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Chaaban T, Mohsen Y, Ezzeddine Z, Ghssein G. Overview of Yersinia pestis Metallophores: Yersiniabactin and Yersinopine. BIOLOGY 2023; 12:biology12040598. [PMID: 37106798 PMCID: PMC10136090 DOI: 10.3390/biology12040598] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 04/05/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023]
Abstract
The pathogenic anaerobic bacteria Yersinia pestis (Y. pestis), which is well known as the plague causative agent, has the ability to escape or inhibit innate immune system responses, which can result in host death even before the activation of adaptive responses. Bites from infected fleas in nature transmit Y. pestis between mammalian hosts causing bubonic plague. It was recognized that a host's ability to retain iron is essential in fighting invading pathogens. To proliferate during infection, Y. pestis, like most bacteria, has various iron transporters that enable it to acquire iron from its hosts. The siderophore-dependent iron transport system was found to be crucial for the pathogenesis of this bacterium. Siderophores are low-molecular-weight metabolites with a high affinity for Fe3+. These compounds are produced in the surrounding environment to chelate iron. The siderophore secreted by Y. pestis is yersiniabactin (Ybt). Another metallophore produced by this bacterium, yersinopine, is of the opine type and shows similarities with both staphylopine and pseudopaline produced by Staphylococcus aureus and Pseudomonas aeruginosa, respectively. This paper sheds light on the most important aspects of the two Y. pestis metallophores as well as aerobactin a siderophore no longer secreted by this bacterium due to frameshift mutation in its genome.
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Affiliation(s)
- Taghrid Chaaban
- Nursing Sciences Department, Faculty of Public Health, Islamic University of Lebanon, Khalde P.O. Box 30014, Lebanon
- Nursing Sciences Research Chair, Laboratory Educations and Health Practices (LEPS), (EA 3412), UFR SMBH, University Paris 13, Sorbonne Paris Cite, F-93017 Bobigny, France
| | - Yehya Mohsen
- Department of Medical Laboratory Technology, College of Health and Medical Technologies, Al-Ayen University, Nasiriyah 64001, Iraq
| | - Zeinab Ezzeddine
- Laboratory Sciences Department, Faculty of Public Health, Islamic University of Lebanon (IUL), Khalde P.O. Box 30014, Lebanon
- Faculty of Sciences V, Lebanese University, Nabatieh 1700, Lebanon
| | - Ghassan Ghssein
- Laboratory Sciences Department, Faculty of Public Health, Islamic University of Lebanon (IUL), Khalde P.O. Box 30014, Lebanon
- Faculty of Sciences V, Lebanese University, Nabatieh 1700, Lebanon
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The biofilm life cycle: expanding the conceptual model of biofilm formation. Nat Rev Microbiol 2022; 20:608-620. [PMID: 35922483 PMCID: PMC9841534 DOI: 10.1038/s41579-022-00767-0] [Citation(s) in RCA: 275] [Impact Index Per Article: 137.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/21/2022] [Indexed: 01/18/2023]
Abstract
Bacterial biofilms are often defined as communities of surface-attached bacteria and are typically depicted with a classic mushroom-shaped structure characteristic of Pseudomonas aeruginosa. However, it has become evident that this is not how all biofilms develop, especially in vivo, in clinical and industrial settings, and in the environment, where biofilms often are observed as non-surface-attached aggregates. In this Review, we describe the origin of the current five-step biofilm development model and why it fails to capture many aspects of bacterial biofilm physiology. We aim to present a simplistic developmental model for biofilm formation that is flexible enough to include all the diverse scenarios and microenvironments where biofilms are formed. With this new expanded, inclusive model, we hereby introduce a common platform for developing an understanding of biofilms and anti-biofilm strategies that can be tailored to the microenvironment under investigation.
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A previously uncharacterized gene, PA2146, contributes to biofilm formation and drug tolerance across the ɣ-Proteobacteria. NPJ Biofilms Microbiomes 2022; 8:54. [PMID: 35798749 PMCID: PMC9262955 DOI: 10.1038/s41522-022-00314-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 06/14/2022] [Indexed: 01/11/2023] Open
Abstract
Transcriptomic studies have revealed a large number of uncharacterized genes that are differentially expressed in biofilms, which may be important in regulating biofilm phenotypes such as resistance to antimicrobial agents. To identify biofilm genes of unknown function in P. aeruginosa, we made use of RNA-seq and selected 27 uncharacterized genes that were induced upon biofilm growth. Biofilms by respective mutants were subsequently analyzed for two biofilm characteristics, the biofilm architecture and drug susceptibility. The screen revealed 12 out of 27 genes to contribute to biofilm formation and 13 drug susceptibility, with 8 genes affecting both biofilm phenotypes. Amongst the genes affecting both biofilm phenotypes was PA2146, encoding a small hypothetical protein that exhibited some of the most substantial increases in transcript abundance during biofilm growth by P. aeruginosa PAO1 and clinical isolates. PA2146 is highly conserved in ɣ-proteobacteria. Inactivation of PA2146 affected both biofilm phenotypes in P. aeruginosa PAO1, with inactivation of homologs in Klebsiella pneumoniae and Escherichia coli having similar effects. Heterologous expression of PA2146 homologs complemented the P. aeruginosa ∆PA2146, suggesting that PA2146 homologs substitute for and play a similar role as PA2146 in P. aeruginosa.
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D'Arpa P, Karna SLR, Chen T, Leung KP. Pseudomonas aeruginosa transcriptome adaptations from colonization to biofilm infection of skin wounds. Sci Rep 2021; 11:20632. [PMID: 34667187 PMCID: PMC8526614 DOI: 10.1038/s41598-021-00073-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 09/07/2021] [Indexed: 11/09/2022] Open
Abstract
In burn patients Pseudomonas aeruginosa infection is a major cause of morbidity. Analysis of the pathogen's gene expression as it transitions from colonization to acute and then biofilm wound infection may provide strategies for infection control. Toward this goal, we seeded log-phase P. aeruginosa (PAO1) into 3-day-old, full-thickness excision wounds (rabbit ear) and harvested the bacteria during colonization (Hrs 2 and 6), acute infection (Hr 24), and biofilm infection (Days 5 and 9) for transcriptome analysis (RNA-Seq). After 2-6 h in the wound, genes for metabolism and cell replication were down-regulated while wound-adaptation genes were up-regulated (vs. expression in log-phase culture). As the infection progressed from acute to biofilm infection, more genes became up-regulated than down-regulated, but the down-regulated genes enriched in more pathways, likely because the genes and pathways that bacteria already colonizing wounds up-regulate to establish biofilm infection are less known. Across the stages of infection, carbon-utilization pathways shifted. During acute infection, itaconate produced by myeloid cells appears to have been a carbon source because myeloid cell infiltration and the expression of the host gene, ACOD1, for itaconate production peaked coincidently with the expression of the PAO1 genes for itaconate transport and catabolism. Additionally, branched-chain amino acids are suggested to be a carbon source in acute infection and in biofilm infection. In biofilm infection, fatty acid degradation was also up-regulated. These carbon sources feed into the glyoxylate cycle that was coincidently up-regulated, suggesting it provided the precursors for P. aeruginosa to synthesize macromolecules in establishing wound infection.
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Affiliation(s)
- Peter D'Arpa
- Combat Wound Repair Group and Tissue Regeneration Department, US Army Institute of Surgical Research, JBSA Fort Sam Houston, San Antonio, TX, USA.,The Geneva Foundation, Tacoma, USA
| | - S L Rajasekhar Karna
- Combat Wound Repair Group and Tissue Regeneration Department, US Army Institute of Surgical Research, JBSA Fort Sam Houston, San Antonio, TX, USA
| | - Tsute Chen
- The Forsyth Institute, Cambridge, MA, USA
| | - Kai P Leung
- Combat Wound Repair Group and Tissue Regeneration Department, US Army Institute of Surgical Research, JBSA Fort Sam Houston, San Antonio, TX, USA.
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Pellissier L, Leoni S, Marcourt L, Ferreira Queiroz E, Lecoultre N, Quiros-Guerrero LM, Barthélémy M, Eparvier V, Chave J, Stien D, Gindro K, Perron K, Wolfender JL. Characterization of Pseudomonas aeruginosa Quorum Sensing Inhibitors from the Endophyte Lasiodiplodia venezuelensis and Evaluation of Their Antivirulence Effects by Metabolomics. Microorganisms 2021; 9:microorganisms9091807. [PMID: 34576706 PMCID: PMC8465504 DOI: 10.3390/microorganisms9091807] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 08/19/2021] [Accepted: 08/20/2021] [Indexed: 11/16/2022] Open
Abstract
The opportunistic pathogen Pseudomonas aeruginosa is one of the "critical priority pathogens" due to its multidrug resistance to a wide range of antibiotics. Its ability to invade and damage host tissues is due to the use of quorum sensing (QS) to collectively produce a plethora of virulence factors. Inhibition of QS is an attractive strategy for new antimicrobial agents because it disrupts the initial events of infection without killing the pathogen. Highly diverse microorganisms as endophytes represent an under-explored source of bioactive natural products, offering opportunities for the discovery of novel QS inhibitors (QSI). In the present work, the objective was to explore selective QSIs within a unique collection of fungal endophytes isolated from the tropical palm Astrocaryum sciophilum. The fungi were cultured, extracted, and screened for their antibacterial and specific anti-QS activities against P. aeruginosa. The endophytic strain Lasiodiplodia venezuelensis was prioritized for scaled-up fractionation for its selective activity, leading to the isolation of eight compounds in a single step. Among them, two pyran-derivatives were found to be responsible for the QSI activity, with an effect on some QS-regulated virulence factors. Additional non-targeted metabolomic studies on P. aeruginosa documented their effects on the production of various virulence-related metabolites.
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Affiliation(s)
- Léonie Pellissier
- School of Pharmaceutical Sciences, University of Geneva, CMU-Rue Michel-Servet 1, CH-1211 Geneva 4, Switzerland; (L.M.); (E.F.Q.); (L.-M.Q.-G.)
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, CMU-Rue Michel Servet 1, CH-1211 Geneva 4, Switzerland
- Correspondence: (L.P.); (J.-L.W.)
| | - Sara Leoni
- Microbiology Unit, Department of Botany and Plant Biology, University of Geneva, CMU-Rue Michel-Servet 1, CH-1211 Geneva 4, Switzerland; (S.L.); (K.P.)
| | - Laurence Marcourt
- School of Pharmaceutical Sciences, University of Geneva, CMU-Rue Michel-Servet 1, CH-1211 Geneva 4, Switzerland; (L.M.); (E.F.Q.); (L.-M.Q.-G.)
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, CMU-Rue Michel Servet 1, CH-1211 Geneva 4, Switzerland
| | - Emerson Ferreira Queiroz
- School of Pharmaceutical Sciences, University of Geneva, CMU-Rue Michel-Servet 1, CH-1211 Geneva 4, Switzerland; (L.M.); (E.F.Q.); (L.-M.Q.-G.)
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, CMU-Rue Michel Servet 1, CH-1211 Geneva 4, Switzerland
| | - Nicole Lecoultre
- Mycology Group, Research Department Plant Protection, Agroscope, Route de Duillier 50, 1260 Nyon, Switzerland; (N.L.); (K.G.)
| | - Luis-Manuel Quiros-Guerrero
- School of Pharmaceutical Sciences, University of Geneva, CMU-Rue Michel-Servet 1, CH-1211 Geneva 4, Switzerland; (L.M.); (E.F.Q.); (L.-M.Q.-G.)
