<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
<ProteomeXchangeDataset id="PXD050885" formatVersion="1.4.0" xsi:noNamespaceSchemaLocation="proteomeXchange-1.4.0.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
<CvList>
<Cv fullName="PSI-MS" uri="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo" id="MS"/>
<Cv fullName="PSI-MOD" uri="https://raw.githubusercontent.com/MICommunity/psidev/master/psi/mod/data/PSI-MOD.obo" id="MOD"/>
<Cv fullName="UNIMOD" uri="http://www.unimod.org/obo/unimod.obo" id="UNIMOD"/>
</CvList>
<DatasetSummary announceDate="2024-06-23" hostingRepository="PRIDE" title="Arabidopsis Lon1 disruption decreases autophagy flux affects seed development through brassinosteroid regulation">
<Description>Arabidopsis Lon1 serves dual roles as a mitochondrial protease and chaperone. Loss of Lon1 function reduced autophagy flux at transcriptional, protein and cellular levels. Meanwhile, changes occurred in the levels of cellular subunit proteins, especially a significant upregulation of mitochondrial proteins overall in lon1 mutants. Lon1 is a key enzyme in maintaining mitochondrial protein homeostasis. In lon1 mutants, other mitochondrial proteases including mitochondrial autophagy receptor proteins showed significant increases in abundance. Mitophagy is an important mechanism for cellular quality control. lon1-2atg5-1 double mutant were constructed to investigate how they cooperatively regulate mitochondrial protein homeostasis. Transcriptome sequencing results revealed that Lon1 inactivation led to widespread unfolded protein responses (UPRs) pathway activation in lon1-2atg5-1, consistent with lon1-2, while loss function of ATG5 inactivation did not affect mitochondrial homeostasis. The double mutant also exhibited independent plant phenotypes from single parents, yet more severe seed number and embryo development issues, suggesting an additive effect of lon1-2 and atg5-1. Protein Storage Vacuole (PSV) and oil body phenotypes also showed more severe developmental damage in the double mutants. Brassinosteroid (BR) acts as a key plant hormone controlling seed and embryo development. GO and KEGG analysis of genes simultaneously downregulated in lon1-2, atg5-1, and lon1-2atg5-1 revealed significant downregulation of genes involved in BR biosynthesis and its homeostasis, indicating that this may be one of the key factors leading to abnormal seed and embryo development in the mutants. In general, the loss function of Lon1 reduces autophagy flux and induces UPRs to regulate protein homeostasis. Meanwhile, the simultaneous absence of Lon1 and autophagy significantly down-regulates the expression of genes related to BR biosynthesis and homeostasis, thereby leading to pronounced blockage in the development of double mutant seeds and embryos.</Description>
<ReviewLevel>
<cvParam cvRef="MS" accession="MS:1002854" name="Peer-reviewed dataset"/>
</ReviewLevel>
<RepositorySupport>
<cvParam cvRef="MS" accession="MS:1002857" name="Unsupported dataset by repository"/>
</RepositorySupport>
</DatasetSummary>
<DatasetIdentifierList>
<DatasetIdentifier>
<cvParam cvRef="MS" accession="MS:1001919" name="ProteomeXchange accession number" value="PXD050885"/>
</DatasetIdentifier>
</DatasetIdentifierList>
<DatasetOriginList>
<DatasetOrigin>
<cvParam cvRef="MS" accession="MS:1002868" name="Original data"/>
</DatasetOrigin>
</DatasetOriginList>
<SpeciesList>
<Species>
<cvParam cvRef="MS" accession="MS:1001469" name="taxonomy: scientific name" value="Arabidopsis thaliana (Mouse-ear cress)"/>
<cvParam cvRef="MS" accession="MS:1001467" name="taxonomy: NCBI TaxID" value="3702"/>
</Species>
</SpeciesList>
<InstrumentList>
<Instrument id="Instrument_1">
<cvParam cvRef="MS" accession="MS:1003094" name="Orbitrap Exploris 240"/>
</Instrument>
</InstrumentList>
<ModificationList>
<cvParam cvRef="MS" accession="MS:1002864" name="No PTMs are included in the dataset"/>
</ModificationList>
<ContactList>
<Contact id="project_submitter">
<cvParam cvRef="MS" accession="MS:1000586" name="contact name" value="Ce Song"/>
<cvParam cvRef="MS" accession="MS:1000589" name="contact email" value="380415874@qq.com"/>
<cvParam cvRef="MS" accession="MS:1000590" name="contact affiliation" value="Nankai University"/>
<cvParam cvRef="MS" accession="MS:1002037" name="dataset submitter"/>
</Contact>
<Contact id="project_lab_head">
<cvParam cvRef="MS" accession="MS:1002332" name="lab head"/>
<cvParam cvRef="MS" accession="MS:1000586" name="contact name" value="Lei Li"/>
