PPARα-mediated peroxisome induction compensates PPARγ-deficiency in bronchiolar club cells

Karnati, Srikanth; Oruqaj, Gani; Janga, Harshavardhan; Colasante, Claudia; Veldhoven, Paul P. Van; Braverman, Nancy; Pilatz, Adrian; Mariani, Thomas J.; Baumgart-Vogt, Eveline

doi:10.1371/journal.pone.0203466

Cited by 3 publications

(2 citation statements)

References 35 publications

(58 reference statements)

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“…Similarly, the means to solubilize EPS enables a range of approaches to be applied for assigning function, not least of all accurate quantification, but also immunofluorescence microscopy 58 , single molecular structural (e.g. circular dichroism) 59 and biophysical (e.g.…”

Section: Discussionmentioning

confidence: 99%

Extracellular protein isolation from the matrix of anammox biofilm using ionic liquid extraction

Wong

Natarajan

Boleij

et al. 2020

Appl Microbiol Biotechnol

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Anaerobic ammonium oxidation (anammox) performing bacteria self-assemble into compact biofilms by expressing extracellular polymeric substances (EPS). Anammox EPS are poorly characterized, largely due to their low solubility in typical aqueous solvents. Pronase digestion achieved 19.5 ± 0.9 and 41.4 ± 1.4% (w/w) more solubilization of Candidatus Brocadia sinicaenriched anammox granules than DNase and amylase respectively. Nuclear magnetic resonance profiling of the granules confirmed that proteins were dominant. We applied ionic liquid (IL) 1-ethyl-3-methylimidazolium acetate and N,N-dimethylacetamide (EMIM-Ac/DMAc) mixture to extract the major structural proteins. Further treatment by anion exchange chromatography isolated homologous S/T-rich proteins BROSI_A1236 and UZ01_01563, which were major components of the extracted proteins and sequentially highly similar to putative anammox surface-layer (S-layer) protein KUSTD1514. EMIM-Ac/DMAc extraction enriched for these putative S-layer proteins against all other major proteins, along with six monosaccharides (i.e. arabinose, xylose, rhamnose, fucose, galactose and mannose). The sugars, however, contributed <0.5% (w/w) of total granular biomass, and were likely coenriched as glycoprotein appendages. This study demonstrates that S-layer proteins are major constituents of anammox biofilms and can be isolated from the matrix using an ionic liquidbased solvent.

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Section: Discussionmentioning

confidence: 99%

Extracellular protein isolation from the matrix of anammox biofilm using ionic liquid extraction

Wong

Natarajan

Boleij

et al. 2020

Appl Microbiol Biotechnol

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“…In nonhaematopoietic cells, a mechanistic understanding of PPARγ is still largely lacking but there is some evidence for a role in the development of emphysema 34 and a minor role in lipid metabolism of club cells. 36 By contrast, in AM it was shown to be crucial for their development by regulating differentiation of lung fetal monocytes after birth. 32 Perinatal induction of granulocyte-macrophage colonystimulating factor (GM-CSF) expression in lung epithelial cells in turn induces PPARγ in lung fetal monocytes, which then give rise to a selfrenewing AM compartment.…”

Section: Transcription Factors: Peroxisome Proliferator-activated Recmentioning

confidence: 98%

What Makes the Lung Unique – Tissue-Specific Immunity in the Respiratory Tract

2020

EMJ

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The immune system constitutes a critical mechanism of the human body to preserve health and mitigate disease. In the lung, immunity is seen as a critical driver in many respiratory diseases, in particular in those characterised by aberrant inflammation, such as chronic obstructive pulmonary disease, fibrosis, and asthma. In this review, the specialised set of immune cells and lung tissue-specific regulators, including key cytokines such as granulocyte-macrophage colony-stimulating factor and transforming growth factor β, that control immune responses in the respiratory tract will be discussed. Furthermore, the current understanding of the impact of key environmental components such as the role of oxygen and lung microbiota on lung immunity will be highlighted. The goal is to identify the unique aspects of lung immune biology to facilitate insights into the aetiology of common lung inflammatory diseases and to provide the basis for a deeper mechanistic understanding of the underlying immune processes. Finally, key future avenues of research such as using more comprehensive quantitative approaches for elucidating molecular disease mechanisms as well as the potential to exploit tissue-specific regulators of immunity for therapy of lung inflammatory disorders will be discussed.