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, CMU-Rue Michel Servet 1, CH-1211 Geneva 4, Switzerland
| | - Morgane Barthélémy
- Institut de Chimie des Substances Naturelles, Université Paris-Saclay, CNRS, UPR 2301, 91198 Gif-sur-Yvette, France; (M.B.); (V.E.)
| | - Véronique Eparvier
- Institut de Chimie des Substances Naturelles, Université Paris-Saclay, CNRS, UPR 2301, 91198 Gif-sur-Yvette, France; (M.B.); (V.E.)
| | - Jérôme Chave
- Laboratoire Evolution et Diversité Biologique (UMR 5174), CNRS, UT3, IRD, Université Toulouse 3, 118 Route de Narbonne, 31062 Toulouse, France;
| | - Didier Stien
- Sorbonne Université, CNRS, Laboratoire de Biodiversité et Biotechnologie Microbiennes, LBBM, Observatoire Océanologique, 66650 Banyuls-Sur-Mer, France;
| | - Katia Gindro
- Mycology Group, Research Department Plant Protection, Agroscope, Route de Duillier 50, 1260 Nyon, Switzerland; (N.L.); (K.G.)
| | - Karl Perron
- Microbiology Unit, Department of Botany and Plant Biology, University of Geneva, CMU-Rue Michel-Servet 1, CH-1211 Geneva 4, Switzerland; (S.L.); (K.P.)
| | - Jean-Luc Wolfender
- School of Pharmaceutical Sciences, University of Geneva, CMU-Rue Michel-Servet 1, CH-1211 Geneva 4, Switzerland; (L.M.); (E.F.Q.); (L.-M.Q.-G.)
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, CMU-Rue Michel Servet 1, CH-1211 Geneva 4, Switzerland
- Correspondence: (L.P.); (J.-L.W.)
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Phenotypic and Genomic Comparison of the Two Most Common ExoU-Positive Pseudomonas aeruginosa Clones, PA14 and ST235. mSystems 2020; 5:5/6/e01007-20. [PMID: 33293405 PMCID: PMC7743143 DOI: 10.1128/msystems.01007-20] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Genotyping of 2,882 Pseudomonas aeruginosa isolates that had been collected during the last 40 years identified the ExoU-positive lineages PA14 (ST253) and ST235 as the second and third most frequent clones in the P. aeruginosa population. Both clones were approximately 2-fold more frequently detected in animate habitats than in soil or aquatic habitats. While ST253 clone isolates were causing mainly acute and chronic infections in humans, ST235 isolates had been preferentially collected from hospitalized patients with severe acute infections, particularly, keratitis, urinary tract infections, burn wounds, and ventilator-associated pneumonia. The two major exoU clones differed substantially in the composition and flexibility of the accessory genome and by more than 8,000 amino acid sequences. Pronounced sequence variation between orthologs was noted in genes encoding elements of secretion systems and secreted effector molecules, including the type III secretion system, indicating the modes of action of the different clones. When comparing representatives of the two clones in batch culture, the PA14 strain orchestrated the quorum sensing circuitry for the expression of pathogenic traits and stopped growing in batch culture when it entered the stationary phase, but the quorum sensing-deficient ST235 strain expressed high type III secretion activity and continued to grow and to divide. In summary, unrestricted growth, high constitutive type III secretion activity, and facilitated uptake of foreign DNA could be major features that have made ST235 a global high-risk clone associated with poor outcomes of acute nosocomial infections.IMPORTANCE The ubiquitous and metabolically versatile environmental bacterium Pseudomonas aeruginosa can cause infections in a wide variety of hosts, including insects, plants, animals, and humans. P. aeruginosa is one of the ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) pathogens that are the major cause of nosocomial infections in the United States and are a threat all over the world because of their capacity to become increasingly resistant to all available antibiotics. Most experimental work on P. aeruginosa has been performed with reference strains PAO1 and PA14, providing deep insight into key metabolic and regulatory pathways thought to be applicable to all P. aeruginosa strains. However, this comparative study on the two most common exoU-positive clones taught us that there are major lineages in the population such as the global high-risk clone ST235 that exhibit uncommon traits of lifestyle, genome mobility, and pathogenicity distinct from those in our knowledge gained from the studies with the reference strains.
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Abstract
Bacteria must acquire essential nutrients, including zinc, from their environment. For bacterial pathogens, this necessitates overcoming the host metal-withholding response known as nutritional immunity. A novel type of zinc uptake mechanism that involves the bacterial production of a small zinc-scavenging molecule was recently described in the human pathogens Staphylococcus aureus, Pseudomonas aeruginosa, and Yersinia pestis, as well as the soil-associated bacterium Paenibacillus mucilaginosus. This suggests that zincophores may be important for zinc acquisition in diverse environments. In this study, we sought to identify other zincophore-producing bacteria using bioinformatics. We identified almost 250 unique zincophore-producing species, including human and animal pathogens, as well as isolates from soil, rhizosphere, plant, and marine habitats. Crucially, we observed diversity at the amino acid and gene organization levels, suggesting that many of these species are producing unique zincophores. Together, our findings highlight the importance of zincophores for a broad array of bacteria living in diverse environments. Zinc is an essential nutrient in biological systems due to its structural or catalytic requirement in proteins involved in diverse cellular processes. To meet this cellular demand, microbes must acquire sufficient zinc from their environment. However, many environments have low zinc availability. One of the mechanisms used by bacteria to acquire zinc is through the production of small molecules known as zincophores. Similar to bacterial siderophores used for iron uptake, zincophores are synthesized by the bacterium and exported and then reimported as zincophore-zinc complexes. Thus far, only four zincophores have been described, including two from the human pathogens Staphylococcus aureus and Pseudomonas aeruginosa, in which they play a critical role in zinc acquisition during infection, and one in a soil bacterium. To determine what other microbes may produce zincophores, we used bioinformatic analyses to identify new zincophore biosynthetic gene clusters (BGCs) and predict the diversity of molecules synthesized. Genome neighborhood network analysis identified approximately 250 unique zincophore-producing species from actinobacteria, firmicutes, proteobacteria, and fusobacteria. This indicates that zincophores are produced by diverse bacteria that inhabit a broad range of ecological niches. Many of the BGCs likely produce characterized zincophores, based on similarity to the characterized systems. However, this analysis also identified numerous BGCs that, based on the colocalization of additional modifying enzymes and sequence divergence of the biosynthetic enzymes, are likely to produce unique zincophores. Collectively, these findings provide a comprehensive understanding of the zincophore biosynthetic landscape that will be invaluable for future research on these important small molecules. IMPORTANCE Bacteria must acquire essential nutrients, including zinc, from their environment. For bacterial pathogens, this necessitates overcoming the host metal-withholding response known as nutritional immunity. A novel type of zinc uptake mechanism that involves the bacterial production of a small zinc-scavenging molecule was recently described in the human pathogens Staphylococcus aureus, Pseudomonas aeruginosa, and Yersinia pestis, as well as the soil-associated bacterium Paenibacillus mucilaginosus. This suggests that zincophores may be important for zinc acquisition in diverse environments. In this study, we sought to identify other zincophore-producing bacteria using bioinformatics. We identified almost 250 unique zincophore-producing species, including human and animal pathogens, as well as isolates from soil, rhizosphere, plant, and marine habitats. Crucially, we observed diversity at the amino acid and gene organization levels, suggesting that many of these species are producing unique zincophores. Together, our findings highlight the importance of zincophores for a broad array of bacteria living in diverse environments.
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Laffont C, Arnoux P. The ancient roots of nicotianamine: diversity, role, regulation and evolution of nicotianamine-like metallophores. Metallomics 2020; 12:1480-1493. [PMID: 33084706 DOI: 10.1039/d0mt00150c] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Nicotianamine (NA) is a metabolite synthesized by all plants, in which it is involved in the homeostasis of different micronutrients such as iron, nickel or zinc. In some plants it also serves as a precursor of phytosiderophores, which are used for extracellular iron scavenging. Previous studies have also established the presence of NA in filamentous fungi and some mosses, whereas an analogue of NA was inferred in an archaeon. More recently, opine-type metallophores with homology to NA were uncovered in bacteria, especially in human pathogens such as Staphylococcus aureus, Pseudomonas aeruginosa or Yersinia pestis, synthesizing respectively staphylopine, pseudopaline and yersinopine. Here, we review the current state of knowledge regarding the discovery, biosynthesis, function and regulation of these metallophores. We also discuss the genomic environment of the cntL gene, which is homologous to the plant NA synthase (NAS) gene, and plays a central role in the synthesis of NA-like metallophores. This reveals a large diversity of biosynthetic, export and import pathways. Using sequence similarity networks, we uncovered that these metallophores are widespread in numerous bacteria thriving in very different environments, such as those living at the host-pathogen interface, but also in the soil. We additionally established a phylogeny of the NAS/cntL gene and, as a result, we propose that this gene is an ancient gene and NA, or its derivatives, is an ancient metallophore that played a prominent role in metal acquisition or metal resistance. Indeed, our phylogenetic analysis suggests an evolutionary model where the possibility to synthesize this metallophore was present early in the appearance of life, although it was later lost by most living microorganisms, unless facing metal starvation such as at the host-pathogen interface or in some soils. According to our model, NA then re-emerged as a central metabolite for metal homeostasis in fungi, mosses and all known higher plants.
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Affiliation(s)
- Clémentine Laffont
- Aix Marseille Univ, CEA, CNRS, BIAM, Saint Paul-Lez-Durance, F-13108, France.
| | - Pascal Arnoux
- Aix Marseille Univ, CEA, CNRS, BIAM, Saint Paul-Lez-Durance, F-13108, France.
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Yung YP, McGill SL, Chen H, Park H, Carlson RP, Hanley L. Reverse diauxie phenotype in Pseudomonas aeruginosa biofilm revealed by exometabolomics and label-free proteomics. NPJ Biofilms Microbiomes 2019; 5:31. [PMID: 31666981 PMCID: PMC6814747 DOI: 10.1038/s41522-019-0104-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 09/25/2019] [Indexed: 12/17/2022] Open
Abstract
Microorganisms enhance fitness by prioritizing catabolism of available carbon sources using a process known as carbon catabolite repression (CCR). Planktonically grown Pseudomonas aeruginosa is known to prioritize the consumption of organic acids including lactic acid over catabolism of glucose using a CCR strategy termed "reverse diauxie." P. aeruginosa is an opportunistic pathogen with well-documented biofilm phenotypes that are distinct from its planktonic phenotypes. Reverse diauxie has been described in planktonic cultures, but it has not been documented explicitly in P. aeruginosa biofilms. Here a combination of exometabolomics and label-free proteomics was used to analyze planktonic and biofilm phenotypes for reverse diauxie. P. aeruginosa biofilm cultures preferentially consumed lactic acid over glucose, and in addition, the cultures catabolized the substrates completely and did not exhibit the acetate secreting "overflow" metabolism that is typical of many model microorganisms. The biofilm phenotype was enabled by changes in protein abundances, including lactate dehydrogenase, fumarate hydratase, GTP cyclohydrolase, L-ornithine N(5)-monooxygenase, and superoxide dismutase. These results are noteworthy because reverse diauxie-mediated catabolism of organic acids necessitates a terminal electron acceptor like O2, which is typically in low supply in biofilms due to diffusion limitation. Label-free proteomics identified dozens of proteins associated with biofilm formation including 16 that have not been previously reported, highlighting both the advantages of the methodology utilized here and the complexity of the proteomic adaptation for P. aeruginosa biofilms. Documenting the reverse diauxic phenotype in P. aeruginosa biofilms is foundational for understanding cellular nutrient and energy fluxes, which ultimately control growth and virulence.
