A direct interaction between a DNA-tracking protein and a promoter recognition protein: implications for searching DNA sequence.

Tinker-Kulberg, Rachel; Fu, Tsu-Ju; Geiduschek, E. Peter; Kassavetis, George A.

doi:10.1002/j.1460-2075.1996.tb00883.x

Cited by 26 publications

(22 citation statements)

References 51 publications

(26 reference statements)

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“…First, heterologous DNA binding proteins were used to trap a putatively tracking MOT1 molecule on DNA. This approach has been used previously to demonstrate DNA tracking by replication and transcription factors (40,41). If MOT1 disrupts TBP-DNA complexes by using ATP hydrolysis to processively track along DNA, we reasoned that it might be possible to detect these putative ATP-dependent MOT1-DNA-tracking complexes with heterologous DNA binding proteins which might prevent MOT1 from translocating off the end of a linear DNA molecule.…”

Section: Resultsmentioning

confidence: 99%

Testing for DNA Tracking by MOT1, a SNF2/SWI2 Protein Family Member

Auble

Steggerda

1999

Molecular and Cellular Biology

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Proteins in the SNF2/SWI2 family use ATP hydrolysis to catalyze rearrangements in diverse protein-DNA complexes. How ATP hydrolysis is coupled to these rearrangements is unknown, however. One attractive model is that these ATPases are ATP-dependent DNA-tracking enzymes. This idea was tested for the SNF2/SWI2 protein family member MOT1. MOT1 is an essential Saccharomyces cerevisiae transcription factor that uses ATP to dissociate TATA binding protein (TBP) from DNA. By using a series of DNA templates with one or two TATA boxes in combination with binding sites for heterologous DNA binding "roadblock" proteins, the ability of MOT1 to track along DNA was assayed. The results demonstrate that, following ATP-dependent TBP-DNA dissociation, MOT1 dissociates rapidly from the DNA by a mechanism that does not require a DNA end. Template commitment footprinting experiments support the conclusion that ATP-dependent DNA tracking by MOT1 does not occur. These results support a model in which MOT1 drives TBP-DNA dissociation by a mechanism that involves a transient, ATP-dependent interaction with TBP-DNA which does not involve ATP-dependent DNA tracking.The SNF2/SWI2 protein family is a large group of evolutionarily conserved ATPases with diverse functions in transcriptional control, DNA repair, and chromosome segregation (10, 30). Genetic and biochemical approaches have revealed that several of these proteins function by using ATP hydrolysis to drive alterations in protein-DNA contacts. For example, SNF2/SWI2 and related proteins in Drosophila melanogaster and humans are components of large macromolecular complexes which can disrupt nucleosome structure in vitro in an ATP-dependent reaction (4,5,7,18,20,24,29,43,44). Another member of this family, ISWI (11), is a component of distinct complexes which can function both in nucleosome remodeling and in the ATP-dependent formation of closely spaced nucleosome arrays (19,28,42,45). All SNF2/SWI2 protein family members which have been tested contain an ATPase which is essential for in vitro and in vivo function (2,21,25). The intrinsic ATPase activity of these proteins is low or undetectable but can be activated by DNA, proteins, or protein-DNA complexes with which these ATPases are known to interact (3,6,15,25,31,39).Based on these data, one hypothesis is that all SNF2/SWI2 family members participate in ATP-dependent reactions which result in alterations of protein-DNA contacts. ATP-dependent alterations of nucleosome structure can explain how SNF2/ SWI2 and related complexes render the chromatin template accessible to the transcription machinery (43). Likewise, the essential transcriptional regulator MOT1 modulates transcription by catalyzing the ATP-dependent dissociation of TATA binding protein (TBP) from DNA (2). By extension, the roles of SNF2/SWI2 family members in DNA repair may reflect ATP-dependent dissociation or rearrangement of proteins on damaged DNA as an obligate part of certain repair pathways. Despite the apparently widespread utilization of the conserved SNF2/SW...

