Ribosome biosynthesis in Tetrahymena thermophila. IV. Regulation of ribosomal RNA synthesis in growing and growth arrested cells

The group I-like ribozyme DiGIR1 mediates alternative processing of pre-rRNA transcripts in Didymium iridis

During starvation induced encystment, cells of the myxomycete Didymium iridis accumulate a 7.5-kb RNA that is the result of alternative processing of pre-rRNA. The 5' end corresponds to an internal processing site cleaved by the group I-like ribozyme DiGIR1, located within the twin-ribozyme intron Dir.S956-1. The RNA retains the majority of Dir.S956-1 including the homing endonuclease gene and a small spliceosomal intron, the internal transcribed spacers ITS1 and ITS2, and the large subunit rRNA lacking its two group I introns. The formation of this RNA implies cleavage by DiGIR1 in a new RNA context, and presents a new example of the cost to the host of intron load. This is because the formation of the 7.5-kb RNA is incompatible with the formation of functional ribosomal RNA from the same transcript. In the formation of the 7.5-kb RNA, DiGIR1 catalysed cleavage takes place without prior splicing performed by DiGIR2. This contrasts with the processing order leading to mature rRNA and I-DirI mRNA in growing cells, suggesting an interplay between the two ribozymes of a twin-ribozyme intron.

Regulation of ribosome synthesis in Tetrahymena pyriformis. 1. Coordination of synthesis of ribosomal proteins and ribosomal RNA during nutritional shift-down

When exponentially growing cells of Tetrahymena pyriformis are transferred to a non-nutrient medium the loss of whole cell RNA, 90% of which is ribosomal RNA, exhibits biphasic kinetics, whereas whole cell protein is lost at a constant rate. The ratio RNA/protein declines during the first 5 h of starvation and then remains constant during the subsequent period of starvation. The synthesis of the majority of the ribosomal proteins is coordinately regulated during a nutritional shift-down. Exponentially growing cells devote 17% of their capacity for protein synthesis to the production of ribosomal proteins. Upon starvation this proportion is rapidly reduced 3.5-fold. In long-time-starved cells the absolute rate of ribosomal protein synthesis is only about 4.5% of that of exponentially growing cells. The synthesis of ribosomal RNA and ribosomal proteins appears tightly coupled during the transition from growth to starvation. In long-time-starved cells the synthesis of ribosomal RNA and ribosomal proteins are stoichiometrically balanced with no significant degradation of de novo synthesized ribosomal proteins.

Regulation of ribosome synthesis in Tetrahymena pyriformis. 2. Coordination of synthesis of ribosomal proteins and ribosomal RNA during nutritional shift-up

The addition of nutrients to long-time-starved cells of Tetrahymena pyriformis leads to a 50-60-fold increase in the rate of synthesis of ribosomal proteins (r-proteins). This is achieved by a 6-fold increase in the relative rate of r-protein synthesis and a 8-10-fold increase in the rate of total protein synthesis. Synthesis of r-proteins constitutes one third of total cellular protein synthesis 2-4 h after refeeding and the absolute rate of r-protein synthesis is approximately three-times greater than in exponentially growing cells. The synthesis of the individual r-proteins is coordinately regulated during a nutritional shift-up, and de novo synthesized r-proteins are stable. Addition of actinomycin D prevents the increase in the rate of r-protein synthesis. The rates of synthesis of rRNA and r-protein increase in concert, implying coordinate regulation. Furthermore, a comparison of the observed accumulation of r-proteins with the predicted accumulation based on the accumulation of rRNA suggests that rRNA and r-protein are synthesized in a stoichiometrically balanced way during the entire refeeding period.

