The role of mRNA and protein stability in gene expression

How important is the stability of gene products in the process of gene expression? We use a dual-compartment mathematical model to demonstrate the effects that changing the rates of synthesis and degradation of hypothetical mRNAs and proteins would have on the final concentration of protein. The model predicts that the concentration of protein at steady state equals the product of the rate constants for synthesis of mRNA and protein (ks1 and ks2) divided by the product of the rate constants for degradation (kd1 and kd2) and that the rate at which protein concentration changes depends on the rate constants for degradation of both the mRNA and the protein. This permits great flexibility in controlling induction kinetics for particular gene products, since their synthesis, translation, and degradation may be regulated coordinately to permit induction to be stable or transient or to amplify the final yield of protein. We suggest single exons may encode structural features that cause both mRNAs and proteins to be labile, thereby ensuring that modal stabilities of highly regulated macromolecules are similar.     

Comparing protein abundance and mRNA expression levels on a genomic scale

Attempts to correlate protein abundance with mRNA expression levels have had variable success. We review the results of these comparisons, focusing on yeast. In the process, we survey experimental techniques for determining protein abundance, principally two-dimensional gel electrophoresis and mass-spectrometry. We also merge many of the available yeast protein-abundance datasets, using the resulting larger 'meta-dataset' to find correlations between protein and mRNA expression, both globally and within smaller categories.     

Inferring gene expression dynamics from reporter protein levels

We present a mathematical method for inferring the dynamics of gene expression from time series of reporter protein assays and cell populations. We show that estimating temporal expression dynamics from direct visual inspection of reporter protein data is unreliable when the half-life of the protein is comparable to the time scale of the expression dynamics. Our method is simple and general because it is designed only to reconstruct the pattern of protein synthesis, without assuming any specific regulatory mechanisms. It can be applied to a wide range of cell types, patterns of expression, and reporter systems, and is implemented in publicly available spreadsheets. We show that our method is robust to a several possible types of error, and argue that uncertainty about the decay kinetics of reporter proteins is the limiting factor in reconstructing the temporal pattern of gene expression dynamics from reporter protein assays. With improved estimates of reporter protein decay rates, our approach could allow for detailed reconstruction of gene expression dynamics from commonly used reporter protein systems.     

Increased expression of polypyrimidine tract binding protein results in higher insulin mRNA levels

The aim of this study was to further elucidate the role of the polypyrimidine tract binding protein (PTB) in the control of insulin mRNA stability. We observed that the glucose- or interleukin-1beta-induced increase in insulin mRNA was paralleled by an increase in PTB mRNA. To further test the hypothesis that PTB controls insulin gene expression, betaTC-6 cells were treated with a PTB-specific siRNA to modify the beta-cell content of PTB. Surprisingly, we observed an increase in PTB mRNA and PTB protein levels in response to the siRNA treatment. In addition, the PTB-siRNA treatment also increased insulin mRNA. We conclude that expression of the PTB gene controls insulin production.     

Dynamical analysis of gene networks requires both mRNA and protein expression information

One of the important goals of biology is to understand the relationship between DNA sequence information and nonlinear cellular responses. This relationship is central to the ability to effectively engineer cellular phenotypes, pathways, and characteristics. Expression arrays for monitoring total gene expression based on mRNA can provide quantitative insight into which gene or genes are on or off; but this information is insufficient to fully predict dynamic biological phenomena. Using nonlinear stability analysis we show that a combination of gene expression information at the message level and at the protein level is required to describe even simple models of gene networks. To help illustrate the need for such information we consider a mechanistic model for circadian rhythmicity which shows agreement with experimental observations when protein and mRNA information are included and we propose a framework for acquiring and analyzing experimental and mathematically derived information about gene networks.     

Wilt-induced ABA biosynthesis, gene expression and down-regulation of rbcS mRNA levels in Arabidopsis thaliana

