Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Proteomic analysis of Naegleria gruberi mitochondria

ABSTRACT: The formation of mitochondria has enabled eukaryotes to thrive and evolve into multitude of unicellular and multicellular species. The nature of the early mitochondria and its relationship to the ancestral host cell is still unknown. Using a phylogenomic approach we have discovered the presence of core subunits of type II secretion pathway (T2SS) in several unicellular eukaryotes (protists) belonging to jakobids, hetereloboseans and malawimonads. We show that the proteins carry mitochondrial signal sequences and are localized in the protist mitochondria.The mitochondria of Nagleria gruberi were isolated by differential centrifugation and analysed by mass spectrometry. The data analyses revealed about 1000 proteins enriched in the mitochondrial fraction including the components of T2SS.

INSTRUMENT(S): Orbitrap Fusion

ORGANISM(S): Naegleria Sp. Nges2

TISSUE(S): Cell Suspension Culture, Cell Culture

SUBMITTER: Karel Harant

LAB HEAD: Mgr. Pavel Doležal, Ph.D.

PROVIDER: PXD007764 | Pride | 2021-05-19

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	fo1510.raw	Raw
	fo1520.raw	Raw
	fo23.raw	Raw
	g1510.raw	Raw
	g1520.raw	Raw

Items per page:

1 - 5 of 22

Similar Datasets

Proteomic interactome of C. elegans Mediator complex subunit 28 (MDT-28) reveals predominant association with a restricted set of core Mediator subunits and an affinity to additional structural and enzymatic proteins

Project description:Transcription factors exert their regulatory potential on RNA Polymerase II machinery through a multiprotein complex called Mediator complex or Mediator. The Mediator complex integrates regulatory signals from cell regulatory cascades with the regulation by transcription factors. The Mediator complex consists of 25 subunits in Saccharomyces cerevisiae and 30 or more subunits in multicellular eukaryotes. Mediator subunit 28 (MED28), along with MED30, MED23, MED25 and MED26 belong to presumably evolutionarily new subunits that seem to be absent in unicellular eukaryotes and are likely to have evolved together with multicellularity and cell differentiation. Previously, we have shown that an originally uncharacterized predicted gene F28F8.5 is the true MED28 orthologue in Caenorhabditis elegans (MDT-28) and showed that it is involved in a spectrum of developmental processes. Here, we studied the proteomic interactome of MDT-28 edited as GFP::MDT-28 using Crispr/Cas9 technology or MDT-28::GFP expressed from extrachromosomal arrays in transgenic C. elegans exploiting the GFP-TRAP system and mass spectrometry. The results show that MDT-28 associates with the Head module subunits MDT-6, MDT-8, MDT-11, MDT-17, MDT-20, MDT-22 and MDT-30 and the Middle module subunit MDT-14. The analyses also identified additional proteins as preferential MDT-28 interactants including chromatin organizing proteins, structural proteins and enzymes. The results provide evidence for MDT-28 engagement in the Mediator Head Module and support the possibility of physical (direct or indirect) interaction of MDT-28 with additional proteins, reflecting a transcription-regulating potential of primarily structural and enzymatic proteins at the level of the Mediator complex.

2020-07-15 | PXD015552 | Pride

Mitochondrial respiration is necessary to combat oxidative stress in quiescent cells

Project description:Mitochondrial oxidative phosphorylation (OXPHOS) makes ATP and supports biosynthesis during proliferation, but its role in non-proliferating cells, beyond ATP production, is less understood. Here we show that OXPHOS protects quiescent (but not proliferating) cells from oxidative stress. Using in vivo models of OXPHOS deficiency (whole body and endothelium-specific) we show that OXPHOS mediated resistance to ROS (i) maintains selectivity of ROS-based anticancer therapy by protecting normal tissues during treatment, and in quiescent endothelium (ii) ameliorates systemic LPS-induced inflammation and (iii) attenuates symptoms of the inflammatory bowel disease. ROS-resistance provided by OXPHOS is independent of its role in biosynthesis or NADH recycling. Instead, in quiescent cells OXPHOS constitutively generates low levels of endogenous ROS that support basal autophagic flux and protect from exogenous ROS challenge. Hence, during evolution cells acquired mitochondria to profit from oxidative metabolism, but also built in an OXPHOS-dependent mechanism to guard against the resulting oxidative stress.

