Structure-function analysis of Hmo1 unveils an ancestral organization of HMG-Box factors involved in ribosomal DNA transcription from yeast to human

Abstract

Ribosome biogenesis is a major metabolic effort for growing cells. In Saccharomyces cerevisiae, Hmo1, an abundant high-mobility group box protein (HMGB) binds to the coding region of the RNA polymerase I transcribed ribosomal RNAs genes and the promoters of ∼70% of ribosomal protein genes. In this study, we have demonstrated the functional conservation of eukaryotic HMGB proteins involved in ribosomal DNA (rDNA) transcription. We have shown that when expressed in budding yeast, human UBF1 and a newly identified Sp-Hmo1 (Schizosaccharomyces pombe) localize to the nucleolus and suppress growth defect of the RNA polymerase I mutant rpa49-Δ. Owing to the multiple functions of both proteins, Hmo1 and UBF1 are not fully interchangeable. By deletion and domains swapping in Hmo1, we identified essential domains that stimulate rDNA transcription but are not fully required for stimulation of ribosomal protein genes expression. Hmo1 is organized in four functional domains: a dimerization module, a canonical HMGB motif followed by a conserved domain and a C-terminal nucleolar localization signal. We propose that Hmo1 has acquired species-specific functions and shares with UBF1 and Sp-Hmo1 an ancestral function to stimulate rDNA transcription.

Both HMG boxes in Hmo1 are essential for DNA binding in vitro and in vivo

“…23) By contrast, we confirmed that the box A mutations described here also impaired binding of Hmo1 to the RPS23A promoter (Fig. 4(C)).…”

“…21,22) It was reported recently that the integrity of box A is required for the function of Hmo1 in the RNA polymerase I transcription in vivo, whereas the requirement of box A in the transcription of RPG (such as RPS23A) by RNA polymerase II is unclear. 23) In contrast to these previous studies, the box A mutations identified in the genetic screen performed here impaired the ability of Hmo1 to bind to DNA. Furthermore, one of the box A Hmo1 mutants was deficient in DNA binding specifically in vivo.…”

Yeast HMO1: Linker Histone Reinvented

“…Comparable functions of UBF and HMO1 are supported by the observation that both proteins are highly enriched in the nucleolus and localized throughout the transcribed rDNA region and that both proteins contain HMG domains that may promote DNA bending and DNA looping (149,150,162,163). Further support for overlapping functions of HMO1 and UBF was provided by the observation that the expression of human UBF1 or S. pombe HMO1 also suppresses the rpa49Δ growth phenotype (130).…”

“…HMO1 has also been identified in closely related species such as Saccharomyces kluyveri (129). In addition, an HMO1 counterpart is encoded in the Schizosaccharomyces pombe genome (130). According to the Saccharomyces Genome Database (131), HMO1 has been reported to exhibit physical or genetic interactions with a total of 290 genes or gene products.…”

“…1). Box A, which has only limited similarity to consensus HMG domains, functions as a dimerization domain; it has a low affinity for DNA but exhibits some structural specificity, including preferred binding to four-way junction DNA, whereas canonical box B has a higher affinity for DNA but a lower structural specificity (130,132). The HMO1 box A domain contributes to DNA bending; in contrast, the box B domain contributes most of the DNA binding affinity but fails to bend linear DNA (133).…”