The heme-binding protein PhuS transcriptionally regulates the Pseudomonas aeruginosa tandem sRNA prrF1,F2 locus

Biosynthesis, acquisition, regulation, and upcycling of heme: recent advances

Heme, an iron-containing tetrapyrrole in hemoproteins, including: hemoglobin, myoglobin, catalase, cytochrome c, and cytochrome P450, plays critical physiological roles in different organisms. Heme-derived chemicals, such as biliverdin, bilirubin, and phycocyanobilin, are known for their antioxidant and anti-inflammatory properties and have shown great potential in fighting viruses and diseases. Therefore, more and more attention has been paid to the biosynthesis of hemoproteins and heme derivatives, which depends on the adequate heme supply in various microbial cell factories. The enhancement of endogenous biosynthesis and exogenous uptake can improve the intracellular heme supply, but the excess free heme is toxic to the cells. Therefore, based on the heme-responsive regulators, several sensitive biosensors were developed to fine-tune the intracellular levels of heme. In this review, recent advances in the: biosynthesis, acquisition, regulation, and upcycling of heme were summarized to provide a solid foundation for the efficient production and application of high-value-added hemoproteins and heme derivatives.

Relationship between Pyochelin and Pseudomonas Quinolone Signal in Pseudomonas aeruginosa: A Direction for Future Research

Pseudomonas aeruginosa is an opportunistic pathogen that requires iron to survive in the host; however, the host immune system limits the availability of iron. Pyochelin (PCH) is a major siderophore produced by P. aeruginosa during infection, which can help P. aeruginosa survive in an iron-restricted environment and cause infection. The infection activity of P. aeruginosa is regulated by the Pseudomonas quinolone signal (PQS) quorum-sensing system. The system uses 2-heptyl-3-hydroxy-4-quinolone (PQS) or its precursor, 2-heptyl-4-quinolone (HHQ), as the signal molecule. PQS can control specific life processes such as mediating quorum sensing, cytotoxicity, and iron acquisition. This review summarizes the biosynthesis of PCH and PQS, the shared transport system of PCH and PQS, and the regulatory relationship between PCH and PQS. The correlation between the PQS and PCH is emphasized to provide a new direction for future research.

The small RNA PrrH aggravates Pseudomonas aeruginosa-induced acute lung injury by regulating the type III secretion system activator ExsA

Pseudomonas aeruginosa is an opportunistic pathogen that causes acute and chronic infections in immunocompromised individuals. Small regulatory RNAs (sRNAs) regulate multiple bacterial adaptations to environmental changes, especially virulence. Our previous study showed that sRNA PrrH negatively regulates the expression of a number of virulence factors, such as pyocyanin, rhamnolipid, biofilm, and elastase in the P. aeruginosa strain PAO1. However, previous studies have shown that the prrH-deficient mutant attenuates virulence in an acute murine lung infection model. All ΔprrH-infected mice survived the entire 28-day course of the experiment, whereas all mice inoculated with the wild-type or the complemented mutant succumbed to lung infection within 4 days of injection, but the specific mechanism is unclear. Herein, we explored how PrrH mediates severe lung injury by regulating the expression of virulence factors. In vivo mouse and in vitro cellular assays demonstrated that PrrH enhanced the pathogenicity of PAO1, causing severe lung injury. Mechanistically, PrrH binds to the coding sequence region of the mRNA of exsA, which encodes the type III secretion system master regulatory protein. We further demonstrated that PrrH mediates a severe inflammatory response and exacerbates the apoptosis of A549 cells. Overall, our results revealed that PrrH positively regulates ExsA, enhances the pathogenicity of P. aeruginosa, and causes severe lung injury.

IMPORTANCE

Pseudomonas aeruginosa is a Gram-negative bacterium and the leading cause of nosocomial pneumonia. The pathogenicity of P. aeruginosa is due to the secretion of many virulence factors. Small regulatory RNAs (sRNAs) regulate various bacterial adaptations, especially virulence. Therefore, understanding the mechanism by which sRNAs regulate virulence is necessary for understanding the pathogenicity of P. aeruginosa and the treatment of the related disease. In this study, we demonstrated that PrrH enhances the pathogenicity of P. aeruginosa by binding to the coding sequence regions of the ExsA, the master regulatory protein of type III secretion system, causing severe lung injury and exacerbating the inflammatory response and apoptosis. These findings revealed that PrrH is a crucial molecule that positively regulates ExsA. Type III-positive strains are often associated with a high mortality rate in P. aeruginosa infections in clinical practice. Therefore, this discovery may provide a new target for treating P. aeruginosa infections, especially type III-positive strains.