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Affiliation(s)
- Yeni P. Yung
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607 USA
| | - S. Lee McGill
- Center for Biofilm Engineering, Montana State University, Bozeman, MT 59717 USA
| | - Hui Chen
- Research Resources Center, University of Illinois at Chicago, Chicago, IL 60607 USA
| | - Heejoon Park
- Center for Biofilm Engineering, Montana State University, Bozeman, MT 59717 USA
| | - Ross P. Carlson
- Center for Biofilm Engineering, Montana State University, Bozeman, MT 59717 USA
| | - Luke Hanley
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607 USA
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Conceptual Model of Biofilm Antibiotic Tolerance That Integrates Phenomena of Diffusion, Metabolism, Gene Expression, and Physiology. J Bacteriol 2019; 201:JB.00307-19. [PMID: 31501280 DOI: 10.1128/jb.00307-19] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 08/28/2019] [Indexed: 01/14/2023] Open
Abstract
Transcriptomic, metabolomic, physiological, and computational modeling approaches were integrated to gain insight into the mechanisms of antibiotic tolerance in an in vitro biofilm system. Pseudomonas aeruginosa biofilms were grown in drip flow reactors on a medium composed to mimic the exudate from a chronic wound. After 4 days, the biofilm was 114 μm thick with 9.45 log10 CFU cm-2 These biofilms exhibited tolerance, relative to exponential-phase planktonic cells, to subsequent treatment with ciprofloxacin. The specific growth rate of the biofilm was estimated via elemental balances to be approximately 0.37 h-1 and with a reaction-diffusion model to be 0.32 h-1, or one-third of the maximum specific growth rate for planktonic cells. Global analysis of gene expression indicated lower transcription of ribosomal genes and genes for other anabolic functions in biofilms than in exponential-phase planktonic cells and revealed the induction of multiple stress responses in biofilm cells, including those associated with growth arrest, zinc limitation, hypoxia, and acyl-homoserine lactone quorum sensing. Metabolic pathways for phenazine biosynthesis and denitrification were transcriptionally activated in biofilms. A customized reaction-diffusion model predicted that steep oxygen concentration gradients will form when these biofilms are thicker than about 40 μm. Mutant strains that were deficient in Psl polysaccharide synthesis, the stringent response, the stationary-phase response, and the membrane stress response exhibited increased ciprofloxacin susceptibility when cultured in biofilms. These results support a sequence of phenomena leading to biofilm antibiotic tolerance, involving oxygen limitation, electron acceptor starvation and growth arrest, induction of associated stress responses, and differentiation into protected cell states.IMPORTANCE Bacteria in biofilms are protected from killing by antibiotics, and this reduced susceptibility contributes to the persistence of infections such as those in the cystic fibrosis lung and chronic wounds. A generalized conceptual model of biofilm antimicrobial tolerance with the following mechanistic steps is proposed: (i) establishment of concentration gradients in metabolic substrates and products; (ii) active biological responses to these changes in the local chemical microenvironment; (iii) entry of biofilm cells into a spectrum of states involving alternative metabolisms, stress responses, slow growth, cessation of growth, or dormancy (all prior to antibiotic treatment); (iv) adaptive responses to antibiotic exposure; and (v) reduced susceptibility of microbial cells to antimicrobial challenges in some of the physiological states accessed through these changes.
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Simple rules govern the diversity of bacterial nicotianamine-like metallophores. Biochem J 2019; 476:2221-2233. [PMID: 31300464 DOI: 10.1042/bcj20190384] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 07/10/2019] [Accepted: 07/11/2019] [Indexed: 11/17/2022]
Abstract
In metal-scarce environments, some pathogenic bacteria produce opine-type metallophores mainly to face the host's nutritional immunity. This is the case of staphylopine, pseudopaline and yersinopine, identified in Staphylococcus aureus, Pseudomonas aeruginosa and Yersinia pestis, respectively. Depending on the species, these metallophores are synthesized by two (CntLM) or three enzymes (CntKLM), CntM catalyzing the last step of biosynthesis using diverse substrates (pyruvate or α-ketoglutarate), pathway intermediates (xNA or yNA) and cofactors (NADH or NADPH). Here, we explored the substrate specificity of CntM by combining bioinformatic and structural analysis with chemical synthesis and enzymatic studies. We found that NAD(P)H selectivity is mainly due to the amino acid at position 33 (S. aureus numbering) which ensures a preferential binding to NADPH when it is an arginine. Moreover, whereas CntM from P. aeruginosa preferentially uses yNA over xNA, the staphylococcal enzyme is not stereospecific. Most importantly, selectivity toward α-ketoacids is largely governed by a single residue at position 150 of CntM (S. aureus numbering): an aspartate at this position ensures selectivity toward pyruvate, whereas an alanine leads to the consumption of both pyruvate and α-ketoglutarate. Modifying this residue in P. aeruginosa led to a complete reversal of selectivity. Thus, the diversity of opine-type metallophore is governed by the absence/presence of a cntK gene encoding a histidine racemase, and the amino acid residue at position 150 of CntM. These two simple rules predict the production of a fourth metallophore by Paenibacillus mucilaginosus, which was confirmed in vitro and called bacillopaline.
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Zhang J, Zhao T, Yang R, Siridechakorn I, Wang S, Guo Q, Bai Y, Shen HC, Lei X. De novo synthesis, structural assignment and biological evaluation of pseudopaline, a metallophore produced by Pseudomonas aeruginosa. Chem Sci 2019; 10:6635-6641. [PMID: 31367316 PMCID: PMC6625496 DOI: 10.1039/c9sc01405e] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 05/27/2019] [Indexed: 12/15/2022] Open
Abstract
Pseudopaline is an opine carboxylate metallophore produced by Pseudomonas aeruginosa for harvesting divalent metals. However, the structure of pseudopaline is not fully elucidated. Herein, we report the first de novo total synthesis and isolation of pseudopaline, which allows unambiguous determination and confirmation of both the absolute and the relative configuration of the natural product. The synthesis highlights an efficient and stereocontrolled route using the asymmetric Tsuji-Trost reaction as the key step. The preliminary structure-activity relationship study indicated that one pseudopaline derivative shows comparable activity to pseudopaline. Moreover, a pseudopaline-fluorescein conjugate was prepared and evaluated, which confirmed that pseudopaline could be transported in the bacteria. Since the metal acquisition by P. aeruginosa is crucial for its ability to cause diseases, our extensive structural and functional studies of pseudopaline may pave the way for developing new therapeutic strategies such as the "Trojan horse" antibiotic conjugate against P. aeruginosa.
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Affiliation(s)
- Jian Zhang
- Beijing National Laboratory for Molecular Sciences , Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education , Department of Chemical Biology , College of Chemistry and Molecular Engineering , Synthetic and Functional Biomolecules Center , Peking-Tsinghua Center for Life Sciences , Peking University , Beijing 100871 , China .
| | - Tianhu Zhao
- Beijing National Laboratory for Molecular Sciences , Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education , Department of Chemical Biology , College of Chemistry and Molecular Engineering , Synthetic and Functional Biomolecules Center , Peking-Tsinghua Center for Life Sciences , Peking University , Beijing 100871 , China .
| | - Rongwen Yang
- Beijing National Laboratory for Molecular Sciences , Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education , Department of Chemical Biology , College of Chemistry and Molecular Engineering , Synthetic and Functional Biomolecules Center , Peking-Tsinghua Center for Life Sciences , Peking University , Beijing 100871 , China .
| | - Ittipon Siridechakorn
- Beijing National Laboratory for Molecular Sciences , Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education , Department of Chemical Biology , College of Chemistry and Molecular Engineering , Synthetic and Functional Biomolecules Center , Peking-Tsinghua Center for Life Sciences , Peking University , Beijing 100871 , China .
| | - Sanshan Wang
- Beijing National Laboratory for Molecular Sciences , Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education , Department of Chemical Biology , College of Chemistry and Molecular Engineering , Synthetic and Functional Biomolecules Center , Peking-Tsinghua Center for Life Sciences , Peking University , Beijing 100871 , China .
| | - Qianqian Guo
- Beijing National Laboratory for Molecular Sciences , Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education , Department of Chemical Biology , College of Chemistry and Molecular Engineering , Synthetic and Functional Biomolecules Center , Peking-Tsinghua Center for Life Sciences , Peking University , Beijing 100871 , China .
| | - Yingjie Bai
- Beijing National Laboratory for Molecular Sciences , Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education , Department of Chemical Biology , College of Chemistry and Molecular Engineering , Synthetic and Functional Biomolecules Center , Peking-Tsinghua Center for Life Sciences , Peking University , Beijing 100871 , China .
| | - Hong C Shen
- Roche Innovation Center Shanghai , Roche Pharma Research & Early Development , Shanghai 201203 , China
| | - Xiaoguang Lei
- Beijing National Laboratory for Molecular Sciences , Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education , Department of Chemical Biology , College of Chemistry and Molecular Engineering , Synthetic and Functional Biomolecules Center , Peking-Tsinghua Center for Life Sciences , Peking University , Beijing 100871 , China .
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13
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Lorenz A, Preuße M, Bruchmann S, Pawar V, Grahl N, Pils MC, Nolan LM, Filloux A, Weiss S, Häussler S. Importance of flagella in acute and chronicPseudomonas aeruginosainfections. Environ Microbiol 2018; 21:883-897. [DOI: 10.1111/1462-2920.14468] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 11/01/2018] [Accepted: 11/02/2018] [Indexed: 12/18/2022]
Affiliation(s)
- Anne Lorenz
- Institute of Molecular BacteriologyHelmholtz Centre for Infection Research Braunschweig Germany
- Institute of Molecular Bacteriology, TWINCORE GmbHCenter for Clinical and Experimental Infection Research Hannover Germany
| | - Matthias Preuße
- Institute of Molecular BacteriologyHelmholtz Centre for Infection Research Braunschweig Germany
- Institute of Molecular Bacteriology, TWINCORE GmbHCenter for Clinical and Experimental Infection Research Hannover Germany
| | - Sebastian Bruchmann
- Institute of Molecular BacteriologyHelmholtz Centre for Infection Research Braunschweig Germany
- Institute of Molecular Bacteriology, TWINCORE GmbHCenter for Clinical and Experimental Infection Research Hannover Germany
- Wellcome Sanger Institute Cambridge UK
| | - Vinay Pawar
- Institute of Molecular BacteriologyHelmholtz Centre for Infection Research Braunschweig Germany
- Institute of Immunology, Medical School Hannover Hannover Germany
| | - Nora Grahl
- Institute of Molecular BacteriologyHelmholtz Centre for Infection Research Braunschweig Germany
- Institute of Molecular Bacteriology, TWINCORE GmbHCenter for Clinical and Experimental Infection Research Hannover Germany
| | - Marina C. Pils
- Mouse PathologyAnimal Experimental Unit, Helmholtz Centre for Infection Research Braunschweig Germany
| | - Laura M. Nolan
- MRC Centre for Molecular Bacteriology and Infection (CMBI), Department of Life SciencesImperial College London London UK
| | - Alain Filloux
- MRC Centre for Molecular Bacteriology and Infection (CMBI), Department of Life SciencesImperial College London London UK
| | - Siegfried Weiss
- Institute of Immunology, Medical School Hannover Hannover Germany
| | - Susanne Häussler
- Institute of Molecular BacteriologyHelmholtz Centre for Infection Research Braunschweig Germany
- Institute of Molecular Bacteriology, TWINCORE GmbHCenter for Clinical and Experimental Infection Research Hannover Germany
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14
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Intergenic evolution during host adaptation increases expression of the metallophore pseudopaline in Pseudomonas aeruginosa. Microbiology (Reading) 2018; 164:1038-1047. [DOI: 10.1099/mic.0.000687] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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15
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Pezzoni M, Pizarro RA, Costa CS. Exposure to low doses of UVA increases biofilm formation in Pseudomonas aeruginosa. BIOFOULING 2018; 34:673-684. [PMID: 30185068 DOI: 10.1080/08927014.2018.1480758] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 05/18/2018] [Indexed: 06/08/2023]
Abstract
The establishment of bacterial biofilms on abiotic surfaces is a complex process regulated by multiple genetic regulators and environmental factors which are able to modulate the passage of planktonic cells to a sessile state. Solar ultraviolet-A radiation (UVA, 315-400) is one of the main environmental stress factors that bacteria must face at the Earth´s surface. The deleterious effects of UVA are mainly due to oxidative damage. This paper reports that exposure to low UVA doses promotes biofilm formation in three prototypical strains of Pseudomonas aeruginosa, a relevant opportunistic human pathogen. It demonstrates that exposure of planktonic cells to sublethal doses of UVA can increase cell surface hydrophobicity and swimming motility, two parameters known to favor cell adhesion. These results suggest that UVA radiation acts, at least in part, by promoting the first stages of biofilm development.
