Browse
Submit Data
Databases
API
Help

Dataset Information

234 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Proteome-based new insights into dimethyl sulfide metabolism of Hyphomicrobium denitrificans

ABSTRACT: To get further insights in the dimethyl sulfide metabolism of Hyphomicrobium denitrificans, a LC-MS proteomic approach was used. The total protein of three biological replicates of H. denitrificans grown on dimethyl sulfide was compared with three biological replicates grown on dimethylamine. This approach resulted in the identification of several new proteins with a potential involvement in dimethyl sulfide degradation.

INSTRUMENT(S): LTQ Orbitrap Velos

ORGANISM(S): Hyphomicrobium Denitrificans Atcc 51888

SUBMITTER: Marc Sylvester

LAB HEAD: Christiane Dahl

PROVIDER: PXD009030 | Pride | 2018-06-14

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Publications

A novel bacterial sulfur oxidation pathway provides a new link between the cycles of organic and inorganic sulfur compounds.

Koch Tobias T Dahl Christiane C

The ISME journal 20180621 10

Dimethylsulfide (DMS) plays a globally significant role in carbon and sulfur cycling and impacts Earth's climate because its oxidation products serve as nuclei for cloud formation. While the initial steps of aerobic DMS degradation and the fate of its carbon atoms are reasonably well documented, oxidation of the contained sulfur is largely unexplored. Here, we identified a novel pathway of sulfur compound oxidation in the ubiquitously occurring DMS-degrader Hyphomicrobium denitrificans X<sup>T</ ...[more]

PMID: 29930335

Similar Datasets

MFSD1 KO Liver - Lysosomes are a major site of intracellular acidic hydrolase-mediated proteolysis and cellular degradation

Project description:Lysosomes are a major site of intracellular acidic hydrolase-mediated proteolysis and cellular degradation. The export of low-molecular catabolic end products from the lysosomal lumen to the cytosol is facilitated by polytopic transmembrane proteins which mediate secondary active or passive transport. One of these proteins is MFSD1, a so far uncharacterized lysosomal 12 transmembrane domain-containing family member of the major facilitator superfamily. MFSD1 is, uncommon for a lysosomal membrane protein, not N-glycosylated. It contains a dileucine-based sorting motif that is essential for its transport to lysosomes. Lysosomes from mouse liver of MFSD1 knock-out mice were isolated and analyzed by TMT labelling, as well as whole liver protein extracts, both in comparison to wildtype controls.

2019-10-28 | PXD014241 | Pride

Disease-linked lysine glutarylation impairs function and interactions of mitochondrial proteins and contribute to mitochondrial heterogeneity

Project description:Inherited deficiencies of the lysine and tryptophan catabolic pathways, due to mutations in the glutaryl-CoA-dehydrogenase (GCDH) gene, cause glutaric aciduria type 1 (GA1). In mammals two metabolic routes for L-lysine oxidation exist, the mitochondrial saccharopine pathway, which is predominant in extracerebral tissue and the peroxysomal/cytosolic pipecolate pathway, the main pathway in adult brain. A unique feature of all pathways is the formation of glutaryl-CoA that is converted into crotonyl-CoA via GCDH. In this study we identified increased lysine glutarylation, a novel reversible post-translational modification, in various tissues and cultured cells of Gcdh KO mice as a result of glutaryl-CoA accumulation. Our analysis revealed that glutarylation is widespread in mitochondria. By using a proteomic approach, we identified 37 and 154 glutarylated mitochondrial proteins in brain and liver tissue from Gcdh KO mice, respectively. We further showed that glutarylation supresses glutamate dehydrogenase (GDH) and carbonic anhydrase 5B activity, plus the direct interaction between GCDH and GDH.

2018-07-11 | PXD007881 | Pride

Transcriptome analysis of Paracoccus denitrificans during Cu-limitation

Project description:Transcriptional profiling of Paracoccus denitrificans PD1222 wild type grown to mid-exponential phase in minimal media with either 13 uM (Cu-H) or 0.5 uM (Cu-L) Cu regimes. The goal was to define the effects of Cu-limitation on denitrification genes Two growth conditions, three biological replicates of each condition. Each sample hybridised in a two-channel hybridization against Paracoccus denitrificans genomic DNA as the comparator/reference, which also acted as a control for spot quality. Cu-concentration 13 uM (Cu-H) versus 0.5 uM Cu (Cu-L) in anaerobic growth conditions.

