Quantitative analysis of peroxisome tracks using a Hidden Markov Model.

Diffusion and mobility are essential for cellular functions, as molecules are usually distributed throughout the cell and have to meet to interact and perform their function. This also involves the cytosolic migration of cellular organelles. However, observing such diffusion and interaction dynamics is challenging due to the high spatial and temporal resolution required and the accurate analysis of the diffusional tracks. The latter is especially important when identifying anomalous diffusion events, such as directed motions, which are often rare. Here, we investigate the migration modes of peroxisome organelles in the cytosol of living cells. Peroxisomes predominantly migrate randomly, but occasionally they bind to the cell's microtubular network and perform directed migration, which is difficult to quantify, and so far, accurate analysis of switching between these migration modes is missing. We set out to solve this limitation by experiments and analysis with high statistical accuracy. Specifically, we collect temporal diffusion tracks of thousands of individual peroxisomes in the HEK 293 cell line using two-dimensional spinning disc fluorescence microscopy at a high acquisition rate of 10 frames/s. We use a Hidden Markov Model with two hidden states to (1) automatically identify directed migration segments of the tracks and (2) quantify the migration properties for comparison between states and between different experimental conditions. Comparing different cellular conditions, we show that the knockout of the peroxisomal membrane protein PEX14 leads to a decrease in the directed movement due to a lowered binding probability to the microtubule. However, it does not eradicate binding, highlighting further microtubule-binding mechanisms of peroxisomes than via PEX14. In contrast, structural changes of the microtubular network explain perceived eradication of directed movement by disassembly of microtubules by Nocodazole-treatment.

Synthesis of an Hsp70 inhibitor and its assessment of lysosomal membrane permeabilization.

Hsp70 inhibitors have great potential as chemical probes and anticancer agents. Thus, it is important to elucidate their modes of action on cancer cell death. This protocol describes a step-by-step process for the synthesis of apoptozole as an inhibitor of Hsp70, analysis of internalization of apoptozole into lysosomes, and assessment of lysosomal membrane permeabilization induced by apoptozole. The current protocol can be used for detailed mechanistic studies of Hsp70 inhibitors and further substances targeting lysosomal proteins on cancer cell death. For complete information on the use and execution of this protocol, please refer to Park et al. (2018).

Assessment of AMPK-Stimulated Cellular Long-Chain Fatty Acid and Glucose Uptake.

Here we describe an assay for simultaneous measurement of cellular uptake rates of long-chain fatty acids (LCFA) and glucose that can be applied to cells in suspension. The uptake assay includes the use of radiolabeled substrates at such concentrations and incubation periods that exact information is provided about unidirectional uptakes rates. Cellular uptake of both substrates is under regulation of AMPK. The underlying mechanism includes the translocation of LCFA and glucose transporters from intracellular membrane compartments to the cell surface, leading to an increase in substrate uptake. In this chapter, we explain the principles of the uptake assay before detailing the exact procedure. We also provide information of the specific LCFA and glucose transporters subject to AMPK-mediated subcellular translocation. Finally, we discuss the application of AMPK inhibitors and activators in combination with cellular substrate uptake assays.

Organelle morphogenesis by active membrane remodeling.

Intracellular organelles are subject to a steady flux of lipids and proteins through active, energy consuming transport processes. Active fission and fusion are promoted by GTPases, e.g., Arf-Coatamer and the Rab-Snare complexes, which both sense and generate local membrane curvature. Here we investigate, through Dynamical Triangulation Monte Carlo simulations, the role that these active processes play in determining the morphology and composition segregation in closed membranes. We find that the steady state shapes obtained as a result of such active processes, bear a striking resemblance to the ramified morphologies of organelles in vivo, pointing to the relevance of nonequilibrium fission-fusion in organelle morphogenesis.

A biomarker of contaminant exposure is effective in large scale assessment of ten estuaries.

