JB Accepted Manuscript Posted Online 28 August 2017 J. Bacteriol. doi:10.1128/JB.00472-17 Copyright © 2017 American Society for Microbiology. All Rights Reserved.
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The ferric uptake regulator Fur is conditionally essential in Pseudomonas aeruginosa
2 Martina Pasquaa, Daniela Visaggiob, Alessandra Lo Sciutoa, Shirley Genaha, Ehud Baninc, Paolo
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Viscab#, Francesco Imperia#
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Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Laboratory
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affiliated to Istituto Pasteur Italia – Fondazione Cenci Bolognetti, Rome, Italya; Department of
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Sciences, University “Roma Tre”, Rome, Italyb; Institute for Nanotechnology and Advanced Materials,
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Bar-Ilan University, Ramat Gan, Israelc.
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Running head: Pyochelin impairs growth in Fur-depleted P. aeruginosa
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#Address correspondence to Francesco Imperi,
[email protected], and/or Paolo Visca,
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[email protected].
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Keywords: biofilm, colony formation, infection, iron uptake, oxidative stress, siderophore.
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Abstract
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In Pseudomonas aeruginosa the ferric uptake regulator protein (Fur) controls both metabolism and
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virulence in response to iron availability. Differently from other bacteria, attempts to obtain fur deletion
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mutants in P. aeruginosa failed, leading to the assumption that Fur is an essential protein in this
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bacterium. By investigating a P. aeruginosa fur conditional mutant, we demonstrate that Fur is not
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essential for P. aeruginosa growth in liquid media, biofilm formation, and pathogenicity in an insect
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model of infection. Conversely, Fur is essential for growth on solid media since Fur-depleted cells are
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severely impaired in colony formation. Transposon-mediated random mutagenesis experiments
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identified pyochelin siderophore biosynthesis as a major cause of the colony growth defect of the fur
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conditional mutant, and deletion mutagenesis confirmed this evidence. Impaired colony growth of
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pyochelin-proficient Fur-depleted cells does not depend on oxidative stress, since Fur-depleted cells do
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not accumulate higher levels of reactive oxygen species (ROS), and are not rescued by antioxidant
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agents or overexpression of ROS-detoxifying enzymes. Ectopic expression of pch genes revealed that
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pyochelin production has no inhibitory effects in a fur deletion mutant of Pseudomonas syringae pv.
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tabaci, suggesting that the toxicity of the pch locus in Fur-depleted cells involves P. aeruginosa-
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specific pathway(s).
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Importance
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Members of the ferric uptake regulator (Fur) protein family are bacterial transcriptional repressors
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which control iron uptake and storage in response to iron availability, thereby playing a crucial role in
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the maintenance of iron homeostasis. While fur null mutants have been obtained in many bacteria, Fur
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appears essential in Pseudomonas aeruginosa for still unknown reasons. We obtained Fur-depleted P.
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aeruginosa cells by conditional mutagenesis, and showed that Fur is dispensable for planktonic growth,
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while it is required for colony formation. This is because Fur protects P. aeruginosa colonies from 2
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toxicity exerted by the pyochelin siderophore. This work provides a functional basis to the essentiality
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of Fur in P. aeruginosa, and highlights unique properties of the Fur regulon in this species.
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Introduction
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Iron is a critical nutrient for almost all forms of life, due to its fundamental role as a redox cofactor of
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important enzymes involved in different cellular functions, such as respiration, catabolism, amino acid
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and nucleoside synthesis, and stress response. Although essential for nutrition, iron can also have
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deleterious effects if supplied in excess to living organisms. Indeed, intracellular Fe2+catalyses the
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formation of reactive oxygen species (ROS) through the Fenton reaction, which can damage biological
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macromolecules, such as proteins and nucleic acids, and lipids (1).
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To reconcile their nutritional iron requirement with the need to maintain the intracellular iron content
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below hazardous levels, bacteria have evolved sophisticated strategies to control iron homeostasis.
