Subcellular Partitioning Research Articles

Correction: Subcellular Partitioning of Protein Tyrosine Phosphatase 1B to the Endoplasmic Reticulum and Mitochondria Depends Sensitively on the Composition of Its Tail Anchor

[This corrects the article DOI: 10.1371/journal.pone.0139429.].

Subcellular partitioning profiles and metallothionein levels in indigenous clams Moerella iridescens from a metal-impacted coastal bay

In this study, the effect of environmental metal exposure on the accumulation and subcellular distribution of metals in the digestive gland of clams with special emphasis on metallothioneins (MTs) was investigated. Specimens of indigenous Moerella iridescens were collected from different natural habitats in Maluan Bay (China), characterized by varying levels of metal contamination. The digestive glands were excised, homogenized and six subcellular fractions were separated by differential centrifugation procedures and analyzed for their Cu, Zn, Cd and Pb contents. MTs were quantified independently by spectrophotometric measurements of thiols. Site-specific differences were observed in total metal concentrations in the tissues, correlating well with variable environmental metal concentrations and reflecting the gradient trends in metal contamination. Concentrations of the non-essential Cd and Pb were more responsive to environmental exposure gradients than were tissue concentrations of the essential metals, Cu and Zn. Subcellular partitioning profiles for Cu, Zn and Cd were relatively similar, with the heat-stable protein (HSP) fraction as the dominant metal-binding compartment, whereas for Pb this fraction was much less important. The variations in proportions and concentrations of metals in this fraction along with the metal bioaccumulation gradients suggested that the induced MTs play an important role in metal homeostasis and detoxification for M. iridescens in the metal-contaminated bay. Nevertheless, progressive accumulation of non-essential metals (Cd, and especially Pb) resulting from “spillover” was observed in putative metal- sensitive (e.g., mitochondria and heat-denaturable protein (HDP)) or lysosome/microsome fractions, demonstrating that metal detoxification was incomplete and increased the toxicological risk to M. iridescens inhabiting the metal-impacted environments. Through multiple stepwise regression analysis, the induction of MTs was statistically correlated with the HSP concentrations of Cu, and to a lesser extent with Zn, and ultimately to the Cd concentrations, exhibiting significant dose-dependent relationships. Overall, these findings not only revealed the fates of accumulated metals, but scientifically favored an improved understanding of the detoxification at the subcellular level in response to metal accumulation, supporting the focus of metabolic availability assessment on the intracellular processes or events occurring within organisms.

Subcellular distribution of trace elements and liver histology of landlocked Arctic char (Salvelinus alpinus) sampled along a mercury contamination gradient

We sampled landlocked Arctic char (Salvelinus alpinus) from four lakes (Small, 9-Mile, North, Amituk) in the Canadian High Arctic that span a gradient of mercury contamination. Metals (Hg, Se, Tl, and Fe) were measured in char tissues to determine their relationships with health indices (relative condition factor and hepatosomatic index), stable nitrogen isotope ratios, and liver histology. A subcellular partitioning procedure was employed to determine how metals were distributed between potentially sensitive and detoxified compartments of Arctic char livers from a low- and high-mercury lake (Small Lake and Amituk Lake, respectively). Differences in health indices and metal concentrations among char populations were likely related to differences in feeding ecology. Concentrations of Hg, Se, and Tl were highest in the livers of Amituk char, whereas concentrations of Fe were highest in Small and 9-Mile char. At the subcellular level we found that although Amituk char had higher concentrations of Tl in whole liver than Small Lake char, they maintained a greater proportion of this metal in detoxified fractions, suggesting an attempt at detoxification. Mercury was found mainly in potentially sensitive fractions of both Small and Amituk Lake char, indicating that Arctic char are not effectively detoxifying this metal. Histological changes in char livers, mainly in the form of melano-macrophage aggregates and hepatic fibrosis, could be linked to the concentrations and subcellular distributions of essential or non-essential metals.