Combining experiment and energy landscapes to explore anaerobic heme breakdown in multifunctional hemoproteins

To survive, many pathogens extract heme from their host organism and break down the porphyrin scaffold to sequester the Fe2+ ion via a heme oxygenase. Recent studies have revealed that certain pathogens can anaerobically degrade heme. Our own research has shown that one such pathway proceeds via NADH-dependent heme degradation, which has been identified in a family of hemoproteins from a range of bacteria. HemS, from Yersinia enterocolitica, is the main focus of this work, along with HmuS (Yersinia pestis), ChuS (Escherichia coli) and ShuS (Shigella dysenteriae). We combine experiments, Energy Landscape Theory, and a bioinformatic investigation to place these homologues within a wider phylogenetic context. A subset of these hemoproteins are known to bind certain DNA promoter regions, suggesting not only that they can catalytically degrade heme, but that they are also involved in transcriptional modulation responding to heme flux. Many of the bacterial species responsible for these hemoproteins (including those that produce HemS, ChuS and ShuS) are known to specifically target oxygen-depleted regions of the gastrointestinal tract. A deeper understanding of anaerobic heme breakdown processes exploited by these pathogens could therefore prove useful in the development of future strategies for disease prevention.

The heme-responsive PrrH sRNA regulates Pseudomonas aeruginosa pyochelin gene expression

Pseudomonas aeruginosa is an opportunistic pathogen that requires iron for growth and virulence, yet this nutrient is sequestered by the innate immune system during infection. When iron is limiting, P. aeruginosa expresses the PrrF1 and PrrF2 small RNAs (sRNAs), which post-transcriptionally repress expression of nonessential iron-containing proteins, thus sparing this nutrient for more critical processes. The genes for the PrrF1 and PrrF2 sRNAs are arranged in tandem on the chromosome, allowing for the transcription of a longer heme-responsive sRNA, termed PrrH. While the functions of PrrF1 and PrrF2 have been extensively studied, the role of PrrH in P. aeruginosa physiology and virulence is not well understood. In this study, we performed transcriptomic and proteomic studies to identify the PrrH regulon. In shaking cultures, the pyochelin synthesis proteins were increased in two distinct prrH mutants compared to the wild type, while the mRNAs for these proteins were not affected by the prrH mutation. We identified complementarity between the PrrH sRNA and the sequence upstream of the pchE mRNA, suggesting the potential for PrrH to directly regulate the expression of genes for pyochelin synthesis. We further showed that pchE mRNA levels were increased in the prrH mutants when grown in static but not shaking conditions. Moreover, we discovered that controlling for the presence of light was critical for examining the impact of PrrH on pchE expression. As such, our study reports on the first likely target of the PrrH sRNA and highlights key environmental variables that will allow for future characterization of PrrH function. IMPORTANCE In the human host, iron is predominantly in the form of heme, which Pseudomonas aeruginosa can acquire as an iron source during infection. We previously showed that the iron-responsive PrrF small RNAs (sRNAs) are critical for mediating iron homeostasis during P. aeruginosa infection; however, the function of the heme-responsive PrrH sRNA remains unclear. In this study, we identified genes for pyochelin siderophore biosynthesis, which mediates uptake of inorganic iron, as a novel target of PrrH regulation. This study therefore highlights a novel relationship between heme availability and siderophore biosynthesis in P. aeruginosa.

Mechanisms of iron homeostasis in Pseudomonas aeruginosa and emerging therapeutics directed to disrupt this vital process

Pseudomonas aeruginosa is an opportunistic pathogen able to infect any human tissue. One of the reasons for its high adaptability and colonization of host tissues is its capacity of maintaining iron homeostasis through a wide array of iron acquisition and removal mechanisms. Due to their ability to cause life-threatening acute and chronic infections, especially among cystic fibrosis and immunocompromised patients, and their propensity to acquire resistance to many antibiotics, the World Health Organization (WHO) has encouraged the scientific community to find new strategies to eradicate this pathogen. Several recent strategies to battle P. aeruginosa focus on targeting iron homeostasis mechanisms, turning its greatest advantage into an exploitable weak point. In this review, we discuss the different mechanisms used by P. aeruginosa to maintain iron homeostasis and the strategies being developed to fight this pathogen by blocking these mechanisms. Among others, the use of iron chelators and mimics, as well as disruption of siderophore production and uptake, have shown promising results in reducing viability and/or virulence of this pathogen. The so-called 'Trojan-horse' strategy taking advantage of the siderophore uptake systems is emerging as an efficient method to improve delivery of antibiotics into the bacterial cells. Moreover, siderophore transporters are considered promising targets for the developing of P. aeruginosa vaccines.

