RNA processing and expression of an intron-encoded protein in yeast mitochondria: role of a conserved dodecamer sequence

Maintenance and expression of the S. cerevisiae mitochondrial genome--from genetics to evolution and systems biology

As a legacy of their endosymbiotic eubacterial origin, mitochondria possess a residual genome, encoding only a few proteins and dependent on a variety of factors encoded by the nuclear genome for its maintenance and expression. As a facultative anaerobe with well understood genetics and molecular biology, Saccharomyces cerevisiae is the model system of choice for studying nucleo-mitochondrial genetic interactions. Maintenance of the mitochondrial genome is controlled by a set of nuclear-coded factors forming intricately interconnected circuits responsible for replication, recombination, repair and transmission to buds. Expression of the yeast mitochondrial genome is regulated mostly at the post-transcriptional level, and involves many general and gene-specific factors regulating splicing, RNA processing and stability and translation. A very interesting aspect of the yeast mitochondrial system is the relationship between genome maintenance and gene expression. Deletions of genes involved in many different aspects of mitochondrial gene expression, notably translation, result in an irreversible loss of functional mtDNA. The mitochondrial genetic system viewed from the systems biology perspective is therefore very fragile and lacks robustness compared to the remaining systems of the cell. This lack of robustness could be a legacy of the reductive evolution of the mitochondrial genome, but explanations involving selective advantages of increased evolvability have also been postulated.

Purification and characterization of an RNA dodecamer sequence binding protein from mitochondria of Saccharomyces cerevisiae

Saccharomyces cerevisiae mitochondrial mRNAs terminate at their 3' ends with a conserved dodecamer sequence, 5'-AAUAA(U/C)AUUCUU-3'. We have identified a nuclear-encoded protein (DBP) which specifically binds to the dodecamer sequence and have purified it to apparent homogeneity by RNA affinity chromatography. DBP consists of a single polypeptide of 55 kDa and binds to its RNA substrate with a 1:1 stoichiometry. Scatchard analysis determines that K(d) is 0.93 nM for the canonical dodecamer sequence (5'-AAUAAUAUUCUU-3') and 0.46 nM for the only naturally occurring variant (5'-AAUAACAUUCUU-3') unique to oli1 gene. Based on the studies using mutant oligonucleotides, DBP appears to recognize primarily the nucleotide sequence of an RNA rather than its potential secondary structure.

Effect of estrogens on IL-1beta promoter activity

It is well documented that steroid hormones modulate cytokine gene expression. In some tissues estrogens are known to suppress cytokine production while in other tissue types, cytokine expression is enhanced by the hormone. This study was conducted to investigate the regulatory mechanisms which underlie the modulation of the interleukin-1beta (IL-1beta) gene at the transcription level. To accomplish this, the macrophage cell line RAW264.7, which appeared insensitive to 17beta-estradiol (E2) treatment, was stably transfected with the human estrogen receptor (ER) and an IL-1beta promoter-CAT reporter construct. E2 markedly enhanced LPS-induced IL-1beta promoter-driven CAT activity in an E2 dose dependent manner. This responsiveness was estrogen specific since no synergism was observed between LPS and the sex steroids testosterone or progesterone while the estrogen analogue 17alpha-estradiol stimulated only at 10 to 100 times the amount required for 17beta-E2. Several antiestrogens, H1285, ICI 182 780, and tamoxifen inhibited the estrogen stimulated enhancement of IL-1beta promoter activity in a dose-dependent manner, indicating that this effect was indeed mediated through the ER in a ligand dependent manner. The estrogenic effect appeared to be indirect and time dependent since the addition of E2 was required hours prior to LPS stimulation; addition of E2 and LPS at the same time resulted in a greatly reduced estrogenic effect. The estrogen metabolites 17-epiestriol and 16-keto-17beta-E2 displayed an estrogenic response virtually indistinguishable from E2. 4-Hydroxyestradiol displayed activity only at 100-fold the concentration of E2 while 2-hydroxyestrone showed no activity at any of the concentrations tested. Overall the results demonstrate that E2 and some metabolites of E2 synergize with LPS to markedly enhance IL-1beta promoter activity through ER mediated processes.

