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Article ; Online: The novel pre-rRNA detection workflow "Riboprobing" allows simple identification of undescribed RNA species.

Gerhalter, Magdalena / Kofler, Lisa / Zisser, Gertrude / Merl-Pham, Juliane / Hauck, Stefanie M / Bergler, Helmut

2024

Abstract: Ribosomes translate mRNA into proteins and are essential for every living organism. In eukaryotes both ribosomal subunits are rapidly assembled in a strict hierarchical order, starting in the nucleolus with transcription of a common precursor ribosomal ... ...

Abstract	Ribosomes translate mRNA into proteins and are essential for every living organism. In eukaryotes both ribosomal subunits are rapidly assembled in a strict hierarchical order, starting in the nucleolus with transcription of a common precursor ribosomal RNA (pre-rRNA). This pre-rRNA encodes three of the four mature rRNAs which are formed by several, consecutive endonucleolytic and exonucleolytic processing steps. Historically, Northern Blots are used to analyze the variety of different pre-rRNA species, only allowing rough length estimations. Although this limitation can be overcome with Primer Extension, both approaches often use radioactivity and are time consuming and costly. Here we present "Riboprobing" a reverse transcription-based workflow extended by linker ligation for easy and fast detection and characterization of various pre-rRNA species and their 5` as well as 3` ends. Using standard molecular biology lab equipment, our technique allows reliable discrimination of pre-rRNA species not resolved by Northern Blotting (e.g.: 27SA2, 27SA3 and 27SB). The method can be successfully used for analysis of total cell extracts as well as purified pre-ribosomes for a straightforward evaluation of the impact of mutant gene versions or inhibitors. In the course of method development, we identified and characterized a hitherto undescribed aberrant pre-rRNA, arising from LiCl inhibition. This pre-rRNA fragment spans from processing site A1 to E, forming a small RNP that is lacking most early joining assembly factors. This finding expands our knowledge of how the cell deals with severe pre-rRNA processing defects and demonstrates the strict requirement for the 5'ETS for the assembly process.
Language	English
Publishing date	2024-04-05
Publishing country	United States
Document type	Journal Article
ZDB-ID	1241540-6
ISSN	1469-9001 ; 1355-8382
ISSN (online)	1469-9001
ISSN	1355-8382
DOI	10.1261/rna.079912.123
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Article: Linking Increased Isotope Fractionation at Low Concentrations to Enzyme Activity Regulation: 4-Cl Phenol Degradation by Arthrobacter chlorophenolicus A6

Kundu, Kankana / Melsbach, Aileen / Heckel, Benjamin / Schneidemann, Sarah / Kanapathi, Dheeraj / Marozava, Sviatlana / Merl-Pham, Juliane / Elsner, Martin

Environmental science & technology. 2022 Feb. 11, v. 56, no. 5

2022

Abstract: Slow microbial degradation of organic trace chemicals (“micropollutants”) has been attributed to either downregulation of enzymatic turnover or rate-limiting substrate supply at low concentrations. In previous biodegradation studies, a drastic decrease ... ...

