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Rose AB, Broach JR. Propagation and expression of cloned genes in yeast: 2-microns circle-based vectors. Methods Enzymol 1990; 185:234-79. [PMID: 2199781 DOI: 10.1016/0076-6879(90)85024-i] [Citation(s) in RCA: 94] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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2
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A region internal to the coding sequences is essential for transcription of the yeast Ty-D15 element. Mol Cell Biol 1989. [PMID: 2550798 DOI: 10.1128/mcb.9.9.3667] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The major transcript of the yeast transposable element Ty1 has its 5' end in one delta and the 3' end in the opposite delta, the direct repeats of about 335 base pairs (bp) at each end of the element. The transcriptional initiation signals of the Ty-D15 element that give rise to this transcript were found to have a number of unusual characteristics. The 5' delta by itself, which contained the initiation site for Ty transcription, gave no detectable transcription. A region internal to the transcript in a translated part of the element and about 140 bp downstream of the 5' delta was essential for initiation of the major Ty transcript. This internal activating region (IAR) had several interesting properties. When the portion of the delta upstream of the initiation site was replaced with DNA fragments that did not by themselves act as promoters, initiation directed by the IAR still occurred at about the same position, 200 to 400 bp upstream of the IAR. If fragments containing the IAR were inverted, transcription could still occur. When 468 or 636 bp was inserted between the delta and the IAR, initiations occurred near the normal delta initiation site and in the inserted DNA. Therefore, the location and properties of transcription signals for Ty-D15 differ considerably from those expected for a yeast gene transcribed by RNA polymerase II.
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3
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Yu K, Elder RT. A region internal to the coding sequences is essential for transcription of the yeast Ty-D15 element. Mol Cell Biol 1989; 9:3667-78. [PMID: 2550798 PMCID: PMC362427 DOI: 10.1128/mcb.9.9.3667-3678.1989] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The major transcript of the yeast transposable element Ty1 has its 5' end in one delta and the 3' end in the opposite delta, the direct repeats of about 335 base pairs (bp) at each end of the element. The transcriptional initiation signals of the Ty-D15 element that give rise to this transcript were found to have a number of unusual characteristics. The 5' delta by itself, which contained the initiation site for Ty transcription, gave no detectable transcription. A region internal to the transcript in a translated part of the element and about 140 bp downstream of the 5' delta was essential for initiation of the major Ty transcript. This internal activating region (IAR) had several interesting properties. When the portion of the delta upstream of the initiation site was replaced with DNA fragments that did not by themselves act as promoters, initiation directed by the IAR still occurred at about the same position, 200 to 400 bp upstream of the IAR. If fragments containing the IAR were inverted, transcription could still occur. When 468 or 636 bp was inserted between the delta and the IAR, initiations occurred near the normal delta initiation site and in the inserted DNA. Therefore, the location and properties of transcription signals for Ty-D15 differ considerably from those expected for a yeast gene transcribed by RNA polymerase II.
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Affiliation(s)
- K Yu
- Department of Molecular Genetics and Cell Biology, University of Chicago, Illinois 60637
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4
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Fulton AM, Rathjen PD, Kingsman SM, Kingsman AJ. Upstream and downstream transcriptional control signals in the yeast retrotransposon, TY. Nucleic Acids Res 1988; 16:5439-58. [PMID: 2838817 PMCID: PMC336777 DOI: 10.1093/nar/16.12.5439] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The yeast retrotransposon, Ty, shares many structural and functional features with retroviral proviruses. These include production of a terminally redundant major transcript. There are also two less abundant transcripts of 5.0 kb and 2.2 kb. Ty transcription is regulated by cell-type, that is it is reduced 5-20 fold in a/alpha diploids as compared to haploids. However control of expression of Ty is not well understood. By deletion analysis we have identified regions of the element which are involved in the activation and regulation of transcription. These signals are found both upstream and downstream of the mRNA start site. The downstream signals are within the region encoding the major Ty proteins. This organisation of transcriptional control signals is discussed with reference to the organisation of control signals in other yeast genes and in retroviral proviruses and other retro-elements.
