1
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Guo Y, Mao Z, Ran F, Sun J, Zhang J, Chai G, Wang J. Nanotechnology-Based Drug Delivery Systems to Control Bacterial-Biofilm-Associated Lung Infections. Pharmaceutics 2023; 15:2582. [PMID: 38004561 PMCID: PMC10674810 DOI: 10.3390/pharmaceutics15112582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/09/2023] [Accepted: 10/17/2023] [Indexed: 11/26/2023] Open
Abstract
Airway mucus dysfunction and impaired immunological defenses are hallmarks of several lung diseases, including asthma, cystic fibrosis, and chronic obstructive pulmonary diseases, and are mostly causative factors in bacterial-biofilm-associated respiratory tract infections. Bacteria residing within the biofilm architecture pose a complex challenge in clinical settings due to their increased tolerance to currently available antibiotics and host immune responses, resulting in chronic infections with high recalcitrance and high rates of morbidity and mortality. To address these unmet clinical needs, potential anti-biofilm therapeutic strategies are being developed to effectively control bacterial biofilm. This review focuses on recent advances in the development and application of nanoparticulate drug delivery systems for the treatment of biofilm-associated respiratory tract infections, especially addressing the respiratory barriers of concern for biofilm accessibility and the various types of nanoparticles used to combat biofilms. Understanding the obstacles facing pulmonary drug delivery to bacterial biofilms and nanoparticle-based approaches to combatting biofilm may encourage researchers to explore promising treatment modalities for bacterial-biofilm-associated chronic lung infections.
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Affiliation(s)
- Yutong Guo
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Zeyuan Mao
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Fang Ran
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Jihong Sun
- Department of Radiology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou 310016, China
| | - Jingfeng Zhang
- The Key Laboratory of Diagnosis and Treatment of Digestive System Tumors of Zhejiang Province, Ningbo 315000, China
| | - Guihong Chai
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Jian Wang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510180, China
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2
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Goodyear MC, Seidel L, Krieger JR, Geddes-McAlister J, Levesque RC, Khursigara CM. Quantitative proteomics reveals unique responses to antimicrobial treatments in clinical Pseudomonas aeruginosa isolates. mSystems 2023; 8:e0049123. [PMID: 37623324 PMCID: PMC10654054 DOI: 10.1128/msystems.00491-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 07/05/2023] [Indexed: 08/26/2023] Open
Abstract
IMPORTANCE Pseudomonas aeruginosa is an important pathogen often associated with hospital-acquired infections and chronic lung infections in people with cystic fibrosis. P. aeruginosa possesses a wide array of intrinsic and adaptive mechanisms of antibiotic resistance, and the regulation of these mechanisms is complex. Label-free quantitative proteomics is a powerful tool to compare susceptible and resistant strains of bacteria and their responses to antibiotic treatments. Here we compare the proteomes of three isolates of P. aeruginosa with different antibiotic resistance profiles in response to five challenge conditions. We uncover unique and shared proteome changes for the widely used laboratory strain PAO1 and two isolates of the Liverpool epidemic strain of P. aeruginosa, LESlike1 and LESB58. Our data set provides insight into antibiotic resistance in clinically relevant Pseudomonas isolates and highlights proteins, including those with uncharacterized functions, which can be further investigated for their role in adaptive responses to antibiotic treatments.
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Affiliation(s)
- Mara C. Goodyear
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Laura Seidel
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | | | | | - Roger C. Levesque
- Institut de biologie integrative et des systems (IBIS), Département de microbiologie-infectiologie et d'immunologie, Université Laval, Laval, Quebec, Canada
| | - Cezar M. Khursigara
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
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3
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Bond JJ, Refshauge G, Newell MT, Holman BWB, Wheeler D, Woodgate S, Kamath KS, Hayes RC. Quantitative Differences in Rumen Epithelium Proteins in Lambs Fed Wheat, Perennial Wheat, or Perennial Wheat plus Lucerne. Proteomes 2023; 11:27. [PMID: 37755706 PMCID: PMC10537991 DOI: 10.3390/proteomes11030027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 09/16/2023] [Accepted: 09/19/2023] [Indexed: 09/28/2023] Open
Abstract
The value of crops such as perennial wheat (PW) for grain and grazing compared to conventional wheat (W), or the addition of lucerne to PW (PWL) is still being determined. This research sought to determine if these diets were associated with changes in the membranebound proteins that transport nutrients in the rumen epithelium (RE). Crossbred ewes (Poll Dorset × Merino) were fed W, PW, or PWL (50:50) fresh-cut forage ad libitum for 4 weeks. Average daily gain (ADG; p < 0.001) was highest in the W-fed lambs compared to the PW and PWL. Metabolisable energy intake (MEI) was higher in lambs fed W (p < 0.001) compared to PW and PWL. In pairwise comparisons of the PW and PWL diet group we found protein abundance was significantly (p < 0.05, FDR < 0.05, Benjamini p < 0.05) different in fatty acid metabolism, oxidative phosphorylation, and biosynthesis of cofactors pathways. There were not any differences in protein abundance related to nutrient transport or energy metabolism in the RE between W- vs. PW- and W- vs. PWL-fed lambs. However, in the PW- vs. PWL-fed lambs, there was a difference in the level of proteins regulating the metabolism of fatty acids and energy production in the mitochondria of the rumen epithelium.
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Affiliation(s)
- Jude Jessie Bond
- NSW Department of Primary Industries, Extensive Livestock Industry Centre, Trevenna Rd, University of New England, Armidale, NSW 2351, Australia
| | - Gordon Refshauge
- Cowra Agricultural Research and Advisory Station, NSW Department of Primary Industries, Cowra, NSW 2794, Australia; (G.R.); (M.T.N.); (R.C.H.)
| | - Matthew T. Newell
- Cowra Agricultural Research and Advisory Station, NSW Department of Primary Industries, Cowra, NSW 2794, Australia; (G.R.); (M.T.N.); (R.C.H.)
| | - Benjamin W. B. Holman
- Wagga Wagga Agricultural Institute, NSW Department of Primary Industries, Wagga Wagga, NSW 2650, Australia;
| | - David Wheeler
- NSW Department of Primary Industries, Orange Agricultural Institute, Orange, NSW 2800, Australia;
| | - Serey Woodgate
- NSW Department of Primary Industries, Extensive Livestock Industry Centre, Trevenna Rd, University of New England, Armidale, NSW 2351, Australia
| | - Karthik S. Kamath
- Australian Proteome Analysis Facility (APAF), Macquarie University, North Ryde, NSW 2109, Australia
| | - Richard C. Hayes
- Cowra Agricultural Research and Advisory Station, NSW Department of Primary Industries, Cowra, NSW 2794, Australia; (G.R.); (M.T.N.); (R.C.H.)
- Wagga Wagga Agricultural Institute, NSW Department of Primary Industries, Wagga Wagga, NSW 2650, Australia;
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4
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Meier-Credo J, Heiniger B, Schori C, Rupprecht F, Michel H, Ahrens CH, Langer JD. Detection of Known and Novel Small Proteins in Pseudomonas stutzeri Using a Combination of Bottom-Up and Digest-Free Proteomics and Proteogenomics. Anal Chem 2023; 95:11892-11900. [PMID: 37535005 PMCID: PMC10433244 DOI: 10.1021/acs.analchem.3c00676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 07/24/2023] [Indexed: 08/04/2023]
Abstract
Small proteins of around 50 aa in length have been largely overlooked in genetic and biochemical assays due to the inherent challenges with detecting and characterizing them. Recent discoveries of their critical roles in many biological processes have led to an increased recognition of the importance of small proteins for basic research and as potential new drug targets. One example is CcoM, a 36 aa subunit of the cbb3-type oxidase that plays an essential role in adaptation to oxygen-limited conditions in Pseudomonas stutzeri (P. stutzeri), a model for the clinically relevant, opportunistic pathogen Pseudomonas aeruginosa. However, as no comprehensive data were available in P. stutzeri, we devised an integrated, generic approach to study small proteins more systematically. Using the first complete genome as basis, we conducted bottom-up proteomics analyses and established a digest-free, direct-sequencing proteomics approach to study cells grown under aerobic and oxygen-limiting conditions. Finally, we also applied a proteogenomics pipeline to identify missed protein-coding genes. Overall, we identified 2921 known and 29 novel proteins, many of which were differentially regulated. Among 176 small proteins 16 were novel. Direct sequencing, featuring a specialized precursor acquisition scheme, exhibited advantages in the detection of small proteins with higher (up to 100%) sequence coverage and more spectral counts, including sequences with high proline content. Three novel small proteins, uniquely identified by direct sequencing and not conserved beyond P. stutzeri, were predicted to form an operon with a conserved protein and may represent de novo genes. These data demonstrate the power of this combined approach to study small proteins in P. stutzeri and show its potential for other prokaryotes.