Abstract	Slow microbial degradation of organic trace chemicals (“micropollutants”) has been attributed to either downregulation of enzymatic turnover or rate-limiting substrate supply at low concentrations. In previous biodegradation studies, a drastic decrease in isotope fractionation of atrazine revealed a transition from rate-limiting enzyme turnover to membrane permeation as a bottleneck when concentrations fell below the Monod constant of microbial growth. With degradation of the pollutant 4-chlorophenol (4-CP) by Arthrobacter chlorophenolicus A6, this study targeted a bacterium which adapts its enzyme activity to concentrations. Unlike with atrazine degradation, isotope fractionation of 4-CP increased at lower concentrations, from ε(C) = −1.0 ± 0.5‰ in chemostats (D = 0.090 h–¹, 88 mg L–¹) and ε(C) = −2.1 ± 0.5‰ in batch (c₀ = 220 mg L–¹) to ε(C) = −4.1 ± 0.2‰ in chemostats at 90 μg L–¹. Surprisingly, fatty acid composition indicated increased cell wall permeability at high concentrations, while proteomics revealed that catabolic enzymes (CphCI and CphCII) were differentially expressed at D = 0.090 h–¹. These observations support regulation on the enzyme activity level─through either a metabolic shift between catabolic pathways or decreased enzymatic turnover at low concentrations─and, hence, reveal an alternative end-member scenario for bacterial adaptation at low concentrations. Including more degrader strains into this multidisciplinary analytical approach offers the perspective to build a knowledge base on bottlenecks of bioremediation at low concentrations that considers bacterial adaptation.
Keywords	4-chlorophenol ; Arthrobacter chlorophenolicus ; analytical methods ; atrazine ; bacteria ; biodegradation ; bioremediation ; cell walls ; enzyme activity ; enzymes ; fatty acid composition ; isotope fractionation ; microbial growth ; permeability ; phenol ; pollutants ; proteomics
Language	English
Dates of publication	2022-0211
Size	p. 3021-3032.
Publishing place	American Chemical Society
Document type	Article
ISSN	1520-5851
DOI	10.1021/acs.est.1c04939
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Fatty acid-binding protein 5 is a functional biomarker and indicator of ferroptosis in cerebral hypoxia.

Peng, Hao / Xin, Shan / Pfeiffer, Susanne / Müller, Constanze / Merl-Pham, Juliane / Hauck, Stefanie M / Harter, Patrick N / Spitzer, Daniel / Devraj, Kavi / Varynskyi, Borys / Arzberger, Thomas / Momma, Stefan / Schick, Joel A

Cell death & disease

2024 Volume 15, Issue 4, Page(s) 286

Abstract: The progression of human degenerative and hypoxic/ischemic diseases is accompanied by widespread cell death. One death process linking iron-catalyzed reactive species with lipid peroxidation is ferroptosis, which shows hallmarks of both programmed and ... ...

Abstract	The progression of human degenerative and hypoxic/ischemic diseases is accompanied by widespread cell death. One death process linking iron-catalyzed reactive species with lipid peroxidation is ferroptosis, which shows hallmarks of both programmed and necrotic death in vitro. While evidence of ferroptosis in neurodegenerative disease is indicated by iron accumulation and involvement of lipids, a stable marker for ferroptosis has not been identified. Its prevalence is thus undetermined in human pathophysiology, impeding recognition of disease areas and clinical investigations with candidate drugs. Here, we identified ferroptosis marker antigens by analyzing surface protein dynamics and discovered a single protein, Fatty Acid-Binding Protein 5 (FABP5), which was stabilized at the cell surface and specifically elevated in ferroptotic cell death. Ectopic expression and lipidomics assays demonstrated that FABP5 drives redistribution of redox-sensitive lipids and ferroptosis sensitivity in a positive-feedback loop, indicating a role as a functional biomarker. Notably, immunodetection of FABP5 in mouse stroke penumbra and in hypoxic postmortem patients was distinctly associated with hypoxically damaged neurons. Retrospective cell death characterized here by the novel ferroptosis biomarker FABP5 thus provides first evidence for a long-hypothesized intrinsic ferroptosis in hypoxia and inaugurates a means for pathological detection of ferroptosis in tissue.
MeSH term(s)	Ferroptosis ; Fatty Acid-Binding Proteins/metabolism ; Animals ; Humans ; Biomarkers/metabolism ; Mice ; Hypoxia, Brain/metabolism ; Hypoxia, Brain/pathology ; Mice, Inbred C57BL ; Lipid Peroxidation ; Male ; Neoplasm Proteins
Chemical Substances	Fatty Acid-Binding Proteins ; Biomarkers ; FABP5 protein, human ; Fabp5 protein, mouse ; Neoplasm Proteins
Language	English
Publishing date	2024-04-23
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2541626-1
ISSN	2041-4889 ; 2041-4889
ISSN (online)	2041-4889
ISSN	2041-4889
DOI	10.1038/s41419-024-06681-y
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Adaptation of Carbon Source Utilization Patterns of

Marozava, Sviatlana / Merl-Pham, Juliane / Müller, Hubert / Meckenstock, Rainer U

Frontiers in microbiology

2020 Volume 11, Page(s) 1271

Abstract: There are two main strategies known how microorganisms regulate substrate utilization: specialization on one preferred substrate at high concentrations in batch cultures or simultaneous utilization of many substrates at low concentrations in chemostats. ... ...

