A conserved hexanucleotide motif is important in UV-inducible promoters in Sulfolobus acidocaldarius

Abstract

Upon DNA damage, Sulfolobales exhibit a global gene regulatory response resulting in the expression of DNA transfer and repair proteins and the repression of the cell division machinery. Because the archaeal DNA damage response is still poorly understood, we investigated the promoters of the highly induced ups operon. Ups pili are involved in cellular aggregation and DNA exchange between cells. With LacS reporter gene assays we identified a conserved, non-palindromic hexanucleotide motif upstream of the ups core promoter elements to be essential for promoter activity. Substitution of this cis regulatory motif in the ups promoters resulted in abolishment of cellular aggregation and reduced DNA transfer. By screening the Sulfolobus acidocaldarius genome we identified a total of 214 genes harbouring the hexanucleotide motif in their respective promoter regions. Many of these genes were previously found to be regulated upon UV light treatment. Given the fact that the identified motif is conserved among S. acidocaldarius and Sulfolobus tokodaii promoters, we speculate that a common regulatory mechanism is present in these two species in response to DNA-damaging conditions.

An Orc1/Cdc6 ortholog functions as a key regulator in the DNA damage response in Archaea

“…Then, promoter sequences (100 bp preceding the start codon) of 21 highly up regulated DDR genes (over 18 folds change, Supplementary Table S6 ) were retrieved from the genome sequence of S. islandicus REY15A ( 20 ) and analyzed for conserved sequence motifs using the MEME (Multiple EM for Motif Elicitation) suite ( 32 ). A 20 bp consensus (5′-AATAGTTTCRGWDTACTCWS-3′) was identified, containing the DNA motif of 5′-ANTTTC-3′ previously reported for UV-responsive gene promoters of S. acidocaldarius ( 51 ). The motif is positioned at –23 to –55 bp upstream of the ATG codon in most identified DDR genes ( Supplementary Figure S3 ).…”

“…Our research has gained important insights into the mechanisms of Orc1-2-dependent regulation in S. islandicus . First, a conserved motif (5′-ANTTTC-3′) is present in the promoters of a number of highly up regulated DDR genes, and it is identical to the motif identified in UV-inducible genes of S. acidocaldarius ( 51 ). Here, we show that the S. islandicus Orc1-2 protein binds specifically to the motif present in a selected set of DDR gene promoters in vitro (Figure 4 ), and inactivation of either component (Orc1-2 deficiency or mutagenesis of the DNA binding motif) abolishes the NQO-responsive expression from all tested promoters in reporter gene assay (Figure 3 ).…”

Effect of UV irradiation on Sulfolobus acidocaldarius and involvement of the general transcription factor TFB3 in the early UV response

“…Previous motif searches identified a non-palindromic hexanucleotide motif in S. acidocaldarius (5′-A(N)TTTC-3′) that was supposed to be important in UV-inducible promoters ( 74 ). The motif is located 30 to 80 bp upstream of the transcription start, and a so far unknown regulator was supposed to bind to the motif and to interact with TFB3, which lacks a DNA binding domain.…”

“…The motif is located 30 to 80 bp upstream of the transcription start, and a so far unknown regulator was supposed to bind to the motif and to interact with TFB3, which lacks a DNA binding domain. It is speculated that TFB3 then interacts with the RNAP and thus activates transcription via bridging the RNAP and TFB1–TBP–DNA complex ( 32 , 74 ). In our study, we performed an automated motif search and identified in total 299 genes in S. acidocaldarius .…”

A CRISPR-associated factor Csa3a regulates DNA damage repair in Crenarchaeon Sulfolobus islandicus

“…On the other hand, the signal of retarded band for each EMSA experiment was completely abolished for all tested promoters in the presence of 2- or 4-fold excess of unlabeled specific competitor DNA (cold probe) (Figure 2A ). Notably, a DNA motif similar to the UV-responsive motif ( 26 ) was identified for all tested promoters. The mutated promoters with transversion mutation at the UV-responsive motif and its flanking region formed a weak shift band with the Csa3a regulator (40, 80 or 120 ng/μl) in EMSA experiment (Figure 2A ).…”