The<i>Arabidopsis thaliana</i>PeptideAtlas; harnessing world-wide proteomics data for a comprehensive community proteomics resource

Kj, van Wijk; Deutsch, Eric W.; Sun, Qing‐Yuan; Sun, Zhonghua; Leppert, M.; As, Boguraev; Mendoza, Luis

doi:10.1101/2021.05.03.442425

Cited by 5 publications

(14 citation statements)

References 125 publications

(138 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Thus, localization of PpAARE1 to the cytoplasm is also possible from the longer splice variant. Alternative translation initiation of AtAARE is further evidenced by proteomics data (www.peptideatlas.org/builds/arabidopsis/, van Wijk et al, 2021). Here, we found evidence for N-terminal acetylation of M 56 which is the initiator methionine of the short variant (e.g., Zhang et al, 2019;PXD012708).…”

Section: Discussionsupporting

confidence: 58%

A deeply conserved protease, acylamino acid-releasing enzyme (AARE), acts in ageing in Physcomitrella and Arabidopsis

Hoernstein

Özdemir

Gessel

et al. 2022

Preprint

View full text Add to dashboard Cite

Protein oxidation results from the reaction of amino-acid side chains with reactive oxygen species (ROS) and is partly irreversible. In non-photosynthetic tissues, mitochondria are a main source of ROS, whereas plastids are the major source in photosynthetic tissues. Oxidized proteins suffer from decreased structural integrity and even loss of function, and their accumulation leads to cytotoxic aggregates. In mammals, aggregate formation correlates with aging and is linked to several age-related pathologies. Mammalian proteolytic pathways for clearance of oxidized proteins are under intensive research, while mechanistic insights into this process in plants is scarce. Acylamino acid-releasing (AARE) enzymes are ATP-independent serine proteases, presumably acting on oxidized proteins and operating in a dual exo-/endopeptidase mode. They are found in all domains of life. Here, we investigated AARE enzymes in the moss Physcomitrella and the angiosperm Arabidopsis and identified three homologous nuclear genes in Physcomitrella (PpAARE1-3) and a single nuclear gene in Arabidopsis (AtAARE). Surprisingly, we observed triple localization of the proteins AtAARE and PpAARE1 to plastids, mitochondria and the cytosol in vivo, likely conserved across the plant lineage. This represents an ATP-independent possibility for degradation of oxidized proteins in the major source organelles of ROS in plants, which is distinct to mammals. Combinatorial knockout plants and protein interaction analysis revealed specific interactions of the moss AARE isoforms and functions in progressive aging. Analysis of an AtAARE T-DNA mutant further suggests the evolutionary conservation of AARE function in age-related development.

show abstract

Section: Discussionsupporting

confidence: 58%

A deeply conserved protease, acylamino acid-releasing enzyme (AARE), acts in ageing in Physcomitrella and Arabidopsis

Hoernstein

Özdemir

Gessel

et al. 2022

Preprint

View full text Add to dashboard Cite

show abstract

“…It should be noted that it in some cases, it is possible that dbTIS were incorrectly annotated, and that the identified “dTIS” actually might represent the correct TIS. For instance, Met17 likely represents the actual start site of the DNA repair protein homolog XRCC4 (AT3G23100) given the absence of preceding Ribo-seq signal and lack of peptide evidence in the Arabidopsis Peptide Atlas (Van Wijk et al, 2021 ) despite theoretical likely identifiable tryptic peptides ( Supplementary Figure 7 ). In contrast, the majority of genes (62/68) with a dTIS called did have a matching Ribo-seq-called dbTIS ( Supplementary Dataset S1 ), and for seven genes, Nt peptides were identified matching both the dTIS and dbTIS, thus indicative of protein translation of both Nt proteoforms.…”

Section: Discussionmentioning

confidence: 99%

To New Beginnings: Riboproteogenomics Discovery of N-Terminal Proteoforms in Arabidopsis Thaliana

