Gene expression changes dramatically over the course of aging. It’s relatively common to find a paper that addresses these alterations in gene expression (especially at the level of transcriptional regulation), but rare to find one that addresses the mechanism of the change. Which factors govern differential gene expression in the aged cell? We don’t know, and in the age of cheaper and cheaper microarrays and increasingly accessible mass-spec for protein expression studies, it seems like we rarely ask.
Hence I was pleased to see today’s paper. Timchenko et al. begin with a few established points of reference (known changes in gene expression and in levels of regulatory proteins) and proceed to systematically identify and characterize a multiprotein complex, involved in translational regulation, that is upregulated in the aged liver. Furthermore, they demonstrate that this complex determines differential translation of multiple isoforms of a broad-spectrum transcription factor:
RNA binding protein, CUGBP1, regulates translation of proteins in a variety of biological processes. In this paper, we show that aging liver increases CUGBP1 translational activities by an induction of a high molecular weight protein-protein complex of CUGBP1. The complex contains CUGBP1, subunits alpha, beta and gamma of the initiation translation factor eIF2 and four proteins of the endoplasmic reticulum, eR90, CRT, eR60 and Grp78. The induction of the CUGBP1-eIF2 complex in old livers is associated with the elevation of protein levels of CUGBP1 and with the hyper-phosphorylation of CUGBP1 by a cyclin D3-cdk4 kinase, activity of which is increased with age. … The CUGBP1-eIF2 complex is bound to C/EBP beta mRNA in the liver of old animals and this binding correlates with the increased amounts of LAP and LIP. Consistent with these observations, the purified CUGBP1-eIF2 complex binds to the 5’ region of C/EBP beta mRNA and significantly increases translation of the three isoforms of C/EBP beta in a cell-free translation system, in cultured cells and in the liver. Thus, these studies demonstrated that age-mediated induction of the CUGBP1-eIF2 complex changes translation of C/EBP beta in old livers.
CUGBP-1 was already known to be upregulated in senescent fibroblasts, where it increases translation of CDK inhibitor p21WAF1. LIP, the C/EBPß isoform whose levels rise, was already known to be upregulated in the aging liver. The novelty here is in mechanistically bridging the two observations, showing that both in vivo and in vitro, the upregulation of a multiprotein complex containing CUGBP-1 increases translation of this specific C/EBPß isoform.
LIP is a dominant negative whose expression presumably represses transcription of genes responsive to other C/EBPß isoforms; the full ramifications of the upregulation of LIP await a detailed transcriptional study, but it’s reasonable to speculate that high LIP results in repression of liver-specific genes in an aged organ.
So I like this preliminary story: A multiprotein complex specific to an aged tissue post-transcriptionally regulates a transcription factor, resulting (presumably) in a dramatic change in transcription throughout the genome. Granted that in one sense it simply pushes the question back one step further (why the upregulation of the CUGBP-1 complex?), it still provides refreshing dose of mechanism in a line of research that sometimes gets bogged down in the lepidopteristic listing of upregulated and downregulated genes.
One point of disgruntlement: The authors used mass spec to identify the subunits of their complex, and confirmed the identifications by Western blot. Strangley, several of the proteins (CUGBP-1 and the subunits of eIF2) are cytosolic — but several others (including Grp78 and calreticulin) live in the endoplasmic reticulum (ER). Now, the cytosol and the ER are separated by a membrane that takes some work to get across, so it’s hard to believe that the native complex actually includes all of these proteins. I would hazard to guess that the cell lysis conditions used here somehow violate the ER membrane and allow abundant chaperones to bind to the cytosolic “half” of the complex. The authors are curiously uncritical about their discovery of a multiprotein complex whose subunits reside in different membrane-bound compartments of the cell, failing to mention this issue even in passing.
Finally, a more general point on the study of gene expression in aging. A question unasked and therefore unanswered in this and many papers is what, if anything, age-related changes in gene expression signify: Are they deleterious, protective, passive responses to damage-induced signals, neutral, or other? It’s a gigantic question, far beyond the scope of any one paper. But since I introduced the discussion of the paper by talking about what I’d like to see more of in the field, it seems an appropriate way to end.
Happy Friday, everyone. Be good to your livers.