The TATA motif, the CAA motif and the poly(T) transcription termination motif are all important for transcription re‐initiation on plant tRNA genes

Yukawa, Yasushi; Sugita, Mamoru; Choisne, Nathalie; Small, Ian; Sugiura, Masahiro

doi:10.1046/j.1365-313x.2000.00752.x

Cited by 44 publications

(64 citation statements)

References 41 publications

(73 reference statements)

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“…1B): (i) the information content is higher at TATA for S. pombe, (ii) the information content is higher at position 10 (greater propensity for G10) in A. thaliana, and (iii) the information content is higher around ϩ1 for A. thaliana. The A. thaliana pattern is consistent with data that show partial or little effect of TATA mutations but larger effects of CAA mutations on plant tRNA expression (9,81). Thus, the cumulative evidence indicates that although fission yeasts and plants exhibit TATA elements upstream of their tRNA genes, S. pombe is more obligatorily dependent on the TATA promoter element for transcription.…”

Section: Species Specificity Of Pol Iii-dependent Trna Transcriptionsupporting

confidence: 87%

“…A CAA motif was noted to be a transcription initiation site for plant tRNA (81). The analysis in Fig.…”

Section: Species Specificity Of Pol Iii-dependent Trna Transcriptionmentioning

confidence: 96%

“…TATA elements have been noted upstream of tRNA genes in A. thaliana, and a TATA element has been reported to effect reinitiation of tRNA transcription in tobacco (13,81). A CAA motif was noted to be a transcription initiation site for plant tRNA (81).…”

Section: Species Specificity Of Pol Iii-dependent Trna Transcriptionmentioning

confidence: 99%

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Widespread Use of TATA Elements in the Core Promoters for RNA Polymerases III, II, and I in Fission Yeast

Hamada

Huang

Lowe

et al. 2001

Molecular and Cellular Biology

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In addition to directing transcription initiation, core promoters integrate input from distal regulatory elements. Except for rare exceptions, it has been generally found that eukaryotic tRNA and rRNA genes do not contain TATA promoter elements and instead use protein-protein interactions to bring the TATA-binding protein (TBP), to the core promoter. Genomewide analysis revealed TATA elements in the core promoters of tRNA and 5S rRNA (Pol III), U1 to U5 snRNA (Pol II), and 37S rRNA (Pol I) genes in Schizosaccharomyces pombe. Using tRNA-dependent suppression and other in vivo assays, as well as in vitro transcription, we demonstrated an obligatory requirement for upstream TATA elements for tRNA and 5S rRNA expression in S. pombe. The Pol III initiation factor Brf is found in complexes with TFIIIC and Pol III in S. pombe, while TBP is not, consistent with independent recruitment of TBP by TATA. Template commitment assays are consistent with this and confirm that the mechanisms of transcription complex assembly and initiation by Pol III in S. pombe differ substantially from those in other model organisms. The results were extended to large-rRNA synthesis, as mutation of the TATA element in the Pol I promoter also abolishes rRNA expression in fission yeast. A survey of other organisms' genomes reveals that a substantial number of eukaryotes may use widespread TATAs for transcription. These results indicate the presence of TATA-unified transcription systems in contemporary eukaryotes and provide insight into the residual need for TBP by all three Pols in other eukaryotes despite a lack of TATA elements in their promoters.Structural similarities shared by the RNA polymerases (Pols) of bacteria, archaea, and eukarya reflect a deep-rooted common ancestry of transcription systems in all organisms on earth. Archaea and eukaryotes exhibit greater similarity to each other in their Pol subunits, accessory transcription factors (TFs), and promoter elements than either does to bacteria (36). In eukaryotes, Pol I synthesizes large rRNA (35S to 45S, depending on the species); Pol II synthesizes mRNAs and some small nuclear (sn) RNAs, such as U1 to U5; and Pol III synthesizes mostly tRNAs and 5S rRNA, as well as U6 snRNA and a few other transcripts (53).The core promoter orchestrates polymerase recruitment, promoter activity, and response to regulatory input (59, 66). In eukaryotes, TATA promoter elements direct transcription by Pol II of a large subset of (but not all) protein-encoding genes, but often not the far fewer snRNA genes that are transcribed by Pol II. While TATA elements are found in a minute fraction of Pol III genes, they are generally not found in the core promoter regions of Pol I genes (53). Intriguingly, despite the lack of TATA promoter elements, Pols I, II, and III all require TATA-binding protein (TBP) for initiation (17). Archaea use widespread TATA-like promoters and a TBP ortholog to direct transcription by a single Pol of all gene types, those encoding tRNA, rRNA, and mRNAs (reviewed in reference 67). Or...