Abstract	There are two main strategies known how microorganisms regulate substrate utilization: specialization on one preferred substrate at high concentrations in batch cultures or simultaneous utilization of many substrates at low concentrations in chemostats. However, it remains unclear how microorganisms utilize substrates at low concentrations in the subsurface: do they focus on a single substrate and exhibit catabolite repression or do they de-repress regulation of all catabolic pathways? Here, we investigated the readiness of
Language	English
Publishing date	2020-06-23
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2587354-4
ISSN	1664-302X
ISSN	1664-302X
DOI	10.3389/fmicb.2020.01271
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Article: High glucose treatment promotes extracellular matrix proteome remodeling in Mller glial cells.

Sagmeister, Sandra / Merl-Pham, Juliane / Petrera, Agnese / Deeg, Cornelia A / Hauck, Stefanie M

PeerJ

2021 Volume 9, Page(s) e11316

Abstract: Background: The underlying pathomechanisms in diabetic retinopathy (DR) remain incompletely understood. The aim of this study was to add to the current knowledge about the particular role of retinal Mller glial cells (RMG) in the initial processes of DR. ...

Abstract	Background: The underlying pathomechanisms in diabetic retinopathy (DR) remain incompletely understood. The aim of this study was to add to the current knowledge about the particular role of retinal Mller glial cells (RMG) in the initial processes of DR. Methods: Applying a quantitative proteomic workflow, we investigated changes of primary porcine RMG under short term high glucose treatment as well as glycolysis inhibition treatment. Results: We revealed significant changes in RMG proteome primarily in proteins building the extracellular matrix (ECM) indicating fundamental remodeling processes of ECM as novel rapid response to high glucose treatment. Among others, Osteopontin (SPP1) as well as its interacting integrins were significantly downregulated and organotypic retinal explant culture confirmed the selective loss of SPP1 in RMG upon treatment. Since SPP1 in the retina has been described neuroprotective for photoreceptors and functions against experimentally induced cell swelling, its rapid loss under diabetic conditions may point to a direct involvement of RMG to the early neurodegenerative processes driving DR. Data are available via ProteomeXchange with identifier PXD015879.
Language	English
Publishing date	2021-05-18
Publishing country	United States
Document type	Journal Article
ZDB-ID	2703241-3
ISSN	2167-8359
ISSN	2167-8359
DOI	10.7717/peerj.11316
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Article ; Online: Linking Increased Isotope Fractionation at Low Concentrations to Enzyme Activity Regulation: 4-Cl Phenol Degradation by

Kundu, Kankana / Melsbach, Aileen / Heckel, Benjamin / Schneidemann, Sarah / Kanapathi, Dheeraj / Marozava, Sviatlana / Merl-Pham, Juliane / Elsner, Martin

Environmental science & technology

2022 Volume 56, Issue 5, Page(s) 3021–3032

Abstract: Slow microbial degradation of organic trace chemicals ("micropollutants") has been attributed to either downregulation of enzymatic turnover or rate-limiting substrate supply at low concentrations. In previous biodegradation studies, a drastic decrease ... ...

Abstract	Slow microbial degradation of organic trace chemicals ("micropollutants") has been attributed to either downregulation of enzymatic turnover or rate-limiting substrate supply at low concentrations. In previous biodegradation studies, a drastic decrease in isotope fractionation of atrazine revealed a transition from rate-limiting enzyme turnover to membrane permeation as a bottleneck when concentrations fell below the Monod constant of microbial growth. With degradation of the pollutant 4-chlorophenol (4-CP) by
MeSH term(s)	Arthrobacter ; Atrazine ; Biodegradation, Environmental ; Carbon Isotopes/metabolism ; Chemical Fractionation ; Isotopes ; Micrococcaceae ; Phenol
Chemical Substances	Carbon Isotopes ; Isotopes ; Phenol (339NCG44TV) ; Atrazine (QJA9M5H4IM)
Language	English
Publishing date	2022-02-11
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1520-5851
ISSN (online)	1520-5851
DOI	10.1021/acs.est.1c04939
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Article: Time-resolved phosphoproteomic analysis elucidates hepatic 11,12-Epoxyeicosatrienoic acid signaling pathways.