Cost-effective and sensitive measures of anthropogenic stress are necessary tools in any environmental monitoring program. When implementing new monitoring tools in a region, rigorous laboratory and field studies are essential for characterizing the sensitivity and efficacy of the approach. We exposed the oyster Saccostrea glomerata to various individual contaminants through multiple exposure pathways (water- and food-borne) in the laboratory and measured two biomarker responses, lysosomal membrane stability (LMS) and lipid peroxidation (LPO). LMS was sensitive to both contaminant exposure pathways. We subsequently measured this biomarker in oysters which had been experimentally deployed at multiple sites in each of ten estuaries with varying levels of contamination associated with re-suspended sediments. There was a strong association between LMS and metal exposure, despite substantial natural variation in water quality parameters. Our results illustrate the potential use of LMS as a pragmatic indicator of biotic injury in environmental monitoring programs for re-suspended contaminated sediments.

Coexistence of fluid and crystalline phases of proteins in photosynthetic membranes.

Photosystem II (PSII) and its associated light-harvesting complex II (LHCII) are highly concentrated in the stacked grana regions of photosynthetic thylakoid membranes. PSII-LHCII supercomplexes can be arranged in disordered packings, ordered arrays, or mixtures thereof. The physical driving forces underlying array formation are unknown, complicating attempts to determine a possible functional role for arrays in regulating light harvesting or energy conversion efficiency. Here, we introduce a coarse-grained model of protein interactions in coupled photosynthetic membranes, focusing on just two particle types that feature simple shapes and potential energies motivated by structural studies. Reporting on computer simulations of the model's equilibrium fluctuations, we demonstrate its success in reproducing diverse structural features observed in experiments, including extended PSII-LHCII arrays. Free energy calculations reveal that the appearance of arrays marks a phase transition from the disordered fluid state to a system-spanning crystal. The predicted region of fluid-crystal coexistence is broad, encompassing much of the physiologically relevant parameter regime; we propose experiments that could test this prediction. Our results suggest that grana membranes lie at or near phase coexistence, conferring significant structural and functional flexibility to this densely packed membrane protein system.

Energetic cost of protein import across the envelope membranes of chloroplasts.

Chloroplasts are the organelles of green plants in which light energy is transduced into chemical energy, forming ATP and reduced carbon compounds upon which all life depends. The expenditure of this energy is one of the central issues of cellular metabolism. Chloroplasts contain ~3,000 proteins, among which less than 100 are typically encoded in the plastid genome. The rest are encoded in the nuclear genome, synthesized in the cytosol, and posttranslationally imported into the organelle in an energy-dependent process. We report here a measurement of the amount of ATP hydrolyzed to import a protein across the chloroplast envelope membranes--only the second complete accounting of the cost in Gibbs free energy of protein transport to be undertaken. Using two different precursors prepared by three distinct techniques, we show that the import of a precursor protein into chloroplasts is accompanied by the hydrolysis of ~650 ATP molecules. This translates to a ΔG(protein) (transport) of some 27,300 kJ/mol protein imported. We estimate that protein import across the plastid envelope membranes consumes ~0.6% of the total light-saturated energy output of the organelle.

Modeling the step of endosomal escape during cell infection by a nonenveloped virus.

Widely disparate viruses enter the host cell through an endocytic pathway and travel the cytoplasm inside an endosome. For the viral genetic material to be delivered into the cytoplasm, these viruses have to escape the endosomal compartment, an event triggered by the conformational changes of viral endosomolytic proteins. We focus here on small nonenveloped viruses such as adeno-associated viruses, which contain few penetration proteins. The first time a penetration protein changes conformation defines the slowest timescale responsible for the escape. To evaluate this time, we construct what to our knowledge is a novel biophysical model based on a stochastic approach that accounts for the small number of proteins, the endosomal maturation, and the protease activation dynamics. We show that the escape time increases with the endosomal size, whereas decreasing with the number of viral particles inside the endosome. We predict that the optimal escape probability is achieved when the number of proteases in the endosome is in the range of 250-350, achieved for three viral particles.

