The glycolytic enzyme ALDOA and the exon junction complex protein RBM8A are regulators of ribosomal biogenesis

Jessica Denise Schwarz; Sören Lukassen; Pranjali Bhandare; Lorenz Eing; Marteinn Thor Snaebjörnsson; Yiliam Cruz García; Jan Philipp Kisker; Almut Schulze; Elmar Wolf

doi:10.3389/fcell.2022.954358

The glycolytic enzyme ALDOA and the exon junction complex protein RBM8A are regulators of ribosomal biogenesis

Front Cell Dev Biol. 2022 Sep 14:10:954358. doi: 10.3389/fcell.2022.954358. eCollection 2022.

Authors

Jessica Denise Schwarz¹, Sören Lukassen², Pranjali Bhandare¹, Lorenz Eing¹, Marteinn Thor Snaebjörnsson³, Yiliam Cruz García¹, Jan Philipp Kisker¹, Almut Schulze³, Elmar Wolf¹

Affiliations

¹ Cancer Systems Biology Group, Theodor Boveri Institute, University of Würzburg, Würzburg, Germany.
² Center for Digital Health, Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany.
³ Tumor Metabolism and Microenvironment, German Cancer Research Center, Heidelberg, Germany.

Abstract

Cellular growth is a fundamental process of life and must be precisely controlled in multicellular organisms. Growth is crucially controlled by the number of functional ribosomes available in cells. The production of new ribosomes depends critically on the activity of RNA polymerase (RNAP) II in addition to the activity of RNAP I and III, which produce ribosomal RNAs. Indeed, the expression of both, ribosomal proteins and proteins required for ribosome assembly (ribosomal biogenesis factors), is considered rate-limiting for ribosome synthesis. Here, we used genetic screening to identify novel transcriptional regulators of cell growth genes by fusing promoters from a ribosomal protein gene (Rpl18) and from a ribosomal biogenesis factor (Fbl) with fluorescent protein genes (RFP, GFP) as reporters. Subsequently, both reporters were stably integrated into immortalized mouse fibroblasts, which were then transduced with a genome-wide sgRNA-CRISPR knockout library. Subsequently, cells with altered reporter activity were isolated by FACS and the causative sgRNAs were identified. Interestingly, we identified two novel regulators of growth genes. Firstly, the exon junction complex protein RBM8A controls transcript levels of the intronless reporters used here. By acute depletion of RBM8A protein using the auxin degron system combined with the genome-wide analysis of nascent transcription, we showed that RBM8A is an important global regulator of ribosomal protein transcripts. Secondly, we unexpectedly observed that the glycolytic enzyme aldolase A (ALDOA) regulates the expression of ribosomal biogenesis factors. Consistent with published observations that a fraction of this protein is located in the nucleus, this may be a mechanism linking transcription of growth genes to metabolic processes and possibly to metabolite availability.

Keywords: AldoA; RBM8A; Ribosomal protein gene; Y14; aldolase A; genetic screen; genome-wide screen; ribosome biogenesis.