86 results on '"subcellular compartment"'
Search Results
2. Cellular and Molecular Mechanisms Underlying Synaptic Subcellular Specificity.
- Author
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Wang, Mengqing, Fan, Jiale, and Shao, Zhiyong
- Subjects
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CEREBRAL cortex , *CAENORHABDITIS elegans , *MOLECULAR pathology , *CELL adhesion molecules - Abstract
Chemical synapses are essential for neuronal information storage and relay. The synaptic signal received or sent from spatially distinct subcellular compartments often generates different outcomes due to the distance or physical property difference. Therefore, the final output of postsynaptic neurons is determined not only by the type and intensity of synaptic inputs but also by the synaptic subcellular location. How synaptic subcellular specificity is determined has long been the focus of study in the neurodevelopment field. Genetic studies from invertebrates such as Caenorhabditis elegans (C. elegans) have uncovered important molecular and cellular mechanisms required for subcellular specificity. Interestingly, similar molecular mechanisms were found in the mammalian cerebellum, hippocampus, and cerebral cortex. This review summarizes the comprehensive advances in the cellular and molecular mechanisms underlying synaptic subcellular specificity, focusing on studies from C. elegans and rodents. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
3. Multiscale Asymptotic Analysis Reveals How Cell Growth and Subcellular Compartments Affect Tissue-Scale Hormone Transport.
- Author
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Kiradjiev, K. B. and Band, L. R.
- Abstract
Determining how cell-scale processes lead to tissue-scale patterns is key to understanding how hormones and morphogens are distributed within biological tissues and control developmental processes. In this article, we use multiscale asymptotic analysis to derive a continuum approximation for hormone transport in a long file of cells to determine how subcellular compartments and cell growth and division affect tissue-scale hormone transport. Focusing our study on plant tissues, we begin by presenting a discrete multicellular ODE model tracking the hormone concentration in each cell’s cytoplasm, subcellular vacuole, and surrounding apoplast, represented by separate compartments in the cell-file geometry. We allow the cells to grow at a rate that can depend both on space and time, accounting for both cytoplasmic and vacuolar expansion. Multiscale asymptotic analysis enables us to systematically derive the corresponding continuum model, obtaining an effective reaction–advection–diffusion equation and revealing how the effective diffusivity, effective advective velocity, and the effective sink term depend on the parameters in the cell-scale model. The continuum approximation reveals how subcellular compartments, such as vacuoles, can act as storage vessels, that significantly alter the effective properties of hormone transport, such as the effective diffusivity and the induced effective velocity. Furthermore, we show how cell growth and spatial variance across cell lengths affect the effective diffusivity and the induced effective velocity, and how these affect the tissue-scale hormone distribution. In particular, we find that cell growth naturally induces an effective velocity in the direction of growth, whereas spatial variance across cell lengths induces effective velocity due to the presence of an extra compartment, such as the apoplast and the vacuole, and variations in the relative sizes between the compartments across the file of cells. It is revealed that hormone transport is faster across cells of decreasing lengths than cells with increasing lengths. We also investigate the effect of cell division on transport dynamics, assuming that each cell divides as soon as it doubles in size, and find that increasing the time between successive cell divisions decreases the growth rate, which enhances the effect of cell division in slowing hormone transport. Motivated by recent experimental discoveries, we discuss particular applications for transport of gibberellic acid (GA), an important growth hormone, within the Arabidopsis root. The model reveals precisely how membrane proteins that mediate facilitated GA transport affect the effective tissue-scale transport. However, the results are general enough to be relevant to other plant hormones, or other substances that are transported in a similar way in any type of cells. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
4. Cellular and Molecular Mechanisms Underlying Synaptic Subcellular Specificity
- Author
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Mengqing Wang, Jiale Fan, and Zhiyong Shao
- Subjects
synaptic specificity ,subcellular compartment ,secreted molecules ,cell adhesion molecules ,development ,Neurosciences. Biological psychiatry. Neuropsychiatry ,RC321-571 - Abstract
Chemical synapses are essential for neuronal information storage and relay. The synaptic signal received or sent from spatially distinct subcellular compartments often generates different outcomes due to the distance or physical property difference. Therefore, the final output of postsynaptic neurons is determined not only by the type and intensity of synaptic inputs but also by the synaptic subcellular location. How synaptic subcellular specificity is determined has long been the focus of study in the neurodevelopment field. Genetic studies from invertebrates such as Caenorhabditis elegans (C. elegans) have uncovered important molecular and cellular mechanisms required for subcellular specificity. Interestingly, similar molecular mechanisms were found in the mammalian cerebellum, hippocampus, and cerebral cortex. This review summarizes the comprehensive advances in the cellular and molecular mechanisms underlying synaptic subcellular specificity, focusing on studies from C. elegans and rodents.
- Published
- 2024
- Full Text
- View/download PDF
5. Subcellular Proteomics as a Unified Approach of Experimental Localizations and Computed Prediction Data for Arabidopsis and Crop Plants
- Author
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Hooper, Cornelia M., Castleden, Ian R., Tanz, Sandra K., Grasso, Sally V., Millar, A. Harvey, Crusio, Wim E., Series Editor, Dong, Haidong, Series Editor, Radeke, Heinfried H., Series Editor, Rezaei, Nima, Series Editor, Steinlein, Ortrud, Series Editor, Xiao, Junjie, Series Editor, and Vischi Winck, Flavia, editor
- Published
- 2021
- Full Text
- View/download PDF
6. Differential accumulation of human β-amyloid and tau from enriched extracts in neuronal and endothelial cells.
- Author
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Rabanal-Ruiz, Y., Pedrero-Prieto, C.M., Sanchez-Rodriguez, L., Flores-Cuadrado, A., Saiz-Sanchez, D., Frontinan-Rubio, J., Ubeda-Banon, I., Duran Prado, M., Martinez-Marcos, A., and Peinado, Juan R.
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ENDOTHELIAL cells , *TAU proteins , *CELL aggregation , *POISONS , *ORGANELLES , *ENDOPLASMIC reticulum - Abstract
While Aβ and Tau cellular distribution has been largely studied, the comparative internalization and subcellular accumulation of Tau and Aβ isolated from human brain extracts in endothelial and neuronal cells has not yet been unveiled. We have previously demonstrated that controlled enrichment of Aβ from human brain extracts constitutes a valuable tool to monitor cellular internalization in vitro and in vivo. Herein, we establish an alternative method to strongly enrich Aβ and Tau aggregates from human AD brains, which has allowed us to study and compare the cellular internalization, distribution and toxicity of both proteins within brain barrier endothelial (bEnd.3) and neuronal (Neuro2A) cells. Our findings demonstrate the suitability of human enriched brain extracts to monitor the intracellular distribution of human Aβ and Tau, which, once internalized, show dissimilar sorting to different organelles within the cell and differential toxicity, exhibiting higher toxic effects on neuronal cells than on endothelial cells. While tau is strongly concentrated preferentially in mitochondria, Aβ is distributed predominantly within the endolysosomal system in endothelial cells, whereas the endoplasmic reticulum was its preferential location in neurons. Altogether, our findings display a picture of the interactions that human Aβ and Tau might establish in these cells. • Human brain extracts reveal Aβ and Tau sorting differences in endolysosomal system, ER, mitochondria and autophagosomes. • Our findings might explain the differential toxicity of both proteins within brain barrier endothelial and neuronal cells. • Differential toxicity of Aβ and Tau in brain endothelial and neuronal cells might be explained by our findings. [ABSTRACT FROM AUTHOR]
- Published
- 2024
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7. Expansion of metabolically labelled endocytic organelles and cytoskeletal cell structures in Giardia lamblia using optimised U-ExM protocols.
- Author
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Jetishi C, Balmer EA, Berger BM, Faso C, and Ochsenreiter T
- Abstract
Understanding cellular ultrastructure is tightly bound to microscopic resolution and the ability to identify individual components at that resolution. Expansion microscopy has revolutionised this topic. Here we present and compare two protocols of ultrastructure expansion microscopy that allow for 4.5-fold mostly isotropic expansion and the use of antibodies, metabolic labelling, and DNA stains to demarcate individual regions such as the endoplasmic reticulum, the nuclei, the peripheral endocytic compartments as well as the ventral disc and the cytoskeleton in Giardia lamblia . We present an optimised, shortened, and modular protocol that can be swiftly adjusted to the investigators needs in this important protozoan model organism., Competing Interests: All authors declare that they have no conflicts of interest.
