51
|
Chowdhury N, Bagchi A. Identification of ligand binding activity and DNA recognition by RhlR protein from opportunistic pathogen Pseudomonas aeruginosa-a molecular dynamic simulation approach. J Mol Recognit 2018; 31:e2738. [PMID: 29968257 DOI: 10.1002/jmr.2738] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 05/21/2018] [Accepted: 06/01/2018] [Indexed: 11/07/2022]
Abstract
RhlR protein from opportunistic pathogen Pseudomonas aeruginosa is involved in the transcription of virulence genes of the organism. The RhlR protein functions as a dimer and binds to the cognate promoter DNA with the help of an autoinducer ligand BHL to initiate the transcription of the virulence genes. Till date, there are no reports that detail the mechanism of virulence gene expression by RhlR protein in P. aeruginosa. In this work, we tried to analyse the molecular aspects of the various binding interactions of the RhlR protein while formimg the dimmer as well as with the promoter DNA. We analysed the mode of dimerisation of the RhlR protein and its binding interactions with the autoinducer BHL ligand. From our analyses, we could identify the potential amino acid residues which are involved in the binding interactions. We also predicted how the autoinducer BHL would help in making contacts with the DNA as well as with itself. Thus, the autoinducer BHL would serve as an important mediator of molecular interactions involved in binding the RhlR protein to itself as well as with the promoter DNA. Therefore, any other molecule which would be able to compete with the autoinducer ligand BHL to bind to RhlR protein but would not let the RhlR protein bind the promoter DNA would be an ideal drug candidate to prevent the transcription process of the virulence genes in P. aeruginosa. Our future aim is to predict suitable ligands which would compete with BHL to thwart the transcription process.
Collapse
Affiliation(s)
- Nilkanta Chowdhury
- Department of Biochemistry and Biophysics, University of Kalyani, Nadia, India
| | - Angshuman Bagchi
- Department of Biochemistry and Biophysics, University of Kalyani, Nadia, India
| |
Collapse
|
52
|
King CD, Singh D, Holden K, Govan AB, Keith SA, Ghazi A, Robinson RA. Proteomic identification of virulence-related factors in young and aging C. elegans infected with Pseudomonas aeruginosa. J Proteomics 2018; 181:92-103. [DOI: 10.1016/j.jprot.2018.04.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 03/26/2018] [Accepted: 04/09/2018] [Indexed: 12/16/2022]
|
53
|
Short SM, van Tol S, MacLeod HJ, Dimopoulos G. Hydrogen cyanide produced by the soil bacterium Chromobacterium sp. Panama contributes to mortality in Anopheles gambiae mosquito larvae. Sci Rep 2018; 8:8358. [PMID: 29844510 PMCID: PMC5974309 DOI: 10.1038/s41598-018-26680-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 05/04/2018] [Indexed: 11/09/2022] Open
Abstract
Mosquito larvae continuously encounter microbes in their aquatic environment, which serve as food and play a critical role in successful development. In previous work, we isolated a Chromobacterium sp. (C.sp_P) with larvicidal activity from the midgut of dengue vector Aedes mosquitoes in Panama. In this study, we found a positive correlation between initial concentrations of C.sp_P and larval mortality rates, and that C.sp_P is more efficient at inducing larval mortality in a high nutrient environment. Multiple Chromobacterium species induce larval mortality with similar efficacy to C.sp_P except for C. subtsugae. We also found that a non-lethal dose of C.sp_P lengthens development time and increases mortality over multiple developmental stages, suggesting persistent effects of exposure. Additionally, we showed that larvicidal activity persists in the larval breeding water after removal of live bacteria, and that the larvicidal factor in C.sp_P-treated water is smaller than 3 kDa, heat resistant to 90 °C, and lost after vacuum centrifugation. We showed that C.sp_P produces hydrogen cyanide in culture and in larval water at concentrations sufficient to kill An. gambiae larvae, and treatment of the larval water with a cyanide antidote eliminated larvicidal activity. We conclude that a potential mechanism by which C.sp_P can induce larval mortality is via production of hydrogen cyanide.
Collapse
Affiliation(s)
- Sarah M Short
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - Sarah van Tol
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA.,Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Hannah J MacLeod
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - George Dimopoulos
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA.
| |
Collapse
|
54
|
Short SM, van Tol S, Smith B, Dong Y, Dimopoulos G. The mosquito adulticidal Chromobacterium sp. Panama causes transgenerational impacts on fitness parameters and elicits xenobiotic gene responses. Parasit Vectors 2018; 11:229. [PMID: 29622036 PMCID: PMC5887189 DOI: 10.1186/s13071-018-2822-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 03/26/2018] [Indexed: 11/22/2022] Open
Abstract
Background Vector control is critical in reducing the disease burden caused by mosquitoes, and insecticides are an effective tool to control vector populations. Resistance to common insecticides is now widespread, and novel classes of insecticides are needed. In previous work, we described the mosquitocidal activity of Chromobacterium sp. Panama (C.sp_P), a bacterium found in association with mosquitoes in natural populations. In the current work, we further explored the effects of exposure to the bacterium on mosquito fitness and mosquito physiology. Results We found that C.sp_P has mosquitocidal activity against a broad range of mosquito taxa. When exposed to C.sp_P as adults, female An. gambiae suffered reduced longevity, but experienced no change in fecundity. The offspring of these females, however, had higher mortality as larvae and were slower to develop compared to offspring of control females. We also found that the mosquitocidal activity of C.sp_P was retained after removal of live cells from biofilm culture media, suggesting the bacteria secrete mosquitocidal compound(s) into the media during growth. Exposure to this cell-free C.sp_P-conditioned media caused female midgut transcriptional changes comprising detoxification, xenobiotic response, and stress response genes, suggesting the physiological response to C.sp_P is similar to that of insecticide exposure. Finally, we found that multiple members of the Chromobacterium genus had mosquitocidal activity, but this activity was highest in mosquitoes treated with C.sp_P. Conclusions Our findings suggest that C.sp_P produces factor(s) with strong effects on mosquito longevity and fitness, which may be of interest for mosquitocide development. More generally, they indicate that further exploration of mosquito-associated and environmental microbes for novel insecticidal compounds or biocontrol agents is warranted. Electronic supplementary material The online version of this article (10.1186/s13071-018-2822-8) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Sarah M Short
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - Sarah van Tol
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA.,Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Brendan Smith
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - Yuemei Dong
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - George Dimopoulos
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA.
| |
Collapse
|
55
|
Haripriyan J, Omanakuttan A, Menon ND, Vanuopadath M, Nair SS, Corriden R, Nair BG, Nizet V, Kumar GB. Clove Bud Oil Modulates Pathogenicity Phenotypes of the Opportunistic Human Pathogen Pseudomonas aeruginosa. Sci Rep 2018; 8:3437. [PMID: 29467483 PMCID: PMC5821892 DOI: 10.1038/s41598-018-19771-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 01/08/2018] [Indexed: 02/01/2023] Open
Abstract
Earlier studies from our laboratory have demonstrated that clove bud oil (CBO) attenuates expression of certain virulence factors of Pseudomonas aeruginosa PAO1. Here, we probe more deeply into the effect of CBO on four pseudomonal proteases - elastase A, elastase B, protease IV and alkaline protease - each known to play key roles in disease pathogenesis. CBO inhibited the activity of these proteases present in the bacterial culture supernatant. Zymography studies indicated that these proteases can activate host matrix metalloproteases (MMPs) to establish infection, through conversion of pro-MMP-2 to active MMP-2. PAO1 is a predominant pathogen in burn wound infections and we show the modulatory effect of CBO on MMPs in an in vitro model of burn injury. Furthermore, CBO induced dose-dependent neutrophil extracellular trap formation in human neutrophils. CBO also increased the survival of C. elegans infected with PAO1, establishing an anti-infective role in a whole animal model of pathogenesis. LC-MS/MS analysis indicated that CBO treatment elicited a significant reduction of signalling molecules (Acyl-Homoserine-Lactone) involved in quorum sensing regulation. Our observations demonstrate that CBO attenuates key virulence mechanisms of this important human pathogen, while concomitantly enhancing host innate immunomodulatory functions, with potential implications for topical therapy against antibiotic-resistant infections.
Collapse
Affiliation(s)
- Jayalekshmi Haripriyan
- School of Biotechnology, Amrita University, Amrita Vishwa Vidyapeetham, Clappana P.O., Kollam, Kerala, 690525, India
| | - Athira Omanakuttan
- School of Biotechnology, Amrita University, Amrita Vishwa Vidyapeetham, Clappana P.O., Kollam, Kerala, 690525, India
| | - Nitasha D Menon
- School of Biotechnology, Amrita University, Amrita Vishwa Vidyapeetham, Clappana P.O., Kollam, Kerala, 690525, India.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Muralidharan Vanuopadath
- School of Biotechnology, Amrita University, Amrita Vishwa Vidyapeetham, Clappana P.O., Kollam, Kerala, 690525, India
| | - Sudarslal Sadasivan Nair
- School of Biotechnology, Amrita University, Amrita Vishwa Vidyapeetham, Clappana P.O., Kollam, Kerala, 690525, India
| | - Ross Corriden
- Department of Pharmacology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Bipin G Nair
- School of Biotechnology, Amrita University, Amrita Vishwa Vidyapeetham, Clappana P.O., Kollam, Kerala, 690525, India
| | - Victor Nizet
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.,Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 920093, USA
| | - Geetha B Kumar
- School of Biotechnology, Amrita University, Amrita Vishwa Vidyapeetham, Clappana P.O., Kollam, Kerala, 690525, India.
| |
Collapse
|
56
|
Kang BR, Anderson AJ, Kim YC. Hydrogen Cyanide Produced by Pseudomonas chlororaphis O6 Exhibits Nematicidal Activity against Meloidogyne hapla. THE PLANT PATHOLOGY JOURNAL 2018; 34:35-43. [PMID: 29422786 PMCID: PMC5796748 DOI: 10.5423/ppj.oa.06.2017.0115] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 11/16/2017] [Accepted: 11/23/2017] [Indexed: 05/09/2023]
Abstract
Root-knot nematodes (Meloidogyne spp.) are parasites that attack many field crops and orchard trees, and affect both the quantity and quality of the products. A root-colonizing bacterium, Pseudomonas chlororaphis O6, possesses beneficial traits including strong nematicidal activity. To determine the molecular mechanisms involved in the nematicidal activity of P. chlororaphis O6, we constructed two mutants; one lacking hydrogen cyanide production, and a second lacking an insecticidal toxin, FitD. Root drenching with wild-type P. chlororaphis O6 cells caused juvenile mortality in vitro and in planta. Efficacy was not altered in the fitD mutant compared to the wild-type but was reduced in both bioassays for the mutant lacking hydrogen cyanide production. The reduced number of galls on tomato plants caused by the wild-type strain was comparable to that of a standard chemical nematicide. These findings suggest that hydrogen cyanide-producing root colonizers, such as P. chlororaphis O6, could be formulated as "green" nematicides that are compatible with many crops and offer agricultural sustainability.
