Proteomic characterization of wheat amyloplasts using identification of proteins by tandem mass spectrometry

Andon, Nancy L.; Hollingworth, Sarah; Koller, Antonius; Greenland, Andrew J.; Yates, John R.; Haynes, Paul A.

doi:10.1002/1615-9861(200209)2:9<1156::aid-prot1156>3.0.co;2-4

Cited by 189 publications

(97 citation statements)

References 26 publications

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“…Initially believed to be restricted to chloroplasts, ferredoxin and the enzyme catalyzing its reduction with NADPH [ferredoxin-NADP reductase (FNR)] were later purified and found to be isoforms specific to nonphotosynthetic tissues (11)(12)(13). In addition to FNR, amyloplasts were found to contain enzymes capable of generating the NADPH needed for reduction of ferredoxin via FNR, namely glucose 6-phosphate dehydrogenase and 6-phosphogluconate dehydrogenase (14)(15)(16)(17).…”

Section: Resultsmentioning

confidence: 99%

A complete ferredoxin/thioredoxin system regulates fundamental processes in amyloplasts

Balmer

Vensel

Cai

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

160

137

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A growing number of processes throughout biology are regulated by redox via thiol-disulfide exchange. This mechanism is particularly widespread in plants, where almost 200 proteins have been linked to thioredoxin (Trx), a widely distributed small regulatory disulfide protein. The current study extends regulation by Trx to amyloplasts, organelles prevalent in heterotrophic plant tissues that, among other biosynthetic activities, catalyze the synthesis and storage of copious amounts of starch. Using proteomics and immunological methods, we identified the components of the ferredoxin͞Trx system (ferredoxin, ferredoxin-Trx reductase, and Trx), originally described for chloroplasts, in amyloplasts isolated from wheat starchy endosperm. Ferredoxin is reduced not by light, as in chloroplasts, but by metabolically generated NADPH via ferredoxin-NADP reductase. However, once reduced, ferredoxin appears to act as established for chloroplasts, i.e., via ferredoxinTrx reductase and a Trx (m-type). A proteomics approach in combination with affinity chromatography and a fluorescent thiol probe led to the identification of 42 potential Trx target proteins, 13 not previously recognized, including a major membrane transporter (Brittle-1 or ADP-glucose transporter). The proteins function in a range of processes in addition to starch metabolism: biosynthesis of lipids, amino acids, and nucleotides; protein folding; and several miscellaneous reactions. The results suggest a mechanism whereby light is initially recognized as a thiol signal in chloroplasts, then as a sugar during transit to the sink, where it is converted again to a thiol signal. In this way, amyloplast reactions in the grain can be coordinated with photosynthesis taking place in leaves.redox regulation ͉ target proteins ͉ ferredoxin-thioredoxin reductase O ur understanding of the function of the regulatory disulfide protein thioredoxin (Trx) has increased dramatically in the past few years, with the advent of new methodologies. Recent approaches make it possible to identify proteins linked to Trx by combining proteomics with affinity chromatography (1) or thiol probes (2-4). These capabilities have defined an extended role of Trx in chloroplasts (1, 5) and helped elucidate its function in other plant systems: mitochondria (6), seeds (2,3,7,8), and seedlings (4, 9). Currently almost 200 proteins appear to be linked to Trx in plants (10). One major organelle that has been neglected, however, is the amyloplast, a plastid of heterotrophic tissues that performs a wide range of biosynthetic reactions, including the synthesis and storage of abundant quantities of starch.To help fill this gap, we have applied proteomic and immunological approaches to investigate the occurrence and function of Trx in amyloplasts. We now report evidence that amyloplasts isolated from wheat starchy endosperm resemble chloroplasts in containing a complete ferredoxin͞Trx system composed of ferredoxin, ferredoxin-Trx reductase (FTR), and Trx (m-type). Application of affinity chromatography and fl...

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Section: Resultsmentioning

confidence: 99%

A complete ferredoxin/thioredoxin system regulates fundamental processes in amyloplasts

Balmer

Vensel

Cai

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

160

137

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“…The peptides were separated by reversed phase HPLC. Data-dependent scanning was performed using Xcalibur v 2.1.0 and a survey mass scan at 30,000 resolution in the Orbitrap analyzer scanning m/z 400 -1600, followed by collision-induced dissociation tandem mass spectrometry (MS/MS) of the 14 most intense ions in the linear ion trap analyzer (32). MS/MS spectra were searched using Thermo Proteome Discoverer 1.2 (Thermo Fisher Scientific).…”

Section: Methodsmentioning

confidence: 99%

Mesencephalic Astrocyte-derived Neurotrophic Factor Protects the Heart from Ischemic Damage and Is Selectively Secreted upon Sarco/endoplasmic Reticulum Calcium Depletion

