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APP Is a Context-Sensitive Regulator of the Hippocampal Presynaptic Active Zone.

Laßek M, Weingarten J, Wegner M, Mueller BF, Rohmer M, Baeumlisberger D, Arrey TN, Hick M, Ackermann J, Acker-Palmer A, Koch I, Müller U, Karas M, Volknandt W - PLoS Comput. Biol. (2016)

Bottom Line: Subsequently, an isobaric labeling was performed using TMT6 for protein identification and quantification by high-resolution mass spectrometry.The impact of APP deletion on the hippocampal PAZ proteome was visualized by creating protein-protein interaction (PPI) networks that incorporated APP into the synaptic vesicle cycle, cytoskeletal organization, and calcium-homeostasis.The combination of subcellular fractionation, immunopurification, proteomic analysis, and bioinformatics allowed us to identify APP as structural and functional regulator in a context-sensitive manner within the hippocampal active zone network.

View Article: PubMed Central - PubMed

Affiliation: Institute for Cell Biology and Neuroscience, Biologicum, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany.

ABSTRACT
The hallmarks of Alzheimer's disease (AD) are characterized by cognitive decline and behavioral changes. The most prominent brain region affected by the progression of AD is the hippocampal formation. The pathogenesis involves a successive loss of hippocampal neurons accompanied by a decline in learning and memory consolidation mainly attributed to an accumulation of senile plaques. The amyloid precursor protein (APP) has been identified as precursor of Aβ-peptides, the main constituents of senile plaques. Until now, little is known about the physiological function of APP within the central nervous system. The allocation of APP to the proteome of the highly dynamic presynaptic active zone (PAZ) highlights APP as a yet unknown player in neuronal communication and signaling. In this study, we analyze the impact of APP deletion on the hippocampal PAZ proteome. The native hippocampal PAZ derived from APP mouse mutants (APP-KOs and NexCreAPP/APLP2-cDKOs) was isolated by subcellular fractionation and immunopurification. Subsequently, an isobaric labeling was performed using TMT6 for protein identification and quantification by high-resolution mass spectrometry. We combine bioinformatics tools and biochemical approaches to address the proteomics dataset and to understand the role of individual proteins. The impact of APP deletion on the hippocampal PAZ proteome was visualized by creating protein-protein interaction (PPI) networks that incorporated APP into the synaptic vesicle cycle, cytoskeletal organization, and calcium-homeostasis. The combination of subcellular fractionation, immunopurification, proteomic analysis, and bioinformatics allowed us to identify APP as structural and functional regulator in a context-sensitive manner within the hippocampal active zone network.

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Subcommunity structure of the network based on Fig 3B.The color code corresponds to the pie chart diagram (cf. Fig 1E). The size of the rings corresponds to the respective number of proteins. Communities (1–7) were subdivided into the following functional clusters (e.g. 1.1–1.12): 1.1 Calcium Signaling, 1.2 Presynaptic Membrane, 1.3 Exocytosis, 1.4 Cytoskeleton Organization, 1.5 Membrane Assembly, 1.6 G-Protein Signaling, 1.7 Organelle Transport, 1.8 Actin Organization, 1.9 Synapse Assembly, 1.10 Membrane Regulation, 1.11 Inhibitory Regulation, 1.12 Vesicle Priming, 2.1 Membrane Trafficking, 2.2 Vesicle Budding, 2.3 Endocytosis, 2.4 Proton Transport, 2.5 Phospholipid Metabolism, 2.6 Vesicle Organization, 2.7 Membrane Organization, 3.1 Electron Transport Chain, 3.2 Energy Metabolism, 3.3 Stress Defense, 4.1 Cellular Respiration, 4.2 Glycolysis, 4.3 Guanine Metabolism, 4.4 Glycerol Metabolism, 4.5 Mitochondrial Metabolism, 4.6 Mitochondrial Assembly, 5.1 Fatty Acid Catabolism, 5.2 Neurotransmitter Metabolism, 5.3 Amino Acid Catabolism, 5.4 Metabolism, 5.5 Fatty Acid Metabolism, 5.6 Mitochondrial Targeting, 6.1 Mitochondrial Protein Trafficking, 6.2 Heatshock Response, 6.3 Neuronal Regulation, 6.4 Protein Folding, 7 Functional Dynamics.
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pcbi.1004832.g004: Subcommunity structure of the network based on Fig 3B.The color code corresponds to the pie chart diagram (cf. Fig 1E). The size of the rings corresponds to the respective number of proteins. Communities (1–7) were subdivided into the following functional clusters (e.g. 1.1–1.12): 1.1 Calcium Signaling, 1.2 Presynaptic Membrane, 1.3 Exocytosis, 1.4 Cytoskeleton Organization, 1.5 Membrane Assembly, 1.6 G-Protein Signaling, 1.7 Organelle Transport, 1.8 Actin Organization, 1.9 Synapse Assembly, 1.10 Membrane Regulation, 1.11 Inhibitory Regulation, 1.12 Vesicle Priming, 2.1 Membrane Trafficking, 2.2 Vesicle Budding, 2.3 Endocytosis, 2.4 Proton Transport, 2.5 Phospholipid Metabolism, 2.6 Vesicle Organization, 2.7 Membrane Organization, 3.1 Electron Transport Chain, 3.2 Energy Metabolism, 3.3 Stress Defense, 4.1 Cellular Respiration, 4.2 Glycolysis, 4.3 Guanine Metabolism, 4.4 Glycerol Metabolism, 4.5 Mitochondrial Metabolism, 4.6 Mitochondrial Assembly, 5.1 Fatty Acid Catabolism, 5.2 Neurotransmitter Metabolism, 5.3 Amino Acid Catabolism, 5.4 Metabolism, 5.5 Fatty Acid Metabolism, 5.6 Mitochondrial Targeting, 6.1 Mitochondrial Protein Trafficking, 6.2 Heatshock Response, 6.3 Neuronal Regulation, 6.4 Protein Folding, 7 Functional Dynamics.