2022-10-13 | PXD021376 | Pride

Project description:Non-photosynthetic plastid-bearing, unicellular eukaryotes

| PRJDB10135 | ENA

unicellular eukaryotes and helminths

Project description:Unicellular eukaryotes and helminths Targeted loci environmental

| PRJNA495046 | ENA

Translocase of the Outer Membrane (TOM complex) of hydrogenosomes in Trichomonas vaginalis

Project description:Mitochondria originated from α-proteobacterial endosymbionts, and the endosymbiont-to-organelle transition is tightly linked to the establishment of protein import pathways. The initial import of most proteins is mediated by the translocase of the outer membrane (TOM). Although TOM is common to all forms of mitochondria, recent studies have shown diversity of TOM subunits between main eukaryotic lineages. However, experimental knowledge is currently limited to a few model organisms. Here, we analysed the TvTOM complex in hydrogenosomes, an anaerobic form of mitochondria found in the excavate Trichomonas vaginalis. Using the pore-forming TvTom40-2 as bait, we immunoprecipitated the high molecular weight TvTOM complex both under crosslinking and native conditions and performed label-free quantitative mass spectrometry (LFQ-MS) to identify the components of the TvTOM complex. Further, we used two proteins that were enriched, Homp36 and Sam50 as baits for reciprocal experiments.

2019-01-07 | PXD010850 | Pride

Comparative integrated omics analysis of the Hfq regulon in Bordetella pertussis

Project description:This study represents the first attempt to characterize the RNA chaperone Hfq regulon in bacterial pathogen using an integrative omics approach. Gene expression profiles were analyzed by RNA-seq and protein amounts in cell-associated and cell-free fractions were determined by LC-MS/MS technique. Comparative analysis of transcriptomic and proteomic data revealed solid correlation considering the role of Hfq in post-transcriptional control of gene expression. Importantly, our study confirms and further enlightens the role of Hfq in pathogenicity of B. pertussis.

2019-07-02 | PXD013953 | Pride

COMPARATIVE OMICS ANALYSIS OF HISTORICAL AND RECENT ISOLATES OF BORDETELLA PERTUSSIS

Project description:Despite high vaccination coverage, pertussis is on the rise in many countries including Czech Republic. To better understand B. pertussis resurgence we compared the changes in genome structures between Czech vaccine and circulating strains and subsequently, we determined how these changes translated into global transcriptomic and proteomic profiles. The whole-genome sequencing revealed that both historical and recent isolates of B. pertussis display substantial variation in genome organization and cluster separately. The RNA-seq and LC-MS/MS analyses indicate that these variations translated into discretely separated transcriptomic and proteomic profiles. Compared to vaccine strains, recent isolates displayed increased expression of flagellar genes and decreased expression of polysaccharide capsule operon. Czech strains (Bp46, K10, Bp155, Bp318 and Bp6242)exhibited increased expression of T3SS and sulphate metabolism genes when compared to Tohama I. In spite of 50 years of vaccination the Czech vaccine strains (VS67, VS393 and VS401) differ from recent isolates to a lesser extent than from another vaccine strain Tohama I.

2021-09-08 | PXD015184 | Pride

Dynamic T. vaginalis secretome and secretion of β-amalyses

Project description:During infection of the urogenital tract, the parasite Trichomonas vaginalis is challenged by factors such as nutrient limitation, the host immune response and coexistence with other members of the microbial fauna. Thus establishment of trichomonad infection depends on multifactorial host-parasite interactions, that involve both contact-dependent mechanisms, such as adherence to vaginal epithelial cells, contact-dependent extracellular killing of host cells, and active phagocytosis of host cells and bacteria, as well as contact independent mechanisms that include secretion of soluble biologically active molecules. To get more insight into the secreted proteome of T. vaginalis we detected and quantified released proteins at consecutive time points. Out of 2072 detected proteins, 89 were estimated to significantly increase in time. These include leishmaniolysin-like metallopeptidases, cathepsin-like cystein peptidases and a number of proteins involved in sugar metabolism, most notably beta-amylases, which may be significant in utilization of host-cell derived glycogen. We further discovered a large group of secreted hypothetical proteins with predicted triple tyrosine domain that may facilitate interaction with the extracellular matrix of the host epithelium.

