Discordance between protein and transcript levels detected by selected reaction monitoring

Abstract

Keywords: absolute protein quantification, Arabidopsis thaliana, mass spectrometry, PDR9/ABCG37, SRM analysis Abbreviations: Fe, iron; iTRAQ, isobaric tags for relative and absolute quantification; LC/MS, high performance liquid chromatography coupled with mass spectrometry; SRM, selected reaction monitoring.Expression levels between transcript and protein are not always correlated. In the present study, the abundance of protein PDR9/ABCG37 in 3 Arabidopsis pdr9/abcg37 mutant alleles was evaluated using selected reaction monitoring analysis. The results showed that protein and mRNA expression levels were similar in 2 mutant alleles. The mRNA expression levels in another mutant, determined by both semi-quantitative and quantitative RT-PCR, were similar to the wild-type, although the abundance of protein was about half the abundance of the wild-type. These results suggested that using only mRNA expression levels to infer protein abundance, compare mutants or responses to various stimuli may lead to incorrect interpretation and conclusions.

Bioorthogonal Noncanonical Amino Acid Tagging (BONCAT) Enables Time-Resolved Analysis of Protein Synthesis in Native Plant Tissue

“…As sessile organisms, plants must retain a high degree of proteomic plasticity to enable rapid responses to a barrage of environmental cues (Huot et al, 2014;Fristedt et al, 2015;Mickelbart et al, 2015). In plants, as in most eukaryotes, mRNA abundance is often a poor proxy for protein levels (Ingolia, 2014;Vélez-Bermúdez and Schmidt, 2014;Fukao, 2015), as indicated by the discordance between total mRNA abundance and polyribosome-associated mRNAs under control and abiotic stress conditions (reviewed by Roy and von Arnim, 2013). To address this issue, we used BONCAT in intact Arabidopsis seedlings to identify and quantify proteins synthesized under conditions of abiotic stress.…”

“…While transcriptomic approaches offer good time resolution (on the minute time scale; Kreps et al, 2002;Preston et al, 2009), transcript abundances and protein levels are frequently discordant (Vélez-Bermúdez and Schmidt, 2014;Fukao, 2015). Translating ribosome affinity purification (Zanetti et al, 2005;Mustroph et al, 2009;Jiao and Meyerowitz, 2010), followed by mRNA quantitation or ribosome footprint mapping (Juntawong et al, 2014), provides proxies for protein synthesis at specific time points in environmental or developmental processes.…”

Reducing the Invasiveness of Low- and High-Grade Endometrial Cancers in Both Primary Human Cancer Biopsies and Cell Lines by the Inhibition of Aquaporin-1 Channels

“…The observed inter- and intra-tumoral heterogeneity and interpatient variability of AQP1 expression emphasizes the importance of combining multiple approaches in cancer treatment. Discrepancies between transcript and protein levels for a given gene product have been described previously [ 74 , 75 ]. The levels of AQP protein expression in EC cells reflect a dynamic balance between processes of transcription, translation, and protein turnover.…”

Peroxisome proliferator‐activated receptor γ coactivator 1‐α overexpression improves angiogenic signalling potential of skeletal muscle‐derived extracellular vesicles

“…Additionally, excess ALIX and TSG101 transcripts likely were not translated into protein as there were no differences in ALIX or TSG101 protein in Ad‐PGC‐1α‐treated cells. Transcript and protein levels are often discordant (Fukao, 2015; Gry et al., 2009), and frequently protein synthesis rate and post‐transcriptional regulation, rather than transcript number, is the main regulator of protein expression (Kristensen et al., 2013).…”