title: Analysis of differential expression patterns of mRNA and protein during cold-acclimation and de-acclimation in Arabidopsis.
abstract: 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 3987 peptides originating from 1569 unique proteins and the corresponding mRNAs were analyzed. Among the 1569 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. In order to confirm the negative correlation of mRNA and protein expression patterns, qRT-PCR and western blot analyses were performed. Mitochondrial malate dehydrogenase 1 (mMDH1) exhibited a negative correlation of mRNA and protein levels, which was characterized by CA-specific mRNA induction and protein accumulation specifically during DA. 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.
authors.affiliation: From the ‡Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, Kanagawa, 230-0045, Japan;
authors.forename: Kentaro
authors.initials: K
authors.lastname: Nakaminami
authors.affiliation: From the ‡Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, Kanagawa, 230-0045, Japan;
authors.forename: Akihiro
authors.initials: A
authors.lastname: Matsui
authors.affiliation: §Plant Proteomics Research Unit, RIKEN CSRS, Yokohama, Kanagawa, 230-0045, Japan;
authors.forename: Hirofumi
authors.initials: H
authors.lastname: Nakagami
authors.affiliation: ¶Cryobiofrontier Research Center, Faculty of Agriculture, Iwate University, Morioka, Iwate, 020-8550, Japan;
authors.forename: Anzu
authors.initials: A
authors.lastname: Minami
authors.affiliation: §Plant Proteomics Research Unit, RIKEN CSRS, Yokohama, Kanagawa, 230-0045, Japan;
authors.forename: Yuko
authors.initials: Y
authors.lastname: Nomura
authors.affiliation: From the ‡Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, Kanagawa, 230-0045, Japan;
authors.forename: Maho
authors.initials: M
authors.lastname: Tanaka
authors.affiliation: From the ‡Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, Kanagawa, 230-0045, Japan;
authors.forename: Taeko
authors.initials: T
authors.lastname: Morosawa
authors.affiliation: From the ‡Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, Kanagawa, 230-0045, Japan;
authors.forename: Junko
authors.initials: J
authors.lastname: Ishida
authors.affiliation: From the ‡Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, Kanagawa, 230-0045, Japan;
authors.forename: Satoshi
authors.initials: S
authors.lastname: Takahashi
authors.affiliation: ¶Cryobiofrontier Research Center, Faculty of Agriculture, Iwate University, Morioka, Iwate, 020-8550, Japan;
authors.forename: Matsuo
authors.initials: M
authors.lastname: Uemura
authors.affiliation: ‖Plant Immunity Research Group, RIKEN CSRS, Yokohama, Kanagawa, 230-0045, Japan;
authors.forename: Ken
authors.initials: K
authors.lastname: Shirasu
authors.affiliation: From the ‡Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, Kanagawa, 230-0045, Japan; ‡‡CREST, JST, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan **Kihara Institute for Biological Research, Yokohama City University, Yokohama, Kanagawa, 244-0813, Japan; motoaki.seki@riken.jp.
authors.forename: Motoaki
authors.initials: M
authors.lastname: Seki
mesh_terms: D000064:Acclimatization / Q000235:genetics*; D017360:Arabidopsis / Q000235:genetics* / Q000378:metabolism; D029681:Arabidopsis Proteins / Q000235:genetics* / Q000378:metabolism; D003080:Cold Temperature; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D063990:Gene Ontology; D008291:Malate Dehydrogenase / Q000235:genetics* / Q000378:metabolism; D008928:Mitochondria / Q000378:metabolism; D014176:Protein Biosynthesis; D020543:Proteome / Q000235:genetics / Q000378:metabolism; D012333:RNA, Messenger / Q000235:genetics* / Q000378:metabolism; D059467:Transcriptome
chemical_list: D029681:Arabidopsis Proteins; D020543:Proteome; D012333:RNA, Messenger; D008291:Malate Dehydrogenase