Effects of progressive depletion of TCM1 or CYH2 mRNA on Saccharomyces cerevisiae ribosomal protein accumulation

H/ACA snoRNA levels are regulated during stem cell differentiation

H/ACA small nucleolar RNAs (snoRNAs) guide pseudouridylation as part of a small nucleolar ribonucleoprotein complex (snoRNP). Disruption of H/ACA snoRNA levels in stem cells impairs pluripotency, yet it remains unclear how H/ACA snoRNAs contribute to differentiation. To determine if H/ACA snoRNA levels are dynamic during differentiation, we comprehensively profiled H/ACA snoRNA abundance in multiple murine cell types and during differentiation in three cellular models, including mouse embryonic stem cells and mouse myoblasts. We determined that the profiles of H/ACA snoRNA abundance are cell-type specific, and we identified a subset of snoRNAs that are specifically regulated during differentiation. Additionally, we demonstrated that a decrease in Snora27 abundance upon differentiation corresponds to a decrease in pseudouridylation of its target site within the E-site transfer RNA (tRNA) binding region of the 28S ribosomal RNA (rRNA) in the large ribosomal subunit. Together, these data point toward a potential model in which H/ACA snoRNAs are specifically regulated during differentiation to alter pseudouridylation and fine tune ribosome function.

Silencing of ribosomal protein L3 genes in N. tabacum reveals coordinate expression and significant alterations in plant growth, development and ribosome biogenesis

The expression of ribosomal protein genes is coordinately regulated in bacteria, yeast, and vertebrates, so that equimolar amounts of ribosomal proteins accumulate for assembly into ribosomes. To understand how expression of ribosomal protein genes is regulated in plants, we altered expression of the large subunit ribosomal protein L3 (RPL3) genes in Nicotiana tabacum using post-transcriptional gene silencing (PTGS). L3 is encoded by two genes, RPL3A and RPL3B, with 80.2% amino acid sequence identity in tobacco. Two types of 'hairpin' RNA (hpRNA) vectors carrying the RPL3A or RPL3B sequences in both sense and antisense orientation were generated in order to alter the expression level of both RPL3 genes. Tobacco plants transformed with a vector containing a 5'-terminal fragment of RPL3A gene displayed decreased RPL3A mRNA levels and a marked increase in the abundance of RPL3B mRNA. These results indicated that expression of the RPL3 genes is coordinately regulated in tobacco. The transgenic plants that contained higher levels of RPL3B mRNA exhibited leaf overgrowth and mottling. Epidermal cells of these plants were increased in number and decreased in size. The precursor rRNA (pre-rRNA) and the mature rRNAs accumulated in these plants, suggesting that ribosome biogenesis is upregulated. Tobacco plants transformed with an hpRNA vector harboring the full-length RPL3B cDNA exhibited efficient silencing of both RPL3A and RPL3B genes, reduced L3 levels, and an abnormal phenotype characterized by a delay in development, stunting, and inhibition of lateral root growth. L3 deficiency led to a reduction in cell number and an increase in cell size, suggesting that L3 positively regulates cell division. Decreasing RPL3 gene expression resulted in a decrease in accumulation of the pre-rRNA, establishing a prominent role for L3 in ribosome biogenesis in plants.

Overexpression of truncated Nmd3p inhibits protein synthesis in yeast

The yeast NMD3 gene was identified in a two-hybrid screen using the nonsense-mediated mRNA decay factor, Upf1p, as bait. NMD3 was shown to encode an essential, highly conserved protein that associated principally with free 60S ribosomal subunits. Overexpression of a truncated form of Nmd3p, lacking 100 C-terminal amino acids and most of its Upf1p-interacting domain, had dominant-negative effects on both cell growth and protein synthesis and promoted the formation of polyribosome half-mers. These effects were eliminated by truncation of an additional 100 amino acids from Nmd3p. Overexpression of the nmd3delta100 allele also led to increased synthesis and destabilization of some ribosomal protein mRNAs, and increased synthesis and altered processing of 35S pre-rRNA. Our data suggest that Nmd3p has a role in the formation, function, or maintenance of the 60S ribosomal subunit and may provide a link for Upf1p to 80S monosomes.

