Homologous proteins encoded by yeast mitochondrial introns and by a group of RNA viruses from plants

Autonomously replicating RNA in mitochondria of maize plants with S-type cytoplasm

Mitochondria isolated from maize plants with S-type male-sterile cytoplasms are capable of synthesizing four species of RNA at concentrations of actinomycin D that eliminate all DNA-directed RNA synthesis. No RNA synthesis occurs under the same conditions with mitochondria from plants possessing normal (N) cytoplasm or with other subcellular fractions from plants with S cytoplasm. The actinomycin D-resistant RNA synthesis occurs within the mitochondria since the labeling of these species is unaffected by inclusion of RNase in the incubation medium and since they become completely sensitive to RNase upon lysis of the mitochondria with low concentrations of Triton X-100. Two of the actinomycin D-resistant products are double stranded. These are 2850 and 900 base pairs in length, whereas the remaining two are 2150 and 850 bases. The synthesis of all four RNAs occurs in at least five different accessions of S cytoplasm, suggesting it is a general feature of S mitochondria. The double-stranded RNAs show homology to single-stranded S mitochondrial RNA but not to N mitochondrial RNA. Our observations indicate that the replication of these RNAs occurs independently of mtDNA and that they thus represent a novel type of inheritable element in organelles, an RNA plasmid.

The reverse transcriptase encoded by ai1 intron is active in trans in the retro-deletion of yeast mitochondrial introns

Genomic mitochondrial intron deletion occurs frequently during the reversion of mitochondrial intronic mutations in Saccharomyces cerevisiae. The multiplicity as well as the apparent polarity of intron deletion led us to propose the implication of reverse transcription in this process. The two first introns of the COX1 (cytochrome oxidase I) gene, ai1 and ai2, are known to be homologous to viral reverse transcriptase and to encode such activity. We have tested the involvement of these introns in the deletion process by constructing three isogenic strains. They contain the same reporter mutation in the second intron of the CYTb (cytochrome b) gene but differ from each other by the presence or the absence of the ai1 and/or ai2 introns in the other gene encoding the COX1 subunit. Only the strain lacking ai1 and ai2 introns is no more able to revert by intron deletion. The strain retaining only the ai1 intron was able to revert by intron deletion. We conclude that the reverse transcriptase activity, even when encoded by only ai1 intron, can act in trans in the intron deletion process, during the reversion of intronic mutations.

The P30 movement protein of tobacco mosaic virus is a single-strand nucleic acid binding protein

The P30 protein of tobacco mosaic virus (TMV) is required for cell to cell movement of viral RNA, which presumably occurs through plant intercellular connections, the plasmodesmata. The mechanism by which P30 mediates transfer of TMV RNA molecules through plasmodesmata channels is unknown. We have identified P30 as an RNA and single-stranded (ss) DNA binding protein. Binding of purified P30 to ss nucleic acids is strong, highly cooperative, and sequence nonspecific with a minimal binding site of 4-7 nucleotides per P30 monomer. In-frame deletions across P30 were used to localize the ss nucleic acid binding domain to within amino acid residues 65-86 of the protein. We propose that binding of P30 to TMV RNA creates an unfolded protein-RNA complex that functions as an intermediate in virus cell to cell movement through plasmodesmata.

Evolution of RNA genomes: does the high mutation rate necessitate high rate of evolution of viral proteins?

RNA genomes have been shown to mutate much more frequently than DNA genomes. It is generally assumed that this results in rapid evolution of RNA viral proteins. Here, an alternative hypothesis is proposed that close cooperation between positive-strand RNA viral proteins and those of the host cells required their coevolution, resulting in similar amino acid substitution rates. Constraints on compatibility with cellular proteins should determine, at any time, the covarion sets in RNA viral proteins. These ideas may be helpful in rationalizing the accumulating data on significant sequence similarities between proteins of positive-strand RNA viruses infecting evolutionarily distant hosts as well as between viral and cellular proteins.

A protein required for splicing group I introns in Neurospora mitochondria is mitochondrial tyrosyl-tRNA synthetase or a derivative thereof

The nuclear cyt-18 mutants of Neurospora crassa are defective in splicing a number of group I introns in mitochondria. Here, cloning and sequencing of the cyt-18 gene show that it contains an open reading frame having significant homology to bacterial tyrosyl-tRNA synthetases. Biochemical and genetic experiments lead to the conclusions that the cyt-18 gene encodes mitochondrial tyrosyl-tRNA synthetase, that mutations in this gene inhibit splicing directly, and that mitochondrial tyrosyl-tRNA synthetase or a derivative of this protein is related to the soluble activity that functions in splicing the mitochondrial large rRNA intron and possibly other group I introns. Analysis of partial revertants provides direct evidence that the cyt-18 gene encodes a protein or proteins with two activities, splicing and aminoacylation, that can be partially separated by mutation. Our findings may be relevant to the evolution of introns and splicing mechanisms in eukaryotes.