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Affiliation(s)
- Jakob Meier-Credo
- Proteomics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Benjamin Heiniger
- Molecular
Ecology, Agroscope & SIB Swiss Institute
of Bioinformatics, 8046 Zürich, Switzerland
| | - Christian Schori
- Molecular
Ecology, Agroscope & SIB Swiss Institute
of Bioinformatics, 8046 Zürich, Switzerland
| | - Fiona Rupprecht
- Proteomics, Max Planck Institute for Brain
Research, 60438 Frankfurt
am Main, Germany
| | - Hartmut Michel
- Department
of Molecular Membrane Biology, Max Planck
Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Christian H. Ahrens
- Molecular
Ecology, Agroscope & SIB Swiss Institute
of Bioinformatics, 8046 Zürich, Switzerland
| | - Julian D. Langer
- Proteomics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
- Proteomics, Max Planck Institute for Brain
Research, 60438 Frankfurt
am Main, Germany
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5
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Kalpana S, Lin WY, Wang YC, Fu Y, Lakshmi A, Wang HY. Antibiotic Resistance Diagnosis in ESKAPE Pathogens-A Review on Proteomic Perspective. Diagnostics (Basel) 2023; 13:1014. [PMID: 36980322 PMCID: PMC10047325 DOI: 10.3390/diagnostics13061014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 02/26/2023] [Accepted: 02/28/2023] [Indexed: 03/11/2023] Open
Abstract
Antibiotic resistance has emerged as an imminent pandemic. Rapid diagnostic assays distinguish bacterial infections from other diseases and aid antimicrobial stewardship, therapy optimization, and epidemiological surveillance. Traditional methods typically have longer turn-around times for definitive results. On the other hand, proteomic studies have progressed constantly and improved both in qualitative and quantitative analysis. With a wide range of data sets made available in the public domain, the ability to interpret the data has considerably reduced the error rates. This review gives an insight on state-of-the-art proteomic techniques in diagnosing antibiotic resistance in ESKAPE pathogens with a future outlook for evading the "imminent pandemic".
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Affiliation(s)
- Sriram Kalpana
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan 333423, Taiwan
| | | | - Yu-Chiang Wang
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Yiwen Fu
- Department of Medicine, Kaiser Permanente Santa Clara Medical Center, Santa Clara, CA 95051, USA
| | - Amrutha Lakshmi
- Department of Biochemistry, University of Madras, Guindy Campus, Chennai 600025, India
| | - Hsin-Yao Wang
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan 333423, Taiwan
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6
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Salvà-Serra F, Jaén-Luchoro D, Marathe NP, Adlerberth I, Moore ERB, Karlsson R. Responses of carbapenemase-producing and non-producing carbapenem-resistant Pseudomonas aeruginosa strains to meropenem revealed by quantitative tandem mass spectrometry proteomics. Front Microbiol 2023; 13:1089140. [PMID: 36845973 PMCID: PMC9948630 DOI: 10.3389/fmicb.2022.1089140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 12/08/2022] [Indexed: 02/11/2023] Open
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen with increasing incidence of multidrug-resistant strains, including resistance to last-resort antibiotics, such as carbapenems. Resistances are often due to complex interplays of natural and acquired resistance mechanisms that are enhanced by its large regulatory network. This study describes the proteomic responses of two carbapenem-resistant P. aeruginosa strains of high-risk clones ST235 and ST395 to subminimal inhibitory concentrations (sub-MICs) of meropenem by identifying differentially regulated proteins and pathways. Strain CCUG 51971 carries a VIM-4 metallo-β-lactamase or 'classical' carbapenemase; strain CCUG 70744 carries no known acquired carbapenem-resistance genes and exhibits 'non-classical' carbapenem-resistance. Strains were cultivated with different sub-MICs of meropenem and analyzed, using quantitative shotgun proteomics based on tandem mass tag (TMT) isobaric labeling, nano-liquid chromatography tandem-mass spectrometry and complete genome sequences. Exposure of strains to sub-MICs of meropenem resulted in hundreds of differentially regulated proteins, including β-lactamases, proteins associated with transport, peptidoglycan metabolism, cell wall organization, and regulatory proteins. Strain CCUG 51971 showed upregulation of intrinsic β-lactamases and VIM-4 carbapenemase, while CCUG 70744 exhibited a combination of upregulated intrinsic β-lactamases, efflux pumps, penicillin-binding proteins and downregulation of porins. All components of the H1 type VI secretion system were upregulated in strain CCUG 51971. Multiple metabolic pathways were affected in both strains. Sub-MICs of meropenem cause marked changes in the proteomes of carbapenem-resistant strains of P. aeruginosa exhibiting different resistance mechanisms, involving a wide range of proteins, many uncharacterized, which might play a role in the susceptibility of P. aeruginosa to meropenem.
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Affiliation(s)
- Francisco Salvà-Serra
- Department of Infectious Diseases, Institute for Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden,Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden,Culture Collection University of Gothenburg (CCUG), Department of Clinical Microbiology, Sahlgrenska University Hospital and Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden,Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden,Microbiology, Department of Biology, University of the Balearic Islands, Palma de Mallorca, Spain,*Correspondence: Francisco Salvà-Serra, ✉
| | - Daniel Jaén-Luchoro
- Department of Infectious Diseases, Institute for Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden,Culture Collection University of Gothenburg (CCUG), Department of Clinical Microbiology, Sahlgrenska University Hospital and Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden,Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
| | | | - Ingegerd Adlerberth
- Department of Infectious Diseases, Institute for Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden,Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden,Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Edward R. B. Moore
- Department of Infectious Diseases, Institute for Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden,Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden,Culture Collection University of Gothenburg (CCUG), Department of Clinical Microbiology, Sahlgrenska University Hospital and Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden,Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Roger Karlsson
- Department of Infectious Diseases, Institute for Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden,Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden,Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden,Nanoxis Consulting AB, Gothenburg, Sweden,Roger Karlsson, ✉
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7
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Martin LW, Gray AR, Brockway B, Lamont IL. Pseudomonas aeruginosa is oxygen-deprived during infection in cystic fibrosis lungs, reducing the effectiveness of antibiotics. FEMS Microbiol Lett 2023; 370:fnad076. [PMID: 37516450 PMCID: PMC10408701 DOI: 10.1093/femsle/fnad076] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 07/04/2023] [Accepted: 07/20/2023] [Indexed: 07/31/2023] Open
Abstract
Pseudomonas aeruginosa infects the lungs of patients with cystic fibrosis. Sputum expectorated from the lungs of patients contains low levels of oxygen, indicating that P. aeruginosa may be oxygen-deprived during infection. During in vitro growth under oxygen-limiting conditions, a P. aeruginosa reference strain increases expression of a cytochrome oxidase with a high affinity for oxygen, and of nitrate and nitrite reductases that enable it to use nitrate instead of oxygen during respiration. Here, we quantified transcription of the genes encoding these three enzymes in sputum samples from 18 infected patients, and in bacteria isolated from the sputum samples and grown in aerobic and anaerobic culture. In culture, expression of all three genes was increased by averages of 20- to 500-fold in anaerobically grown bacteria compared with those grown aerobically, although expression levels varied greatly between isolates. Expression of the same genes in sputum was similar to that of the corresponding bacteria in anaerobic culture. The isolated bacteria were less susceptible to tobramycin and ciprofloxacin, two widely used anti-pseudomonal antibiotics, when grown anaerobically than when grown aerobically. Our findings show that P. aeruginosa experiences oxygen starvation during infection in cystic fibrosis, reducing the effectiveness of antibiotic treatment.
