The Sulfolobus Initiator Element Is an Important Contributor to Promoter Strength

Ao, Xiang; Li, Yingjun; Wang, Fan; Mao, Feng; Lin, Yanxu; Zhao, Siming; Liang, Yunxiang; Peng, Nan

doi:10.1128/jb.00768-13

Cited by 20 publications

(22 citation statements)

References 46 publications

(67 reference statements)

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“…Total RNA was isolated from exponentially growing Sulfolobus cultures in SCVy medium or ACVy medium for induction of csa3a gene under control of araS promoter (OD 600 = 0.2) as described previously ( 45 ). Genomic DNA in the total RNA sample was removed using DNase I (Roche, Basel, Switzerland).…”

Section: Methodsmentioning

confidence: 99%

“…Each real-time quantification reaction was carried out as described above for the ChIP-qPCR assay using the first-strand cDNAs as template and each forward primer ( csa1 qF, cas1 qF, cas2 qF, cas4 qF or csa3a qF) in combination with the reverse primers listed above along with csa3a qR. The transcripts of the albA gene were used as the control ( 45 ) and the cycle threshold (Ct) values of the control transcript albA were used to normalize the Ct values of the csa1, cas1, cas2, cas4 and csa3a transcripts.…”

Section: Methodsmentioning

confidence: 99%

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Transcriptional regulator-mediated activation of adaptation genes triggers CRISPR de novo spacer acquisition

Liu

Wang

et al. 2015

Nucleic Acids Research

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100

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Acquisition of de novo spacer sequences confers CRISPR-Cas with a memory to defend against invading genetic elements. However, the mechanism of regulation of CRISPR spacer acquisition remains unknown. Here we examine the transcriptional regulation of the conserved spacer acquisition genes in Type I-A of Sulfolobus islandicus REY15A. Csa3a, a MarR-like transcription factor encoded by the gene located adjacent to csa1, cas1, cas2 and cas4 cluster, but on the reverse strand, was demonstrated to specifically bind to the csa1 and cas1 promoters with the imperfect palindromic sequence. Importantly, it was demonstrated that the transcription level of csa1, cas1, cas2 and cas4 was significantly enhanced in a csa3a-overexpression strain and, moreover, the Csa1 and Cas1 protein levels were increased in this strain. Furthermore, we demonstrated the hyperactive uptake of unique spacers within both CRISPR loci in the presence of the csa3a overexpression vector. The spacer acquisition process is dependent on the CCN PAM sequence and protospacer selection is random and non-directional. These results suggested a regulation mechanism of CRISPR spacer acquisition where a single transcriptional regulator senses the presence of an invading element and then activates spacer acquisition gene expression which leads to de novo spacer uptake from the invading element.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Transcriptional regulator-mediated activation of adaptation genes triggers CRISPR de novo spacer acquisition

Liu

Wang

et al. 2015

Nucleic Acids Research

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100

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“…In contrast to M2, in transformants carrying the promoter mutant M1 that is located upstream to TSS, xacR promoter activity was completely abolished rather than increased. This might be explained by mutation of putative proximal promoter element or initiator element, essential for transcription (Brenneis et al, 2007;Grohmann and Werner, 2011;Ao et al, 2013).…”

Section: Xacr Acts As Repressor For Its Own Synthesismentioning

confidence: 99%

XacR – a novel transcriptional regulator of D‐xylose and L‐arabinose catabolism in the haloarchaeon Haloferax volcanii

Johnsen

Sutter

Schulz

et al. 2014

Environmental Microbiology

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The haloarchaeon Haloferax volcanii degrades D-xylose and L-arabinose via oxidative pathways to α-ketoglutarate. The genes involved in these pathways are clustered and were transcriptionally upregulated by both D-xylose and L-arabinose suggesting a common regulator. Adjacent to the gene cluster, a putative IclR-like transcriptional regulator, HVO_B0040, was identified. It is shown that HVO_B0040, designated xacR, encodes an activator of both D-xylose and L-arabinose catabolism: in ΔxacR cells, transcripts of genes involved in pentose catabolism could not be detected; transcript formation could be recovered by complementation, indicating XacR dependent transcriptional activation. Upstream activation promoter regions and nucleotide sequences that were essential for XacR-mediated activation of pentose-specific genes were identified by in vivo deletion and scanning mutagenesis. Besides its activator function XacR acted as repressor of its own synthesis: xacR deletion resulted in an increase of xacR promoter activity. A palindromic sequence was identified at the operator site of xacR promoter, and mutation of this sequence also resulted in an increase and thus derepression of xacR promoter activity. It is concluded that the palindromic sequence represents the binding site of XacR as repressor. This is the first report of a transcriptional regulator of pentose catabolism in the domain of archaea.

