Proteomic analysis of the mitochondria from embryonic and postnatal rat brains reveals response to developmental changes in energy demands

Villeneuve, Lance M.; Stauch, Kelly L.; Fox, Howard S.

doi:10.1016/j.jprot.2014.07.011

Cited by 19 publications

(27 citation statements)

References 69 publications

(77 reference statements)

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“…Details on the composition of and the methods utilized to build the SWATH-MS library have been previously published [29]. Additional samples were added to the SWATH-MS library to enrich for synaptic mitochondrial proteins.…”

Section: Methodsmentioning

confidence: 99%

“…Sample preparation was conducted by using a modified version of the filter-aided sample preparation (FASP) protocol as previously described [29, 33, 34]. In short, samples were loaded onto a 20-μm filter (Pall Corporation, Ann Arbor, MI), trypsin digested (Promega, Madison, WI), and the resulting peptides were cleaned with an Oasis mixed-mode weak cation exchange cartridge (Waters, Milford, MA).…”

Section: Methodsmentioning

confidence: 99%

“…SWATH-MS data-independent analysis (DIA) was conducted as previously performed [29]. In short, 5 μg of peptide from each sample was resuspended in 6 μL of 0.1% formic acid (Honeywell, Muskegon, MI).…”

Section: Methodsmentioning

confidence: 99%

“…No data processing (neither denoising nor smoothing) of any kind was applied to the extracted ion chromatograms. Retention time was calibrated as previously stated [29] using synthetic peptides (BiognoSYS; Zurich, Switzerland) spiked-in samples in accordance with the manufacturer’s protocol. Quantitative analysis for each protein was set at 5 peptides and 5 transitions in accordance with previously published work [29, 39] for targeted data extraction.…”

Section: Methodsmentioning

confidence: 99%

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HIV-1 transgenic rats display mitochondrial abnormalities consistent with abnormal energy generation and distribution

et al. 2016

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With the advent of the combination antiretroviral therapy era (cART), the development of AIDS has been largely limited in the United States. Unfortunately, despite the development of efficacious treatments, HIV-1 associated neurocognitive disorders (HAND) can still develop and as many HIV-1 positive individuals age, the prevalence of HAND is likely to rise because HAND manifests in the brain with very low levels of virus. However, the mechanism producing this viral disorder is still debated. Interestingly, HIV-1 infection exposes neurons to proteins including Tat, Nef, Vpr which can drastically alter mitochondrial properties. Mitochondrial dysfunction has been posited to be a cornerstone of the development of numerous neurodegenerative diseases. Therefore, we investigated mitochondria in an animal model of HAND. Using an HIV-1 transgenic rat model expressing 7 of the 9 HIV-1 viral proteins, mitochondrial functional and proteomic analysis were performed on a subset of mitochondria that are particularly sensitive to cellular changes, the neuronal synaptic mitochondria. Quantitative mass spectroscopic studies followed by statistical analysis revealed extensive proteome alteration in this model paralleling mitochondrial abnormalities identified in HIV-1 animal models and HIV-1 infected humans. Novel mitochondrial protein changes were discovered in the electron transport chain (ETC), the glycolytic pathways, mitochondrial trafficking proteins, and proteins involved in various energy pathways, and these findings correlated well with the function of the mitochondria as assessed by a mitochondrial coupling and flux assay. By targeting these proteins and proteins upstream in the same pathway, we may be able to limit the development of HAND.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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HIV-1 transgenic rats display mitochondrial abnormalities consistent with abnormal energy generation and distribution

et al. 2016

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“…In the neuroprotomics area, it is already possible to find some reports, such as the work published by our group [209], where we presented a pipeline for reproducible quantitative screenings using a membrane-enriched sample from rat cortex, indicating that our approach is suitable for evaluation of membrane proteins, key players in the majority of neuronal dysfunctions. There are also two other works from Fox's group regarding mitochondrial alterations: one of them corresponding to an exhaustive characterization of mitochondrial proteome from embryonic and postnatal rat brain revealing a rearrangement of proteins from glycolysis and mitochondrial trafficking/dynamics, which may suggest a development change to accommodate the required energy demands in different developmental stages [210]. Another study focused on mitochondrial functional alterations associated with deregulation of PTEN-induced kinase 1 (PINK1), a Parkinson's disease-associated protein [211].…”

Section: Sequential Window Acquisition Of All Theoretical Fragment-iomentioning

confidence: 99%

Neuroproteomics — LC-MS Quantitative Approaches

Santa¹,

Anjo²,

Mendes³

et al. 2015

Recent Advances in Proteomics Research

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Neuroproteomics is a scientific field that aims to study all the proteins of the central nervous system, their expression, function, and interactions. The central nervous system is intricate and heterogeneous, and the study of its proteome is consequently complex, with many biological questions still requiring deep investigation. For this, mass spectrometry approaches, most often coupled with liquid chromatography (LC-MS), have been the number one choice in proteomics, and over the years it has added many important findings to the field. At this point it is important that proteomics turns to the quantitative expression of proteins instead of only identifying which proteins are present in a given sample, much because the most important alterations may be slight alterations in the quantity of a protein in a given situation. Therefore, many LC-MS quantitative approaches have been developed relying on the labeling of the proteins or even by using label-free techniques.In this chapter, a brief description of the principles and procedures of several approaches used for relative and absolute, targeted and untargeted quantification of proteins is presented, complemented with a literature revision of their application in the neurosciences field.

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Quantitative Proteomics of Presynaptic Mitochondria Reveal an Overexpression and Biological Relevance of Neuronal MitoNEET in Postnatal Brain Development

Stauch

Villeneuve

Totusek

et al. 2019

Developmental Neurobiology

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Although it has been recognized that energy metabolism and mitochondrial structure and functional activity in the immature brain differs from that of the adult, few studies have examined mitochondria specifically at the neuronal synapse during postnatal brain development. In this study, we examined the presynaptic mitochondrial proteome in mice at postnatal day 7 and 42, a period that involves the formation and maturation of synapses. Application of two independent quantitative proteomics approaches – SWATH‐MS and super‐SILAC – revealed a total of 40 proteins as significantly differentially expressed in the presynaptic mitochondria. In addition to elevated levels of proteins known to be involved in ATP metabolic processes, our results identified increased levels of mitoNEET (Cisd1), an iron‐sulfur containing protein that regulates mitochondrial bioenergetics. We found that mitoNEET overexpression plays a cell‐type specific role in ATP synthesis and in neuronal cells promotes ATP generation. The elevated ATP levels in SH‐SY5Y neuroblastoma cells were associated with increased mitochondrial membrane potential and a fragmented mitochondrial network, further supporting a role for mitoNEET as a key regulator of mitochondrial function.

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Proteomic analysis of the mitochondria from embryonic and postnatal rat brains reveals response to developmental changes in energy demands

Cited by 19 publications

References 69 publications

HIV-1 transgenic rats display mitochondrial abnormalities consistent with abnormal energy generation and distribution

HIV-1 transgenic rats display mitochondrial abnormalities consistent with abnormal energy generation and distribution

Neuroproteomics — LC-MS Quantitative Approaches

Quantitative Proteomics of Presynaptic Mitochondria Reveal an Overexpression and Biological Relevance of Neuronal MitoNEET in Postnatal Brain Development

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