Protein-coat dynamics and cluster phases in intracellular trafficking.

Clustering of membrane proteins is a hallmark of biological membranes' lateral organization and crucial to their function. However, the physical properties of these protein aggregates remain poorly understood. Ensembles of coat proteins, the example considered here, are necessary for intracellular transport in eukaryotic cells. Assembly and disassembly rates for coat proteins involved in intracellular vesicular trafficking must be carefully controlled: their assembly deforms the membrane patch and drives vesicle formation, yet the protein coat must rapidly disassemble after vesiculation. Motivated by recent experimental findings for protein-coat dynamics, we study a dynamical Ising-type model for coat assembly and disassembly, and demonstrate how simple dynamical rules generate a robust, steady-state distribution of protein clusters (corresponding to intermediate budded shapes) and how cluster sizes are controlled by the kinetics. We interpret the results in terms of both vesiculation and the coupling to cargo proteins.

Diffusion in cytoplasm: effects of excluded volume due to internal membranes and cytoskeletal structures.

The intricate geometry of cytoskeletal networks and internal membranes causes the space available for diffusion in cytoplasm to be convoluted, thereby affecting macromolecule diffusivity. We present a first systematic computational study of this effect by approximating intracellular structures as mixtures of random overlapping obstacles of various shapes. Effective diffusion coefficients are computed using a fast homogenization technique. It is found that a simple two-parameter power law provides a remarkably accurate description of effective diffusion over the entire range of volume fractions and for any given composition of structures. This universality allows for fast computation of diffusion coefficients, once the obstacle shapes and volume fractions are specified. We demonstrate that the excluded volume effect alone can account for a four-to-sixfold reduction in diffusive transport in cells, relative to diffusion in vitro. The study lays the foundation for an accurate coarse-grain formulation that would account for cytoplasm heterogeneity on a micron scale and binding of tracers to intracellular structures.

Peptide probe study of the role of interaction between the cytoplasmic and transmembrane domains of the ryanodine receptor in the channel regulation mechanism.

Ryanodine receptor (RyR) mutations linked with some congenital skeletal and cardiac diseases are localized to three easily definable regions: region 1 (N-terminal domain), region 2 (central domain), and a rather broad region 3 containing the channel pore. As shown in our recent studies, the interdomain interaction between regions 1 and 2 plays a critical role in channel regulation and pathogenesis. Here we present evidence that within region 3 there is a similar channel regulation mechanism mediated by an interdomain interaction. DP15, a peptide corresponding to RyR1 residues 4820-4841, produced significant activation of [3H]ryanodine binding above threshold Ca2+ concentrations (>or=0.3 microM), but MH mutations (L4823P or L4837V) made in DP15 almost completely abolished its channel activating function. To identify the DP15 binding site(s) within RyR1, DP15 (labeled with a fluorescent probe Alexa Fluor 680 and a photoaffinity cross-linker APG) was cross-linked to RyR1, and the site of cross-linking was identified by gel analysis of fluorescently labeled proteolytic fragments with the aid of Western blotting with site-specific antibodies. The shortest fluorescently labeled band was a 96 kDa fragment which was stained with an antibody directed to the region of residues 4114-4142 of RyR1, indicating that the interaction between the region of residues 4820-4841 adjacent to the channel pore and the 96 kDa segment containing the region of residues 4114-4142 is involved in the mechanism of Ca2+-dependent channel regulation. In further support of this concept, anti-DP15 antibody and cardiac counterpart of DP15 produced channel activation similar to that of DP15.

The dynamics of stochastic attrition viewed as an absorption time on a terminating Markov chain.