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While most bacteria have the genetic potential to express different mechanisms for iron acquisition, as
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a general rule the expression of iron uptake genes is repressed when sufficient amounts of intracellular
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iron are available. This negative control occurs through the activity of a transcriptional repressor of the
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Fur (or DtxR) family (2). When loaded with Fe2+, this repressor forms homodimers that bind the
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operator sequence (Fur box) within target promoters, thereby blocking transcription of iron uptake
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genes (3). In addition to this pivotal regulatory mechanism, which is responsible for the restricted
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expression of iron uptake genes under conditions of iron starvation, iron acquisition is also regulated by
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additional mechanisms which overall allow optimal expression of a given iron uptake system only
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when it is effective in delivering iron to the cell (4). In many bacteria Fur also positively controls the
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expression of non-essential iron-using proteins or ROS detoxifying enzymes, by repressing the
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transcription of small RNA(s) which in turn inhibits the translation of target mRNAs (3,5). As a result,
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genes that are involved in iron storage and/or detoxification are induced in the presence of high
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intracellular iron levels, thus counteracting free iron toxicity as well as decreasing the amount of
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sequestered (protein-bound) iron under low-iron conditions.
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In spite of the crucial role of Fur in preserving iron homeostasis in bacterial cells, knock-out mutants in
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the fur gene have been obtained in several bacterial species. These mutants showed variable and
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species-specific phenotypes, ranging from constitutive expression of iron-uptake systems and/or
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virulence factors to impaired acid, serum or oxidative stress resistance, defective motility and/or
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biofilm formation (3). In general, fur deletion has minor effects on bacterial growth in vitro though it
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can affect pathogenicity, since fur mutants of some pathogenic species appear less virulent and/or
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invasive than their wild type counterparts (3,6). However, this is not a rule given that some bacterial
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pathogens, such as pathogenic Escherichia coli strains and Vibrio vulnificus, showed no differences in
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infectivity between wild type and fur mutant strains in animal models (7-9), suggesting that the
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relevance of Fur during bacterial infections is species- and, likely, infection-model specific.
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Notably, fur (or its analogous gene ideR) has been described as an essential gene in few bacterial
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species, such as Pseudomonas aeruginosa and Mycobacterium tuberculosis, due to the inability to
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obtain viable fur knock-out mutants (10-12). The relevance of fur for the fitness of the opportunistic
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human pathogen P. aeruginosa was recently corroborated by two independent transposon sequencing
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(Tn-seq) studies reporting that fur insertion mutants were outcompeted in transposon mutant pools
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under several different growth conditions (13-14). In silico predictions and in vitro experiments,
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including microarray comparison of gene expression between iron-replete and iron-depleted cells and
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Fur-DNA pull down experiments, were used to define the Fur regulon in P. aeruginosa (15-18).
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Overall, these and further confirmatory studies revealed that Fur, directly or indirectly via Fur-
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regulated alternative sigma factors or AraC-like transcriptional regulators, basically represses all iron-
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uptake genes, including those for biosynthesis and transport of the endogenous siderophores
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pyoverdine and pyochelin, heme uptake and transport of exogenous iron chelators, and some virulence
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factors. Moreover, Fur positively regulates iron-storage proteins (bacterioferritins), some enzymes
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involved in carbon catabolism and respiration, and ROS-scavenging enzymes through Fur-mediated 5
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repression of the two sRNAs PrrF1/2 (reviewed in refs. 19,20). This led to the proposal that Fur
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essentiality could be related to the inability of P. aeruginosa to grow through fermentation and, thus, its
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strict requirement to respire, which generates considerable potential for generation of ROS that would
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not be efficiently detoxified in Fur-deficient cells (20,21). However, while the importance of Fur for
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resistance to oxidative stress is overall conserved in bacteria (3), it should be noted that fur knock out
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mutants have been obtained in other non-fermenting Gram-negative bacteria (e.g., Burkholderia
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multivorans, Moraxella catarrhalis and some Pseudomonas species; 22-26), suggesting that alternative,
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more specific harmful effect(s) could account for the critical role of Fur in P. aeruginosa physiology.