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Affiliation(s)
- Lois W Martin
- Department of Biochemistry, University of Otago, Dunedin, 9016, New Zealand
| | - Andrew R Gray
- Biostatistics Centre, University of Otago, Dunedin 9016, New Zealand
| | - Ben Brockway
- Medicine, University of Otago, Dunedin 9016, New Zealand
| | - Iain L Lamont
- Department of Biochemistry, University of Otago, Dunedin, 9016, New Zealand
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8
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Quantification of cytosol and membrane proteins in rumen epithelium of sheep with low or high CH4 emission phenotype. PLoS One 2022; 17:e0273184. [PMID: 36256644 PMCID: PMC9578583 DOI: 10.1371/journal.pone.0273184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 08/03/2022] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Ruminant livestock are a major contributor to Australian agricultural sector carbon emissions. Variation in methane (CH4) produced from enteric microbial fermentation of feed in the reticulo-rumen of sheep differs with different digestive functions. METHOD We isolated rumen epithelium enzymatically to extract membrane and cytosol proteins from sheep with high (H) and low (L) CH4 emission. Protein abundance was quantified using SWATH-mass spectrometry. RESULTS The research found differences related to the metabolism of glucose, lactate and processes of cell defence against microbes in sheep from each phenotype. Enzymes in the methylglyoxal pathway, a side path of glycolysis, resulting in D-lactate production, differed in abundance. In the H CH4 rumen epithelium the enzyme hydroxyacylglutathione hydrolase (HAGH) was 2.56 fold higher in abundance, whereas in the L CH4 epithelium lactate dehydrogenase D (LDHD) was 1.93 fold higher. Malic enzyme 1 which converts D-lactate to pyruvate via the tricarboxylic cycle was 1.57 fold higher in the L CH4 phenotype. Other proteins that are known to regulate cell defence against microbes had differential abundance in the epithelium of each phenotype. CONCLUSION Differences in the abundance of enzymes involved in the metabolism of glucose were associated with H and L CH4 phenotype sheep. Potentially this represents an opportunity to use protein markers in the rumen epithelium to select low CH4 emitting sheep.
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9
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de Jesus Salazar-Estrada I, Kamath KS, Liu F. Precision Targeting of Endogenous Epidermal Growth Factor Receptor (EGFR) by Structurally Aligned Dual-Modifier Labeling. ACS Pharmacol Transl Sci 2022; 5:859-871. [PMID: 36268127 PMCID: PMC9578136 DOI: 10.1021/acsptsci.2c00155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Indexed: 11/28/2022]
Abstract
Covalent modification of endogenous proteins by chemical probes is used for proteome-wide profiling of cellular protein function and drug discovery. However, probe selectivity in the complex cellular environment is a challenge, and new probes with better target selectivity are continuously needed. On the basis of the success of monocovalent activity-based and reactivity-based probes, an approach of structurally aligned dual-modifier labeling (SADL) was investigated here on its potential in improving target precision. Two reactive groups, based on the acrylamide and NHS ester chemistry, were linked with structural alignment to be under the same anilinoquinazoline ligand-directive for targeting the epidermal growth factor receptor (EGFR) protein kinase as the model system for proteome-wide profiling. The SADL approach was compared with its monocovalent precursors in a label-free MaxLFQ workflow using MDA-MB-468 triple negative breast cancer cells. The dual-modifier probe consistently showed labeling of EGFR with improved precision over both monocovalent precursors under various controls. The workflow also labeled endogenous USP34 and PKMYT1 with high selectivity. Precision labeling with two covalent modifiers under a common ligand directive may broaden protein identification opportunities in the native environment to complement genetic and antibody-based approaches for elucidating biological or disease mechanisms, as well as accelerating drug target discovery.
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Affiliation(s)
| | | | - Fei Liu
- School
of Natural Sciences, Macquarie University, Sydney, NSW 2109, Australia
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10
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Nitrate respiration occurs throughout the depth of mucoid and non-mucoid Pseudomonas aeruginosa submerged agar colony biofilms including the oxic zone. Sci Rep 2022; 12:8557. [PMID: 35595796 PMCID: PMC9123002 DOI: 10.1038/s41598-022-11957-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 04/19/2022] [Indexed: 11/15/2022] Open
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen and well characterized biofilm former. P. aeruginosa forms strong oxygen gradients inside biofilms due to rapid oxygen respiration in the top layers and the poor solubility of oxygen coupled with diffusion limited transport. Transcriptomic evidence from in vitro and ex vivo sampling suggests that denitrification is occurring in biofilms in ostensibly oxic environments. It is hypothesized that in the presence of nitrate there is stratification with aerobic respiration occurring in the outer oxic layer and denitrification in the lower anoxic zone. We used submerged agar colony biofilms grown from mucoid (FRD1) and non-mucoid (PAO1) strains to simultaneously measure depth microprofiles of oxygen and nitrous oxide in the same colony with microelectrodes. Oxygen respiration occurred at the top of the colony as expected but denitrification occurred throughout the entire depth, even in the oxic region. Local denitrification rates were highly variable suggesting heterogenous metabolic activity within the colony. We also assessed the short-term influence of tobramycin on aerobic respiration within a PAO1 colony. Although there was an immediate reduction in respiration it was never completely arrested over a 2 h period. On tobramycin removal the oxygen gradient steadily reestablished, demonstrating immediate recovery of metabolic activity.
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11
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Monteagudo-Cascales E, Santero E, Canosa I. The Regulatory Hierarchy Following Signal Integration by the CbrAB Two-Component System: Diversity of Responses and Functions. Genes (Basel) 2022; 13:genes13020375. [PMID: 35205417 PMCID: PMC8871633 DOI: 10.3390/genes13020375] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 02/14/2022] [Accepted: 02/16/2022] [Indexed: 02/04/2023] Open
Abstract
CbrAB is a two-component system, unique to bacteria of the family Pseudomonaceae, capable of integrating signals and involved in a multitude of physiological processes that allow bacterial adaptation to a wide variety of varying environmental conditions. This regulatory system provides a great metabolic versatility that results in excellent adaptability and metabolic optimization. The two-component system (TCS) CbrA-CbrB is on top of a hierarchical regulatory cascade and interacts with other regulatory systems at different levels, resulting in a robust output. Among the regulatory systems found at the same or lower levels of CbrAB are the NtrBC nitrogen availability adaptation system, the Crc/Hfq carbon catabolite repression cascade in Pseudomonas, or interactions with the GacSA TCS or alternative sigma ECF factor, such as SigX. The interplay between regulatory mechanisms controls a number of physiological processes that intervene in important aspects of bacterial adaptation and survival. These include the hierarchy in the use of carbon sources, virulence or resistance to antibiotics, stress response or definition of the bacterial lifestyle. The multiple actions of the CbrAB TCS result in an important competitive advantage.
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Affiliation(s)
| | - Eduardo Santero
- Departamento de Biología Molecular e Ingeniería Bioquímica, Universidad Pablo de Olavide, Centro Andaluz de Biología del Desarrollo, CSIC, Junta de Andalucía, 41013 Seville, Spain;
| | - Inés Canosa
- Departamento de Biología Molecular e Ingeniería Bioquímica, Universidad Pablo de Olavide, Centro Andaluz de Biología del Desarrollo, CSIC, Junta de Andalucía, 41013 Seville, Spain;
- Correspondence: ; Tel.: +34-954349052
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12
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Identification of a Novel Ciprofloxacin Tolerance Gene, aciT, Which Contributes to Filamentation in Acinetobacter baumannii. Antimicrob Agents Chemother 2021; 65:AAC.01400-20. [PMID: 33820764 PMCID: PMC8316044 DOI: 10.1128/aac.01400-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 03/20/2021] [Indexed: 01/19/2023] Open
Abstract
Fluoroquinolones are one of the most prescribed broad-spectrum antibiotics. However, their effectiveness is being compromised by high rates of resistance in clinically important organisms, including Acinetobacter baumannii. We sought to investigate the transcriptomic and proteomic responses of the clinical A. baumannii strain AB5075-UW upon exposure to subinhibitory concentrations of ciprofloxacin. Our transcriptomics and proteomics analyses found that the most highly expressed genes and proteins were components of the intact prophage phiOXA. The next most highly expressed gene (and its protein product) under ciprofloxacin stress was a hypothetical gene, ABUW_0098, named here the Acinetobacterciprofloxacin tolerance (aciT) gene. Disruption of this gene resulted in higher susceptibility to ciprofloxacin, and complementation of the mutant with a cloned aciT gene restored ciprofloxacin tolerance to parental strain levels. Microscopy studies revealed that aciT is essential for filamentation during ciprofloxacin stress in A. baumannii. Sequence analysis of aciT indicates the encoded protein is likely to be localized to the cell membrane. Orthologs of aciT are found widely in the genomes of species from the Moraxellaceae family and are well conserved in Acinetobacter species, suggesting an important role. With these findings taken together, this study has identified a new gene conferring tolerance to ciprofloxacin, likely by enabling filamentation in response to the antibiotic.