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- 2024
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8. The Effect of Single and Multiple SERAT Mutants on Serine and Sulfur Metabolism
- Abstract
The gene family of serine acetyltransferases (SERATs) constitutes an interface between the plant pathways of serine and sulfur metabolism. SERATs provide the activated precursor, O-acetylserine for the fixation of reduced sulfur into cysteine by exchanging the serine hydroxyl moiety by a sulfhydryl moiety, and subsequently all organic compounds containing reduced sulfur moieties. We investigate here, how manipulation of the SERAT interface results in metabolic alterations upstream or downstream of this boundary and the extent to which the five SERAT isoforms exert an effect on the coupled system, respectively. Serine is synthesized through three distinct pathways while cysteine biosynthesis is distributed over the three compartments cytosol, mitochondria, and plastids. As the respective mutants are viable, all necessary metabolites can obviously cross various membrane systems to compensate what would otherwise constitute a lethal failure in cysteine biosynthesis. Furthermore, given that cysteine serves as precursor for multiple pathways, cysteine biosynthesis is highly regulated at both, the enzyme and the expression level. In this study, metabolite profiles of a mutant series of the SERAT gene family displayed that levels of the downstream metabolites in sulfur metabolism were affected in correlation with the reduction levels of SERAT activities and the growth phenotypes, while levels of the upstream metabolites in serine metabolism were unchanged in the serat mutants compared to wild-type plants. These results suggest that despite of the fact that the two metabolic pathways are directly connected, there seems to be no causal link in metabolic alterations. This might be caused by the difference of their pool sizes or the tight regulation by homeostatic mechanisms that control the metabolite concentration in plant cells. Additionally, growth conditions exerted an influence on metabolic compositions.
- Published
- 2023
9. Subcellular engineering of lipase dependent pathways directed towards lipid related organelles for highly effectively compartmentalized biosynthesis of triacylglycerol derived products in Yarrowia lipolytica.
- Author
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Yang, Kaixin, Qiao, Yangge, Li, Fei, Xu, Yun, Yan, Yunjun, Madzak, Catherine, and Yan, Jinyong
- Subjects
- *
ORGANELLES , *BIOSYNTHESIS , *FATTY acid methyl esters , *LIPIDS - Abstract
As an alternative to in vitro lipase dependent biotransformation and to traditional assembly of pathways in cytoplasm, the present study focused on targeting lipase dependent pathways to a subcellular compartment lipid body (LB), in combination with compartmentalization of associated pathways in other lipid relevant organelles including endoplasmic reticulum (ER) and peroxisome for efficient in vivo biosynthesis of fatty acid methyl esters (FAMEs) and hydrocarbons, in the context of improving Yarrowia lipolytica lipid pool. Through knock in and knock out of key genes involved in triacylglycerols (TAGs) biosynthesis and degradation, the TAGs content was increased to 51.5%, from 7.2% in parent strain. Targeting lipase dependent pathway to LB gave a 10-fold higher FAMEs titer (1028.0 mg/L) compared to cytosolic pathway (102.8 mg/L). Furthermore, simultaneously targeting lipase dependent pathway to LB, ER and peroxisome gave rise to the highest FAMEs titer (1644.8 mg/L). The subcellular compartment engineering strategy was extended to other lipase dependent pathways for fatty alkene and alkane biosynthesis, which resulted in a 14-fold titer enhancement compared to traditional cytosolic pathways. We developed yeast subcellular cell factories by directing lipase dependent pathways towards the TAGs storage organelle LB for efficient biosynthesis of TAG derived chemicals for the first time. The successful exploration of targeting metabolic pathways towards LB centered organelles is expected to promote subcellular compartment engineering for other lipid derived product biosynthesis. • Engineering lipase dependent pathways for biosynthesis of products. • Exploring lipid body for subcellular compartmentalization. • Simultaneously targeting subcellular compartments to improve product titers. [ABSTRACT FROM AUTHOR]
- Published
- 2019
- Full Text
- View/download PDF
10. Advances in the Mechanisms of Plant Tolerance to Manganese Toxicity
- Author
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Jifu Li, Yidan Jia, Rongshu Dong, Rui Huang, Pandao Liu, Xinyong Li, Zhiyong Wang, Guodao Liu, and Zhijian Chen
- Subjects
manganese toxicity ,mn detoxification ,tolerance mechanism ,gene function ,subcellular compartment ,Biology (General) ,QH301-705.5 ,Chemistry ,QD1-999 - Abstract
Manganese (Mn) is an essential element for plant growth due to its participation in a series of physiological and metabolic processes. Mn is also considered a heavy metal that causes phytotoxicity when present in excess, disrupting photosynthesis and enzyme activity in plants. Thus, Mn toxicity is a major constraint limiting plant growth and production, especially in acid soils. To cope with Mn toxicity, plants have evolved a wide range of adaptive strategies to improve their growth under this stress. Mn tolerance mechanisms include activation of the antioxidant system, regulation of Mn uptake and homeostasis, and compartmentalization of Mn into subcellular compartments (e.g., vacuoles, endoplasmic reticulum, Golgi apparatus, and cell walls). In this regard, numerous genes are involved in specific pathways controlling Mn detoxification. Here, we summarize the recent advances in the mechanisms of Mn toxicity tolerance in plants and highlight the roles of genes responsible for Mn uptake, translocation, and distribution, contributing to Mn detoxification. We hope this review will provide a comprehensive understanding of the adaptive strategies of plants to Mn toxicity through gene regulation, which will aid in breeding crop varieties with Mn tolerance via genetic improvement approaches, enhancing the yield and quality of crops.
- Published
- 2019
- Full Text
- View/download PDF
11. The Effect of Single and Multiple SERAT Mutants on Serine and Sulfur Metabolism
- Author
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Mutsumi Watanabe, Takayuki Tohge, Alisdair R. Fernie, and Rainer Hoefgen
- Subjects
serine acetyltransferase ,serine ,O-acetylserine ,cysteine ,subcellular compartment ,Plant culture ,SB1-1110 - Abstract
The gene family of serine acetyltransferases (SERATs) constitutes an interface between the plant pathways of serine and sulfur metabolism. SERATs provide the activated precursor, O-acetylserine for the fixation of reduced sulfur into cysteine by exchanging the serine hydroxyl moiety by a sulfhydryl moiety, and subsequently all organic compounds containing reduced sulfur moieties. We investigate here, how manipulation of the SERAT interface results in metabolic alterations upstream or downstream of this boundary and the extent to which the five SERAT isoforms exert an effect on the coupled system, respectively. Serine is synthesized through three distinct pathways while cysteine biosynthesis is distributed over the three compartments cytosol, mitochondria, and plastids. As the respective mutants are viable, all necessary metabolites can obviously cross various membrane systems to compensate what would otherwise constitute a lethal failure in cysteine biosynthesis. Furthermore, given that cysteine serves as precursor for multiple pathways, cysteine biosynthesis is highly regulated at both, the enzyme and the expression level. In this study, metabolite profiles of a mutant series of the SERAT gene family displayed that levels of the downstream metabolites in sulfur metabolism were affected in correlation with the reduction levels of SERAT activities and the growth phenotypes, while levels of the upstream metabolites in serine metabolism were unchanged in the serat mutants compared to wild-type plants. These results suggest that despite of the fact that the two metabolic pathways are directly connected, there seems to be no causal link in metabolic alterations. This might be caused by the difference of their pool sizes or the tight regulation by homeostatic mechanisms that control the metabolite concentration in plant cells. Additionally, growth conditions exerted an influence on metabolic compositions.
- Published
- 2018
- Full Text
- View/download PDF
12. Effects of Phosphoinositides and Their Derivatives on Membrane Morphology and Function
- Author
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Larijani, Banafshé, Poccia, Dominic L., and FALASCA, MARCO, editor
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- 2012
- Full Text
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13. Metabolic process of raffinose family oligosaccharides during cold stress and recovery in cucumber leaves.
- Author
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Gu, Hao, Lu, Man, Zhang, Zhiping, Xu, Jinjin, Cao, Wenhua, and Miao, Minmin
- Subjects
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CUCUMBERS , *OLIGOSACCHARIDES , *PHYSIOLOGICAL effects of cold temperatures , *GALACTINOL synthase , *CHLOROPLASTS - Abstract
Raffinose family oligosaccharides (RFOs) accumulate under stress conditions in many plants and have been suggested to act as stress protectants. To elucidate the metabolic process of RFOs under cold stress, levels of RFOs, and related carbohydrates, the expression and activities of main metabolic enzymes and their subcellular compartments were investigated during low-temperature treatment and during the recovery period in cucumber leaves. Cold stress induced the accumulation of stachyose in vacuoles, galactinol in vacuoles and cytosol, and sucrose and raffinose in vacuoles, cytosol, and chloroplasts. After cold stress removal, levels of these sugars decreased gradually in the respective compartments. Among four galactinol synthase genes ( CsGS ), CsGS1 was not affected by cold stress, while the other three CsGSs were up-regulated by low temperature. RNA levels of acid-α-galactosidase ( GAL ) 3 and alkaline-α-galactosidase ( AGA) 2 and 3 , and the activities of GAL and AGA, were up-regulated after cold stress removal. GAL3 protein and GAL activity were exclusively located in vacuoles, whereas AGA2 and AGA 3 proteins were found in cytosol and chloroplasts, respectively. The results indicate that RFOs, which accumulated during cold stress in different subcellular compartments in cucumber leaves, could be catabolized in situ by different galactosidases after stress removal. [ABSTRACT FROM AUTHOR]
- Published
- 2018
- Full Text
- View/download PDF
14. Cellular and Subcellular Distribution of Selenium and Selenium-Containing Proteins in the Rat
- Author
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Behne, Dietrich, Pfeifer, Henning, Röthlein, Doris, Kyriakopoulos, Antonios, Roussel, A. M., editor, Anderson, R. A., editor, and Favier, A. E., editor
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- 2002
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15. Indication for differential sorting of the rat v-SNARE splice isoforms VAMP-1a and -1b.