The heme-responsive PrrH sRNA regulates Pseudomonas aeruginosa pyochelin gene expression

Pseudomonas aeruginosa is an opportunistic pathogen that requires iron for growth and virulence, yet this nutrient is sequestered by the innate immune system during infection. When iron is limiting, P. aeruginosa expresses the PrrF1 and PrrF2 small regulatory RNAs (sRNAs), which post-transcriptionally repress expression of non-essential iron-containing proteins thus sparing this nutrient for more critical processes. The genes for the PrrF1 and PrrF2 sRNAs are arranged in tandem on the chromosome, allowing for the transcription of a longer heme-responsive sRNA, termed PrrH. While the functions of PrrF1 and PrrF2 have been studied extensively, the role of PrrH in P. aeruginosa physiology and virulence is not well understood. In this study, we performed transcriptomic and proteomic studies to identify the PrrH regulon. In shaking cultures, the pyochelin synthesis proteins were increased in two distinct prrH mutants compared to wild type, while the mRNAs for these proteins were not affected by prrH mutation. We identified complementarity between the PrrH sRNA and sequence upstream of the pchE mRNA, suggesting potential for PrrH to directly regulate expression of genes for pyochelin synthesis. We further showed that pchE mRNA levels were increased in the prrH mutants when grown in static but not shaking conditions. Moreover, we discovered controlling for the presence of light was critical for examining the impact of PrrH on pchE expression. As such, our study reports on the first likely target of the PrrH sRNA and highlights key environmental variables that will allow for future characterization of PrrH function.

The role of host heme in bacterial infection

Heme is an indispensable cofactor for almost all aerobic life, including the human host and many bacterial pathogens. During infection, heme and hemoproteins are the largest source of bioavailable iron, and pathogens have evolved various heme acquisition pathways to satisfy their need for iron and heme. Many of these pathways are regulated transcriptionally by intracellular iron levels, however, host heme availability and intracellular heme levels have also been found to regulate heme uptake in some species. Knowledge of these pathways has helped to uncover not only how these bacteria incorporate host heme into their metabolism but also provided insight into the importance of host heme as a nutrient source during infection. Within this review is covered multiple aspects of the role of heme at the host pathogen interface, including the various routes of heme biosynthesis, how heme is sequestered by the host, and how heme is scavenged by bacterial pathogens. Also discussed is how heme and hemoproteins alter the behavior of the host immune system and bacterial pathogens. Finally, some unanswered questions about the regulation of heme uptake and how host heme is integrated into bacterial metabolism are highlighted.

The function of small RNA in Pseudomonas aeruginosa

Pseudomonas aeruginosa, the main conditional pathogen causing nosocomial infection, is a gram-negative bacterium with the largest genome among the known bacteria. The main reasons why Pseudomonas aeruginosa is prone to drug-resistant strains in clinic are: the drug-resistant genes in its genome and the drug resistance easily induced by single antibiotic treatment. With the development of high-throughput sequencing technology and bioinformatics, the functions of various small RNAs (sRNA) in Pseudomonas aeruginosa are being revealed. Different sRNAs regulate gene expression by binding to protein or mRNA to play an important role in the complex regulatory network. In this article, first, the importance and biological functions of different sRNAs in Pseudomonas aeruginosa are explored, and then the evidence and possibilities that sRNAs served as drug therapeutic targets are discussed, which may introduce new directions to develop novel disease treatment strategies.

Posttranscriptional Regulation in Response to Different Environmental Stresses in Campylobacter jejuni