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“…The INR has been shown to be targeted by some transcriptional activators, and its high AT content may facilitate promoter opening in some instances. Many archaeal transcripts are leaderless, so the INR is not consistently identifiable, and the regulatory influence of INR sequences does not appear to extend to RNA half-life or alter the translational capacity (70). PPEs, centered approximately 10 bps upstream of the site of initiation, have been shown to increase transcription output through recruitment of TFB (67,68).…”

Section: Dna Elementsmentioning

confidence: 99%

Transcription Regulation in Archaea

2016

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The known diversity of metabolic strategies and physiological adaptations of archaeal species to extreme environments is extraordinary. Accurate and responsive mechanisms to ensure that gene expression patterns match the needs of the cell necessitate regulatory strategies that control the activities and output of the archaeal transcription apparatus. Archaea are reliant on a single RNA polymerase for all transcription, and many of the known regulatory mechanisms employed for archaeal transcription mimic strategies also employed for eukaryotic and bacterial species. Novel mechanisms of transcription regulation have become apparent by increasingly sophisticated in vivo and in vitro investigations of archaeal species. This review emphasizes recent progress in understanding archaeal transcription regulatory mechanisms and highlights insights gained from studies of the influence of archaeal chromatin on transcription. RNA polymerase (RNAP) is a well-conserved, multisubunit essential enzyme that transcribes DNA to generate RNA in all cells. Although RNA synthesis is carried out by RNAP, the activities of RNAP during each phase of transcription are subject to basal and regulatory transcription factors. Substantial differences in transcription regulatory strategies exist in the three domains (Bacteria, Archaea, and Eukarya). Only a single transcription factor (NusG or Spt5) is universally conserved (1, 2), and the roles of many archaeon-encoded factors have not been evaluated using in vivo and in vitro techniques. Archaea are reliant on a transcription apparatus that is homologous to the eukaryotic transcription machinery; similarities include additional RNAP subunits that form a discrete subdomain of RNAP (3, 4) as well as basal transcription factors that direct transcription initiation and elongation (5-8).The shared homology of archaeal-eukaryotic transcription components aligns with the shared ancestry of Archaea and Eukarya, and this homology often is exclusive of Bacteria. Archaea are prokaryotic, but the transcription apparatus of Bacteria differs significantly from that of Archaea and Eukarya.The archaeal transcription apparatus is most commonly summarized as a simplified version of the eukaryotic machinery. In some respects this is true, as homologs of only a few eukaryotic transcription factors are encoded in archaeal genomes, and archaeal transcription in vitro can be supported by just a few transcription factors. However, much regulatory activity in eukaryotes is devoted to posttranslational modifications of chromatin, RNAP, and transcription factors, and this complexity seemingly does not transfer to the Archaea, where few posttranslational modifications or chromatin-imposed regulation events are currently known. The ostensible simplicity of archaeal transcription is under constant revision, as more detailed examinations of archaeon-encoded factors become possible through increasingly sophisticated in vivo and in vitro techniques. This review will highlight the current understanding of archaeal transcriptio...

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The Sulfolobus Initiator Element Is an Important Contributor to Promoter Strength

Cited by 20 publications

References 46 publications

Transcriptional regulator-mediated activation of adaptation genes triggers CRISPR de novo spacer acquisition

Transcriptional regulator-mediated activation of adaptation genes triggers CRISPR de novo spacer acquisition

XacR – a novel transcriptional regulator of D‐xylose and L‐arabinose catabolism in the haloarchaeon Haloferax volcanii

Transcription Regulation in Archaea

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