Allele-specific protein-DNA interactions between the single-stranded DNA-binding protein, ssA-TIBF, and DNA replication determinants in Tetrahymena 1 1Edited by T. Richmond

Saha, Swati; Kapler, Geoffrey M.

doi:10.1006/jmbi.1999.3365

Cited by 9 publications

(17 citation statements)

References 46 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In contrast to previously described replication initiation factors, these proteins bind exclusively to single-stranded DNA, specifically recognizing the A-rich strand of type I elements (33,46,52). Affinity-purified TIF1 also binds to the T-rich type I element strand in vitro.…”

mentioning

confidence: 78%

Characterization of a Novel Origin Recognition Complex-Like Complex: Implications for DNA Recognition, Cell Cycle Control, and Locus-Specific Gene Amplification

Mohammad

York

Hommel

et al. 2003

Molecular and Cellular Biology

View full text Add to dashboard Cite

The origin recognition complex (ORC) plays a central role in eukaryotic DNA replication. Here we describe a unique ORC-like complex in Tetrahymena thermophila, TIF4, which bound in an ATP-dependent manner to sequences required for cell cycle-controlled replication and gene amplification (ribosomal DNA [rDNA] type I elements). TIF4's mode of DNA recognition was distinct from that of other characterized ORCs, as it bound exclusively to single-stranded DNA. In contrast to yeast ORCs, TIF4 DNA binding activity was cell cycle regulated and peaked during S phase, coincident with the redistribution of the Orc2-related subunit, p69, from the cytoplasm to the macronucleus. Origin-binding activity and nuclear p69 immunoreactivity were further regulated during development, where they distinguished replicating from nonreplicating nuclei. Both activities were lost from germ line micronuclei following the programmed arrest of micronuclear replication. Replicating macronuclei stained with Orc2 antibodies throughout development in wild-type cells but failed to do so in the amplification-defective rmm11 mutant. Collectively, these findings indicate that the regulation of TIF4 is intimately tied to the cell cycle and developmentally programmed replication cycles. They further implicate TIF4 in rDNA gene amplification. As type I elements interact with other sequence-specific single-strand breaks (in vitro and in vivo), the dynamic interplay of Orc-like (TIF4) and non-ORC-like proteins with this replication determinant may provide a novel mechanism for regulation.

show abstract

mentioning

confidence: 78%

Characterization of a Novel Origin Recognition Complex-Like Complex: Implications for DNA Recognition, Cell Cycle Control, and Locus-Specific Gene Amplification

Mohammad

York

Hommel

et al. 2003

Molecular and Cellular Biology

View full text Add to dashboard Cite

show abstract

“…TIF1 was previously shown to bind to essential replication determinants in the T. thermophila rDNA minichromosome (Umthun et al, 1994;Saha and Kapler, 2000) and generate in vivo marks that distinguish the sites for replication and transcription initiation (Saha et al, 2001). In the work presented here we provide evidence that TIF1 regulates rDNA origin firing.…”

Section: Discussionmentioning

confidence: 99%

“…Promoter-proximal type I elements are also required for rRNA transcription (Gallagher and Blackburn, 1998 Umthun et al, 1994;Mohammad et al, 2000). In contrast to ORC and non-ORC replicator proteins in other systems, all four TIFs associate exclusively with single-stranded DNA in vitro (Mohammad et al, 2000(Mohammad et al, , 2003Saha and Kapler, 2000). Consistent with an in vivo role for these sequence-specific single-stranded DNA binding proteins (ss-SSBs), in vivo footprinting studies indicate that the Tetrahymena rDNA origin and promoter regions are naturally unwound in native chromosomes (Saha et al, 2001).…”

mentioning

confidence: 99%

TIF1 Represses rDNA Replication Initiation, but Promotes Normal S Phase Progression and Chromosome Transmission inTetrahymena

