Mycobacterium smegmatis PhoU Proteins Have Overlapping Functions in Phosphate Signaling and Are Essential

Phycospheric bacteria limits the effect of nitrogen and phosphorus imbalance on diatom bloom

Human activities have caused an imbalance in the input nitrogen and phosphorus (N/P) in the biosphere. The imbalance of N/P is one of the characteristics of water eutrophication, which is the fundamental factor responsible for the blooms. The effects of the N/P imbalance on diatom and phycospheric bacteria in blooms are poorly understood. In this study, the N/P molar ratio in real water (14:1) and the predicted N/P molar ratio in future water (65:1) were simulated to analyze the response of Cyclotella sp. and phycospheric bacteria to the N/P imbalance. The results showed that the N/P imbalance inhibited the growth of Cyclotella sp., but prolonged diatom bloom duration. The resistance of Cyclotella sp. to the N/P imbalance is related to phycospheric bacteria, and there are dynamic regulatory mechanisms within the phycospheric bacteria community to resist the N/P imbalance: (1) the increase of HNA bacterial density, the decrease of LNA bacterial density, (2) the increase of phycospheric bacterial diversity and eutrophic bacteria abundance, and the change of denitrifying bacteria abundance, (3) the activity of nitrogen and phosphorus metabolism of HNA bacteria enhanced, while that of LNA bacteria decreased. And the gene hosts of nitrogen and phosphorus metabolism were most enriched in Proteobacteria, indicating that Proteobacteria played an important role in maintaining the stability of phycospheric bacteria and was the dominant phylum resistant to the N/P imbalance. This study clarified that the algal-bacteria system was resistant to the N/P imbalance and implied that the N/P imbalance had little effect on the occurrence of diatom bloom events due to the presence of phycospheric bacteria.

PhoU: a multifaceted regulator in microbial signaling and homeostasis

Inorganic phosphate (Pi) is a fundamental molecule crucial for numerous biological processes, such as ATP synthesis and phospholipid formation. To prevent cellular toxicity, Pi transport is often linked to counterion transport within the bacterium. This review discusses the multifaceted functions of the PhoU protein in bacterial regulation, focusing on its role in coordinating Pi transport with counterions, controlling polyphosphate accumulation, and regulating secondary metabolite biosynthesis and DNA repair. We also explore recent findings that challenge the conventional view of PhoU simply as a negative regulator in phosphate signaling, suggesting its broader impact on bacterial physiology and stress response. Understanding the diverse functions of PhoU provides new insight into bacterial biology and offers potential therapeutic implications.

Devosia aquimaris sp. nov., isolated from seawater of the Changjiang River estuary of China

A gram-stain-negative, aerobic, rod-shaped bacterium strain CJK-A8-3T was isolated from a polyamine-enriched seawater sample collected from the Changjiang River estuary of China. The colonies were white and circular. Strain CJK-A8-3T grew optimally at 35 °C, pH 7.0 and 1.5% NaCl. Its polar lipids contained phosphatidylglycerol, phosphatidic acid, unidentified glycolipids, and a combination of phospholipids and glycolipids. The respiratory quinone was ubiquinone-10, and its main fatty acids were C16:0, 11-methyl C18:1ω7c and Summed Feature 8 (including C18:1ω7c/C18:1ω6c). The phylogenetic tree based on 16S rRNA genes placed strain CJK-A8-3T in a new linage within the genus Devosia. 16S rRNA gene sequence of strain CJK-A8-3T showed identities of 98.50% with Devosia beringensis S02T, 98.15% with D. oryziradicis, and 98.01% with D. submarina JCM 18935T. The genome size of strain CJK-A8-3T was 3.81 Mb with the DNA G + C content 63.9%, higher than those of the reference strains (60.4-63.8%). The genome contained genes functional in the metabolism of terrigenous aromatic compounds, alkylphosphonate and organic nitrogen, potentially beneficial for nutrient acquirement and environmental remediation. It also harbored genes functional in antibiotics resistance and balance of osmotic pressure, enhancing their adaptation to estuarine environments. Both genomic investigation and experimental verification showed that strain CJK-A8-3T could be versatile and efficient to use diverse organic nitrogen compounds as carbon and nitrogen sources. Based on phenotypic, chemotaxonomic, phylogenetic and genomic characteristics, strain CJK-A8-3T was identified as a novel Devosia species, named as Devosia aquimaris sp. nov. The type strain is CJK-A8-3T (= MCCC 1K06953T = KCTC 92162T).

