Comparative proteomic analysis of autotetraploid and diploid Paulownia tomentosa reveals proteins associated with superior photosynthetic characteristics and stress adaptability in autotetraploid Paulownia

Abstract

To enlarge the germplasm resource of plants, we used colchicine to induce autotetraploid, as reported previously. Compared with its diploid progenitor, autotetraploid exhibits better photosynthetic characteristics and higher stress resistance. However, the underlying mechanism for its predominant characteristics has not been determined at the proteome level. In this study, isobaric tag for relative and absolute quantitation coupled with liquid chromatography-tandem mass spectrometry was employed to compare proteomic changes between autotetraploid and diploid. A total of 1427 proteins were identified in our study, of which 130 proteins were differentially expressed between autotetraploid and diploid . Functional analysis of differentially expressed proteins revealed that photosynthesis-related proteins and stress-responsive proteins were significantly enriched among the differentially expressed proteins, suggesting they may be responsible for the photosynthetic characteristics and stress adaptability of autotetraploid. The correlation analysis between transcriptome and proteome data revealed that only 15 (11.5%) of the differentially expressed proteins had corresponding differentially expressed unigenes between diploid and autotetraploid . These results indicated that there was a limited correlation between the differentially expressed proteins and the previously reported differentially expressed unigenes. This work provides new clues to better understand the superior traits in autotetraploid and lays a theoretical foundation for developing breeding strategies in the future.

The photo-inhibition of camphor leaves (Cinnamomum camphora L.) by NaCl stress based on physiological, chloroplast structure and comparative proteomic analysis

“…It has been reported that the upregulation of some above proteins can provide protection from stress during photosynthesis. For example, the polyploidy of autotetraploid Paulownia tomentosa (PT4) was more vigorous, adaptive, and capable of surviving better than diploid P. tomentosa (PT2) in harsher environment because of some upregulated DEPs such as photosystem I reaction center subunit IV B (PsaE-2), and putative cytochrome b6f Rieske iron-sulfur subunit ( Yan et al, 2017 ); heat stress recovery caused a 5.1-fold expression of PsaH and a 28.1-fold increase in expression of PsaN to get more temperature resistance of grapevine ( Liu et al, 2014 ). Therefore, it inferred salinity induced the photo-inhibition in camphor seedlings by the downregulation of proteins in PSI, PSII, the cytochrome b6/f complex, ATP synthase without a protective role.…”

“…Two criteria were to screen the DEPs: (1) a protein must contain at least two unique spectra, and only these unique spectra are for the quantification of proteins; (2) the protein ratio standard had to have a fold-change ≥2.0 or ≤0.5. The proteins that met both criteria were considered as the differential proteins ( Yan et al, 2017 ).…”

“…After carrying out the quality control of raw data by a hierarchical cluster analysis algorithm ( Yan et al, 2017 ), all the credible and different proteins were carried on to the Gene Ontology (GO) analysis based on DAVID 6.7 and the pathway analysis by the Kyoto Encyclopedia of Genes and Genome (KEGG) database ( Kanehisa & Goto, 2000 ).…”

Peer Review #1 of "The photo-inhibition of camphor leaves (Cinnamomum camphora L.) by NaCl stress based on physiological, chloroplast structure and comparative proteomic analysis (v0.1)"

“…After carrying out the quality control of raw data by a hierarchical cluster analysis algorithm (Yan et al, 2017), all the credible and different proteins were carried on to the Gene Ontology PeerJ reviewing PDF | (2019:02:34911:3:0:NEW 29 May 2020)…”

Gene Balance Predicts Transcriptional Responses Immediately Following Ploidy Change InArabidopsis thaliana

“…Such decoupling is evident in response to polyploidy because not all genes show identical expression responses following duplication -whether measured at the level of transcript abundance (e.g. Pirrello et al (2018);Hou et al (2018);Guo et al (1996); Riddle et al (2006); Robinson et al (2018); Stupar et al (2007); Yu et al (2010), additional references in Doyle and Coate (2019)) or protein abundance (Birchler and Newton 1981;Yao et al 2011;Zhu et al 2012;Soltis et al 2016;55 Deng et al 2017;Wang et al 2017;Yan et al 2017). Consequently, WGD does not necessarily preserve protein dosage balance, and the extent to which dosage responses following WGD are coordinated amongst genes encoding interacting proteins is unknown.…”