Localized Ca(2+) elevations known as Ca(2+) puffs and sparks are cellular signals that arise from the cooperative activity of clusters of inositol 1,4,5-trisphosphate receptors and ryanodine receptors clustered at Ca(2+) release sites on the surface of the endoplasmic reticulum or sarcoplasmic reticulum. When Markov chain models of these intracellular Ca(2+)-regulated Ca(2+) channels are coupled via a mathematical representation of Ca(2+) microdomain, simulated Ca(2+) release sites may exhibit the phenomenon of "stochastic Ca(2+) excitability" where the inositol 1,4,5-trisphosphate receptors (IP(3)Rs) or ryanodine receptors (RyRs) open and close in a concerted fashion. Interestingly, under some conditions simulated puffs and sparks can be observed even when the single-channel model used does not include slow Ca(2+) inactivation or, indeed, any long-lived closed/refractory state [V. Nguyen, R. Mathias, G. Smith, Stochastic automata network descriptor for Markov chain models of instantaneously-coupled intracellular Ca(2+) channels, Bull. Math. Biol. 67 (2005) 393-432]. In this case, termination of the localized Ca(2+) elevation occurs when all of the intracellular channels at a release site simultaneously close through a process referred to as stochastic attrition [M. Stern, Theory of excitation-contraction coupling in cardiac muscle, Biophys. J. 63 (1992) 497-517]. In this paper, we investigate the statistical properties of stochastic attrition viewed as an absorption time on a terminating Markov chain that represents a Ca(2+) release site composed of N two-state channels that are activated by Ca(2+). Assuming that the local [Ca(2+)] experienced by a channel depends only on the number of open channels at the Ca(2+) release site (i.e., instantaneous mean-field coupling [ibid.], we derive the probability distribution function for the time until stochastic attrition occurs and present an analytical formula for the expectation of this random variable. We explore how the contribution of stochastic attrition to the termination of Ca(2+) puffs and sparks depends on the number of channels at a release site, the source amplitude of the channels (i.e., the strength of the coupling), the background [Ca(2+)], channel kinetics, and the cooperactivity of Ca(2+) binding. Because we explicitly model the Ca(2+) regulation of the intracellular channels, our results differ markedly from (and in fact generalize) preliminary analyses that assume the intracellular Ca(2+) channels are uncoupled and consequently independent.

Thiazide-like diuretics attenuate agonist-induced vasoconstriction by calcium desensitization linked to Rho kinase.

Lowering blood pressure using thiazide-like diuretics, including chlorthalidone and hydrochlorothiazide, has been proven to be effective in clinical studies. However, the mechanisms by which thiazide-like diuretics lower blood pressure are still poorly understood. To evaluate whether thiazide-like diuretics cause calcium desensitization in smooth muscle cells, we measured their effects on agonist-induced increase of blood pressure in Wistar rats in vivo and on agonist-induced vasoconstriction of aortic rings, DNA synthesis, and protein synthesis, RhoA, Rho kinase, and intracellular calcium in vascular smooth muscle cells in vitro. Thiazide-like diuretics significantly attenuated angiotensin II-induced or norepinephrine-induced increase of systolic blood pressure in rats. Thiazide-like diuretics inhibited agonist-induced vasoconstriction of aortic rings in a concentration-dependent manner in the presence and absence of endothelium. The inhibitory effects of thiazide-like diuretics were similar to that of the specific Rho kinase inhibitor Y27632. RT-PCR and immunoblotting showed that RhoA and Rho kinase were significantly reduced in vascular smooth muscle cells after administration of thiazide-like diuretics. In contrast, thiazide-like diuretics did not affect protein tyrosine phosphatase-2 (SHP-2) expression. Agonist-induced changes of intracellular calcium were not affected by thiazide-like diuretics. The study indicates that thiazide-like diuretics inhibit agonist-induced vasoconstriction by calcium desensitization in smooth muscle cells linked to the Rho-Rho kinase pathway.

In vivo and in organello assessment of OXPHOS activities.

Mitochondrial OXPHOS defects are responsible for a large group of human diseases and have been associated with degenerative disorders and aging. The accurate in vivo and in organello biochemical assessment of the OXPHOS system is necessary for the diagnosis and investigation of such conditions. Here I describe a set of accurate polarographic and spectrophotometric assays that use relatively small amounts of biological material (cells or isolated mitochondria) and discuss the biochemical parameters appropriate for discriminating partial OXPHOS defects.