The DExH box protein Suv3p is a component of a yeast mitochondrial 3'-to-5' exoribonuclease that suppresses group I intron toxicity

The yeast mitochondrial protein Suv3p is a putative NTP-dependent RNA helicase. Here we report that in cells lacking Suv3p, there is an approximately 50-fold increase in the excised form of the group I intron omega of the mitochondrial 31S rRNA gene. Surprisingly, little mature 21S rRNA accumulates in those cells; instead, unligated 21S rRNA exons appear. Intron overaccumulation could lead to spliced exon reopening via a reaction known to be catalyzed by group I introns in vitro. We also show that Suv3p is a functional component of a novel mitochondrial NTP-dependent 3'-to-5' exoribonuclease activity that can degrade group I intron RNAs. These findings account for group I intron overaccumulation in cells lacking Suv3p and define a novel function for putative RNA helicases in direct RNA degradation.

The suv3 nuclear gene product is required for the in vivo processing of the yeast mitochondrial 21s rRNA transcripts containing the r1 intron

We have constructed a yeast mitochondrial genome containing only one group-I intron, r1, from the 21s rRNA gene and introduced this genome into a strain bearing a disruption of the suv3 gene. The presence of the r1 intron alone causes a block in respiration, while the isogenic strain containing the intronless genome is respiratory competent. Northern analysis indicates that the functional suv3 protein is necessary for the yeast cell in order to process the r1-containing transcripts: in the absence of the suv3 protein the hybridization pattern of the excised r1 intron is altered and the amount of mature 21s rRNA is 50-fold lower. We suggest that the multifunctional suv3 protein, which displays motifs of ATP-dependent RNA helicases, is necessary for the in vivo pathway leading to formation of mature 21s rRNA from the transcripts containing the r1 intron in mitochondria of Saccharomyces cerevisiae.

Formation of the 3' end of yeast mitochondrial mRNAs occurs by site-specific cleavage two bases downstream of a conserved dodecamer sequence

Mitochondrial mRNAs in yeast arise by processing of polygenic primary transcripts at a conserved dodecamer sequence (5'-AAUAAPyAUUCUU-3'). Previous results indicated that processing at dodecamer sites interrupted the sequence implying that it functioned primarily as a signal for 3' end formation of mRNAs. We have determined the precise cleavage site for RNAs processed at the dodecamer sequences associated with the oli1 gene and the omega intron of the 21S rRNA gene. In both cases cleavage occurred two bases downstream of the site. Hydrolysis left the PO4 group attached to the 3' terminus of the cleavage products. These results demonstrate for the first time that mature mitochondrial mRNAs terminate with an intact dodecamer sequence. In light of the recent identification of a protein complex within mitochondria that binds to RNAs terminating with an intact dodecamer sequence, these results support the idea that the dodecamer sequence functions not only within pre-mRNAs as a processing site, but within mature mRNAs as well, possibly for the stabilization and/or translation.

Genetic approaches to the study of mitochondrial biogenesis in yeast

In contrast to most other organisms, the yeast Saccharomyces cerevisiae can survive without functional mitochondria. This ability has been exploited in genetic approaches to the study of mitochondrial biogenesis. In the last two decades, mitochondrial genetics have made major contributions to the identification of genes on the mitochondrial genome, the mapping of these genes and the establishment of structure-function relationships in the products they encode. In parallel, more than 200 complementation groups, corresponding to as many nuclear genes necessary for mitochondrial function or biogenesis have been described. Many of the latter are required for post-transcriptional events in mitochondrial gene expression, including the processing of mitochondrial pre-RNAs, the translation of mitochondrial mRNAs, or the assembly of mitochondrial translation products into the membrane. The aim of this review is to describe the genetic approaches used to unravel the intricacies of mitochondrial biogenesis and to summarize recent insights gained from their application.

Expression of the oxi1 and maturase-related RF1 genes in yeast mitochondria

Transcription of the yeast mitochondrial oxi1 gene (cytochrome oxidase subunit 2) is initiated at a variant non anucleotide sequence, TTAAAAGTA, located 54 bp upstream from the protein-coding gene. Transcriptional initiation at this site gives rise to a 2,500 nucleotide primary transcript containing both the oxi1 gene and the downstream maturase-related reading frame, RF1. Precise transcript mapping has revealed that the 3'-end of the mature oxi1 mRNA is generated by an endonucleolytic cleavage which takes place after the conserved dodecamer sequence, AAUAAUAUUCUU (End-of-Messenger signal), 75 nucleotides downstream from the oxi1 stop codon. Since the RF1 5'-terminal coding region overlaps the oxi1 3'-terminal coding sequence, cleavage at this motif truncates the RF1 message suggesting that the expression of the putative RF1 protein is controlled at the level of dodecamer processing.