Genome-Scale Proteomics Reveals Arabidopsis thaliana Gene Models and Proteome Dynamics

Abstract

We have assembled a proteome map for Arabidopsis thaliana from high-density, organ-specific proteome catalogs that we generated for different organs, developmental stages, and undifferentiated cultured cells. We matched 86,456 unique peptides to 13,029 proteins and provide expression evidence for 57 gene models that are not represented in the TAIR7 protein database. Analysis of the proteome identified organ-specific biomarkers and allowed us to compile an organ-specific set of proteotypic peptides for 4105 proteins to facilitate targeted quantitative proteomics surveys. Quantitative information for the identified proteins was used to establish correlations between transcript and protein accumulation in different plant organs. The Arabidopsis proteome map provides information about genome activity and proteome assembly and is available as a resource for plant systems biology.

Plastid Proteome Assembly without Toc159: Photosynthetic Protein Import and Accumulation of N-Acetylated Plastid Precursor Proteins

“…The remaining proteins include established chloroplast proteins, such as a photosystem II oxygen-evolving complex protein (AT5G66570), RNA binding protein 29 (AT2G37220), or phosphoglycerate kinase (AT3G12780), which have predicted transit sequences of 29, 47, and 75 amino acids, respectively. Peptides within the cleaved transit peptide sequences were not found in the wild type or in the Arabidopsis proteome map (Baerenfaller et al, 2008), indicating that normally the transit sequences are efficiently cleaved and degraded. Their detection in ppi2 and Toc159cs therefore provides a first hint that precursor proteins accumulate in these two genotypes (Table 1).…”

“…In total, 4582 different proteins were identified (wild type, 2760;wtS, 2882;ppi2, 3150;Toc159cs, 3119) (Figure 1F; see Supplemental Data Set 1 online). Quantitative information was obtained for all identified proteins using normalized spectral counting (nSpC) (Baerenfaller et al, 2008). Since our experiment was designed to analyze the consequences of Toc159 depletion for the assembly of the quantitative plastid proteome, we grouped the proteomics data of the wild type (wild type and wtS) and the Toc159-deficient plants (ppi2 and Toc159cs) and compared the protein identification and accumulation within and between these two groups.…”

“…Of these proteins, 708 were identified in the wild type, 737 in ppi2, and 589 in both Cytosolic location of plastid proteins was assessed by detection of N-acetylation within the predicted transit peptide (TP). Provided is also the minimal position of detected peptides in wild-type leaves and in AtProteome (Baerenfaller et al, 2008). Data "Wild Type" encompass data from wild type and wtS, and "toc159" data from ppi2 and Toc159cs, respectively.…”

“…Protein quantification with nSpC was done according to Baerenfaller et al (2008). Briefly, the expected contribution of each individual protein to the samples total peptide pool was calculated correcting the values with a normalization factor, which balances for the theoretical number of tryptic peptides per protein and sample depth according to the following formula:…”

Unique and Overlapping Expression Patterns among Members of Photosynthesis-Associated Nuclear Gene Families in Arabidopsis

“…Presence of RbcS and Lhcb1 transcripts was also detected (Supplemental Table S3), but their identity could not unambiguously be ascertained because, in the ATH1 GeneChip, the same Affymetrix locus identifier is assigned to all the RbcS genes on the one hand and to Lhcb1.1, Lhcb1.2, and Lhcb1.3, collectively, on the other. Finally, more recent proteomics efforts have identified RbcL, RbcS1A, and Lhcb4.1 polypeptides in the Arabidopsis root (Baerenfaller et al, 2008), suggesting that in Arabidopsis Rbc and Lhc gene expression data largely mirror protein accumulation profiles. Because RbcS and Lhc activity is subject to extensive control at the posttranslational level (Tobin and Silverthorne, 1985;Thompson and White, 1991), even patterns of protein abundance alone may, however, not necessarily reflect levels of functional RbcS and Lhc proteins.…”