SAGA mediates transcription from the TATA-like element independently of Taf1p/TFIID but dependent on core promoter structures in Saccharomyces cerevisiae

RESEARCH ARTICLE SAGA mediates transcription from the TATAlike element independently of Taf1p/TFIID but dependent on core promoter structures in Saccharomyces cerevisiae Kiyoshi Watanabe, Tetsuro Kokubo* a1111111111 a1111111111 a1111111111 a1111111111 a1111111111 OPEN ACCESS Citation: Watanabe K, Kokubo T (2017) SAGA mediates transcription from the TATA-like element independently of Taf1p/TFIID but dependent on core promoter structures in Saccharomyces cerevisiae. PLoS ONE 12(11): e0188435. https:// doi.org/10.1371/journal.pone.0188435 Editor: Laszlo Tora, Institute of Genetics and Molecular and Cellular Biology, FRANCE Received: October 3, 2017 Accepted: November 7, 2017 Published: November 27, 2017 Copyright: © 2017 Watanabe, Kokubo. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Data Availability Statement: All relevant data are within the paper and its Supporting Information files. Funding: This study was supported by grants from the Japan Society for the Promotion of Science (15K06953) and the AMED-CREST program (JPMJCR11J4) of the Japan Agency for Medical Research and Development, AMED. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Molecular and Cellular Biology Laboratory, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa, Japan * Abstract In Saccharomyces cerevisiae, core promoters of class II genes contain a TATA element, either a TATA box (TATA[A/T]A[A/T][A/G]) or TATA-like element (1 or 2 bp mismatched version of the TATA box). The TATA element directs the assembly of the preinitiation complex (PIC) to ensure accurate transcriptional initiation. It has been proposed the PIC is assembled by two distinct pathways in which TBP is delivered by TFIID or SAGA, leading to the widely accepted model that these complexes mediate transcription mainly from TATA-like element- or TATA box-containing promoters, respectively. Although both complexes are involved in transcription of nearly all class II genes, it remains unclear how efficiently SAGA mediates transcription from TATA-like element-containing promoters independently of TFIID. We found that transcription from the TATA box-containing AGP1 promoter was greatly stimulated in a Spt3p-dependent manner after inactivation of Taf1p/TFIID. Thus, this promoter provides a novel experimental system in which to evaluate SAGA-mediated transcription from TATA-like element(s). We quantitatively measured transcription from various TATA-like elements in the Taf1p-dependent CYC1 promoter and Taf1p-independent AGP1 promoter. The results revealed that SAGA could mediate transcription from at least some TATA-like elements independently of Taf1p/TFIID, and that Taf1p-dependence or -independence is highly robust with respect to variation of the TATA sequence. Furthermore, chimeric promoter mapping revealed that Taf1p-dependence or independence was conferred by the upstream activating sequence (UAS), whereas Spt3p-dependent transcriptional stimulation after inactivation of Taf1p/TFIID was specific to the AGP1 promoter and dependent on core promoter regions other than the TATA box. These results suggest that TFIID and/or SAGA are regulated in two steps: the UAS first specifies TFIID or SAGA as the predominant factor on a given promoter, and then the core promoter structure guides the pertinent factor to conduct transcription in an appropriate manner. PLOS ONE | https://doi.org/10.1371/journal.pone.0188435 November 27, 2017 1 / 27 SAGA-mediated transcription from the TATA-like element Competing interests: The authors have declared that no competing interests exist. Introduction In eukaryotes, general transcription factors (GTFs), Mediator, and RNA polymerase II (pol II) assemble on the core promoter to form a preinitiation complex (PIC) that directs accurate transcriptional initiation [1–5]. In the first step of PIC assembly, TBP is recruited to the core promoter as a subunit of TFIID or via physical association with the SPT module of the SAGA (SptAda-Gcn5-acetyltransferase) complex [6–9]. TFIID and SAGA are structurally related large multi-protein complexes that mediate basal and/or activated transcription [2, 10–12]. They share five Taf subunits that form a scaffold for the assembly of other complex-specific subunits [9, 13–16], and the two complexes define two distinct PIC assembly pathways [4, 8, 17]. Genome-wide studies revealed that SAGA-dominated promoters (i.e., those whose transcriptional activities are primarily supported by SAGA rather than by TFIID) prefer the TATA box (TATAWAWR; W = A/T, R = A/G), whereas TFIID-dominated promoters prefer the TATA-like element (a 1 or 2 bp mismatched version of the TATA box) [7, 8]. According to the nomenclature proposed by Rhee and Pugh [8], the TATA element includes the TATA box and the TATA-like element. More recent studies indicate that TFIID and SAGA are both involved in transcription of nearly all class II genes [18–21]. Consistent with this, it is well established that TFIID can mediate transcription from various types of promoters, both in vivo and in vitro, regardless of whether they contain the TATA box or not [22–28]. However, it remains unclear how efficiently SAGA can mediate transcription from TATA-less promoters that do not contain the TATA box but instead contain TATA-like elements or other less well-characterized core promoter elements (CEs) [25, 29, 30], especially in a manner independent of TFIID. One reason for this ambiguity is the scarcity of in vitro experiments that scrutinize the requirements of the TATA sequence for SAGA-dependent transcription. In an in vitro SAGAdependent transcription system, SAGA can mediate transcription from the TATA-containing HIS4 promoter [31] but not from the TATA-less RPS5 promoter [24]. However, it remains to be determined whether SAGA can mediate transcription from a HIS4 promoter containing a TATA-like element (off-consensus TATA) or a RPS5 promoter containing a consensus TATA box under the same conditions. Other studies showed that several sequences isolated as active CEs in a random screen using the gal-his3 hybrid promoter [32] have significant transcriptional activities in vitro, even if they do not contain a consensus TATA box [33], but it remains unclear whether the in vitro transcription system used in the latter experiment is SAGAdependent. Another reason for the ambiguity is the functional redundancy between TFIID and SAGA [7, 34]. In general, SAGA-dependent promoters are highly regulated [7, 35] and require the TATA box for transcriptional activation [35, 36], as observed for the GAL1 promoter [37–40]. Consistent with this, mutational studies of the partially (i.e., subunit-specifically) SAGAdependent [11] but TFIID-i (...truncated)