Transfer RNA genes from Dictyostelium discoideum are frequently associated with repetitive elements and contain consensus boxes in their 5′ and 3′-flanking regions

Hofmann, Jörg; Schumann, Gerald G.; Borschet, Gabi; Gösseringer, Roger; Bach, M. C.; Bertling, Wolf; Marschalek, Rolf; Dingermann, Theo

doi:10.1016/0022-2836(91)90495-r

Cited by 44 publications

(49 citation statements)

References 69 publications

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“…The derived B-box consensus GTCNNNNG 53 T TCRANYC closely matches B-box sequences from the tRNA genes of other eukaryotes. The presence of "extra" B (exB) boxes located downstream of D. discoideum tRNA genes has been previously noted (25). We inspected the complete list of D. discoideum tRNA genes and confirmed the presence of tRNA gene-associated exB boxes that are 41 bp on average (ranging from 33 to 60 bp; n ϭ 261) downstream of the geneinternal B boxes of 66% of all D. discoideum tRNA genes.…”

Section: Resultssupporting

confidence: 67%

Role of RNA Polymerase III Transcription Factors in the Selection of Integration Sites by the Dictyostelium Non-Long Terminal Repeat Retrotransposon TRE5-A

Siol

Boutliliss

Chung

et al. 2006

Molecular and Cellular Biology

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In the compact Dictyostelium discoideum genome, non-long terminal repeat (non-LTR) retrotransposons known as TREs avoid accidental integration-mediated gene disruption by targeting the vicinity of tRNA genes. In this study we provide the first evidence that proteins of a non-LTR retrotransposon interact with a target-specific transcription factor to direct its integration. We applied an in vivo selection system that allows for the isolation of natural TRE5-A integrations into a known genomic location upstream of tRNA genes. TRE5-A frequently modified the integration site in a way characteristic of other non-LTR retrotransposons by adding nontemplated extra nucleotides and generating small and extended target site deletions. Mutations within the B-box promoter of the targeted tRNA genes interfered with both the in vitro binding of RNA polymerase III transcription factor TFIIIC and the ability of TRE5-A to target these genes. An isolated B box was sufficient to enhance TRE5-A integration in the absence of a surrounding tRNA gene. The RNA polymerase III-transcribed ribosomal 5S gene recruits TFIIIC in a B-box-independent manner, yet it was readily targeted by TRE5-A in our assay. These results suggest a direct role of an RNA polymerase III transcription factor in the targeting process.

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Section: Resultssupporting

confidence: 67%

Role of RNA Polymerase III Transcription Factors in the Selection of Integration Sites by the Dictyostelium Non-Long Terminal Repeat Retrotransposon TRE5-A

Siol

Boutliliss

Chung

et al. 2006

Molecular and Cellular Biology

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“…Yeast Ty1-4 and Dictyostelium TRE5 and TRE3 are targeted to tDNAs (141)(142)(143)(144)(145); Ty5 integrates into heterochromatin (146); Maggy chromodomain element targets H3K9Me (147), and Tf1 targets intergenic regions (see Levin,Chapter 43). Of the characterized retroelements, Ty3 has the most specific pattern of integration.…”

Section: Integrase and Integration Functions Of Integrasementioning

confidence: 99%

Ty3, a Position-specific Retrotransposon in Budding Yeast

Sandmeyer

Patterson²,

Bilanchone³

2015

Microbiol Spectr

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Long terminal repeat (LTR) retrotransposons constitute significant fractions of many eukaryotic genomes. Two ancient families are Ty1/Copia (Pseudoviridae) and Ty3/Gypsy (Metaviridae). The Ty3/Gypsy family probably gave rise to retroviruses based on the domain order, similarity of sequences, and the envelopes encoded by some members. The Ty3 element of Saccharomyces cerevisiae is one of the most completely characterized elements at the molecular level. Ty3 is induced in mating cells by pheromone stimulation of the mitogen-activated protein kinase pathway as cells accumulate in G1. The two Ty3 open reading frames are translated into Gag3 and Gag3-Pol3 polyprotein precursors. In haploid mating cells Gag3 and Gag3-Pol3 are assembled together with Ty3 genomic RNA into immature virus-like particles in cellular foci containing RNA processing body proteins. Virus-like particle Gag3 is then processed by Ty3 protease into capsid, spacer, and nucleocapsid, and Gag3-Pol3 into those proteins and additionally, protease, reverse transcriptase, and integrase. After haploid cells mate and become diploid, genomic RNA is reverse transcribed into cDNA. Ty3 integration complexes interact with components of the RNA polymerase III transcription complex resulting in Ty3 integration precisely at the transcription start site. Ty3 activation during mating enables proliferation of Ty3 between genomes and has intriguing parallels with metazoan retrotransposon activation in germ cell lineages. Identification of nuclear pore, DNA replication, transcription, and repair host factors that affect retrotransposition has provided insights into how hosts and retrotransposons interact to balance genome stability and plasticity.