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Rodepeter, Fiona R., Wiegand, Susanne, Lüers, Hans-Georg, Bonaterra, Gabriel A., Lowe, Anson W., Bette, Michael, Jacob, Ralf, and Mandic, Robert
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PROTEIN receptors , *FLOW cytometry , *GREEN fluorescent protein , *GOLGI apparatus , *PEROXISOMES , *INTRACELLULAR membranes , *FLUORESCENCE microscopy - Abstract
Soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) proteins are essential constituents of the intracellular trafficking machinery. The variable C-terminus in the 2 rat VAMP-1 splice isoforms VAMP-1a and -1b potentially acts as a sorting signal, because similar changes at the C-terminal end of a human VAMP-1 splice isoform resulted in its sorting to mitochondria. To evaluate the differences in the subcellular localization of these two v-SNARE proteins, VAMP-1a and -1b proteins tagged with green fluorescent protein (GFP) and red fluorescent protein (RFP) were expressed in HeLa, COS-7, and MDCK cells and evaluated by conventional confocal as well as total internal reflection fluorescence microscopy. Regions consistent with the endoplasmic reticulum and Golgi apparatus demonstrated a major overlap of both signals. In the periphery, vesicular structures were observed that mainly expressed one of the 2 isoforms. Within our experimental settings, we could not observe sorting of any of the 2 isoforms to mitochondria or peroxisomes, whereas both isoforms were found expressed in a minor subset of singular vesicles, which sporadically appeared to co-localize with the exocyst marker EXOC3/Sec6. Because vesicular structures were seen that expressed only one of the two splice variants, it is possible that VAMP-1a and VAMP-1b are sorted to distinct cellular compartments that require further characterization. [ABSTRACT FROM AUTHOR]
- Published
- 2017
- Full Text
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16. Cytosolic and Nuclear Co-localization of Betalain Biosynthetic Enzymes in Tobacco Suggests that Betalains Are Synthesized in the Cytoplasm and/or Nucleus of Betalainic Plant Cells.
- Author
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Ning Chen, Zhi-Hai Yu, and Xing-Guo Xiao
- Subjects
BETALAINS ,PLANT cytoplasm ,PLANT cells & tissues - Abstract
Betalains replace anthocyanins as color pigments in most families of Caryophyllales. Unlike anthocyanins, betalains are derived from tyrosine via three enzymatic steps: hydroxylation of L-tyrosine to L-3,4-dihydroxyphenylalanine (L-DOPA; step 1), and conversion of L-DOPA to betalamic acid (step 2), and to cyclo-DOPA (cDOPA; step 3). The principal enzymes responsible for these reactions have been elucidated at the molecular level, but their subcellular localizations have not been explored; hence, the intracellular compartments wherein betalains are biosynthesized remain unknown. Here, we report on the subcellular localization of these principal enzymes. Bioinformatic predictors and N- and C-terminal GFP tagging in transgenic tobacco, showed that Beta vulgaris CYP76AD1 which mediates both steps 1 and 3, DODA1 that catalyzes step 2, and CYP76AD6 which also mediates step 1, were similarly localized to the cytoplasm and nucleus (although the P450s were also weakly present in the endoplasmic reticulum). These two compartments were also the principal locations of Mirabilis jalapa cDOPA5GT. The cytoplasmic and nuclear co-localization of these key enzymes in tobacco suggests that betalains are biosynthesized in the cytoplasm and/or nucleus of betalain-containing plant cells. Elucidation of the subcellular compartmentation of betalain biosynthesis will facilitate the bioengineering of the betalain biosynthetic pathway in non-betalain-containing plants. [ABSTRACT FROM AUTHOR]
- Published
- 2017
- Full Text
- View/download PDF
17. Mitochondrial acetyl-CoA utilization pathway for terpenoid productions.
- Author
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Yuan, Jifeng and Ching, Chi-Bun
- Subjects
- *
MITOCHONDRIAL proteins , *ACETYL compounds , *TERPENES , *CELL metabolism , *BIOSYNTHESIS , *PYROPHOSPHATES - Abstract
Acetyl-CoA is a central molecule in the metabolism of the cell, which is also a precursor molecule to a variety of value-added products such as terpenoids and fatty acid derived molecules. Considering subcellular compartmentalization of metabolic pathways allows higher concentrations of enzymes, substrates and intermediates, and bypasses competing pathways, mitochondrion-compartmentalized acetyl-CoA utilization pathways might offer better pathway activities with improved product yields. As a proof-of-concept, we sought to explore a mitochondrial farnesyl pyrophosphate (FPP) biosynthetic pathway for the biosynthesis of amorpha-4,11-diene in budding yeast. In the present study, the eight-gene FPP biosynthetic pathway was successfully expressed inside yeast mitochondria to enable high-level amorpha-4,11-diene production. In addition, we also found the mitochondrial compartment serves as a partial barrier for the translocation of FPP from mitochondria into the cytosol, which would potentially allow minimized loss of FPP to cytosolic competing pathways. To our best knowledge, this is the first report to harness yeast mitochondria for terpenoid productions from the mitochondrial acetyl-CoA pool. We envision subcellular metabolic engineering might also be employed for an efficient production of other bio-products from the mitochondrial acetyl-CoA in other eukaryotic organisms. [ABSTRACT FROM AUTHOR]
- Published
- 2016
- Full Text
- View/download PDF
18. Effect of Continuous Melatonin Infusions on Steady-State Plasma Melatonin Levels, Metabolic Fate and Tissue Retention in Rats Under Near Physiological Conditions
- Author
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Messner, M., Hardeland, R., Rodenbeck, A., Huether, G., Huether, Gerald, editor, Kochen, Walter, editor, Simat, Thomas J., editor, and Steinhart, Hans, editor
- Published
- 1999
- Full Text
- View/download PDF
19. Cytoplasmic Ion Imaging: Evidence for Intracellular Calibration Heterogeneities of Ion-Sensitive Fluoroprobes
- Author
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Opitz, N., Porwol, T., Merten, E., Acker, H., and Slavík, Jan, editor
- Published
- 1996
- Full Text
- View/download PDF
20. Biogenesis of Peribacteroid Membrane (PBM) Forming a Subcellular Compartment Essential for Symbiotic Nitrogen Fixation
- Author
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Verma, D. P. S., Cheon, C.-I., Lee, N.-G., Hong, Z., Miao, G.-H., Palacios, Rafael, editor, Mora, Jaime, editor, and Newton, William E., editor
- Published
- 1993
- Full Text
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21. Exploring the proteomic characteristics of the Escherichia coli B and K-12 strains in different cellular compartments.
- Author
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Han, Mee-Jung
- Subjects
- *
PROTEOMICS , *ESCHERICHIA coli , *INDUSTRIAL applications , *BIOTECHNOLOGY , *BACTERIAL cells , *CELL growth , *RECOMBINANT proteins - Abstract
Escherichia coli , one of the well-characterized prokaryotes, has been the most widely used bacterial host in scientific studies and industrial applications. Many different strains have been developed for the widespread use of E. coli in biotechnology, and selecting an ideal host to produce a specific protein of interest is a critical step in developing a production process. The E. coli B and K-12 strains are among the most frequently used bacterial hosts for the production of recombinant proteins as well as small-molecule metabolites such as amino acids, biofuels, carboxylic acids, diamines, and others. However, both strains have distinctive differences in genotypic and phenotypic attributes, and their behaviors can still be unpredictable at times, especially while expressing a recombinant protein. Therefore, in this review, an in-depth analysis of the physiological behavior on the proteomic level was performed, wherein the particularly distinct proteomic differences between the E. coli B and K-12 strains were investigated in the four distinctive cellular compartments. Interesting differences in the proteins associated with key cellular properties including cell growth, protein production and quality, cellular tolerance, and motility were observed between the two representative strains. The resulting enhancement of knowledge regarding host physiology that is summarized herein is expected to contribute to the acceleration of strain improvements and optimization for biotechnology-related processes. [ABSTRACT FROM AUTHOR]
- Published
- 2016
- Full Text
- View/download PDF
22. The S-100 Protein Family: A Biochemical and Functional Overview
- Author
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Hilt, Dana C., Kligman, Douglas, and Heizmann, Claus W., editor
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- 1991
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23. Photorespiratory Dependent Leaf Mitochondrial ATP Production
- Author
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Gardeström, Per, Wigge, Bosse, and Baltscheffsky, M., editor
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- 1990
- Full Text
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24. Membrane remodeling in plant salt tolerance
- Author
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Guo, Qi
- Subjects
Sequential Window Acquisition of All Theoretical Mass Spectra ,Phospholipid ,CAM ,Lipid metabolism ,Crassulacean acid metabolism ,Subcellular compartment ,Quantitative proteomics ,SWATH-MS ,Salt tolerance ,Lipid signalling ,Membrane markers - Abstract
Soil salinisation is a serious land degradation issue worldwide, limiting the productivity of crops. Understanding the tolerance mechanisms employed by halophytes is of great value for ultimately identifying biomarkers for salt-tolerant crop breeding. This PhD project capitalised on the use of innovative membrane isolation technology Free-Flow Electrophoresis, next-generation proteomic technology SWATH-MS, and mass spectrometry-based lipidomic analyses to investigate changes in proteins and lipids in leaf tissue of the halophyte Mesembryanthemum crystallinum grown under salt conditions. Results provided a framework to develop a model for salinity-induced membrane remodelling at the subcellular level and will inform future work to engineer salt-tolerant crops.