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Affiliation(s)
- Magdalena Pezzoni
- a Dpto. de Radiobiología , Comisión Nacional de Energía Atómica , General San Martín , Argentina
| | - Ramón A Pizarro
- a Dpto. de Radiobiología , Comisión Nacional de Energía Atómica , General San Martín , Argentina
| | - Cristina S Costa
- a Dpto. de Radiobiología , Comisión Nacional de Energía Atómica , General San Martín , Argentina
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16
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McFarlane JS, Davis CL, Lamb AL. Staphylopine, pseudopaline, and yersinopine dehydrogenases: A structural and kinetic analysis of a new functional class of opine dehydrogenase. J Biol Chem 2018; 293:8009-8019. [PMID: 29618515 PMCID: PMC5971449 DOI: 10.1074/jbc.ra118.002007] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 04/03/2018] [Indexed: 11/06/2022] Open
Abstract
Opine dehydrogenases (ODHs) from the bacterial pathogens Staphylococcus aureus, Pseudomonas aeruginosa, and Yersinia pestis perform the final enzymatic step in the biosynthesis of a new class of opine metallophores, which includes staphylopine, pseudopaline, and yersinopine, respectively. Growing evidence indicates an important role for this pathway in metal acquisition and virulence, including in lung and burn-wound infections (P. aeruginosa) and in blood and heart infections (S. aureus). Here, we present kinetic and structural characterizations of these three opine dehydrogenases. A steady-state kinetic analysis revealed that the three enzymes differ in α-keto acid and NAD(P)H substrate specificity and nicotianamine-like substrate stereoselectivity. The structural basis for these differences was determined from five ODH X-ray crystal structures, ranging in resolution from 1.9 to 2.5 Å, with or without NADP+ bound. Variation in hydrogen bonding with NADPH suggested an explanation for the differential recognition of this substrate by these three enzymes. Our analysis further revealed candidate residues in the active sites required for binding of the α-keto acid and nicotianamine-like substrates and for catalysis. This work reports the first structural kinetic analyses of enzymes involved in opine metallophore biosynthesis in three important bacterial pathogens of humans.
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Affiliation(s)
- Jeffrey S McFarlane
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045
| | - Cara L Davis
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045
| | - Audrey L Lamb
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045; Department of Chemistry, University of Kansas, Lawrence, Kansas 66045.
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17
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Affiliation(s)
- Henrik H. De Fine Licht
- Section for Organismal Biology, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
- * E-mail:
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18
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Gonzalez MR, Ducret V, Leoni S, Fleuchot B, Jafari P, Raffoul W, Applegate LA, Que YA, Perron K. Transcriptome Analysis of Pseudomonas aeruginosa Cultured in Human Burn Wound Exudates. Front Cell Infect Microbiol 2018. [PMID: 29535973 PMCID: PMC5835353 DOI: 10.3389/fcimb.2018.00039] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Pseudomonas aeruginosa is a severe opportunistic pathogen and is one of the major causes of hard to treat burn wound infections. Herein we have used an RNA-seq transcriptomic approach to study the behavior of P. aeruginosa PAO1 growing directly on human burn wound exudate. A chemical analysis of compounds used by this bacterium, coupled with kinetics expression of central genes has allowed us to obtain a global view of P. aeruginosa physiological and metabolic changes occurring while growing on human burn wound exudate. In addition to the numerous virulence factors and their secretion systems, we have found that all iron acquisition mechanisms were overexpressed. Deletion and complementation with pyoverdine demonstrated that iron availability was a major limiting factor in burn wound exudate. The quorum sensing systems, known to be important for the virulence of P. aeruginosa, although moderately induced, were activated even at low cell density. Analysis of bacterial metabolism emphasized importance of lactate, lipid and collagen degradation pathways. Overall, this work allowed to designate, for the first time, a global view of P. aeruginosa characteristics while growing in human burn wound exudate and highlight the possible therapeutic approaches to combat P. aeruginosa burn wound infections.
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Affiliation(s)
- Manuel R Gonzalez
- Microbiology Unit, Department of Botany and Plant Biology, Sciences III, University of Geneva, Geneva, Switzerland
| | - Verena Ducret
- Microbiology Unit, Department of Botany and Plant Biology, Sciences III, University of Geneva, Geneva, Switzerland
| | - Sara Leoni
- Microbiology Unit, Department of Botany and Plant Biology, Sciences III, University of Geneva, Geneva, Switzerland
| | - Betty Fleuchot
- Microbiology Unit, Department of Botany and Plant Biology, Sciences III, University of Geneva, Geneva, Switzerland
| | - Paris Jafari
- Plastic, Reconstructive and Hand Surgery, Unit of Regenerative Therapy, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Wassim Raffoul
- Plastic, Reconstructive and Hand Surgery, Unit of Regenerative Therapy, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Lee A Applegate
- Plastic, Reconstructive and Hand Surgery, Unit of Regenerative Therapy, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Yok-Ai Que
- Department of Intensive Care Medicine, Bern University Hospital, Bern, Switzerland
| | - Karl Perron
- Microbiology Unit, Department of Botany and Plant Biology, Sciences III, University of Geneva, Geneva, Switzerland.,School of Pharmaceutical Sciences, University of Geneva and Centre Hospitalier Universitaire Vaudois, Geneva, Switzerland
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19
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Gonzalez MR, Ducret V, Leoni S, Perron K. Pseudomonas aeruginosa zinc homeostasis: Key issues for an opportunistic pathogen. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1862:722-733. [PMID: 29410128 DOI: 10.1016/j.bbagrm.2018.01.018] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 01/26/2018] [Indexed: 12/13/2022]
Abstract
Zinc is an essential trace element for almost all living organisms. In the opportunistic bacterial pathogen Pseudomonas aeruginosa, zinc has been shown to play an important role in virulence, in colonization of the host organism and has also been shown to be involved in antibiotic resistance. P. aeruginosa possesses numerous systems enabling it to thrive in zinc-depleted conditions as well as high-zinc situations, two environments that are encountered during human infection. These capabilities account for its pathogenic strength. The main aim of this review is to focus on zinc homeostasis in P. aeruginosa and the genetic regulation of the systems involved. The interconnection with virulence, as well as the mechanism of co-regulation between metal and antibiotic resistance, are of prime interest for understanding the molecular mechanisms allowing P. aeruginosa to switch from its existence as a common environmental bacterium to a severe opportunistic pathogen. This article is part of a Special Issue entitled: Dynamic gene expression, edited by Prof. Patrick Viollier.
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Affiliation(s)
- Manuel R Gonzalez
- Microbiology Unit, Department of Botany and Plant Biology, Sciences III, University of Geneva, Geneva, Switzerland
| | - Verena Ducret
- Microbiology Unit, Department of Botany and Plant Biology, Sciences III, University of Geneva, Geneva, Switzerland
| | - Sara Leoni
- Microbiology Unit, Department of Botany and Plant Biology, Sciences III, University of Geneva, Geneva, Switzerland
| | - Karl Perron
- Microbiology Unit, Department of Botany and Plant Biology, Sciences III, University of Geneva, Geneva, Switzerland; School of Pharmaceutical Sciences, University of Geneva and University of Lausanne, Geneva, Switzerland.
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20
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Lhospice S, Gomez NO, Ouerdane L, Brutesco C, Ghssein G, Hajjar C, Liratni A, Wang S, Richaud P, Bleves S, Ball G, Borezée-Durant E, Lobinski R, Pignol D, Arnoux P, Voulhoux R. Pseudomonas aeruginosa zinc uptake in chelating environment is primarily mediated by the metallophore pseudopaline. Sci Rep 2017; 7:17132. [PMID: 29214991 PMCID: PMC5719457 DOI: 10.1038/s41598-017-16765-9] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 11/16/2017] [Indexed: 11/09/2022] Open
Abstract
Metal uptake is vital for all living organisms. In metal scarce conditions a common bacterial strategy consists in the biosynthesis of metallophores, their export in the extracellular medium and the recovery of a metal-metallophore complex through dedicated membrane transporters. Staphylopine is a recently described metallophore distantly related to plant nicotianamine that contributes to the broad-spectrum metal uptake capabilities of Staphylococcus aureus. Here we characterize a four-gene operon (PA4837-PA4834) in Pseudomonas aeruginosa involved in the biosynthesis and trafficking of a staphylopine-like metallophore named pseudopaline. Pseudopaline differs from staphylopine with regard to the stereochemistry of its histidine moiety associated with an alpha ketoglutarate moiety instead of pyruvate. In vivo, the pseudopaline operon is regulated by zinc through the Zur repressor. The pseudopaline system is involved in nickel uptake in poor media, and, most importantly, in zinc uptake in metal scarce conditions mimicking a chelating environment, thus reconciling the regulation of the cnt operon by zinc with its function as the main zinc importer under these metal scarce conditions.
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Affiliation(s)
- Sébastien Lhospice
- CNRS et Aix-Marseille Université, Laboratoire d'Ingénierie des Systèmes Macromoléculaires (UMR7255), Institut de Microbiologie de la Méditerranée, Marseille, France
| | - Nicolas Oswaldo Gomez
- CNRS et Aix-Marseille Université, Laboratoire d'Ingénierie des Systèmes Macromoléculaires (UMR7255), Institut de Microbiologie de la Méditerranée, Marseille, France
| | - Laurent Ouerdane
- Université de Pau et des Pays de l'Adour/CNRS, Laboratoire de Chimie Analytique Bio-inorganique et Environnement, IPREM-UMR5254, Hélioparc, 2, Avenue Angot, 64053, Pau, France
| | - Catherine Brutesco
- CEA, CNRS and Aix-Marseille Université, Institut de Biosciences et Biotechnologies d'Aix-Marseille, UMR 7265 LBC, CEA Cadarache, Saint-Paul-lez-Durance, F-13108, France
| | - Ghassan Ghssein
- CEA, CNRS and Aix-Marseille Université, Institut de Biosciences et Biotechnologies d'Aix-Marseille, UMR 7265 LBC, CEA Cadarache, Saint-Paul-lez-Durance, F-13108, France
| | - Christine Hajjar
- CEA, CNRS and Aix-Marseille Université, Institut de Biosciences et Biotechnologies d'Aix-Marseille, UMR 7265 LBC, CEA Cadarache, Saint-Paul-lez-Durance, F-13108, France
| | - Ahmed Liratni
- CNRS et Aix-Marseille Université, Laboratoire d'Ingénierie des Systèmes Macromoléculaires (UMR7255), Institut de Microbiologie de la Méditerranée, Marseille, France
| | - Shuanglong Wang
- Université de Pau et des Pays de l'Adour/CNRS, Laboratoire de Chimie Analytique Bio-inorganique et Environnement, IPREM-UMR5254, Hélioparc, 2, Avenue Angot, 64053, Pau, France
| | - Pierre Richaud
- CEA, CNRS and Aix-Marseille Université, Institut de Biosciences et Biotechnologies d'Aix-Marseille, UMR 7265 LB3M, CEA Cadarache, Saint-Paul-lez Durance, F-13108, France
| | - Sophie Bleves
- CNRS et Aix-Marseille Université, Laboratoire d'Ingénierie des Systèmes Macromoléculaires (UMR7255), Institut de Microbiologie de la Méditerranée, Marseille, France
| | - Geneviève Ball
- CNRS et Aix-Marseille Université, Laboratoire d'Ingénierie des Systèmes Macromoléculaires (UMR7255), Institut de Microbiologie de la Méditerranée, Marseille, France
| | - Elise Borezée-Durant
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Ryszard Lobinski
- Université de Pau et des Pays de l'Adour/CNRS, Laboratoire de Chimie Analytique Bio-inorganique et Environnement, IPREM-UMR5254, Hélioparc, 2, Avenue Angot, 64053, Pau, France
| | - David Pignol
- CEA, CNRS and Aix-Marseille Université, Institut de Biosciences et Biotechnologies d'Aix-Marseille, UMR 7265 LBC, CEA Cadarache, Saint-Paul-lez-Durance, F-13108, France
| | - Pascal Arnoux
- CEA, CNRS and Aix-Marseille Université, Institut de Biosciences et Biotechnologies d'Aix-Marseille, UMR 7265 LBC, CEA Cadarache, Saint-Paul-lez-Durance, F-13108, France.
| | - Romé Voulhoux
- CNRS et Aix-Marseille Université, Laboratoire d'Ingénierie des Systèmes Macromoléculaires (UMR7255), Institut de Microbiologie de la Méditerranée, Marseille, France.
