Translation control: bridging the gap between genomics and proteomics?

doi:10.1016/S0968-0004(00)01776-X

Trends in Biochemical Sciences

Volume 26, Issue 4, 1 April 2001, Pages 225-229

https://doi.org/10.1016/S0968-0004(00)01776-X Get rights and content

Abstract

mRNA profiling enables the expression levels of thousands of transcripts in a cell to be monitored simultaneously. Nevertheless, analyses in yeast and mammalian cells have demonstrated that mRNA levels alone are unreliable indicators of the corresponding protein abundances. This discrepancy between mRNA and protein levels argues for the relevance of additional control mechanisms besides transcription. As translational control is a major mechanism regulating gene expression, the use of translated mRNA in profiling experiments might depict the proteome more closely than does the use of total mRNA. This would combine the technical potential of genomics with the physiological relevance of 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

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Trends in Biochemical Sciences

OpinionTranslation control: bridging the gap between genomics and proteomics?

Abstract

Section snippets

Do mRNA expression levels faithfully reflect protein abundance?

Technical limitations to proteome analysis

Expression profiling of polysome-bound mRNAs: a closer representation of the proteome?

Conclusion

Acknowledgements

Curr. Opin. Genet. Dev.

Trends Cell Biol.

J. Mol. Biol.

FEBS Lett.

J. Biol. Chem.

Tissue Cell

J. Biol. Chem.

J. Biol. Chem.

Cell

Curr. Biol.

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

Opinion
Translation control: bridging the gap between genomics and proteomics?