- Published
- 2021
- Full Text
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25. Subcellular distribution of FTY720 and FTY720-phosphate in immune cells - another aspect of Fingolimod action relevant for therapeutic application.
- Author
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Schröder, Matthias, Arlt, Olga, Schmidt, Helmut, Huwiler, Andrea, Angioni, Carlo, Pfeilschifter, Josef M., Schwiebs, Anja, and Radeke, Heinfried H.
- Subjects
- *
MULTIPLE sclerosis , *PHOSPHATES , *FINGOLIMOD , *PRODRUGS , *IMMUNOREGULATION , *SPHINGOSINE-1-phosphate , *THERAPEUTICS - Abstract
FTY720 (Fingolimod; Gilenya®) is an immunemodulatory prodrug which, after intracellular phosphorylation by sphingosine kinase 2 (SphK2) and export, mimics effects of the endogenous lipid mediator sphingosine-1-phosphate. Fingolimod has been introduced to treat relapsing-remitting multiple sclerosis. However, little has been published about the immune cell membrane penetration and subcellular distribution of FTY720 and FTY720-P. Thus, we applied a newly established LC-MS/MS method to analyze the subcellular distribution of FTY720 and FTY720-P in subcellular compartments of spleen cells of wild type, SphK1- and SphK2-deficient mice. These studies demonstrated that, when normalized to the original cell volume and calculated on molar basis, FTY720 and FTY720-P dramatically accumulated several hundredfold within immune cells reaching micromolar concentrations. The amount and distribution of FTY720 was differentially affected by SphK1- and SphK2-deficiency On the background of recently described relevant intracellular FTY720 effects in the nanomolar range and the prolonged application in multiple sclerosis, this data showing a substantial intracellular accumulation of FTY720, has to be considered for benefit/risk ratio estimates. [ABSTRACT FROM AUTHOR]
- Published
- 2015
- Full Text
- View/download PDF
26. ER to synapse trafficking of NMDA receptors.
- Author
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Horak, Martin, Petralia, Ronald S., Kaniakova, Martina, and Sans, Nathalie
- Subjects
GLUTAMATE receptors ,METHYL aspartate receptors ,DIZOCILPINE ,NEURAL transmission ,NEURAL circuitry - Abstract
Glutamate is the major excitatory neurotransmitter in the mammalian central nervous system. There are three distinct subtypes of ionotropic glutamate receptors (GluRs) that have been identified including 2-amino-3-(5-methyl-3-oxo-1,2-oxazol-4-yl)propanoic acid receptors (AMPARs), N-methyl-D-aspartate receptors (NMDARs) and kainate receptors. The most common GluRs in mature synapses are AMPARs that mediate the fast excitatory neurotransmission and NMDARs that mediate the slow excitatory neurotransmission. There have been large numbers of recent reports studying how a single neuron regulates synaptic numbers and types of AMPARs and NMDARs. Our current research is centered primarily on NMDARs and, therefore, we will focus in this review on recent knowledge of molecular mechanisms occurring (1) early in the biosynthetic pathway of NMDARs, (2) in the transport of NMDARs after their release from the endoplasmic reticulum (ER); and (3) at the plasma membrane including excitatory synapses. Because a growing body of evidence also indicates that abnormalities in NMDAR functioning are associated with a number of human psychiatric and neurological diseases, this review together with other chapters in this issue may help to enhance research and to gain further knowledge of normal synaptic physiology as well as of the etiology of many human brain diseases. [ABSTRACT FROM AUTHOR]
- Published
- 2014
- Full Text
- View/download PDF
27. SpiCee: A Genetic Tool for Subcellular and Cell-Specific Calcium Manipulation
- Author
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Ros, Oriol, Baudet, Sarah, Zagar, Yvrick, Loulier, Karine, Roche, Fiona, Couvet, Sandrine, Aghaie, Alain, Atkins, Melody, Louail, Alice, Petit, Christine, Metin, Christine, Mechulam, Yves, Nicol, Xavier, Institut de la Vision, Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Institut National de la Santé et de la Recherche Médicale (INSERM), UMRS 1120, Institut National de la Santé et de la Recherche Médicale de Paris, Ecole des Neurosciences de Paris Île de France (ENP), Ecole des Neurosciences de Paris, Chaire Génétique et physiologie cellulaire, Collège de France (CdF (institution)), Laboratoire de Biologie Structurale de la Cellule (BIOC), École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS), Nicol, Xavier, Collège de France - Chaire Génétique et physiologie cellulaire, and Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)
- Subjects
Cell Survival ,subcellular compartment ,[SDV.BC]Life Sciences [q-bio]/Cellular Biology ,Adenosine Triphosphate ,subcellular calcium manipulation ,Cell Movement ,calcium buffer ,[SDV.BDD] Life Sciences [q-bio]/Development Biology ,Animals ,Humans ,Calcium Signaling ,[SDV.BC] Life Sciences [q-bio]/Cellular Biology ,[SDV.BDD]Life Sciences [q-bio]/Development Biology ,single-cell pharmacology ,Chelating Agents ,Neurons ,neuronal migration ,calcium ,Cell Death ,EF hand ,axon guidance ,[SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology ,Mice, Inbred C57BL ,parvalbumin calmodulin ,HEK293 Cells ,Genetic Techniques ,Thapsigargin ,Signal Transduction ,Subcellular Fractions - Abstract
International audience; Calcium is a second messenger crucial to a myriad of cellular processes ranging from regulation of metabolism and cell survival to vesicle release and motility. Current strategies to directly manipulate endogenous calcium signals lack cellular and subcellular specificity. We introduce SpiCee, a versatile and genetically encoded chelator combining low- and high-affinity sites for calcium. This scavenger enables altering endogenous calcium signaling and functions in single cells in vitro and in vivo with biochemically controlled subcellular resolution. SpiCee paves the way to investigate local calcium signaling in vivo and directly manipulate this second messenger for therapeutic use.
- Published
- 2020
28. Proteomics methods for subcellular proteome analysis.
- Author
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Drissi, Romain, Dubois, Marie‐Line, and Boisvert, François‐Michel
- Subjects
- *
PROTEOMICS , *CELL culture , *PROTEIN fractionation , *SODIUM dodecyl sulfate , *POLYACRYLAMIDE gel electrophoresis , *SOLUBILIZATION , *GEL permeation chromatography - Abstract
The elucidation of the subcellular distribution of proteins under different conditions is a major challenge in cell biology. This challenge is further complicated by the multicompartmental and dynamic nature of protein localization. To address this issue, quantitative proteomics workflows have been developed to reliably identify the protein complement of whole organelles, as well as for protein assignment to subcellular location and relative protein quantification based on different cell culture conditions. Here, we review quantitative MS-based approaches that combine cellular fractionation with proteomic analysis. The application of these methods to the characterization of organellar composition and to the determination of the dynamic nature of protein complexes is improving our understanding of protein functions and dynamics. [ABSTRACT FROM AUTHOR]
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- 2013
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- View/download PDF
29. Robust prediction of protein subcellular localization combining PCA and WSVMs
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Tian, Jiang, Gu, Hong, Liu, Wenqi, and Gao, Chiyang
- Subjects
- *
PROTEINS , *SUPPORT vector machines , *ROBUST control , *PRINCIPAL components analysis , *PROBLEM solving , *GENERALIZATION , *ALGORITHMS , *OUTLIERS (Statistics) - Abstract
Abstract: Automated prediction of protein subcellular localization is an important tool for genome annotation and drug discovery, and Support Vector Machines (SVMs) can effectively solve this problem in a supervised manner. However, the datasets obtained from real experiments are likely to contain outliers or noises, which can lead to poor generalization ability and classification accuracy. To explore this problem, we adopt strategies to lower the effect of outliers. First we design a method based on Weighted SVMs, different weights are assigned to different data points, so the training algorithm will learn the decision boundary according to the relative importance of the data points. Second we analyse the influence of Principal Component Analysis (PCA) on WSVM classification, propose a hybrid classifier combining merits of both PCA and WSVM. After performing dimension reduction operations on the datasets, kernel-based possibilistic c-means algorithm can generate more suitable weights for the training, as PCA transforms the data into a new coordinate system with largest variances affected greatly by the outliers. Experiments on benchmark datasets show promising results, which confirms the effectiveness of the proposed method in terms of prediction accuracy. [Copyright &y& Elsevier]
- Published
- 2011
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30. Ras and Rap Signaling in Synaptic Plasticity and Mental Disorders.