Subcellular partitioning kinetics, metallothionein response and oxidative damage in the marine mussel Mytilus galloprovincialis exposed to cadmium-based quantum dots

The environmental health impact of metal-based nanomaterials is of emerging concern, but their metabolism and detoxification pathways in marine bioindicator species remain unclear. This study investigated the role of subcellular partitioning kinetics, metallothioneins (MTs) response and oxidative damage (lipid peroxidation – LPO) in the marine mussel Mytilus galloprovincialis exposed to CdTe quantum dots (QDs) in comparison with its dissolved counterpart. Mussels were exposed to QDs and dissolved Cd for 21days at 10μgCdL−1 followed by a 50days depuration. Higher Cd concentrations were detected in fractions containing mitochondria, nucleus and lysosomes, suggesting potential subcellular targets of QDs toxicity in mussel tissues. Tissue specific metabolism patterns were observed in mussels exposed to both Cd forms. Although MT levels were directly associated with Cd in both forms, QDs subcellular partitioning is linked to biologically active metal (BAM), but no increase in LPO occurred, while in the case of dissolved Cd levels are in the biologically detoxified metal (BDM) form, indicating nano-specific effects. Mussel gills showed lower detoxification capability of QDs, while the digestive gland is the major tissue for storage and detoxification of both Cd forms. Both mussel tissues were unable to completely eliminate the Cd accumulated in the QDs form (estimated half-life time>50days), highlighting the potential source of Cd and QDs toxicity for human and environmental health. Results indicate tissue specific metabolism patterns and nano-specific effects in marine mussel exposed to QDs.

Toxicokinetic Modeling Challenges for Aquatic Nanotoxicology

Nanotoxicity has become of increasing concern since the rapid development of metal nanoparticles (NPs). Aquatic nanotoxicity depends on crucial qualitative and quantitative properties of nanomaterials that induce adverse effects on subcellular, tissue, and organ level. The dose-response effects of size-dependent metal NPs, however, are not well investigated in aquatic organisms. In order to determine the uptake and elimination rate constants for metal NPs in the metabolically active/ detoxified pool of tissues, a one-compartmental toxicokinetic model can be applied when subcellular partitioning of metal NPs data would be available. The present review is an attempt to describe the nano-characteristics of toxicokinetics and subcellular partitioning on aquatic organisms with the help of the mechanistic modeling for NP size-dependent physiochemical properties and parameters. Physiologically-based pharmacokinetic (PBPK) models can provide an effective tool to estimate the time course of NP accumulation in target organs and is useful in quantitative risk assessments. NP accumulation in fish should take into account different effects of different NP sizes to better understand tissue accumulative capacities and dynamics. The size-dependent NP partition coefficient is a crucial parameter that influences tissue accumulation levels in PBPK modeling. Further research is needed to construct the effective systems-level oriented toxicokinetic model that can provide a useful tool to develop quantitatively the robustly approximate relations that convey a better insight into the impacts of environmental metal NPs on subcellular and tissue/organ responses in aquatic organisms.

Quantitative Analysis of Subcellular Distribution of the SUMO Conjugation System by Confocal Microscopy Imaging.

Different studies point to an enrichment in SUMO conjugation in the cell nucleus, although non-nuclear SUMO targets also exist. In general, the study of subcellular localization of proteins is essential for understanding their function within a cell. Fluorescence microscopy is a powerful tool for studying subcellular protein partitioning in living cells, since fluorescent proteins can be fused to proteins of interest to determine their localization. Subcellular distribution of proteins can be influenced by binding to other biomolecules and by posttranslational modifications. Sometimes these changes affect only a portion of the protein pool or have a partial effect, and a quantitative evaluation of fluorescence images is required to identify protein redistribution among subcellular compartments. In order to obtain accurate data about the relative subcellular distribution of SUMO conjugation machinery members, and to identify the molecular determinants involved in their localization, we have applied quantitative confocal microscopy imaging. In this chapter, we will describe the fluorescent protein fusions used in these experiments, and how to measure, evaluate, and compare average fluorescence intensities in cellular compartments by image-based analysis. We show the distribution of some components of the Arabidopsis SUMOylation machinery in epidermal onion cells and how they change their distribution in the presence of interacting partners or even when its activity is affected.

Integration of copper subcellular distribution and chemical forms to understand copper toxicity in apple trees

Little information is known about the tolerance mechanisms of apple trees growing in soils with excess Cu. This study investigated not only the accumulation and translocation of Cu in the organs of two apple tree cultivars (Fuji and Ralls), but also the detoxification mechanisms of their roots at the cell level. Most accumulated Cu was within apple tree root, especially in the fibrous root, for both cultivars. Compared with Fuji, Ralls had significantly higher Cu concentrations in roots, especially for fibrous roots, while lower concentrations in the aboveground parts. Combining the results from subcellular distribution and chemical forms in the fibrous roots of two apple tree cultivars, more Cu amounts were sequestrated in cell wall and vacuole for Ralls and Cu accumulated in the fibrous root of Fuji had higher in vivo mobility. The results of this study implied that different apple tree cultivars differ in the accumulation, transportation and tolerance to toxic levels of soil Cu, and the chemical forms and subcellular partitioning of Cu in the fibrous roots can elucidate some of the variation of apple trees in Cu sensitivity.