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13
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Camus L, Vandenesch F, Moreau K. From genotype to phenotype: adaptations of Pseudomonas aeruginosa to the cystic fibrosis environment. Microb Genom 2021; 7:mgen000513. [PMID: 33529147 PMCID: PMC8190622 DOI: 10.1099/mgen.0.000513] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 12/21/2020] [Indexed: 12/12/2022] Open
Abstract
Pseudomonas aeruginosa is one of the main microbial species colonizing the lungs of cystic fibrosis patients and is responsible for the decline in respiratory function. Despite the hostile pulmonary environment, P. aeruginosa is able to establish chronic infections thanks to its strong adaptive capacity. Various longitudinal studies have attempted to compare the strains of early infection with the adapted strains of chronic infection. Thanks to new '-omics' techniques, convergent genetic mutations, as well as transcriptomic and proteomic dysregulations have been identified. As a consequence of this evolution, the adapted strains of P. aeruginosa have particular phenotypes that promote persistent infection.
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Affiliation(s)
- Laura Camus
- CIRI – Centre International de Recherche en Infectiologie, Université de Lyon/Inserm U1111/Université Claude Bernard Lyon 1/CNRS UMR5308/ENS de Lyon, Lyon, France
| | - François Vandenesch
- CIRI – Centre International de Recherche en Infectiologie, Université de Lyon/Inserm U1111/Université Claude Bernard Lyon 1/CNRS UMR5308/ENS de Lyon, Lyon, France
- Centre National de Référence des Staphylocoques, Hospices Civils de Lyon, Lyon, France
- Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France
| | - Karen Moreau
- CIRI – Centre International de Recherche en Infectiologie, Université de Lyon/Inserm U1111/Université Claude Bernard Lyon 1/CNRS UMR5308/ENS de Lyon, Lyon, France
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Neill CJ, Harris S, Goldstone RJ, Lau ECHT, Henry TB, Yiu HHP, Smith DGE. Antibacterial Activities of Ga(III) against E. coli Are Substantially Impacted by Fe(III) Uptake Systems and Multidrug Resistance in Combination with Oxygen Levels. ACS Infect Dis 2020; 6:2959-2969. [PMID: 32960047 DOI: 10.1021/acsinfecdis.0c00425] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The continued emergence and spread of antimicrobial resistance (AMR), particularly multidrug resistant (MDR) bacteria, are increasing threats driving the search for additional and alternative antimicrobial agents. The World Health Organization (WHO) has categorized bacterial risk levels and includes Escherichia coli among the highest priority, making this both a convenient model bacterium and a clinically highly relevant species on which to base investigations of antimicrobials. Among many compounds examined for use as antimicrobials, Ga(III) complexes have shown promise. Nonetheless, the spectrum of activities, susceptibility of bacterial species, mechanisms of antimicrobial action, and bacterial characteristics influencing antibacterial actions are far from being completely understood; these are important considerations for any implementation of an effective antibacterial agent. In this investigation, we show that an alteration in growth conditions to physiologically relevant lowered oxygen (anaerobic) conditions substantially increases the minimum inhibitory concentrations (MICs) of Ga(III) required to inhibit growth for 46 wild-type E. coli strains. Several studies have implicated a Trojan horse hypothesis wherein bacterial Fe uptake systems have been linked to the promotion of Ga(III) uptake and result in enhanced antibacterial activity. Our studies show that, conversely, the carriage of accessory Fe uptake systems (Fe_acc) significantly increased the concentrations of Ga(III) required for antibacterial action. Similarly, it is shown that MDR strains are more resistant to Ga(III). The increased tolerance of Fe_acc/MDR strains was apparent under anaerobic conditions. This phenomenon of heightened tolerance has not previously been shown although the mechanisms remain to be defined. Nonetheless, this further highlights the significant contributions of bacterial metabolism, fitness, and AMR characteristics and their implications in evaluating novel antimicrobials.
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Affiliation(s)
- Christopher J. Neill
- The Institute of Biological Chemistry, Biophysics and Bioengineering (IB3), School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh EH14 4AS, United Kingdom
| | - Susan Harris
- The Institute of Biological Chemistry, Biophysics and Bioengineering (IB3), School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh EH14 4AS, United Kingdom
| | - Robert J. Goldstone
- The Institute of Biological Chemistry, Biophysics and Bioengineering (IB3), School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh EH14 4AS, United Kingdom
| | - Elizabeth C. H. T. Lau
- Chemical Engineering, School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh EH14 4AS, United Kingdom
| | - Theodore B. Henry
- The Institute of Life and Earth Sciences (ILES), School of Energy, Geoscience, Infrastructure and Society, Heriot-Watt University, Edinburgh EH14 4AS, United Kingdom
| | - Humphrey H. P. Yiu
- Chemical Engineering, School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh EH14 4AS, United Kingdom
| | - David G. E. Smith
- The Institute of Biological Chemistry, Biophysics and Bioengineering (IB3), School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh EH14 4AS, United Kingdom
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15
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Mechanisms controlling bacterial infection in myeloid cells under hypoxic conditions. Cell Mol Life Sci 2020; 78:1887-1907. [PMID: 33125509 PMCID: PMC7966188 DOI: 10.1007/s00018-020-03684-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 09/08/2020] [Accepted: 10/09/2020] [Indexed: 12/12/2022]
Abstract
Various factors of the tissue microenvironment such as the oxygen concentration influence the host-pathogen interaction. During the past decade, hypoxia-driven signaling via hypoxia-inducible factors (HIF) has emerged as an important factor that affects both the pathogen and the host. In this chapter, we will review the current knowledge of this complex interplay, with a particular emphasis given to the impact of hypoxia and HIF on the inflammatory and antimicrobial activity of myeloid cells, the bacterial responses to hypoxia and the containment of bacterial infections under oxygen-limited conditions. We will also summarize how low oxygen concentrations influence the metabolism of neutrophils, macrophages and dendritic cells. Finally, we will discuss the consequences of hypoxia and HIFα activation for the invading pathogen, with a focus on Pseudomonas aeruginosa, Mycobacterium tuberculosis, Coxiella burnetii, Salmonella enterica and Staphylococcus aureus. This includes a description of the mechanisms and microbial factors, which the pathogens use to sense and react to hypoxic conditions.
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16
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Ye C, Ge Y, Zhang Y, Zhou L, Chen W, Zhu X, Pan J. Deletion of vp0057, a Gene Encoding a Ser/Thr Protein Kinase, Impacts the Proteome and Promotes Iron Uptake and Competitive Advantage in Vibrio parahaemolyticus. J Proteome Res 2020; 20:250-260. [PMID: 33112629 DOI: 10.1021/acs.jproteome.0c00361] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The marine bacterial pathogen Vibrio parahaemolyticus is a major cause of food-borne gastroenteritis. Recent findings have demonstrated that protein phosphorylation is fundamental to the regulation of many physiological processes in pathogenic bacteria, including bacterial virulence. However, the underlying mechanisms remain to be completely clarified. Using bioinformatics analysis, we found that VP0057 may be a potential Ser/Thr protein kinase with phosphorylation activity. Thus, we constructed the vp0057-deletion mutant (Δvp0057) from the wild-type V. parahaemolyticus serotype O3:K6 and employed a mass spectrometry-based proteomic strategy to characterize proteome-wide changes in response to vp0057 deletion, owing to the potential roles of VP0057 in V. parahaemolyticus. One hundred ninety-seven differentially expressed proteins were identified in the Δvp0057 strain compared with the wild-type strain, among which 135 proteins were upregulated and 62 proteins were downregulated. Detailed annotation of these differentially expressed proteins was conducted. Notably, iron-related and T6SS1-related proteins were upregulated in the Δvp0057 strain, corroborating the results by quantitative PCR. Further experiments proved that vp0057 deletion promotes Fe2+ and Fe3+ uptake and provides a growth competition advantage, which is controlled by iron-related and T6SS1-related proteins, respectively. Although the regulatory roles and mechanisms of VP0057 remain to be revealed in V. parahaemolyticus, our systemic analysis of the protein profile of Δvp0057 provides a promising starting point for the intensive exploration of VP0057.