Collapse
Affiliation(s)
- Beom Ryong Kang
- Institute of Environmentally-Friendly Agriculture, Chonnam National University, Gwangju 61186,
Korea
| | - Anne J. Anderson
- Department of Biology, Utah State University, Logan, UT 84322-5305,
USA
| | - Young Cheol Kim
- Institute of Environmentally-Friendly Agriculture, Chonnam National University, Gwangju 61186,
Korea
- Corresponding author. Phone) +82-62-530-2071, FAX) +82-62-530-0208, E-mail)
| |
Collapse
|
57
|
Regulation of ribonucleotide synthesis by the Pseudomonas aeruginosa two-component system AlgR in response to oxidative stress. Sci Rep 2017; 7:17892. [PMID: 29263410 PMCID: PMC5738425 DOI: 10.1038/s41598-017-17917-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 12/04/2017] [Indexed: 11/11/2022] Open
Abstract
Ribonucleotide reductases (RNR) catalyze the last step of deoxyribonucleotide synthesis, and are therefore essential to DNA-based life. Three forms of RNR exist: classes I, II, and III. While eukaryotic cells use only class Ia RNR, bacteria can harbor any combination of classes, granting them adaptability. The opportunistic pathogen Pseudomonas aeruginosa surprisingly encodes all three classes, allowing it to thrive in different environments. Here we study an aspect of the complex RNR regulation whose molecular mechanism has never been elucidated, the well-described induction through oxidative stress, and link it to the AlgZR two-component system, the primary regulator of the mucoid phenotype. Through bioinformatics, we identify AlgR binding locations in RNR promoters, which we characterize functionally through EMSA and physically through AFM imaging. Gene reporter assays in different growth models are used to study the AlgZR-mediated control on the RNR network under various environmental conditions and physiological states. Thereby, we show that the two-component system AlgZR, which is crucial for bacterial conversion to the mucoid phenotype associated with chronic disease, controls the RNR network and directs how the DNA synthesis pathway is modulated in mucoid and non-mucoid biofilms, allowing it to respond to oxidative stress.
Collapse
|
58
|
Baker YR, Hodgkinson JT, Florea BI, Alza E, Galloway WRJD, Grimm L, Geddis SM, Overkleeft HS, Welch M, Spring DR. Identification of new quorum sensing autoinducer binding partners in Pseudomonas aeruginosa using photoaffinity probes. Chem Sci 2017; 8:7403-7411. [PMID: 29163891 PMCID: PMC5674140 DOI: 10.1039/c7sc01270e] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 08/26/2017] [Indexed: 12/20/2022] Open
Abstract
Many bacterial species, including the human pathogen Pseudomonas aeruginosa, employ a mechanism of intercellular communication known as quorum sensing (QS), which is mediated by signalling molecules termed autoinducers. The Pseudomonas Quinolone Signal (PQS) and 2-Heptyl-3H-4-Quinolone (HHQ) are autoinducers in P. aeruginosa, and they are considered important factors in the progress of infections by this clinically relevant organism. Herein, we report the development of HHQ and PQS photoaffinity-based probes for chemical proteomic studies. Application of these probes led to the identification of previously unsuspected putative HHQ and PQS binders, thereby providing new insights into QS at a proteomic level and revealing potential new small molecule targets for virulence attenuation strategies. Notably, we found evidence that PQS binds RhlR, the cognate receptor in the Rhl QS sub-system of P. aeruginosa. This is the first indication of interaction between the Rhl and PQS systems at the protein/ligand level, which suggests that RhlR should be considered a highly attractive target for antivirulence strategies.
Collapse
Affiliation(s)
- Y R Baker
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge , CB2 1EW , UK .
- Leiden Institute of Chemistry , Leiden University , Einsteinweg 55 , 2333 CC Leiden , The Netherlands
- Department of Biochemistry , University of Cambridge , 80 Tennis Court Road , Cambridge , CB2 1GA , UK .
| | - J T Hodgkinson
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge , CB2 1EW , UK .
- Department of Biochemistry , University of Cambridge , 80 Tennis Court Road , Cambridge , CB2 1GA , UK .
| | - B I Florea
- Leiden Institute of Chemistry , Leiden University , Einsteinweg 55 , 2333 CC Leiden , The Netherlands
| | - E Alza
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge , CB2 1EW , UK .
| | - W R J D Galloway
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge , CB2 1EW , UK .
| | - L Grimm
- Department of Biochemistry , University of Cambridge , 80 Tennis Court Road , Cambridge , CB2 1GA , UK .
| | - S M Geddis
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge , CB2 1EW , UK .
| | - H S Overkleeft
- Leiden Institute of Chemistry , Leiden University , Einsteinweg 55 , 2333 CC Leiden , The Netherlands
| | - M Welch
- Department of Biochemistry , University of Cambridge , 80 Tennis Court Road , Cambridge , CB2 1GA , UK .
| | - D R Spring
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge , CB2 1EW , UK .
| |
Collapse
|
59
|
Borrero-de Acuña JM, Timmis KN, Jahn M, Jahn D. Protein complex formation during denitrification by Pseudomonas aeruginosa. Microb Biotechnol 2017; 10:1523-1534. [PMID: 28857512 PMCID: PMC5658584 DOI: 10.1111/1751-7915.12851] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 08/08/2017] [Accepted: 08/09/2017] [Indexed: 12/18/2022] Open
Abstract
The most efficient means of generating cellular energy is through aerobic respiration. Under anaerobic conditions, several prokaryotes can replace oxygen by nitrate as final electron acceptor. During denitrification, nitrate is reduced via nitrite, NO and N2O to molecular nitrogen (N2) by four membrane‐localized reductases with the simultaneous formation of an ion gradient for ATP synthesis. These four multisubunit enzyme complexes are coupled in four electron transport chains to electron donating primary dehydrogenases and intermediate electron transfer proteins. Many components require membrane transport and insertion, complex assembly and cofactor incorporation. All these processes are mediated by fine‐tuned stable and transient protein–protein interactions. Recently, an interactomic approach was used to determine the exact protein–protein interactions involved in the assembly of the denitrification apparatus of Pseudomonas aeruginosa. Both subunits of the NO reductase NorBC, combined with the flavoprotein NosR, serve as a membrane‐localized assembly platform for the attachment of the nitrate reductase NarGHI, the periplasmic nitrite reductase NirS via its maturation factor NirF and the N2O reductase NosZ through NosR. A nitrate transporter (NarK2), the corresponding regulatory system NarXL, various nitrite (NirEJMNQ) and N2O reductase (NosFL) maturation proteins are also part of the complex. Primary dehydrogenases, ATP synthase, most enzymes of the TCA cycle, and the SEC protein export system, as well as a number of other proteins, were found to interact with the denitrification complex. Finally, a protein complex composed of the flagella protein FliC, nitrite reductase NirS and the chaperone DnaK required for flagella formation was found in the periplasm of P. aeruginosa. This work demonstrated that the interactomic approach allows for the identification and characterization of stable and transient protein–protein complexes and interactions involved in the assembly and function of multi‐enzyme complexes.
Collapse
Affiliation(s)
| | - Kenneth N Timmis
- Institute of Microbiology, Technische Universität Braunschweig, Spielmannstr. 7, Braunschweig, Germany
| | - Martina Jahn
- Institute of Microbiology, Technische Universität Braunschweig, Spielmannstr. 7, Braunschweig, Germany
| | - Dieter Jahn
- Institute of Microbiology, Technische Universität Braunschweig, Spielmannstr. 7, Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology BRICS, Technische Universität Braunschweig, Rebenring 56, Braunschweig, Germany
| |
Collapse
|
60
|
Nandi M, Selin C, Brawerman G, Fernando WGD, de Kievit TR. The global regulator ANR is essential for Pseudomonas chlororaphis strain PA23 biocontrol. MICROBIOLOGY-SGM 2017; 162:2159-2169. [PMID: 27998371 DOI: 10.1099/mic.0.000391] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Pseudomonas chlororaphis PA23 is a biocontrol agent capable of protecting canola from stem rot disease caused by the fungus Sclerotinia sclerotiorum. The focus of the current study was to elucidate the role of the transcriptional regulator ANR in the biocontrol capabilities of this bacterium. An anr mutant was created, PA23anr, that was devoid antifungal activity. In other pseudomonads, ANR is essential for regulating HCN production. Characterization of PA23anr revealed that, in addition to HCN, ANR controls phenazine (PHZ), pyrrolnitrin (PRN), protease and autoinducer (AHL) signal molecule production. In gene expression studies, hcnA, phzA, prnA and phzI were found to be downregulated, consistent with our endproduct analysis. Because the phenotype of PA23anr closely resembles that of quorum sensing (QS)-deficient strains, we explored whether there is a connection between ANR and the PhzRI QS system. Both phzI and phzR are positively regulated by ANR, whereas PhzR represses anr transcription. Complementation of PA23anr with pUCP-phzR, C6-HSL or both yielded no change in phenotype. Conversely, PA23phzR harbouring pUCP23-anr exhibited partial-to-full restoration of antifungal activity, HCN, PRN and AHL production together with hcnA, prnA, phzI and rpoS expression. PHZ and protease production remained unchanged indicating that ANR can complement the QS-deficient phenotype with respect to some but not all traits. Our experiments were conducted at atmospheric O2 levels underscoring the fact that ANR has a profound effect on PA23 physiology under aerobic conditions.
Collapse
Affiliation(s)
- Munmun Nandi
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Carrie Selin
- Department of Plant Science, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Gabriel Brawerman
- Department of Pharmacology and Therapeutics, University of Manitoba, Winnipeg, Manitoba, Canada
| | | | - Teresa R de Kievit
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| |
Collapse
|
61
|
Schuster M, Sexton DJ, Hense BA. Why Quorum Sensing Controls Private Goods. Front Microbiol 2017; 8:885. [PMID: 28579979 PMCID: PMC5437708 DOI: 10.3389/fmicb.2017.00885] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 05/02/2017] [Indexed: 12/22/2022] Open
Abstract
Cell-cell communication, also termed quorum sensing (QS), is a widespread process that coordinates gene expression in bacterial populations. The generally accepted view is that QS optimizes the cell density-dependent benefit attained from cooperative behaviors, often in the form of secreted products referred to as "public goods." This view is challenged by an increasing number of cell-associated products or "private goods" reported to be under QS-control for which a collective benefit is not apparent. A prominent example is nucleoside hydrolase from Pseudomonas aeruginosa, a periplasmic enzyme that catabolizes adenosine. Several recent studies have shown that private goods can function to stabilize cooperation by co-regulated public goods, seemingly explaining their control by QS. Here we argue that this property is a by-product of selection for other benefits rather than an adaptation. Emphasizing ecophysiological context, we propose alternative explanations for the QS control of private goods. We suggest that the benefit attained from private goods is associated with high cell density, either because a relevant ecological condition correlates with density, or because the private good is, directly or indirectly, involved in cooperative behavior. Our analysis helps guide a systems approach to QS, with implications for antivirulence drug design and synthetic biology.