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“…To date, attempts to study in vitro transcription using whole cell extracts have been unsuccessful. This system would be especially helpful to study in vitro the position-specific integration mechanism of the Dictyostelium repetitive element upstream of tRNA genes, since it appears to use RNA polymerase I11 transcription factors assembled on tRNA genes as a landmark in this process (Hofmann et al, 1991). An in vitro transcription system would also allow a detailed analysis of the possible involvement in transcriptional regulation of an external B-block sequence identified at the 3' end of D. discoideum tRNA genes.…”

Section: Isolation Of Transcription Factor Iiic From Dictyostelium DImentioning

confidence: 99%

“…An in vitro transcription system would also allow a detailed analysis of the possible involvement in transcriptional regulation of an external B-block sequence identified at the 3' end of D. discoideum tRNA genes. These so called exB motifs are present in approximately 80% of the tRNA genes analysed so far and may be a unique feature of the D. discoideum genome (Hofmann et a]., 1991).…”

Section: Isolation Of Transcription Factor Iiic From Dictyostelium DImentioning

confidence: 99%

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Isolation of transcription factor IIIC from Dictyostelium discoideum

Bukenberger

Dingermann

Meißner³

et al. 1994

European Journal of Biochemistry

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Transcription factor IIIC (TFIIIC) binds in a sequence-specific manner to RNA-polymerase-IIItranscribed genes (e.g. tRNA genes). It sequesters other transcription factors into the preformed complex, thereby activating transcription by RNA polymerase 111. The Dictyostelium discoideum homologue of TFIIIC was highly purified by af€inity chromatography based on its tDNA-binding activity. This TFIIIC homologue is a multicomponent factor (molecular mass 380 kDa), which binds to the B-box element of the internal tRNA gene promoter without significant A-box interaction. Partially purified D. discoideum TFIIIC is able to functionally complement a human RNA polymerase I11 in vitro transcription system depleted of human TFIIIC. We provide evidence that partially purified D. discoideum TFIIIC interacts in vitro with gene-external B-box elements present downstream of many D. discoideum tRNA genes.DNA-dependent RNA polymerase I11 of eukaryotes catalyses the synthesis of tRNA, 5s rRNA, some small cellular RNAs (e.g. U6 snRNA), and some small viral transcripts (e.g. the adenovirus VA1 RNA; Geiduschek and TocchiniValentini, 1988 ;Willis, 1993). TFIIIC is a universally needed, sequence-specific RNA polymerase I11 transcription factor and is the first protein that binds to the internal promoter sequence of tRNA and viral VA1 genes. The TFIIIC . DNA complex sequesters TFIIIB, a factor that determines RNA polymerase I11 specificity and initiates transcription.TFIIIC has been characterised in considerable detail in several organisms. In all analysed cases, TFIIIC is a multimeric protein complex of at least five proteins (Gabrielsen et al., 1989;Kassavetis et al., 1990;Dean and Berk, 1987;Yoshinaga et al., 1989). A model derived from data using the yeast factor (also called z factor) suggests that TFIIIC may be composed of two functional domains (z, and tB), interacting with the A-block and B-block elements of the internal RNA polymerase I11 promoters (Marzouki et al., 1986;Bartholomew et al., 1990). Affinity-labeling experiments determined that the 138-kDa and 95-kDa subunits of Saccharomyces cerevisiae TFIIIC bind to the B-block and Ablock sequence of the internal promoter, respectively (Bartholomew et al., 1990). Recently, the primary structures of the 138-, 131-and 95-kDa subunits of yeast TFIIIC were reported, deduced from cDNA cloning of the respective genes (Lefebvre et al., 1992). Unlike the yeast factor , human TFIIIC (hTFIIIC) can be separated by chromatography into two domains. TFIIIC2 binds exclu-

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Transfer RNA genes from Dictyostelium discoideum are frequently associated with repetitive elements and contain consensus boxes in their 5′ and 3′-flanking regions

Cited by 44 publications

References 69 publications

Role of RNA Polymerase III Transcription Factors in the Selection of Integration Sites by the Dictyostelium Non-Long Terminal Repeat Retrotransposon TRE5-A

Role of RNA Polymerase III Transcription Factors in the Selection of Integration Sites by the Dictyostelium Non-Long Terminal Repeat Retrotransposon TRE5-A

Ty3, a Position-specific Retrotransposon in Budding Yeast

Isolation of transcription factor IIIC from Dictyostelium discoideum

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