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Affiliation(s)
- Chen Ye
- Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Yongze Ge
- Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Yue Zhang
- Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Lantian Zhou
- Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Wei Chen
- Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Xuan Zhu
- Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Jianyi Pan
- Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
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Vrla GD, Esposito M, Zhang C, Kang Y, Seyedsayamdost MR, Gitai Z. Cytotoxic alkyl-quinolones mediate surface-induced virulence in Pseudomonas aeruginosa. PLoS Pathog 2020; 16:e1008867. [PMID: 32925969 PMCID: PMC7515202 DOI: 10.1371/journal.ppat.1008867] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 09/24/2020] [Accepted: 08/04/2020] [Indexed: 12/28/2022] Open
Abstract
Surface attachment, an early step in the colonization of multiple host environments, activates the virulence of the human pathogen P. aeruginosa. However, the downstream toxins that mediate surface-dependent P. aeruginosa virulence remain unclear, as do the signaling pathways that lead to their activation. Here, we demonstrate that alkyl-quinolone (AQ) secondary metabolites are rapidly induced upon surface association and act directly on host cells to cause cytotoxicity. Surface-induced AQ cytotoxicity is independent of other AQ functions like quorum sensing or PQS-specific activities like iron sequestration. We further show that packaging of AQs in outer-membrane vesicles (OMVs) increases their cytotoxicity to host cells but not their ability to stimulate downstream quorum sensing pathways in bacteria. OMVs lacking AQs are significantly less cytotoxic, suggesting these molecules play a role in OMV cytotoxicity, in addition to their previously characterized role in OMV biogenesis. AQ reporters also enabled us to dissect the signal transduction pathways downstream of the two known regulators of surface-dependent virulence, the quorum sensing receptor, LasR, and the putative mechanosensor, PilY1. Specifically, we show that PilY1 regulates surface-induced AQ production by repressing the AlgR-AlgZ two-component system. AlgR then induces RhlR, which can induce the AQ biosynthesis operon under specific conditions. These findings collectively suggest that the induction of AQs upon surface association is both necessary and sufficient to explain surface-induced P. aeruginosa virulence. Pseudomonas aeruginosa is one of the most intensely studied bacterial pathogens and is a leading cause of hospital-acquired infections in the United States. An intriguing aspect of P. aeruginosa is its ability increase its virulence following attachment to a solid surface, suggesting that these bacteria use mechano-transduction to regulate pathogenesis. However, the cytotoxins that mediate host-cell killing in response to surface attachment remain unknown. Here, we use a microscopy-based host-cell killing assay to show that the alkyl-quinolone (AQ) family of secreted small molecules is both necessary and sufficient to explain surface-induced virulence. We further show that these compounds are upregulated rapidly following bacterial surface attachment and that packaging of AQs into secreted outer membrane vesicles enhances AQ cytotoxicity. This work thus fills a major gap in our understanding of surface sensing in P. aeruginosa and provides new methods for investigating surface-dependent signaling pathways.
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Affiliation(s)
- Geoffrey D. Vrla
- Department of Molecular Biology, Princeton University, Princeton, NJ, Unites States of America
| | - Mark Esposito
- Department of Molecular Biology, Princeton University, Princeton, NJ, Unites States of America
| | - Chen Zhang
- Department of Chemistry, Princeton University, Princeton, NJ, Unites States of America
| | - Yibin Kang
- Department of Molecular Biology, Princeton University, Princeton, NJ, Unites States of America
| | | | - Zemer Gitai
- Department of Molecular Biology, Princeton University, Princeton, NJ, Unites States of America
- * E-mail:
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18
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Barbosa RRB, Liberato FMG, de Freitas Coelho P, Vidal PDR, de Carvalho RBCO, Donadio MVF. Sleep-disordered breathing and markers of morbidity in children and adolescents with cystic fibrosis. Pediatr Pulmonol 2020; 55:1974-1983. [PMID: 32364318 DOI: 10.1002/ppul.24780] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 04/01/2020] [Accepted: 04/05/2020] [Indexed: 11/10/2022]
Abstract
BACKGROUND Studies have shown that sleep disorders occur in cystic fibrosis (CF) patients and may be present before daytime clinical manifestations. OBJECTIVES To evaluate the presence of sleep disorders among children and adolescents with CF, attempting to identify associations with pulmonary function, nutritional status, days in hospital, and days taking antibiotics. METHODS Individuals with a diagnosis of CF aged between 6 and 18 years were included. Information on sociodemographic, clinical profile, history of hospitalizations, and use of antibiotics in the last year were collected. Spirometry, bioimpedance, and polysomnography were performed. The presence of nocturnal hypoxemia and obstructive sleep apnea syndrome (OSAS) were evaluated and participants divided according to their presence. RESULTS Thirty-one patients were included. The prevalence of OSAS was 32.3% and nocturnal hypoxemia was 29.0%. Average nocturnal peripheral oxyhemoglobin saturation (SpO2 ) correlated (P < .001) with forced vital capacity (r = .55) and forced expiratory volume in the first second (r = .62). The higher the percentage of total sleep time (TST) with SpO2 less than 90%, the lower the pulmonary function. Individuals with OSAS and nocturnal hypoxemia had lower spirometric values compared to patients without these disorders, but the nocturnal hypoxemia group also had lower Shwachman-Kulczycki score, longer hospitalization time and antibiotic use. TST with SpO2 less than 90% was associated with length of hospitalization (r2 = .53). CONCLUSION Children and adolescents with CF have sleep disorders, including OSAS (32.3%) and nocturnal hypoxemia (29%). Individuals with nocturnal hypoxemia presented lower lung function, worse clinical score, and higher morbidity. TST with SpO2 less than 90% was associated with length of hospitalization.
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Affiliation(s)
- Roberta Ribeiro Batista Barbosa
- Department of Physiotherapy, Escola Superior de Ciências da Santa Casa de Misericórdia de Vitória, Vitória, Espírito Santo, Brazil
| | | | - Pitiguara de Freitas Coelho
- Department of Physiotherapy, Escola Superior de Ciências da Santa Casa de Misericórdia de Vitória, Vitória, Espírito Santo, Brazil
| | - Pâmela Dos Reis Vidal
- Department of Physiotherapy, Escola Superior de Ciências da Santa Casa de Misericórdia de Vitória, Vitória, Espírito Santo, Brazil
| | | | - Márcio Vinícius Fagundes Donadio
- Laboratory of Pediatric Physical Activity, Centro Infant, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Rio Grande do Sul, Brazil
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19
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Zhang Y, Pan X, Liao S, Jiang C, Wang L, Tang Y, Wu G, Dai G, Chen L. Quantitative Proteomics Reveals the Mechanism of Silver Nanoparticles against Multidrug-Resistant Pseudomonas aeruginosa Biofilms. J Proteome Res 2020; 19:3109-3122. [PMID: 32567865 DOI: 10.1021/acs.jproteome.0c00114] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The decline of clinically effective antibiotics has made it necessary to develop more effective antimicrobial agents, especially for refractory biofilm-related infections. Silver nanoparticles (AgNPs) are a new type of antimicrobial agent that can eradicate biofilms and reduce bacterial resistance, but its anti-biofilm mechanism has not been elucidated. In this study, we investigated the molecular mechanism of AgNPs against multidrug-resistant Pseudomonas aeruginosa by means of anti-biofilm tests, scanning electron microscopy (SEM), and tandem mass tag (TMT)-labeled quantitative proteomics. The results of anti-biofilm tests demonstrated that AgNPs inhibited the formation of P. aeruginosa biofilm and disrupted its preformed biofilm. SEM showed that when exposed to AgNPs, the structure of the P. aeruginosa biofilm was destroyed, along with significant reduction of its biomass. TMT-labeled quantitative proteomic analysis revealed that AgNPs could defeat the P. aeruginosa biofilm in multiple ways by inhibiting its adhesion and motility, stimulating strong oxidative stress response, destroying iron homeostasis, blocking aerobic and anaerobic respiration, and affecting quorum sensing systems. Our findings offer a new insight into clarifying the mechanism of AgNPs against biofilms, thus providing a theoretical basis for its clinical application.