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Isolation of a putative S-layer protein from anammox biofilm extracellular matrix using ionic liquid extraction

Wong

Natarajan

Boleij

et al. 2019

Preprint

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25Anaerobic ammonium oxidation (anammox) performing bacteria self-assemble into compact 26 biofilms by expressing extracellular polymeric substances (EPS). Anammox EPS are poorly 27 characterized, largely due to their low solubility in typical aqueous solvents. Pronase digestion 28 cationic exchange resin (CER) 23 , physical methods such as centrifugation, heating and 74 sonication or chemical methods by using organic solvents (detergents and ethanol), have been 75 made. However, to date no exopolymer has been isolated from the matrix of anammox biofilms, 76 which is a minimum requirement for subsequent biophysical and functional analysis. 77 While some metabolic proteins are conserved between anammox species (e.g. the c-type heme 78 proteins) 24 , it is unknown whether any extracellular proteins are similarly conserved. It has been 79 reported that surface layer (S-layer) proteins may be common to anammox biofilms as a 80 structural component of the cell. For example, KUSTD1514 forms a shell on the outside of the 81 cell envelope of Ca. Kuenenia stuttgartsiensis 25 , while a homologous S-layer protein is a major 82 EPS constituent of Ca. Brocadia-enriched granular biofilm and hypothesized to also contribute 83 to biofilm matrix structure (i.e. following shedding) 26 . S-layer proteins could be important to 84 biofilm formation more broadly 27 . Describing a function for S-layer proteins in biofilm 85formation is confounded by the fact that they are embedded in EPS and the S-layer protein has 86 not been isolated from the anammox biofilm matrix. 87To address the challenge of processing anammox EPS, we used ionic liquid 1-ethyl-3-methyl 88 imidazolium acetate (EMIM-Ac) to dissolve a laboratory anammox granular biofilm. 89Imidazolium-based ionic liquids are green solvents that have also been applied to process 90 similarly recalcitrant biopolymers (e.g. cellulose and chitosan) 28 , as protein stabilizers and co-91 solvents, and enzyme catalysts. We extracted and purified the putative S-layer protein from a 92 laboratory anammox granular biofilm. We found a putative S-layer protein to be the dominant 93 polymer in our biofilm extract. While six monosaccharides were co-enriched with the EPS, they 94 contributed <0.5% (w/w) of total granular biomass and were all common protein o-95 glycosylating sugars. It is thus likely that they were enriched as glycoprotein appendages rather 96 than free exopolysaccharides. We provide further support for an important role for S-layer 97 proteins in anammox biofilms, and present a method, involving EMIM-Ac, that allows for S-98 5 layer proteins to be isolated from complex matrices such as biofilm EPS. This will inform on 99 the role of S-layer proteins in anammox biofilm formation. 100 Materials and methods 101 102 Figure 1: Schematic diagram of anammox extracellular polymeric substances (EPS) extraction and 103 purification with ionic liquid (IL) 104 105 Anammox granular sludge enrichment 106 Anammox granular sludges (GR) were cultivated in a 4 L reactor seeded with activated s...

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PPARα-mediated peroxisome induction compensates PPARγ-deficiency in bronchiolar club cells

Cited by 3 publications

References 35 publications

Extracellular protein isolation from the matrix of anammox biofilm using ionic liquid extraction

Extracellular protein isolation from the matrix of anammox biofilm using ionic liquid extraction

What Makes the Lung Unique – Tissue-Specific Immunity in the Respiratory Tract

Isolation of a putative S-layer protein from anammox biofilm extracellular matrix using ionic liquid extraction

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