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21
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McFarlane JS, Lamb AL. Biosynthesis of an Opine Metallophore by Pseudomonas aeruginosa. Biochemistry 2017; 56:5967-5971. [PMID: 29091735 DOI: 10.1021/acs.biochem.7b00804] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Bacterial pathogenesis frequently requires metal acquisition by specialized, small-molecule metallophores. We hypothesized that the Gram-negative Pseudomonas aeruginosa encodes the enzymes nicotianamine synthase (NAS) and opine dehydrogenase (ODH), biosynthesizing a new class of opine metallophore, previously characterized only in the unrelated Gram-positive organism Staphylococcus aureus. The identity of this metallophore, herein named pseudopaline, was determined through measurements of binding affinity, the in vitro reconstitution of the biosynthetic pathway to screen potential substrates, and the confirmation of product formation by mass spectrometry. Pseudopaline and the S. aureus metallophore staphylopine exhibit opposite stereochemistry for the histidine moiety, indicating unique recognition by NAS. Additionally, we demonstrate SaODH catalysis in the presence of pyruvate, as previously shown, but also oxaloacetate, suggesting the potential for the production of a variant form of staphylopine, while PaODH specifically recognizes α-ketoglutarate. Both the staphylopine and pseudopaline operons have been implicated in the pathogenesis of key infectious disease states and warrant further study.
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Affiliation(s)
- Jeffrey S McFarlane
- Department of Molecular Biosciences, University of Kansas , Lawrence, Kansas 66045, United States
| | - Audrey L Lamb
- Department of Molecular Biosciences, University of Kansas , Lawrence, Kansas 66045, United States
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22
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Robbe-Saule M, Babonneau J, Sismeiro O, Marsollier L, Marion E. An Optimized Method for Extracting Bacterial RNA from Mouse Skin Tissue Colonized by Mycobacterium ulcerans. Front Microbiol 2017; 8:512. [PMID: 28392785 PMCID: PMC5364165 DOI: 10.3389/fmicb.2017.00512] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 03/13/2017] [Indexed: 11/13/2022] Open
Abstract
Bacterial transcriptome analyses during host colonization are essential to decipher the complexity of the relationship between the bacterium and its host. RNA sequencing (RNA-seq) is a promising approach providing valuable information about bacterial adaptation, the host response and, in some cases, mutual tolerance underlying crosstalk, as recently observed in the context of Mycobacterium ulcerans infection. Buruli ulcer is caused by M. ulcerans. This neglected disease is the third most common mycobacterial disease worldwide. Without treatment, M. ulcerans provokes massive skin ulcers. A healing process may be observed in 5% of Buruli ulcer patients several months after the initiation of disease. This spontaneous healing process suggests that some hosts can counteract the development of the lesions caused by M. ulcerans. Deciphering the mechanisms involved in this process should open up new treatment possibilities. To this end, we recently developed the first mouse model for studies of the spontaneous healing process. We have shown that the healing process is based on mutual tolerance between the bacterium and its host. In this context, RNA-seq seems to be the most appropriate method for deciphering bacterial adaptation. However, due to the low bacterial load in host tissues, the isolation of mycobacterial RNA from skin tissue for RNA-seq analysis remains challenging. We developed a method for extracting and purifying mycobacterial RNA whilst minimizing the amount of host RNA in the sample. This approach was based on the extraction of bacterial RNA by a differential lysis method. The challenge in the development of this method was the choice of a lysis system favoring the removal of host RNA without damage to the bacterial cells. We made use of the thick, resistant cell wall of M. ulcerans to achieve this end.
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Affiliation(s)
- Marie Robbe-Saule
- Center for Research in Cancerology and Immunology Nantes-Angers, Institut National de la Santé et de la Recherche Médicale, Université de Nantes, Université d'AngersAngers, France; Equipe Atip-Avenir, Center for Research in Cancerology and Immunology Nantes-Angers, Institut National de la Santé et de la Recherche Médicale, Centre Hospitalier Universitaire et Université d'AngersAngers, France
| | - Jérémie Babonneau
- Center for Research in Cancerology and Immunology Nantes-Angers, Institut National de la Santé et de la Recherche Médicale, Université de Nantes, Université d'AngersAngers, France; Equipe Atip-Avenir, Center for Research in Cancerology and Immunology Nantes-Angers, Institut National de la Santé et de la Recherche Médicale, Centre Hospitalier Universitaire et Université d'AngersAngers, France
| | - Odile Sismeiro
- Transcriptome and Epigenome Platform, Biomics, Center for Innovation and Technological Research, Institut Pasteur Paris, France
| | - Laurent Marsollier
- Center for Research in Cancerology and Immunology Nantes-Angers, Institut National de la Santé et de la Recherche Médicale, Université de Nantes, Université d'AngersAngers, France; Equipe Atip-Avenir, Center for Research in Cancerology and Immunology Nantes-Angers, Institut National de la Santé et de la Recherche Médicale, Centre Hospitalier Universitaire et Université d'AngersAngers, France
| | - Estelle Marion
- Center for Research in Cancerology and Immunology Nantes-Angers, Institut National de la Santé et de la Recherche Médicale, Université de Nantes, Université d'AngersAngers, France; Equipe Atip-Avenir, Center for Research in Cancerology and Immunology Nantes-Angers, Institut National de la Santé et de la Recherche Médicale, Centre Hospitalier Universitaire et Université d'AngersAngers, France
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23
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Dual-seq transcriptomics reveals the battle for iron during Pseudomonas aeruginosa acute murine pneumonia. Sci Rep 2016; 6:39172. [PMID: 27982111 PMCID: PMC5159919 DOI: 10.1038/srep39172] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 11/18/2016] [Indexed: 12/21/2022] Open
Abstract
Determining bacterial gene expression during infection is fundamental to understand pathogenesis. In this study, we used dual RNA-seq to simultaneously measure P. aeruginosa and the murine host’s gene expression and response to respiratory infection. Bacterial genes encoding products involved in metabolism and virulence were differentially expressed during infection and the type III and VI secretion systems were highly expressed in vivo. Strikingly, heme acquisition, ferric-enterobactin transport, and pyoverdine biosynthesis genes were found to be significantly up-regulated during infection. In the mouse, we profiled the acute immune response to P. aeruginosa and identified the pro-inflammatory cytokines involved in acute response to the bacterium in the lung. Additionally, we also identified numerous host iron sequestration systems upregulated during infection. Overall, this work sheds light on how P. aeruginosa triggers a pro-inflammatory response and competes for iron with the host during infection, as iron is one of the central elements for which both pathogen and host fight during acute pneumonia.
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24
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Effect of Human Burn Wound Exudate on Pseudomonas aeruginosa Virulence. mSphere 2016; 1:mSphere00111-15. [PMID: 27303724 PMCID: PMC4894682 DOI: 10.1128/msphere.00111-15] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 04/03/2016] [Indexed: 11/20/2022] Open
Abstract
Burn wound sepsis is currently the main cause of morbidity and mortality after burn trauma. Infections by notorious pathogens such as Pseudomonas aeruginosa, Staphylococcus aureus, and Acinetobacter baumannii impair patient recovery and can even lead to fatality. In this study, we investigated the effect of burn wound exudates (BWEs) on the virulence of those pathogens. BWEs were collected within 7 days after burn trauma from 5 burn patients. We first monitored their effect on pathogen growth. In contrast to A. baumannii and S. aureus, P. aeruginosa was the only pathogen able to grow within these human fluids. Expression of typical virulence factors such as pyocyanin and pyoverdine was even enhanced compared the levels seen with standard laboratory medium. A detailed chemical composition analysis of BWE was performed, which enabled us to determine the major components of BWE and underline the metabolic modifications induced by burn trauma. These data are essential for the development of an artificial medium mimicking the burn wound environment and the establishment of an in vitro system to analyze the initial steps of burn wound infections. IMPORTANCE Microbial infection of severe burn wounds is currently a major medical challenge. Of the infections by bacteria able to colonize such injuries, those by Pseudomonas aeruginosa are among the most severe, causing major delays in burn patient recovery or leading to fatal issues. In this study, we investigated the growth properties of several burn wound pathogens in biological fluids secreted from human burn wounds. We found that P. aeruginosa strains were able to proliferate but not those of the other pathogens tested. In addition, burn wound exudates (BWEs) stimulate the expression of virulence factors in P. aeruginosa. The chemical composition analysis of BWEs enabled us to determine the major components of these fluids. These data are essential for the development of an artificial medium mimicking the burn wound environment and for in vitro analysis of the initial step in the development of burn wound infections.
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McNally L, Brown SP. Building the microbiome in health and disease: niche construction and social conflict in bacteria. Philos Trans R Soc Lond B Biol Sci 2016; 370:rstb.2014.0298. [PMID: 26150664 PMCID: PMC4528496 DOI: 10.1098/rstb.2014.0298] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Microbes collectively shape their environment in remarkable ways via the products of their metabolism. The diverse environmental impacts of macro-organisms have been collated and reviewed under the banner of ‘niche construction’. Here, we identify and review a series of broad and overlapping classes of bacterial niche construction, ranging from biofilm production to detoxification or release of toxins, enzymes, metabolites and viruses, and review their role in shaping microbiome composition, human health and disease. Some bacterial niche-constructing traits can be seen as extended phenotypes, where individuals actively tailor their environment to their benefit (and potentially to the benefit of others, generating social dilemmas). Other modifications can be viewed as non-adaptive by-products from a producer perspective, yet they may lead to remarkable within-host environmental changes. We illustrate how social evolution and niche construction perspectives offer complementary insights into the dynamics and consequences of these traits across distinct timescales. This review highlights that by understanding the coupled bacterial and biochemical dynamics in human health and disease we can better manage host health.