Subcellular Partitioning of Protein Tyrosine Phosphatase 1B to the Endoplasmic Reticulum and Mitochondria Depends Sensitively on the Composition of Its Tail Anchor.

The canonical protein tyrosine phosphatase PTP1B is an important regulator of diverse cellular signaling networks. PTP1B has long been thought to exert its influence solely from its perch on the endoplasmic reticulum (ER); however, an additional subpopulation of PTP1B has recently been detected in mitochondria extracted from rat brain tissue. Here, we show that PTP1B’s mitochondrial localization is general (observed across diverse mammalian cell lines) and sensitively dependent on the transmembrane domain length, C-terminal charge and hydropathy of its short (≤35 amino acid) tail anchor. Our electron microscopy of specific DAB precipitation revealed that PTP1B localizes via its tail anchor to the outer mitochondrial membrane (OMM), with fluorescence lifetime imaging microscopy establishing that this OMM pool contributes to the previously reported cytoplasmic interaction of PTP1B with endocytosed epidermal growth factor receptor. We additionally examined the mechanism of PTP1B’s insertion into the ER membrane through heterologous expression of PTP1B’s tail anchor in wild-type yeast and yeast mutants of major conserved ER insertion pathways: In none of these yeast strains was ER targeting significantly impeded, providing in vivo support for the hypothesis of spontaneous membrane insertion (as previously demonstrated in vitro). Further functional elucidation of the newly recognized mitochondrial pool of PTP1B will likely be important for understanding its complex roles in cellular responses to external stimuli, cell proliferation and diseased states.

Subcellular cadmium distribution and antioxidant enzymatic activities in the leaves of two castor (Ricinus communis L.) cultivars exhibit differences in Cd accumulation

The aims of this study were: (1) the study of cadmium (Cd) accumulation and toxicity in different castor cultivars (Ricinus communis L.); (2) to investigate changes in antioxidant enzymatic activities and the subcellular distribution of Cd in young and old leaves from two different castor cultivars, after exposure to two different Cd concentrations, and explore the underlying mechanism of Cd detoxification focusing on antioxidant enzymes and subcellular compartmentalization. The Cd concentration, toxicity, and subcellular distribution, as well as superoxide dismutase (SOD), catalase (CAT), and peroxidase (POD) activities were measured in Zibo-3 and Zibo-9 cultivars after exposure to two different concentrations of Cd (2mg/L and 5mg/L) for 10 days. This research revealed Cd accumulation characteristics in castor are root>stem>young leaf>old leaf. Castor tolerance was Cd dose exposure and the cultivars themselves dependent. Investigation of subcellular Cd partitioning showed that Cd accumulated mainly in the heat stable protein (HSP) and cellular debris fractions, followed by the Cd rich granule (MRG), heat denatured protein (HDP), and organelle fractions. With increasing Cd concentration in nutrient solution, the decreased detoxified fractions (BDM) and the increased Cd-sensitive fractions (MSF) in young leaves may indicate the increased Cd toxicity in castor cultivars. The BDM-Cd fractions or MSF-Cd in old leaves may be linked with Cd tolerance of different cultivars of castor. The antioxidant enzymes that govern Cd detoxification were not found to be active in leaves. Taken together, these results indicate Cd tolerance and toxicity in castor can be explained by subcellular partitioning.

Internal distribution of Cd in lettuce and resulting effects on Cd trophic transfer to the snail: Achatina fulica

The mechanisms underlying Cd trophic transfer along the soil–lettuce–snail food chain were investigated. The fate of Cd within cells, revealed by assessment of Cd chemical forms and of subcellular partitioning, differed between the two examined lettuce species that we examined (L. longifolia and L. crispa). The species-specific internal Cd fate not only influenced Cd burdens in lettuce, with higher Cd levels in L. crispa, but also affected Cd transfer efficiency to the consumer snail (Achatina fulica). Especially, the incorporation of Cd chemical forms (Cd in the inorganic, water-soluble and pectates and protein-integrated forms) in lettuce could best explain Cd trophic transfer, when compared to dietary Cd levels alone and/or subcellular Cd partitioning. Trophically available metal on the subcellular partitioning base failed to shed light on Cd transfer in this study. After 28-d of exposure, most Cd was trapped in the viscera of Achatina fulica, and cadmium bio-magnification was noted in the snails, as the transfer factor of lettuce-to-snail soft tissue was larger than one. This study provides a first step to apply a chemical speciation approach to dictate the trophic bioavailability of Cd through the soil–plant–snail system, which might be an important pre-requisite for mechanistic understanding of metal trophic transfer.