Hydroperoxyl, superoxide and pH gradients in the mitochondrial matrix: a theoretical assessment.

The negative surface charge of many cellular membranes concentrates protons and rarefies superoxide in their vicinity. It was speculated that the low pH near membranes should facilitate superoxide protonation, thereby concentrating hydroperoxyl radical in this region. This process would exacerbate both lipid peroxidation and the transfer of oxidative damage between cellular compartments, as hydroperoxyl is a good initiator of lipid peroxidation and permeates lipid bilayers. Surface-charge-enhancement of hydroperoxyl production in mitochondria--which are main intracellular sources of superoxide--should be particularly relevant. Using a simple model of superoxide metabolism in the mitochondrial matrix, we calculated the gradients of pH, superoxide, and hydroperoxyl, and assessed the previous hypothesis in the light of available experimental data. The following predictions ensued: (i) Near the mitochondrial inner membrane, gradients of superoxide concentration with amplitude up to 36% of the maximal concentration, and pH gradients of up to 0.19 units between membrane and bulk. (ii) These electrostatically induced gradients die out within approximately 4 nm of the membrane. (iii) At high (hundreds of nanometres) inter-cristae separations, owing to enzyme-catalyzed dismutation of superoxide, both superoxide and hydroperoxyl become rarefied towards the midpoint between cristae. (iv) Surface charge should neither enhance superoxide protonation nor concentrate hydroperoxyl near biological membranes.

Assessment of mechanisms of thyroid hormone action in mouse Leydig cells: regulation of the steroidogenic acute regulatory protein, steroidogenesis, and luteinizing hormone receptor function.

Recently, we demonstrated that triiodothyronine (T(3)) stimulated steroid hormone biosynthesis and steroidogenic acute regulatory (StAR) protein expression in mLTC-1 mouse Leydig tumor cells through the mediation of steroidogenic factor 1 (SF-1). We now report a dual response mechanism of T(3) on steroidogenesis and StAR expression, and on LH receptor (LHR) expression and binding in mLTC-1 cells. T(3) acutely (8 h), induced a 260% increase in StAR messenger RNA (mRNA) expression over the basal level which was coincident with an increase in progesterone (P) production. In contrast, chronic stimulation with T(3) (beyond 8 h), resulted in an attenuation of StAR expression and P production. This attenuation was most likely caused by a decrease in cholesterol delivery to the inner mitochondrial membrane as demonstrated by incubations with the hydrophilic steroid precursors, 22R hydroxycholesterol and pregnenolone, which restored P synthesis. In similar studies, chronic treatment with T(3) increased the levels of cytochrome P450scc mRNA by 83%, whereas those of cytochrome P450 17alpha-hydroxylase and 3ss-hydroxysteroid dehydrogenase decreased. The diminished response in steroidogenesis following chronic T(3) exposure was not a result of alterations in StAR mRNA stability, but rather was due to inhibition of transcription of the StAR gene. Similar acute stimulatory and chronic inhibitory responses to T(3) were found when LHR mRNA expression and LHR ligand binding were examined. Transfections with an LHR or StAR promoter/luciferase reporter construct demonstrated that a 173-bp fragment of the LHR promoter containing an SF-1 binding motif was involved in T(3) response, as was the SF-1 recognition site at -135 bp in the StAR promoter. Furthermore, the importance of SF-1 in T(3) function was also verified employing mutation in the bases of SF-1 sequences using electrophoretic mobility shift assays. The potential physiological relevance of these findings was demonstrated when similar responses were obtained in mice rendered hypo and hyperthyroid. Collectively, these observations further characterize the thyroid-gonadal connection and provide insights into the mechanisms for a dual regulatory role of thyroid hormone in Leydig cell functions.

Computational prediction of membrane-tethered transcription factors.