The survival strategies that Campylobacter jejuni (C. jejuni) employ throughout its transmission and infection life cycles remain largely elusive. Specifically, there is a lack of understanding about the posttranscriptional regulation of stress adaptations resulting from small noncoding RNAs (sRNAs). Published C. jejuni sRNAs have been discovered in specific conditions but with limited insights into their biological activities. Many more sRNAs are yet to be discovered as they may be condition-dependent. Here, we have generated transcriptomic data from 21 host- and transmission-relevant conditions. The data uncovered transcription start sites, expression patterns and posttranscriptional regulation during various stress conditions. This data set helped predict a list of putative sRNAs. We further explored the sRNAs' biological functions by integrating differential gene expression analysis, coexpression analysis, and genome-wide sRNA target prediction. The results showed that the C. jejuni gene expression was influenced primarily by nutrient deprivation and food storage conditions. Further exploration revealed a putative sRNA (CjSA21) that targeted tlp1 to 4 under food processing conditions. tlp1 to 4 are transcripts that encode methyl-accepting chemotaxis proteins (MCPs), which are responsible for chemosensing. These results suggested CjSA21 inhibits chemotaxis and promotes survival under food processing conditions. This study presents the broader research community with a comprehensive data set and highlights a novel sRNA as a potential chemotaxis inhibitor. IMPORTANCE The foodborne pathogen C. jejuni is a significant challenge for the global health care system. It is crucial to investigate C. jejuni posttranscriptional regulation by small RNAs (sRNAs) in order to understand how it adapts to different stress conditions. However, limited data are available for investigating sRNA activity under stress. In this study, we generate gene expression data of C. jejuni under 21 stress conditions. Our data analysis indicates that one of the novel sRNAs mediates the adaptation to food processing conditions. Results from our work shed light on the posttranscriptional regulation of C. jejuni and identify an sRNA associated with food safety.

Modeling the native ensemble of PhuS using enhanced sampling MD and HDX-ensemble reweighting

The cytoplasmic heme binding protein from Pseudomonas aeruginosa, PhuS, plays two essential roles in regulating heme uptake and iron homeostasis. First, PhuS shuttles exogenous heme to heme oxygenase (HemO) for degradation and iron release. Second, PhuS binds DNA and modulates the transcription of the prrF/H small RNAs (sRNAs) involved in the iron-sparing response. Heme binding to PhuS regulates this dual function, as the unliganded form binds DNA, whereas the heme-bound form binds HemO. Crystallographic studies revealed nearly identical structures for apo- and holo-PhuS, and yet numerous solution-based measurements indicate that heme binding is accompanied by large conformational rearrangements. In particular, hydrogen-deuterium exchange mass spectrometry (HDX-MS) of apo- versus holo-PhuS revealed large differences in deuterium uptake, notably in α-helices 6, 7, and 8 (α6,7,8), which contribute to the heme binding pocket. These helices were mostly labile in apo-PhuS but largely protected in holo-PhuS. In contrast, in silico-predicted deuterium uptake levels of α6,7,8 from molecular dynamics (MD) simulations of the apo- and holo-PhuS structures are highly similar, consistent only with the holo-PhuS HDX-MS data. To rationalize this discrepancy between crystal structures, simulations, and observed HDX-MS, we exploit a recently developed computational approach (HDXer) that fits the relative weights of conformational populations within an ensemble of structures to conform to a target set of HDX-MS data. Here, a combination of enhanced sampling MD, HDXer, and dimensionality reduction analysis reveals an apo-PhuS conformational landscape in which α6, 7, and 8 are significantly rearranged compared to the crystal structure, including a loss of secondary structure in α6 and the displacement of α7 toward the HemO binding interface. Circular dichroism analysis confirms the loss of secondary structure, and the extracted ensembles of apo-PhuS and of heme-transfer-impaired H212R mutant, are consistent with known heme binding and transfer properties. The proposed conformational landscape provides structural insights into the modulation by heme of the dual function of PhuS.

Screening and functional identification of antioxidant microRNA-size sRNAs from Spirulina platensis using high-throughput sequencing

MiRNA-size small RNAs, abbreviated as sRNAs, are increasingly being discovered as research progresses and omics technologies development in prokaryotes. However, there is a paucity of data concerning whether or not sRNAs exist in cyanobacteria and regulate the resistance to oxidative stress. In this investigation, small RNA libraries were constructed from the control, 50-nM and 100-nM H2O2 treatments of Spirulina platensis. By high-throughput sequencing, 23 candidate sRNAs showed significantly differential expression under oxidative stress, among which eight sRNAs were identified with the similar expression patterns as the sequencing results by real-time qPCR. By nucleic acid hybridisation, the corresponding expression changes also demonstrated that sequencing results of sRNAs were feasible and credible. By bioinformatics prediction and structure identification, 43 target genes were predicted for 8 sRNAs in plant miRNA database, among which 29 were annotated into the genome and related metabolic pathways of S. platensis. By COG functional classification and KEGG pathway analysis, 31 target genes were predicted to be directly or indirectly involved in the defence mechanism of H2O2 stress. Thirteen target genes displayed reversely changing patterns compared with those of their sRNAs under H2O2 treatment. These findings provide compelling evidence that these sRNAs in S. platensis play a crucial role in oxidative stress responses, and thus provide a theoretical reference for improving the stress-triggering physiological regulation.