The sub-cellular fate of mercury in the liver of wild mullets (Liza aurata) – Contribution to the understanding of metal-induced cellular toxicity

Mercury is a recognized harmful pollutant in aquatic systems but still little is known about its sub-cellular partitioning in wild fish. Mercury concentrations in liver homogenate (whole organ load) and in six sub-cellular compartments were determined in wild Liza aurata from two areas – contaminated (LAR) and reference. Water and sediment contamination was also assessed. Fish from LAR displayed higher total mercury (tHg) organ load as well as in sub-cellular compartments than those from the reference area, reflecting environmental differences. However, spatial differences in percentage of tHg were only observed for mitochondria (Mit) and lysosomes plus microsomes (Lys+Mic). At LAR, Lys+Mic exhibited higher levels of tHg than the other fractions. Interestingly, tHg in Mit, granules (Gran) and heat-denaturable proteins was linearly correlated with the whole organ. Low tHg concentrations in heat stable proteins and Gran suggests that accumulated levels might be below the physiological threshold to activate those detoxification fractions.

Subcellular partitioning of metals in Aporrectodea caliginosa along a gradient of metal exposure in 31 field-contaminated soils

Subcellular fractionation of metals in organisms was proposed as a better way to characterize metal bioaccumulation. Here we report the impact of a laboratory exposure to a wide range of field-metal contaminated soils on the subcellular partitioning of metals in the earthworm Aporrectodea caliginosa. Soils moderately contaminated were chosen to create a gradient of soil metal availability; covering ranges of both soil metal contents and of several soil parameters. Following exposure, Cd, Pb and Zn concentrations were determined both in total earthworm body and in three subcellular compartments: cytosolic, granular and debris fractions. Three distinct proxies of soil metal availability were investigated: CaCl2-extractable content dissolved content predicted by a semi-mechanistic model and free ion concentration predicted by a geochemical speciation model. Subcellular partitionings of Cd and Pb were modified along the gradient of metal exposure, while stable Zn partitioning reflected regulation processes. Cd subcellular distribution responded more strongly to increasing soil Cd concentration than the total internal content, when Pb subcellular distribution and total internal content were similarly affected. Free ion concentrations were better descriptors of Cd and Pb subcellular distribution than CaCl2 extractable and dissolved metal concentrations. However, free ion concentrations and soil total metal contents were equivalent descriptors of the subcellular partitioning of Cd and Pb because they were highly correlated. Considering lowly contaminated soils, our results raise the question of the added value of three proxies of metal availability compared to soil total metal content in the assessment of metal bioavailability to earthworm.

Human regulator of telomere elongation helicase 1 (RTEL1) is required for the nuclear and cytoplasmic trafficking of pre-U2 RNA.

Hoyeraal-Hreidarsson syndrome (HHS) is a severe form of Dyskeratosis congenita characterized by developmental defects, bone marrow failure and immunodeficiency and has been associated with telomere dysfunction. Recently, mutations in Regulator of Telomere ELongation helicase 1 (RTEL1), a helicase first identified in Mus musculus as being responsible for the maintenance of long telomeres, have been identified in several HHS patients. Here we show that RTEL1 is required for the export and the correct cytoplasmic trafficking of the small nuclear (sn) RNA pre-U2, a component of the major spliceosome complex. RTEL1-HHS cells show abnormal subcellular partitioning of pre-U2, defects in the recycling of ribonucleotide proteins (RNP) in the cytoplasm and splicing defects. While most of these phenotypes can be suppressed by re-expressing the wild-type protein in RTEL1-HHS cells, expression of RTEL1 mutated variants in immortalized cells provokes cytoplasmic mislocalizations of pre-U2 and other RNP components, as well as splicing defects, thus phenocopying RTEL1-HHS cellular defects. Strikingly, expression of a cytoplasmic form of RTEL1 is sufficient to correct RNP mislocalizations both in RTEL1–HHS cells and in cells expressing nuclear mutated forms of RTEL1. This work unravels completely unanticipated roles for RTEL1 in RNP trafficking and strongly suggests that defects in RNP biogenesis pathways contribute to the pathology of HHS.

