Dataset Information

Arabidopsis thaliana, Silene conica, and Agrostemma githago mitochondrial and chloroplast proteomes

ABSTRACT: LC-MS/MS analysis of purified mitochondria, purified chloroplast, and total leaf tissue from three species of flowering plants (Arabidopsis thaliana, Silene conica, and Agrostemma githago)

INSTRUMENT(S):

ORGANISM(S): Agrostemma Githago Silene Conica Arabidopsis Thaliana (mouse-ear Cress)

TISSUE(S): Plant Cell, Leaf

SUBMITTER: Daniel Sloan

LAB HEAD: Daniel B. Sloan

PROVIDER: PXD071069 | Pride | 2025-12-11

REPOSITORIES: Pride

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Dataset's files

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			Action	DRS
	Dan_20240412_QE_AurTS25_2hr_AgithagoChloro_01.mzML	Mzml
	Dan_20240412_QE_AurTS25_2hr_AgithagoChloro_01.mzid	Mzid
	Dan_20240412_QE_AurTS25_2hr_AgithagoChloro_01.raw	Raw
	Dan_20240412_QE_AurTS25_2hr_AgithagoChloro_02.mzML	Mzml
	Dan_20240412_QE_AurTS25_2hr_AgithagoChloro_02.mzid	Mzid

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Project description:Chloroplast is a major plant cell organelle that fulfills essential metabolic and biosynthetic functions. Located at the interface between the chloroplast and other cell compartments, the chloroplast envelope system is a strategic barrier controlling exchanges of ions, metabolites and proteins, thus regulating essential metabolic functions (synthesis of hormones precursors, amino acids, pigments, sugars, vitamins, lipids, nucleotides…) of the plant cell. However, chloroplast envelope membranes remain the hidden part of the chloroplast proteome and many envelope proteins remain to be characterized (known but uncharacterized envelope proteins) or identified (orphan known envelope-associated functions carried by unidentified proteins) Indeed, the envelope contains only 1% of the chloroplast proteins (i.e. 0.25% of the whole cell proteome). When comparing the composition crude leaf extract and purified envelope vesicles, a high theoretical enrichment factor (EF) of specific envelope proteins is thus expected. This is especially true for minor envelope proteins (e.g. representing 1/100 or 1/1000 of the envelope protein content). Sensitivity of MS technique has been greatly improved during the last decade. Today, thanks to the continuous improvement of MS techniques, we are able to detect more components in a complex sample, to generate quantitative data and to statistically validate above-cited enrichment factor. Here, we have taken advantage of present-days better MS sensitivity towards a better definition (differentiate genuine envelope proteins from contaminants) of the chloroplast envelope proteome. This MS- and statistical-based analysis relied on an enrichment factor calculated for each protein identified in purified envelope fractions when compared to the value obtained for the same protein in crude cell extracts. Using this approach, a total of 1376 proteins was detected in purified envelope fractions, of which, more than 500 could be assigned an envelope localization combining MS-based statistical analyses and manual annotation using data from the literature or prediction tools. Interestingly, many of such proteins being unknown or unexpected envelope components, these data constitute a new resource of significant value to the broader plant science community aiming to define principles and molecular mechanisms controlling fundamental aspects of plastid biogenesis and functions.

Project description:Plastids contain multiple copies of the plastid chromosome, folded together with proteins and RNA into nucleoids. The degree to which components of the plastid gene expression and protein biogenesis machineries are nucleoid associated, and the factors involved in plastid DNA organization, repair, and replication, are poorly understood. To provide a conceptual framework for nucleoid function, we characterized the proteomes of highly enriched nucleoid fractions of proplastids and mature chloroplasts isolated from the maize (Zea mays) leaf base and tip, respectively, using mass spectrometry. Quantitative comparisons with proteomes of unfractionated proplastids and chloroplasts facilitated the determination of nucleoid-enriched proteins. This nucleoid-enriched proteome included proteins involved in DNA replication, organization, and repair as well as transcription, mRNA processing, splicing, and editing. Many proteins of unknown function, including pentatricopeptide repeat (PPR), tetratricopeptide repeat (TPR), DnaJ, and mitochondrial transcription factor (mTERF) domain proteins, were identified. Strikingly, 70S ribosome and ribosome assembly factors were strongly overrepresented in nucleoid fractions, but protein chaperones were not. Our analysis strongly suggests that mRNA processing, splicing, and editing, as well as ribosome assembly, take place in association with the nucleoid, suggesting that these processes occur cotranscriptionally. The plastid developmental state did not dramatically change the nucleoid-enriched proteome but did quantitatively shift the predominating function from RNA metabolism in undeveloped plastids to translation and homeostasis in chloroplasts. This study extends the known maize plastid proteome by hundreds of proteins, including more than 40 PPR and mTERF domain proteins, and provides a resource for targeted studies on plastid gene expression. Details of protein identification and annotation are provided in the Plant Proteome Database.

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Arabidopsis thaliana, Silene conica, and Agrostemma githago mitochondrial and chloroplast proteomes

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