Functional Whole Genome Screen of Nutrient-Starved Mycobacterium tuberculosis Identifies Genes Involved in Rifampin Tolerance

Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), poses a global health challenge and is responsible for over a million deaths each year. Current treatment is lengthy and complex, and new, abbreviated regimens are urgently needed. Mtb adapts to nutrient starvation, a condition experienced during host infection, by shifting its metabolism and becoming tolerant to the killing activity of bactericidal antibiotics. An improved understanding of the mechanisms mediating antibiotic tolerance in Mtb can serve as the basis for developing more effective therapies. We performed a forward genetic screen to identify candidate Mtb genes involved in tolerance to the two key first-line antibiotics, rifampin and isoniazid, under nutrient-rich and nutrient-starved conditions. In nutrient-rich conditions, we found 220 mutants with differential antibiotic susceptibility (218 in the rifampin screen and 2 in the isoniazid screen). Following Mtb adaptation to nutrient starvation, 82 mutants showed differential antibiotic susceptibility (80 in the rifampin screen and 2 in the isoniazid screen). Using targeted mutagenesis, we validated the rifampin-hypersusceptible phenotype under nutrient starvation in Mtb mutants lacking the following genes: ercc3, moeA1, rv0049, and rv2179c. These findings shed light on potential therapeutic targets, which could help shorten the duration and complexity of antitubercular regimens.

Identification of Arginine Phosphorylation in Mycolicibacterium smegmatis

Tuberculosis is a leading cause of worldwide infectious mortality. The prevalence of multidrug-resistant Mycobacterium tuberculosis infections drives an urgent need to exploit new drug targets. One such target is the ATP-dependent protease ClpC1P1P2, which is strictly essential for viability. However, few proteolytic substrates of mycobacterial ClpC1P1P2 have been identified to date. Recent studies in Bacillus subtilis have shown that the orthologous ClpCP protease recognizes proteolytic substrates bearing posttranslational arginine phosphorylation. While several lines of evidence suggest that ClpC1P1P2 is similarly capable of recognizing phosphoarginine-bearing proteins, the existence of phosphoarginine modifications in mycobacteria has remained in question. Here, we confirm the presence of posttranslational phosphoarginine modifications in Mycolicibacterium smegmatis, a nonpathogenic surrogate of M. tuberculosis. Using a phosphopeptide enrichment workflow coupled with shotgun phosphoproteomics, we identified arginine phosphosites on several functionally diverse targets within the M. smegmatis proteome. Interestingly, phosphoarginine modifications are not upregulated by heat stress, suggesting divergent roles in mycobacteria and Bacillus. Our findings provide new evidence supporting the existence of phosphoarginine-mediated proteolysis by ClpC1P1P2 in mycobacteria and other actinobacterial species. IMPORTANCE Mycobacteria that cause tuberculosis infections employ proteolytic pathways that modulate cellular behavior by destroying specific proteins in a highly regulated manner. Some proteolytic enzymes have emerged as novel antibacterial targets against drug-resistant tuberculosis infections. However, we have only a limited understanding of how these enzymes function in the cell and how they select proteins for destruction. Some proteolytic enzymes are capable of recognizing proteins that carry an unusual chemical modification, arginine phosphorylation. Here, we confirm the existence of arginine phosphorylation in mycobacterial proteins. Our work expands our understanding of a promising drug target in an important global pathogen.

