Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Subcellular distribution of enzymes determined by rapid digitonin fractionation of isolated hepatocytes.

ABSTRACT: Conditions were determined for rapid separation of cytosolic and mitochondrial compartments by digitonin fractionation of rat hepatocytes. The minimum time required for separation of mitochondrial and cytosolic enzyme markers decreased rapidly with increasing temperature. Kyro EOB, a non-ionic detergent, increases the release of cytosolic enzymes, particularly at lower temperatures. Experimental procedures are described for greater than 90% release of cytosolic enzymes and less than 2% release of mitochondrial enzymes in 3s. By using appropriate concentrations of digitonin and Kyro EOB in a fractionation medium maintained at 1 degrees C and a minimum time of exposure to the medium, nearly separate patterns of release were obtained for enzyme markers for the cytosol, mitochondrial matrix and mitochondrial intermembrane space. The distribution of enzymes that exist in more than one of these compartments was quantified by comparing their rates of release with those of marker enzymes. The cytosol/mitochondrial-matrix distributions for such enzymes in hepatocytes from starved rats were 16%/84% for aspartate aminotransferase, 34%/66% for fumarase and 77%/23% for ATP citrate lyase. In hepatocytes from rats that were induced to synthesize ATP citrate lyase by starvation and re-feeding, the ratio had increased to 95%/5%. The maximum cytosol/intermembrane-space ratio for adenylate kinase was 8%/92%. A procedure is also described for treating commercial digitonin that increases its solubility in water from about 1mg/ml to more than 800mg/ml.

SUBMITTER: Janski AM

PROVIDER: S-EPMC1161592 | biostudies-other | 1980 Feb

REPOSITORIES: biostudies-other

ACCESS DATA

Json Xml

Similar Datasets

Cadmium accumulation, subcellular distribution and chemical fractionation in hydroponically grown Sesuvium portulacastrum [Aizoaceae].

Project description:Sesuvium portulacastrum is a well-known halophyte with considerable Cd accumulation and tolerance under high Cd stress. This species is also considered as a good candidate of Cd phytoremediation in the polluted soils. However, the mechanism of Cd accumulation, distribution and fractionation in different body parts still remain unknown. Seedlings of Sesuvium portulacastrum were studied hydroponically under exposure to a range of Cd concentrations (50 μM or μmol/L to 600 μM or μmol/L) for 28 days to investigate the potential accumulation capability and tolerance mechanisms of this species. Cd accumulation in roots showed that the bio-concentration factor was > 10, suggesting a strong ability to absorb and accumulate Cd. Cd fractionation in the aboveground parts showed the following order of distribution: soluble fraction > cell wall > organelle > cell membrane. In roots, soluble fraction was mostly predominant than other fractions. Cd speciation in leaves and stems was mainly contained of sodium chloride and deionised water extracted forms, suggesting a strong binding ability with pectin and protein as well as with organic acids. In the roots, inorganic form of Cd was dominant than other forms of Cd. It could be suggested that sodium chloride, deionised water and inorganic contained form of Cd are mainly responsible for the adaption of this plant in the Cd stress environment and alleviating Cd toxicity.

| S-EPMC7769616 | biostudies-literature

Mitochondrial and cytosolic ATP/ADP ratios in isolated hepatocytes. A comparison of the digitonin method and the non-aqueous fractionation procedure.

Project description:The ratio of ATP content/ADP content in the mitochondrial matrix was found to be 2.07 +/- 0.21 and 2.26 +/- 0.22 as determined with six different preparations of isolated hepatocytes subfractionated with the digitonin and non-aqueous-fractionation procedures, respectively. In contrast, the mitochondrial matrix ATP/ADP determined with isolated haemoglobin-free perfused liver by using the non-aqueous-fractionation procedure was about 0.2, whereas the cytosolic values obtained with isolated cells and with the intact organ were similar. It is concluded that the relatively higher ATP/ADP ratio in the mitochondrial matrix of isolated hepatocytes represents a biochemical difference due to properties of the model rather than a methodological artifact.

| S-EPMC1162423 | biostudies-other

Validity of the digitonin method for metabolite compartmentation in isolated hepatocytes.

Project description:1. A modification of the digitonin method of Zuurendonk & Tager (1974) (Biochim. Biophys. Acta 333, 393-399) (i.e. the 'convaentional' method) was developed that allows the fractionation of isolated hepatocytes at -5 degrees C (i.e. 'low-temperature' method). 2. With respect to compartmentation of adenine nucleotides, glutamate and citrate, the two methods yielded very similar results. 3. In contrast, the mitochondrial amounts of aspartate and malate, as revealed by the low-temperature method, were about twice as high as those found by the conventional procedure. No change in the total cellular content occurred. 4. With n-butylmalonate and glisoxepid present in the conventional digitonin medium, significantly higher amounts of malate and aspartate respectively were found in the mitochondrial pellets. The results obtained by the low-temperature method, however, were not influenced by the these inhibitors. 5. It is concluded that under the conventional conditions of cell fractionation no appreciable redistribution of adenine nucleotides, glutamate and citrate occurs.

| S-EPMC1162557 | biostudies-other

Subcellular distribution of hepatic bile acid-conjugating enzymes.