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Affiliation(s)
- Yapeng Zhang
- Department of Medical Microbiology, School of Basic Medical Sciences, Central South University, Changsha 410013, China
| | - Xuanhe Pan
- Department of Medical Microbiology, School of Basic Medical Sciences, Central South University, Changsha 410013, China
| | - Shijing Liao
- Department of Clinical Laboratory, The First People's Hospital of Yueyang, Yueyang 414000, China
| | - Congyuan Jiang
- Hunan Anson Biotechnology Company Ltd., Changsha 410008, China
| | - Linqian Wang
- Department of Clinical Laboratory, Hunan Cancer Hospital, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, China
| | - Yurong Tang
- Department of Medical Microbiology, School of Basic Medical Sciences, Central South University, Changsha 410013, China
| | - Guojun Wu
- Department of Medical Microbiology, School of Basic Medical Sciences, Central South University, Changsha 410013, China
| | - Gan Dai
- Department of Medical Microbiology, School of Basic Medical Sciences, Central South University, Changsha 410013, China
| | - Liyu Chen
- Department of Medical Microbiology, School of Basic Medical Sciences, Central South University, Changsha 410013, China
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20
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Mielko KA, Jabłoński SJ, Wojtowicz W, Milczewska J, Sands D, Łukaszewicz M, Młynarz P. Possible metabolic switch between environmental and pathogenic Pseudomonas aeruginosa strains: 1H NMR based metabolomics study. J Pharm Biomed Anal 2020; 188:113369. [PMID: 32534405 DOI: 10.1016/j.jpba.2020.113369] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 05/11/2020] [Accepted: 05/14/2020] [Indexed: 10/24/2022]
Abstract
The study aimed to assess whether Pseudomonas aeruginosa strains from different sources can be distinguished by the metabolomic fingerprint and to check whether antibiotic susceptibility distinctions are available through metabolomic analysis. 1H NMR spectroscopy analysis of the bacteria metabolites was performed. Twenty-nine strains were tested (18 isolated form cystic fibrosis patients and 11 environmental). Thirty-one metabolites were identified, 12 were up-regulated in strains from CF patients, while 2 were higher level in strains from the environment. Changed carbohydrate catabolic metabolism and the metabolic shift toward the utilization of amino acids is suggested in strains from CF patients.
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Affiliation(s)
- Karolina Anna Mielko
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Sławomir Jan Jabłoński
- Biotransformation Department, University of Wroclaw, Plac Uniwersytecki 1, 50-137 Wrocław Poland
| | - Wojciech Wojtowicz
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Justyna Milczewska
- Cystic Fibrosis Department, Institute of Mother and Child, Kasprzaka 17a, 01-211 Warszawa, Poland
| | - Dorota Sands
- Cystic Fibrosis Department, Institute of Mother and Child, Kasprzaka 17a, 01-211 Warszawa, Poland
| | - Marcin Łukaszewicz
- Biotransformation Department, University of Wroclaw, Plac Uniwersytecki 1, 50-137 Wrocław Poland
| | - Piotr Młynarz
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland.
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Pseudomonas aeruginosa lasR mutant fitness in microoxia is supported by an Anr-regulated oxygen-binding hemerythrin. Proc Natl Acad Sci U S A 2020; 117:3167-3173. [PMID: 31980538 DOI: 10.1073/pnas.1917576117] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Pseudomonas aeruginosa strains with loss-of-function mutations in the transcription factor LasR are frequently encountered in the clinic and the environment. Among the characteristics common to LasR-defective (LasR-) strains is increased activity of the transcription factor Anr, relative to their LasR+ counterparts, in low-oxygen conditions. One of the Anr-regulated genes found to be highly induced in LasR- strains was PA14_42860 (PA1673), which we named mhr for microoxic hemerythrin. Purified P. aeruginosa Mhr protein contained the predicted di-iron center and bound molecular oxygen with an apparent K d of ∼1 µM. Both Anr and Mhr were necessary for fitness in lasR+ and lasR mutant strains in colony biofilms grown in microoxic conditions, and the effects were more striking in the lasR mutant. Among genes in the Anr regulon, mhr was most closely coregulated with the Anr-controlled high-affinity cytochrome c oxidase genes. In the absence of high-affinity cytochrome c oxidases, deletion of mhr no longer caused a fitness disadvantage, suggesting that Mhr works in concert with microoxic respiration. We demonstrate that Anr and Mhr contribute to LasR- strain fitness even in biofilms grown in normoxic conditions. Furthermore, metabolomics data indicate that, in a lasR mutant, expression of Anr-regulated mhr leads to differences in metabolism in cells grown on lysogeny broth or artificial sputum medium. We propose that increased Anr activity leads to higher levels of the oxygen-binding protein Mhr, which confers an advantage to lasR mutants in microoxic conditions.
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22
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Proteomic response of Euglena gracilis to heavy metal exposure – Identification of key proteins involved in heavy metal tolerance and accumulation. ALGAL RES 2020. [DOI: 10.1016/j.algal.2019.101764] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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23
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Deschamps E, Schmitz-Afonso I, Schaumann A, Dé E, Loutelier-Bourhis C, Alexandre S, Afonso C. Determination of the collision cross sections of cardiolipins and phospholipids from Pseudomonas aeruginosa by traveling wave ion mobility spectrometry-mass spectrometry using a novel correction strategy. Anal Bioanal Chem 2019; 411:8123-8131. [DOI: 10.1007/s00216-019-02194-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 09/16/2019] [Accepted: 10/07/2019] [Indexed: 12/15/2022]
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24
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Pseudomonas aeruginosa Ethanol Oxidation by AdhA in Low-Oxygen Environments. J Bacteriol 2019; 201:JB.00393-19. [PMID: 31527114 DOI: 10.1128/jb.00393-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 09/11/2019] [Indexed: 12/26/2022] Open
Abstract
Pseudomonas aeruginosa has a broad metabolic repertoire that facilitates its coexistence with different microbes. Many microbes secrete products that P. aeruginosa can then catabolize, including ethanol, a common fermentation product. Here, we show that under oxygen-limiting conditions P. aeruginosa utilizes AdhA, an NAD-linked alcohol dehydrogenase, as a previously undescribed means for ethanol catabolism. In a rich medium containing ethanol, AdhA, but not the previously described PQQ-linked alcohol dehydrogenase, ExaA, oxidizes ethanol and leads to the accumulation of acetate in culture supernatants. AdhA-dependent acetate accumulation and the accompanying decrease in pH promote P. aeruginosa survival in LB-grown stationary-phase cultures. The transcription of adhA is elevated by hypoxia and under anoxic conditions, and we show that it is regulated by the Anr transcription factor. We have shown that lasR mutants, which lack an important quorum sensing regulator, have higher levels of Anr-regulated transcripts under low-oxygen conditions than their wild-type counterparts. Here, we show that a lasR mutant, when grown with ethanol, has an even larger decrease in pH than the wild type (WT) that is dependent on both anr and adhA The large increase in AdhA activity is similar to that of a strain expressing a hyperactive Anr-D149A variant. Ethanol catabolism in P. aeruginosa by AdhA supports growth on ethanol as a sole carbon source and electron donor in oxygen-limited settings and in cells growing by denitrification under anoxic conditions. This is the first demonstration of a physiological role for AdhA in ethanol oxidation in P. aeruginosa IMPORTANCE Ethanol is a common product of microbial fermentation, and the Pseudomonas aeruginosa response to and utilization of ethanol are relevant to our understanding of its role in microbial communities. Here, we report that the putative alcohol dehydrogenase AdhA is responsible for ethanol catabolism and acetate accumulation under low-oxygen conditions and that it is regulated by Anr.
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Conceptual Model of Biofilm Antibiotic Tolerance That Integrates Phenomena of Diffusion, Metabolism, Gene Expression, and Physiology. J Bacteriol 2019; 201:JB.00307-19. [PMID: 31501280 DOI: 10.1128/jb.00307-19] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 08/28/2019] [Indexed: 01/14/2023] Open
Abstract
Transcriptomic, metabolomic, physiological, and computational modeling approaches were integrated to gain insight into the mechanisms of antibiotic tolerance in an in vitro biofilm system. Pseudomonas aeruginosa biofilms were grown in drip flow reactors on a medium composed to mimic the exudate from a chronic wound. After 4 days, the biofilm was 114 μm thick with 9.45 log10 CFU cm-2 These biofilms exhibited tolerance, relative to exponential-phase planktonic cells, to subsequent treatment with ciprofloxacin. The specific growth rate of the biofilm was estimated via elemental balances to be approximately 0.37 h-1 and with a reaction-diffusion model to be 0.32 h-1, or one-third of the maximum specific growth rate for planktonic cells. Global analysis of gene expression indicated lower transcription of ribosomal genes and genes for other anabolic functions in biofilms than in exponential-phase planktonic cells and revealed the induction of multiple stress responses in biofilm cells, including those associated with growth arrest, zinc limitation, hypoxia, and acyl-homoserine lactone quorum sensing. Metabolic pathways for phenazine biosynthesis and denitrification were transcriptionally activated in biofilms. A customized reaction-diffusion model predicted that steep oxygen concentration gradients will form when these biofilms are thicker than about 40 μm. Mutant strains that were deficient in Psl polysaccharide synthesis, the stringent response, the stationary-phase response, and the membrane stress response exhibited increased ciprofloxacin susceptibility when cultured in biofilms. These results support a sequence of phenomena leading to biofilm antibiotic tolerance, involving oxygen limitation, electron acceptor starvation and growth arrest, induction of associated stress responses, and differentiation into protected cell states.IMPORTANCE Bacteria in biofilms are protected from killing by antibiotics, and this reduced susceptibility contributes to the persistence of infections such as those in the cystic fibrosis lung and chronic wounds. A generalized conceptual model of biofilm antimicrobial tolerance with the following mechanistic steps is proposed: (i) establishment of concentration gradients in metabolic substrates and products; (ii) active biological responses to these changes in the local chemical microenvironment; (iii) entry of biofilm cells into a spectrum of states involving alternative metabolisms, stress responses, slow growth, cessation of growth, or dormancy (all prior to antibiotic treatment); (iv) adaptive responses to antibiotic exposure; and (v) reduced susceptibility of microbial cells to antimicrobial challenges in some of the physiological states accessed through these changes.