The Global Regulator PhoU Positively Controls Growth and Butenyl-Spinosyn Biosynthesis in Saccharopolyspora pogona

Butenyl-spinosyn, a highly effective biological insecticide, is produced by Saccharopolyspora pogona. However, its application has been severely hampered by its low yield. Recent studies have shown that PhoU plays a pivotal role in regulating cell growth, secondary metabolite biosynthesis and intracellular phosphate levels. Nevertheless, the function of PhoU remains ambiguous in S. pogona. In this study, we investigated the effects of PhoU on the growth and the butenyl-spinosyn biosynthesis of S. pogona by constructing the mutants. Overexpression of phoU increased the production of butenyl-spinosyn to 2.2-fold that of the wild-type strain. However, the phoU deletion resulted in a severe imbalance of intracellular phosphate levels, and suppression of the growth and butenyl-spinosyn biosynthesis. Quantitative Real-time PCR (qRT-PCR) analysis, distinctive protein detection and mass spectrometry revealed that PhoU widely regulated primary metabolism, energy metabolism and DNA repair, which implied that PhoU influences the growth and butenyl-spinosyn biosynthesis of S. pogona as a global regulator.

Comparative Analysis on Proteomics Profiles of Intracellular and Extracellular M.tb and BCG From Infected Human Macrophages

Tuberculosis is the second cause in infectious diseases leading to human death. Understanding the virulence mechanism is inevitable if the disease needs to be fully cured. Therefore, this study aimed to reveal this mechanism by comparing proteomic profiles of intracellular and extracellular virulent strain M.tb and bacille Calmette–Guérin (BCG) from infected THP-1cells. First, M.tb and BCG infected THP-1 at MOI 10:1. Twelve hours postinfection, intracellular bacteria of M.tb and BCG were collected, whereas the two bacilli cultured in 7H9 broth media were used as the control. Then four groups of bacilli were subjected to proteomic analysis, and differential proteomic profiles between M.tb and BCG were comparatively analyzed with bioinformatics tools. As a result, we identified a total of 1,557 proteins. Further, they were divided into four groups for comparison of M.tb versus BCG under 7H9 culture (shorten as out), M.tb in (intracellular) versus M.tb out, BCG in versus BCG out and M.tb in versus BCG in. Between M.tb in versus BCG in, a total of 211 differentially expressed proteins were found. Eight proteins like ESAT-6 distributed in six RDs and some known proteins related to virulence. Besides, five uncharacterized proteins were differentially expressed. Further analysis revealed enriched pathways were associated with glyoxylate and dicarboxylate metabolism pathways. In M.tb out versus BCG out, a total of 144 differential proteins were identified and mainly involved in metabolism pathways. Then, 121 differential proteins in the group of M.tb in versus M.tb out were enriched in ribosome and oxidative phosphorylation related to adaptation to the host environment. The group of BCG in versus BCG out shared the same trend of different pathways to the M.tb in versus M.tb out. Finally, 42 proteins were identified to be up-regulated only in intracellular M.tb including eight RD proteins, whereas 22 up-regulated uniquely in intracellular BCG. Besides, only two proteins (Pks13 and Rv1405c) were commonly up-regulated in intracellular M.tb and BCG. Further, some unknown proteins were uniquely up-regulated in the intracellular M.tb and BCG. These findings provide valuable data for further exploration of molecular mechanism for M.tb virulence and BCG immune response.

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.

