Trends in Biochemical Sciences
OpinionTranslation control: bridging the gap between genomics and proteomics?
Section snippets
Do mRNA expression levels faithfully reflect protein abundance?
A recurring criticism to the use of mRNA expression profiling in characterizing cellular phenotypes has been that the transcriptome does not faithfully represent the proteome 16. A limited number of reports have compared the steady-state levels of proteins with those of their corresponding mRNAs. Results from these studies have suggested that mRNA abundance is a poor indicator of the levels of the corresponding protein 17, 18, 19, 20. As it is the proteome that determines cell phenotype, this
Technical limitations to proteome analysis
As a consequence of the discrepancies between the levels of mRNAs and their proteins, the most meaningful approach to describe cell phenotypes would be an exhaustive, quantitative analysis of the proteome. Proteomics, a term covering all the technology currently available to analyse global patterns of gene expression at the protein level 23, usually involves separation of proteins from cells or cell fractions in 2D gels, followed by identification of individual spots by mass-spectrometry.
Expression profiling of polysome-bound mRNAs: a closer representation of the proteome?
The above considerations suggest that expression profiling data would be more meaningful if mRNA samples could be enriched for transcripts that are being translated. This can be achieved by fractionation of cytoplasmic extracts in sucrose gradients, enabling the separation of free mRNPs (ribonucleoprotein particles) both from mRNAs in ribosomal pre-initiation complexes and from mRNAs fully loaded with ribosomes (i.e. polysomes). As only polysomes represent actively translated transcripts, this
Conclusion
Polysome-bound mRNAs obtained by sucrose-gradient fractionation can be used for quantitative analysis in mRNA profiling experiments. This methodology integrates every level of regulation from transcription to translation. It also combines the technical potential offered by genomics in terms of high throughput, feasibility, reproducibility, sensitivity, target identification, and adaptability to new cell systems, with the physiological relevance of proteomics analysis. This translational
Acknowledgements
We are grateful to S. Hunt and D. Jones for critically reviewing the manuscript, and to our colleagues M. Jechlinger, M. von Lindern and N. Kraut for allowing us to discuss their unpublished results. J.A.G–S. especially thanks C. Martinez-A. for continuous support and encouragement. Research in the authors’ laboratories is partially supported by an EU TMR Network grant (contract number ERBFMRXCT980197) (to H.B, J.A.G–S. and E.W.M.) and by the Austrian ‘Fonds zur Foerderung der
References (43)
- et al.
Mechanisms of RNA localization and translational regulation
Curr. Opin. Genet. Dev.
(2000) Intracellular proteolysis
Trends Cell Biol.
(1999)- et al.
Accumulation of rare and moderately abundant mRNAs in mouse L-cells is mainly post-transcriptionally regulated
J. Mol. Biol.
(1984) Gene expression profiling: monitoring transcription and translation products using DNA microarrays and proteomics
FEBS Lett.
(2000)The fas-induced apoptosis analyzed by high-throughput proteome analysis
J. Biol. Chem.
(2000)Effects of serum deprivation, insulin and dexamethasone on polysome percentages in C2C12 myoblasts and differentiating myoblasts
Tissue Cell
(1999)Translational control of arylsulfatase A expression in mouse testis
J. Biol. Chem.
(1994)Elongation factor-1α mRNA is selectively translated following mitogenic stimulation
J. Biol. Chem.
(1994)Characterization of the yeast transcriptome
Cell
(1997)TGFβ signalling is essential for carcinoma cell invasiveness and metastasis
Curr. Biol.
(1998)
Progress with proteome projects: why all proteins expressed by a genome should be identified and how to do it
Biotechnol. Genet. Eng. Rev.
The proteasome
Annu. Rev. Biophys. Biomolec. Struct.
The 26S proteasome: a molecular machine designed for controlled proteolysis
Annu. Rev. Biochem.
Proteomics: capacity versus utility
Electrophoresis
Post-transcriptional regulatory mechanisms in eukaryotes: an overview
J. Endocrinol.
Origins and principles of translational control
Control of translation initiation in animals
Annu. Rev. Cell Dev. Biol.
Translational control of developmental decisions
Influence of polyadenylation-induced translation of metazoa development and neuronal synaptic function
Cited by (320)
Acute restraint stress regulates brain DNMT3a and promotes defensive behaviors in male rats
2024, Neuroscience LettersLabel-free quantitative proteomics reveals the antibacterial effects of benzyl isothiocyanate against Vibrio parahaemolyticus
2022, LWTCitation Excerpt :In bacteria, there is not a substantial link between mRNA and protein abundances (Gygi, Corthals, Zhang, Rochon, & Aebersold, 2000). By examining transcript abundances and gene modifications, it was also unable to identify the levels of proteins and their functional activities (Pradet-Balade, Boulmé, Beug, Müllner, & Garcia-Sanz, 2001). While transcriptome profiling can be comprehensive, it may be subject to posttranscriptional and posttranslational modifications (Gygi, Rochon, Franza, & Aebersold, 1999).
Proteomic profiling of Deinococcus radiodurans with response to thioredoxin reductase inhibitor and ionizing radiation treatment
2022, Journal of ProteomicsCitation Excerpt :Usually, the protein functions are activated by post-translational modifications, protein-protein interactions, and proteolysis [17]. Protein's functional activity could not be determined by transcriptome and gene knockout analysis [17]. Therefore, the systematic and comprehensive proteomic analysis might help reveal the role of proteome content in the resistance against oxidative stress.
Complex response to physiological and drug-induced hepatic heme demand in monoallelic ALAS1 mice
2021, Molecular Genetics and Metabolism Reports