sorting signals, n-terminal modifications and abundance of the chloroplast proteome分拣信号,叶绿体蛋白质组的氨基端修改和丰富.pdf

Sorting Signals, N-Terminal Modifications and Abundance of the Chloroplast Proteome 1 1 1 1¤ 2 3 Boris Zybailov , Heidi Rutschow , Giulia Friso , Andrea Rudella , Olof Emanuelsson , Qi Sun , Klaas J. van Wijk1* 1 Department of Plant Biology, Cornell University, Ithaca, New York, United States of America, 2 Stockholm Bioinformatics Center, AlbaNova, Stockholm University, Stockholm, Sweden, 3 Computation Biology Service Unit, Cornell Theory Center, Cornell University, Ithaca, New York, United States of America Abstract Characterization of the chloroplast proteome is needed to understand the essential contribution of the chloroplast to plant growth and development. Here we present a large scale analysis by nanoLC-Q-TOF and nanoLC-LTQ-Orbitrap mass spectrometry (MS) of ten independent chloroplast preparations from Arabidopsis thaliana which unambiguously identified 1325 proteins. Novel proteins include various kinases and putative nucleotide binding proteins. Based on repeated and independent MS based protein identifications requiring multiple matched peptide sequences, as well as literature, 916 nuclear-encoded proteins were assigned with high confidence to the plastid, of which 86% had a predicted chloroplast transit peptide (cTP). The protein abundance of soluble stromal proteins was calculated from normalized spectral counts from LTQ-Obitrap analysis and was found to cover four orders of magnitude. Comparison to gel-based quantification demonstrates that ‘spectral counting’ can provide large scale protein quantification for Arabidopsis. This quantitative information was used to determine possible b