Transcription and sequence studies of a 4.3-kbp fragment from a ds-DNA eukaryotic algal virus.

A 4.3-kbp portion of the genome from the Chlorella virus, PBCV-1, has been cloned and sequenced. Minimally, five open reading frames (ORFs) were identified on this fragment. Transcriptional analysis indicates that each ORF encodes complex patterns of RNA. The total length of transcribed RNA exceeds that of the ORF indicating either post-transcriptional modification or multiple transcriptional start/stop sites. The sequence TTTTTNT, previously described as the transcriptional stop site for the early genes of vaccinia virus, is also found downstream of each of our ORFs. The regions 5' to each ORF were very A + T-rich (approx 80%) but distinct promoter sequences were not unambiguously identified.

The chloroplast genome of an exsymbiotic Chlorella-like green alga.

Chloroplast DNA was isolated and cloned from Chlorella, strain N1a, exsymbiotic with Paramecium bursaria. BamHI, SalI, KpnI and Xho I restriction fragments of the DNA were assembled into a circular map. The genome consists of approximately 120 kbp of DNA, has a G/C content of 38%, and contains only a single copy of the rRNA cistron. The rRNA cistron is small, 5000-8000 bp, and the 16S and 23S gene are separated by less than 2000 bp.

5-Azacytidine-resistant mutants of Chlorella virus IL-3A.

Many dsDNA-containing viruses which infect the unicellular, eukaryotic Chlorella-like green alga strain NC64A encode for DNA methyltransferases and DNA site-specific (restriction) endonucleases. We have hypothesized that these endonucleases help degrade host DNA permitting deoxynucleotides to recycle into virus DNA. This hypothesis was tested by isolating deletion mutants of Chlorella virus IL-3A lacking functional genes for the cytosine methyltransferase M.CviJI and the cognate site-specific endonuclease CviJI. The growth and burst sizes of the mutants and parent virus were identical. Also host nuclear and chloroplast DNAs disappeared from infected cells at the same rates. Thus M.CviJI and CviJI activities are not required for IL-3A replication and CviJI activity is not essential for host DNA degradation.

The mitochondrial genome of an exsymbiotic Chlorella-like green alga.

Mitochondrial (mt) DNA from the unicellular, exsymbiotic Chlorella-like green alga, strain Nla was isolated and cloned. The mtDNA has a buoyant density of 1.692 g/ml in CsCl and an apparent G/C base composition of 32.5%. The genome contains approximately 76 kbp of DNA based on restriction fragment summation and electron microscopic measurements. A map of restriction endonuclease sites using Sst I, Bam I, Sal I and Xho I was generated. The genome maps as a circular molecule and appears as such under the electron microscope. Eight genes were assigned to the map by hybridization to specific restriction fragments using heterologous mt-encoded specific probes. These include the genes for subunits 6, 9, and alpha of the F0-F1 ATPase complex, the large and small subunit rRNAs, cytochrome oxidase subunits I and II, and apocytochrome b.

Characterization of viruses infecting a eukaryotic Chlorella-like green alga.

Nineteen plaque-forming viruses of the unicellular, eukaryotic Chlorella-like green alga, strain NC64A, were isolated from various geographic regions in the United States and characterized. Like the previously described virus, PBCV-1, all of the new viruses were large polyhedrons, sensitive to chloroform, and contained large dsDNA genomes of ca. 300 kbp. All of the viral DNAs contained 5-methyldeoxycytidine which varied from 0.1 to 47% of the deoxycytidine. In addition, 10 of the viral DNAs contained N6-methyldeoxyadenosine which varied from 8.1 to 37% of the deoxyadenosine. These viruses, along with 11 previously described viruses which replicate in the same Chlorella host, were grouped into 11 classes based on at least one of the following properties: plaque size, reaction with PBCV-1 antiserum, or the nature and abundance of methylated bases in their genomic DNA.

Infection of a Chlorella-like alga with the virus PBCV-1: transcriptional studies.

Infection of the unicellular, eukaryotic Chlorella-like green alga NC64A by the large dsDNA containing virus PBCV-1 immediately reduced host RNA synthesis. Chloroplast rRNAs, but not cytosolic rRNAs, were degraded following viral infection. Northern blot analysis utilizing four cloned fragments of PBCV-1 DNA as probes, which represent about 12% of the viral genome, revealed several properties of PBCV-1 transcription: A few viral transcripts were detected within 5 min after infection. Each PBCV-1 DNA clone hybridized to both early and late transcripts which implies that early and late genes are dispersed throughout the viral genome. The transition from early to late transcription occurred between 40 and 60 min after infection coincident with the onset of viral DNA synthesis. Three of the four DNA clones hybridized to transcripts which additively were larger than the corresponding DNA probe. This could reflect RNA processing, presence of overlapping genes, or transcription from both DNA strands. A few, but not all, early transcripts were synthesized in the presence of cycloheximide. This suggests that the virus either carries in its own RNA polymerase or uses a host RNA polymerase for very early viral transcription and that synthesis of additional, later transcripts depends on translation of an early gene product(s).

