PXD002866

PXD002866 is an original dataset announced via ProteomeXchange.

Title	The Physcomitrella patens chloroplast proteome changes in response to short-term stress
Description	Plants often face more than one type of stress at a time, and how plants respond to combined stress factors is therefore of great interest. Here, we used protoplasts of the moss Physcomitrella patens as a model to study the effects of short-term combined stress on the chloroplast proteome. In this system, biotic stress is mimicked by exposure to cell wall-hydrolyzing enzymes, and abiotic stress is related to plasmolysis. We used SWATH-MS to perform label-free comparative quantitative proteomic analysis of the chloroplast proteome. Overall, we quantified 480 chloroplast proteins, 220 of which showed a more than 1.4-fold change in abundance in protoplasts. We additionally quantified 1422 chloroplast proteins using emPAI. We observed degradation of a significant portion of the chloroplast proteome during the first hour of stress. Electron-transport chain (ETC) components underwent the heaviest degradation, resulting in the decline of photosynthetic activity. We also compared the proteome changes to those in the transcriptional level of nuclear-encoded chloroplast genes. Globally, the levels of the quantified proteins and their corresponding mRNAs showed limited correlation. Genes involved in the biosynthesis of chlorophyll and components of the outer chloroplast membrane showed decreases in both transcript and protein abundance. However, proteins like dehydroascorbate reductase 1 and 2-cys peroxiredoxin B responsible for ROS detoxification increased in abundance. Further, genes such as thylakoid ascorbate peroxidase were induced at the transcriptional level but down-regulated at the proteomic level. Together, our results demonstrate that the initial chloroplast reaction to stress is due changes at the proteomic level.
HostingRepository	PRIDE
AnnounceDate	2017-10-24
AnnouncementXML	Submission_2017-10-24_03:29:19.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD002866
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Georgij Arapidi
SpeciesList	scientific name: Physcomitrella patens subsp. patens (Moss); NCBI TaxID: 3218;
ModificationList	Ammonia-loss; Dehydrated; Acetyl; Carbamidomethyl
Instrument	TripleTOF 5600

Revision	Datetime	Status	ChangeLog Entry
0	2015-09-07 03:27:54	ID requested
1	2017-01-03 03:01:40	announced
⏵ 2	2017-10-24 03:29:21	announced	Updated project metadata.

Fesenko I, Seredina A, Arapidi G, Ptushenko V, Urban A, Butenko I, Kovalchuk S, Babalyan K, Knyazev A, Khazigaleeva R, Pushkova E, Anikanov N, Ivanov V, Govorun VM, Chloroplast Proteome Changes in Response to Protoplastation. Front Plant Sci, 7():1661(2016) [pubmed]

curator keyword: Biological

submitter keyword: SWATH-MS, chloroplast proteome, moss Physcomitrella patens, label-free quantification, stress

Georgij Arapidi
contact affiliation	Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences
contact email	arapidi@gmail.com
lab head
Georgij Arapidi
contact affiliation	IBCH RAS
contact email	arapidi@gmail.com
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/12/PXD002866

PRIDE project URI

• PRIDE
  1. PXD002866
     1. Label: PRIDE project
     2. Name: The Physcomitrella patens chloroplast proteome changes in response to short-term stress