Prokaryotic mechanisms in eukaryotes?

Prokaryotic mechanisms in eukaryotes: experimental data and speculations

Surprising experimental data recently provided could indicate ancestral genes common to mammals and bacteria. The detection of prokaryotic structures and/or mechanisms even in higher eukaryotes shows the extreme conservation of gene structures throughout evolution. The occurrence of common structures in pro- and eukaryotes is in good agreement with the new view concerning the early steps of cellular evolution. Because of the relative paucity of research in this area, further prokaryotic features of transcription and translation process may also be evolutionarily conserved in eukaryotes.

Tandemly repeated exons encode 81-base repeats in multiple, developmentally regulated Schistosoma mansoni transcripts

The adult Schistosoma mansoni cDNA clone 10-3 encodes an antigen that is recognized by sera from infected humans. We characterized multiple developmentally regulated transcripts homologous to the 10-3 cDNA and portions of the complex genomic loci encoding those transcripts. Transcripts of approximately 950, 870, and 780 nucleotides were expressed in adults, whereas only the 780-nucleotide transcript was observed in the larval stage. These transcripts were highly similar, containing variable numbers of identical direct tandem repeats of 81 bases. Although the sequence of the repeating elements and sequences 3' to them were identical in all the transcripts, sequences 5' of the repeating elements exhibited variations, including a 27-base insertion, alternative start sites for transcription, and alternate 5' exon usage. These transcripts appeared to be derived in part by the developmentally controlled alternative splicing of small exons and the use of alternative transcription initiation sites from the one or two complex loci of at least 40 kilobase pairs. Each 81-base repeat in the transcripts was encoded by three dispersed 27-base-pair exons. These 27-base-pair exons were contained within highly conserved, reiterated 3-kilobase-pair genomic tandem arrays.

Tandemly repeated exons encode 81-base repeats in multiple, developmentally regulated Schistosoma mansoni transcripts

The adult Schistosoma mansoni cDNA clone 10-3 encodes an antigen that is recognized by sera from infected humans. We characterized multiple developmentally regulated transcripts homologous to the 10-3 cDNA and portions of the complex genomic loci encoding those transcripts. Transcripts of approximately 950, 870, and 780 nucleotides were expressed in adults, whereas only the 780-nucleotide transcript was observed in the larval stage. These transcripts were highly similar, containing variable numbers of identical direct tandem repeats of 81 bases. Although the sequence of the repeating elements and sequences 3' to them were identical in all the transcripts, sequences 5' of the repeating elements exhibited variations, including a 27-base insertion, alternative start sites for transcription, and alternate 5' exon usage. These transcripts appeared to be derived in part by the developmentally controlled alternative splicing of small exons and the use of alternative transcription initiation sites from the one or two complex loci of at least 40 kilobase pairs. Each 81-base repeat in the transcripts was encoded by three dispersed 27-base-pair exons. These 27-base-pair exons were contained within highly conserved, reiterated 3-kilobase-pair genomic tandem arrays.

RNA polymerase II interacts with the promoter region of the noninduced hsp70 gene in Drosophila melanogaster cells

By using a protein-DNA cross-linking method (D. S. Gilmour and J. T. Lis, Mol. Cell. Biol. 5:2009-2018, 1985), we examined the in vivo distribution of RNA polymerase II on the hsp70 heat shock gene in Drosophila melanogaster Schneider line 2 cells. In heat shock-induced cells, a high level of RNA polymerase II was detected on the entire gene, while in noninduced cells, the RNA polymerase II was confined to the 5' end of the hsp70 gene, predominantly between nucleotides -12 and +65 relative to the start of transcription. This association of RNA polymerase II was apparent whether the cross-linking was performed by a 10-min UV irradiation of chilled cells with mercury vapor lamps or by a 40-microsecond irradiation of cells with a high-energy xenon flash lamp. We hypothesize that RNA polymerase II has access to, and a high affinity for, the promoter region of this gene before induction, and this poised RNA polymerase II may be critical in the mechanism of transcription activation.