2013-11-18 | E-GEOD-48577 | biostudies-arrayexpress

RNA-seq of Paracoccus denitrificans Pd1222 and a ramB deletion mutant during growth on succinate and acetate

Project description:The alphaproteobacterium Paracoccus denitrificans Pd1222 has two different, yet functionally redundant acetyl-CoA assimilation routes: the Ethylmalonyl-CoA pathway (EMCP) and the glyoxylate cycle (GC). The EMPC and the GC each tightly control the balance between catabolism and anabolism by shifting flux away from the oxidation of acetyl-CoA in the tricarboxylic acid (TCA) cycle towards biomass formation. RamB (encoded by Pden_1365), a member of the ScfR family, is a transcriptional regulator in P. denitrificans Pd1222 that controls expression of GC. To analyze the role of RamB in the coordinated regulation of metabolic plasticity, we analyzed the global transcriptome of P. denitrificans Pd1222, as well as the ramB-deletion strain during mid-exponential growth phase on defined minimal medium with acetate or succinate as carbon sources.

2023-06-06 | E-MTAB-12482 | biostudies-arrayexpress

Differential proteome between ejaculate and epididymal sperm represents a key factor for sperm freezability in wild small ruminants

Project description:The proteome of two sperm sources, epididymal and ejaculated sperm, was compared and associated with sperm freezing capacity using samples collected from three wild small ruminants species. Protein identification was performed using two databases separately (Ovis aries and Capra hircus NCBI) and results were later combined.

2021-05-04 | PXD017462 | Pride

Proteomic characterization of Hsp78-interacting proteins highlights chaperone role during protein aggregation in mitochondria under heat stress - Part B Aggregation

Project description:Chaperones of the Hsp100 chaperone family support protein homeostasis, the maintenance of protein activity under stress, by refolding aggregated proteins or targeting them for degradation. Hsp78, the ClpB-type mitochondrial member of the Hsp100 family, can be found in lower eukaryotes like yeast. Although Hsp78 has been shown to contribute to protection against elevated temperatures in yeast, the biochemical mechanisms underlying this mitochondria-specific thermotolerance are still largely unclear. To identify endogenous chaperone substrate proteins, we generated an Hsp78-ATPase mutant with a stabilized substrate binding behavior. We used two SILAC-based quantitative mass spectrometry approaches to analyze the role of Hsp78 during heat stress-induced mitochondrial protein aggregation and disaggregation processes on a proteomic level. In the first setup, Hsp78-interacting polypeptides were identified to reveal the endogenous substrate spectrum of the chaperone. Our analysis revealed that Hsp78 is interacting with a wide variety of proteins related to metabolic functions including energy production and protein synthesis, as well as other chaperones, thus maintaining crucial functions for mitochondrial stress resistance. We compared these interaction data with a second experimental setup that focused on the on overall aggregation and disaggregation processes in mitochondria under heat stress on a proteomic level. This revealed specific aggregation-prone protein populations and demonstrated the direct quantitative impact of Hsp78 on stress-dependent protein solubility different conditions and. We conclude that Hsp78 together with its cofactors represents a recovery system that protects major mitochondrial metabolic functions during as well restores protein biogenesis capacity after heat stress.

2022-09-20 | PXD030436 | Pride

Proteomic characterization of Hsp78-interacting proteins highlights chaperone role during protein aggregation in mitochondria under heat stress - Part A Protein Interactions

2022-09-20 | PXD030405 | Pride

Transcriptomic and Proteomic Insight into the Mechanism of Cyclooctasulfur- versus Thiosulfate-Oxidation by the Chemolithoautotroph Sulfurimonas denitrificans