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Section: Resultsmentioning

confidence: 99%

Testing for DNA Tracking by MOT1, a SNF2/SWI2 Protein Family Member

Auble

Steggerda

1999

Molecular and Cellular Biology

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“…Activated late promoters outcompete middle promoters on the same plasmid in vitro, especially at higher ionic strengths. This advantage is enhanced by ADP-ribosylation of RNAP ␣ subunits and by binding of the phage-encoded RpbA protein to the RNAP core (552,1082,1173). DsbA protein is thought to also affect transcription from some late promoters (995), although it is not essential (1114).…”

Section: Late Transcriptionmentioning

confidence: 99%

Bacteriophage T4 Genome

Miller

Kutter

Mosig

et al. 2003

Microbiol Mol Biol Rev

701

801

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SUMMARY Phage T4 has provided countless contributions to the paradigms of genetics and biochemistry. Its complete genome sequence of 168,903 bp encodes about 300 gene products. T4 biology and its genomic sequence provide the best-understood model for modern functional genomics and proteomics. Variations on gene expression, including overlapping genes, internal translation initiation, spliced genes, translational bypassing, and RNA processing, alert us to the caveats of purely computational methods. The T4 transcriptional pattern reflects its dependence on the host RNA polymerase and the use of phage-encoded proteins that sequentially modify RNA polymerase; transcriptional activator proteins, a phage sigma factor, anti-sigma, and sigma decoy proteins also act to specify early, middle, and late promoter recognition. Posttranscriptional controls by T4 provide excellent systems for the study of RNA-dependent processes, particularly at the structural level. The redundancy of DNA replication and recombination systems of T4 reveals how phage and other genomes are stably replicated and repaired in different environments, providing insight into genome evolution and adaptations to new hosts and growth environments. Moreover, genomic sequence analysis has provided new insights into tail fiber variation, lysis, gene duplications, and membrane localization of proteins, while high-resolution structural determination of the “cell-puncturing device,” combined with the three-dimensional image reconstruction of the baseplate, has revealed the mechanism of penetration during infection. Despite these advances, nearly 130 potential T4 genes remain uncharacterized. Current phage-sequencing initiatives are now revealing the similarities and differences among members of the T4 family, including those that infect bacteria other than Escherichia coli. T4 functional genomics will aid in the interpretation of these newly sequenced T4-related genomes and in broadening our understanding of the complex evolution and ecology of phages—the most abundant and among the most ancient biological entities on Earth.

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Section: T4 Late Transcription-continuedmentioning

confidence: 99%

“…Clearly, the enhancer-like single-strand break of our activable DNA templates was serving as the loading site for the sliding clamp, and the strand specificity of break placement reflected the polarity of clamp loading as well as the specific interaction of one lateral face of gp45 with the T4 late RNA polymerase holoenzyme (95,96). While devising an assay for clamp sliding along DNA (by photochemical cross-linking), Rachel Tinker found that gp45 can carry gp55 along with it, implying a unique mode of promoter searching for the T4 late RNA polymerase (96). Tsu-Ju Fu found the gp45 sliding clamp prone to falling off DNA, suggesting the mechanistic basis for coupling T4 late transcription to concurrent DNA replication (97); gp33 was found to repress basal transcription (93), consistent with the different phenotypes of the "maturation-defective" gene 55 and gene 33 mutants; gp33 and gp55 were found to attach the sliding-clamp activator to the T4 late RNA polymerase holoenzyme through their carboxy termini (98,99).…”

Section: T4 Late Transcription-continuedmentioning

confidence: 99%

Without a License, or Accidents Waiting to Happen

Geiduschek

2009

Annu. Rev. Biochem.

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This is a memoir of circumstances that have shaped my life as a scientist, some of the questions that have excited my interest, and some of the people with whom I have shared that pursuit. I was introduced to transcription soon after the discovery of RNA polymerase and have been fascinated by questions relating to gene regulation since that time. My account touches on early experiments dealing with the ability of RNA polymerase to selectively transcribe its DNA template. Temporal programs of transcription that control the multiplication cycles of viruses (phages) and the precise mechanisms generating this regulation have been a continuing source of fascination and new challenges. A longtime interest in eukaryotic RNA polymerase III has centered on yeast and on the enumeration and properties of its transcription initiation factors, the architecture of its promoter complexes, and the mechanism of transcriptional initiation. These areas of research are widely regarded as separate, but to my thinking they have posed similar questions, and I have been unwilling or unable to abandon either one for the other. An additional interest in archaeal transcription can be seen as stemming naturally from this point of view.

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A direct interaction between a DNA-tracking protein and a promoter recognition protein: implications for searching DNA sequence.

Cited by 26 publications

References 51 publications

Testing for DNA Tracking by MOT1, a SNF2/SWI2 Protein Family Member

Testing for DNA Tracking by MOT1, a SNF2/SWI2 Protein Family Member

Bacteriophage T4 Genome

Without a License, or Accidents Waiting to Happen

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