Collapse
Affiliation(s)
- Martin Schuster
- Department of Microbiology, Oregon State UniversityCorvallis, OR, United States
| | - D Joseph Sexton
- Department of Microbiology, Oregon State UniversityCorvallis, OR, United States
| | - Burkhard A Hense
- Institute of Computational Biology, Helmholtz Zentrum MünchenNeuherberg, Germany
| |
Collapse
|
62
|
Ossowicki A, Jafra S, Garbeva P. The antimicrobial volatile power of the rhizospheric isolate Pseudomonas donghuensis P482. PLoS One 2017; 12:e0174362. [PMID: 28358818 PMCID: PMC5373542 DOI: 10.1371/journal.pone.0174362] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 03/07/2017] [Indexed: 11/19/2022] Open
Abstract
Soil and rhizosphere bacteria produce an array of secondary metabolites including a wide range of volatile organic compounds (VOCs). These compounds play an important role in the long-distance interactions and communication between (micro)organisms. Furthermore, bacterial VOCs are involved in plant pathogens inhibition and induction of soil fungistasis and suppressivenes. In the present study, we analysed the volatile blend emitted by the rhizospheric isolate Pseudomonas donghuensis P482 and evaluated the volatile effect on the plant pathogenic fungi and bacteria as well as one oomycete. Moreover, we investigated the role of the GacS/GacA system on VOCs production in P. donghuensis P482. The results obtained demonstrated that VOCs emitted by P. donghuensis P482 have strong antifungal and antioomycete, but not antibacterial activity. The production of certain volatiles such as dimethyl sulfide, S-methyl thioacetate, methyl thiocyanate, dimethyl trisulfide, 1-undecan and HCN is depended on the GacS/GacA two-component regulatory system. Apparently, these compounds play an important role in the pathogens suppression as the gacA mutant entirely lost the ability to inhibit via volatiles the growth of tested plant pathogens.
Collapse
Affiliation(s)
- Adam Ossowicki
- Laboratory of Biological Plant Protection, Department of Biotechnology, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, Gdansk, Poland
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Sylwia Jafra
- Laboratory of Biological Plant Protection, Department of Biotechnology, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, Gdansk, Poland
- * E-mail: (PG); (SJ)
| | - Paolina Garbeva
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
- * E-mail: (PG); (SJ)
| |
Collapse
|
63
|
Lauridsen RK, Sommer LM, Johansen HK, Rindzevicius T, Molin S, Jelsbak L, Engelsen SB, Boisen A. SERS detection of the biomarker hydrogen cyanide from Pseudomonas aeruginosa cultures isolated from cystic fibrosis patients. Sci Rep 2017; 7:45264. [PMID: 28349938 PMCID: PMC5368648 DOI: 10.1038/srep45264] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 02/27/2017] [Indexed: 11/09/2022] Open
Abstract
Pseudomonas aeruginosa is the primary cause of chronic airway infections in cystic fibrosis (CF) patients. Persistent infections are seen from the first P. aeruginosa culture in about 75% of young CF patients, and it is important to discover new ways to detect P. aeruginosa at an earlier stage. The P. aeruginosa biomarker hydrogen cyanide (HCN) contains a triple bond, which is utilized in this study because of the resulting characteristic C≡N peak at 2135 cm-1 in a Raman spectrum. The Raman signal was enhanced by surface-enhanced Raman spectroscopy (SERS) on a Au-coated SERS substrate. After long-term infection, a mutation in the patho-adaptive lasR gene can alter the expression of HCN, which is why it is sometimes not possible to detect HCN in the breath of chronically infected patients. Four P. aeruginosa reference strains and 12 clinical P. aeruginosa strains isolated from CF children were evaluated, and HCN was clearly detected from overnight cultures of all wild type-like isolates and half of the later isolates from the same patients. The clinical impact could be that P. aeruginosa infections could be detected at an earlier stage, because daily breath sampling with an immediate output could be possible with a point-of-care SERS device.
Collapse
Affiliation(s)
- Rikke Kragh Lauridsen
- DTU Nanotech, Technical University of Denmark, Ørsteds Plads 345B, 2800 Lyngby, Denmark
| | - Lea M. Sommer
- DTU Biosustain, Technical University of Denmark, Novo Nordisk Foundation Center for Biosustainability, Kogle Allé 6, 2970 Hørsholm, Denmark
| | - Helle Krogh Johansen
- DTU Biosustain, Technical University of Denmark, Novo Nordisk Foundation Center for Biosustainability, Kogle Allé 6, 2970 Hørsholm, Denmark
- Department of Clinical Microbiology 9301, Rigshospitalet, Juliane Maries Vej 22, 2100 København Ø, Denmark
| | - Tomas Rindzevicius
- DTU Nanotech, Technical University of Denmark, Ørsteds Plads 345B, 2800 Lyngby, Denmark
| | - Søren Molin
- DTU Biosustain, Technical University of Denmark, Novo Nordisk Foundation Center for Biosustainability, Kogle Allé 6, 2970 Hørsholm, Denmark
| | - Lars Jelsbak
- DTU Systems Biology, Technical University of Denmark, Matematiktorvet 301, 2800 Lyngby, Denmark
| | - Søren Balling Engelsen
- Department of Food Science, University of Copenhagen, Rolighedsvej 26, 1958 Frederiksberg C, Denmark
| | - Anja Boisen
- DTU Nanotech, Technical University of Denmark, Ørsteds Plads 345B, 2800 Lyngby, Denmark
| |
Collapse
|
64
|
Cyclic-di-GMP regulates lipopolysaccharide modification and contributes to Pseudomonas aeruginosa immune evasion. Nat Microbiol 2017; 2:17027. [PMID: 28263305 PMCID: PMC5341770 DOI: 10.1038/nmicrobiol.2017.27] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Accepted: 01/31/2017] [Indexed: 11/18/2022]
Abstract
Pseudomonas aeruginosa is a Gram-negative bacterial pathogen associated with acute and chronic infections. The universal c-di-GMP second messenger is instrumental in the switch from a motile lifestyle to resilient biofilm as in the cystic fibrosis lung. The SadC diguanylate cyclase is associated with this patho-adaptive transition. Here we identified an unrecognized SadC partner, WarA, which we show is a methyltransferase in complex with a putative kinase WarB. We established that WarA binds to c-di-GMP, which potentiates its methyltransferase activity. Together, WarA and WarB have structural similarities with the bi-functional Escherichia coli LPS O antigen regulator WbdD. Strikingly, WarA influences P. aeruginosa O antigen modal distribution and interacts with the LPS biogenesis machinery. LPS is known to modulate the immune response in the host, and by using a zebrafish infection model, we implicate WarA in the ability of P. aeruginosa to evade detection by the host.
Collapse
|
65
|
Moradali MF, Ghods S, Rehm BHA. Pseudomonas aeruginosa Lifestyle: A Paradigm for Adaptation, Survival, and Persistence. Front Cell Infect Microbiol 2017; 7:39. [PMID: 28261568 PMCID: PMC5310132 DOI: 10.3389/fcimb.2017.00039] [Citation(s) in RCA: 793] [Impact Index Per Article: 113.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 02/02/2017] [Indexed: 12/16/2022] Open
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen affecting immunocompromised patients. It is known as the leading cause of morbidity and mortality in cystic fibrosis (CF) patients and as one of the leading causes of nosocomial infections. Due to a range of mechanisms for adaptation, survival and resistance to multiple classes of antibiotics, infections by P. aeruginosa strains can be life-threatening and it is emerging worldwide as public health threat. This review highlights the diversity of mechanisms by which P. aeruginosa promotes its survival and persistence in various environments and particularly at different stages of pathogenesis. We will review the importance and complexity of regulatory networks and genotypic-phenotypic variations known as adaptive radiation by which P. aeruginosa adjusts physiological processes for adaptation and survival in response to environmental cues and stresses. Accordingly, we will review the central regulatory role of quorum sensing and signaling systems by nucleotide-based second messengers resulting in different lifestyles of P. aeruginosa. Furthermore, various regulatory proteins will be discussed which form a plethora of controlling systems acting at transcriptional level for timely expression of genes enabling rapid responses to external stimuli and unfavorable conditions. Antibiotic resistance is a natural trait for P. aeruginosa and multiple mechanisms underlying different forms of antibiotic resistance will be discussed here. The importance of each mechanism in conferring resistance to various antipseudomonal antibiotics and their prevalence in clinical strains will be described. The underlying principles for acquiring resistance leading pan-drug resistant strains will be summarized. A future outlook emphasizes the need for collaborative international multidisciplinary efforts to translate current knowledge into strategies to prevent and treat P. aeruginosa infections while reducing the rate of antibiotic resistance and avoiding the spreading of resistant strains.
Collapse
Affiliation(s)
| | | | - Bernd H. A. Rehm
- Institute of Fundamental Sciences, Massey UniversityPalmerston North, New Zealand
| |
Collapse
|
66
|
Chowdhury N, Bagchi A. Structural Insight into the Gene Expression Profiling of the hcn Operon in Pseudomonas aeruginosa. Appl Biochem Biotechnol 2017; 182:1144-1157. [DOI: 10.1007/s12010-016-2388-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 12/28/2016] [Indexed: 11/29/2022]
|
67
|
Fong J, Yuan M, Jakobsen TH, Mortensen KT, Delos Santos MMS, Chua SL, Yang L, Tan CH, Nielsen TE, Givskov M. Disulfide Bond-Containing Ajoene Analogues As Novel Quorum Sensing Inhibitors of Pseudomonas aeruginosa. J Med Chem 2016; 60:215-227. [PMID: 27977197 DOI: 10.1021/acs.jmedchem.6b01025] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Since its discovery 22 years ago, the bacterial cell-to-cell communication system, termed quorum sensing (QS), has shown potential as antipathogenic target. Previous studies reported that ajoene from garlic inhibits QS in opportunistic human pathogen Pseudomonas aeruginosa. In this study, screening of an in-house compound library revealed two sulfur-containing compounds which possess structural resemblance with ajoene and inhibit QS in bioreporter assay. Following a quantitative structure-activity relationship (SAR) study, 25 disulfide bond-containing analogues were synthesized and tested for QS inhibition activities. SAR study indicated that the allyl group could be replaced with other substituents, with the most active being benzothiazole derivative (IC50 = 0.56 μM). The compounds were able to reduce QS-regulated virulence factors (elastase, rhamnolipid, and pyocyanin) and successfully inhibit P. aeruginosa infection in murine model of implant-associated infection. Altogether, the QS inhibition activity of the synthesized compounds is encouraging for further exploration of novel analogues in antimicrobial drug development.