Methylation of ribosomal RNA genes in the macronucleus of Tetrahymena thermophila

We have investigated the occurrence of methylated adenine residues in the macronuclear ribosomal RNA genes of Tetrahymena thermophila. It has been shown previously that macronuclear DNA, including the palindromic ribosomal RNA genes (rDNA), of Tetrahymena thermophila contains the modified base N-6-methyladenine, but no 5-methylcytosine. Purified rDNA was digested with restriction enzymes Sau 3AI, MboI and DpnI to map the positions and levels of N-6-methyladenine in the sequence 5' GATC 3'. A specific pattern of doubly methylated GATC sequences was found; hemimethylated sites were not detected. The patterns and levels of methylation of these sites did not change significantly in different physiological states. A molecular form of the rDNA found in the newly developing macronucleus and for several generations following the sexual process, conjugation, contained no detectably methylated GATC sites. However, both the bulk macronuclear DNA and palindromic rDNA from the same macronuclei were methylated. Possible roles for N-6-methyladenine in macronuclear DNA are discussed in light of these findings.

Complex endonucleolytic cleavage pattern during early events in the processing of pre-rRNA in the lower eukaryote, Tetrahymena thermophila

We have analysed nuclear RNA from T. thermophila by RNA transfer hybridization using cloned rDNA fragments. A very high number of in vivo intermediates and by-products of rRNA processing were identified. These include putative intermediates of the splicing process and alternative products resulting from temporal variability in various endonucleolytic cleavages. In addition, four small RNA species including only transcribed spacer sequences were detected. These are (1) the IVS RNA (approximately 400 bases), the by-product of the splicing process, (2) a fragment from the internal transcribed spacer (approximately 360 bases), possibly resulting from 3'-end processing of pre-17S rRNA, (3) a fragment comprising most or all of the external transcribed spacer (approximately 600 bases) obviously representing the major by-product of 5'-end processing, and, in addition, (4) a small fragment from the initiation region (approximately 230 bases) which might be a product of premature transcription termination.

Fate of an intervening sequence ribonucleic acid: excision and cyclization of the Tetrahymena ribosomal ribonucleic acid intervening sequence in vivo

In previous studies of RNA splicing in vitro, we have shown that the intervening sequence (IVS) of the Tetrahymena rRNA precursor is excised as a unique linear RNA molecule and subsequently cyclized. In the present work, we have investigated the occurrence and stability of these RNA species in vivo. RNA was separated by gel electrophoresis, transferred to diazotized paper, and hybridized with 32P-labeled DNA probes. RNA molecules containing the IVS were found to reside within the nucleus and not in the cytoplasm. The species found in nucleus include both the linear and circular forms of the excised IVS RNA, as well as the unspliced precursor. On the basis of quantitation of the hybridization, the half-lives of the IVS-containing pre-rRNA and the excised IVS RNA in rapidly growing cells were estimated as 2 and 6 s, respectively. We conclude that splicing is not a rate-limiting step in rRNA maturation and that the IVS RNA is quickly degraded after its excision. When the deproteinized nuclear RNA was incubated at 37 degrees C in a Mg2+-containing solution, a substantial portion of the linear IVS RNA was converted to the circular form. Autocyclization, previously characterized with IVS RNA produced by splicing in vitro, is therefore also a property of IVS RNA produced in vivo.

Different nucleosome spacing in transcribed and non-transcribed regions of the ribosomal RNA gene in Tetrahymena thermophila

The chromatin structure of the palindromic macronuclear ribosomal RNA genes of Tetrahymena thermophila was probed with micrococcal nuclease. Independent of the state of transcriptional activity, the transcribed region had a shorter nucleosome repeat (184 +/- 3 base pairs) than the non-transcribed central spacer or bulk chromatin (both 200 base pairs). The transcribed region displayed an increased sensitivity to micrococcal nuclease in rapidly growing cells, which suggested an altered chromatin structure during transcription. At early stages of nuclease digestion, the central spacer appeared to be in a highly structured nucleosomal array. Based on the differences in nucleosome repeat distance and sensitivity to nuclease, we conclude that quite different chromatin structures are maintained in two adjacent regions of the Tetrahymena ribosomal RNA gene. The DNA of the non-transcribed terminal spacer was found to contain sequences which are highly susceptible to micrococcal nuclease, precluding any conclusions about nucleosome structure in this region.