Relationship of viroids and certain other plant pathogenic nucleic acids to group I and II introns

The nucleotide sequences of viroids contain features believed to be essential for the splicing of group I introns. Common sequence elements include a 16-nucleotide consensus sequence and three pairs of short sequences arranged in the same sequential order in both types of RNAs. The calculated probability of finding sequences resembling the 16-nucleotide consensus sequence in random nucleotide chains showed that at low fidelity (up to 5 mismatched nucleotides), the number of such sequences in viroids, plant viral satellite RNAs, plant viral RNAs and one plant viral DNA, group I introns and flanking exons does not significantly differ from the number expected at random. As the degree of fidelity is increased, the number in both introns and viroids, but not in exons or the other plant pathogens examined, greatly exceeds that expected in random chains. These findings suggest that viroids may have evolved from group I introns and/or that processing of viroid oligomers to monomers may have structural requirements similar to those of group I introns. The nucleotide sequences of viroids do not show close homology with two conserved regions of group II introns, the 14-base pair consensus region and the 5' terminal segment. However, close homology does exist between the conserved sequence of the 3' terminal segment of group II introns and viroids thus suggesting a possible evolutionary or functional relationship.

Circular plasmid DNAs from mitochondria of Sorghum bicolor

Agarose gel electrophoresis of mitochondrial DNA (mtDNA) from the IS1112C male-sterile cytoplasm of Sorghum bicolor (S. bicolor) revealed plasmid-like DNAs additional to the linear N1 and N2 molecules. Mitochondrial plasmids were separated from the principal mitochondrial genome and used in the construction of molecular clones. Clones with EcoRI inserts of 1.7 and 2.3 kb were recovered. Hybridization of these clones to Southern blots of unrestricted and EcoRI-digested IS1112C mitochondrial plasmids indicated the cloned inserts were complete or nearly-complete copies of minicircular DNA molecules. These clones were used to probe Southern blots of mitochondrial genomes from six cytoplasmic male-sterile (CMS) and five male-fertile (MF) lines of S. bicolor, as well as Southern blots of IS1112C chloroplast, kafir chloroplast, IS1112C nuclear, and kafir nuclear genomes. The 2.3 and 1.7 kb plasmids had a very limited distribution among the sorghum entries we examined. We found no evidence for integrated copies of these sequences in any of the mitochondrial, chloroplast, or nuclear genomes probed in this study. However, the 2.3 kb sorghum minicircle did hybridize to the 1.94 kb minicircle from maize mitochondria. Hybridization of the 1.7 and 2.3 kb clones to IS111L2C mitochondrial RNA reveal a transcript of 1.1 kb from the 1.7 kb minicircle and transcripts of 1.9 and 1.4 kb from the 2.3 kb molecule.

Nucleotide sequence of the satellite of peanut stunt virus reveals structural homologies with viroids and certain nuclear and mitochondrial introns

Peanut stunt virus-associated RNA 5 (PARNA 5), the satellite of a plant cucumovirus, is a linear RNA of 393 nucleotides with a 5' cap and a 3' hydroxyl group. Determination of its nucleotide sequence has revealed two consecutive open reading frames that together extend most of its length. Sequences at the 5' and 3' ends are homologous with those of the satellite of the related cucumber mosaic virus, and the double-stranded forms of both satellites contain an unpaired guanosine at the 3' end of the minus strand. However, little other homology exists between the two satellites. In contrast, PARNA 5 has several regions of 90% sequence homology with various plant viroids, including sequences of the conserved central region of most viroids. Such homologies suggest a common origin with viroids coupled with specific adaptation as a linear RNA. The presence within PARNA 5 of conserved intron sequences essential to proper RNA processing suggests a possible origin from plant introns and/or involvement of such sequences in the processing of PARNA 5 multimers to monomers at some stage of replication.

The DNA sequence and genetic organization of a Neurospora mitochondrial plasmid suggest a relationship to introns and mobile elements

We have determined the complete 3581 bp sequence of the mitochondrial plasmid from Neurospora crassa strain Mauriceville-1c. The plasmid contains a long open reading frame that is expressed in its major transcript and could encode a hydrophilic protein of 710 amino acids. Two characteristics of the plasmid--codon usage and the presence of conserved sequence elements--suggest that it is related to Group I mtDNA introns. The major transcripts of the plasmid are approximately full-length, colinear RNAs that have heterogenous 5' ends and a single major 3' end. The major 5' and 3' ends are adjacent and slightly overlapping. The Mauriceville plasmid may belong to a class of genetic elements that were or are the progenitors of mtDNA introns.