Collapse
Affiliation(s)
- July Fong
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University , 60 Nanyang Drive, Singapore 637551, Singapore.,School of Biological Sciences, Nanyang Technological University , 60 Nanyang Drive, Singapore 637551, Singapore
| | - Mingjun Yuan
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University , 60 Nanyang Drive, Singapore 637551, Singapore
| | - Tim Holm Jakobsen
- Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen , 2200 København N, Denmark
| | - Kim T Mortensen
- Department of Chemistry, Technical University of Denmark , Kemitorvet, 2800 Kgs Lyngby, Denmark
| | - May Margarette Salido Delos Santos
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University , 60 Nanyang Drive, Singapore 637551, Singapore
| | - Song Lin Chua
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University , 60 Nanyang Drive, Singapore 637551, Singapore
| | - Liang Yang
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University , 60 Nanyang Drive, Singapore 637551, Singapore.,School of Biological Sciences, Nanyang Technological University , 60 Nanyang Drive, Singapore 637551, Singapore
| | - Choon Hong Tan
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University , 60 Nanyang Drive, Singapore 637551, Singapore.,Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University , 21 Nanyang Link, Singapore 637371, Singapore
| | - Thomas E Nielsen
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University , 60 Nanyang Drive, Singapore 637551, Singapore.,Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen , 2200 København N, Denmark
| | - Michael Givskov
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University , 60 Nanyang Drive, Singapore 637551, Singapore.,Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen , 2200 København N, Denmark
| |
Collapse
|
68
|
Ganesh PS, Rai RV. Inhibition of quorum-sensing-controlled virulence factors of Pseudomonas aeruginosa by Murraya koenigii essential oil: a study in a Caenorhabditis elegans infectious model. J Med Microbiol 2016; 65:1528-1535. [DOI: 10.1099/jmm.0.000385] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- P. Sankar Ganesh
- Department of Studies in Microbiology, University of Mysore, Manasagangotri, Mysore 570006, Karnataka, India
| | - Ravishankar Vittal Rai
- Department of Studies in Microbiology, University of Mysore, Manasagangotri, Mysore 570006, Karnataka, India
| |
Collapse
|
69
|
Cupp-Sutton KA, Ashby MT. Biological Chemistry of Hydrogen Selenide. Antioxidants (Basel) 2016; 5:E42. [PMID: 27879667 PMCID: PMC5187540 DOI: 10.3390/antiox5040042] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 11/04/2016] [Accepted: 11/08/2016] [Indexed: 12/13/2022] Open
Abstract
There are no two main-group elements that exhibit more similar physical and chemical properties than sulfur and selenium. Nonetheless, Nature has deemed both essential for life and has found a way to exploit the subtle unique properties of selenium to include it in biochemistry despite its congener sulfur being 10,000 times more abundant. Selenium is more easily oxidized and it is kinetically more labile, so all selenium compounds could be considered to be "Reactive Selenium Compounds" relative to their sulfur analogues. What is furthermore remarkable is that one of the most reactive forms of selenium, hydrogen selenide (HSe- at physiologic pH), is proposed to be the starting point for the biosynthesis of selenium-containing molecules. This review contrasts the chemical properties of sulfur and selenium and critically assesses the role of hydrogen selenide in biological chemistry.
Collapse
Affiliation(s)
- Kellye A Cupp-Sutton
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019, USA.
| | - Michael T Ashby
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019, USA.
| |
Collapse
|
70
|
Rijavec T, Lapanje A. Hydrogen Cyanide in the Rhizosphere: Not Suppressing Plant Pathogens, but Rather Regulating Availability of Phosphate. Front Microbiol 2016; 7:1785. [PMID: 27917154 PMCID: PMC5114478 DOI: 10.3389/fmicb.2016.01785] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 10/24/2016] [Indexed: 01/22/2023] Open
Abstract
Plant growth promoting rhizobacteria produce chemical compounds with different benefits for the plant. Among them, HCN is recognized as a biocontrol agent, based on its ascribed toxicity against plant pathogens. Based on several past studies questioning the validity of this hypothesis, we have re-addressed the issue by designing a new set of in vitro experiments, to test if HCN-producing rhizobacteria could inhibit the growth of phytopathogens. The level of HCN produced by the rhizobacteria in vitro does not correlate with the observed biocontrol effects, thus disproving the biocontrol hypothesis. We developed a new concept, in which HCN does not act as a biocontrol agent, but rather is involved in geochemical processes in the substrate (e.g., chelation of metals), indirectly increasing the availability of phosphate. Since this scenario can be important for the pioneer plants living in oligotrophic alpine environments, we inoculated HCN producing bacteria into sterile mineral sand together with germinating plants and showed that the growth of the pioneer plant French sorrel was increased on granite-based substrate. No such effect could be observed for maize, where plantlets depend on the nutrients stored in the endosperm. To support our concept, we used KCN and mineral sand and showed that mineral mobilization and phosphate release could be caused by cyanide in vitro. We propose that in oligotrophic alpine environments, and possibly elsewhere, the main contribution of HCN is in the sequestration of metals and the consequential indirect increase of nutrient availability, which is beneficial for the rhizobacteria and their plant hosts.
Collapse
Affiliation(s)
- Tomaž Rijavec
- Institute of Metagenomics and Microbial TechnologiesLjubljana, Slovenia; Department of Environmental Sciences, Jožef Stefan InstituteLjubljana, Slovenia
| | - Aleš Lapanje
- Institute of Metagenomics and Microbial TechnologiesLjubljana, Slovenia; Department of Environmental Sciences, Jožef Stefan InstituteLjubljana, Slovenia; Remote Controlled Theranostic Systems Lab, Saratov State UniversitySaratov, Russia
| |
Collapse
|
71
|
The Diguanylate Cyclase HsbD Intersects with the HptB Regulatory Cascade to Control Pseudomonas aeruginosa Biofilm and Motility. PLoS Genet 2016; 12:e1006354. [PMID: 27792789 PMCID: PMC5085249 DOI: 10.1371/journal.pgen.1006354] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 09/09/2016] [Indexed: 11/19/2022] Open
Abstract
The molecular basis of second messenger signaling relies on an array of proteins that synthesize, degrade or bind the molecule to produce coherent functional outputs. Cyclic di-GMP (c-di-GMP) has emerged as a eubacterial nucleotide second messenger regulating a plethora of key behaviors, like the transition from planktonic cells to biofilm communities. The striking multiplicity of c-di-GMP control modules and regulated cellular functions raised the question of signaling specificity. Are c-di-GMP signaling routes exclusively dependent on a central hub or can they be locally administrated? In this study, we show an example of how c-di-GMP signaling gains output specificity in Pseudomonas aeruginosa. We observed the occurrence in P. aeruginosa of a c-di-GMP synthase gene, hsbD, in the proximity of the hptB and flagellar genes cluster. We show that the HptB pathway controls biofilm formation and motility by involving both HsbD and the anti-anti-sigma factor HsbA. The rewiring of c-di-GMP signaling into the HptB cascade relies on the original interaction between HsbD and HsbA and on the control of HsbD dynamic localization at the cell poles.
Collapse
|
72
|
Expression of multiple cbb3 cytochrome c oxidase isoforms by combinations of multiple isosubunits in Pseudomonas aeruginosa. Proc Natl Acad Sci U S A 2016; 113:12815-12819. [PMID: 27791152 DOI: 10.1073/pnas.1613308113] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The ubiquitous opportunistic human pathogen Pseudomonas aeruginosa has five terminal oxidases for aerobic respiration and uses them under different growth conditions. Two of them are cbb3-type cytochrome c oxidases encoded by the gene clusters ccoN1O1Q1P1 and ccoN2O2Q2P2, which are the main terminal oxidases under high- and low-oxygen conditions, respectively. P. aeruginosa also has two orphan gene clusters, ccoN3Q3 and ccoN4Q4, encoding the core catalytic CcoN isosubunits, but the roles of these genes have not been clarified. We found that 16 active cbb3 isoforms could be produced by combinations of four CcoN, two CcoO, and two CcoP isosubunits. The CcoN3- or CcoN4-containing isoforms were produced in the WT cell membrane in response to nitrite and cyanide, respectively. The strains carrying these isoforms were more resistant to nitrite or cyanide under low-oxygen conditions. These results indicate that P. aeruginosa gains resistance to respiratory inhibitors using multiple cbb3 isoforms with different features, which are produced through exchanges of multiple core catalytic isosubunits.
Collapse
|
73
|
Corral Lugo A, Daddaoua A, Ortega A, Morel B, Díez Peña AI, Espinosa-Urgel M, Krell T. Purification and characterization of Pseudomonas aeruginosa LasR expressed in acyl-homoserine lactone free Escherichia coli cultures. Protein Expr Purif 2016; 130:107-114. [PMID: 27756565 DOI: 10.1016/j.pep.2016.10.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 10/06/2016] [Accepted: 10/14/2016] [Indexed: 11/25/2022]
Abstract
Quorum sensing systems are essential for bacterial communication. We report here the purification and characterization of the Pseudomonas aeruginosa LasR quorum sensing regulator purified from lysates of E. coli cultures grown in the absence of added acyl-homoserine lactones (AHL). We show by isothermal titration calorimetry that LasR recognizes different AHLs with an affinity of approximately 1 μM. The affinity of LasR for its cognate 3-Oxo-C12-AHL was similar to that of other AHLs, indicating that this regulator has not evolved to preferentially recognize its cognate AHL. The α-helical content as determined by CD spectroscopy was found to be in agreement with the corresponding value derived from the homology model. Analytical ultracentrifugation studies show that LasR is a mixture of monomers and dimers and that AHL binding does not alter its oligomeric state. Thermal unfolding studies indicate that LasR has a significant thermal stability and that AHL binding does not significantly alter the unfolding temperature. Two LasR-DNA complexes were observed in electrophoretic mobility shift assays using the hcnABC promoter that has two lux boxes. Taken together, data indicate that the presence of AHLs is not a requisite for correct LasR protein folding. The protein is able to bind AHL ligands in a reversible manner, revising initial concepts of this regulator. The availability of AHL-free protein will permit further studies to determine more precisely its mode of action.
Collapse
Affiliation(s)
- Andrés Corral Lugo
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/ Prof. Albareda, 1, 18008 Granada, Spain
| | - Abdelali Daddaoua
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/ Prof. Albareda, 1, 18008 Granada, Spain
| | - Alvaro Ortega
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/ Prof. Albareda, 1, 18008 Granada, Spain
| | - Bertrand Morel
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/ Prof. Albareda, 1, 18008 Granada, Spain
| | - Ana Isabel Díez Peña
- Department of Physical Chemistry, Faculty of Chemistry, Regional Campus of International Excellence "Campus Mare Nostrum", University of Murcia, 30071 Murcia, Spain
| | - Manuel Espinosa-Urgel
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/ Prof. Albareda, 1, 18008 Granada, Spain
| | - Tino Krell
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/ Prof. Albareda, 1, 18008 Granada, Spain.
| |
Collapse
|
74
|
Sethupathy S, Prasath KG, Ananthi S, Mahalingam S, Balan SY, Pandian SK. Proteomic analysis reveals modulation of iron homeostasis and oxidative stress response in Pseudomonas aeruginosa PAO1 by curcumin inhibiting quorum sensing regulated virulence factors and biofilm production. J Proteomics 2016; 145:112-126. [DOI: 10.1016/j.jprot.2016.04.019] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Revised: 04/15/2016] [Accepted: 04/17/2016] [Indexed: 01/01/2023]
|
75
|
Metabolism and Pathogenicity of Pseudomonas aeruginosa Infections in the Lungs of Individuals with Cystic Fibrosis. Microbiol Spectr 2016; 3. [PMID: 26350318 DOI: 10.1128/microbiolspec.mbp-0003-2014] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Individuals with the genetic disease cystic fibrosis (CF) accumulate mucus or sputum in their lungs. This sputum is a potent growth substrate for a range of potential pathogens, and the opportunistic bacterium Pseudomonas aeruginosa is generally most difficult of these to eradicate. As a result, P. aeruginosa infections are frequently maintained in the CF lung throughout life, and are the leading cause of death for these individuals. While great effort has been expended to better understand and treat these devastating infections, only recently have researchers begun to rigorously examine the roles played by specific nutrients in CF sputum to cue P. aeruginosa pathogenicity. This chapter summarizes the current state of knowledge regarding how P. aeruginosa metabolism in CF sputum affects initiation and maintenance of these infections. It contains an overview of CF lung disease and the mechanisms of P. aeruginosa pathogenicity. Several model systems used to study these infections are described with emphasis on the challenge of replicating the chronic infections observed in humans with CF. Nutrients present in CF sputum are surveyed, and the impacts of these nutrients on the infection are discussed. The chapter concludes by addressing the future of this line of research including the use of next-generation technologies and the potential for metabolism-based therapeutics.