Mentions: The community structure provided by Radatools does not resolve the functional structure unambiguously. Within the community structures individual protein groups (functional clusters) are represented, e. g. synaptic vesicle exo- and endocytosis, Ca2+-homeostasis and cytoskeleton. Therefore, each community structure consists of a collection of proteins that belongs to individual functional cluster. This collection of proteins can be summarized under the term heterogeneity to emphasize this complex and diverse layout of the community structures. For better visualization of this “heterogenic nature”, we created a subcommunity layout representing all individual functional clusters (Fig 4).


APP Is a Context-Sensitive Regulator of the Hippocampal Presynaptic Active Zone.

Laßek M, Weingarten J, Wegner M, Mueller BF, Rohmer M, Baeumlisberger D, Arrey TN, Hick M, Ackermann J, Acker-Palmer A, Koch I, Müller U, Karas M, Volknandt W - PLoS Comput. Biol. (2016)

Subcommunity structure of the network based on Fig 3B.The color code corresponds to the pie chart diagram (cf. Fig 1E). The size of the rings corresponds to the respective number of proteins. Communities (1–7) were subdivided into the following functional clusters (e.g. 1.1–1.12): 1.1 Calcium Signaling, 1.2 Presynaptic Membrane, 1.3 Exocytosis, 1.4 Cytoskeleton Organization, 1.5 Membrane Assembly, 1.6 G-Protein Signaling, 1.7 Organelle Transport, 1.8 Actin Organization, 1.9 Synapse Assembly, 1.10 Membrane Regulation, 1.11 Inhibitory Regulation, 1.12 Vesicle Priming, 2.1 Membrane Trafficking, 2.2 Vesicle Budding, 2.3 Endocytosis, 2.4 Proton Transport, 2.5 Phospholipid Metabolism, 2.6 Vesicle Organization, 2.7 Membrane Organization, 3.1 Electron Transport Chain, 3.2 Energy Metabolism, 3.3 Stress Defense, 4.1 Cellular Respiration, 4.2 Glycolysis, 4.3 Guanine Metabolism, 4.4 Glycerol Metabolism, 4.5 Mitochondrial Metabolism, 4.6 Mitochondrial Assembly, 5.1 Fatty Acid Catabolism, 5.2 Neurotransmitter Metabolism, 5.3 Amino Acid Catabolism, 5.4 Metabolism, 5.5 Fatty Acid Metabolism, 5.6 Mitochondrial Targeting, 6.1 Mitochondrial Protein Trafficking, 6.2 Heatshock Response, 6.3 Neuronal Regulation, 6.4 Protein Folding, 7 Functional Dynamics.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4836664&req=5