The kinetics of wilt-induced abscisic acid (ABA) biosynthesis were investigated in shoots of Arabidopsis thaliana (L.) Heynh Landsberg erecta. ABA concentrations were measured using a radioimmunoassay (RIA) based on the monoclonal antibody MAC 252, and the RIA validated by comparison with combined gas chromatography-mass spectrometry using a [²H₃] labelled internal standard. The basal ABA content of Arabidopsis shoots was ca 10 ng g^?1 fresh weight; the concentrations had increased ca 4-fold within 30 min of the initiation of wilting, increased ca 8-fold after 4 h and 11-fold after 8 h. This stress-induced ABA production was dependent on de novo gene expression; pre-treatment of leaves and shoots with the metabolic inhibitors cordycepin and cycloheximide reduced the rate of subsequent stress-induced ABA biosynthesis from 12.5 ng g^?1 h^?1 to 1 ng g^?1 h^?1 and 0 ng g^?1 h^?1, respectively. In vitro translation of mRNA isolated from shoots subjected to wilting or ABA treatment followed by one-dimensional sodium dodecyl sulphate polyacrylamide gel electrophoresis revealed only minor changes. The effects of wilting and ABA on the content of total ribulose 1,5-bisphosphate carboxylase/oxygenase small sub-unit (rbcS) mRNA were also determined. Both wilting and exogenous ABA resulted in a substantial reduction in the amount of rbcS mRNA, an effect readily reversed by rehydration of wilted shoots. However, the effects of wilting were not mediated solely by newly-synthesised endogenous ABA, as wilting also reduced rbcS mRNA levels in the ABA-deficient aba-1 mutant, which did not produce ABA in response to loss of turgor. The amount of rbcS mRNA was higher in aba-1 shoots, suggesting that cellular rbcS mRNA levels are normally down-regulated by ABA. Cold treatment induced ABA production in wild type shoots only, but resulted in an increased rbcS mRNA content of both wild type and aba-1 shoots.     

Metabolism of c-myc gene products: c-myc mRNA and protein expression in the cell cycle.

The presence and synthesis of c-myc protein and mRNA in the cell cycle has been studied. We find that c-myc mRNA is present, at equivalent levels, at all times in the cell cycle with the possible exception of mitosis. Furthermore, we demonstrate that this mRNA is transcribed in both G1 and G2 phases. An analysis of the c-myc protein in vivo shows that de novo synthesis occurs in G1 and G2 and the protein turns over with a half-life of approximately 20-30 min in both phases. Furthermore, the level of c-myc protein rapidly increases in cell populations when they re-initiate the cell cycle, thereafter decreasing as the culture reaches quiescence. The results therefore suggest that expression of c-myc can be rapidly modulated and that it is activated during the G0 to G1 transition, but is expressed thereafter in the cell cycle.     

Control of gene expression during induction of cultured peanut cells: mRNA levels,protein synthesis and enzyme activity of stilbene synthase

Stilbene synthase is an inducible enzyme occurring in a small number of plants. The enzyme is amenable to analysis and biochemical studies only after the cells are subjected to induction. Cell suspension cultures of peanut react very selectively if elicited with biotic inducers. Just as intact peanut plants produce stilbene phytoalexins when attacked by fungi so also do sterile cultured cells when treated with sterilized insoluble fungal cell walls. Both systems react by synthesizing stilbene synthase. The time courses of increase in enzyme activity, protein synthesis and mRNA activity were studied, and their relation to other activities of the cells was elaborated. The results show that, after applying the fungal elicitor, the system responds very quickly and selectively: within 2 hours the synthesis rate of stilbene synthase protein is increased more than 30-fold, the increase being detectable 40 min after induction. The first increase in translatable mRNA for stilbene synthase can be seen 20 min after application of the stimulus. Stilbene synthase synthesized in vivo was compared to stilbene synthase prepared by translation in vitro. There was no difference in size, and limited proteolysis did not indicate significant differences in the peptide structure of the primary translation product and the active enzyme.     

Utility of low-copy nuclear gene sequences in plant phylogenetics

Low-copy nuclear genes in plants are a rich source of phylogenetic information. They hold a great potential to improve the robustness of phylogenetic reconstruction at all taxonomic levels, especially where universal markers such as cpDNA and nrDNA are unable to generate strong phylogenetic hypotheses. Low-copy nuclear genes, however, remain underused in plant phylogenetic studies due to practical and theoretical complications in unraveling the evolutionary dynamics of nuclear gene families. The lack of the universal markers or universal PCR primers of low-copy nuclear genes has also hampered their phylogenetic utility. It has recently become clear that low-copy nuclear genes are particularly helpful in resolving close interspecific relationships and in reconstructing allopolyploidization in plants. Gene markers that are widely, if not universally, useful have begun to emerge. Although utilizing low-copy nuclear genes usually requires extra lab work such as designing PCR primers, PCR-cloning, and/or Southern blotting, rapid accumulation of gene sequences in the databases and advances in cloning techniques have continued to make such studies more feasible. With the growing number of theoretical studies devoted to the gene tree and species tree problem, a solid foundation for reconstructing complex plant phylogenies based on multiple gene trees began to build. It is also realized increasingly that fast evolving introns of the low-copy nuclear genes will provide much needed phylogenetic information around the species boundary and allow us to address fundamental questions concerning processes of plant speciation. Phylogenetic and molecular evolutionary analyses of developmentally important genes will add a new dimension to systematic and evolutionary studies of plant diversity.