Distinct modes of TATA box utilization by the RNA polymerase III transcription machineries from budding yeast and higher plants

Dieci, Giorgio; Yukawa, Yasushi; Alzapiedi, Mircko; Guffanti, Elisa; Ferrari, Roberto; Sugiura, Masahiro; Ottonello, Simone

doi:10.1016/j.gene.2006.03.013

Cited by 17 publications

(7 citation statements)

References 53 publications

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“…Evidence that plant tRNA genes rely on upstream TATA elements for pol III transcription ((47, 94), and refs therein) were supported by genome-wide analysis (42, 86). A majority of human tRNA genes engage TBP at upstream TATA promoters (43).…”

Section: Nonsense Suppressionmentioning

confidence: 84%

“…Thus, while TFIIIB subunits share sequence homology in the two yeasts, they differ in interaction mechanisms. Similarly, features specific to plant TBP and Brf1 rather than tRNA gene upstream architecture per se , are responsible for TATA box dependence (47). The physiologic ramifications of these differences in TBP recruitment mechanisms remain to be uncovered.…”

Section: Nonsense Suppressionmentioning

confidence: 99%

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A methods review on use of nonsense suppression to study 3′ end formation and other aspects of tRNA biogenesis

Rijal

Maraia

Arimbasseri

2015

Gene

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Suppressor tRNAs bear anticodon mutations that allow them to decode premature stop codons in metabolic marker gene mRNAs, that can be used as in vivo reporters of functional tRNA biogenesis. Here, we review key components of a suppressor tRNA system specific to S. pombe and its adaptations for use to study specific steps in tRNA biogenesis. Eukaryotic tRNA biogenesis begins with transcription initiation by RNA polymerase (pol) III. The nascent pre-tRNAs must undergo folding, 5′ and 3′ processing to remove the leader and trailer, nuclear export, and splicing if applicable, while multiple complex chemical modifications occur throughout the process. We review evidence that precursor-tRNA processing begins with transcription termination at the oligo(T) terminator element, which forms a 3′ oligo(U) tract on the nascent RNA, a sequence-specific binding site for the RNA chaperone, La protein. The processing pathway bifurcates depending on a poorly understood property of pol III termination that determines the 3′ oligo(U) length and therefore the affinity for La. We thus review the pol III termination process and the factors involved including advances using gene-specific random mutagenesis by dNTP analogs that identify key residues important for transcription termination in certain pol III subunits. The review ends with a ‘technical approaches’ section that includes a parts lists of suppressor-tRNA alleles, strains and plasmids, and graphic examples of its diverse uses.

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Section: Nonsense Suppressionmentioning

confidence: 84%

Section: Nonsense Suppressionmentioning

confidence: 99%

A methods review on use of nonsense suppression to study 3′ end formation and other aspects of tRNA biogenesis

Rijal

Maraia

Arimbasseri

2015

Gene

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“…Therefore, TATA-like sequence-dependent transcription of tRNA genes may predominate in algae. This possibility is supported by the fact that an upstream TATA box is well conserved and functionally important for transcription of tRNA genes in some plants and fungi (Choisne et al, 1997, 1998; Yukawa et al, 2000; Hamada et al, 2001; Dieci et al, 2006). In addition, transcription of Saccharomyces cerevisiae tRNA genes harboring an upstream TATA box proceeds without TFIIIC in vitro (Dieci et al, 2000).…”

Section: Transcription Of Permuted Trna Genesmentioning

confidence: 99%

“…Polymerase III C (TFIIIC), a multi-subunit complex of transcription factors that is essential for transcription by RNAPIII, binds to the A and B boxes simultaneously and promotes binding of the TFIIIB complex, which includes the TATA-box binding protein, to the region upstream of the tRNA sequence, followed by recruitment of RNAPIII. The dependency of transcription of tRNA genes on the A and B boxes is predominantly conserved; however, the additional requirements for transcription are diverse among organisms and the upstream region sometimes contributes to the efficiency of the initiation step (Choisne et al, 1998; Yukawa et al, 2000; Hamada et al, 2001; Giuliodori et al, 2003; Dieci et al, 2006). …”

Section: Transcription Of Permuted Trna Genesmentioning

confidence: 99%

Circularly permuted tRNA genes: their expression and implications for their physiological relevance and development

Soma

2014

Front. Genet.

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A number of genome analyses and searches using programs that focus on the RNA-specific bulge-helix-bulge (BHB) motif have uncovered a wide variety of disrupted tRNA genes. The results of these analyses have shown that genetic information encoding functional RNAs is described in the genome cryptically and is retrieved using various strategies. One such strategy is represented by circularly permuted tRNA genes, in which the sequences encoding the 5′-half and 3′-half of the specific tRNA are separated and inverted on the genome. Biochemical analyses have defined a processing pathway in which the termini of tRNA precursors (pre-tRNAs) are ligated to form a characteristic circular RNA intermediate, which is then cleaved at the acceptor-stem to generate the typical cloverleaf structure with functional termini. The sequences adjacent to the processing site located between the 3′-half and the 5′-half of pre-tRNAs potentially form a BHB motif, which is the dominant recognition site for the tRNA-intron splicing endonuclease, suggesting that circularization of pre-tRNAs depends on the splicing machinery. Some permuted tRNAs contain a BHB-mediated intron in their 5′- or 3′-half, meaning that removal of an intron, as well as swapping of the 5′- and 3′-halves, are required during maturation of their pre-tRNAs. To date, 34 permuted tRNA genes have been identified from six species of unicellular algae and one archaeon. Although their physiological significance and mechanism of development remain unclear, the splicing system of BHB motifs seems to have played a key role in the formation of permuted tRNA genes. In this review, current knowledge of circularly permuted tRNA genes is presented and some unanswered questions regarding these species are discussed.

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“…When present, the TATA box profoundly influences TSS selection by Pol III, in cooperation with the A box-bound τA sub-complex of TFIIIC. In particular, τA is thought to open a window within which TBP selects a TATA (or a TATA-like) sequence onto which TFIIIB assembles; Pol III is then recruited by TFIIIB and initiates transcription 28-30 bp downstream of the 5′ end of the TATA element (Dieci et al, 2006;Joazeiro et al, 1996).…”

Section: Upstream Elements In Tfiiic-dependent Pol III Transcriptionmentioning

confidence: 99%

RNA polymerase III transcription control elements: Themes and variations

Orioli

Pascali

Pagano

et al. 2012

Gene

Self Cite

126

113

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Distinct modes of TATA box utilization by the RNA polymerase III transcription machineries from budding yeast and higher plants

Cited by 17 publications

References 53 publications

A methods review on use of nonsense suppression to study 3′ end formation and other aspects of tRNA biogenesis

A methods review on use of nonsense suppression to study 3′ end formation and other aspects of tRNA biogenesis

Circularly permuted tRNA genes: their expression and implications for their physiological relevance and development

RNA polymerase III transcription control elements: Themes and variations

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