Dataset Information

Arabidopsis thaliana Cytochrome c Novel Partners Identification by LTQ

ABSTRACT: Programmed cell death is an event displayed by many different organisms along the evolutionary scale. In plants, it is necessary for development and for the hypersensitive response to stress or pathogenic infection. A common feature to programmed cell death among organisms is the mitochondria-to-cytosol translocation of cytochrome c. To understand the role of cytochrome c in the onset of plant programmed cell death, a proteomic approach based on affinity chromatography has been developed, using Arabidopsis cytochrome c as bait. Eleven putative, new cytochrome c partners have been identified. Nine of them bind the heme protein in plant protoplasts and in human cells, as a heterologous system, according to Bimolecular Fluorescence Complementation. The binding affinities and the kinetic rate constants of three cytochrome c - target complexes have been estimated by Surface Plasmon Resonance. Our data suggest that the role of cytochrome c as a programmed cell death-signaling messenger could be evolutionarily well-conserved. Data Processing & data analysis: Peptides were analyzed using a nanoliquid chromatography-MS/MS on an LTQ linear ion trap mass spectrometer (Thermo Electron San Jose, CA, USA). The mass spectrometer was operated in the data-dependent mode to automatically switch between full MS and MS/MS acquisition. The parameters for ion scanning were the following: Full-scan MS(400-1800 m/z) plus top seven peaks Zoom/MS/MS (isolation width 2 m/z), normalized collision energy 35%. The scanning was performed using a dynamic exclusion list (120s exclusion list size of 50). Peak lists from all MS/MS spectra were extracted from the Xcalibur RAW files using a freely available program DTAsupercharge v.1.19 (http://msquant.sourceforge.net/). MASCOT 2.1 was used to search the Uniprot_Arabidopsis protein database 100323 (90895 sequences). Database search parameters used were the following: trypsin as enzyme; peptide tolerance, 300ppm; fragment ion tolerance, 0.6 Da; missed cleavage sites,1; fixed modification, carbamidomethyl cysteine and variable modifications, methionine oxidation. In all protein identifications the probability scores were greater than the score fixed by MASCOT (30) as significant with a p-value <0.05.

INSTRUMENT(S): LTQ

ORGANISM(S): Arabidopsis Thaliana (mouse-ear Cress)

TISSUE(S): Plant Cell, Cell Suspension Culture

SUBMITTER: Jonathan Martinez Fabregas

LAB HEAD: Jonathan Martinez Fabregas

PROVIDER: PXD000280 | Pride | 2013-11-11

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	JM-Control-AIIIC-2horas-ok.RAW	Raw
	JM-Control-AIIIC-2horas-ok.dat	Other
	JM-Control-AIIIC-2horas-ok.mgf	Mgf
	JM-Control-AIIIC-2horas.RAW	Raw
	JM-Control-AIIIC-2horas.dat	Other

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Publications

New Arabidopsis thaliana cytochrome c partners: a look into the elusive role of cytochrome c in programmed cell death in plants.

Martínez-Fábregas Jonathan J Díaz-Moreno Irene I González-Arzola Katiuska K Janocha Simon S Navarro José A JA Hervás Manuel M Bernhardt Rita R Díaz-Quintana Antonio A De la Rosa Miguel Á MÁ

Molecular & cellular proteomics : MCP 20130909 12

Programmed cell death is an event displayed by many different organisms along the evolutionary scale. In plants, programmed cell death is necessary for development and the hypersensitive response to stress or pathogenic infection. A common feature in programmed cell death across organisms is the translocation of cytochrome c from mitochondria to the cytosol. To better understand the role of cytochrome c in the onset of programmed cell death in plants, a proteomic approach was developed based on ...[more]

PMID: 24019145

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