Morrison

Yakisich

Cassidy-Hanley

et al. 2005

MBoC

View full text Add to dashboard Cite

The non-ORC protein, TIF1, recognizes sequences in the Tetrahymena thermophila ribosomal DNA (rDNA) minichromosome that are required for origin activation. We show here that TIF1 represses rDNA origin firing, but is required for proper macronuclear S phase progression and division. TIF1 mutants exhibit an elongated macronuclear S phase and diminished rate of DNA replication. Despite this, replication of the rDNA minichromosome initiates precociously. Because rDNA copy number is unaffected in the polyploid macronucleus, mechanisms that prevent reinitiation appear intact. Although mutants exit macronuclear S with a wild-type DNA content, division of the amitotic macronucleus is both delayed and abnormal. Nuclear defects are also observed in the diploid mitotic micronucleus, as TIF1 mutants lose a significant fraction of their micronuclear DNA. Hence, TIF1 is required for the propagation and subsequent transmission of germline chromosomes. The broad phenotypes associated with a TIF1-deficiency suggest that this origin binding protein is required globally for the proper execution and/or monitoring of key chromosomal events during S phase and possibly at later stages of the cell cycle. We propose that micro-and macronuclear defects result from exiting the respective nuclear S phases with physically compromised chromosomes. INTRODUCTIONThe initiation of eukaryotic DNA replication is regulated by protein-DNA interactions that occur within defined chromosomal domains, termed replicators or replicons. Eukaryotic replicators are modular and contain binding sites for the conserved six-subunit origin recognition complex (ORC;Bell and Stillman, 1992) and non-ORC DNA binding proteins (Marahrens and Stillman, 1992). ORC plays a central role, recruiting proteins involved in replication initiation and elongation to form the prereplicative complex (pre-RC). These proteins include a replicative helicase-the minichromosome maintenance (MCM) complex (Ishimi, 1997;Labib et al., 2000) and factors that regulate origin activation, such as Cdc6 and Cdt1 (Nishitani et al., 2000;Oehlmann et al., 2004).Although ORC binding sites are plentiful in the Saccharomyces cerevisiae (Sc) genome, only a fraction are routinely engaged in replication initiation (Theis and Newlon, 1993;Wyrick et al., 2001). Genetic studies indicate that ScORC binding is necessary, but not sufficient, to confer replicator status to a chromosomal domain. Although ScORC binds DNA in a sequence-specific manner, metazoan ORCs exhibit no obvious sequence-specificity, displaying a preference for degenerate, asymmetric A:T-rich sequences in vitro (Austin et al., 1999;Chesnokov et al., 2001;Vashee et al., 2001) and in vivo (Kong et al., 2003;Vashee et al., 2003). This relaxed specificity is similar to Schizosaccharomyces pombe (Sp) ORC, which binds DNA via an unusual A-T hook domain in its Orc4 subunit (Chuang and Kelly, 1999;Kong and DePamphilis, 2001). Although metazoan ORCs lack AT hooks, they still associate with specific replicator domains in vivo (Austin et al., 1999;Abdur...

show abstract

“…Furthermore, promoter-proximal type I elements are the only genetically defined components of the rRNA promoter (23,24). Sequences immediately downstream of type I elements are important for their recognition by sequence-specific DNA-binding proteins (25). Mutations in these downstream sequences can confer different cellular phenotypes.…”

mentioning

confidence: 99%

“…The most extensively studied type I element binding activity, TIF1 (previously designated ssA-TIBF), is a homotetramer with a subunit molecular mass of 21 kDa (25,28,29). Purified TIF1 binds in a sequence-specific manner to single-stranded DNA corresponding to either the A-rich or T-rich strand of the type I elements, raising the possibility that it stabilizes replication origins in an unwound state (25).…”

mentioning

confidence: 99%

Cloning and Biochemical Analysis of the TetrahymenaOrigin Binding Protein TIF1

Saha

Nicholson

Kapler

2001

Journal of Biological Chemistry

Self Cite

View full text Add to dashboard Cite

Cis-acting type I elements regulate the initiation of DNA replication, replication fork movement, and transcription of the Tetrahymena thermophila rDNA minichromosome and are required for cell cycle-controlled replication and developmentally programmed gene amplification. Previous studies identified three in vitro single-stranded type I element binding activities that were proposed to play distinct roles in replication control. Here we describe the cloning of one of these genes, TIF1, and we provide evidence for its association with type I elements in vivo. Furthermore, we show that TIF1 interacts (in vitro and in vivo) with pause site elements (PSE), which co-localize with replication initiation and fork arrest sites, and are shown to be essential. The in vivo accessibility of PSE and type I elements to potassium permanganate suggests that origin regions are frequently unwound in native chromatin. TIF1 contains sequence similarity to the Solanum tuberosum single strand-specific transcription factor, p24, and a related Arabidopsis protein. Antisense inhibition studies suggest that TIF1 competes with other proteins for PSE and type I element binding. TIF1 displays a marked strand bias in vivo, discriminating between origin-and promoter-proximal type I elements. We propose that this bias selectively modulates the binding of a different subset of proteins to the respective regulatory elements.

show abstract

Allele-specific protein-DNA interactions between the single-stranded DNA-binding protein, ssA-TIBF, and DNA replication determinants in Tetrahymena 1 1Edited by T. Richmond

Cited by 9 publications

References 46 publications

Characterization of a Novel Origin Recognition Complex-Like Complex: Implications for DNA Recognition, Cell Cycle Control, and Locus-Specific Gene Amplification

Characterization of a Novel Origin Recognition Complex-Like Complex: Implications for DNA Recognition, Cell Cycle Control, and Locus-Specific Gene Amplification

TIF1 Represses rDNA Replication Initiation, but Promotes Normal S Phase Progression and Chromosome Transmission inTetrahymena

Cloning and Biochemical Analysis of the TetrahymenaOrigin Binding Protein TIF1

Contact Info

Product

Resources

About