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Stornetta, Ruth L. and Zhu, J. Julius
- Subjects
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RAS proteins , *GUANOSINE triphosphatase , *MITOGEN-activated protein kinases , *MENTAL illness , *NEUROPLASTICITY - Abstract
The Ras family GTPases (Ras, Rap1, and Rap2) and their downstream mitogen-activated protein kinases (ERK, JNK, and p38MAPK) and PI3K signaling cascades control various physiological processes. In neuronal cells, recent studies have shown that these parallel cascades signal distinct forms of AMPA-sensitive glutamate receptor trafficking during experience-dependent synaptic plasticity and adaptive behavior. Interestingly, both hypo- and hyperactivation of Ras/ Rap signaling impair the capacity of synaptic plasticity, underscoring the importance of a “happy-medium” dynamic regulation of the signaling. Moreover, accumulating reports have linked various genetic defects that either up- or down-regulate Ras/Rap signaling with several mental disorders associated with learning disability (e.g., Alzheimer’s disease, Angelman syndrome, autism, cardio-facio-cutaneous syndrome, Coffin-Lowry syndrome, Costello syndrome, Cowden and Bannayan-Riley-Ruvalcaba syndromes, fragile X syndrome, neurofibromatosis type 1, Noonan syndrome, schizophrenia, tuberous sclerosis, and X-linked mental retardation), highlighting the necessity of happy-medium dynamic regulation of Ras/Rap signaling in learning behavior. Thus, the recent advances in understanding of neuronal Ras/Rap signaling provide a useful guide for developing novel treatments for mental diseases. [ABSTRACT FROM PUBLISHER]
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- 2011
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- View/download PDF
31. Deregulation of Rab5 and Rab4 proteins in p85R274A-expressing cells alters PDGFR trafficking
- Author
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Chamberlain, M. Dean, Oberg, Jennifer C., Furber, Levi A., Poland, Sharon F., Hawrysh, Andrea D., Knafelc, Stacey M., McBride, Heidi M., and Anderson, Deborah H.
- Subjects
- *
GUANOSINE triphosphatase , *ENZYME regulation , *CELLULAR signal transduction , *RAS proteins , *PLATELET-derived growth factor , *CELL receptors , *PROTEIN-tyrosine kinases , *ENDOCYTOSIS - Abstract
Abstract: Activated receptor tyrosine kinases recruit many signaling proteins to activate downstream cell proliferation and survival pathways, including phosphatidylinositol 3-kinase (PI3K) consisting of a p85 regulatory protein and a p110 catalytic protein. We have recently shown the p85α protein also has in vitro GTPase activating protein (GAP) activity towards Rab5 and Rab4, small GTPases that regulate vesicle trafficking events for activated receptors. Expression of a GAP-defective mutant, p85R274A, resulted in sustained levels of activated platelet-derived growth factor receptors (PDGFRs) and enhanced downstream signaling. In this report we have characterized Rab5- and Rab4-mediated PDGFR trafficking in cells expressing wild type p85 and GAP-defective mutant p85R274A. Wild type p85 overexpressing cells had slower PDGFR trafficking consistent with enhanced GAP activity deactivating Rab5 and Rab4 to block their vesicle trafficking functions. Mutant p85R274A expression increased the internalization rate of PDGFRs, a Rab5-dependent process, without preventing PDGFR ubiquitination. Immunofluorescence studies further demonstrated that p85R274A-expressing cells showed Rab5 accumulation at intracellular locations. Pull-down and FRAP (fluorescence recovery after photobleaching) experiments indicate this is likely membrane-associated Rab5-GTP, sustained due to decreased p85 GAP activity for the p85R274A mutant. These cells also had substantial amounts of activated PDGFRs in Rab4-positive recycling endosomes, a compartment that usually contains primarily deactivated/dephosphorylated receptors. Our results suggest that the PDGFR-associated GAP activity of p85 regulates both Rab5 and Rab4 functions in cells to influence the movement of activated PDGFR through endosomal compartments. Disruption of this regulation by p85R274A expression impacts PDGFR phosphorylation/dephosphorylation, degradation kinetics and downstream signaling by altering the time receptors spend in specific intracellular endosomal compartments. These results demonstrate that the p85α protein is an important regulator of Rab-mediated PDGFR trafficking, which significantly impacts receptor signaling and degradation. [Copyright &y& Elsevier]
- Published
- 2010
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32. Transglutaminase 2: a multi-functional protein in multiple subcellular compartments.
- Author
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Donghyun Park, Sun Shim Choi, and Kwon-Soo Ha
- Subjects
- *
G proteins , *PROTEIN kinases , *CYTOSOL , *CELL membranes , *MITOCHONDRIA - Abstract
Transglutaminase 2 (TG2) is a multifunctional protein that can function as a transglutaminase, G protein, kinase, protein disulfide isomerase, and as an adaptor protein. These multiple biochemical activities of TG2 account for, at least in part, its involvement in a wide variety of cellular processes encompassing differentiation, cell death, inflammation, cell migration, and wound healing. The individual biochemical activities of TG2 are regulated by several cellular factors, including calcium, nucleotides, and redox potential, which vary depending on its subcellular location. Thus, the microenvironments of the subcellular compartments to which TG2 localizes, such as the cytosol, plasma membrane, nucleus, mitochondria, or extracellular space, are important determinants to switch on or off various TG2 biochemical activities. Furthermore, TG2 interacts with a distinct subset of proteins and/or substrates depending on its subcellular location. In this review, the biological functions and molecular interactions of TG2 will be discussed in the context of the unique environments of the subcellular compartments to which TG2 localizes. [ABSTRACT FROM AUTHOR]
- Published
- 2010
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- View/download PDF
33. Changing transcriptional initiation sites and alternative 5′- and 3′-splice site selection of the first intron deploys Arabidopsis PROTEIN ISOASPARTYL METHYLTRANSFERASE2 variants to different subcellular compartments.
- Author
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Dinkins, Randy D., Majee, Susmita Maitra, Nayak, Nihar R., Martin, David, Xu, Qilong, Belcastro, Marisa P., Houtz, Robert L., Beach, Carol M., and Downie, A. Bruce
- Subjects
- *
ARABIDOPSIS thaliana , *METHYLTRANSFERASES , *ASPARTATE aminotransferase , *PLANT physiology , *TRANSCRIPTION factors - Abstract
Arabidopsis thaliana (L.) Heynh. possesses two PROTEIN-L-ISOASPARTATE METHYLTRANSFERASE ( PIMT) genes encoding enzymes (EC 2.1.1.77) capable of converting uncodedl-isoaspartyl residues, arising spontaneously atl-asparaginyl andl-aspartyl sites in proteins, tol-aspartate. PIMT2 produces at least eight transcripts by using four transcriptional initiation sites (TIS; resulting in three different initiating methionines) and both 5′- and 3′-alternative splice site selection of the first intron. The transcripts produce mature proteins capable of convertingl-isoaspartate tol-aspartate in small peptide substrates. PIMT:GFP fusion proteins generated a detectable signal in the nucleus. However, whether the protein was also detectable in the cytoplasm, endo-membrane system, chloroplasts, and/or mitochondria, depended on the transcript from which it was produced. On-blot-methylation of proteins, prior to the completion of germination, indicated that cruciferin subunits contain isoaspartate. The implications of using transcriptional mechanisms to expand a single gene’s repertoire to protein variants capable of entry into the cell’s various compartments are discussed in light of PIMT’s presumed role in repairing the proteome. [ABSTRACT FROM AUTHOR]
- Published
- 2008
- Full Text
- View/download PDF
34. Subcellular segregation of distinct heteromeric NMDA glutamate receptors in the striatum.
- Author
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Dunah, Anthone W. and Standaert, David G.