pcbi.1004832.g004: Subcommunity structure of the network based on Fig 3B.The color code corresponds to the pie chart diagram (cf. Fig 1E). The size of the rings corresponds to the respective number of proteins. Communities (1–7) were subdivided into the following functional clusters (e.g. 1.1–1.12): 1.1 Calcium Signaling, 1.2 Presynaptic Membrane, 1.3 Exocytosis, 1.4 Cytoskeleton Organization, 1.5 Membrane Assembly, 1.6 G-Protein Signaling, 1.7 Organelle Transport, 1.8 Actin Organization, 1.9 Synapse Assembly, 1.10 Membrane Regulation, 1.11 Inhibitory Regulation, 1.12 Vesicle Priming, 2.1 Membrane Trafficking, 2.2 Vesicle Budding, 2.3 Endocytosis, 2.4 Proton Transport, 2.5 Phospholipid Metabolism, 2.6 Vesicle Organization, 2.7 Membrane Organization, 3.1 Electron Transport Chain, 3.2 Energy Metabolism, 3.3 Stress Defense, 4.1 Cellular Respiration, 4.2 Glycolysis, 4.3 Guanine Metabolism, 4.4 Glycerol Metabolism, 4.5 Mitochondrial Metabolism, 4.6 Mitochondrial Assembly, 5.1 Fatty Acid Catabolism, 5.2 Neurotransmitter Metabolism, 5.3 Amino Acid Catabolism, 5.4 Metabolism, 5.5 Fatty Acid Metabolism, 5.6 Mitochondrial Targeting, 6.1 Mitochondrial Protein Trafficking, 6.2 Heatshock Response, 6.3 Neuronal Regulation, 6.4 Protein Folding, 7 Functional Dynamics.
Mentions: The community structure provided by Radatools does not resolve the functional structure unambiguously. Within the community structures individual protein groups (functional clusters) are represented, e. g. synaptic vesicle exo- and endocytosis, Ca2+-homeostasis and cytoskeleton. Therefore, each community structure consists of a collection of proteins that belongs to individual functional cluster. This collection of proteins can be summarized under the term heterogeneity to emphasize this complex and diverse layout of the community structures. For better visualization of this “heterogenic nature”, we created a subcommunity layout representing all individual functional clusters (Fig 4).

Bottom Line: Subsequently, an isobaric labeling was performed using TMT6 for protein identification and quantification by high-resolution mass spectrometry.The impact of APP deletion on the hippocampal PAZ proteome was visualized by creating protein-protein interaction (PPI) networks that incorporated APP into the synaptic vesicle cycle, cytoskeletal organization, and calcium-homeostasis.The combination of subcellular fractionation, immunopurification, proteomic analysis, and bioinformatics allowed us to identify APP as structural and functional regulator in a context-sensitive manner within the hippocampal active zone network.

View Article: PubMed Central - PubMed

Affiliation: Institute for Cell Biology and Neuroscience, Biologicum, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany.

ABSTRACT
The hallmarks of Alzheimer's disease (AD) are characterized by cognitive decline and behavioral changes. The most prominent brain region affected by the progression of AD is the hippocampal formation. The pathogenesis involves a successive loss of hippocampal neurons accompanied by a decline in learning and memory consolidation mainly attributed to an accumulation of senile plaques. The amyloid precursor protein (APP) has been identified as precursor of Aβ-peptides, the main constituents of senile plaques. Until now, little is known about the physiological function of APP within the central nervous system. The allocation of APP to the proteome of the highly dynamic presynaptic active zone (PAZ) highlights APP as a yet unknown player in neuronal communication and signaling. In this study, we analyze the impact of APP deletion on the hippocampal PAZ proteome. The native hippocampal PAZ derived from APP mouse mutants (APP-KOs and NexCreAPP/APLP2-cDKOs) was isolated by subcellular fractionation and immunopurification. Subsequently, an isobaric labeling was performed using TMT6 for protein identification and quantification by high-resolution mass spectrometry. We combine bioinformatics tools and biochemical approaches to address the proteomics dataset and to understand the role of individual proteins. The impact of APP deletion on the hippocampal PAZ proteome was visualized by creating protein-protein interaction (PPI) networks that incorporated APP into the synaptic vesicle cycle, cytoskeletal organization, and calcium-homeostasis. The combination of subcellular fractionation, immunopurification, proteomic analysis, and bioinformatics allowed us to identify APP as structural and functional regulator in a context-sensitive manner within the hippocampal active zone network.

Show MeSH
Related in: MedlinePlus