Transcription terminator-like element within a Saccharomyces cerevisiae promoter region

We analyzed a cloned fragment of the yeast URA3 promoter region that contains a sequence of DNA capable of functioning as a highly efficient transcription terminator. BAL 31 deletions have shown the signal for the transcription termination activity is less than or equal to 110 base pairs and resides between bases 45 and 155 upstream of the URA3 primary ATG codon at base 227. In our in vivo assay system, the DNA fragment is able to terminate transcripts very efficiently in either orientation. The terminated transcripts bind to oligodeoxythymidylate cellulose columns and promote the synthesis of full-length cDNAs, suggesting that the transcripts are polyadenylated. The 110-base-pair region contains no sequence resembling terminator consensus sequences described by Zaret and Sherman (K.S. Zaret and F. Sherman, Cell, 28:563-573, 1982) or Henikoff and Cohen (S. Henikoff and E.H. Cohen, Mol. Cell. Biol., 4:1515-1520, 1984). We discuss the possible physiological relevance of this sequence to bona fide termination of transcription and to URA3 regulation in Saccharomyces cerevisiae.

RNA polymerase II interacts with the promoter region of the noninduced hsp70 gene in Drosophila melanogaster cells

By using a protein-DNA cross-linking method (D. S. Gilmour and J. T. Lis, Mol. Cell. Biol. 5:2009-2018, 1985), we examined the in vivo distribution of RNA polymerase II on the hsp70 heat shock gene in Drosophila melanogaster Schneider line 2 cells. In heat shock-induced cells, a high level of RNA polymerase II was detected on the entire gene, while in noninduced cells, the RNA polymerase II was confined to the 5' end of the hsp70 gene, predominantly between nucleotides -12 and +65 relative to the start of transcription. This association of RNA polymerase II was apparent whether the cross-linking was performed by a 10-min UV irradiation of chilled cells with mercury vapor lamps or by a 40-microsecond irradiation of cells with a high-energy xenon flash lamp. We hypothesize that RNA polymerase II has access to, and a high affinity for, the promoter region of this gene before induction, and this poised RNA polymerase II may be critical in the mechanism of transcription activation.

Cancer: involvement of replicative origins?

The assumption is made that movable genetic elements related to cancer are replicons and/or replicative origins. Some evidence is provided that certain mobile Alu-origins may represent candidates for precursors of chromosomal insertions. They could incorporate and interact with "fixed" chromosomal origins converting them to "procaryotic" ones. In other words, cancer is considered the result of a short and compact "re-evolution" from eucaryotic to "procaryotic" replication units.

Transcription terminator-like element within a Saccharomyces cerevisiae promoter region

We analyzed a cloned fragment of the yeast URA3 promoter region that contains a sequence of DNA capable of functioning as a highly efficient transcription terminator. BAL 31 deletions have shown the signal for the transcription termination activity is less than or equal to 110 base pairs and resides between bases 45 and 155 upstream of the URA3 primary ATG codon at base 227. In our in vivo assay system, the DNA fragment is able to terminate transcripts very efficiently in either orientation. The terminated transcripts bind to oligodeoxythymidylate cellulose columns and promote the synthesis of full-length cDNAs, suggesting that the transcripts are polyadenylated. The 110-base-pair region contains no sequence resembling terminator consensus sequences described by Zaret and Sherman (K.S. Zaret and F. Sherman, Cell, 28:563-573, 1982) or Henikoff and Cohen (S. Henikoff and E.H. Cohen, Mol. Cell. Biol., 4:1515-1520, 1984). We discuss the possible physiological relevance of this sequence to bona fide termination of transcription and to URA3 regulation in Saccharomyces cerevisiae.

Attenuation may regulate gene expression in animal viruses and cells

In eukaryotes, an abundant population of promoter-proximal RNA chains have been observed and studied, mainly in whole nuclear RNA, in denovirus type 2, and in SV40. On the basis of these results it has been suggested that a premature termination process resembling attenuation in prokaryotes occurs in eukaryotes. Moreover, these studies have shown that the adenosine analog 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole (DRB) enhances premature termination, but its mode of action is not understood. The determination of the nucleotide sequences of SV40 and other viruses and cellular genes provide means for elucidating the nucleotide sequences involved in the attenuation mechanism. A model has recently been described in which attenuation and mRNA modulation in a feedback control system quantitatively regulate SV40 gene expression. The suggested mechanism described in this model opens up approaches to the investigation of attenuation and mRNA modulation as a possible mechanism whereby eukaryotes may regulate transcription in a variety of different circumstances.