BACKGROUND: Sequestration of transcription factors in the membrane is emerging as an important mechanism for the regulation of gene expression. A handful of membrane-spanning transcription factors has been previously identified whose access to the nucleus is regulated by proteolytic cleavage from the membrane. To investigate the existence of other transmembrane transcription factors, we analyzed computationally all proteins in SWISS-PROT/TrEMBL for the combined presence of a DNA-binding domain and a transmembrane segment. RESULTS: Using Pfam hidden Markov models and four transmembrane-prediction programs, we identified with high confidence 76 membrane-spanning transcription factors in SWISS-PROT/TrEMBL. Analysis of the distribution of two proteins predicted by our method, MTJ1 and DMRT2, confirmed their localization to intracellular membrane compartments. Furthermore, elimination of the predicted transmembrane segment led to nuclear localization for each of these proteins. CONCLUSIONS: Our analysis uncovered a wealth of predicted membrane-spanning transcription factors that are structurally and taxonomically diverse, 56 of which lack experimental annotation. Seventy-five of the proteins are modular in structure, suggesting that a single proteolysis may be sufficient to liberate a DNA-binding domain from the membrane. This study provides grounds for investigations into the stimuli and mechanisms that release this intriguing class of transcription factors from membranes.

Differential role for competitive reverse transcriptase-polymerase chain reaction and intracellular cytokine staining as diagnostic tools for the assessment of intragraft cytokine profiles in rejecting and nonrejecting heart allografts.

The early and reliable diagnosis of allograft rejection is a difficult task and the assessment of cytokine expression in the grafts can be a helpful parameter. We have compared competitive reverse transcriptase-polymerase chain reaction (RT-PCR) with intracellular cytokine staining by flow cytometry as tools to measure cytokine expression in rejecting and nonrejecting murine cardiac allografts. Both techniques gave comparable results for cytokine expression in rejecting allografts and syngeneic controls. Grafts from mice pretreated with anti-CD4 antibody and donor-specific blood transfusion showed a marked reduction in cytokine expression, as assessed by competitive RT-PCR, even though a cellular infiltrate was present in the graft. In contrast, the cytokine production measured by intracellular cytokine staining of the isolated graft-infiltrating cells was high and exceeded even that of the rejecting allografts. We conclude that intracellular cytokine staining of graft-infiltrating leukocytes by flow cytometry does not necessarily reflect accurately the cytokine milieu in the graft. This technique might therefore have a limited clinical application in contrast to competitive RT-PCR for the differentiation between graft acceptance and graft rejection.

Cyclic ADP-ribose induces a larger than normal calcium release in malignant hyperthermia-susceptible skeletal muscle fibers.

Malignant hyperthermia (MH) is associated with abnormal regulation of intracellular calcium in skeletal muscle fibers. Cyclic adenosine diphosphate-ribose (cADPR) is an endogenous metabolite of beta-NAD+ that induces Ca2+ release from intracellular stores in many tissues. Microinjection of cADPR (0.5 or 1 microM) increased the intracellular resting Ca2+ concentration ([Ca2+]i) in intact swine skeletal muscle in a dose-dependent manner. However, the increase in [Ca2+]i was greater in malignant-hyperthermia-susceptible (MHS) fibers than in non-susceptible (MHN) fibers. Incubation of muscle fibers in low external Ca2+ solution or in the presence of L-type Ca2+ channel entry blockers, or intracellular microinjection of heparin or ruthenium red did not modify the effect of cADPR on [Ca2+]i. Dantrolene (50 microM), a known inhibitor of intracellular Ca2+ release, decreased resting [Ca2+]i and prevented the cADPR-induced increase in [Ca2+]i. These results provide evidence: (1) for the existence of Ca2+ release mechanisms occurring via non-ryanodine or inositol 1,4,5-trisphosphate (InsP3) receptor mechanisms; (2) that MHS skeletal muscles exhibit a higher responsiveness to cADP-ribose-induced release of Ca2+ and (3) that the ability of dantrolene to block cADP-ribose-induced release of Ca2+ could be related to its pharmacologic effect on resting [Ca2+]i.