Topic
B recognition element
About: B recognition element is a research topic. Over the lifetime, 6 publications have been published within this topic receiving 216 citations.
Papers
TL;DR: To identify the element responsible for the cold response, a pTKR expression probe plasmid was constructed using thermostable catalase from Pyrobaculum calidifontis as a reporter and indicated that the regulatory element is located in the region between the SD region and the initiation codon (ATG).
Abstract: Thermococcus kodakarensis, which grows optimally at 85°C, expresses cold stress-inducible DEAD box RNA helicase (Tk-deaD) when shifted to 60°C. A DDA1 deletion (ΔTk-deaD) mutant exhibited decreased cell growth, and cells underwent lysis at 60°C in nutrient broth in the absence of elemental sulfur. In contrast, cells in medium containing elemental sulfur at 60°C did not undergo lysis, suggesting that Tk-deaD is necessary for cell growth in sulfur-free medium. To identify the element responsible for the cold response, a pTKR expression probe plasmid was constructed using thermostable catalase from Pyrobaculum calidifontis as a reporter. The plasmid pTKRD, which contained the transcription factor B recognition element, TATA region, and Shine-Dalgarno (SD) region, including the initiation codon of the Tk-deaD gene, exhibited cold inducibility. We also constructed a series of deletion and chimeric constructs with the glutamate dehydrogenase (gdh) promoter, whose expression is constitutive independent of culture temperatures and catalase expression. Reporter assay experiments indicated that the regulatory element is located in the region between the SD region and the initiation codon (ATG). Nucleotide sequences in the upstream regions of Tk-deaD and gdh were compared and revealed a five-adenosine (AAAAA) sequence between SD and ATG of Tk-deaD that was not present in gdh. Replacement of the repeated adenosine sequence with other sequences revealed that the AAAAA sequence is important for cold induction. This sequence-specific mechanism is unique and is one that has not been identified in other known cold-inducible genes.
22 citations
TL;DR: The basal and GvpE-induced activities of P(A) and P(D) were investigated in Haloferax volcanii transformants and it was shown that a complete UAS is required for activation.
Abstract: Gas vesicle formation in haloarchaea involves 14 gas vesicle protein (gvp) genes. The strong promoter PA drives the expression of gvpACNO, which encodes the major gas vesicle structural proteins GvpA and GvpC, whereas the oppositely oriented promoter PD initiates the synthesis of the two regulator proteins, GvpD and GvpE. GvpE activates PA and PD , and requires a 20 nt upstream activator sequence (UAS). UASA and UASD partially overlap in the centre of the 35 bp intergenic region. The basal and GvpE-induced activities of PA and PD were investigated in Haloferax volcanii transformants. Each UAS consists of two 8 nt portions (PA , 1A+2A; PD , 1D+2D), and mutations in the overlapping 1A and 1D portions affected the GvpE induction of both promoters. Substitution of one of the UAS portions by a nonsense sequence showed that a complete UAS is required for activation. The activation of PA was more efficient compared with PD . Promoter PA with UASA in configuration 1A+1A was still activated by GvpE, but PD was not inducible with UASD in configuration 1D+1D. The TATA box and/or transcription factor B recognition element (BRE) were exchanged between PA and PD. All elements of PA functioned well in the environment of ‘PD ’ and transferred the stronger PA activity to ‘PD ’. In contrast, the respective ‘PA ’ chimeras were less active, and BRED was not functional in the environment of ‘PA’. The relative strengths of the two promoters were substantially determined by the BRE. A 4 nt scanning mutagenesis uncovered an additional regulatory element in the region between TATAD and the transcriptional start site of gvpD.
13 citations
TL;DR: Among the Archaea with the genes, those from the mesophilic methanogen Methanosarcina mazeii are the only ones whose basal (constitutive) and stress-induced transcription patterns have been determined, and factor(s)-DNA modeling predicted that modifications of H bonds are caused by TBP binding, and that these modifications are distinctive for each promoter.
13 citations
TL;DR: A spontaneous mutant of a ΔearA mutant is isolated in which the restoration of the transcription and translation of the fla operon, archaella formation and swarming motility were all restored even in the absence of EarA, suggesting that EarA may help recruit transcription factor B to a weak BRE in theFla promoter of wild-type cells but is not required for transcription from the flA promoter with a strong BRE.
Abstract: 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 (∆earA), 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 ∆earA 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 ∆earA 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 helps recruit transcription factor B to a weak BRE in the fla promoter of wildtype 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.
TL;DR: The primary transcriptome of the H2-producing archaeon Thermococcus onnurineus NA1 is determined, demonstrating that transcription of orthologous genes are initiated by highly conserved promoter sequences, however their upstream sequences for transcriptional and translational regulation are largely diverse.
Abstract: In spite of their pivotal roles in transcriptional and post-transcriptional processes, the regulatory elements of archaeal genomes are not yet fully understood. Here, we determine the primary transcriptome of the H2-producing archaeon Thermococcus onnurineus NA1. We identified 1,082 purine-rich transcription initiation sites along with well-conserved TATA box, A-rich B recognition element (BRE), and promoter proximal element (PPE) motif in promoter regions, a high pyrimidine nucleotide content (T/C) at the -1 position, and Shine-Dalgarno (SD) motifs (GGDGRD) in 5' untranslated regions (5' UTRs). Along with differential transcript levels, 117 leaderless genes and 86 non-coding RNAs (ncRNAs) were identified, representing diverse cellular functions and potential regulatory functions under the different growth conditions. Interestingly, we observed low GC content in ncRNAs for RNA-based regulation via unstructured forms or interaction with other cellular components. Further comparative analysis of T. onnurineus upstream regulatory sequences with those of closely related archaeal genomes demonstrated that transcription of orthologous genes are initiated by highly conserved promoter sequences, however their upstream sequences for transcriptional and translational regulation are largely diverse. These results provide the genetic information of T. onnurineus for its future application in metabolic engineering.
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Performance Metrics
| Year | Papers |
|---|---|
| 2017 | 2 |
| 2013 | 1 |
| 2012 | 1 |
| 2001 | 1 |
| 1999 | 1 |