Dataset Information

LC-MS Based Draft Map of the Arabidopsis thaliana Nuclear Proteome and Protein Import in Pattern Triggered Immunity

ABSTRACT: An LC-MS based discovery proteomics approach was used to measure the nuclear proteome fractions of Arabidopsis thaliana cell culture. An enrichment score based on the relative abundance of cytoplasmic, mitochondrial and golgi markers in the nuclear protein fraction allowed us to curate the nuclear proteome producing high quality catalogs of around 3,000 nuclear proteins under untreated and both PTI conditions (flg22 and nlp20). The measurements also covered low abundant proteins including more than 100 transcription factors and transcriptional co-activators. Here we sought to gain a broader impression of protein import to the nucleus upon stimulus with flg22 and nlp20. Furthermore, the abundance of 93 proteins changed significantly in the nucleus following elicitation of immunity. These results suggest promiscuous ribosome assembly and retrograde signaling from the mitochondrion to the nucleus including Prohibitins and Cytochrome C, in the two forms of PTI.

INSTRUMENT(S): Q Exactive Plus

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

TISSUE(S): Plant Cell, Cell Culture

SUBMITTER: Steffen Neumann

LAB HEAD: Wolfgang Hoehenwarter

PROVIDER: PXD024349 | Pride | 2021-11-08

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	AYM_Control_cellular_1.msf	Msf
	AYM_Control_cellular_1.raw	Raw
	AYM_Control_cellular_2.msf	Msf
	AYM_Control_cellular_2.raw	Raw
	AYM_Control_cellular_3.msf	Msf

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LC-MS Based Draft Map of the <i>Arabidopsis thaliana</i> Nuclear Proteome and Protein Import in Pattern Triggered Immunity.

Ayash Mohamed M Abukhalaf Mohammad M Thieme Domenika D Proksch Carsten C Heilmann Mareike M Schattat Martin Hartmut MH Hoehenwarter Wolfgang W

Frontiers in plant science 20211108

Despite its central role as the ark of genetic information and gene expression the plant nucleus is surprisingly understudied. We isolated nuclei from the <i>Arabidopsis thaliana</i> dark grown cell culture left untreated and treated with flg22 and nlp20, two elicitors of pattern triggered immunity (PTI) in plants, respectively. An liquid chromatography mass spectrometry (LC-MS) based discovery proteomics approach was used to measure the nuclear proteome fractions. An enrichment score based on t ...[more]

PMID: 34858452

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Project description:During early embryonic cell divisions, the total nuclear volume doubles with each cycle. At a critical volume ratio between the nucleus and cytoplasm, embryos start transcribing their genome in a reproducible and sequential manner. However, the underlying molecular mechanism for these well-timed events remains unclear. Previous studies proposed that titration of a regulatory factor by the exponentially increasing DNA content of the system triggers the onset of the first transcripts. Nevertheless, a systematic investigation of nuclear proteome changes during development is still missing. In this study, we perform this investigation and find that differential nuclear import timing can largely explain the sequential onset of transcription. First, we investigated nuclear proteome changes in early development. We found that nuclear proteins sequentially titrate into the embryonic nuclei. Interestingly, transcription factors and RNA polymerases enter the nucleus at different times, which correspond to the activation of their nuclear functions. Notably, we observed a high correlation between when transcription factors enter the nucleus and the order in which they activate downstream transcription. Time-lapse imaging of protein import into nuclei encapsulated in droplets of cytoplasmic extract validated our discovery of the sequential nuclear import by mass spectrometry. Lastly, we investigated the underlying molecular mechanism responsible for the differential timing of protein entry into embryonic nuclei. To this end, we quantified the relative affinity of substrates to importin and observe that high-affinity substrates tend to enter the nucleus earlier than low-affinity substrates. Notably, we can explain > 36% of the observed time-variation of when proteins enter the nucleus in the embryo with this simple affinity assay. Together, our results suggest that embryos control protein entry into the nucleus by modulating importin affinities, which then determines the timing of essential nuclear processes in early development.