- Subjects
- *
BRAIN , *METHYL aspartate - Abstract
Abstract Functional N-methyl- d-aspartate (NMDA) glutamate receptors are composed of heteromeric complexes of NR1, the obligatory subunit for channel activity, and NR2 or NR3 family members, which confer variability in the properties of the receptors. Recent studies have provided evidence for the existence of both binary (containing NR1 and either NR2A or NR2B) and ternary (containing NR1, NR2A, and NR2B) receptor complexes in the adult mammalian brain. However, the mechanisms regulating subunit assembly and receptor localization are not well understood. In the CNS, NMDA subunits are present both at intracellular sites and the post-synaptic membrane of neurons. Using biochemical protein fractionation and co-immunoprecipitation approaches we have found that in rat striatum binary NMDA receptors are widely distributed, and can be identified in the light membrane, synaptosomal membrane, and synaptic vesicle-enriched subcellular compartments. In contrast, ternary receptors are found exclusively in the synaptosomal membranes. When striatal proteins are chemically cross-linked prior to subcellular fractionation, ternary NMDA receptors can be precipitated from the light membrane and synaptic vesicle-enriched fractions where this type of receptor complex is not detectable under normal conditions. These findings suggest differential targeting of distinct types of NMDA receptor assemblies between intracellular and post-synaptic sites based on subunit composition. This targeting may underlie important differences in the regulation of the transport pathways involved in both normal as well as pathological receptor functions. [ABSTRACT FROM AUTHOR]
- Published
- 2003
- Full Text
- View/download PDF
35. SponGee: A Genetic Tool for Subcellular and Cell-Specific cGMP Manipulation
- Author
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Karine Loulier, Oriol Ros, Sandrine Couvet, Christine Petit, Alice Louail, Yves Mechulam, Delphine Ladarre, Sarah Baudet, Solène Ribes, Alain Aghaie, Zsolt Lenkei, Xavier Nicol, Yvrick Zagar, Institut de la Vision, Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Laboratoire Plasticité du Cerveau Brain Plasticity (UMR 8249) (PdC), Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Chaire Génétique et physiologie cellulaire, Collège de France (CdF (institution)), Laboratoire de Biochimie de l'Ecole polytechnique (BIOC), Centre National de la Recherche Scientifique (CNRS)-École polytechnique (X), This work was supported by grants from Agence Nationale de la Recherche (ANR-15-CE16-0007-01), Retina France, and Sorbonne Université (FCS-SU IDEX SUPER SU-15-R-PERSU-17) to X.N. This work was performed in the frame of the LABEX LIFESENSES (ANR-10-LABX-65) and IHU FOReSIGHT (ANR-18-IAHU-0001), supported by French state funds managed by the Agence Nationale de la Recherche within the Investissements d’Avenir program. A.L. and S.B. were supported by a fellowship from the ED3C doctoral program (Sorbonne Université)., ANR-15-CE16-0007,MessengerCodes,Régulation de la connectivité neuronale par les seconds messagers: décryptage des codes(2015), ANR-10-LABX-0065,LIFESENSES,DES SENS POUR TOUTE LA VIE(2010), ANR-18-IAHU-0001,FOReSIGHT,Enabling Vision Restoration(2018), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Collège de France - Chaire Génétique et physiologie cellulaire, and École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS)
- Subjects
0301 basic medicine ,[SDV.BIO]Life Sciences [q-bio]/Biotechnology ,[SDV.NEU.NB]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology ,Endogeny ,subcellular compartment ,[SDV.BC]Life Sciences [q-bio]/Cellular Biology ,Models, Biological ,Second Messenger Systems ,General Biochemistry, Genetics and Molecular Biology ,Rats, Sprague-Dawley ,03 medical and health sciences ,Cyclic nucleotide ,chemistry.chemical_compound ,Mice ,0302 clinical medicine ,In vivo ,Cyclic AMP ,Animals ,single cell pharmacology ,lcsh:QH301-705.5 ,Cyclic GMP ,genetically encoded ,[SDV.BDD]Life Sciences [q-bio]/Development Biology ,Cell specific ,neuronal migration ,Chemistry ,axon guidance ,PKG ,(T)hPDE5(VV) ,Cgmp signaling ,cGMP buffer ,In vitro ,Cell biology ,Rats ,030104 developmental biology ,Förster resonance energy transfer ,lipid grafts ,lcsh:Biology (General) ,FRET ,Axon guidance ,030217 neurology & neurosurgery - Abstract
Summary: cGMP is critical to a variety of cellular processes, but the available tools to interfere with endogenous cGMP lack cellular and subcellular specificity. We introduce SponGee, a genetically encoded chelator of this cyclic nucleotide that enables in vitro and in vivo manipulations in single cells and in biochemically defined subcellular compartments. SponGee buffers physiological changes in cGMP concentration in various model systems while not affecting cAMP signals. We provide proof-of-concept strategies by using this tool to highlight the role of cGMP signaling in vivo and in discrete subcellular domains. SponGee enables the investigation of local cGMP signals in vivo and paves the way for therapeutic strategies that prevent downstream signaling activation. : Ros et al. developed SponGee, a genetically encoded cGMP chelator that enables the manipulation of this second messenger in single cells with subcellular specificity. SponGee alters the migration of developing cortical neurons in vivo. Lipid raft targeting of SponGee prevents axon repulsion, in contrast to exclusion from this subcellular compartment. Keywords: cGMP buffer, subcellular compartment, single cell pharmacology, axon guidance, neuronal migration, lipid grafts, genetically encoded, FRET, ThPDE5VV, PKG
- Published
- 2019
36. Subcellular engineering of lipase dependent pathways directed towards lipid related organelles for highly effectively compartmentalized biosynthesis of triacylglycerol derived products in Yarrowia lipolytica
- Author
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Kaixin Yang, Yangge Qiao, Fei Li, Yun Xu, Yunjun Yan, Jinyong Yan, Catherine Madzak, Key Lab of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology [Wuhan] (HUST), Génie et Microbiologie des Procédés Alimentaires (GMPA), and Institut National de la Recherche Agronomique (INRA)-AgroParisTech
- Subjects
0106 biological sciences ,[SDV]Life Sciences [q-bio] ,Yarrowia ,Bioengineering ,Biosynthesis ,01 natural sciences ,Applied Microbiology and Biotechnology ,Fungal Proteins ,03 medical and health sciences ,chemistry.chemical_compound ,010608 biotechnology ,Subcellular compartment ,Organelle ,[SDV.IDA]Life Sciences [q-bio]/Food engineering ,[SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering ,Lipase ,Triglycerides ,030304 developmental biology ,Lipid body ,0303 health sciences ,biology ,Peroxisome ,biology.organism_classification ,Metabolic pathway ,Cytosol ,Metabolic Engineering ,Biochemistry ,chemistry ,Cytoplasm ,biology.protein ,Microorganisms, Genetically-Modified ,Biotechnology - Abstract
International audience; As an alternative to in vitro lipase dependent biotransformation and to traditional assembly of pathways in cytoplasm, the present study focused on targeting lipase dependent pathways to a subcellular compartment lipid body (LB), in combination with compartmentalization of associated pathways in other lipid relevant organelles including endoplasmic reticulum (ER) and peroxisome for efficient in vivo biosynthesis of fatty acid methyl esters (FAMEs) and hydrocarbons, in the context of improving Yarrowia lipolytica lipid pool. Through knock in and knock out of key genes involved in triacylglycerols (TAGs) biosynthesis and degradation, the TAGs content was increased to 51.5%, from 7.2% in parent strain. Targeting lipase dependent pathway to LB gave a 10-fold higher FAMEs titer (1028.0 mg/L) compared to cytosolic pathway (102.8 mg/L). Furthermore, simultaneously targeting lipase dependent pathway to LB, ER and peroxisome gave rise to the highest FAMEs titer (1644.8 mg/L). The subcellular compartment engineering strategy was extended to other lipase dependent pathways for fatty alkene and alkane biosynthesis, which resulted in a 14-fold titer enhancement compared to traditional cytosolic pathways. We developed yeast subcellular cell factories by directing lipase dependent pathways towards the TAGs storage organelle LB for efficient biosynthesis of TAG derived chemicals for the first time. The successful exploration of targeting metabolic pathways towards LB centered organelles is expected to promote subcellular compartment engineering for other lipid derived product biosynthesis.
- Published
- 2019
37. The Effect of Single and Multiple SERAT Mutants on Serine and Sulfur Metabolism
- Abstract
The gene family of serine acetyltransferases (SERATs) constitutes an interface between the plant pathways of serine and sulfur metabolism. SERATs provide the activated precursor, O-acetylserine for the fixation of reduced sulfur into cysteine by exchanging the serine hydroxyl moiety by a sulfhydryl moiety, and subsequently all organic compounds containing reduced sulfur moieties. We investigate here, how manipulation of the SERAT interface results in metabolic alterations upstream or downstream of this boundary and the extent to which the five SERAT isoforms exert an effect on the coupled system, respectively. Serine is synthesized through three distinct pathways while cysteine biosynthesis is distributed over the three compartments cytosol, mitochondria, and plastids. As the respective mutants are viable, all necessary metabolites can obviously cross various membrane systems to compensate what would otherwise constitute a lethal failure in cysteine biosynthesis. Furthermore, given that cysteine serves as precursor for multiple pathways, cysteine biosynthesis is highly regulated at both, the enzyme and the expression level. In this study, metabolite profiles of a mutant series of the SERAT gene family displayed that levels of the downstream metabolites in sulfur metabolism were affected in correlation with the reduction levels of SERAT activities and the growth phenotypes, while levels of the upstream metabolites in serine metabolism were unchanged in the serat mutants compared to wild-type plants. These results suggest that despite of the fact that the two metabolic pathways are directly connected, there seems to be no causal link in metabolic alterations. This might be caused by the difference of their pool sizes or the tight regulation by homeostatic mechanisms that control the metabolite concentration in plant cells. Additionally, growth conditions exerted an influence on metabolic compositions.
