PXD001216

PXD001216 is an original dataset announced via ProteomeXchange.

Title	Analysis of differential expression patterns of mRNA and protein during cold- and de-acclimation in Arabidopsis
Description	Overwintering plants are capable of exhibiting high levels of cold tolerance, which is acquired through the process of cold acclimation (CA). In contrast to CA, the acquired freezing tolerance is rapidly reduced during cold de-acclimation (DA) and plants resume growth after sensing warm temperatures. In order to better understand plant growth and development, and to aid in the breeding of cold-tolerant plants, it is important to decipher the functional mechanisms of the DA process. In this study, we performed comparative transcriptomic and proteomic analyses during CA and DA. As revealed by shotgun proteomics, we identified 3,987 peptides originating from 1,569 unique proteins and the corresponding mRNAs were analyzed. Among the 1,569 genes, 658 genes were specifically induced at the transcriptional level during the process of cold acclimation. In order to investigate the relationship between mRNA and the corresponding protein expression pattern, a Pearson correlation was analyzed. Interestingly, 199 genes showed a positive correlation of mRNA and protein expression pattern, indicating that both their transcription and translation occurred during CA. However, 226 genes showed a negative correlation of mRNA and protein expression pattern, indicating that their mRNAs were transcribed during CA and were stored for the subsequent DA step. Under this scenario, those proteins were specifically increased during DA without additional transcription of mRNA. These data indicate that the expression of specific mRNAs and subsequent accumulation of corresponding proteins are not always in accordance under low temperature stress conditions in plants.
HostingRepository	PRIDE
AnnounceDate	2014-10-02
AnnouncementXML	Submission_2015-06-01_06:21:54.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Kentaro Nakaminami
SpeciesList	scientific name: Arabidopsis thaliana (Mouse-ear cress); NCBI TaxID: 3702;
ModificationList	iodoacetamide derivatized residue
Instrument	LTQ Orbitrap XL

Revision	Datetime	Status	ChangeLog Entry
0	2014-08-08 03:34:24	ID requested
1	2014-10-02 02:44:54	announced
⏵ 2	2015-06-01 06:21:55	announced	Updated publication reference for PubMed record(s): 25277243.

Nakaminami K, Matsui A, Nakagami H, Minami A, Nomura Y, Tanaka M, Morosawa T, Ishida J, Takahashi S, Uemura M, Shirasu K, Seki M, Analysis of differential expression patterns of mRNA and protein during cold-acclimation and de-acclimation in Arabidopsis. Mol Cell Proteomics, 13(12):3602-11(2014) [pubmed]

curator keyword: Biological

submitter keyword: Arabidopsis, Cold acclimation, Cold deacclimation, nano-LC-MS/MS

Motoaki Seki
contact affiliation	Plant Genomic Network Research Team, RIKEN CSRS, JAPAN
contact email	motoaki.seki@riken.jp
lab head
Kentaro Nakaminami
contact affiliation	RIKEN CSRS
contact email	nm_ken@psc.riken.jp
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/2014/10/PXD001216

PRIDE project URI

• PRIDE
  1. PXD001216
     1. Label: PRIDE project
     2. Name: Analysis of differential expression patterns of mRNA and protein during cold- and de-acclimation in Arabidopsis