Glembotski

Thuerauf

Huang

et al. 2012

Journal of Biological Chemistry

171

221

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“…The resulting peptides were analyzed by either liquid chromatographyelectrospray tandem MS (MS/MS) or matrix-assisted laser-desorption ionization MS (MALDI-TOF). For MS/MS analysis, peptides were initially separated using a microbore high pressure liquid chromatography system (Surveyor, ThermoFinnigan, San Jose, CA), and the eluent from the high pressure liquid chromatography column was eluted directly into the electrospray ionization source of a ThermoFinnigan LCQ-Deca ion trap mass spectrometer (ThermoFinnigan, San Jose, CA) as described previously (22). MS/MS data were analyzed using the SE-QUEST algorithm, and positive sequence identifications were based on established criteria such as a cross-correlation factor (Xcorr) greater than 2.5, a ⌬ cross-correlation factor (⌬Xcorr) greater than 0.1, and a minimum of one tryptic peptide terminus.…”

Section: Methodsmentioning

confidence: 99%

Protein Disulfide Bond Formation in the Cytoplasm during Oxidative Stress

Cumming

Andon

Haynes

et al. 2004

Journal of Biological Chemistry

Self Cite

404

358

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The majority of disulfide-linked cytosolic proteins are thought to be enzymes that transiently form disulfide bonds while catalyzing oxidation-reduction (redox) processes. Recent evidence indicates that reactive oxygen species can act as signaling molecules by promoting the formation of disulfide bonds within or between select redox-sensitive proteins. However, few studies have attempted to examine global changes in disulfide bond formation following reactive oxygen species exposure. Here we isolate and identify disulfide-bonded proteins (DSBP) in a mammalian neuronal cell line (HT22) exposed to various oxidative insults by sequential nonreducing/reducing two-dimensional SDS-PAGE combined with mass spectrometry. By using this strategy, several known cytosolic DSBP, such as peroxiredoxins, thioredoxin reductase, nucleoside-diphosphate kinase, and ribonucleotide-diphosphate reductase, were identified. Unexpectedly, a large number of previously unknown DSBP were also found, including those involved in molecular chaperoning, translation, glycolysis, cytoskeletal structure, cell growth, and signal transduction. Treatment of cells with a wide range of hydrogen peroxide concentrations either promoted or inhibited disulfide bonding of select DSBP in a concentration-dependent manner. Decreasing the ratio of reduced to oxidized glutathione also promoted select disulfide bond formation within proteins from cytoplasmic extracts. In addition, an epitope-tagged version of the molecular chaperone HSP70 forms mixed disulfides with both ␤4-spectrin and adenomatous polyposis coli protein in the cytosol. Our findings indicate that disulfide bond formation within families of cytoplasmic proteins is dependent on the nature of the oxidative insult and may provide a common mechanism used to control multiple physiological processes.Oxidative stress occurs when the rate of reactive oxygen species (ROS) 1 generation exceeds the detoxification abilities of the cell, and it has been implicated in many degenerative diseases. It is frequently argued that ROS cause relatively nonspecific damage to vital cellular components such as lipids, DNA, and proteins. However, emerging evidence indicates that ROS can cause specific protein modifications that may lead to a change in the activity or function of the oxidized protein (1, 2). Several major forms of oxidative modifications can occur on amino acid residue side chains including carbonylation, nitrosylation, and oxidation of methionine to methionine sulfoxide (3). Protein sulfhydryls can be oxidized to protein disulfides and sulfenic acids as well as more highly oxidized states such as the sulfinic and sulfonic acid forms of protein cysteines (4). Under non-stressed conditions, disulfide bond formation occurs primarily in the oxidizing environment of the endoplasmic reticulum (ER) in eukaryotic cells (5). The sulfhydryl groups in the vast majority of protein cysteine residues (Cys-SH) have a pK a Ͼ8.0 and, in the reducing environment of the cytoplasm, remain protonated at physiological pH. Thus,...

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Proteomic characterization of wheat amyloplasts using identification of proteins by tandem mass spectrometry

Cited by 189 publications

References 26 publications

A complete ferredoxin/thioredoxin system regulates fundamental processes in amyloplasts

A complete ferredoxin/thioredoxin system regulates fundamental processes in amyloplasts

Mesencephalic Astrocyte-derived Neurotrophic Factor Protects the Heart from Ischemic Damage and Is Selectively Secreted upon Sarco/endoplasmic Reticulum Calcium Depletion

Protein Disulfide Bond Formation in the Cytoplasm during Oxidative Stress

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