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Affiliation(s)
- Luke McNally
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh EH9 3FL, UK Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Sam P Brown
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh EH9 3FL, UK Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
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Molina L, Udaondo Z, Duque E, Fernández M, Bernal P, Roca A, de la Torre J, Ramos JL. Specific Gene Loci of Clinical Pseudomonas putida Isolates. PLoS One 2016; 11:e0147478. [PMID: 26820467 PMCID: PMC4731212 DOI: 10.1371/journal.pone.0147478] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 01/05/2016] [Indexed: 11/18/2022] Open
Abstract
Pseudomonas putida are ubiquitous inhabitants of soils and clinical isolates of this species have been seldom described. Clinical isolates show significant variability in their ability to cause damage to hosts because some of them are able to modulate the host’s immune response. In the current study, comparisons between the genomes of different clinical and environmental strains of P. putida were done to identify genetic clusters shared by clinical isolates that are not present in environmental isolates. We show that in clinical strains specific genes are mostly present on transposons, and that this set of genes exhibit high identity with genes found in pathogens and opportunistic pathogens. The set of genes prevalent in P. putida clinical isolates, and absent in environmental isolates, are related with survival under oxidative stress conditions, resistance against biocides, amino acid metabolism and toxin/antitoxin (TA) systems. This set of functions have influence in colonization and survival within human tissues, since they avoid host immune response or enhance stress resistance. An in depth bioinformatic analysis was also carried out to identify genetic clusters that are exclusive to each of the clinical isolates and that correlate with phenotypical differences between them, a secretion system type III-like was found in one of these clinical strains, a determinant of pathogenicity in Gram-negative bacteria.
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Affiliation(s)
- Lázaro Molina
- Environmental Protection Department, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas. C/ Profesor Albareda 1, Granada, Spain
- * E-mail:
| | - Zulema Udaondo
- Environmental Protection Department, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas. C/ Profesor Albareda 1, Granada, Spain
- Abengoa Research, Campus de las Palmas Altas, Sevilla, Spain
| | - Estrella Duque
- Environmental Protection Department, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas. C/ Profesor Albareda 1, Granada, Spain
- Abengoa Research, Campus de las Palmas Altas, Sevilla, Spain
| | - Matilde Fernández
- Environmental Protection Department, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas. C/ Profesor Albareda 1, Granada, Spain
| | - Patricia Bernal
- Environmental Protection Department, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas. C/ Profesor Albareda 1, Granada, Spain
- Imperial College London, South Kensington Campus, London, United Kingdom
| | - Amalia Roca
- Bio-Iliberis R&D, C/ Capileira 7, 18210 Peligros, Granada, Spain
| | - Jesús de la Torre
- Environmental Protection Department, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas. C/ Profesor Albareda 1, Granada, Spain
| | - Juan Luis Ramos
- Environmental Protection Department, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas. C/ Profesor Albareda 1, Granada, Spain
- Abengoa Research, Campus de las Palmas Altas, Sevilla, Spain
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Varga JJ, Barbier M, Mulet X, Bielecki P, Bartell JA, Owings JP, Martinez-Ramos I, Hittle LE, Davis MR, Damron FH, Liechti GW, Puchałka J, dos Santos VAPM, Ernst RK, Papin JA, Albertí S, Oliver A, Goldberg JB. Genotypic and phenotypic analyses of a Pseudomonas aeruginosa chronic bronchiectasis isolate reveal differences from cystic fibrosis and laboratory strains. BMC Genomics 2015; 16:883. [PMID: 26519161 PMCID: PMC4628258 DOI: 10.1186/s12864-015-2069-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 10/03/2015] [Indexed: 01/24/2023] Open
Abstract
Background Pseudomonas aeruginosa is an environmentally ubiquitous Gram-negative bacterium and important opportunistic human pathogen, causing severe chronic respiratory infections in patients with underlying conditions such as cystic fibrosis (CF) or bronchiectasis. In order to identify mechanisms responsible for adaptation during bronchiectasis infections, a bronchiectasis isolate, PAHM4, was phenotypically and genotypically characterized. Results This strain displays phenotypes that have been associated with chronic respiratory infections in CF including alginate over-production, rough lipopolysaccharide, quorum-sensing deficiency, loss of motility, decreased protease secretion, and hypermutation. Hypermutation is a key adaptation of this bacterium during the course of chronic respiratory infections and analysis indicates that PAHM4 encodes a mutated mutS gene responsible for a ~1,000-fold increase in mutation rate compared to wild-type laboratory strain P. aeruginosa PAO1. Antibiotic resistance profiles and sequence data indicate that this strain acquired numerous mutations associated with increased resistance levels to β-lactams, aminoglycosides, and fluoroquinolones when compared to PAO1. Sequencing of PAHM4 revealed a 6.38 Mbp genome, 5.9 % of which were unrecognized in previously reported P. aeruginosa genome sequences. Transcriptome analysis suggests a general down-regulation of virulence factors, while metabolism of amino acids and lipids is up-regulated when compared to PAO1 and metabolic modeling identified further potential differences between PAO1 and PAHM4. Conclusions This work provides insights into the potential differential adaptation of this bacterium to the lung of patients with bronchiectasis compared to other clinical settings such as cystic fibrosis, findings that should aid the development of disease-appropriate treatment strategies for P. aeruginosa infections. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2069-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- John J Varga
- Department of Pediatrics, Division of Pulmonology, Allergy/Immunology, Cystic Fibrosis and Sleep, Children's Healthcare of Atlanta, Atlanta, GA, USA. .,Emory + Children's Center for Cystic Fibrosis Research, Emory University and Children's Healthcare of Atlanta, Atlanta, GA, USA. .,Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA, USA.
| | - Mariette Barbier
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA, USA. .,Department of Microbiology, Immunology and Cell Biology, West Virginia University School of Medicine, Morgantown, WV, USA.
| | - Xavier Mulet
- Servicio de Microbiología and Unidad de Investigación, Hospital Son Espases, Instituto de Investigación Sanitaria de Palma (IdISPa), Palma, de Mallorca, Spain.
| | - Piotr Bielecki
- Synthetic and Systems Biology Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany. .,Present address: Immunobiology Department, Yale University, School of Medicine, New Haven, CT, 06511, USA.
| | - Jennifer A Bartell
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA.
| | - Joshua P Owings
- Department of Pediatrics, Division of Pulmonology, Allergy/Immunology, Cystic Fibrosis and Sleep, Children's Healthcare of Atlanta, Atlanta, GA, USA. .,Emory + Children's Center for Cystic Fibrosis Research, Emory University and Children's Healthcare of Atlanta, Atlanta, GA, USA. .,Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA, USA.
| | | | - Lauren E Hittle
- Department of Microbial Pathogenesis, University of Maryland School of Dentistry, University of Maryland, Baltimore, MD, USA.
| | - Michael R Davis
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA, USA.
| | - F Heath Damron
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA, USA. .,Department of Microbiology, Immunology and Cell Biology, West Virginia University School of Medicine, Morgantown, WV, USA.
| | - George W Liechti
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA, USA.
| | - Jacek Puchałka
- Servicio de Microbiología and Unidad de Investigación, Hospital Son Espases, Instituto de Investigación Sanitaria de Palma (IdISPa), Palma, de Mallorca, Spain. .,Present address: Dr. von Hauner Children's Hospital, Ludwig Maximilians University, Munich, Germany.
| | - Vitor A P Martins dos Santos
- Systems and Synthetic Biology, Wageningen University, Wageningen, Netherlands. .,Present address: Chair of Systems and Synthetic Biology, Wageningen University, Wageningen, The Netherlands. .,Present address: LifeGlimmer GmbH, Berlin, Germany.
| | - Robert K Ernst
- Department of Microbial Pathogenesis, University of Maryland School of Dentistry, University of Maryland, Baltimore, MD, USA.
| | - Jason A Papin
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA.
| | - Sebastian Albertí
- IUNICS, University of the Balearic Islands, Palma, de Mallorca, Spain.
| | - Antonio Oliver
- Servicio de Microbiología and Unidad de Investigación, Hospital Son Espases, Instituto de Investigación Sanitaria de Palma (IdISPa), Palma, de Mallorca, Spain.
| | - Joanna B Goldberg
- Department of Pediatrics, Division of Pulmonology, Allergy/Immunology, Cystic Fibrosis and Sleep, Children's Healthcare of Atlanta, Atlanta, GA, USA. .,Emory + Children's Center for Cystic Fibrosis Research, Emory University and Children's Healthcare of Atlanta, Atlanta, GA, USA. .,Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA, USA.
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A novel siderophore system is essential for the growth of Pseudomonas aeruginosa in airway mucus. Sci Rep 2015; 5:14644. [PMID: 26446565 PMCID: PMC4597187 DOI: 10.1038/srep14644] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 09/02/2015] [Indexed: 12/25/2022] Open
Abstract
Pseudomonas aeruginosa establishes airway infections in Cystic Fibrosis patients. Here, we investigate the molecular interactions between P. aeruginosa and airway mucus secretions (AMS) derived from the primary cultures of normal human tracheal epithelial (NHTE) cells. PAO1, a prototype strain of P. aeruginosa, was capable of proliferating during incubation with AMS, while all other tested bacterial species perished. A PAO1 mutant lacking PA4834 gene became susceptible to AMS treatment. The ΔPA4834 mutant was grown in AMS supplemented with 100 μM ferric iron, suggesting that the PA4834 gene product is involved in iron metabolism. Consistently, intracellular iron content was decreased in the mutant, but not in PAO1 after the AMS treatment. Importantly, a PAO1 mutant unable to produce both pyoverdine and pyochelin remained viable, suggesting that these two major siderophore molecules are dispensable for maintaining viability during incubation with AMS. The ΔPA4834 mutant was regrown in AMS amended with 100 μM nicotianamine, a phytosiderophore whose production is predicted to be mediated by the PA4836 gene. Infectivity of the ΔPA4834 mutant was also significantly compromised in vivo. Together, our results identify a genetic element encoding a novel iron acquisition system that plays a previously undiscovered role in P. aeruginosa airway infection.
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Contribution of stress responses to antibiotic tolerance in Pseudomonas aeruginosa biofilms. Antimicrob Agents Chemother 2015; 59:3838-47. [PMID: 25870065 DOI: 10.1128/aac.00433-15] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 04/07/2015] [Indexed: 11/20/2022] Open
Abstract
Enhanced tolerance of biofilm-associated bacteria to antibiotic treatments is likely due to a combination of factors, including changes in cell physiology as bacteria adapt to biofilm growth and the inherent physiological heterogeneity of biofilm bacteria. In this study, a transcriptomics approach was used to identify genes differentially expressed during biofilm growth of Pseudomonas aeruginosa. These genes were tested for statistically significant overlap, with independently compiled gene lists corresponding to stress responses and other putative antibiotic-protective mechanisms. Among the gene groups tested were those associated with biofilm response to tobramycin or ciprofloxacin, drug efflux pumps, acyl homoserine lactone quorum sensing, osmotic shock, heat shock, hypoxia stress, and stationary-phase growth. Regulons associated with Anr-mediated hypoxia stress, RpoS-regulated stationary-phase growth, and osmotic stress were significantly enriched in the set of genes induced in the biofilm. Mutant strains deficient in rpoS, relA and spoT, or anr were cultured in biofilms and challenged with ciprofloxacin and tobramycin. When challenged with ciprofloxacin, the mutant strain biofilms had 2.4- to 2.9-log reductions in viable cells compared to a 0.9-log reduction of the wild-type strain. Interestingly, none of the mutants exhibited a statistically significant alteration in tobramycin susceptibility compared to that with the wild-type biofilm. These results are consistent with a model in which multiple genes controlled by overlapping starvation or stress responses contribute to the protection of a P. aeruginosa biofilm from ciprofloxacin. A distinct and as yet undiscovered mechanism protects the biofilm bacteria from tobramycin.
