Ribin, a Protein Encoded by a Message Complementary to rRNA, Modulates Ribosomal Transcription and Cell Proliferation

Abstract

The control of rRNA transcription, tightly coupled to the cell cycle and growth state of the cell, is a key process for understanding the mechanisms that drive cell proliferation. Here we describe a novel protein, ribin, found in rodents, that binds to the rRNA promoter and stimulates its activity. The protein also interacts with the basal rRNA transcription factor UBF. The open reading frame encoding ribin is 96% complementary to a central region of the large rRNA. This demonstrates that ribosomal DNA-related sequences in higher eukaryotes can be expressed as protein-coding messages. Ribin contains two predicted nuclear localization sequence elements, and green fluorescent protein-ribin fusion proteins localize in the nucleus. Cell lines overexpressing ribin exhibit enhanced rRNA transcription and faster growth. Furthermore, these cells significantly overcome the suppression of rRNA synthesis caused by serum deprivation. On the other hand, the endogenous ribin level correlates positively with the amount of serum in the medium. The data show that ribin is a limiting stimulatory factor for rRNA synthesis in vivo and suggest its involvement in the pathway that adapts ribosomal transcription and cell proliferation to physiological changes.A major class of housekeeping genes, highly repeated and clustered in the nucleolus in eukaryotes, encode rRNA. The transcription of these genes, executed by RNA polymerase I (Pol I) and assisting factors, is strictly cell cycle and growth regulated (reviewed in references15, 32, and 34). It has been demonstrated that both activating factors and repressors are involved in a rapid adjustment of Pol I activity to the growth state of the cell (9,16,23,39). A Pol I-associated factor, TIF-IA/C*, implicated in the growth regulation of rRNA transcription in mammals, has recently been cloned (8). The activity of this factor fluctuates with the growth conditions, and its binding to the polymerase is required for a transcription-competent complex to form on the rRNA promoter (9, 39). Recent studies have shown that other Pol I transcription factors are also targets of regulation, finding that the phosphorylation status and activity of UBF, SL1, and TTFI are cell cycle controlled through cyclin-dependent kinases (20,24,41,44). Ribosomal transcription is a target of variety of factors affecting cell proliferation, such as hormones and phorbol esters, viral antigens, and the tumor suppressor proteins p53 and Rb (10,15,16,48,49).Pol I transcription machinery is generally species specific (15, 32). The structure divergence found in rRNA promoters of different species could partially account for this. SL1 has been shown to play a major role in selection of the rRNA promoter by homologous Pol I transcription apparatus, although UBF and Pol I can also contribute to this selectivity (5, 15, 37). The DNA-protein and protein-protein aspects of specific recognition of the rRNA promoter are not yet clear. Previous data demonstrated that UBF and SL1 can interact with the rRNA promoter. This interaction is...

Expression of the rDNA-encoded mitochondrial protein Tar1p is stringently controlled and responds differentially to mitochondrial respiratory demand and dysfunction

“…Thus, it will be of great interest to understand how such factors reciprocally impact rRNA and Tar1p expression from this dynamic locus, as well as how and why these changes are linked to mitochondrial metabolism, perhaps as one means to link the expensive process of ribosome biogenesis to the primary energy generator, the mitochondrion. Interestingly, the mammalian ribin protein (Kermekchiev and Ivanova 2001), the mRNA for which is in part complementary to rRNA and hence analogous to Tar1p, is involved in the response to growth factors, suggesting that mechanisms that link rDNA-related transcripts to cellular metabolism may be conserved. Finally, both respiration and extrachromosomal rDNA circles (ERCs), which contain TAR1 , have profound effects on yeast replicative life span (Sinclair and Guarente 1997; Lin et al 2002).…”

A positive role for yeast extrachromosomal rDNA circles?

“…ERC production would already have been a byproduct of rDNA array copy number maintenance, and the rDNA locus would have already been subject to Sir2p-dependent pol-II transcription silencing. We envisage that the TAR1 open reading frame emerged by chance (other overprinted genes are known at the rDNA locus 31) and acquired suppression of drive function. Selection would then have favoured retrograde response-dependent control of ERC production/rDNA pol-II transcription.…”

Ribosome Assembly

“…Remarkably, two proteins encoded within rDNA or rDNA-like sequences (Tar1p and Ribin, respectively) have recently been identified; these are transcribed in the antisense direction with respect to 25S or 25S-like sequences [43,119]. Yeast Tar1p is a mitochondrial protein that is capable of rescuing respiration-deficient strains.…”