Project description:1. The subcellular location of enzymes conjugating bile acids with glycine or taurine was investigated by centrifugation of rat liver homogenates. 2. [14C]Cholic acid-conjugating activity was predominantly associated with the soluble-microsomal region of the gradient after centrifugation in a Ti-15 zonal rotor but the bulk of the conjugating activity sedimented with mitochondrial-lysosomal fractions in differential pelleting experiments. 3. Cholate: CoA ligase (EC 6.2.1.7) and cholyltransferase (EC 2.3.1) were not enriched in purified Golgi or plasma-membrane fractions. Cholate: CoA ligase was distributed evenly between rough- and smooth-surfaced microsomal subfractions but cholyltransferase showed a dual soluble-rough microsomal activity distribution. 4. Sedimentation of cholyltransferase in mitochondria-enriched fractions prepared by differential centrifugation appears to be an artefact of sedimentation of rough microsomal membranes in mitochondrial fractions. 5. The subcellular distribution of bile acid-conjugating enzymes is discussed with reference to hepatic processing of bile acids.

| S-EPMC1163172 | biostudies-other

Nonaqueous fractionation and overexpression of fluorescent-tagged enzymes reveals the subcellular sites of L-theanine biosynthesis in tea.

Project description:l-Theanine is a specialized metabolite in the tea (Camellia sinensis) plant which can constitute over 50% of the total amino acids. This makes an important contribution to tea functionality and quality, but the subcellular location and mechanism of biosynthesis of l-theanine are unclear. Here, we identified five distinct genes potentially capable of synthesizing l-theanine in tea. Using a nonaqueous fractionation method, we determined the subcellular distribution of l-theanine in tea shoots and roots and used transient expression in Nicotiana or Arabidopsis to investigate in vivo functions of l-theanine synthetase and also to determine the subcellular localization of fluorescent-tagged proteins by confocal laser scanning microscopy. In tea root tissue, the cytosol was the main site of l-theanine biosynthesis, and cytosol-located CsTSI was the key l-theanine synthase. In tea shoot tissue, l-theanine biosynthesis occurred mainly in the cytosol and chloroplasts and CsGS1.1 and CsGS2 were most likely the key l-theanine synthases. In addition, l-theanine content and distribution were affected by light in leaf tissue. These results enhance our knowledge of biochemistry and molecular biology of the biosynthesis of functional tea compounds.

| S-EPMC7769230 | biostudies-literature

Subcellular distribution of chelatable iron: a laser scanning microscopic study in isolated hepatocytes and liver endothelial cells.

Project description:The pool of cellular chelatable iron ('free iron', 'low-molecular-weight iron', the 'labile iron pool') is usually considered to reside mainly within the cytosol. For the present study we adapted our previously established Phen Green method, based on quantitative laser scanning microscopy, to examine the subcellular distribution of chelatable iron in single intact cells for the first time. These measurements, performed in isolated rat hepatocytes and rat liver endothelial cells, showed considerable concentrations of chelatable iron, not only in the cytosol but also in several other subcellular compartments. In isolated rat hepatocytes we determined a chelatable iron concentration of 5.8+/-2.6 microM within the cytosol and of at least 4.8 microM in mitochondria. The hepatocellular nucleus contained chelatable iron at the surprisingly high concentration of 6.6+/-2.9 microM. In rat liver endothelial cells, the concentration of chelatable iron within all these compartments was even higher (cytosol, 7.3+/-2.6 microM; nucleus, 11.8+/-3.9 microM; mitochondria, 9.2+/-2.7 microM); in addition, chelatable iron (approx. 16+/-4 microM) was detected in a small subpopulation of the endosomal/lysosomal apparatus. Hence there is an uneven distribution of subcellular chelatable iron, a fact that is important to consider for (patho)physiological processes and that also has implications for the use of iron chelators to inhibit oxidative stress.

| S-EPMC1221812 | biostudies-other

Non-aqueous fractionation revealed changing subcellular metabolite distribution during apple fruit development.

