Our laboratory is studying the pathway of assembly of ribosomes in eukaryotes. We use the yeast Saccharomyces cerevisiae as an experimental organism in which to study this essential and highly conserved process. Thus we can utilize state-of-the-art genomics, proteomics, and molecular biology, as well as classical genetic and biochemical approaches.

Ribosomes consist of two ribonucleoprotein subunits. In eukaryotes, the 40S subunit contains a single 18S rRNA and 32 different ribosomal proteins, while the 60S subunit contains the 5S, 5.8S, and 25S rRNAs and 48 different ribosomal proteins. The 18S, 5.8S, and 25S rRNAs are derived from a single 35S transcript, by a series of endonucleolytic and exonucleolytic processing steps. The 5S pre-rRNA is synthesized from separate genes. The genes for 5S and 35S rRNA are linked in yeast and present in ~100 to 150 tandem repeats on chromosome XII. Transcription and processing of pre-rRNA and most steps of assembly of ribosomal proteins with rRNA occur in the nucleolus, a subdomain of the nucleus. Late steps in ribosome assembly occur upon release of the immature ribosomal subunits from the nucleolus into the nucleoplasm, including changes that allow the subunits to be exported from the nucleus to the cytoplasm. Several final steps of cytoplasmic maturation are required to produce ribosomal subunits capable of functioning in protein synthesis.

Our goals are to identify and characterize proteins that are necessary for the biogenesis of ribosomes but do not end up as constituents of the mature ribosomes. Such "non-ribosomal" molecules might be required for a number of processes in order to assemble a ribosome. These include: (1) rearrangements of rRNA structure or of protein-rRNA interactions that occur during sequential assembly of ribosomal proteins with rRNA (e.g. RNA-dependent helicases/ATPases, GTPases or protein isomerases), (2) cleavage and processing of RNA, (3) sensing and reporting the progress and fidelity of RNA processing and ribosome assembly (quality control, kinases, phosphatases, GTPases) and (4) transport of nascent ribosomes within the nucleolus and nucleoplasm and export to the cytoplasm.

We have identified a number of such factors in genetic screens or selections for mutants defective in ribosome biogenesis. Most of these proteins are essential and have homologues in humans, as well as in other metazoans. An important recent breakthrough in our lab has been the development of methods to purify ribosome assembly intermediates and identify their RNA and protein constituents. These genetic and biochemical tools now enable us to investigate in much more detail than before the order in which ribosomes assemble and the precise function of each non-ribosomal protein in the biogenesis of ribosomes.

An interesting outcome of this much expanded catalogue of ribosome assembly factors is the discovery that many of these proteins are also important for cell growth or proliferation. This should not be entirely surprising, since ribosome biogenesis was known to be tightly coordinated with cell growth and cell cycle progression. We are beginning to investigate in more detail how ribosome biogenesis and cell growth and proliferation might be coordinated through these molecules.

Tang L, Sahasranaman A, Jakovljevic J, Schleifman E, Woolford Jr JL. 2008. Interactions among Ytm1, Erb1, and Nop7 Required for Assembly of the Nop7-Subcomplex in Yeast Preribosomes. Molecular Biology of the Cell 19: 2844-2856.

Zhang J, Harnpicharnchai P, Jakovljevic J, Tang L, Guo Y, Oeffinger M, Rout MP, Hiley SL, Hughes T, Woolford Jr JL. 2007. Assembly factors Rpf2 and Rrs1 recruit 5S rRNA and ribosomal proteins rpL5 and rpL11 into nascent ribosomes. Genes and Development 21: 2580-2592.

Miles,TD, Jakovljevic, J, Horsey, E, Harnpicharnchai, P, Tang, L, and Woolford, JL, Jr. Ytm1,Nop7,and Erb1 Form a Complex Necessary for Maturation of 66S Preribosomes. Molecular and Cellular Biology 2005; 25: 10419-10432.

Jakovljevic J, Antunez de Mayolo P, Miles TD, Nguyen TM-L, Leger-Silvestre, I, Gas N, Woolford, JL Jr. The carboxyl-terminal extension of yeast ribosomal protein S14 is necessary for maturation of 43S preribosomes. Molecular Cell 2004; 14: 331-342.

Horsey EW, Jakovljevic J, Miles TD, Harnpicharnchai P, Woolford JL Jr. Role of the Yeast Rrp1 Protein in the dynamics of pre-ribosome maturation. RNA 2004; 10:813-827.

Farach-Colton M, Huang Y, Woolford JL Jr. Discovering temporal relations in molecular pathways using protein-protein interactions. RECOMB Proceedings of International Conference on Computational Molecular Biology. 2004.

Antunez de Mayolo P, Woolford JL Jr. Interactions of yeast ribosomal protein S14 with RNA. Journal of Molecular Biology 2003; 333:697-709.