<cvParam cvRef="MS" accession="MS:1000589" name="contact email" value="lei.li@nankai.edu.cn"/>
<cvParam cvRef="MS" accession="MS:1000590" name="contact affiliation" value="Frontiers Science Center for Cell Responses, Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, 300071 Tianjin, China"/>
</Contact>
</ContactList>
<PublicationList>
<Publication id="PMID38791463">
<cvParam cvRef="MS" accession="MS:1000879" name="PubMed identifier" value="38791463"/>
<cvParam cvRef="MS" accession="MS:1002866" name="Reference" value="Song C, Hou Y, Li T, Liu Y, Wang XA, Qu W, Li L. Lon1 Inactivation Downregulates Autophagic Flux and Brassinosteroid Biogenesis, Modulating Mitochondrial Proportion and Seed Development in <i>Arabidopsis</i>. Int J Mol Sci. 2024 25(10):5425"/>
</Publication>
<Publication id="DOI-10_3390_ijms25105425">
<cvParam cvRef="MS" accession="MS:1001922" name="Digital Object Identifier (DOI)" value="10.3390/ijms25105425"/>
</Publication>
</PublicationList>
<KeywordList>
<cvParam cvRef="MS" accession="MS:1001925" name="submitter keyword" value="Lon1, autophagy,Arabidopsis, UPRs, seed, brassinosteroid"/>
</KeywordList>
<FullDatasetLinkList>
<FullDatasetLink>
<cvParam cvRef="MS" accession="MS:1002852" name="Dataset FTP location" value="ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2024/06/PXD050885"/>
</FullDatasetLink>
<FullDatasetLink>
<cvParam cvRef="MS" accession="MS:1001930" name="PRIDE project URI" value="http://www.ebi.ac.uk/pride/archive/projects/PXD050885"/>
</FullDatasetLink>
</FullDatasetLinkList>
<DatasetFileList>
<DatasetFile id="FILE_1" name="lon1-1_2.raw">
<cvParam cvRef="MS" accession="MS:1002846" name="Associated raw file URI" value="ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2024/06/PXD050885/lon1-1_2.raw"/>
</DatasetFile>
<DatasetFile id="FILE_2" name="checksum.txt">
<cvParam cvRef="MS" accession="MS:1002851" name="Other type file URI" value="ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2024/06/PXD050885/checksum.txt"/>
</DatasetFile>
<DatasetFile id="FILE_3" name="Col-0_3.raw">
<cvParam cvRef="MS" accession="MS:1002846" name="Associated raw file URI" value="ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2024/06/PXD050885/Col-0_3.raw"/>
</DatasetFile>
<DatasetFile id="FILE_4" name="Col-0_2.raw">
<cvParam cvRef="MS" accession="MS:1002846" name="Associated raw file URI" value="ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2024/06/PXD050885/Col-0_2.raw"/>
</DatasetFile>
<DatasetFile id="FILE_5" name="lon1-1_3.raw">
<cvParam cvRef="MS" accession="MS:1002846" name="Associated raw file URI" value="ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2024/06/PXD050885/lon1-1_3.raw"/>
</DatasetFile>
<DatasetFile id="FILE_6" name="Lon1-autophagy.msf">
<cvParam cvRef="MS" accession="MS:1002849" name="Search engine output file URI" value="ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2024/06/PXD050885/Lon1-autophagy.msf"/>
</DatasetFile>
<DatasetFile id="FILE_7" name="lon1-2_2.raw">
<cvParam cvRef="MS" accession="MS:1002846" name="Associated raw file URI" value="ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2024/06/PXD050885/lon1-2_2.raw"/>
</DatasetFile>
<DatasetFile id="FILE_8" name="lon1-1_1.raw">
<cvParam cvRef="MS" accession="MS:1002846" name="Associated raw file URI" value="ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2024/06/PXD050885/lon1-1_1.raw"/>
</DatasetFile>
<DatasetFile id="FILE_9" name="Col-0_1.raw">
<cvParam cvRef="MS" accession="MS:1002846" name="Associated raw file URI" value="ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2024/06/PXD050885/Col-0_1.raw"/>
</DatasetFile>
<DatasetFile id="FILE_10" name="lon1-2_1.raw">
<cvParam cvRef="MS" accession="MS:1002846" name="Associated raw file URI" value="ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2024/06/PXD050885/lon1-2_1.raw"/>
</DatasetFile>
<DatasetFile id="FILE_11" name="lon1-2_3.raw">
<cvParam cvRef="MS" accession="MS:1002846" name="Associated raw file URI" value="ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2024/06/PXD050885/lon1-2_3.raw"/>
</DatasetFile>
</DatasetFileList>
<RepositoryRecordList>
<RepositoryRecord name="Arabidopsis Lon1 disruption decreases autophagy flux affects seed development through brassinosteroid regulation" label="PRIDE project" recordID="PXD050885" repositoryID="PRIDE" uri="http://www.ebi.ac.uk/pride/archive/projects/PXD050885"/>
</RepositoryRecordList>
</ProteomeXchangeDataset>