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Section: Species Specificity Of Pol Iii-dependent Trna Transcriptionsupporting

confidence: 87%

“…A CAA motif was noted to be a transcription initiation site for plant tRNA (81). The analysis in Fig.…”

Section: Species Specificity Of Pol Iii-dependent Trna Transcriptionmentioning

confidence: 96%

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Widespread Use of TATA Elements in the Core Promoters for RNA Polymerases III, II, and I in Fission Yeast

Hamada

Huang

Lowe

et al. 2001

Molecular and Cellular Biology

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“…There are hybrid promoters like the U6 snRNA gene in S. cerevisiae that contain both internal promoters and a TATA box 61,62 which contributes to better transcription. 63,64,65 Microsatellites -The different microsatellites arrangements between genera at the NTS region are the main contributors to the variation in the NTS length. It has been shown that there is a correlation between the length of the NTS region and the number of motif repetitions within each region of microsatellites in Rajiformes.…”

Section: Nts Regionmentioning

confidence: 99%

Molecular organization of the 5S rDNA gene type II in elasmobranchs

et al. 2015

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The 5S rDNA gene is a non-coding RNA that can be found in 2 copies (type I and type II) in bony and cartilaginous fish. Previous studies have pointed out that type II gene is a paralog derived from type I. We analyzed the molecular organization of 5S rDNA type II in elasmobranchs. Although the structure of the 5S rDNA is supposed to be highly conserved, our results show that the secondary structure in this group possesses some variability and is different than the consensus secondary structure. One of these differences in Selachii is an internal loop at nucleotides 7 and 112. These mutations observed in the transcribed region suggest an independent origin of the gene among Batoids and Selachii. All promoters were highly conserved with the exception of BoxA, possibly due to its affinity to polymerase III. This latter enzyme recognizes a dT 4 sequence as stop signal, however in Rajiformes this signal was doubled in length to dT 8. This could be an adaptation toward a higher efficiency in the termination process. Our results suggest that there is no TATA box in elasmobranchs in the NTS region. We also provide some evidence suggesting that the complexity of the microsatellites present in the NTS region play an important role in the 5S rRNA gene since it is significantly correlated with the length of the NTS.

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“…24 and references therein). In some eukaryotic genomes, the upstream regions of ICR-containing class III genes are characterized by the presence of a TATA box, starting at around Ϫ30, which strongly contributes to transcription efficiency as an essential component of the promoter (25,26). In some cases, the upstream TATA element can even allow for TFIIIC-independent in vitro transcription (27,28).…”

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confidence: 99%

A Minimal Promoter for TFIIIC-dependent in Vitro Transcription of snoRNA and tRNA Genes by RNA Polymerase III

Guffanti

Ferrari

Preti

et al. 2006

Journal of Biological Chemistry

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The Saccharomyces cerevisiae SNR52 gene is unique among the snoRNA coding genes in being transcribed by RNA polymerase III. The primary transcript of SNR52 is a 250-nucleotide precursor RNA from which a long leader sequence is cleaved to generate the mature snR52 RNA. We found that the box A and box B sequence elements in the leader region are both required for the in vivo accumulation of the snoRNA. As expected box B, but not box A, was absolutely required for stable TFIIIC, yet in vitro. Surprisingly, however, the box B was found to be largely dispensable for in vitro transcription of SNR52, whereas the box A-mutated template effectively recruited TFIIIB; yet it was transcriptionally inactive. Even in the complete absence of box B and both upstream TATA-like and T-rich elements, the box A still directed efficient, TFIIIC-dependent transcription. Box B-independent transcription was also observed for two members of the tRNA Asn (GTT) gene family, but not for two tRNA Pro (AGG) gene copies. Fully recombinant TFIIIC supported box B-independent transcription of both SNR52 and tRNA Asn genes, but only in the presence of TFIIIB reconstituted with a crude B؆ fraction. Non-TFIIIB component(s) in this fraction were also required for transcription of wild-type SNR52. Transcription of the box B-less tRNA Asn genes was strongly influenced by their 5-flanking regions, and it was stimulated by TBP and Brf1 proteins synergistically. The box A can thus be viewed as a core TFIIICinteracting element that, assisted by upstream TFIIIB-DNA contacts, is sufficient to promote class III gene transcription.RNA polymerase (Pol) 3 III synthesizes tRNA, 5 S rRNA, and a variety of other types of small nuclear and cytoplasmic RNAs. In general, the transcription of class III genes is under the control of internal control regions (ICR) characterized by discontinuous structures, with essential boxes separated by non-essential nucleotides (1). In the case of tRNA and 5 S rRNA genes, the ICRs are highly conserved and comprise the binding sites for the general transcription factor TFIIIC (box A and box B) and for the 5 S-specific factor TFIIIA (box C). Once assembled, TFIIIC recruits TFIIIB upstream of the transcription start site (TSS); TFIIIB in turn recruits Pol III for transcription initiation. The strong conservation of the ICRs likely reflects their dual function as both nucleation sites for transcription complex assembly and key determinants of tRNA and 5 S rRNA structure. An indication of the constraints imposed on ICR by their overlapping structural and functional roles comes from the variability of promoter organizations displayed by the minority of class III genes not coding for tRNA and 5 S rRNA. In some of these genes, the TFIIIC-interacting control regions (box A and box B) have been maintained within the transcribed region, and adapted to the structure of the small RNA without losing the transcriptional function. For example, in the Saccharomyces cerevisiae SCR1 gene, coding for the 7SL RNA, box A and box B are both intragenic an...

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The TATA motif, the CAA motif and the poly(T) transcription termination motif are all important for transcription re‐initiation on plant tRNA genes

Cited by 44 publications

References 41 publications

Widespread Use of TATA Elements in the Core Promoters for RNA Polymerases III, II, and I in Fission Yeast

Widespread Use of TATA Elements in the Core Promoters for RNA Polymerases III, II, and I in Fission Yeast

Molecular organization of the 5S rDNA gene type II in elasmobranchs

A Minimal Promoter for TFIIIC-dependent in Vitro Transcription of snoRNA and tRNA Genes by RNA Polymerase III

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