Ribosome concentration contributes to discrimination against poly(A)- mRNA during translation initiation in Saccharomyces cerevisiae

Inactivation of Saccharomyces cerevisiae poly(A) polymerase in a strain bearing the temperature-sensitive lethal pap1-1 mutation results in the synthesis of poly(A)- mRNAs that initiate translation with surprising efficiency. Translation of poly(A)- mRNAs after polyadenylation shut-off might result from an increase in the ratio of ribosomes and associated translation factors to mRNA, caused by the inability of poly(A)- mRNAs to accumulate to normal levels. To test this hypothesis, we used ribosomal subunit protein gene mutations to decrease either 40 or 60 S ribosomal subunit concentrations in strains carrying the pap1-1 mutation. Polyadenylation shut-off in such cells results in a nearly normal ratio of ribosomes to mRNA as revealed by polyribosome sedimentation analysis. Ribonuclease protection and Northern blot analyses showed that a significant percentage of poly(A)-deficient and poly(A)- mRNA associate with smaller polyribosomes compared with cells with normal ribosome levels. Analysis of the ratio of poly(A)-deficient and poly(A)- forms of a specific mRNA showed relatively more poly(A)- mRNA sedimenting with 20-60 S complexes than do poly(A)+ forms, suggesting a block in an early step of the translation initiation of the poly(A)- transcripts. These findings support models featuring the poly(A) tail as an enhancer of translation and suggest that the full effect of a poly(A) tail on the initiation strength of a mRNA may require competition for a limited number of free ribosomes or translation factors.

Multiple regions of yeast ribosomal protein L1 are important for its interaction with 5 S rRNA and assembly into ribosomes

Yeast ribosomal protein L1 binds to 5 S rRNA and can be released from 60 S ribosomal subunits as an intact ribonucleoprotein particle. To identify residues important for binding of Saccharomyces cerevisiae rpL1 to 5 S rRNA and assembly into functional ribosomes, we have isolated mutant alleles of the yeast RPL1 gene by site-directed and random mutagenesis. The rpl1 mutants were assayed for association of rpL1 with 5 S rRNA in vivo and in vitro and assembly of rpL1 into functional 60 S ribosomal subunits. Consistent with previous data implicating the importance of the carboxyl-terminal 47 amino acids of rpL1 for binding to 5 S rRNA in vitro, we find that deletion of the carboxyl-terminal 8, 25, or 44 amino acids of rpL1 confers lethality in vivo. Missense mutations elsewhere in rpL1 also affect its function, indicating that multiple regions of rpL1 are important for its association with 5 S rRNA and assembly into ribosomes.

Processing of pre-ribosomal RNA in Saccharomyces cerevisiae

Post-transcriptional processing of precursor-ribosomal RNA comprises a complex pathway of endonucleolytic cleavages, exonucleolytic digestion and covalent modifications. The general order of the various processing steps is well conserved in eukaryotic cells, but the underlying mechanisms are largely unknown. Recent analysis of pre-rRNA processing, mainly in the yeast Saccharomyces cerevisiae, has significantly improved our understanding of this important cellular activity. Here we will review the data that have led to our current picture of yeast pre-rRNA processing.

Proline biosynthesis in Saccharomyces cerevisiae: molecular analysis of the PRO1 gene, which encodes gamma-glutamyl kinase

The PRO1 gene of Saccharomyces cerevisiae encodes the 428-amino-acid protein gamma-glutamyl kinase (ATP:L-glutamate 5-phosphotransferase, EC 2.7.2.11), which catalyzes the first step in proline biosynthesis. Amino acid sequence comparison revealed significant homology between the yeast and Escherichia coli gamma-glutamyl kinases throughout their lengths. Four close matches to the consensus sequence for GCN4 protein binding and one close match to the RAP1 protein-binding site were found in the PRO1 upstream region. The response of the PRO1 gene to changes in the growth medium was analyzed by measurement of steady-state mRNA levels and of beta-galactosidase activity encoded by a PRO1-lacZ gene fusion. PRO1 expression was not repressed by exogenous proline and was not induced by the presence of glutamate in the growth medium. Although expression of the PRO1 gene did not change in response to histidine starvation, both steady-state PRO1 mRNA levels and beta-galactosidase activities were elevated in a gcd1 strain and reduced in a gcn4 strain. In addition, a pro1 bradytrophic strain became completely auxotrophic for proline in a gcn4 strain background. These results indicate that PRO1 is regulated by the general amino acid control system.

Downregulation of messenger RNA levels for ribosomal proteins in differentiating HL-60 cells

After differentiation induction in HL-60 cells by treatment with retinoic acid, phorbol ester, or dimethyl sulfoxide strong downregulation of the steady state mRNA level of the putative protein No. 3 of the large ribosomal subunit (rpL3) was observed. Downregulation was also observed in other hemopoietic human cell lines, although to a lesser extent. Four ribosomal protein mRNAs were compared in their degree of downregulation after differentiation induction or actinomycin D treatment. The comparatively fast response of rpL3 mRNA observed could indicate a regulatory function of rpL3 protein.

Immunological homologies between yeast ribosomal protein L2 and rat liver ribosomal proteins L4 and L24

Polyclonal antibodies raised against ribosomal protein (r-protein) L2 of Schizosaccharomyces pombe were used to check for cross-reactions with total r-proteins of rat liver. Using this procedure, the rat liver r-proteins, L4 and L24, were identified as being immunologically related to yeast L2. In additional, homologies between rat liver L4 and L24 were detected. The possible implications for the regulation of r-protein synthesis are discussed.