et al. 2022

View full text Add to dashboard Cite

Alternative translation initiation is a widespread event in biology that can shape multiple protein forms or proteoforms from a single gene. However, the respective contribution of alternative translation to protein complexity remains largely enigmatic. By complementary ribosome profiling and N-terminal proteomics (i.e., riboproteogenomics), we provide clear-cut evidence for ~90 N-terminal proteoform pairs shaped by (alternative) translation initiation in Arabidopsis thaliana. Next to several cases additionally confirmed by directed mutagenesis, identified alternative protein N-termini follow the enzymatic rules of co-translational N-terminal protein acetylation and initiator methionine removal. In contrast to other eukaryotic models, N-terminal acetylation in plants cannot generally be considered as a proxy of translation initiation because of its posttranslational occurrence on mature proteolytic neo-termini (N-termini) localized in the chloroplast stroma. Quantification of N-terminal acetylation revealed differing co- vs. posttranslational N-terminal acetylation patterns. Intriguingly, our data additionally hints to alternative translation initiation serving as a common mechanism to supply protein copies in multiple cellular compartments, as alternative translation sites are often in close proximity to cleavage sites of N-terminal transit sequences of nuclear-encoded chloroplastic and mitochondrial proteins. Overall, riboproteogenomics screening enables the identification of (differential localized) N-terminal proteoforms raised upon alternative translation.

show abstract

“…Both Figure 3A and 3B indicate that future incorporation of newer PXDs into maize PeptideAtlas will likely lead to significant increase in newly identified distinct peptides and proteins. This contrasts the current status for the 2 nd release of the Arabidopsis PeptideAtlas https://peptideatlas.org/builds/arabidopsis/, where incorporation of additional and high quality PXD data set resulted in only small increases in distinct peptides and canonical proteins 28 . Details about these maize PXDs, including how many new distinct peptides and proteins they identified, can be found in Table 1 and Supplemental Data Set S1.…”

Section: Search Results For the First Maize Peptideatlasmentioning

confidence: 60%

“…Therefore, the impact of alternative splicing for the cellular proteome in eukaryotes is still under debate [13][14][15] . In addition, plant genomes may also contain an unknown number of various types of small Open Reading Frames (sORFs) encoding for small proteins or peptides, that could be detected by MS [16][17][18] . The use of proteomics data for plant genome annotation is summarized under the term 'proteogenomics' 19 , and has been applied for the genomes of Arabidopsis (Arabidopsis thaliana) 20,21 , rice (Oryza sativa) 22,23 , maize 24 , grape (Vitis vinifera) 25 , and sweet potato (Ipomoea batatas) 26 and the perennial fruit cherry 27 .…”

Section: Introductionmentioning

confidence: 99%

TheZea maysPeptideAtlas – a new maize community resource

van Wijk,

Leppert,

Sun

et al. 2023

Preprint

Self Cite

View full text Add to dashboard Cite

We developed the Maize PeptideAtlas resource (www.peptideatlas.org/builds/maize) to help solve questions about the maize proteome. Publicly available raw tandem mass spectrometry (MS/MS) data for maize were collected from ProteomeXchange and reanalyzed through a uniform processing and metadata annotation pipeline. These data are from a wide range of genetic backgrounds, including the inbred lines B73 and W22, many hybrids and their respective parents. Samples were collected from field trials, controlled environmental conditions, a range of (a)biotic conditions and different tissues, cell types and subcellular fractions. The protein search space included different maize genome annotations for the B73 inbred line from MaizeGDB, UniProtKB, NCBI RefSeq and for the W22 inbred line. 445 million MS/MS spectra were searched, of which 120 million were matched to 0.37 million distinct peptides. Peptides were matched to 66.2% of the proteins (one isoform per protein coding gene) in the most recent B73 nuclear genome annotation (v5). Furthermore, most conserved plastid- and mitochondrial-encoded proteins (NCBI RefSeq annotations) were identified. Peptides and proteins identified in the other searched B73 genome annotations will aid to improve maize genome annotation. We also illustrate high confidence detection of unique SNPs in the W22 proteome as compared to the B73 proteome. N-terminal acetylation, phosphorylation, ubiquitination, and three lysine acylations (K-acetyl, K-malonyl, K-hydroxybutyryl) were identified and can be inspected through a PTM viewer in PeptideAtlas. All matched MS/MS-derived peptide data are linked to spectral, technical and biological metadata. This new PeptideAtlas will be integrated with community resources including MaizeGDB athttps://www.maizegdb.org/and its JBrowse tracks.

show abstract

TheArabidopsis thalianaPeptideAtlas; harnessing world-wide proteomics data for a comprehensive community proteomics resource

Cited by 5 publications

References 125 publications

A deeply conserved protease, acylamino acid-releasing enzyme (AARE), acts in ageing in Physcomitrella and Arabidopsis

A deeply conserved protease, acylamino acid-releasing enzyme (AARE), acts in ageing in Physcomitrella and Arabidopsis

To New Beginnings: Riboproteogenomics Discovery of N-Terminal Proteoforms in Arabidopsis Thaliana

TheZea maysPeptideAtlas – a new maize community resource

Contact Info

Product

Resources

About