Transcription Regulation in the Third Domain

Karr, Elizabeth A.

doi:10.1016/b978-0-12-800259-9.00003-2

Cited by 30 publications

(20 citation statements)

References 153 publications

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“…The TATA box is the site of binding of the TATA-binding protein TBP while the BRE sequence is the site of binding for TFB (Peeters et al, 2013). While relatively few transcriptional activators have been studied in Archaea, the mechanism of activation in these limited studies has been shown to involve recruitment of TBP or TFB to the TATA box or BRE (Karr, 2014). Consensus TATA box sequences vary for different subgroups of Archaea and mutations in the TATA box can reduce transcription efficiency (Soppa, 1999; Bartlett, 2005; van de Werken et al, 2006).…”

Section: Discussionmentioning

confidence: 99%

“…Transcriptional activators typically bind to sites located upstream of the BRE and help in the recruitment of TBP or TFB. In contrast, repressors can bind to either the promoter region where they interfere with TFB or TBP binding by steric hindrance, or downstream of the promoter, sometimes even after the TSS, to prevent RNA polymerase recruitment or transcription elongation (Bell, 2005; Peeters et al, 2013; Karr, 2014). Transcriptional activators are often associated with promoters that have TATA box or BRE sequences that deviate from consensus sequences (Ochs et al, 2012; Peeters et al, 2013).…”

Section: Introductionmentioning

confidence: 99%

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Bypassing the Need for the Transcriptional Activator EarA through a Spontaneous Deletion in the BRE Portion of the fla Operon Promoter in Methanococcus maripaludis

et al. 2017

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In Methanococcus maripaludis, the euryarchaeal archaellum regulator A (EarA) is required for the transcription of the fla operon, which is comprised of a series of genes which encode most of the proteins needed for the formation of the archaeal swimming organelle, the archaellum. In mutants deleted for earA (ΔearA), there is almost undetectable transcription of the fla operon, Fla proteins are not synthesized and the cells are non-archaellated. In this study, we have isolated a spontaneous mutant of a ΔearA mutant in which the restoration of the transcription and translation of the fla operon (using flaB2, the second gene of the operon, as a reporter), archaella formation and swarming motility were all restored even in the absence of EarA. Analysis of the DNA sequence from the fla promoter of this spontaneous mutant revealed a deletion of three adenines within a string of seven adenines in the transcription factor B recognition element (BRE). When the three adenine deletion in the BRE was regenerated in a stock culture of the ΔearA mutant, very similar phenotypes to that of the spontaneous mutant were observed. Deletion of the three adenines in the fla promoter BRE resulted in the mutant BRE having high sequence identity to BREs from promoters that have strong basal transcription level in Mc. maripaludis and Methanocaldococcus jannaschii. These data suggest that EarA may help recruit transcription factor B to a weak BRE in the fla promoter of wild-type cells but is not required for transcription from the fla promoter with a strong BRE, as in the three adenine deletion version in the spontaneous mutant.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Bypassing the Need for the Transcriptional Activator EarA through a Spontaneous Deletion in the BRE Portion of the fla Operon Promoter in Methanococcus maripaludis

et al. 2017

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“…The basal promoter and transcription machinery in Archaea are reminiscent of those found in Eukaryotes, yet bacteria-like transcription regulators are used for regulation Karr, 2014). The activators usually bind upstream of the factor B recognition element (BRE) and help in the recruitment of the general transcription factors, while repressors can bind to either the promoter or downstream to prevent transcription by steric hindrance (Bell, 2005;Peeters et al, 2013).…”

Section: Introductionmentioning

confidence: 99%

Identification of the first transcriptional activator of an archaellum operon in a euryarchaeon

Ding

Nash

Berezuk

et al. 2016

Molecular Microbiology

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The archaellum is the swimming organelle of the third domain, the Archaea. In the euryarchaeon Methanococcus maripaludis, genes involved in archaella formation, including the three archaellins flaB1, flaB2 and flaB3, are mainly located in the fla operon. Previous studies have shown that transcription of fla genes and expression of Fla proteins are regulated under different growth conditions. In this study, we identify MMP1718 as the first transcriptional activator that directly regulates the fla operon in M. maripaludis. Mutants carrying an in-frame deletion in mmp1718 did not express FlaB2 detected by western blotting. Quantitative reverse transcription PCR analysis of purified RNA from the Δmmp1718 mutant showed that transcription of flaB2 was negligible compared to wildtype cells. In addition, no archaella were observed on the cell surface of the Δmmp1718 mutant. FlaB2 expression and archaellation were restored when the Δmmp1718 mutant was complemented with mmp1718 in trans. Electrophoretic motility shift assay and isothermal titration calorimetry results demonstrated the specific binding of purified MMP1718 to DNA fragments upstream of the fla promoter. Four 6 bp consensus sequences were found immediately upstream of the fla promoter and are considered the putative MMP1718-binding sites. Herein, we designate MMP1718 as EarA, the first euryarchaeal archaellum regulator.

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“…The minimal, necessary proteins and DNA elements for archaeal transcription initiation are now well defined and characterized (21)(22)(23)(24)(25)(26)(27)(28). A recent excellent review (29) summarizes the actions of repressors and activators that function during initiation in archaeal species. We focus here on the roles of new DNA elements and newly discovered strategies of basal initiation factors.…”

Section: Regulated Transcription Initiationmentioning

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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Transcription Regulation in the Third Domain

Cited by 30 publications

References 153 publications

Bypassing the Need for the Transcriptional Activator EarA through a Spontaneous Deletion in the BRE Portion of the fla Operon Promoter in Methanococcus maripaludis

Bypassing the Need for the Transcriptional Activator EarA through a Spontaneous Deletion in the BRE Portion of the fla Operon Promoter in Methanococcus maripaludis

Identification of the first transcriptional activator of an archaellum operon in a euryarchaeon

Transcription Regulation in Archaea

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