The conundrum of discordant protein and mRNA expression. Are plants special?

Vélez‐Bermúdez, Isabel Cristina; Schmidt, Wolfgang

doi:10.3389/fpls.2014.00619

Cited by 48 publications

(42 citation statements)

References 31 publications

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“…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.…”

Section: Discussionmentioning

confidence: 99%

“…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.…”

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confidence: 99%

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

Glenn

Stone

et al. 2017

Plant Physiol.

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Proteomic plasticity undergirds stress responses in plants, and understanding such responses requires accurate measurement of the extent to which proteins levels are adjusted to counter external stimuli. Here, we adapt bioorthogonal noncanonical amino acid tagging (BONCAT) to interrogate protein synthesis in vegetative Arabidopsis (Arabidopsis thaliana) seedlings. BONCAT relies on the translational incorporation of a noncanonical amino acid probe into cellular proteins. In this study, the probe is the Met surrogate azidohomoalanine (Aha), which carries a reactive azide moiety in its amino acid side chain. The azide handle in Aha can be selectively conjugated to dyes and functionalized beads to enable visualization and enrichment of newly synthesized proteins. We show that BONCAT is sensitive enough to detect Arabidopsis proteins synthesized within a 30-min interval defined by an Aha pulse and that the method can be used to detect proteins made under conditions of light stress, osmotic shock, salt stress, heat stress, and recovery from heat stress. We further establish that BONCAT can be coupled to tandem liquid chromatography-mass spectrometry to identify and quantify proteins synthesized during heat stress and recovery from heat stress. Our results are consistent with a model in which, upon the onset of heat stress, translation is rapidly reprogrammed to enhance the synthesis of stress mitigators and is again altered during recovery. All experiments were carried out with commercially available reagents, highlighting the accessibility of the BONCAT method to researchers interested in stress responses as well as translational and posttranslational regulation in plants.

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Section: Discussionmentioning

confidence: 99%

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confidence: 99%

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

Glenn

Stone

et al. 2017

Plant Physiol.

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“…PAV among defence response (biotic stress) genes has been observed in several plant species 5,8,17,18 . The PA of resistance genes could partially be due to their overlapping roles and large number following recent genome triplication in B. oleracea 1,[19][20][21] , however the presence of pathogens is also likely to impact gene retention due to strong selection for corresponding resistance genes. In total, 441 resistance genes were identified (Supplementary Table 8 Tables 9 and 10).…”

Section: Resultsmentioning

confidence: 99%

Construction and analysis of the Brassica oleracea pangenome

Golicz¹

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This thesis describes the construction and analysis of a first Brassica oleracea pangenome. It also presents a pipeline that was developed and implemented in order to build and analyse the pangenome.B. oleracea is a species of high economic importance encompassing crops like broccoli, Brussels sprout, cabbage, cauliflower, kale and kohlrabi. Additionally, it is of high interest to the scientific community because the crops display remarkable morphological and physiological variation and the genetic underpinning of this variation is not fully understood.Recent years have seen an explosion of genome sequencing projects. It has also become clear that there is a significant amount of presence/absence and copy number variation between individuals of the same species, and a reference sequence from a single individual is unable to capture all of the genomic information necessary to fully characterize a species. The term pangenome was coined to describe all the genomic (genic) sequence information found within species.We have hypothesized that some of the phenotypic variation found in the B. oleracea crops might be due to presence/absence variants and therefore we have set out to construct and analyse the B. oleracea pangenome.The pipeline designed was composed of three main steps 1. Pangenome assembly using an iterative mapping and assembly approach and pangenome annotation. Chalhoub, B., Denoeud, F., Liu, S., Parkin, I.A.P., Tang, H., Wang, X., Chiquet, J., Belcram, H., Tong, C., Samans, B., Corréa, M., Da Silva, C., Just, J., Falentin, C., Koh, C.S., Le Clainche, I., Bernard, M., Bento, P., Noel, B., Labadie, K., Alberti, A., Charles, M., Arnaud, D., Guo, H., Daviaud, C., Alamery, S., Jabbari, K., Zhao, M., Edger, P.P., Chelaifa, H., Tack, D., Lassalle, G., Mestiri, I., Schnel, N., Le Paslier, M.-C., Fan, G., Renault, V., Bayer, P.E., Golicz, A.A., Manoli, S., Lee, T.-H., Thi, V.H.D., Chalabi, S., Hu, Q., Fan, C., Tollenaere, R., Lu, Y., Battail, C., Shen, J., Sidebottom, C.H.D., Wang, X., Canaguier, A., Chauveau, A., Bérard, A., Deniot, G., Guan, M., Liu, Z., Sun, F., Lim, Y.P., Lyons, E., Town, C.D., Bancroft, I., Wang, X., Meng, J., Ma, J., Pires, J.C., King, G.J., Brunel, D., Delourme, R., Renard, M.,

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“…These aspects involve changes at the level of transcription and translation . It has well documented that the changes in gene expression at the transcriptional level have a low correlation with changes at the protein level . Unlike transcripts, proteins are the direct effectors of the crop stress response.…”

Section: Introductionmentioning

confidence: 99%

Advances in crop proteomics: PTMs of proteins under abiotic stress

Gong

Cao

et al. 2016

Proteomics

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Under natural conditions, crop plants are frequently subjected to various abiotic environmental stresses such as drought and heat wave, which may become more prevalent in the coming decades. Plant acclimation and tolerance to an abiotic stress are always associated with significant changes in PTMs of specific proteins. PTMs are important for regulating protein function, subcellular localization and protein activity and stability. Studies of plant responses to abiotic stress at the PTMs level are essential to the process of plant phenotyping for crop improvement. The ability to identify and quantify PTMs on a large-scale will contribute to a detailed protein functional characterization that will improve our understanding of the processes of crop plant stress acclimation and stress tolerance acquisition. Hundreds of PTMs have been reported, but it is impossible to review all of the possible protein modifications. In this review, we briefly summarize several main types of PTMs regarding their characteristics and detection methods, review the advances in PTMs research of crop proteomics, and highlight the importance of specific PTMs in crop response to abiotic stress.

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The conundrum of discordant protein and mRNA expression. Are plants special?

Cited by 48 publications

References 31 publications

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

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

Construction and analysis of the Brassica oleracea pangenome

Advances in crop proteomics: PTMs of proteins under abiotic stress

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