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In this work, we used a fur conditional mutant of the reference strain P. aeruginosa PAO1 to
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investigate the effect of Fur depletion both in vitro and in vivo, and employed a transposon mutagenesis
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approach to identify genetic determinants affecting growth of Fur-depleted cells. Our results revealed
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that Fur-depleted P. aeruginosa cells are similar to the wild type with regard to planktonic growth,
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biofilm formation and pathogenicity in an insect model of infection. In contrast, we found that Fur is
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essential for colony growth on agar plates, and that biosynthesis of the pyochelin siderophore is
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partially responsible for this defect, through a mechanism that apparently does not depend on ROS
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generation.
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Results
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Validation of the fur conditional mutant to investigate the effect of Fur depletion in P.
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aeruginosa. In an attempt to investigate the possible involvement of Fur in cell aggregation-mediated
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induction of iron uptake and virulence genes in P. aeruginosa, we recently generated a fur conditional
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mutant in P. aeruginosa PAO1. This mutant carries an arabinose-inducible copy of the fur coding
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sequence inserted into a neutral site (attB) of the PAO1 genome and an in-frame deletion in the 6
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endogenous fur gene (27). With the aim of corroborating the suitability of the fur conditional mutant to
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study the effect of Fur depletion in P. aeruginosa cells, we analyzed this mutant for (i) the effect of
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arabinose on growth, (ii) Fur intracellular levels and (iii) expression of Fur-repressed genes in response
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to iron. As shown in Figure 1A, the growth of the fur conditional mutant in microtiter plates in
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Mueller-Hinton (MH) was impaired with respect to the parental strain PAO1, and was gradually
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restored by arabinose in a dose dependent manner. In the absence of arabinose Fur was undetectable by
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Western blot in cells of the fur conditional mutant, while it was detected at wild type levels in mutant
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cells cultured in the presence of an arabinose concentration (0.5%; Fig. 1B) which completely restored
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the growth of the fur conditional mutant. Since the inability to immunodetect a given protein is not
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sufficient to rule out that basal protein levels potentially present in the conditional mutant could still
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have an effect on Fur-dependent genes, we also monitored pyoverdine production, an easily-detectable
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phenotype that is promptly repressed by Fur in response to iron (28). Pyoverdine production was about
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10-fold higher in the fur mutant than in PAO1, but it decreased to wild type levels in the presence of
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0.5% arabinose (Fig. 1C). More importantly, while addition of 50 µM FeCl3 to the medium shut down
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pyoverdine production by wild type cells, it had no effect on the pyoverdine levels of the fur mutant
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grown in the absence of arabinose (Fig. 1C), indicating that iron-mediated repression of Fur-regulated
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genes is abrogated in the conditional mutant. This was confirmed by the observation that exogenously-
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added iron was unable to repress transcription from promoters of genes directly repressed by Fur (pvdS
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and pchR) in the fur conditional mutant (Fig. 1D). Taken together, these preliminary experiments
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provide evidence that our fur conditional mutant can be used as a tool to investigate the effect of Fur
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depletion in P. aeruginosa.
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Fur-depleted P. aeruginosa cells show severe growth defects on solid media. In order to investigate
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more in depth the effect of Fur depletion in P. aeruginosa, we compared planktonic growth of the wild 7
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type strain PAO1 and the fur conditional mutant in flask cultures using different media containing
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different iron concentrations. The fur conditional mutant was able to grow in the complex medium MH
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(about 5-10 µM iron concentration; 29), although with lower growth rates and about 50% reduction in
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growth yields with respect to the wild type PAO1 (Fig. 2A). The differences in growth rates and yields
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between the two strains were markedly reduced in the iron-deprived complex medium TSBD (ca. 1.5
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µM iron concentration; 30) (Fig. 2B), while no differences were observed in the iron-depleted minimal
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medium DCAA, where iron concentration is very low (