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26
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Erdmann J, Thöming JG, Pohl S, Pich A, Lenz C, Häussler S. The Core Proteome of Biofilm-Grown Clinical Pseudomonas aeruginosa Isolates. Cells 2019; 8:E1129. [PMID: 31547513 PMCID: PMC6829490 DOI: 10.3390/cells8101129] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 09/18/2019] [Accepted: 09/19/2019] [Indexed: 12/13/2022] Open
Abstract
Comparative genomics has greatly facilitated the identification of shared as well as unique features among individual cells or tissues, and thus offers the potential to find disease markers. While proteomics is recognized for its potential to generate quantitative maps of protein expression, comparative proteomics in bacteria has been largely restricted to the comparison of single cell lines or mutant strains. In this study, we used a data independent acquisition (DIA) technique, which enables global protein quantification of large sample cohorts, to record the proteome profiles of overall 27 whole genome sequenced and transcriptionally profiled clinical isolates of the opportunistic pathogen Pseudomonas aeruginosa. Analysis of the proteome profiles across the 27 clinical isolates grown under planktonic and biofilm growth conditions led to the identification of a core biofilm-associated protein profile. Furthermore, we found that protein-to-mRNA ratios between different P. aeruginosa strains are well correlated, indicating conserved patterns of post-transcriptional regulation. Uncovering core regulatory pathways, which drive biofilm formation and associated antibiotic tolerance in bacterial pathogens, promise to give clues to interactions between bacterial species and their environment and could provide useful targets for new clinical interventions to combat biofilm-associated infections.
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Affiliation(s)
- Jelena Erdmann
- Institute for Molecular Bacteriology, TWINCORE GmbH, Centre for Experimental and Clinical Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover 30625, Germany.
- Research Core Unit Proteomics and Institute of Toxicology, Hannover Medical School, Hannover 30625, Germany.
| | - Janne G Thöming
- Institute for Molecular Bacteriology, TWINCORE GmbH, Centre for Experimental and Clinical Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover 30625, Germany.
| | - Sarah Pohl
- Institute for Molecular Bacteriology, TWINCORE GmbH, Centre for Experimental and Clinical Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover 30625, Germany.
- Department of Molecular Bacteriology, Helmholtz Center for Infection Research, Braunschweig 38124, Germany.
| | - Andreas Pich
- Research Core Unit Proteomics and Institute of Toxicology, Hannover Medical School, Hannover 30625, Germany.
| | - Christof Lenz
- Institute of Clinical Chemistry, Bioanalytics, University Medical Center Göttingen, Göttingen 37075, Germany.
- Max Planck Institute for Biophysical Chemistry, Bioanalytical Mass Spectrometry, Göttingen 37077, Germany.
| | - Susanne Häussler
- Institute for Molecular Bacteriology, TWINCORE GmbH, Centre for Experimental and Clinical Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover 30625, Germany.
- Department of Molecular Bacteriology, Helmholtz Center for Infection Research, Braunschweig 38124, Germany.
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27
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Vincent RM, Wright BW, Jaschke PR. Measuring Amber Initiator tRNA Orthogonality in a Genomically Recoded Organism. ACS Synth Biol 2019; 8:675-685. [PMID: 30856316 DOI: 10.1021/acssynbio.9b00021] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Using engineered initiator tRNA for precise control of protein translation within cells has great promise within future orthogonal translation systems to decouple housekeeping protein metabolism from that of engineered genetic systems. Previously, E. coli strain C321.ΔA. exp lacking all UAG stop codons was created, freeing this "amber" stop codon for other purposes. An engineered "amber initiator" tRNACUAfMet that activates translation at UAG codons is available, but little is known about this tRNA's orthogonality. Here, we combine for the first time the amber initiator tRNACUAfMet in C321.ΔA. exp and measure its cellular effects. We found that the tRNACUAfMet expression resulted in a nearly 200-fold increase in fluorescent reporter expression with a unimodal population distribution and no apparent cellular fitness defects. Proteomic analysis revealed upregulated ribosome-associated, tRNA degradation, and amino acid biosynthetic proteins, with no evidence for off-target translation initiation. In contrast to previous work, we show that UAG-initiated proteins carry N-terminal methionine, but have no evidence for glutamine. Together, our results identify beneficial features of using the amber initiator tRNACUAfMet to control gene expression while also revealing fundamental challenges to using engineered initiator tRNAs as the basis for orthogonal translation initiation systems.
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Affiliation(s)
- Russel M. Vincent
- Department of Molecular Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Bradley W. Wright
- Department of Molecular Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Paul R. Jaschke
- Department of Molecular Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
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28
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Vipin C, Mujeeburahiman M, Arun AB, Ashwini P, Mangesh SV, Rekha PD. Adaptation and diversification in virulence factors among urinary catheter-associated Pseudomonas aeruginosa isolates. J Appl Microbiol 2018; 126:641-650. [PMID: 30372578 DOI: 10.1111/jam.14143] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 10/11/2018] [Accepted: 10/23/2018] [Indexed: 12/13/2022]
Abstract
AIM The aim of this study was to investigate the natural variation in the antibiotic sensitivity, biofilm formation and virulence among Pseudomonas aeruginosa isolated from the catheter-associated urinary tract infection (CAUTI) from a single centre. METHODS AND RESULTS Pseudomonas aeruginosa strains were isolated from the patients with CAUTI after obtaining informed consent. These isolates were identified by routine biochemical methods and 16S rRNA gene sequencing. Antibiotic sensitivity and virulence factors were measured using standard protocols. Crystal violet staining, scanning electron microscopy and confocal laser scanning microscopy were used for the biofilm studies. The extent of infectivity of the strains to induce cell lysis was studied in vitro using the Human Embryonic Kidney cells (HEK 293T). Association between virulence factors, biofilm formation and antibiotic resistance among the strains was analysed statistically. Among the 1266 patients admitted during the 2016-2017 period, 98 cases of CAUTI were reported and 18·36% (n = 18) was due to P. aeruginosa infection. Antibiogram showed that 94·4% of isolates were resistant to multiple antibiotics and 73·7% were carbapenem-resistant. All the isolates formed biofilm on different material surfaces with varying intensity (OD580 ≥0·20-1·11). The biofilm intensity on silicone-latex material was significantly higher compared to the polystyrene surface (P > 0·05). All the strains were highly virulent and able to cause cell killing of HEK 293T cells with a rate ranging from 69·35 to 100% and showed very low sensitivity to healthy human serum. CONCLUSIONS Antibiotic sensitivity and association between the virulence factors and biofilm formation in the P. aeruginosa clinical strains showed complex natural diversity. SIGNIFICANCE AND IMPACT OF THE STUDY This study demonstrates the natural diversity and adaptation in virulence factors, biofilm formation and host-pathogen interaction among catheter-associated P. aeruginosa strains. The findings from the study urge for developing individualized drug strategy for targeting these multidrug-resistant pathogens.