Rahm, Marco / Merl-Pham, Juliane / Adamski, Jerzy / Hauck, Stefanie M

Prostaglandins & other lipid mediators

2019 Volume 146, Page(s) 106387

Abstract: Epoxyeicosatrienoic acids (EETs) are potent lipid mediators with well-established effects in vascular tissues. Recent studies indicated an emerging role of these eicosanoids in metabolic diseases and the EET signaling pathway was shown to be involved in ... ...

Abstract	Epoxyeicosatrienoic acids (EETs) are potent lipid mediators with well-established effects in vascular tissues. Recent studies indicated an emerging role of these eicosanoids in metabolic diseases and the EET signaling pathway was shown to be involved in hepatic insulin sensitivity. However, compared to vascular tissues, there is only limited knowledge about the underlying signaling pathways in the liver. Therefore, we employed an LC-MS/MS-based time-resolved phosphoproteomics approach to characterize 11,12-EET-mediated signaling events in the liver cell line Hepa 1-6. 11,12-EET treatment resulted in the time-dependent regulation of phosphopeptides involved in processes as yet unknown to be affected by EETs, including RNA processing, splicing and translation regulation. Pathway analysis combined with western blot-based validation revealed enhanced AKT/mTOR/p70S6K signaling as demonstrated by increased acute phosphorylation of AKT (Ser473) and p70S6K (Thr389). In addition, 11,12-EET treatment led to differential regulation of phosphopeptides including important mediators of the DNA damage response and we observed a prolonged induction of the etoposide-induced DNA damage marker γH2AX in response to 11,12-EET. In summary, our findings extend current knowledge of 11,12-EET signaling events and emphasize the importance of the AKT/mTOR/p70S6K pathway in hepatic 11,12-EET signaling. Based on the results presented in this study, we furthermore propose a novel role of EET signaling in the regulation of the DNA damage response.
MeSH term(s)	8,11,14-Eicosatrienoic Acid/analogs & derivatives ; 8,11,14-Eicosatrienoic Acid/metabolism ; Cell Line ; Humans ; Liver/metabolism ; Phosphoproteins ; Proteomics ; Signal Transduction
Chemical Substances	Phosphoproteins ; 11,12-epoxy-5,8,14-eicosatrienoic acid (5DOQ38R4UW) ; 8,11,14-Eicosatrienoic Acid (FC398RK06S)
Language	English
Publishing date	2019-10-24
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1426962-4
ISSN	2212-196X ; 1098-8823 ; 0090-6980
ISSN (online)	2212-196X
ISSN	1098-8823 ; 0090-6980
DOI	10.1016/j.prostaglandins.2019.106387
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Zs.A 815: Show issues

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Article: Late Effects of Chronic Low Dose Rate Total Body Irradiation on the Heart Proteome of ApoE

Azimzadeh, Omid / Merl-Pham, Juliane / Subramanian, Vikram / Oleksenko, Kateryna / Krumm, Franziska / Mancuso, Mariateresa / Pasquali, Emanuela / Tanaka, Ignacia B / Tanaka, Satoshi / Atkinson, Michael J / Tapio, Soile / Moertl, Simone

Cancers

2023 Volume 15, Issue 13

Abstract: Recent epidemiologic studies support an association between chronic low-dose radiation exposure and the development of cardiovascular disease (CVD). The molecular mechanisms underlying the adverse effect of chronic low dose exposure are not fully ... ...

Abstract	Recent epidemiologic studies support an association between chronic low-dose radiation exposure and the development of cardiovascular disease (CVD). The molecular mechanisms underlying the adverse effect of chronic low dose exposure are not fully understood. To address this issue, we have investigated changes in the heart proteome of ApoE deficient (ApoE
Language	English
Publishing date	2023-06-29
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2527080-1
ISSN	2072-6694
ISSN	2072-6694
DOI	10.3390/cancers15133417
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Article: Activation of PPARα by Fenofibrate Attenuates the Effect of Local Heart High Dose Irradiation on the Mouse Cardiac Proteome.