Collapse
|
76
|
Biotechnological potential of a rhizosphere Pseudomonas aeruginosa strain producing phenazine-1-carboxylic acid and phenazine-1-carboxamide. World J Microbiol Biotechnol 2016; 32:50. [DOI: 10.1007/s11274-015-1987-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 11/26/2015] [Indexed: 12/31/2022]
|
77
|
Chowdhury N, Bagchi A. Molecular insight into the activity of LasR protein from Pseudomonas aeruginosa in the regulation of virulence gene expression by this organism. Gene 2016; 580:80-7. [PMID: 26768577 DOI: 10.1016/j.gene.2015.12.067] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 11/09/2015] [Accepted: 12/30/2015] [Indexed: 10/22/2022]
Abstract
Pseudomonas aeruginosa is an opportunistic human pathogen. This organism attacks human patients suffering from diseases like AIDS, cancer, cystic fibrosis, etc. One of the important virulent factors produced by this organism is Hydrogen Cyanide. This is expressed from the genes encoded by the hcnABC operon. The expressions of the genes encoded by hcnABC operon are mediated mainly by the interactions of LasR protein with the corresponding promoter region of the hcnABC operon. The LasR protein acts as a dimer and binds to the promoter DNA with the help of an autoinducer ligand. However, till date the detailed molecular mechanism of how the LasR protein interacts with the promoter DNA is not clearly known. Therefore, in this work, an attempt has been made to analyze the mode of interactions of the LasR protein with the promoter DNA region of the hcnABC operon. We analyzed the three dimensional structure of the LasR protein from Pseudomonas aeruginosa and docked the protein with the autoinducer ligand. We then docked the ligand-bound-LasR-protein as well the LasR-protein-without-the-autoinducer-ligand on to the promoter DNA region of hcnABC operon. We analyzed the details of the interaction profiles of LasR protein with the autoinducer ligand. We also deciphered the details of the LasR promoter-DNA interactions. We compared the modes of DNA bindings by the LasR protein in presence and absence of the autoinducer ligand and tried to analyze the molecular details of the binding of LasR protein with the promoter DNA region of hcnABC operon during hcnABC gene expression. This study may therefore pave the pathway for future experiments to determine the relative effects of the amino acid residues of LasR protein in DNA binding during the transcription of hcnABC operon.
Collapse
Affiliation(s)
- Nilkanta Chowdhury
- Department of Biochemistry and Biophysics, University of Kalyani, Kalyani, Nadia 741235, India
| | - Angshuman Bagchi
- Department of Biochemistry and Biophysics, University of Kalyani, Kalyani, Nadia 741235, India.
| |
Collapse
|
78
|
Corral-Lugo A, Daddaoua A, Ortega A, Espinosa-Urgel M, Krell T. Rosmarinic acid is a homoserine lactone mimic produced by plants that activates a bacterial quorum-sensing regulator. Sci Signal 2016; 9:ra1. [PMID: 26732761 DOI: 10.1126/scisignal.aaa8271] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023]
Abstract
Quorum sensing is a bacterial communication mechanism that controls genes, enabling bacteria to live as communities, such as biofilms. Homoserine lactone (HSL) molecules function as quorum-sensing signals for Gram-negative bacteria. Plants also produce previously unidentified compounds that affect quorum sensing. We identified rosmarinic acid as a plant-derived compound that functioned as an HSL mimic. In vitro assays showed that rosmarinic acid bound to the quorum-sensing regulator RhlR of Pseudomonas aeruginosa PAO1 and competed with the bacterial ligand N-butanoyl-homoserine lactone (C4-HSL). Furthermore, rosmarinic acid stimulated a greater increase in RhlR-mediated transcription in vitro than that of C4-HSL. In P. aeruginosa, rosmarinic acid induced quorum sensing-dependent gene expression and increased biofilm formation and the production of the virulence factors pyocyanin and elastase. Because P. aeruginosa PAO1 infection induces rosmarinic acid secretion from plant roots, our results indicate that rosmarinic acid secretion is a plant defense mechanism to stimulate a premature quorum-sensing response. P. aeruginosa is a ubiquitous pathogen that infects plants and animals; therefore, identification of rosmarinic acid as an inducer of premature quorum-sensing responses may be useful in agriculture and inform human therapeutic strategies.
Collapse
Affiliation(s)
- Andrés Corral-Lugo
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/ Prof. Albareda, 1, 18008 Granada, Spain
| | - Abdelali Daddaoua
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/ Prof. Albareda, 1, 18008 Granada, Spain
| | - Alvaro Ortega
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/ Prof. Albareda, 1, 18008 Granada, Spain
| | - Manuel Espinosa-Urgel
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/ Prof. Albareda, 1, 18008 Granada, Spain
| | - Tino Krell
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/ Prof. Albareda, 1, 18008 Granada, Spain.
| |
Collapse
|
79
|
Lidor O, Al-Quntar A, Pesci EC, Steinberg D. Mechanistic analysis of a synthetic inhibitor of the Pseudomonas aeruginosa LasI quorum-sensing signal synthase. Sci Rep 2015; 5:16569. [PMID: 26593271 PMCID: PMC4655403 DOI: 10.1038/srep16569] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 10/14/2015] [Indexed: 01/24/2023] Open
Abstract
Pseudomonas aeruginosa is an opportunistic Gram-negative pathogen responsible for many human infections. LasI is an acyl-homoserine lactone synthase that produces a quorum-sensing (QS) signal that positively regulates numerous P. aeruginosa virulence determinants. The inhibition of the LasI protein is therefore an attractive drug target. In this study, a novel in silico to in vitro complementation was applied to screen thiazolidinedione-type compounds for their ability to inhibit biofilm formation at concentrations not affecting bacterial growth. The compound (z)-5-octylidenethiazolidine-2, 4-dione (TZD-C8) was a strong inhibitor of biofilm formation and chosen for further study. Structural exploration of in silico docking predicted that the compound had high affinity for the LasI activity pocket. The TZD-C8 compound was also predicted to create hydrogen bonds with residues Arg30 and Ile107. Site-directed mutagenesis (SDM) of these two sites demonstrated that TZD-C8 inhibition was abolished in the lasI double mutant PAO-R30D, I107S. In addition, in vitro swarming motility and quorum sensing signal production were affected by TZD-C 8, confirming this compound alters the cell to cell signalling circuitry. Overall, this novel inhibitor of P. aeruginosa quorum sensing shows great promise and validates our mechanistic approach to discovering inhibitors of LuxI-type acyl-homoserine lactone synthases.
Collapse
Affiliation(s)
- O. Lidor
- Biofilm Research Laboratory, Institute of Dental Sciences, Faculty of Dental Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - A. Al-Quntar
- Biofilm Research Laboratory, Institute of Dental Sciences, Faculty of Dental Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
- Institute of Drug Research, School of Pharmacy, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - E. C. Pesci
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, USA
| | - D. Steinberg
- Biofilm Research Laboratory, Institute of Dental Sciences, Faculty of Dental Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| |
Collapse
|
80
|
Engineering the central biosynthetic and secondary metabolic pathways of Pseudomonas aeruginosa strain PA1201 to improve phenazine-1-carboxylic acid production. Metab Eng 2015; 32:30-38. [PMID: 26369437 DOI: 10.1016/j.ymben.2015.09.003] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 08/10/2015] [Accepted: 09/02/2015] [Indexed: 11/24/2022]
Abstract
The secondary metabolite phenazine-1-carboxylic acid (PCA) is an important component of the newly registered biopesticide Shenqinmycin. We used a combined method involving gene, promoter, and protein engineering to modify the central biosynthetic and secondary metabolic pathways in the PCA-producing Pseudomonas aeruginosa strain PA1201. The PCA yield of the resulting strain PA-IV was increased 54.6-fold via the following strategies: (1) blocking PCA conversion and enhancing PCA efflux pumping; (2) increasing metabolic flux towards the PCA biosynthetic pathway through the over-production of two DAHP synthases and blocking the synthesis of 21 secondary metabolites; (3) increasing the PCA precursor supply through the engineering of five chorismate-utilizing enzymes; (4) engineering the promoters of two PCA biosynthetic gene clusters. Strain PA-IV produced 9882 mg/L PCA in fed-batch fermentation, which is twice as much as that produced by the current industrial strain. Strain PA-IV was also genetically stable and comparable to Escherichia coli in cytotoxicity.
Collapse
|
81
|
Plyuta VA, Lipasova VA, Koksharova OA, Veselova MA, Kuznetsov AE, Khmel IA. The effect of introduction of the Heterologous gene encoding the N-acyl-homoserine lactonase (aiiA) on the properties of Burkholderia cenocepacia 370. RUSS J GENET+ 2015. [DOI: 10.1134/s1022795415080062] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
|
82
|
Quorum Sensing Protects Pseudomonas aeruginosa against Cheating by Other Species in a Laboratory Coculture Model. J Bacteriol 2015. [PMID: 26195596 DOI: 10.1128/jb.00482-15] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Many species of bacteria use a cell-cell communication system called quorum sensing (QS) to coordinate group activities. QS systems frequently regulate the production of exoproducts. Some of these products, such as proteases, are "public goods" that are shared among the population and vulnerable to cheating by nonproducing members of the population. Because the QS system of the opportunistic pathogen Pseudomonas aeruginosa regulates several public goods, it can serve as a model for studying cooperation. Bacteria also commonly regulate antimicrobial production through QS. In this study, we focused on the hypothesis that QS-regulated antimicrobials may be important for P. aeruginosa to protect against cheating by another bacterial species, Burkholderia multivorans. We assessed laboratory cocultures of P. aeruginosa and B. multivorans and investigated the importance of three P. aeruginosa QS-regulated antimicrobials, hydrogen cyanide, rhamnolipids, and phenazines, for competition. We found that P. aeruginosa dominates cocultures with B. multivorans and that the three antimicrobials together promote P. aeruginosa competitiveness, with hydrogen cyanide contributing the greatest effect. We show that these QS-regulated antimicrobials are also critical for P. aeruginosa to prevent B. multivorans from cheating under nutrient conditions where both species require a P. aeruginosa quorum-regulated protease for growth. Together our results highlight the importance of antimicrobials in protecting cooperating populations from exploitation by other species that can act as cheaters. IMPORTANCE Cooperative behaviors are threatened by social cheating, wherein individuals do not produce but nonetheless benefit from shared public goods. Bacteria have been shown to use several genetic mechanisms to restrain the emergence of cheaters from within the population, but public goods might also be used by other bacterial species in the vicinity. We demonstrate that a public good produced by Pseudomonas aeruginosa can be used by another species, Burkholderia multivorans, to obtain carbon and energy. We also show that P. aeruginosa antimicrobials that are coregulated with the public good prevent invasion by the cheating species. Our results demonstrate that cross-species cheating can occur and that coregulation of public goods with antimicrobials may stabilize cooperative behavior in mixed microbial communities.