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Affiliation(s)
- A M Fulton
- Department of Biochemistry, University of Oxford, UK
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5
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Rathjen PD, Kingsman AJ, Kingsman SM. The yeast ROAM mutation--identification of the sequences mediating host gene activation and cell-type control in the yeast retrotransposon, Ty. Nucleic Acids Res 1987; 15:7309-24. [PMID: 2821507 PMCID: PMC306250 DOI: 10.1093/nar/15.18.7309] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
When the yeast retrotransposon, Ty, integrates into the 5' flanking region of a gene it can activate the expression of that gene. At the same time the activated gene is brought under cell-type specific control such that expression is high in haploid a or alpha cells but low in a/alpha diploids. These Ty mediated mutations are known as ROAM mutations. In this study we have used a ROAM mutation created in vitro to identify the sequences within Ty that mediate this phenomenon. We show that a single activator located within the coding region of the Ty element is responsible for ROAM activation. This sequence, which is regulated by the mating type of the cell, differs from classical enhancer elements in that its activity is strictly orientation dependent. An independent activator located downstream of the ROAM sequence activated transcription only in the non-ROAM orientation. This sequence may be part of an internal promoter that controls expression of the sub-genomic 5.0kb Ty transcript.
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Affiliation(s)
- P D Rathjen
- Department of Biochemistry, University of Oxford, UK
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6
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Adams SE, Kingsman SM, Kingsman AJ. The yeast Ty element: recent advances in the study of a model retro-element. Bioessays 1987; 7:3-9. [PMID: 2820390 DOI: 10.1002/bies.950070102] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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7
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Wilson W, Malim MH, Mellor J, Kingsman AJ, Kingsman SM. Expression strategies of the yeast retrotransposon Ty: a short sequence directs ribosomal frameshifting. Nucleic Acids Res 1986; 14:7001-16. [PMID: 3020502 PMCID: PMC311713 DOI: 10.1093/nar/14.17.7001] [Citation(s) in RCA: 59] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The Ty element of yeast is a member of a class of eukaryotic transposons which bear a striking resemblance to retroviral proviruses in their structure and expression strategies (1,2). A direct comparison can be drawn between the production of a fusion protein encoded by Ty, resulting from a frameshift event which fuses two out-of-phase open reading frames TYA and TYB, and the production of Pr180gag-pol in a retrovirus such as Rous Sarcoma Virus (RSV) (3,4). We present data which shows, definitively, that RNA splicing is not responsible for the frameshift in Ty. By in vitro mutation of a class I element, Ty1-15, we demonstrate that 31 nucleotides contained within the region where the TYA and TYB open reading frames overlap direct the frameshift. Within this short sequence there is a region of homology with a class II element which we show is also able to frameshift.
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8
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Affiliation(s)
- J Mellor
- Department of Biochemistry, Oxford, U.K
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9
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Polumienko AL, Grigor'eva SP, Lushnikov AA, Domaradskij IV. The kanamycin resistance gene expression in Escherichia coli as affected by specific yeast sequences. Biochem Biophys Res Commun 1986; 136:529-34. [PMID: 3010983 DOI: 10.1016/0006-291x(86)90472-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
It was shown that the transcription initiation of the kanamycin resistance gene (the Km gene) from transposon Tn5 in E.coli HB101 strain can be provided by specific yeast sequences. To localize a region of the yeast DNA involved in transcription initiation, a number of hybrid plasmids containing promoterless part of the Km gene fused with DNA sequences from chromosome III of the yeast Saccharomyces cerevisiae was constructed. Comparison of nucleotide sequences lying in the LTR of the yeast transposon Tyl-17 with the consensus bacterial promoter revealed strong similarities.
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10
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Parent SA, Fenimore CM, Bostian KA. Vector systems for the expression, analysis and cloning of DNA sequences in S. cerevisiae. Yeast 1985; 1:83-138. [PMID: 3916863 DOI: 10.1002/yea.320010202] [Citation(s) in RCA: 239] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Affiliation(s)
- S A Parent
- Section of Biochemistry, Brown University, Providence, Rhode Island 02912
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11
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Kingsman SM, Kingsman AJ, Dobson MJ, Mellor J, Roberts NA. Heterologous gene expression in Saccharomyces cerevisiae. Biotechnol Genet Eng Rev 1985; 3:377-416. [PMID: 2418856 DOI: 10.1080/02648725.1985.10647819] [Citation(s) in RCA: 65] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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12
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Fulton AM, Mellor J, Dobson MJ, Chester J, Warmington JR, Indge KJ, Oliver SG, de la Paz P, Wilson W, Kingsman AJ. Variants within the yeast Ty sequence family encode a class of structurally conserved proteins. Nucleic Acids Res 1985; 13:4097-112. [PMID: 2989787 PMCID: PMC341298 DOI: 10.1093/nar/13.11.4097] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The Ty transposable elements of Saccharomyces cerevisiae form a heterogeneous family within which two broad structural classes (I and II) exist. The two classes differ by two large substitutions and many restriction sites. We show that, like class I elements a class II element, Tyl-17, also appears to contain at least two major protein coding regions, designated TYA and TYB, and the organisational relationship of these regions has been conserved. The TYA genes of both classes encode proteins, designated p1 proteins, with an approximate molecular weight of 50 Kd and, despite considerable variation between the TYA regions at the DNA level, the structures of these proteins are remarkably similar. These observations strongly suggest that the p1 proteins of Ty elements are functionally significant and that they have been subject to selection.