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Affiliation(s)
- C Vipin
- Yenepoya Research Centre, Yenepoya University, Mangalore, Karnataka, India.,Department of Urology, Yenepoya Medical College, Yenepoya University, Mangalore, Karnataka, India
| | - M Mujeeburahiman
- Department of Urology, Yenepoya Medical College, Yenepoya University, Mangalore, Karnataka, India
| | - A B Arun
- Yenepoya Research Centre, Yenepoya University, Mangalore, Karnataka, India
| | - P Ashwini
- Yenepoya Research Centre, Yenepoya University, Mangalore, Karnataka, India
| | - S V Mangesh
- Yenepoya Research Centre, Yenepoya University, Mangalore, Karnataka, India
| | - P D Rekha
- Yenepoya Research Centre, Yenepoya University, Mangalore, Karnataka, India
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29
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Krasny L, Bland P, Kogata N, Wai P, Howard BA, Natrajan RC, Huang PH. SWATH mass spectrometry as a tool for quantitative profiling of the matrisome. J Proteomics 2018; 189:11-22. [PMID: 29501709 PMCID: PMC6215756 DOI: 10.1016/j.jprot.2018.02.026] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Revised: 02/16/2018] [Accepted: 02/19/2018] [Indexed: 12/16/2022]
Abstract
Proteomic analysis of extracellular matrix (ECM) and ECM-associated proteins, collectively known as the matrisome, is a challenging task due to the inherent complexity and insolubility of these proteins. Here we present sequential window acquisition of all theoretical fragment ion spectra mass spectrometry (SWATH MS) as a tool for the quantitative analysis of matrisomal proteins in both non-enriched and ECM enriched tissue without the need for prior fractionation. Utilising a spectral library containing 201 matrisomal proteins, we compared the performance and reproducibility of SWATH MS over conventional data-dependent analysis mass spectrometry (DDA MS) in unfractionated murine lung and liver. SWATH MS conferred a 15-20% increase in reproducible peptide identification across replicate experiments in both tissue types and identified 54% more matrisomal proteins in the liver versus DDA MS. We further use SWATH MS to evaluate the quantitative changes in matrisome content that accompanies ECM enrichment. Our data shows that ECM enrichment led to a systematic increase in core matrisomal proteins but resulted in significant losses in matrisome-associated proteins including the cathepsins and proteins of the S100 family. Our proof-of-principle study demonstrates the utility of SWATH MS as a versatile tool for in-depth characterisation of the matrisome in unfractionated and non-enriched tissues. SIGNIFICANCE: The matrisome is a complex network of extracellular matrix (ECM) and ECM-associated proteins that provides scaffolding function to tissues and plays important roles in the regulation of fundamental cellular processes. However, due to its inherent complexity and insolubility, proteomic studies of the matrisome typically require the application of enrichment workflows prior to MS analysis. Such enrichment strategies often lead to losses in soluble matrisome-associated components. In this study, we present sequential window acquisition of all theoretical fragment ion spectra mass spectrometry (SWATH MS) as a tool for the quantitative analysis of matrisomal proteins. We show that SWATH MS provides a more reproducible coverage of the matrisome compared to data-dependent analysis (DDA) MS. We also demonstrate that SWATH MS is capable of accurate quantification of matrisomal proteins without prior ECM enrichment and fractionation, which may simplify sample handling workflows and avoid losses in matrisome-associated proteins commonly linked to ECM enrichment.
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Affiliation(s)
- Lukas Krasny
- Division of Molecular Pathology, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Philip Bland
- The Breast Cancer Now Toby Robins Research Centre, Division of Breast Cancer Research, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Naoko Kogata
- The Breast Cancer Now Toby Robins Research Centre, Division of Breast Cancer Research, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Patty Wai
- Division of Molecular Pathology, The Institute of Cancer Research, London, SW3 6JB, UK; The Breast Cancer Now Toby Robins Research Centre, Division of Breast Cancer Research, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Beatrice A Howard
- The Breast Cancer Now Toby Robins Research Centre, Division of Breast Cancer Research, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Rachael C Natrajan
- Division of Molecular Pathology, The Institute of Cancer Research, London, SW3 6JB, UK; The Breast Cancer Now Toby Robins Research Centre, Division of Breast Cancer Research, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Paul H Huang
- Division of Molecular Pathology, The Institute of Cancer Research, London, SW3 6JB, UK.
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30
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Erdmann J, Preusse M, Khaledi A, Pich A, Häussler S. Environment-driven changes of mRNA and protein levels in Pseudomonas aeruginosa. Environ Microbiol 2018; 20:3952-3963. [DOI: 10.1111/1462-2920.14419] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 09/13/2018] [Accepted: 09/15/2018] [Indexed: 12/27/2022]
Affiliation(s)
- Jelena Erdmann
- Centre for Experimental and Clinical Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Centre for Infection Research; Institute for Molecular Bacteriology, TWINCORE GmbH; Hannover Germany
- Centre for Pharmacology and Toxicology; Research Core Unit Proteomics and Institute of Toxicology, Hannover Medical School; Hannover Germany
| | - Matthias Preusse
- Centre for Experimental and Clinical Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Centre for Infection Research; Institute for Molecular Bacteriology, TWINCORE GmbH; Hannover Germany
- Department of Molecular Bacteriology, Helmholtz Center for Infection Research; Braunschweig Germany
| | - Ariane Khaledi
- Department of Molecular Bacteriology, Helmholtz Center for Infection Research; Braunschweig Germany
| | - Andreas Pich
- Centre for Pharmacology and Toxicology; Research Core Unit Proteomics and Institute of Toxicology, Hannover Medical School; Hannover Germany
| | - Susanne Häussler
- Centre for Experimental and Clinical Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Centre for Infection Research; Institute for Molecular Bacteriology, TWINCORE GmbH; Hannover Germany
- Department of Molecular Bacteriology, Helmholtz Center for Infection Research; Braunschweig Germany
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31
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Gaviard C, Jouenne T, Hardouin J. Proteomics ofPseudomonas aeruginosa: the increasing role of post-translational modifications. Expert Rev Proteomics 2018; 15:757-772. [DOI: 10.1080/14789450.2018.1516550] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Charlotte Gaviard
- Normandie Univ, UNIROUEN, INSA Rouen, CNRS, PBS, 76000, Rouen, France
- PISSARO proteomic facility, IRIB, 76821 Mont-Saint-Aignan, France
| | - Thierry Jouenne
- Normandie Univ, UNIROUEN, INSA Rouen, CNRS, PBS, 76000, Rouen, France
- PISSARO proteomic facility, IRIB, 76821 Mont-Saint-Aignan, France
| | - Julie Hardouin
- Normandie Univ, UNIROUEN, INSA Rouen, CNRS, PBS, 76000, Rouen, France
- PISSARO proteomic facility, IRIB, 76821 Mont-Saint-Aignan, France
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32
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Shakkottai A, O'Brien LM, Nasr SZ, Chervin RD. Sleep disturbances and their impact in pediatric cystic fibrosis. Sleep Med Rev 2018; 42:100-110. [PMID: 30093360 DOI: 10.1016/j.smrv.2018.07.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 06/15/2018] [Accepted: 07/03/2018] [Indexed: 12/14/2022]
Abstract
Cystic fibrosis is a chronic, life-shortening illness that affects multiple systems and results in frequent respiratory infections, chronic cough, fat malabsorption and malnutrition. Poor sleep is often reported by patients with cystic fibrosis. Although objective data to explain these complaints have been limited, they do show poor sleep efficiency and frequent arousals. Abnormalities in gas exchange are also observed during sleep in patients with cystic fibrosis. The potential impact of these abnormalities in sleep on health and quality of life remains largely unstudied. This review summarizes what is known about sleep in children with cystic fibrosis, and implications for clinical practice. This report also highlights new evidence on the impact of sleep problems on disease-specific outcomes such as lung function, and identifies areas that need further exploration.
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Affiliation(s)
- Aarti Shakkottai
- Sleep Disorders Center and Department of Neurology, Michigan Medicine, Ann Arbor, MI, USA; Pediatric Pulmonology, Department of Pediatrics and Communicable Diseases, Michigan Medicine, Ann Arbor, MI, USA.
| | - Louise M O'Brien
- Sleep Disorders Center and Department of Neurology, Michigan Medicine, Ann Arbor, MI, USA; Department of Obstetrics and Gynecology, Michigan Medicine, Ann Arbor, MI, USA; Department of Oral and Maxillofacial Surgery, Michigan Medicine, Ann Arbor, MI, USA
| | - Samya Z Nasr
- Pediatric Pulmonology, Department of Pediatrics and Communicable Diseases, Michigan Medicine, Ann Arbor, MI, USA
| | - Ronald D Chervin
- Sleep Disorders Center and Department of Neurology, Michigan Medicine, Ann Arbor, MI, USA
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