Collapse
|
83
|
Pyoverdine and proteases affect the response of Pseudomonas aeruginosa to gallium in human serum. Antimicrob Agents Chemother 2015; 59:5641-6. [PMID: 26149986 DOI: 10.1128/aac.01097-15] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 06/26/2015] [Indexed: 11/20/2022] Open
Abstract
Gallium is an iron mimetic which has recently been repurposed as an antibacterial agent due to its capability to disrupt bacterial iron metabolism. In this study, the antibacterial activity of gallium nitrate [Ga(NO3)3] was investigated in complement-free human serum (HS) on 55 Pseudomonas aeruginosa clinical isolates from cystic fibrosis and non-cystic fibrosis patients. The susceptibility of P. aeruginosa to Ga(NO3)3 in HS was dependent on the bacterial ability to acquire iron from serum binding proteins (i.e., transferrin). The extent of serum protein degradation correlated well with P. aeruginosa growth in HS, while pyoverdine production did not. However, pyoverdine-deficient P. aeruginosa strains were unable to grow in HS and overcome iron restriction, albeit capable of releasing proteases. Predigestion of HS with proteinase K promoted the growth of all strains, irrespective of their ability to produce proteases and/or pyoverdine. The MICs of Ga(NO3)3 were higher in HS than in an iron-poor Casamino Acids medium, where proteolysis does not affect iron availability. Coherently, strains displaying high proteolytic activity were less susceptible to Ga(NO3)3 in HS. Our data support a model in which both pyoverdine and proteases affect the response of P. aeruginosa to Ga(NO3)3 in HS. The relatively high Ga(NO3)3 concentration required to inhibit the growth of highly proteolytic P. aeruginosa isolates in HS poses a limitation to the potential of Ga(NO3)3 in the treatment of P. aeruginosa bloodstream infections.
Collapse
|
84
|
Links between Anr and Quorum Sensing in Pseudomonas aeruginosa Biofilms. J Bacteriol 2015; 197:2810-20. [PMID: 26078448 DOI: 10.1128/jb.00182-15] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 06/10/2015] [Indexed: 12/23/2022] Open
Abstract
UNLABELLED In Pseudomonas aeruginosa, the transcription factor Anr controls the cellular response to low oxygen or anoxia. Anr activity is high in oxygen-limited environments, including biofilms and populations associated with chronic infections, and Anr is necessary for persistence in a model of pulmonary infection. In this study, we characterized the Anr regulon in biofilm-grown cells at 1% oxygen in the laboratory strain PAO1 and in a quorum sensing (QS)-deficient clinical isolate, J215. As expected, transcripts related to denitrification, arginine fermentation, high-affinity cytochrome oxidases, and CupA fimbriae were lower in the Δanr derivatives. In addition, we observed that transcripts associated with quorum sensing regulation, iron acquisition and storage, type VI secretion, and the catabolism of aromatic compounds were also differentially expressed in the Δanr strains. Prior reports have shown that quorum sensing-defective mutants have higher levels of denitrification, and we found that multiple Anr-regulated processes, including denitrification, were strongly inversely proportional to quorum sensing in both transcriptional and protein-based assays. We also found that in LasR-defective strains but not their LasR-intact counterparts, Anr regulated the production of the 4-hydroxy-2-alkylquinolines, which play roles in quorum sensing and interspecies interactions. These data show that Anr was required for the expression of important metabolic pathways in low-oxygen biofilms, and they reveal an expanded and compensatory role for Anr in the regulation of virulence-related genes in quorum sensing mutants, such as those commonly isolated from infections. IMPORTANCE Pseudomonas aeruginosa causes acute ocular, soft tissue, and pulmonary infections, as well as chronic infections in the airways of cystic fibrosis patients. P. aeruginosa uses quorum sensing (QS) to regulate virulence, but mutations in the gene encoding the master regulator of QS, lasR, are frequently observed in clinical isolates. We demonstrated that the regulon attributed to Anr, an oxygen-sensitive transcription factor, was more highly expressed in lasR mutants. Furthermore, we show that Anr regulates the production of several different secreted factors in lasR mutants. These data demonstrate the importance of Anr in naturally occurring quorum sensing mutants in the context of chronic infections.
Collapse
|
85
|
Volatile affairs in microbial interactions. ISME JOURNAL 2015; 9:2329-35. [PMID: 26023873 DOI: 10.1038/ismej.2015.42] [Citation(s) in RCA: 241] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Revised: 02/15/2015] [Accepted: 02/23/2015] [Indexed: 12/31/2022]
Abstract
Microorganisms are important factors in shaping our environment. One key characteristic that has been neglected for a long time is the ability of microorganisms to release chemically diverse volatile compounds. At present, it is clear that the blend of volatiles released by microorganisms can be very complex and often includes many unknown compounds for which the chemical structures remain to be elucidated. The biggest challenge now is to unravel the biological and ecological functions of these microbial volatiles. There is increasing evidence that microbial volatiles can act as infochemicals in interactions among microbes and between microbes and their eukaryotic hosts. Here, we review and discuss recent advances in understanding the natural roles of volatiles in microbe-microbe interactions. Specific emphasis will be given to the antimicrobial activities of microbial volatiles and their effects on bacterial quorum sensing, motility, gene expression and antibiotic resistance.
Collapse
|
86
|
Mousa WK, Raizada MN. Biodiversity of genes encoding anti-microbial traits within plant associated microbes. FRONTIERS IN PLANT SCIENCE 2015; 6:231. [PMID: 25914708 PMCID: PMC4392301 DOI: 10.3389/fpls.2015.00231] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 03/23/2015] [Indexed: 05/10/2023]
Abstract
The plant is an attractive versatile home for diverse associated microbes. A subset of these microbes produces a diversity of anti-microbial natural products including polyketides, non-ribosomal peptides, terpenoids, heterocylic nitrogenous compounds, volatile compounds, bacteriocins, and lytic enzymes. In recent years, detailed molecular analysis has led to a better understanding of the underlying genetic mechanisms. New genomic and bioinformatic tools have permitted comparisons of orthologous genes between species, leading to predictions of the associated evolutionary mechanisms responsible for diversification at the genetic and corresponding biochemical levels. The purpose of this review is to describe the biodiversity of biosynthetic genes of plant-associated bacteria and fungi that encode selected examples of antimicrobial natural products. For each compound, the target pathogen and biochemical mode of action are described, in order to draw attention to the complexity of these phenomena. We review recent information of the underlying molecular diversity and draw lessons through comparative genomic analysis of the orthologous coding sequences (CDS). We conclude by discussing emerging themes and gaps, discuss the metabolic pathways in the context of the phylogeny and ecology of their microbial hosts, and discuss potential evolutionary mechanisms that led to the diversification of biosynthetic gene clusters.
Collapse
Affiliation(s)
- Walaa K. Mousa
- Department of Plant Agriculture, University of GuelphGuelph, ON, Canada
- Department of Pharmacognosy, Faculty of Pharmacy, Mansoura UniversityMansoura, Egypt
| | - Manish N. Raizada
- Department of Plant Agriculture, University of GuelphGuelph, ON, Canada
| |
Collapse
|
87
|
Kuroki M, Igarashi Y, Ishii M, Arai H. Fine-tuned regulation of the dissimilatory nitrite reductase gene by oxygen and nitric oxide in Pseudomonas aeruginosa. ENVIRONMENTAL MICROBIOLOGY REPORTS 2014; 6:792-801. [PMID: 25186017 DOI: 10.1111/1758-2229.12212] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Revised: 08/21/2014] [Accepted: 08/23/2014] [Indexed: 06/03/2023]
Abstract
Nitrite reductase (NIR) catalyses the reduction of nitrite to nitric oxide (NO) in the denitrification pathway. In Pseudomonas aeruginosa, expression of the gene encoding NIR (nirS) is induced by NO and is under control of the NO-sensing regulator DNR (dissimilatory nitrate respiration regulator). Because DNR is under control of the oxygen-sensing regulator ANR (anaerobic regulator of arginine deiminase and nitrate reductase), nirS is expressed only under low oxygen and anaerobic conditions. Both ANR and DNR are FNR (fumarate and nitrate reductase regulator)-type regulators and recognize the consensus FNR-binding motif. The motif of the nirS promoter is thought to be recognized only by DNR, and not by ANR. Here, mutant strains expressing either ANR or DNR were constructed and used to analyse the role of ANR and DNR in the activation of nirS expression. Analysis of transcriptional activity by microarray and quantitative reverse transcription polymerase chain reaction revealed that nirS is transcribed under low oxygen conditions in an ANR-dependent manner, although the expression level was 10-fold lower than that of the DNR-dependent expression. An artificial promoter containing the FNR-binding motif of the nirS promoter was also twofold upregulated by ANR. These results indicate that low-level expression of NIR in the presence of nitrite may provide NO as a trigger for the full expression of denitrification genes when oxygen is depleted.
Collapse
Affiliation(s)
- Miho Kuroki
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan
| | | | | | | |
Collapse
|
88
|
The hierarchy quorum sensing network in Pseudomonas aeruginosa. Protein Cell 2014; 6:26-41. [PMID: 25249263 PMCID: PMC4286720 DOI: 10.1007/s13238-014-0100-x] [Citation(s) in RCA: 747] [Impact Index Per Article: 74.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 08/28/2014] [Indexed: 12/13/2022] Open
Abstract
Pseudomonas aeruginosa causes severe and persistent infections in immune compromised individuals and cystic fibrosis sufferers. The infection is hard to eradicate as P. aeruginosa has developed strong resistance to most conventional antibiotics. The problem is further compounded by the ability of the pathogen to form biofilm matrix, which provides bacterial cells a protected environment withstanding various stresses including antibiotics. Quorum sensing (QS), a cell density-based intercellular communication system, which plays a key role in regulation of the bacterial virulence and biofilm formation, could be a promising target for developing new strategies against P. aeruginosa infection. The QS network of P. aeruginosa is organized in a multi-layered hierarchy consisting of at least four interconnected signaling mechanisms. Evidence is accumulating that the QS regulatory network not only responds to bacterial population changes but also could react to environmental stress cues. This plasticity should be taken into consideration during exploration and development of anti-QS therapeutics.