Project description:Chemoautotrophic bacteria belonging to the genus Sulfurimonas in the class Campylobacteria (formerly classified as Epsilonproteobacteria) play a key role in the sulfur cycle in a variety of oxygen-deficient or –limited and sulfide-rich marine and terrestrial environments. Previously, they were identified as key players in the turnover of zero-valence sulfur, a central intermediate in the marine sulfur cycle, and S. denitrificans was further shown to be able to oxidize cyclooctasulfur. However, at present the mechanism involved in the activation and metabolism of cyclooctasulfur is not known. To this end, we assessed the transcriptome and proteome of S. denitrificans grown with either thiosulfate or cyclooctasulfur as the electron donor. While the overall profiles under the two growth conditions were rather similar, distinct differences were observed that could be attributed to the utilization of cyclooctasulfur. This included a higher abundance of expressed genes and proteins related to attachment in the presence of cyclooctasulfur and the differential expression of the sulfur-oxidation multienzyme complex (SOX). S. denitrificans uses the SOX system for the oxidation of reduced sulfur compounds, including two copies of the sulfur-binding SoxYZ proteins, encoded in two gene clusters: soxABXYZ1 and soxCDYZ2. While the proteins of both operons of the SOX system were detected in the presence of thiosulfate, only proteins of the soxCDYZ2 operon were detected when grown with cylcooctasulfur. Based on these findings a model for the oxidation of cylcooctasulfur is being proposed that might also apply to other Campylobacteria that share the same arrangement of the SOX system. Our results have implications for interpreting metatranscriptomic and -proteomic data and for the observed high level of diversification of soxYZ2 among sulfur-oxidizing Campylobacteria.

2019-07-22 | PXD009127 | Pride

Proteomic analysis of the role of the quality control protease LONP1 in mitochondrial protein aggregation

Project description:The mitochondrial matrix protease LONP1 is an essential part of the organellar protein quality control system. LONP1 has been shown to be involved in respiration control and apoptosis. Furthermore, a reduction in LONP1 level correlates with ageing processes. Up to now, the effects of a LONP1 defect were mostly studied by utilizing transient, siRNA-mediated knockdown approaches. We generated a new cellular model system for studying the impact of LONP1 on mitochondrial protein homeostasis by a CRISPR/Cas-mediated genetic knockdown (gKD). These cells show a stable reduction of LONP1 along with a mild phenotype characterized by absent morphological differences and only small negative effects on mitochondrial functions under normal culture conditions. To assess the consequences of a permanent LONP1 depletion on the mitochondrial proteome, we analyzed the alterations of protein levels by quantitative mass spectrometry, demonstrating small adaptive changes, in particular concerning mitochondrial protein biogenesis. In an additional proteomic analysis, we determined the temperature-dependent aggregation behavior of mitochondrial proteins and its dependence on a reduction of LONP1 activity, demonstrating the important role of the protease for mitochondrial protein homeostasis in mammalian cells. We identified a significant number of mitochondrial proteins that are affected by LONP1 activity concerning their stressinduced solubility. Taken together, our results suggest a very good applicability of the LONP1 gKD cell line as a model system for human ageing processes.

2022-01-31 | PXD026941 | Pride

Effect of sulfide on growth physiology and gene expression of Desulfovibrio vulgaris Hildenborough

Project description:The effect of sulfide stress on Desulfovibrio vulgaris Hildenborough (DvH) gene expression was determined by comparing the gene expression profiles of DvH under conditions in which sulfide was allowed to accumulate (high sulfide, average concentration 10 mM) against DvH cells grown under conditions in which sulfide was removed by continuous gassing (low sulfide, average concentration 1 mM). High sulfide significantly decreased the instantaneous growth rate constant and final cell density of the culture indicating a decreased bioenergetic fitness. Changes in gene expression caused by exposure to high sulfide were determined using full-genome DvH microarrays. The transcription of ribosomal protein-encoding genes was decreased, in agreement with the lower growth rate of DvH under high sulfide conditions. Interestingly, expression of the gene for DsrD, located downstream of the genes for dissimilatory sulfite reductase (DsrAB) was also strongly down-regulated. In contrast, the expression of many genes involved in iron accumulation, stress response and proteolysis, and chemotaxis were increased. This indicates that high sulfide represents a significant stress condition, in which the bioavailability of metals like iron may be lowered and in which proteins (e.g. metalloenzymes) may need to be refolded, or proteolytically degraded. Overall this leads to a reduced growth rate and less efficient biomass production with available resources. For each condition 2 unique biological samples were hybridized to 4 arrays that each contained duplicate spots. Genomic DNA was used as universal reference.

2010-05-06 | E-GEOD-15073 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data