Dual control of RegX3 transcriptional activity by SenX3 and PknB

The mycobacterial SenX3-RegX3 two-component system consists of the SenX3 sensor histidine kinase and its cognate RegX3 response regulator. This system is a phosphorelay-based regulatory system involved in sensing environmental P_i levels and induction of genes required for P_i acquisition under P_i-limiting conditions. Here we demonstrate that overexpression of the kinase domain of Mycobacterium tuberculosis PknB (PknB-KD^Mtb) inhibits the transcriptional activity of RegX3 of both M. tuberculosis and Mycobacterium smegmatis (RegX3^Mtb and RegX3^Ms, respectively). Mass spectrometry results, along with those of in vitro phosphorylation and complementation analyses, revealed that PknB kinase activity inhibits the transcriptional activity of RegX3^Mtb through phosphorylation events at Thr-100, Thr-191, and Thr-217. Electrophoretic mobility shift assays disclosed that phosphorylation of Thr-191 and Thr-217 abolishes the DNA-binding ability of RegX3^Mtb and that Thr-100 phosphorylation likely prevents RegX3^Mtb from being activated through conformational changes induced by SenX3-mediated phosphorylation. We propose that the convergence of the PknB and SenX3-RegX3 signaling pathways might enable mycobacteria to integrate environmental P_i signals with the cellular replication state to adjust gene expression in response to P_i availability.

The relevance of persisters in tuberculosis drug discovery

Bacterial persisters are a subpopulation of cells that exhibit phenotypic resistance during exposure to a lethal dose of antibiotics. They are difficult to target and thought to contribute to the long treatment duration required for tuberculosis. Understanding the molecular and cellular biology of persisters is critical to finding new tuberculosis drugs that shorten treatment. This review focuses on mycobacterial persisters and describes the challenges they pose in tuberculosis therapy, their characteristics and formation, how persistence leads to resistance, and the current approaches being used to target persisters within mycobacterial drug discovery.

Elucidating the role of (p)ppGpp in mycobacterial persistence against antibiotics

Bacterial persistence, the ability of bacteria to survive high concentrations of antibiotics for extended periods of time, is an important contributing factor to therapy failure and development of chronic and recurrent infections. Several recent studies have suggested that this persistence is mediated primarily by (p)ppGpp, through its interactions with toxin-antitoxin modules and polyphosphates. In this study, we address whether these key players play a role in mycobacterial persistence against antibiotics. We targeted these specific pathways in Mycobacterium smegmatis by constructing deletion strains of (p)ppGpp synthetase/hydrolase (relA), polyphosphate kinases (ppk1 and ppk2), exopolyphosphatases (ppx1 and ppx2), and the lon protease. None of these mutant strains exhibited altered levels of persisters against isoniazid and ciprofloxacin, when compared with wild-type strain. Even under conditions in which the stringent response usually gets activated, these strains displayed wild-type persister levels. Interestingly, we also found that unlike Escherichia coli, maintaining M. smegmatis in exponential phase by repeated passaging does not eliminate persisters suggesting that at least against the antibiotics tested, stationary-phase dependent persisters (type I) are not the major contributors. Thus, our data demonstrate that multiple mechanisms of antibiotic persistence exist and that these vary widely among different bacterial species. © 2018 IUBMB Life, 70(9):836-844, 2018.

No wisdom in the crowd: genome annotation in the era of big data - current status and future prospects

Science and engineering rely on the accumulation and dissemination of knowledge to make discoveries and create new designs. Discovery-driven genome research rests on knowledge passed on via gene annotations. In response to the deluge of sequencing big data, standard annotation practice employs automated procedures that rely on majority rules. We argue this hinders progress through the generation and propagation of errors, leading investigators into blind alleys. More subtly, this inductive process discourages the discovery of novelty, which remains essential in biological research and reflects the nature of biology itself. Annotation systems, rather than being repositories of facts, should be tools that support multiple modes of inference. By combining deduction, induction and abduction, investigators can generate hypotheses when accurate knowledge is extracted from model databases. A key stance is to depart from 'the sequence tells the structure tells the function' fallacy, placing function first. We illustrate our approach with examples of critical or unexpected pathways, using MicroScope to demonstrate how tools can be implemented following the principles we advocate. We end with a challenge to the reader.