Nucleotide sequence of the 3' terminal region of the LEU2 gene from Saccharomyces cerevisiae

The 3' terminal region from the LEU2 gene of yeast has been sequenced. Two open reading frames (ORF) have been identified, one of which constitutes the 3' terminus of beta-isopropylmalate dehydrogenase, the product of the LEU2 gene. A noncoding spacer region located between the ORFs contains two consensus-type transcriptional terminators. The terminator-like sequences are oriented in opposing directions on opposite DNA strands. The noncoding spacer region may represent a single terminator for the LEU2 gene or two separate terminators involved in blocking convergent transcription from an as yet unidentified yeast gene.

Specific changes in lactate levels, lactate dehydrogenase patterns and cytochrome b559 in Dictyostelium discoideum caused by queuine

Higher eukaryotes contain tRNA transglycosylases that incorporate the guanine derivative queuine from the nutritional environment into specific tRNAs by exchange with guanine at position 34. Alterations in the queuosine content of specific tRNAs are suggested to be involved in regulatory mechanisms of major routes of metabolism during differentiation. Dictyostelium discoideum has been applied as a model to investigate the function of queuine or queuine-containing tRNAs. Axenic strains are supplied with queuine by peptone, but they grow equally well in a defined queuine-free medium. Queuine-lacking amoebae, starved in suspension culture for 24 h, lose their ability to differentiate into stalk cells and spores, whereas amoebae sufficiently supplied with queuine will overcome this metabolic stress and undergo further development when plated on agar. The results presented here show that D(-)-lactate occurs in the slime mould in millimolar amounts and that its level is remarkably decreased in queuine-lacking cells after 24 h of starvation in suspension culture. On isoelectric-focusing polyacrylamide gels, nine different forms of NAD-dependent D(-)-lactate dehydrogenase can be separated from extracts of vegetative cells, and six forms from extracts of the starved cells. Under queuine limitation, one form is missing in the starved cells. Low amounts of L(+)-lactate are usually found in vegetative amoebae but significantly less in queuine-lacking cells. Five forms of NAD-dependent L(+)-lactate dehydrogenase are detectable in extracts from vegetative, queuine-treated cells, and slight alterations occur in queuine-deficient amoebae. In the starved cells only one form of L(+)-lactate dehydrogenase is found, irrespective of the supply of queuine to the cells. A cytochrome of type b with an absorption maximum at 559 nm accumulates during starvation only in queuine-lacking cells; it might be a component of an NAD-independent lactic acid oxidoreductase as is cytochrome b 557 in yeast and be responsible for the reduced level of lactate in cells lacking queuine in tRNA.

Role of an upstream regulatory element in leucine repression of the Saccharomyces cerevisiae leu2 gene

The expression of a number of eukaryotic genes has been shown to involve at least two sequences located upstream of the actual transcription unit: one of these sequences, centred on a widely conserved TATAAT sequence, is thought to be involved in determining the precise site of initiation of transcription; the other has a gene-specific sequence, can function at a variable distance upstream of the initiation site, and is involved in the regulation of transcription. By constructing beta-galactosidase gene fusions, to facilitate measuring gene expression in vivo, we have now defined a cis-acting regulatory element of the Saccharomyces cerevisiae leu2 gene. This element is located within a 280 base pair (bp) fragment which occurs 125 bp upstream of the leu2 translation initiation codon and which contains a short G + C-rich palindromic sequence. A fragment of the Escherichia coli transposable element Tn9 which contains a similar palindromic sequence can functionally replace the natural leu2 regulatory element. Our results are contrary to previous speculations that the leu2 gene is regulated by an attenuation mechanism.