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Hilker R, Munder A, Klockgether J, Losada PM, Chouvarine P, Cramer N, Davenport CF, Dethlefsen S, Fischer S, Peng H, Schönfelder T, Türk O, Wiehlmann L, Wölbeling F, Gulbins E, Goesmann A, Tümmler B. Interclonal gradient of virulence in thePseudomonas aeruginosapangenome from disease and environment. Environ Microbiol 2014; 17:29-46. [DOI: 10.1111/1462-2920.12606] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Accepted: 07/05/2014] [Indexed: 11/28/2022]
Affiliation(s)
- Rolf Hilker
- Department of Bioinformatics and Systems Biology; University of Giessen; Gießen D-35392 Germany
| | - Antje Munder
- Clinical Research Group; ‘Molecular Pathology of Cystic Fibrosis and Pseudomonas Genomics’; Hannover Medical School; OE 6710 Hannover D-30625 Germany
| | - Jens Klockgether
- Clinical Research Group; ‘Molecular Pathology of Cystic Fibrosis and Pseudomonas Genomics’; Hannover Medical School; OE 6710 Hannover D-30625 Germany
| | - Patricia Moran Losada
- Clinical Research Group; ‘Molecular Pathology of Cystic Fibrosis and Pseudomonas Genomics’; Hannover Medical School; OE 6710 Hannover D-30625 Germany
| | - Philippe Chouvarine
- Clinical Research Group; ‘Molecular Pathology of Cystic Fibrosis and Pseudomonas Genomics’; Hannover Medical School; OE 6710 Hannover D-30625 Germany
| | - Nina Cramer
- Clinical Research Group; ‘Molecular Pathology of Cystic Fibrosis and Pseudomonas Genomics’; Hannover Medical School; OE 6710 Hannover D-30625 Germany
| | - Colin F. Davenport
- Clinical Research Group; ‘Molecular Pathology of Cystic Fibrosis and Pseudomonas Genomics’; Hannover Medical School; OE 6710 Hannover D-30625 Germany
| | - Sarah Dethlefsen
- Clinical Research Group; ‘Molecular Pathology of Cystic Fibrosis and Pseudomonas Genomics’; Hannover Medical School; OE 6710 Hannover D-30625 Germany
| | - Sebastian Fischer
- Clinical Research Group; ‘Molecular Pathology of Cystic Fibrosis and Pseudomonas Genomics’; Hannover Medical School; OE 6710 Hannover D-30625 Germany
| | - Huiming Peng
- Department of Molecular Biology; University Hospital Essen; University of Duisburg-Essen; Essen D-45122 Germany
| | - Torben Schönfelder
- Clinical Research Group; ‘Molecular Pathology of Cystic Fibrosis and Pseudomonas Genomics’; Hannover Medical School; OE 6710 Hannover D-30625 Germany
| | - Oliver Türk
- Clinical Research Group; ‘Molecular Pathology of Cystic Fibrosis and Pseudomonas Genomics’; Hannover Medical School; OE 6710 Hannover D-30625 Germany
| | - Lutz Wiehlmann
- Clinical Research Group; ‘Molecular Pathology of Cystic Fibrosis and Pseudomonas Genomics’; Hannover Medical School; OE 6710 Hannover D-30625 Germany
| | - Florian Wölbeling
- Clinical Research Group; ‘Molecular Pathology of Cystic Fibrosis and Pseudomonas Genomics’; Hannover Medical School; OE 6710 Hannover D-30625 Germany
| | - Erich Gulbins
- Department of Molecular Biology; University Hospital Essen; University of Duisburg-Essen; Essen D-45122 Germany
| | - Alexander Goesmann
- Department of Bioinformatics and Systems Biology; University of Giessen; Gießen D-35392 Germany
| | - Burkhard Tümmler
- Clinical Research Group; ‘Molecular Pathology of Cystic Fibrosis and Pseudomonas Genomics’; Hannover Medical School; OE 6710 Hannover D-30625 Germany
- Biomedical Research in Endstage and Obstructive Lung Disease (BREATH); German Center for Lung Research; Hannover Germany
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Kim S, Park J, Lee J, Shin D, Park DS, Lim JS, Choi IY, Seo YS. Understanding pathogenic Burkholderia glumae metabolic and signaling pathways within rice tissues through in vivo transcriptome analyses. Gene 2014; 547:77-85. [PMID: 24949534 DOI: 10.1016/j.gene.2014.06.029] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Revised: 06/10/2014] [Accepted: 06/16/2014] [Indexed: 11/15/2022]
Abstract
Burkholderia glumae is a causal agent of rice grain and sheath rot. Similar to other phytopathogens, B. glumae adapts well to the host environment and controls its biology to induce diseases in the host plant; however, its molecular mechanisms are not yet fully understood. To gain a better understating of the actual physiological changes that occur in B. glumae during infection, we analyzed B. glumae transcriptome from infected rice tissues using an RNA-seq technique. To accomplish this, we analyzed differentially expressed genes (DEGs) and identified 2653 transcripts that were significantly altered. We then performed KEGG pathway and module enrichment of the DEGs. Interestingly, most genes involved bacterial chemotaxis-mediated motility, ascorbate and trehalose metabolisms, and sugar transporters including l-arabinose and d-xylose were found to be highly enriched. The in vivo transcriptional profiling of pathogenic B. glumae will facilitate elucidation of unknown plant-pathogenic bacteria interactions, as well as the overall infection processes.
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Affiliation(s)
- Sunyoung Kim
- Department of Microbiology, Pusan National University, Busan 609-735, Republic of Korea
| | - Jungwook Park
- Department of Microbiology, Pusan National University, Busan 609-735, Republic of Korea
| | - Jongyun Lee
- Department of Microbiology, Pusan National University, Busan 609-735, Republic of Korea
| | - Dongjin Shin
- Department of Functional Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang, Gyeongnam, 627-803, Republic of Korea
| | - Dong-Soo Park
- Department of Functional Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang, Gyeongnam, 627-803, Republic of Korea
| | - Jong-Sung Lim
- NICEM, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Republic of Korea
| | - Ik-Young Choi
- NICEM, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Republic of Korea
| | - Young-Su Seo
- Department of Microbiology, Pusan National University, Busan 609-735, Republic of Korea.
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Leggett HC, Brown SP, Reece SE. War and peace: social interactions in infections. Philos Trans R Soc Lond B Biol Sci 2014; 369:20130365. [PMID: 24686936 PMCID: PMC3982666 DOI: 10.1098/rstb.2013.0365] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
One of the most striking facts about parasites and microbial pathogens that has emerged in the fields of social evolution and disease ecology in the past few decades is that these simple organisms have complex social lives, indulging in a variety of cooperative, communicative and coordinated behaviours. These organisms have provided elegant experimental tests of the importance of relatedness, kin discrimination, cooperation and competition, in driving the evolution of social strategies. Here, we briefly review the social behaviours of parasites and microbial pathogens, including their contributions to virulence, and outline how inclusive fitness theory has helped to explain their evolution. We then take a mechanistically inspired ‘bottom-up’ approach, discussing how key aspects of the ways in which parasites and pathogens exploit hosts, namely public goods, mobile elements, phenotypic plasticity, spatial structure and multi-species interactions, contribute to the emergent properties of virulence and transmission. We argue that unravelling the complexities of within-host ecology is interesting in its own right, and also needs to be better incorporated into theoretical evolution studies if social behaviours are to be understood and used to control the spread and severity of infectious diseases.
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Affiliation(s)
- Helen C Leggett
- Department of Zoology, Oxford University, , South Parks Road, Oxford OX1 3PS, UK
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Barbier M, Damron FH, Bielecki P, Suárez-Diez M, Puchałka J, Albertí S, dos Santos VM, Goldberg JB. From the environment to the host: re-wiring of the transcriptome of Pseudomonas aeruginosa from 22°C to 37°C. PLoS One 2014; 9:e89941. [PMID: 24587139 PMCID: PMC3933690 DOI: 10.1371/journal.pone.0089941] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2013] [Accepted: 01/25/2014] [Indexed: 11/18/2022] Open
Abstract
Pseudomonas aeruginosa is a highly versatile opportunistic pathogen capable of colonizing multiple ecological niches. This bacterium is responsible for a wide range of both acute and chronic infections in a variety of hosts. The success of this microorganism relies on its ability to adapt to environmental changes and re-program its regulatory and metabolic networks. The study of P. aeruginosa adaptation to temperature is crucial to understanding the pathogenesis upon infection of its mammalian host. We examined the effects of growth temperature on the transcriptome of the P. aeruginosa PAO1. Microarray analysis of PAO1 grown in Lysogeny broth at mid-exponential phase at 22°C and 37°C revealed that temperature changes are responsible for the differential transcriptional regulation of 6.4% of the genome. Major alterations were observed in bacterial metabolism, replication, and nutrient acquisition. Quorum-sensing and exoproteins secreted by type I, II, and III secretion systems, involved in the adaptation of P. aeruginosa to the mammalian host during infection, were up-regulated at 37°C compared to 22°C. Genes encoding arginine degradation enzymes were highly up-regulated at 22°C, together with the genes involved in the synthesis of pyoverdine. However, genes involved in pyochelin biosynthesis were up-regulated at 37°C. We observed that the changes in expression of P. aeruginosa siderophores correlated to an overall increase in Fe²⁺ extracellular concentration at 37°C and a peak in Fe³⁺ extracellular concentration at 22°C. This suggests a distinct change in iron acquisition strategies when the bacterium switches from the external environment to the host. Our work identifies global changes in bacterial metabolism and nutrient acquisition induced by growth at different temperatures. Overall, this study identifies factors that are regulated in genome-wide adaptation processes and discusses how this life-threatening pathogen responds to temperature.
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Affiliation(s)
- Mariette Barbier
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, Virginia, United States of America
| | - F. Heath Damron
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, Virginia, United States of America
| | - Piotr Bielecki
- Synthetic and Systems Biology Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - María Suárez-Diez
- Systems and Synthetic Biology, Wageningen University, Wageningen, Netherlands
| | - Jacek Puchałka
- Synthetic and Systems Biology Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Sebastian Albertí
- IUNICS, University of the Balearic Islands, Palma de Mallorca, Spain
| | - Vitor Martins dos Santos
- Synthetic and Systems Biology Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Systems and Synthetic Biology, Wageningen University, Wageningen, Netherlands
- LifeGlimmer GmbH, Berlin, Germany
| | - Joanna B. Goldberg
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, Virginia, United States of America
- Department of Pediatrics, and Center for Cystic Fibrosis Research, Emory University School of Medicine, Children’s Healthcare of Atlanta, Inc., Atlanta, Georgia, United States of America
- * E-mail: .