Transcribed and non-transcribed regions of Tetrahymena ribosomal gene chromatin have different accessibilities to micrococcal nuclease

DNA renaturation kinetics was used to examine the relative accessibility of various regions of the Tetrahymena ribosomal RNA gene (rDNA) chromatin to micrococcal nuclease. In nuclei from cells active in rRNA transcription, the transcribed region of the rDNA chromatin was as much as 5-fold more accessible than the average of the total chromatin. As few as 20% inactive genes in the population could have accounted for all of the hybridization, so the transcribed region of the active units may be totally unprotected from nuclease degradation. The terminal non-transcribed spacer downstream from the transcription unit was also preferentially digested, but to a smaller degree. The central non-transcribed spacer was degraded to the same extent as total chromatin after a high degree of nuclease digestion. In nuclei from starved cells, which have 96% reduced rRNA transcription, the transcribed and terminal spacer regions of the rDNA were again more accessible than the total chromatin from the same nuclei, but the difference did not exceed 2-fold. We conclude that transcriptional activation is accompanied by major changes in the structure of the ribosomal gene chromatin, and that the extent and/or type of structural alteration differs in each functionally defined region of the rDNA.

Replication of the extrachromosomal ribosomal RNA genes of Tetrahymena thermophilia

Cultures of Tetrahymena thermophila were deprived of nutrients and later refed with enriched medium to obtain partial synchrony of DNA replication. Preferential replication of the extrachromosomal, macronuclear ribosomal RNA genes (rDNA) was found to occur at 40-80 min after refeeding. The rDNA accounted for one half of the label incorporated into cellular DNA during this period. Electron microscopy of the purified rDNA showed 1% replicative intermediates. Their structure was that expected for bidirectional replication of the linear rDNA from an origin or origins located in the central nontranscribed region of the palindromic molecule. Similar forms had previously been observed for the rDNA of a related species, Tetrahymena pyriformis. The electron microscopic data was consistent with an origin of replication located approximatley 600 base pairs from the center of the rDNA of T. thermophila, in contrast to a more central location in the rDNA of T. pyriformis. One implication of an off-center origin of replication is that there are two such sequences per palindromic molecule.

In vitro splicing of the ribosomal RNA precursor in nuclei of Tetrahymena

The macronuclear rRNA genes of Tetrahymena thermophila contain a 0.4 kb intervening sequence. In this paper we present evidence that the excision of the intervening sequence from pre-rRNA occurs in vitro in isolated T. thermophila nuclei. The transcription-processing system includes alpha-amanitin to inhibit non-rRNA synthesis and aurintricarboxylic acid to inhibit endogenous nucleases. A discrete 0.4 kb RNA comprises up to 6% of the RNA synthesized in this system. Southern hybridization with restriction fragments of the rDNA (rRNA genes) shows that the 0.4 kb RNA contains the intervening sequence. The size of the 0.4 kb RNA, 410-425 nucleotides, is the size predicted if the entire intervening sequence were excised as a single linear molecule. The 0.4 kb RNA accumulates post-transcriptionally and appears to be stable in vitro. T. pigmentosa strain 6UM, whose rDNA has an intervening sequence of the same size and location as that of T. thermophila, also produces a 0.4 kb RNA in vitro; T. pigmentosa strain 8ALP, with not rDNA intervening sequence, produces no such RNA. The measurement of the accumulation of the excised intervening sequence is a convenient assay for the pre-rRNA splicing activity and a means for characterizing some of the details of the reaction. The resistance of the splicing acticity to concentrations of aurintricarboxylic acid that inhibit other endogenous nucleases should be useful in assaying the splicing enzyme during purification.