DNA methylation of viruses infecting a eukaryotic Chlorella-like green alga.

The genomic DNAs of the eukaryotic Chlorella-like green alga, strain NC64A, and eleven of its viruses all contain significant levels of 5-methyldeoxycytidine. In addition, the host DNA as well as six of the viral DNAs also contain N6-methyldeoxyadenosine. At least some of the methylated bases in the host reside in different base sequences than the methylated bases in the viruses as shown by differential susceptibility to restriction endonuclease enzymes. This suggests that the viruses encode for DNA methyltransferases with sequence specificities different from that of the host enzyme.

Nucleotide sequence of F(0)-ATPase proteolipid (subunit 9) gene of maize mitochondria.

The F(0)-ATPase proteolipid, also referred to as subunit 9 or the dicyclohexylcarbodiimide-binding protein, is encoded by a mitochondrial gene in maize that we have designated atp 9. The clone containing atp 9 was selected for investigation from a mitochondrial DNA library because of its abundant transcript in total maize mitochondrial RNA preparations. Sequence analysis of the clone revealed an open reading frame that was readily identified by its nucleotide homology with the ATPase subunit 9 gene of yeast. As deduced from the nucleotide sequence, the maize ATPase subunit 9 protein contains 74 amino acids with a molecular weight of 7368. Substantial amino acid sequence homology is conserved among maize, yeast, bovine, and Neurospora mitochondrial ATPase subunit 9 proteins, regardless of whether the gene is nuclearly encoded (bovine and Neurospora) or mitochondrially encoded (yeast and maize). RNA transfer blot analysis indicated that the gene sequence is actively transcribed, producing an initial transcript that is large and extensively processed.

Lytic viruses infecting a Chlorella-like alga.

A number of viruses which form plaques on the unicellular, eukaryotic, Chlorella-like green alga, strain NC64A, were isolated from fresh water ponds and rivers in Illinois, North Carolina, and South Carolina. The viruses were large polyhedrons (160 to 190 nm in diameter) and contained dsDNA genomes of ca. 300 kbp. All of the viral DNAs hybridized with DNA from the previously described PBCV-1 virus. However, the viruses, even many of those isolated from the same water sample, could be distinguished from one another by DNA restriction endonuclease digestion. The viruses, including PBCV-1, were grouped into five classes by their resistance to certain DNA restriction endonucleases. Presumably the DNAs in the five classes contain different types or amounts of modified bases.

Ribonucleic Acid and protein metabolism in pea epicotyls : I. The aging process.

Aging of actively growing, etiolated pea Pisum sativum L. var Alaska plants was initiated by removing the plumules of plants in the third internode stage, and applying lanolin to the cut apices of otherwise intact plants. During the subsequent 4-day aging period, several degenerative events occurred in this apical 10-millimeter region. Ribosomal RNA and messenger RNA contents declined, polyribosomes disaggregated, and the protein synthesizing capacity of the polysomes decreased.Two-dimensional, silver-stained protein patterns revealed that aging altered the relative amounts of specific cellular proteins accumulated in vivo. In addition, polypeptide patterns generated by cell-free translation of total and polysomal RNA, isolated from unaged and aged tissues, showed major modifications. More than 200 spots could be resolved by two-dimensional gel fluorography of translation products using RNA from fresh tissues. Of these 200 spots, about eight appeared or increased when total RNA from aged tissue was used, and about 58 disappeared or declined. When polysomal RNA from aged tissue was used as template, about 12 spots appeared or increased, whereas about 64 disappeared or decreased. In general, the products which increased after aging were lower molecular weight and those that decreased were higher molecular weight.

Ribonucleic Acid and Protein Metabolism in Pea Epicotyls : II. Response to Wounding in Aged Tissue.

Aged pea Pisum sativum L. var Alaska epicotyl tissue was wounded by excising the apical 10 or 20 millimeters and incubating the excised segments upright in buffer. Wounding induced a very rapid formation of polysomes which was accompanied by minor increases in ribosomes, mRNA, and poly(A) and by a doubling of the in vivo protein synthesizing capacity. This increase in protein synthesis in vivo was matched by a similar increase in polypeptide synthesis in vitro in wheat germ reactions primed by polysomes. However, in vitro reactions primed by total and polysomal RNA from wounded tissue were affected much less.Two-dimensional gel patterns of silver-stained proteins accumulated in vivo were almost unchanged, even after 6 hours of wounding, since only two spots decreased in intensity and none increased. In contrast, two-dimensional gel fluorographs of polypeptides generated in vitro by both total RNA and polysomal RNA showed numerous changes within 3 hours of wounding. Of the more than 200 spots visualized by fluorography, 17 decreased and 26 increased when total RNA from wounded tissue was used; 15 decreased and 10 increased when polysomal RNA was used. Those polypeptides that decreased after wounding were generally of lower molecular weight; those which increased were of higher molecular weight.Although wounding must be affecting transcription insofar as different mRNAs must be present to encode different polypeptides, its major effect appears to be on translation, presumably through formation of ribosomes with greater translational efficiency.