Azimzadeh, Omid / Subramanian, Vikram / Sievert, Wolfgang / Merl-Pham, Juliane / Oleksenko, Kateryna / Rosemann, Michael / Multhoff, Gabriele / Atkinson, Michael J / Tapio, Soile

Biomedicines

2021 Volume 9, Issue 12

Abstract: Radiation-induced cardiovascular disease is associated with metabolic remodeling in the heart, mainly due to the inactivation of the transcription factor peroxisome proliferator-activated receptor alpha (PPARα), thereby inhibiting lipid metabolic enzymes. ...

Abstract	Radiation-induced cardiovascular disease is associated with metabolic remodeling in the heart, mainly due to the inactivation of the transcription factor peroxisome proliferator-activated receptor alpha (PPARα), thereby inhibiting lipid metabolic enzymes. The objective of the present study was to investigate the potential protective effect of fenofibrate, a known agonist of PPARα on radiation-induced cardiac toxicity. To this end, we compared, for the first time, the cardiac proteome of fenofibrate- and placebo-treated mice 20 weeks after local heart irradiation (16 Gy) using label-free proteomics. The observations were further validated using immunoblotting, enzyme activity assays, and ELISA. The analysis showed that fenofibrate restored signalling pathways that were negatively affected by irradiation, including lipid metabolism, mitochondrial respiratory chain, redox response, tissue homeostasis, endothelial NO signalling and the inflammatory status. The results presented here indicate that PPARα activation by fenofibrate attenuates the cardiac proteome alterations induced by irradiation. These findings suggest a potential benefit of fenofibrate administration in the prevention of cardiovascular diseases, following radiation exposure.
Language	English
Publishing date	2021-12-06
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2720867-9
ISSN	2227-9059
ISSN	2227-9059
DOI	10.3390/biomedicines9121845
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Article: Proteomic Profiling of Cigarette Smoke Induced Changes in Retinal Pigment Epithelium Cells.

Merl-Pham, Juliane / Gruhn, Fabian / Hauck, Stefanie M

Advances in experimental medicine and biology

2016 Volume 854, Page(s) 785–791

Abstract: Age-related macular degeneration (AMD) is a medical condition usually affecting older adults and resulting in a loss of vision in the macula, the center of the visual field. The dry form of this disease presents with atrophy of the retinal pigment ... ...

Abstract	Age-related macular degeneration (AMD) is a medical condition usually affecting older adults and resulting in a loss of vision in the macula, the center of the visual field. The dry form of this disease presents with atrophy of the retinal pigment epithelium, resulting in the detachment of the retina and loss of photoreceptors. Cigarette smoke is one main risk factor for dry AMD and increases the risk of developing the disease by three times. In order to understand the influence of cigarette smoke on retinal pigment epithelial cells, cultured human ARPE-19 cells were treated with cigarette smoke extract for 24 h. Using quantitative mass spectrometry more than 3000 proteins were identified and their respective abundances were compared between cigarette smoke-treated and untreated cells. Altogether 1932 proteins were quantified with at least two unique peptides, with 686 proteins found to be significantly differentially abundant with p > 0.05. Of these proteins the abundance of 64 proteins was at least 2-fold down-regulated after cigarette smoke treatment while 120 proteins were 2-fold up-regulated. The analysis of associated biological processes revealed an alteration of proteins involved in RNA processing and transport as well as extracellular matrix remodelling in response to cigarette smoke treatment.
MeSH term(s)	Cell Line ; Cell Survival ; Chromatography, Liquid ; Epithelial Cells/metabolism ; Humans ; Proteome/metabolism ; Proteomics/methods ; Retinal Pigment Epithelium/cytology ; Retinal Pigment Epithelium/metabolism ; Smoke ; Tandem Mass Spectrometry ; Tobacco Products
Chemical Substances	Proteome ; Smoke
Language	English
Publishing date	2016
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2214-8019 ; 0065-2598
ISSN (online)	2214-8019
ISSN	0065-2598
DOI	10.1007/978-3-319-17121-0_105
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