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Hauber J, Nelböck-Hochstetter P, Feldmann H. Nucleotide sequence and characteristics of a Ty element from yeast. Nucleic Acids Res 1985; 13:2745-58. [PMID: 2987866 PMCID: PMC341191 DOI: 10.1093/nar/13.8.2745] [Citation(s) in RCA: 85] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
We have determined the nucleotide sequence of a complete yeast Ty element (Ty-pY109) which is located near a tRNA(Lys1) gene. The element is 5912 bp in length; the internal domain is flanked by two identical delta sequences of 331 bp. Ty-pY109 contains two large open reading frames (ORFs) which overlap by 38 bp; the putative proteins consist of 440 and 1328 amino acid residues, respectively. The organisation of the coding sequences in Ty resembles that found in retroviral proviruses and the copia-like elements in Drosophila. Partial homologies have been found between Ty-ORF1 and tnpA from Tn3, and Ty-ORF2 and a reverse transcriptase-like domain (1,2).
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Mellor J, Fulton SM, Dobson MJ, Wilson W, Kingsman SM, Kingsman AJ. A retrovirus-like strategy for expression of a fusion protein encoded by yeast transposon Ty1. Nature 1985; 313:243-6. [PMID: 2982101 DOI: 10.1038/313243a0] [Citation(s) in RCA: 159] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Eukaryotic transposons such as the Ty element of yeast or the copia-like sequences of Drosophila show structural and functional similarities to both prokaryotic transposons and retroviral proviruses, but the prokaryotic transposons and retroviral proviruses use markedly different expression strategies which yield products having entirely different functions. To determine the phylogenetic relationship between eukaryotic transposons, prokaryotic transposons and retroviruses, we have sought to identify and characterize the proteins encoded by the yeast Ty element and to describe the strategies used to express these proteins. We show here that the yeast transposon produces a fusion protein by a specific frameshifting event that fuses two out-of-phase open reading frames (ORFs). The process is remarkably similar to that used by retroviruses such as Rous sarcoma virus (RSV) to produce Pr180gag-pol.
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Mellor J, Dobson MJ, Roberts NA, Kingsman AJ, Kingsman SM. Factors affecting heterologous gene expression in Saccharomyces cerevisiae. Gene 1985; 33:215-26. [PMID: 3888784 DOI: 10.1016/0378-1119(85)90096-4] [Citation(s) in RCA: 101] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The 'promoter' fragment from the yeast phosphoglycerate kinase (PGK) gene has been used to direct the expression of human interferon-alpha-2 (IFN alpha 2) on a high-copy-number plasmid in yeast. The yields of IFN alpha 2 are only 1-3% of yeast total protein, whereas the maximum yield of PGK produced by the PGK gene on a high-copy-number plasmid is at least 50%. IFN alpha 2 is turned over more rapidly than PGK but in addition a major reason for the relatively low level of IFN alpha 2 is that IFN-specific RNA levels are much lower. This does not reflect differences in plasmid copy number or integrity, or differences in the 5' and 3' untranslated regions of the transcripts or DNA flanking regions. It appears that the presence of heterologous coding sequences, or the absence of specific yeast sequences causes a reduction in heterologous RNA levels in yeast.
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Piper PW, Lockheart A, Patel N. A minor class of 5S rRNA genes in Saccharomyces cerevisiae X2180-1B, one member of which lies adjacent to a Ty transposable element. Nucleic Acids Res 1984; 12:4083-96. [PMID: 6328410 PMCID: PMC318818 DOI: 10.1093/nar/12.10.4083] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
In Saccharomyces cerevisiae the majority of the genes for 5S rRNA lie within a 9kb rDNA sequence that is present as 100-200 tandemly-repeated copies on Chromosome XII. Following our observations that about 10% of yeast 5S rRNA exists as minor variant sequences, we screened a collection of yeast DNA fragments cloned in lambda gt for 5S rRNA genes whose flanking sequences differed from those adjacent to 5S rRNA genes of the rDNA repeat. Three variant 5S rRNA genes were isolated on the basis of such dissimilarity to rDNA repeat sequences. They display a remarkable conservation of their DNA in the vicinity of the 5S coding region, and are examples of a minor form of 5S rRNA coding sequence present in a small number of copies in the yeast genome. These variant sequences appear to be transcribed as efficiently as 5S rRNA genes of the rDNA repeat. In one of our isolates of the variant sequence a Ty transposable element is inserted 145bp upstream of the initiation point for 5S rRNA synthesis.
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