2017-12-19 | PXD007034 | Pride

Resolving oxidative damage to methionine by an unexpected membrane-associated stereoselective reductase discovered using chiral fluorescent probes

Project description:Non-enzymatic oxidative processes in living organisms are one of the inevitable consequences of respiration and environmental conditions. They can lead to the formation of two stereoisomers (R and S) of methionine sulfoxide, and the redox balance between methionine and methionine sulfoxide in proteins has profound functional consequences. Methionine oxidation can be reverted enzymatically by methionine sulfoxide reductases (Msrs). The two enzyme classes known to fulfil this role are MsrA (reducing (S)-sulfoxides), and MsrB (reducing (R)-sulfoxides). They are strictly stereoselective and conserved throughout the tree of life. Under stress conditions such as stationary phase and nutrient starvation, E.coli upregulates expression of MsrA but similar effect has not been described for MsrB, raising a conundrum of the pathway enabling reduction of the (R)-isomer of methionine sulfoxide in these conditions. Using the recently developed chiral fluorescent probes Sulfox-1 we show that in stationary phase stressed E. coli, MsrA does have a stereocomplementary, (R)-sulfoxide-reducing counterpart. However, this activity is not provided by MsrB as expected, but instead by the DMSO reductase complex DmsABC, widely conserved in bacteria. This finding reveals an unexpected diversity in the metabolic enzymes of redox regulation concerning methionine, which should be taken into account in any antibacterial strategies exploiting oxidative stress.

2019-06-12 | PXD013610 | Pride

Beyond self-resistance: ABCF ATPase LmrC is a signal-transducing component of an antibiotic-driven signaling cascade hastening the onset of lincomycin biosynthesis

Project description:In natural environments, antibiotics are an important instrument of inter-species competition. At subinhibitory concentrations, they act as cues or signals inducing antibiotic production: however, our knowledge of well-documented antibiotic-based sensing systems is limited. Here, for the soil actinobacterium Streptomyces lincolnensis we describe a fundamentally new ribosome-mediated signaling cascade that accelerates the onset of lincomycin production in response to an external ribosome-targeting antibiotic to synchronize the antibiotic production within the population. The entire cascade is encoded within the lincomycin biosynthetic gene cluster (BGC) and besides the transcriptional regulator, LmbU it consists of three lincomycin resistance proteins: a lincomycin transporter, LmrA, a 23S rRNA methyltransferase, LmrB, both conferring a high resistance, and an ABCF ATPase LmrC that confers only moderate resistance but is indispensable for the antibiotic-induced signal transduction. Specifically, the antibiotic sensing occurs via a ribosome-mediated attenuation, which activates LmrC production in response to lincosamide, streptogramin A, or pleuromutilin antibiotics. Then, the ribosome-operating LmrC ATPase activity triggers the transcription of lmbU and consequently the expression of lincomycin BGC. Finally, the production of LmrC is downregulated by LmrA and LmrB which reduces the amount of the ribosome-bound antibiotic and thus fine-tune the cascade. We propose that analogous ABCF-mediated signaling systems are relatively common because many BGCs for ribosome-targeting antibiotics encode an ABCF-protein accompanied by additional resistance protein(s) and transcriptional regulators. Moreover, we revealed that three of eight co-produced ABCF proteins of S. lincolnensis are clindamycin-responsive thus the ABCF-mediated antibiotic signaling might be generally utilized tool of chemical communication.

2021-08-18 | PXD026093 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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