Collapse
|
89
|
Valentini M, García-Mauriño SM, Pérez-Martínez I, Santero E, Canosa I, Lapouge K. Hierarchical management of carbon sources is regulated similarly by the CbrA/B systems in Pseudomonas aeruginosa and Pseudomonas putida. MICROBIOLOGY-SGM 2014; 160:2243-2252. [PMID: 25031426 DOI: 10.1099/mic.0.078873-0] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The CbrA/B system in pseudomonads is involved in the utilization of carbon sources and carbon catabolite repression (CCR) through the activation of the small RNAs crcZ in Pseudomonas aeruginosa, and crcZ and crcY in Pseudomonas putida. Interestingly, previous works reported that the CbrA/B system activity in P. aeruginosa PAO1 and P. putida KT2442 responded differently to the presence of different carbon sources, thus raising the question of the exact nature of the signal(s) detected by CbrA. Here, we demonstrated that the CbrA/B/CrcZ(Y) signal transduction pathway is similarly activated in the two Pseudomonas species. We show that the CbrA sensor kinase is fully interchangeable between the two species and, moreover, responds similarly to the presence of different carbon sources. In addition, a metabolomics analysis supported the hypothesis that CCR responds to the internal energy status of the cell, as the internal carbon/nitrogen ratio seems to determine CCR and non-CCR conditions. The strong difference found in the 2-oxoglutarate/glutamine ratio between CCR and non-CCR conditions points to the close relationship between carbon and nitrogen availability, or the relationship between the CbrA/B and NtrB/C systems, suggesting that both regulatory systems sense the same sort or interrelated signal.
Collapse
Affiliation(s)
- Martina Valentini
- Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Sofía M García-Mauriño
- Centro Andaluz de Biología del Desarollo/CSIC/Universidad Pablo de Olavide, 41013 Seville, Spain
| | - Isabel Pérez-Martínez
- Centro Andaluz de Biología del Desarollo/CSIC/Universidad Pablo de Olavide, 41013 Seville, Spain
| | - Eduardo Santero
- Centro Andaluz de Biología del Desarollo/CSIC/Universidad Pablo de Olavide, 41013 Seville, Spain
| | - Inés Canosa
- Centro Andaluz de Biología del Desarollo/CSIC/Universidad Pablo de Olavide, 41013 Seville, Spain
| | - Karine Lapouge
- Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland
| |
Collapse
|
90
|
Okkotsu Y, Little AS, Schurr MJ. The Pseudomonas aeruginosa AlgZR two-component system coordinates multiple phenotypes. Front Cell Infect Microbiol 2014; 4:82. [PMID: 24999454 PMCID: PMC4064291 DOI: 10.3389/fcimb.2014.00082] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 06/02/2014] [Indexed: 01/28/2023] Open
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen that causes a multitude of infections. These infections can occur at almost any site in the body and are usually associated with a breach of the innate immune system. One of the prominent sites where P. aeruginosa causes chronic infections is within the lungs of cystic fibrosis patients. P. aeruginosa uses two-component systems that sense environmental changes to differentially express virulence factors that cause both acute and chronic infections. The P. aeruginosa AlgZR two component system is one of its global regulatory systems that affects the organism's fitness in a broad manner. This two-component system is absolutely required for two P. aeruginosa phenotypes: twitching motility and alginate production, indicating its importance in both chronic and acute infections. Additionally, global transcriptome analyses indicate that it regulates the expression of many different genes, including those associated with quorum sensing, type IV pili, type III secretion system, anaerobic metabolism, cyanide and rhamnolipid production. This review examines the complex AlgZR regulatory network, what is known about the structure and function of each protein, and how it relates to the organism's ability to cause infections.
Collapse
Affiliation(s)
- Yuta Okkotsu
- Department of Microbiology, University of Colorado School of Medicine Aurora, CO, USA
| | - Alexander S Little
- Department of Microbiology, University of Colorado School of Medicine Aurora, CO, USA
| | - Michael J Schurr
- Department of Microbiology, University of Colorado School of Medicine Aurora, CO, USA
| |
Collapse
|
91
|
Ryall B, Carrara M, Zlosnik JEA, Behrends V, Lee X, Wong Z, Lougheed KE, Williams HD. The mucoid switch in Pseudomonas aeruginosa represses quorum sensing systems and leads to complex changes to stationary phase virulence factor regulation. PLoS One 2014; 9:e96166. [PMID: 24852379 PMCID: PMC4031085 DOI: 10.1371/journal.pone.0096166] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Accepted: 04/03/2014] [Indexed: 01/04/2023] Open
Abstract
The opportunistic pathogen Pseudomonas aeruginosa chronically infects the airways of Cystic Fibrosis (CF) patients during which it adapts and undergoes clonal expansion within the lung. It commonly acquires inactivating mutations of the anti-sigma factor MucA leading to a mucoid phenotype, caused by excessive production of the extracellular polysaccharide alginate that is associated with a decline in lung function. Alginate production is believed to be the key benefit of mucA mutations to the bacterium in the CF lung. A phenotypic and gene expression characterisation of the stationary phase physiology of mucA22 mutants demonstrated complex and subtle changes in virulence factor production, including cyanide and pyocyanin, that results in their down-regulation upon entry into stationary phase but, (and in contrast to wildtype strains) continued production in prolonged stationary phase. These findings may have consequences for chronic infection if mucoid P. aeruginosa were to continue to make virulence factors under non-growing conditions during infection. These changes resulted in part from a severe down-regulation of both AHL-and AQ (PQS)-dependent quorum sensing systems. In trans expression of the cAMP-dependent transcription factor Vfr restored both quorum sensing defects and virulence factor production in early stationary phase. Our findings have implications for understanding the evolution of P. aeruginosa during CF lung infection and it demonstrates that mucA22 mutation provides a second mechanism, in addition to the commonly occurring lasR mutations, of down-regulating quorum sensing during chronic infection this may provide a selection pressure for the mucoid switch in the CF lung.
Collapse
Affiliation(s)
- Ben Ryall
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, Sir Alexander Fleming Building, London, United Kingdom
| | - Marta Carrara
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, Sir Alexander Fleming Building, London, United Kingdom
| | - James E. A. Zlosnik
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, Sir Alexander Fleming Building, London, United Kingdom
| | - Volker Behrends
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, Sir Alexander Fleming Building, London, United Kingdom
- Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, Sir Alexander Fleming Building, London, United Kingdom
| | - Xiaoyun Lee
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, Sir Alexander Fleming Building, London, United Kingdom
| | - Zhen Wong
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, Sir Alexander Fleming Building, London, United Kingdom
| | - Kathryn E. Lougheed
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, Sir Alexander Fleming Building, London, United Kingdom
| | - Huw D. Williams
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, Sir Alexander Fleming Building, London, United Kingdom
- * E-mail:
| |
Collapse
|
92
|
Spence C, Alff E, Johnson C, Ramos C, Donofrio N, Sundaresan V, Bais H. Natural rice rhizospheric microbes suppress rice blast infections. BMC PLANT BIOLOGY 2014; 14:130. [PMID: 24884531 PMCID: PMC4036093 DOI: 10.1186/1471-2229-14-130] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Accepted: 04/28/2014] [Indexed: 05/20/2023]
Abstract
BACKGROUND The natural interactions between plant roots and their rhizospheric microbiome are vital to plant fitness, modulating both growth promotion and disease suppression. In rice (Oryza sativa), a globally important food crop, as much as 30% of yields are lost due to blast disease caused by fungal pathogen Magnaporthe oryzae. Capitalizing on the abilities of naturally occurring rice soil bacteria to reduce M. oryzae infections could provide a sustainable solution to reduce the amount of crops lost to blast disease. RESULTS Naturally occurring root-associated rhizospheric bacteria were isolated from California field grown rice plants (M-104), eleven of which were taxonomically identified by 16S rRNA gene sequencing and fatty acid methyl ester (FAME) analysis. Bacterial isolates were tested for biocontrol activity against the devastating foliar rice fungal pathogen, M. oryzae pathovar 70-15. In vitro, a Pseudomonas isolate, EA105, displayed antibiosis through reducing appressoria formation by nearly 90% as well as directly inhibiting fungal growth by 76%. Although hydrogen cyanide (HCN) is a volatile commonly produced by biocontrol pseudomonads, the activity of EA105 seems to be independent of its HCN production. During in planta experiments, EA105 reduced the number of blast lesions formed by 33% and Pantoea agglomerans isolate, EA106 by 46%. Our data also show both EA105 and EA106 trigger jasmonic acid (JA) and ethylene (ET) dependent induced systemic resistance (ISR) response in rice. CONCLUSIONS Out of 11 bacteria isolated from rice soil, pseudomonad EA105 most effectively inhibited the growth and appressoria formation of M. oryzae through a mechanism that is independent of cyanide production. In addition to direct antagonism, EA105 also appears to trigger ISR in rice plants through a mechanism that is dependent on JA and ET signaling, ultimately resulting in fewer blast lesions. The application of native bacteria as biocontrol agents in combination with current disease protection strategies could aid in global food security.
Collapse
Affiliation(s)
- Carla Spence
- Department of Biological Sciences, University of Delaware, Newark, USA
- Delaware Biotechnology Institute, Newark, USA
| | - Emily Alff
- Delaware Biotechnology Institute, Newark, USA
- Department of Plant and Soil Sciences, University of Delaware, Newark, USA
| | - Cameron Johnson
- Department of Plant Biology, University of California, Davis, USA
| | - Cassandra Ramos
- Department of Plant Biology, University of California, Davis, USA
| | - Nicole Donofrio
- Department of Plant and Soil Sciences, University of Delaware, Newark, USA
| | | | - Harsh Bais
- Delaware Biotechnology Institute, Newark, USA
- Department of Plant and Soil Sciences, University of Delaware, Newark, USA
| |
Collapse
|
93
|
Dingemans J, Ye L, Hildebrand F, Tontodonati F, Craggs M, Bilocq F, De Vos D, Crabbé A, Van Houdt R, Malfroot A, Cornelis P. The deletion of TonB-dependent receptor genes is part of the genome reduction process that occurs during adaptation of Pseudomonas aeruginosa to the cystic fibrosis lung. Pathog Dis 2014; 71:26-38. [PMID: 24659602 DOI: 10.1111/2049-632x.12170] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Revised: 03/12/2014] [Accepted: 03/13/2014] [Indexed: 01/02/2023] Open
Abstract
Chronic Pseudomonas aeruginosa infections are the main cause of morbidity among patients with cystic fibrosis (CF) due to persistent lung inflammation caused by interaction between this bacterium and the immune system. Longitudinal studies of clonally related isolates of a dominant CF clone have indicated that genome reduction frequently occurs during adaptation of P. aeruginosa in the CF lung. In this study, we have evaluated the P. aeruginosa population structure of patients attending the Universitair Ziekenhuis Brussel (UZ Brussel) CF reference center using a combination of genotyping methods. Although the UZ Brussel P. aeruginosa CF population is characterized by the absence of a dominant CF clone, some potential interpatient transmissions could be detected. Interestingly, one of these clones showed deletion of the alternative type I ferripyoverdine receptor gene fpvB. Furthermore, we found that several other TonB-dependent receptors are deleted as well. The genome of one potentially transmissible CF clone was sequenced, revealing large deleted regions including all type III secretion system genes and several virulence genes. Remarkably, a large number of deleted genes are shared between the P. aeruginosa CF clone described in this study and isolates belonging to the dominant Copenhagen CF DK2 clone, suggesting parallel evolution.
