Retrotransposons are a class of mobile genetic elements that replicate through an RNA intermediate and resemble retroviruses from many points of view. Five different families of retrotransposons (Ty1 to Ty5) have been identified in the genome of the yeast Saccharomyces cerevisiae
(reviewed in references 31
, and 57
). They all share the same basic structure, consisting of two direct long terminal repeats (LTR) flanking the TYA
open reading frames, which are analogous to the retroviral gag
genes. Ty1 is the most abundant of the retrotransposon families, with around 30 copies per haploid genome, and is a model for LTR-containing elements. Ty1 is transcribed from LTR to LTR by RNA polymerase II, with the resulting transcript serving as a template for both translation and reverse transcription. Translation leads to the synthesis of Ty1Ap, the structural component of the virus-like particle and of the Ty1A-Ty1B polyprotein containing protease (PR), integrase (IN), reverse transcriptase (RT), and RNase H (RH) catalytic domains, all of which are essential for retrotransposition. The linear double-stranded cDNA molecule, produced by reverse transcription within the virus-like particle, enters the genome either by integrase-mediated integration or, to a lesser extent, by homologous recombination with genomic elements. Ty1 preferentially integrates next to RNA polymerase III-dependent promoters, but less frequent insertions into, or upstream of, genes transcribed by RNA polymerase II have been reported. In these cases, Ty1 insertions have been shown to alter the expression of the neighboring genes by activating or inactivating them or by importing new regulatory mechanisms on their expression. Such insertions may provide a means of evolution to the yeast genome. The Ty1 element and its host have evolved numerous control systems that keep retrotransposition at a low level, yet allowing it to be activated under stress (10
). In contrast to the host defense, which acts mainly at the posttranscriptional level, the Ty1 response to stress generally involves activation of transcription.
The promoter of Ty1 is complex, and its structure is very similar to that of higher eukaryotes. It extends over 1 kb, both upstream and downstream of two TATA boxes, and includes the 5′ LTR and part of the TY1A
open reading frame. At least eight transcription factors (Gcr1, Ste12, Tec1, Mcm1, Tea1, Rap1, Gcn4, and Mot3), which bind to the Ty1 promoter (15
), and three chromatin-remodeling complexes (Swi/Snf, SAGA, and ISWI) regulate Ty1 transcription in haploid cells (7
). The activation of Ty1 transcription by the invasive/filamentous pathway in response to environmental signals, such as nitrogen starvation, occurs through the transcriptional activators Ste12 and Tec1 (9
). These proteins recognize a sequence called FRE (filamentous responsive element), located in TY1A
sequences downstream of the TATA boxes of the Ty1 promoter (2
). In addition to their role in Ty1 activation by the invasive/filamentous signaling pathway, Ste12 and Tec1 are important for basal levels of Ty1 transcription in haploid cells (29
). Exposure of yeast cells to DNA-damaging agents also increases Ty transcript levels and activates Ty retrotransposition (5
). The mechanism of transcriptional activation by DNA damage has not been elucidated, however.
Insights into the transcription of individual Ty1 elements have recently been obtained using a set of haploid strains, each expressing lacZ
from the transcription control signals of a specific Ty1 element at its native location. This set of 31 strains allows study of the transcription of all but one of the Ty1 elements present in the genome of S288C (36
). The comparison of lacZ
expression in these strains identified two basic classes of Ty1 elements according to their level of expression: weakly and highly expressed elements. Based on genetic data, it was proposed that repression of transcription of the highly expressed Ty1 elements by chromatin structures is antagonized by Swi/Snf and SAGA. In addition, several endogenous Ty1 elements, mostly those expressed at high levels, contain five potential Gcn4 binding sites in their 5′ LTR (36
). Gcn4 is a transcriptional activator that binds to multiple sites upstream of amino acid biosynthetic genes (25
). The transcription of the highly expressed Ty1 elements depends on GCN4
in the absence of amino acids and is activated when GCN4
The Bas1 transcriptional activator recognizes a DNA sequence (TGACTC) (13
) similar to the Gcn4 binding site [TGA(C/G)TCA] (39
). The difference is that an A nucleotide is generally present at the 3′ extremity of Gcn4 binding sites but is never found in Bas1 binding sites. All but one of the Gcn4 binding sites located in Ty1 elements contain a T nucleotide at the last position and could be recognized by Bas1, suggesting that Bas1 could potentially activate Ty1 transcription. Bas1, together with Bas2, is required for the regulated activation of the ADE
genes of the de novo AMP biosynthesis pathway (13
). When adenine is provided in the environment, it enters the yeast cells and is converted to AMP and then to other adenine nucleotides. In the absence of purines, Bas1 and Bas2 interact to activate the ADE
). Since the Gcn4 binding sites located in Ty1 were potentially recognized by Bas1, we asked whether Ty1 transcription was stimulated under conditions of adenine starvation.
We discovered that although Bas1 does not activate Ty1 transcription, severe adenine starvation does. Our results indicate that activation occurs mainly on poorly expressed elements, whose transcription is repressed by chromatin. We also show that the activation of transcription of individual Ty1 elements under severe adenine starvation correlates with a proportional increase in their retrotransposition. Finally, we provide evidence that the activation mechanism requires chromatin remodeling at Ty1 promoters.