Project description:In developing apple fruit, metabolic compartmentation is poorly understood due to the lack of experimental data. Distinguishing subcellular compartments in fruit using non-aqueous fractionation has been technically difficult due to the excess amount of sugars present in the different subcellular compartments limiting the resolution of the technique. The work described in this study represents the first attempt to apply non-aqueous fractionation to developing apple fruit, covering the major events occurring during fruit development (cell division, cell expansion, and maturation). Here we describe the non-aqueous fractionation method to study the subcellular compartmentation of metabolites during apple fruit development considering three main cellular compartments (cytosol, plastids, and vacuole). Evidence is presented that most of the sugars and organic acids were predominantly located in the vacuole, whereas some of the amino acids were distributed between the cytosol and the vacuole. The results showed a shift in the plastid marker from the lightest fractions in the early growth stage to the dense fractions in the later fruit growth stages. This implies that the accumulation of starch content with progressing fruit development substantially influenced the distribution of plastidial fragments within the non-aqueous density gradient applied. Results from this study provide substantial baseline information on assessing the subcellular compartmentation of metabolites in apple fruit in general and during fruit growth in particular.

| S-EPMC6804870 | biostudies-other

Distribution of albumin, alpha 1-inhibitor 3 and their respective mRNAs in periportal and perivenous rat hepatocytes isolated by the digitonin-collagenase technique.

Project description:The expression of albumin and alpha 1-inhibitor 3 genes was investigated in rat cell suspensions enriched in periportal (n = 10) and perivenous (n = 10) hepatocytes obtained by the digitonin-collagenase technique. The degree of enrichment of the cell suspensions was assessed: (1) by enzymic assays for the periportal marker alanine aminotransferase and for the perivenous marker glutamine synthetase; and (2) by their content of mRNAs for the periportal marker hepatic glutaminase and for glutamine synthetase. The existence of an antegrade intra-lobular gradient for albumin and alpha 1-inhibitor 3 mRNAs was demonstrated, with periportal:perivenous ratios of 2.33 and 3.80, respectively. However, no gradient was demonstrated for the respective protein contents with corresponding ratios of 0.98 and 1.21. A certain degree of overlap existed between periportal and perivenous suspensions for their content in albumin and alpha 1-inhibitor 3 mRNAs. A morphometrical analysis of the surface of digitonin-permeabilized hepatic tissue revealed that this overlap could be explained by a variable extent of permeabilization of the mediolobular zone from one rat to another and from one lobule to another in a given animal. These results suggest that while the digitonin-collagenase technique is well suited for studies in vitro of proteins expressed in sharp intra-lobular gradients or restricted to an intra-lobular compartment, it is not completely reliable for proteins distributed in continuous moderate intra-lobular gradients, such as albumin and alpha 1-inhibitor 3.

| S-EPMC1136458 | biostudies-other

Subcellular RNA localization during Drosophila embryonic neurogenesis [fractionation-Seq]

Project description:We isolated whole embryo, nuclear, and cytoplasmic lysates from Drosophila embryos during early and late embryogenesis In Drosophila melanogaster, cell-type specification during early nervous system development requires precise regulation of gene expression in time and space. To investigate the gene regulation patterns in early neuronal development, we developed a method 'DIV-SortSeq' to enrich for specific neuroglial cell types for RNA sequencing: from early columnar subdivision and specification, through neuroglial differentiation. DIV-SortSeq recapitulates many of the known protein-coding transcriptome dynamics, as well as novel transcriptional regulatory patterns. We also performed nuclear-cytoplasmic fractionation of whole embryos - Fractionation-Seq - to assess temporal changes in subcellular localization of transcripts during embryogenesis. We present these data as a resource to permit further in-depth investigation into the functional roles of the coding and noncoding transcriptome during early Drosophila neurogenesis.

2019-02-19 | GSE106094 | GEO

Subcellular fractionation enhances proteome coverage of pancreatic duct cells.

Project description:Subcellular fractionation of whole cell lysates offers a means of simplifying protein mixtures, potentially permitting greater depth of proteomic analysis. Here we compare proteins identified from pancreatic duct cells (PaDC) following organelle enrichment to those identified from PaDC whole cell lysates to determine if the additional procedures of subcellular fractionation increase proteome coverage.We used differential centrifugation to enrich for nuclear, mitochondrial, membrane, and cytosolic proteins. We then compared - via mass spectrometry-based analysis - the number of proteins identified from these four fractions with four biological replicates of PaDC whole cell lysates.We identified similar numbers of proteins among all samples investigated. In total, 1658 non-redundant proteins were identified in the replicate samples, while 2196 were identified in the subcellular fractionation samples, corresponding to a 30% increase. Additionally, we noted that each organelle fraction was in fact enriched with proteins specific to the targeted organelle.Subcellular fractionation of PaDC resulted in greater proteome coverage compared to PaDC whole cell lysate analysis. Although more labor intensive and time consuming, subcellular fractionation provides greater proteome coverage, and enriches for compartmentalized sub-populations of proteins. Application of this subcellular fractionation strategy allows for a greater depth of proteomic analysis and thus a better understanding of the cellular mechanisms of pancreatic disease.

| S-EPMC3618666 | biostudies-literature

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