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Nayak N, Lenka RK, Padhy RN. Surveillance of multidrug resistant suppurative infection causing bacteria in hospitalized patients in an Indian tertiary care hospital. JOURNAL OF ACUTE DISEASE 2014. [DOI: 10.1016/s2221-6189(14)60033-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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Djonović S, Urbach JM, Drenkard E, Bush J, Feinbaum R, Ausubel JL, Traficante D, Risech M, Kocks C, Fischbach MA, Priebe GP, Ausubel FM. Trehalose biosynthesis promotes Pseudomonas aeruginosa pathogenicity in plants. PLoS Pathog 2013; 9:e1003217. [PMID: 23505373 PMCID: PMC3591346 DOI: 10.1371/journal.ppat.1003217] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 01/13/2013] [Indexed: 01/22/2023] Open
Abstract
Pseudomonas aeruginosa strain PA14 is a multi-host pathogen that infects plants, nematodes, insects, and vertebrates. Many PA14 factors are required for virulence in more than one of these hosts. Noting that plants have a fundamentally different cellular architecture from animals, we sought to identify PA14 factors that are specifically required for plant pathogenesis. We show that synthesis by PA14 of the disaccharide trehalose is required for pathogenesis in Arabidopsis, but not in nematodes, insects, or mice. In-frame deletion of two closely-linked predicted trehalose biosynthetic operons, treYZ and treS, decreased growth in Arabidopsis leaves about 50 fold. Exogenously co-inoculated trehalose, ammonium, or nitrate, but not glucose, sulfate, or phosphate suppressed the phenotype of the double ΔtreYZΔtreS mutant. Exogenous trehalose or ammonium nitrate does not suppress the growth defect of the double ΔtreYZΔtreS mutant by suppressing the plant defense response. Trehalose also does not function intracellularly in P. aeruginosa to ameliorate a variety of stresses, but most likely functions extracellularly, because wild-type PA14 rescued the in vivo growth defect of the ΔtreYZΔtreS in trans. Surprisingly, the growth defect of the double ΔtreYZΔtreS double mutant was suppressed by various Arabidopsis cell wall mutants that affect xyloglucan synthesis, including an xxt1xxt2 double mutant that completely lacks xyloglucan, even though xyloglucan mutants are not more susceptible to pathogens and respond like wild-type plants to immune elicitors. An explanation of our data is that trehalose functions to promote the acquisition of nitrogen-containing nutrients in a process that involves the xyloglucan component of the plant cell wall, thereby allowing P. aeruginosa to replicate in the intercellular spaces in a leaf. This work shows how P. aeruginosa, a multi-host opportunistic pathogen, has repurposed a highly conserved "house-keeping" anabolic pathway (trehalose biosynthesis) as a potent virulence factor that allows it to replicate in the intercellular environment of a leaf.
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Affiliation(s)
- Slavica Djonović
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jonathan M. Urbach
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Eliana Drenkard
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jenifer Bush
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Rhonda Feinbaum
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jonathan L. Ausubel
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - David Traficante
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
| | - Martina Risech
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
| | - Christine Kocks
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Michael A. Fischbach
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, United States of America
| | - Gregory P. Priebe
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
- Division of Critical Care Medicine, Department of Anesthesiology, Perioperative and Pain Medicine, Boston Children's Hospital, Boston, Massachusetts, United States of America
| | - Frederick M. Ausubel
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail:
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Roca A, Pizarro-Tobías P, Udaondo Z, Fernández M, Matilla MA, Molina-Henares MA, Molina L, Segura A, Duque E, Ramos JL. Analysis of the plant growth-promoting properties encoded by the genome of the rhizobacterium Pseudomonas putida BIRD-1. Environ Microbiol 2012. [PMID: 23206161 DOI: 10.1111/1462-2920.12037] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Pseudomonas putida BIRD-1 is a plant growth-promoting rhizobacterium whose genome size is 5.7 Mbp. It adheres to plant roots and colonizes the rhizosphere to high cell densities even in soils with low moisture. This property is linked to its ability to synthesize trehalose, since a mutant deficient in the synthesis of trehalose exhibited less tolerance to desiccation than the parental strain. The genome of BIRD-1 encodes a wide range of proteins that help it to deal with reactive oxygen stress generated in the plant rhizosphere. BIRD-1 plant growth-promoting rhizobacteria properties derive from its ability to enhance phosphorous and iron solubilization and to produce phytohormones. BIRD-1 is capable of solubilizing insoluble inorganic phosphate forms through acid production. The genome of BIRD-1 encodes at least five phosphatases related to phosphorous solubilization, one of them being a phytase that facilitates the utilization of phytic acid, the main storage form of phosphorous in plants. Pyoverdine is the siderophore produced by this strain, a mutant that in the FvpD siderophore synthase failed to grow on medium without supplementary iron, but the mutant was as competitive as the parental strain in soils because it captures the siderophores produced by other microbes. BIRD-1 overproduces indole-3-acetic acid through convergent pathways.
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Affiliation(s)
- Amalia Roca
- Polígono Industrial Juncaril, Bio-Iliberis R&D, 18210, Peligros, Granada, Spain
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Bielecki P, Komor U, Bielecka A, Müsken M, Puchałka J, Pletz MW, Ballmann M, Martins dos Santos VAP, Weiss S, Häussler S. Ex vivo transcriptional profiling reveals a common set of genes important for the adaptation of Pseudomonas aeruginosa to chronically infected host sites. Environ Microbiol 2012; 15:570-87. [PMID: 23145907 DOI: 10.1111/1462-2920.12024] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Revised: 10/04/2012] [Accepted: 10/06/2012] [Indexed: 01/16/2023]
Abstract
The opportunistic bacterium Pseudomonas aeruginosa is a major nosocomial pathogen causing both devastating acute and chronic persistent infections. During the course of an infection, P. aeruginosa rapidly adapts to the specific conditions within the host. In the present study, we aimed at the identification of genes that are highly expressed during biofilm infections such as in chronically infected lungs of patients with cystic fibrosis (CF), burn wounds and subcutaneous mouse tumours. We found a common subset of differentially regulated genes in all three in vivo habitats and evaluated whether their inactivation impacts on the bacterial capability to form biofilms in vitro and to establish biofilm-associated infections in a murine model. Additive effects on biofilm formation and host colonization were discovered by the combined inactivation of several highly expressed genes. However, even combined inactivation was not sufficient to abolish the establishment of an infection completely. These findings can be interpreted as evidence that either redundant traits encode functions that are essential for in vivo survival and chronic biofilm infections and/or bacterial adaptation is considerably achieved independently of transcription levels. Supplemental screens, will have to be applied in order to identify the minimal set of key genes essential for the establishment of chronic infectious diseases.
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Affiliation(s)
- Piotr Bielecki
- Institute for Molecular Bacteriology, Twincore, Center for Clinical and Experimental Infection Research, a joint venture of the Helmholtz Center of Infection Research and the Hannover Medical School, Hannover, 30625, Germany
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Petrova OE, Schurr JR, Schurr MJ, Sauer K. Microcolony formation by the opportunistic pathogen Pseudomonas aeruginosa requires pyruvate and pyruvate fermentation. Mol Microbiol 2012; 86:819-35. [PMID: 22931250 DOI: 10.1111/mmi.12018] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/27/2012] [Indexed: 12/30/2022]
Abstract
A hallmark of the biofilm architecture is the presence of microcolonies. However, little is known about the underlying mechanisms governing microcolony formation. In the pathogen Pseudomonas aeruginosa, microcolony formation is dependent on the two-component regulator MifR, with mifR mutant biofilms exhibiting an overall thin structure lacking microcolonies, and overexpression of mifR resulting in hyper-microcolony formation. Using global transcriptomic and proteomic approaches, we demonstrate that microcolony formation is associated with stressful, oxygen-limiting but electron-rich conditions, as indicated by the activation of stress response mechanisms and anaerobic and fermentative processes, in particular pyruvate fermentation. Inactivation of genes involved in pyruvate utilization including uspK, acnA and ldhA abrogated microcolony formation in a manner similar to mifR inactivation. Moreover, depletion of pyruvate from the growth medium impaired biofilm and microcolony formation, while addition of pyruvate significantly increased microcolony formation. Addition of pyruvate to or expression of mifR in lactate dehydrogenase (ldhA) mutant biofilms did not restore microcolony formation, while addition of pyruvate partly restored microcolony formation in mifR mutant biofilms. In contrast, expression of ldhA in mifR::Mar fully restored microcolony formation by this mutant strain. Our findings indicate the fermentative utilization of pyruvate to be a microcolony-specific adaptation of the P. aeruginosa biofilm environment.
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Affiliation(s)
- Olga E Petrova
- Department of Biological Sciences, Binghamton University, Binghamton, NY 13902, USA
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Evolution of virulence in opportunistic pathogens: generalism, plasticity, and control. Trends Microbiol 2012; 20:336-42. [PMID: 22564248 PMCID: PMC3491314 DOI: 10.1016/j.tim.2012.04.005] [Citation(s) in RCA: 241] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2012] [Revised: 03/30/2012] [Accepted: 04/12/2012] [Indexed: 01/15/2023]
Abstract
Standard virulence evolution theory assumes that virulence factors are maintained because they aid parasitic exploitation, increasing growth within and/or transmission between hosts. An increasing number of studies now demonstrate that many opportunistic pathogens (OPs) do not conform to these assumptions, with virulence factors maintained instead because of advantages in non-parasitic contexts. Here we review virulence evolution theory in the context of OPs and highlight the importance of incorporating environments outside a focal virulence site. We illustrate that virulence selection is constrained by correlations between these external and focal settings and pinpoint drivers of key environmental correlations, with a focus on generalist strategies and phenotypic plasticity. We end with a summary of key theoretical and empirical challenges to be met for a fuller understanding of OPs.
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Hall-Stoodley L, Stoodley P, Kathju S, Høiby N, Moser C, Costerton JW, Moter A, Bjarnsholt T. Towards diagnostic guidelines for biofilm-associated infections. ACTA ACUST UNITED AC 2012; 65:127-45. [PMID: 22469292 DOI: 10.1111/j.1574-695x.2012.00968.x] [Citation(s) in RCA: 240] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Revised: 03/21/2012] [Accepted: 03/25/2012] [Indexed: 12/17/2022]
Abstract
Biofilms associated with the human body, particularly in typically sterile locations, are difficult to diagnose and treat effectively because of their recalcitrance to conventional antibiotic therapy and host immune responses. The study of biofilms in medicine today requires a translational approach, with examination of clinically relevant biofilms in the context of specific anatomic sites, host tissues, and diseases, focusing on what can be done to mitigate their pathologic consequences. This review, which grew out of a discussion session on clinical biofilms at the 5th ASM Biofilm Conference in Cancun, Mexico, is designed to give an overview of biofilm-associated infections (BAI) and to propose a platform for further discussion that includes clinicians, medical microbiologists, and biofilm researchers who are stakeholders in advancing the scientific pursuit of better diagnosis and treatment of BAI to mitigate their human and healthcare costs. It also highlights the need for better diagnostic markers, which exploit the difference between planktonic and biofilm cells.
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Affiliation(s)
- Luanne Hall-Stoodley
- Wellcome Trust Clinical Research Facility, University Hospital Southampton Foundation Trust, Southampton, UK.
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Diversity of potential pathogenicity and biofilm formation among Burkholderia cepacia complex water, clinical, and agricultural isolates in China. World J Microbiol Biotechnol 2012; 28:2113-23. [PMID: 22806034 DOI: 10.1007/s11274-012-1016-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2011] [Accepted: 01/30/2012] [Indexed: 01/31/2023]
Abstract
A collection of 70 Burkholderia cepacia complex isolates, recovered from clinical, water, and agricultural resources in China in our previous studies, were tested to assess their potential pathogenicity and association of biofilm formation with pathogenicity. The pathogenicity was tested in the alternative infection models alfalfa, detached lettuce midrib, Galleria mellonella (wax moth), rat agar bead, and lettuce intact leaves. Severe to moderate pathogenicity were observed for isolates of clinical and water origin compared to agricultural isolates, with the exception of a few clinical isolates exhibiting reduced pathogenicity. Virulent isolates persisted in rat lungs until 21 days post infection causing histopathological changes like inflammation, while in lettuce midrib tissues invasion, localization, and replication of bacteria were observed. Biofilm formation ability was also documented in high frequency among water and clinical virulent isolates compared to agricultural isolates. Although variations in pathogenicity were observed for a few isolates, results obtained from different model systems including lettuce were consistent. Our studies indicate that water and clinical isolates showed severe virulence and strong biofilm formation ability compared to agricultural isolates. The results also show lettuce as a promising infection model not only to study the pathogenicity factors used by Bcc bacteria but also for characterization the in vivo transcriptional profile for different niches adaptation of this opportunistic pathogen.
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