosphorus sources that IP and cNMP encouraged Enterobacter and Aeromonas, respectively. The abundance of phoA and phoU genes was higher in IP treatments, whereas phoD and phoX genes dominated OP treatments. Our findings suggested that the performance of WWTPs was dependent on phosphorus sources and provided new insights into effective WWTP management.

Physiological Roles of the Dual Phosphate Transporter Systems in Low and High Phosphate Conditions and in Capsule Maintenance of Streptococcus pneumoniae D39

Unlike most bacteria, Streptococcus pneumoniae (pneumococcus) has two evolutionarily distinct ABC transporters (Pst1 and Pst2) for inorganic phosphate (P_i) uptake. The genes encoding a two-component regulator (PnpRS) are located immediately upstream of the pst1 operon. Both the pst1 and pst2 operons encode putative PhoU-family regulators (PhoU1 and PhoU2) at their ends. This study addresses why S. pneumoniae contains dual P_i uptake systems and the regulation and contribution of the Pst1 and Pst2 systems in conditions of high (mM) P_i amount and low (μM) P_i amount. We show that in unencapsulated mutants, both pst1 and pst2 can be deleted, and P_i is taken up by a third Na⁺/P_i co-transporter, designated as NptA. In contrast, either pst1 or pst2 is unexpectedly required for the growth of capsule producing strains. We used a combination of mutational analysis, transcript level determinations by qRT-PCR and RNA-Seq, assays for cellular PnpR~P amounts by SDS-PAGE, and pulse-P_i uptake experiments to study the regulation of P_i uptake. In high P_i medium, PhoU2 serves as the master negative regulator of Pst2 transporter function and PnpR~P levels (post-transcriptionally). ΔphoU2 mutants have high PnpR~P levels and induction of the pst1 operon, poor growth, and sensitivity to antibiotics, possibly due to high P_i accumulation. In low P_i medium, Pst2 is still active, but PnpR~P amount and pst1 operon levels increase. Together, these results support a model in which pneumococcus maintains high P_i transport in high and low P_i conditions that is required for optimal capsule biosynthesis.