- Published
- 2018
38. The Effect of Single and Multiple SERAT Mutants on Serine and Sulfur Metabolism
- Abstract
The gene family of serine acetyltransferases (SERATs) constitutes an interface between the plant pathways of serine and sulfur metabolism. SERATs provide the activated precursor, O-acetylserine for the fixation of reduced sulfur into cysteine by exchanging the serine hydroxyl moiety by a sulfhydryl moiety, and subsequently all organic compounds containing reduced sulfur moieties. We investigate here, how manipulation of the SERAT interface results in metabolic alterations upstream or downstream of this boundary and the extent to which the five SERAT isoforms exert an effect on the coupled system, respectively. Serine is synthesized through three distinct pathways while cysteine biosynthesis is distributed over the three compartments cytosol, mitochondria, and plastids. As the respective mutants are viable, all necessary metabolites can obviously cross various membrane systems to compensate what would otherwise constitute a lethal failure in cysteine biosynthesis. Furthermore, given that cysteine serves as precursor for multiple pathways, cysteine biosynthesis is highly regulated at both, the enzyme and the expression level. In this study, metabolite profiles of a mutant series of the SERAT gene family displayed that levels of the downstream metabolites in sulfur metabolism were affected in correlation with the reduction levels of SERAT activities and the growth phenotypes, while levels of the upstream metabolites in serine metabolism were unchanged in the serat mutants compared to wild-type plants. These results suggest that despite of the fact that the two metabolic pathways are directly connected, there seems to be no causal link in metabolic alterations. This might be caused by the difference of their pool sizes or the tight regulation by homeostatic mechanisms that control the metabolite concentration in plant cells. Additionally, growth conditions exerted an influence on metabolic compositions., journal article
- Published
- 2018
39. Advances in the Mechanisms of Plant Tolerance to Manganese Toxicity
- Author
-
Zhiyong Wang, Guodao Liu, Rui Huang, Jifu Li, Rongshu Dong, Xinyong Li, Zhijian Chen, Pandao Liu, and Yidan Jia
- Subjects
0106 biological sciences ,0301 basic medicine ,Review ,subcellular compartment ,Vacuole ,Photosynthesis ,01 natural sciences ,Antioxidants ,Catalysis ,lcsh:Chemistry ,Inorganic Chemistry ,manganese toxicity ,03 medical and health sciences ,symbols.namesake ,Cell Wall ,Metals, Heavy ,Homeostasis ,Physical and Theoretical Chemistry ,lcsh:QH301-705.5 ,Molecular Biology ,Spectroscopy ,Regulation of gene expression ,Manganese ,Chemistry ,Endoplasmic reticulum ,Organic Chemistry ,food and beverages ,Biological Transport ,tolerance mechanism ,General Medicine ,Plants ,Compartmentalization (fire protection) ,Golgi apparatus ,Computer Science Applications ,gene function ,030104 developmental biology ,lcsh:Biology (General) ,lcsh:QD1-999 ,Biochemistry ,Toxicity ,symbols ,Mn detoxification ,Phytotoxicity ,010606 plant biology & botany - Abstract
Manganese (Mn) is an essential element for plant growth due to its participation in a series of physiological and metabolic processes. Mn is also considered a heavy metal that causes phytotoxicity when present in excess, disrupting photosynthesis and enzyme activity in plants. Thus, Mn toxicity is a major constraint limiting plant growth and production, especially in acid soils. To cope with Mn toxicity, plants have evolved a wide range of adaptive strategies to improve their growth under this stress. Mn tolerance mechanisms include activation of the antioxidant system, regulation of Mn uptake and homeostasis, and compartmentalization of Mn into subcellular compartments (e.g., vacuoles, endoplasmic reticulum, Golgi apparatus, and cell walls). In this regard, numerous genes are involved in specific pathways controlling Mn detoxification. Here, we summarize the recent advances in the mechanisms of Mn toxicity tolerance in plants and highlight the roles of genes responsible for Mn uptake, translocation, and distribution, contributing to Mn detoxification. We hope this review will provide a comprehensive understanding of the adaptive strategies of plants to Mn toxicity through gene regulation, which will aid in breeding crop varieties with Mn tolerance via genetic improvement approaches, enhancing the yield and quality of crops.
- Published
- 2019
40. Cytosolic and Nuclear Co-localization of Betalain Biosynthetic Enzymes in Tobacco Suggests that Betalains Are Synthesized in the Cytoplasm and/or Nucleus of Betalainic Plant Cells
- Author
-
Zhi-Hai Yu, Xing-Guo Xiao, and Ning Chen
- Subjects
0301 basic medicine ,DODA1 (DOD) ,betalain biosynthesis ,subcellular compartment ,Plant Science ,lcsh:Plant culture ,Biology ,CYP76AD1 ,Hydroxylation ,03 medical and health sciences ,chemistry.chemical_compound ,Biosynthesis ,Betalain ,subcellular localization ,lcsh:SB1-1110 ,Original Research ,chemistry.chemical_classification ,Endoplasmic reticulum ,nucleus ,Subcellular localization ,cDOPA5GT ,Cytosol ,030104 developmental biology ,Enzyme ,chemistry ,Biochemistry ,Cytoplasm ,cytoplasm - Abstract
Betalains replace anthocyanins as color pigments in most families of Caryophyllales. Unlike anthocyanins, betalains are derived from tyrosine via three enzymatic steps: hydroxylation of L-tyrosine to L-3,4-dihydroxyphenylalanine (L-DOPA; step 1), and conversion of L-DOPA to betalamic acid (step 2), and to cyclo-DOPA (cDOPA; step 3). The principal enzymes responsible for these reactions have been elucidated at the molecular level, but their subcellular localizations have not been explored; hence, the intracellular compartments wherein betalains are biosynthesized remain unknown. Here, we report on the subcellular localization of these principal enzymes. Bioinformatic predictors and N- and C-terminal GFP tagging in transgenic tobacco, showed that Beta vulgaris CYP76AD1 which mediates both step 1 and step 3, DODA1 that catalyzes step 2, and CYP76AD6 which also mediates step 1, were similarly localized to the cytoplasm and nucleus (although the P450s were also weakly present in the endoplasmic reticulum). These two compartments were also the principal locations of Mirabilis jalapa cDOPA5GT. The cytoplasmic and nuclear co-localization of these key enzymes in tobacco suggests that betalains are biosynthesized in the cytoplasm and/or nucleus of betalain-containing plant cells. Elucidation of the subcellular compartmentation of betalain biosynthesis will facilitate the bioengineering of the betalain biosynthetic pathway in non-betalain-containing plants.
- Published
- 2017
41. Does the proteome encode organellar pH?
- Author
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Brett, Christopher L., Donowitz, Mark, and Rao, Rajini
- Subjects
- *
ORGANELLES , *PROTEINS , *BIOMOLECULES , *HYDROGEN-ion concentration - Abstract
Abstract: Inherent to the proteome itself, may be information that enables proteins to buffer pH at a level that promotes their own function within a specialized compartment. We observe that the distribution of computed isoelectric points in the yeast proteome matches experimentally derived organellar pH estimates across distinct subcellular compartments. This raises an interesting evolutionary question: did the pI of proteins and the pH of organelles co-evolve to optimize function? [Copyright &y& Elsevier]
- Published
- 2006
- Full Text
- View/download PDF
42. Advances in the Mechanisms of Plant Tolerance to Manganese Toxicity.
- Author
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Li, Jifu, Jia, Yidan, Dong, Rongshu, Huang, Rui, Liu, Pandao, Li, Xinyong, Wang, Zhiyong, Liu, Guodao, and Chen, Zhijian
- Subjects
- *
GOLGI apparatus , *MANGANESE , *CROP quality , *PLANT breeding , *PHYTOTOXICITY , *ACID soils , *PLANT enzymes - Abstract
Manganese (Mn) is an essential element for plant growth due to its participation in a series of physiological and metabolic processes. Mn is also considered a heavy metal that causes phytotoxicity when present in excess, disrupting photosynthesis and enzyme activity in plants. Thus, Mn toxicity is a major constraint limiting plant growth and production, especially in acid soils. To cope with Mn toxicity, plants have evolved a wide range of adaptive strategies to improve their growth under this stress. Mn tolerance mechanisms include activation of the antioxidant system, regulation of Mn uptake and homeostasis, and compartmentalization of Mn into subcellular compartments (e.g., vacuoles, endoplasmic reticulum, Golgi apparatus, and cell walls). In this regard, numerous genes are involved in specific pathways controlling Mn detoxification. Here, we summarize the recent advances in the mechanisms of Mn toxicity tolerance in plants and highlight the roles of genes responsible for Mn uptake, translocation, and distribution, contributing to Mn detoxification. We hope this review will provide a comprehensive understanding of the adaptive strategies of plants to Mn toxicity through gene regulation, which will aid in breeding crop varieties with Mn tolerance via genetic improvement approaches, enhancing the yield and quality of crops. [ABSTRACT FROM AUTHOR]
- Published
- 2019
- Full Text
- View/download PDF
43. Specimen Preparation and Other Limitations in Quantitative Eletron Probe X-Ray Microanalysis (EPXMA) Using Ultrathin Sections
- Author
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Roos, Norbert, Bayley, P. M., editor, Zierold, Karl, editor, and Hagler, Herbert K., editor