Importance of subcellular metal partitioning and kinetics to predicting sublethal effects of copper in two deposit-feeding organisms.

The role of subcellular partitioning of copper on the sublethal effects to two deposit-feeding organisms (41-day growth in the bivalve Tellina deltoidalis and 11-day reproduction in the amphipod Melita plumulosa) was assessed for copper-spiked sediments with different geochemical properties. Large differences in bioaccumulation and detoxification strategies were observed. The bivalve accumulated copper faster than the amphipod, and can be considered a relatively strong net bioaccumulator. The bivalve, however, appears to regulate the metabolically available fraction (MAF) of the total metal pool by increasing the net accumulation rate of copper in the biologically detoxified metal pool (BDM), where most of the copper is stored. In the amphipod, BDM concentration remained constant with increasing copper exposures and it can be considered a very weak net bioaccumulator of copper. This regulation of copper, with relatively little stored in detoxified forms, appears to best describe the strategy applied by the amphipod to minimize the potential toxic effects of copper. When the EC50 values for growth and reproduction are expressed based on the MAF of copper, the sensitivity of the two species appears similar, however when expressed based on the net accumulation rate of copper in the metabolically available fraction (MAFrate), the bivalve appears more sensitive to copper. These results indicate that describing the causality of metal effects in terms of kinetics of uptake, detoxification, and excretion rather than threshold metal body concentrations is more effective in predicting the toxic effects of copper. Although the expression of metal toxicity in terms of the rate at which the metal is bioaccumulated into metabolically available forms may not be feasible for routine assessments, a deeper understanding of uptake rates from all exposure routes may improve our ability to assess the risk posed by metal-contaminated sediments.

Plastid-cytosol partitioning and integration of metabolic pathways for APS/PAPS biosynthesis in Arabidopsis thaliana.

Plants assimilate sulfate from the environment to synthesize biologically active sulfur-containing compounds required for growth and cellular development. The primary steps of sulfur metabolism involve sequential enzymatic reactions synthesizing adenosine 5′-phosphosulfate (APS) and 3′-phosphoadenosine 5’-phosphosulfate (PAPS). Recent finding suggests that an adenosine nucleotide transport system facilitating the exchange of PAPS and 3′-phosphoadenosine 5′-phosphate across the plastid envelope is essential for establishing an intimate connection between the plastidic and cytosolic sulfate assimilation pathways in plants. Subcellular partitioning and integration of metabolic pathways provide focal points for investigating metabolic flux regulations. This perspective article presents an integrative view of sulfur metabolic flux control mechanisms with an emphasis on subcellular partitioning of APS/PAPS biosynthetic pathways in Arabidopsis thaliana.

Molecular mechanisms for mediating light-dependent nucleo/cytoplasmic partitioning of phytochrome photoreceptors.

The photoreceptors phytochromes monitor the red/far-red part of the spectrum, exist in the biologically active Pfr (far-red absorbing) or inactive Pr (red absorbing) forms, and function as red/far-red light-regulated molecular switches to modulate plant development and growth. Phytochromes are synthesized in the cytoplasm, and light induces translocation of the Pfr conformer into the nucleus. Nuclear import of phytochromes is a highly regulated process and is fine-tuned by the quality and quantity of light. It appears that phytochrome A (phyA) and phytochrome B (phyB) do not possess active endogenous nuclear import signals (NLSs), thus light-induced translocation of these photoreceptors into the nucleus requires direct protein–protein interactions with their NLS-containing signaling partners. Sub-cellular partitioning of the various phytochrome species is mediated by different molecular machineries. Translocation of phyA into the nucleus is promoted by FAR-RED ELONGATED HYPOCOTYL 1 (FHY1) and FHY1-LIKE (FHL), but the identity of nuclear transport facilitators mediating the import of phyB-E into the nucleus remains elusive. Phytochromes localized in the nucleus are associated with specific protein complexes, termed photobodies. The size and distribution of these structures are regulated by the intensity and duration of irradiation, and circumstantial evidence indicates that they are involved in fine-tuning phytochrome signaling.