Collapse
Affiliation(s)
- Jozef Dingemans
- Department of Bioengineering Sciences, Research Group Microbiology, Vrije Universiteit Brussel and VIB Structural Biology, Brussels, Belgium; Unit of Microbiology, Expert Group Molecular and Cellular Biology, Institute for Environment, Health and Safety, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
94
|
Frangipani E, Pérez-Martínez I, Williams HD, Cherbuin G, Haas D. A novel cyanide-inducible gene cluster helps protect Pseudomonas aeruginosa from cyanide. ENVIRONMENTAL MICROBIOLOGY REPORTS 2014; 6:28-34. [PMID: 24596260 DOI: 10.1111/1758-2229.12105] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Revised: 08/03/2013] [Accepted: 09/13/2013] [Indexed: 06/03/2023]
Abstract
Pseudomonas aeruginosa produces the toxic secondary metabolite hydrogen cyanide (HCN) at high cell population densities and low aeration. Here, we investigated the impact of HCN as a signal in cell-cell communication by comparing the transcriptome of the wild-type strain PAO1 to that of an HCN-negative mutant under cyanogenic conditions. HCN repressed four genes and induced 12 genes. While the individual functions of these genes are unknown, with one exception (i.e. a ferredoxin-dependent reductase), a highly inducible six-gene cluster (PA4129-PA4134) was found to be crucial for protection of P. aeruginosa from external HCN intoxication. A double mutant deleted for PA4129-PA4134 and cioAB (encoding cyanide-insensitive oxidase) did not grow with 100 μM KCN, whereas the corresponding single mutants were essentially unaffected, suggesting a synergistic action of the PA4129-PA4134 gene products and cyanide-insensitive oxidase.
Collapse
Affiliation(s)
- Emanuela Frangipani
- Département de Microbiologie Fondamentale, Université de Lausanne, CH-1015, Lausanne, Switzerland
| | | | | | | | | |
Collapse
|
95
|
Husain FM, Ahmad I, Asif M, Tahseen Q. Influence of clove oil on certain quorum-sensing-regulated functions and biofilm of Pseudomonas aeruginosa and Aeromonas hydrophila. J Biosci 2013; 38:835-44. [DOI: 10.1007/s12038-013-9385-9] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
96
|
Banderas A, Guiliani N. Bioinformatic prediction of gene functions regulated by quorum sensing in the bioleaching bacterium Acidithiobacillus ferrooxidans. Int J Mol Sci 2013; 14:16901-16. [PMID: 23959118 PMCID: PMC3759942 DOI: 10.3390/ijms140816901] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Revised: 07/18/2013] [Accepted: 07/22/2013] [Indexed: 12/14/2022] Open
Abstract
The biomining bacterium Acidithiobacillus ferrooxidans oxidizes sulfide ores and promotes metal solubilization. The efficiency of this process depends on the attachment of cells to surfaces, a process regulated by quorum sensing (QS) cell-to-cell signalling in many Gram-negative bacteria. At. ferrooxidans has a functional QS system and the presence of AHLs enhances its attachment to pyrite. However, direct targets of the QS transcription factor AfeR remain unknown. In this study, a bioinformatic approach was used to infer possible AfeR direct targets based on the particular palindromic features of the AfeR binding site. A set of Hidden Markov Models designed to maintain palindromic regions and vary non-palindromic regions was used to screen for putative binding sites. By annotating the context of each predicted binding site (PBS), we classified them according to their positional coherence relative to other putative genomic structures such as start codons, RNA polymerase promoter elements and intergenic regions. We further used the Multiple EM for Motif Elicitation algorithm (MEME) to further filter out low homology PBSs. In summary, 75 target-genes were identified, 34 of which have a higher confidence level. Among the identified genes, we found afeR itself, zwf, genes encoding glycosyltransferase activities, metallo-beta lactamases, and active transport-related proteins. Glycosyltransferases and Zwf (Glucose 6-phosphate-1-dehydrogenase) might be directly involved in polysaccharide biosynthesis and attachment to minerals by At. ferrooxidans cells during the bioleaching process.
Collapse
Affiliation(s)
- Alvaro Banderas
- Authors to whom correspondence should be addressed; E-Mails: (A.B.); (N.G.); Tel.: +49-06221-546846 (A.B.); +56-2-2978-7241 (N.G.)
| | - Nicolas Guiliani
- Laboratory of Bacterial Communication, Department of Biology, Faculty of Sciences, University of Chile, Santiago 780-0024, Chile
| |
Collapse
|
97
|
Dunlap WC, Starcevic A, Baranasic D, Diminic J, Zucko J, Gacesa R, van Oppen MJH, Hranueli D, Cullum J, Long PF. KEGG orthology-based annotation of the predicted proteome of Acropora digitifera: ZoophyteBase - an open access and searchable database of a coral genome. BMC Genomics 2013; 14:509. [PMID: 23889801 PMCID: PMC3750612 DOI: 10.1186/1471-2164-14-509] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Accepted: 07/15/2013] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Contemporary coral reef research has firmly established that a genomic approach is urgently needed to better understand the effects of anthropogenic environmental stress and global climate change on coral holobiont interactions. Here we present KEGG orthology-based annotation of the complete genome sequence of the scleractinian coral Acropora digitifera and provide the first comprehensive view of the genome of a reef-building coral by applying advanced bioinformatics. DESCRIPTION Sequences from the KEGG database of protein function were used to construct hidden Markov models. These models were used to search the predicted proteome of A. digitifera to establish complete genomic annotation. The annotated dataset is published in ZoophyteBase, an open access format with different options for searching the data. A particularly useful feature is the ability to use a Google-like search engine that links query words to protein attributes. We present features of the annotation that underpin the molecular structure of key processes of coral physiology that include (1) regulatory proteins of symbiosis, (2) planula and early developmental proteins, (3) neural messengers, receptors and sensory proteins, (4) calcification and Ca2+-signalling proteins, (5) plant-derived proteins, (6) proteins of nitrogen metabolism, (7) DNA repair proteins, (8) stress response proteins, (9) antioxidant and redox-protective proteins, (10) proteins of cellular apoptosis, (11) microbial symbioses and pathogenicity proteins, (12) proteins of viral pathogenicity, (13) toxins and venom, (14) proteins of the chemical defensome and (15) coral epigenetics. CONCLUSIONS We advocate that providing annotation in an open-access searchable database available to the public domain will give an unprecedented foundation to interrogate the fundamental molecular structure and interactions of coral symbiosis and allow critical questions to be addressed at the genomic level based on combined aspects of evolutionary, developmental, metabolic, and environmental perspectives.
Collapse
Affiliation(s)
- Walter C Dunlap
- Centre for Marine Microbiology and Genetics, Australian Institute of Marine Science, PMB No. 3 Townsville MC, Townsville 4810, Queensland, Australia
- Institute of Pharmaceutical Science, King’s College London, Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, United Kingdom
| | - Antonio Starcevic
- Section for Bioinformatics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Damir Baranasic
- Section for Bioinformatics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Janko Diminic
- Section for Bioinformatics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Jurica Zucko
- Section for Bioinformatics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Ranko Gacesa
- Section for Bioinformatics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Madeleine JH van Oppen
- Centre for Marine Microbiology and Genetics, Australian Institute of Marine Science, PMB No. 3 Townsville MC, Townsville 4810, Queensland, Australia
| | - Daslav Hranueli
- Section for Bioinformatics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - John Cullum
- Department of Genetics, University of Kaiserslautern, Postfach 3049, 67653 Kaiserslautern, Germany
| | - Paul F Long
- Institute of Pharmaceutical Science, King’s College London, Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, United Kingdom
- Department of Chemistry King’s College London, Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, United Kingdom
| |
Collapse
|
98
|
Groenhagen U, Baumgartner R, Bailly A, Gardiner A, Eberl L, Schulz S, Weisskopf L. Production of bioactive volatiles by different Burkholderia ambifaria strains. J Chem Ecol 2013; 39:892-906. [PMID: 23832658 DOI: 10.1007/s10886-013-0315-y] [Citation(s) in RCA: 130] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2013] [Revised: 06/14/2013] [Accepted: 06/24/2013] [Indexed: 12/28/2022]
Abstract
Increasing evidence indicates that volatile compounds emitted by bacteria can influence the growth of other organisms. In this study, the volatiles produced by three different strains of Burkholderia ambifaria were analysed and their effects on the growth of plants and fungi, as well as on the antibiotic resistance of target bacteria, were assessed. Burkholderia ambifaria emitted highly bioactive volatiles independently of the strain origin (clinical environment, rhizosphere of pea, roots of maize). These volatile blends induced significant biomass increase in the model plant Arabidopsis thaliana as well as growth inhibition of two phytopathogenic fungi (Rhizoctonia solani and Alternaria alternata). In Escherichia coli exposed to the volatiles of B. ambifaria, resistance to the aminoglycoside antibiotics gentamicin and kanamycin was found to be increased. The volatile blends of the three strains were similar, and dimethyl disulfide was the most abundant compound. Sulfur compounds, ketones, and aromatic compounds were major groups in all three volatile profiles. When applied as pure substance, dimethyl disulfide led to increased plant biomass, as did acetophenone and 3-hexanone. Significant fungal growth reduction was observed with high concentrations of dimethyl di- and trisulfide, 4-octanone, S-methyl methanethiosulphonate, 1-phenylpropan-1-one, and 2-undecanone, while dimethyl trisulfide, 1-methylthio-3-pentanone, and o-aminoacetophenone increased resistance of E. coli to aminoglycosides. Comparison of the volatile profile produced by an engineered mutant impaired in quorum-sensing (QS) signalling with the corresponding wild-type led to the conclusion that QS is not involved in the regulation of volatile production in B. ambifaria LMG strain 19182.
Collapse
Affiliation(s)
- Ulrike Groenhagen
- Institute of Organic Chemistry, Technische Universität Braunschweig, Hagenring 30, 38106, Braunschweig, Germany
| | | | | | | | | | | | | |
Collapse
|
99
|
Affiliation(s)
- Mohammad Asif
- Department of Pharmacy, GRD (PG) Institute of Management and Technology, Dehradun, Uttarakhand, India
| | | |
Collapse
|
100
|
Matcher GF, Jiwaji M, de la Mare JA, Dorrington RA. Complex pathways for regulation of pyrimidine metabolism by carbon catabolite repression and quorum sensing in Pseudomonas putida RU-KM3S. Appl Microbiol Biotechnol 2013; 97:5993-6007. [DOI: 10.1007/s00253-013-4862-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2013] [Accepted: 03/13/2013] [Indexed: 11/28/2022]
|