Methods for monitoring and measurement of protein translation in time and space

Dermit, Maria; Dodel, Martin; Mardakheh, Faraz K.

doi:10.1039/c7mb00476a

Cited by 32 publications

(33 citation statements)

References 79 publications

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“…For this reason, the concentration of mRNA was used as a reflection of the levels and activity of the encoded proteins [3]. However, transcriptome analyses revealed that the regulation of gene expression at the mRNA level exists [51], as there are differences in protein levels over time and between clonally identical cells that may result from, e.g. promoter binding, decay of mRNA, translational rate, and protein degradation index [52].…”

Section: Mrna-protein Correlationmentioning

confidence: 99%

Is it useful to use several “omics” for obtaining valuable results?

et al. 2019

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The integration of cell communication and the transfer of signals from stimuli via transcription to translation and further to activation of new protein is crucial for appropriate metabolism and function of living organisms. The overall elucidation and the examination of these complex processes require multistep laboratory approaches in order to obtain results which will not only detect particular stage but also indicate the mechanisms lying upon this process. Such results will be reliable because they will cover multidirectional methods and approaches. The analysis of currently available results already provided with the conclusion that often single omics approach does not correspond with other expected information and may bring misinterpretations. That is why the integration of several "omics" is useful for searching entire explanations and answers as well as appropriate interpretation of obtained complex results. The hypothesis was stated that "from transcriptomics can not be concluded to proteomics". This review focuses on the reasons for the integration of transcriptomic, proteomic and other-omics analysis. Moreover it also describes the examples of clinical meanings and mentions some methods used in these approaches.Publisher's Note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

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Section: Mrna-protein Correlationmentioning

confidence: 99%

Is it useful to use several “omics” for obtaining valuable results?

et al. 2019

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“…To study the effect of CR on the temporal protein translation, we decided to isolate mRNA associated with ribosomes. There are several methods for isolation of ribosome-loaded mRNA (24,25,33), and we analyzed polysome-associated transcripts. It is generally accepted, with few exceptions, that mRNAs associated with polysomes are actively translated (26).…”

Section: Effect Of Cr On Differential Mrna Translation In the Livermentioning

confidence: 99%

“…It is generally accepted, with few exceptions, that mRNAs associated with polysomes are actively translated (26). While some of the transcripts might escape the analysis because of some limitations of this approach, but generally changes in the transcript abundance in polysomes provide the information on the state of the cellular translatome (25). We isolated polyribosomes from livers of wild-type mice on AL and CR diets.…”

Section: Effect Of Cr On Differential Mrna Translation In the Livermentioning

confidence: 99%

“…To further unravel the molecular pathways that contribute to the adaptation of organism physiology to CR and establish a mechanistic connection between the CR-induced changes in the expression and metabolism, we studied the effect of CR on differential translation. Polysome association of mRNAs is a good reflection of active translation (24)(25)(26), and here, we assayed the polysome-associated mRNAs (P-mRNAs) in the livers of mice fed AL and CR diets across the day using RNA sequencing (RNA-seq). We found significant changes in the translational for many transcripts whose products are known to be associated with CR, such as components of insulin, AMPK, and forkhead box signaling pathways (27).…”

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Calorie restriction reprograms diurnal rhythms in protein translation to regulate metabolism

et al. 2018

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Calorie restriction (CR) delays aging and affects the circadian clocks by reprogramming circadian rhythms in gene expression. To expand on the circadian mechanisms in CR, we assayed rhythms in the protein translation by analyzing polysome‐associated mRNAs in the liver of mice fed ad libitum (AL) and CR diets. Global comparison of the diets revealed that <1% of transcripts were differentially abundant in the polysomes. In contrast, the large differential, up to 10%, was detected when CR and AL diets were compared at individual times throughout the day. Most transcripts that were rhythmic under AL lost their rhythms, and many new transcripts gained rhythms under CR. Only a small fraction of transcripts, including the circadian clock genes, were rhythmic under both diets. Thus, CR strongly reprograms translation. CR affected translation of enzymes regulating long‐chain acetyl‐coenzyme A (Acyl‐CoA) metabolism. The expression of the Acyl‐CoA thioesterase (ACOT) family was induced upon CR, leading to the increased transcriptional activity of peroxisome proliferator‐activated receptor α, the transcriptional factor regulated by the ACOT products. We propose that the differential translation induced by CR leads to a temporal partition and reprogramming of metabolic processes and provides a link between CR, lipid metabolism, and the circadian clock.—Makwana, K., Gosai, N., Poe, A., Kondratov, R. V. Calorie restriction reprograms diurnal rhythms in protein translation to regulate metabolism. FASEB J. 33, 4473–4489 (2019). http://www.fasebj.org

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“…mass cytometry | protein synthesis | tellurium M easuring spatial and temporal changes in protein synthesis is necessary to understand the function and dysfunction of multicellular organisms. Protein synthesis can be monitored using radiolabeled amino acids, functional noncognate amino acids, sequencing data from ribosome-associated mRNA, or puromycin labeling approaches (1). However, application of these methods can be complicated by the limitations of the experimental protocols.…”

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TePhe, a tellurium-containing phenylalanine mimic, allows monitoring of protein synthesis in vivo with mass cytometry

Bassan

Willis

Vellanki

et al. 2019

Proc. Natl. Acad. Sci. U.S.A.

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Protein synthesis is central to maintaining cellular homeostasis and its study is critical to understanding the function and dysfunction of eukaryotic systems. Here we report L-2-tellurienylalanine (TePhe) as a noncanonical amino acid for direct measurement of protein synthesis. TePhe is synthetically accessible, nontoxic, stable under biological conditions, and the tellurium atom allows its direct detection with mass cytometry, without postexperiment labeling. TePhe labeling is competitive with phenylalanine but not other large and aromatic amino acids, demonstrating its molecular specificity as a phenylalanine mimic; labeling is also abrogated in vitro and in vivo by the protein synthesis inhibitor cycloheximide, validating TePhe as a translation reporter. In vivo, imaging mass cytometry with TePhe visualizes translation dynamics in the mouse gut, brain, and tumor. The strong performance of TePhe as a probe for protein synthesis, coupled with the operational simplicity of its use, suggests TePhe could become a broadly applied molecule for measuring translation in vitro and in vivo. mass cytometry | protein synthesis | tellurium

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Methods for monitoring and measurement of protein translation in time and space

Abstract: Regulation of protein translation constitutes a crucial step in control of gene expression. Here we review recent methods for system-wide monitoring and measurement of protein translation.

Cited by 32 publications

References 79 publications

Is it useful to use several “omics” for obtaining valuable results?

Is it useful to use several “omics” for obtaining valuable results?

Calorie restriction reprograms diurnal rhythms in protein translation to regulate metabolism

TePhe, a tellurium-containing phenylalanine mimic, allows monitoring of protein synthesis in vivo with mass cytometry

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