Submembranous recruitment of creatine kinase B supports formation of dynamic actin-based protrusions of macrophages and relies on its C-terminal flexible loop

Subcellular partitioning of creatine kinase contributes to the formation of patterns in intracellular ATP distribution and the fuelling of cellular processes with a high and sudden energy demand. We have previously shown that brain-type creatine kinase (CK-B) accumulates at the phagocytic cup in macrophages where it is involved in the compartmentalized generation of ATP for actin remodeling. Here, we report that CK-B catalytic activity also helps in the formation of protrusive ruffle structures which are actin-dependent and abundant on the surface of both unstimulated and LPS-activated macrophages. Recruitment of CK-B to these structures occurred transiently and inhibition of the enzyme's catalytic activity with cyclocreatine led to a general smoothening of surface morphology as visualized by scanning electron microscopy. Comparison of the dynamics of distribution of YFP-tagged CK-mutants and isoforms by live imaging revealed that amino acid residues in the C-terminal segment (aa positions 323–330) that forms one of the protein's two mobile loops are involved in partitioning over inner regions of the cytosol and nearby sites where membrane protrusions occur during induction of phagocytic cup formation. Although wt CK-B, muscle-type CK (CK-M), and a catalytically dead CK-B-E232Q mutant with intact loop region were normally recruited from the cytosolic pool, no dynamic transition to the phagocytic cup area was seen for the CK-homologue arginine kinase and a CK-B-D326A mutant protein. Bioinformatics analysis helped us to predict that conformational flexibility of the C-terminal loop, independent of conformational changes induced by substrate binding or catalytic activity, is likely involved in exposing the enzyme for binding at or near the sites of membrane protrusion formation.

Profiling of sugar transporter genes in grapevine coping with water deficit

The profiling of grapevine (Vitis vinifera L.) genes under water deficit was specifically targeted to sugar transporters. Leaf water status was characterized by physiological parameters and soluble sugars content. The expression analysis provided evidence that VvHT1 hexose transporter gene was strongly down-regulated by the increased sugar content under mild water-deficit. The genes of monosaccharide transporter VvHT5, sucrose carrier VvSUC11, vacuolar invertase VvGIN2 and grape ASR (ABA, stress, ripening) were up-regulated under severe water stress. Their regulation in a drought-ABA signalling network and possible roles in complex interdependence between sugar subcellular partitioning and cell influx/efflux under Grapevine acclimation to dehydration are discussed.

Integration of metal chemical forms and subcellular partitioning to understand metal toxicity in two lettuce (Lactuca sativa L.) cultivars

Metal chemical forms and subcellular partitioning model (SPM) in organisms can provide valuable insights into metal toxicity. Two cultivars of lettuce (Lactuca sativa L.) were grown in Cd and Cu contaminated soils and chemical forms and subcellular distribution of Cd and Cu within the lettuce shoots were determined. Examination of the inhibition of superoxide dismutase (SOD) and catalase (CAT) activities, as well as the production of H2O2 showed that Lactuca sativa L. var. longifolia is more sensitive to metal-stress than is Lactuca sativa L. var. crispa. In L. crispa, the majority of accumulated Cd was in the pectate- and protein-integrated forms (53.7–62.9 %), while in L. longifolia, a higher proportion of the Cd was in the water soluble forms (33.0–39.2 %) and in the organelles fraction – these forms being potentially associated with toxicity. The chemically-based chemical form approach agreed closely with independent biologically-based SPM, as demonstrated by their significant linear relationships. This study provides a first step towards the integration of chemical form approach and SPM into a common mechanistic framework, which is important for predicting the likelihood of toxic effects of metals in the environment of interest.

Assessment of a subcellular metal partitioning protocol for aquatic invertebrates: preservation, homogenization, and subcellular fractionation

Measurements of the subcellular partitioning of trace metals have been used to predict assimilation efficiencies for metals between trophic levels and to evaluate metal detoxification mechanisms in aquatic organisms. Using field‐collected larvae of the insect Chaoborus, we assessed the performance of two preservation protocols, three homogenization treatments, and a cell fractionation protocol to determine the best combination of techniques for assessing the subcellular partitioning of Cd, Cu, Ni, and Zn. Preservation of larval samples for either 2 years at −80°C or 1 year at −80°C or −196°C had little influence on the subcellular partitioning of these metals. Using several marker enzymes, i.e., cytochrome C oxidase and citrate synthase for mitochondria, β‐hexosaminidase for lysosomes, and lactate dehydrogenase for the cytosol, we show that optimal and high‐yield homogenization is achieved using a combination of mechanical disruption using a micro‐pestle followed by vortexing and that the subsequent fractionation procedure employing differential centrifugation/NaOH digestion was effective. We conclude that the preservation and homogenization protocols as well as the fractionation procedure that we tested using Chaoborus larvae can serve as a model approach for improving current protocols and for designing protocols for previously untested biological samples.