- Published
- 1989
- Full Text
- View/download PDF
44. SpiCee: A Genetic Tool for Subcellular and Cell-Specific Calcium Manipulation.
- Author
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Ros O, Baudet S, Zagar Y, Loulier K, Roche F, Couvet S, Aghaie A, Atkins M, Louail A, Petit C, Metin C, Mechulam Y, and Nicol X
- Subjects
- Adenosine Triphosphate metabolism, Animals, Calcium Signaling drug effects, Cell Death drug effects, Cell Movement drug effects, Cell Survival drug effects, Chelating Agents pharmacology, HEK293 Cells, Humans, Mice, Inbred C57BL, Neurons cytology, Neurons drug effects, Signal Transduction drug effects, Subcellular Fractions metabolism, Thapsigargin pharmacology, Calcium metabolism, Genetic Techniques
- Abstract
Calcium is a second messenger crucial to a myriad of cellular processes ranging from regulation of metabolism and cell survival to vesicle release and motility. Current strategies to directly manipulate endogenous calcium signals lack cellular and subcellular specificity. We introduce SpiCee, a versatile and genetically encoded chelator combining low- and high-affinity sites for calcium. This scavenger enables altering endogenous calcium signaling and functions in single cells in vitro and in vivo with biochemically controlled subcellular resolution. SpiCee paves the way to investigate local calcium signaling in vivo and directly manipulate this second messenger for therapeutic use., Competing Interests: Declaration of Interests A patent application, listing O.R. and X.N. as inventors, describing the development and applications of SpiCee as a Ca(2+) chelator is pending., (Copyright © 2020 The Authors. Published by Elsevier Inc. All rights reserved.)
- Published
- 2020
- Full Text
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45. SponGee: A Genetic Tool for Subcellular and Cell-Specific cGMP Manipulation.
- Author
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Ros, Oriol, Zagar, Yvrick, Ribes, Solène, Baudet, Sarah, Loulier, Karine, Couvet, Sandrine, Ladarre, Delphine, Aghaie, Alain, Louail, Alice, Petit, Christine, Mechulam, Yves, Lenkei, Zsolt, and Nicol, Xavier
- Abstract
cGMP is critical to a variety of cellular processes, but the available tools to interfere with endogenous cGMP lack cellular and subcellular specificity. We introduce SponGee, a genetically encoded chelator of this cyclic nucleotide that enables in vitro and in vivo manipulations in single cells and in biochemically defined subcellular compartments. SponGee buffers physiological changes in cGMP concentration in various model systems while not affecting cAMP signals. We provide proof-of-concept strategies by using this tool to highlight the role of cGMP signaling in vivo and in discrete subcellular domains. SponGee enables the investigation of local cGMP signals in vivo and paves the way for therapeutic strategies that prevent downstream signaling activation. • SponGee is a genetically encoded cGMP scavenger • SponGee inhibits cGMP-dependent downstream pathways • SponGee enables cell-specific manipulation of cGMP-dependent processes in vivo • Subcellular targeting confers cell compartment specificity to SponGee Ros et al. developed SponGee, a genetically encoded cGMP chelator that enables the manipulation of this second messenger in single cells with subcellular specificity. SponGee alters the migration of developing cortical neurons in vivo. Lipid raft targeting of SponGee prevents axon repulsion, in contrast to exclusion from this subcellular compartment. [ABSTRACT FROM AUTHOR]
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- 2019
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46. Transglutaminase 2: a multi-functional protein in multiple subcellular compartments
- Author
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Park, Donghyun, Choi, Sun Shim, and Ha, Kwon-Soo
- Published
- 2010
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47. ER to synapse trafficking of NMDA receptors
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Nathalie Sans, Martina Kaniakova, Martin Horak, and Ronald S. Petralia
- Subjects
glutamate receptor ,intracellular trafficking ,Kainate receptor ,Review Article ,subcellular compartment ,Neurotransmission ,Biology ,lcsh:RC321-571 ,Synapse ,Cellular and Molecular Neuroscience ,medicine ,lcsh:Neurosciences. Biological psychiatry. Neuropsychiatry ,5-HT2 receptor ,musculoskeletal, neural, and ocular physiology ,Glutamate receptor ,excitatory neurotransmission ,3. Good health ,internalization ,medicine.anatomical_structure ,nervous system ,Silent synapse ,ion channel ,Neuron ,Neuroscience ,Ionotropic effect - Abstract
Glutamate is the major excitatory neurotransmitter in the mammalian central nervous system. There are three distinct subtypes of ionotropic glutamate receptors (GluRs) that have been identified including 2-amino-3-(5-methyl-3-oxo-1,2-oxazol-4-yl)propanoic acid receptors (AMPARs), N-methyl-D-aspartate receptors (NMDARs) and kainate receptors. The most common GluRs in mature synapses are AMPARs that mediate the fast excitatory neurotransmission and NMDARs that mediate the slow excitatory neurotransmission. There have been large numbers of recent reports studying how a single neuron regulates synaptic numbers and types of AMPARs and NMDARs. Our current research is centered primarily on NMDARs and, therefore, we will focus in this review on recent knowledge of molecular mechanisms occurring (1) early in the biosynthetic pathway of NMDARs, (2) in the transport of NMDARs after their release from the endoplasmic reticulum (ER); and (3) at the plasma membrane including excitatory synapses. Because a growing body of evidence also indicates that abnormalities in NMDAR functioning are associated with a number of human psychiatric and neurological diseases, this review together with other chapters in this issue may help to enhance research and to gain further knowledge of normal synaptic physiology as well as of the etiology of many human brain diseases.
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- 2014
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48. Does the proteome encode organellar pH?
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Rajini Rao, Mark Donowitz, and Christopher L. Brett
- Subjects
Proteome ,Evolution ,Biophysics ,Yeast proteome ,Biology ,ENCODE ,Biochemistry ,03 medical and health sciences ,Structural Biology ,Subcellular compartment ,Organelle ,Genetics ,Compartment (development) ,Animals ,Humans ,Molecular Biology ,030304 developmental biology ,Organelles ,0303 health sciences ,030306 microbiology ,pH ,pI ,Cell Biology ,Hydrogen-Ion Concentration ,Biological Evolution ,Yeast ,Cell biology ,Isoelectric point ,Function (biology) - Abstract
Inherent to the proteome itself, may be information that enables proteins to buffer pH at a level that promotes their own function within a specialized compartment. We observe that the distribution of computed isoelectric points in the yeast proteome matches experimentally derived organellar pH estimates across distinct subcellular compartments. This raises an interesting evolutionary question: did the pI of proteins and the pH of organelles co-evolve to optimize function?
- Published
- 2005
49. The Effect of Single and Multiple SERAT Mutants on Serine and Sulfur Metabolism.
- Author
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Watanabe M, Tohge T, Fernie AR, and Hoefgen R
- Abstract
The gene family of serine acetyltransferases (SERATs) constitutes an interface between the plant pathways of serine and sulfur metabolism. SERATs provide the activated precursor, O -acetylserine for the fixation of reduced sulfur into cysteine by exchanging the serine hydroxyl moiety by a sulfhydryl moiety, and subsequently all organic compounds containing reduced sulfur moieties. We investigate here, how manipulation of the SERAT interface results in metabolic alterations upstream or downstream of this boundary and the extent to which the five SERAT isoforms exert an effect on the coupled system, respectively. Serine is synthesized through three distinct pathways while cysteine biosynthesis is distributed over the three compartments cytosol, mitochondria, and plastids. As the respective mutants are viable, all necessary metabolites can obviously cross various membrane systems to compensate what would otherwise constitute a lethal failure in cysteine biosynthesis. Furthermore, given that cysteine serves as precursor for multiple pathways, cysteine biosynthesis is highly regulated at both, the enzyme and the expression level. In this study, metabolite profiles of a mutant series of the SERAT gene family displayed that levels of the downstream metabolites in sulfur metabolism were affected in correlation with the reduction levels of SERAT activities and the growth phenotypes, while levels of the upstream metabolites in serine metabolism were unchanged in the serat mutants compared to wild-type plants. These results suggest that despite of the fact that the two metabolic pathways are directly connected, there seems to be no causal link in metabolic alterations. This might be caused by the difference of their pool sizes or the tight regulation by homeostatic mechanisms that control the metabolite concentration in plant cells. Additionally, growth conditions exerted an influence on metabolic compositions.
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- 2018
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50. The Control of Calmodulin Synthesis and Localisation in Pea Root Tissue
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Butcher, Russell, Evans, David E., and Trewavas, A. J., editor
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- 1986
- Full Text
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