Unraveling the role of helicases in transcription

Eisen, Arri; Lucchesi, John C.

doi:10.1002/(sici)1521-1878(199808)20:8<634::aid-bies6>3.0.co;2-i

Cited by 51 publications

(19 citation statements)

References 78 publications

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“…[88] reported that the TFIIH XPB DNA helicase was primarily responsible for preventing premature arrest of early elongation intermediates during the exit of the polymerase from the promoter. TFIIH is also required for transcription‐coupled nucleotide excision repair [87,88]. Finally in E. coli , the Rho protein, a RNA/DNA helicase, and in Drosophila , Factor 2 are required for transcription termination [57,87].…”

Section: Role Of Dna Helicases In Transcriptionmentioning

confidence: 99%

“…TFIIH is also required for transcription‐coupled nucleotide excision repair [87,88]. Finally in E. coli , the Rho protein, a RNA/DNA helicase, and in Drosophila , Factor 2 are required for transcription termination [57,87].…”

Section: Role Of Dna Helicases In Transcriptionmentioning

confidence: 99%

“…TFIIH, ERCC6/RAD26) and termination (e.g. Factor 2, Rho) [72,73,[87][88][89]. Transcription activation involves the formation of a preinitiation complex, its association with ssDNA activation, and promoter clearance.…”

Section: Role Of Dna Helicases In Transcriptionmentioning

confidence: 99%

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Unraveling DNA helicases

Tuteja

2004

European Journal of Biochemistry

168

148

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DNA helicases are molecular ÔmotorÕ enzymes that use the energy of NTP hydrolysis to separate transiently energetically stable duplex DNA into single strands. They are therefore essential in nearly all DNA metabolic transactions. They act as essential molecular tools for the cellular machinery. Since the discovery of the first DNA helicase in Escherichia coli in 1976, several have been isolated from both prokaryotic and eukaryotic systems. DNA helicases generally bind to ssDNA or ssDNA/dsDNA junctions and translocate mainly unidirectionally along the bound strand and disrupt the hydrogen bonds between the duplexes. Most helicases contain conserved motifs which act as an engine to drive DNA unwinding. Crystal structures have revealed an underlying common structural fold for their function. These structures suggest the role of the helicase motifs in catalytic function and offer clues as to how these proteins can translocate and unwind DNA. The genes containing helicase motifs may have evolved from a common ancestor. In this review we cover the conserved motifs, structural information, mechanism of DNA unwinding and translocation, and functional aspects of DNA helicases.Keywords: crystal structure; DEAD-box protein; DNA helicase; helicase motifs; unwinding enzyme.DNA helicases are motor proteins that can transiently catalyze the unwinding of energetically stable duplex DNA molecules using NTP hydrolysis as the source of energy [1,2]. They are important enzymatic tools for the cellular DNA machinery. They are known to play essential roles in nearly all aspects of nucleic acid metabolism, such as DNA replication, repair, recombination, and transcription. All helicases share at least three common biochemical properties: (a) nucleic acid binding; (b) NTP/dNTP binding and hydrolysis; (c) NTP/dNTP hydrolysis-dependent unwinding of duplex nucleic acids in the 3¢ to 5¢ or 5¢ to 3¢ direction [3]. Therefore, all DNA helicases described to date also have intrinsic DNA-dependent NTPase activity [4,5]. These enzymes usually act in concert with other enzymes or proteins in DNA metabolic activity. Multiple DNA helicases have been isolated from single-cell types because of different structural requirements of the substrate at various stages of the DNA transaction. For example, at least 14 different DNA helicases have been isolated from a simple single-cell organism such as Escherichia coli, six from bacteriophages, 12 from viruses, 15 from yeast, eight from plants, 11 from calf thymus, and as many as 24 from human cells. These have been described in the preceding review.Most helicases from many different organisms contain about nine short conserved amino-acid sequence fingerprints (designated Q, I, Ia, Ib, II, III, IV, V and VI), called Ôhelicase motifsÕ [6][7][8][9][10]. These motifs are usually clustered in a region of 200-700 amino acids called the core region. Because of the sequence of motif II (DEAD or DEAH or DEXH), the helicase family is also called the DEAD-box protein family. The crystal structures of some of the DNA hel...

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Section: Role Of Dna Helicases In Transcriptionmentioning

confidence: 99%

Section: Role Of Dna Helicases In Transcriptionmentioning

confidence: 99%

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Unraveling DNA helicases

Tuteja

2004

European Journal of Biochemistry

168

148

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“…The requirement for MER3 for both the DSB transition and crossover control supports this hypothesis. However, we cannot rule out the possibility that MER3 affects the expression of other genes and thus is required for different steps of recombination, as some proteins containing helicase domains are known to regulate gene expression (Eisen and Lucchesi, 1998).…”

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confidence: 99%

The Saccharomyces cerevisiae MER3 gene, encoding a novel helicase-like protein, is required for crossover control in meiosis

1999

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The MER3 gene is identified as a novel meiosis-specific gene, whose transcript is spliced in an MRE2/MER1-dependent manner. The predicted Mer3 protein contains the seven motifs characteristic of the DExHbox type of helicases as well as a putative zinc finger. Double strand breaks (DSBs), the initial changes of DNA in meiotic recombination, do not disappear completely and are hyperresected late in mer3 meiosis, indicating that MER3 is required for the transition of DSBs to later intermediates. A mer3 mutation reduces crossover frequencies, and the remaining crossovers show random distribution along a chromosome, resulting in a high incidence of non-disjunction of homologous chromosomes at the first meiotic division. MER3 appears to be very important for both the DSB transition and crossover control.

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“…Factors with helicase activity and/or helicase motifs have been found to regulate transcription including XPB and XPD of the TFIIH and SW12/SNF2 of the chromatin remodeling complex SWI/SNF complex [28–30]. It has been proposed that helicase‐domain‐containing proteins facilitate transcription by altering chromatin structure, thus increasing the accessibility of other transcription factors to the basic transcription apparatus [31]. The winter flounder AFP genes are organized in tandem, direct 8‐kb repeats with 30–40 copies [7].…”

Section: Discussionmentioning

confidence: 99%

The rat ortholog of the presumptive flounder antifreeze enhancer‐binding protein is a helicase domain‐containing protein

Miao

Chan

Fletcher

et al. 2000

European Journal of Biochemistry

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The expression of winter flounder liver-type antifreeze protein (wflAFP) genes is tissue-specific and under seasonal and hormonal regulation. The only intron of the major wflAFP gene was demonstrated to be a liverspecific enhancer in both mammalian cell lines and flounder hepatocytes. Element B, the core enhancer sequence, was shown to interact specifically with a liver-enriched transcription factor, CCAAT/enhancer-binding protein a (C/EBPa), as well as a presumptive antifreeze enhancer-binding protein (AEP). In this study, the identity of the rat AEP ortholog was revealed via its DNA±protein interaction with element B. It is a helicasedomain-containing protein, 988 amino acids in length, and is homologous to mouse Smubp-2, hamster Rip-1 and human Smubp-2. The specific binding between element B and AEP was confirmed by South-Western analysis and gel retardation assays. Residues in element B important to this interaction were identified by methylation interference assays. Mutation on one of the residues disrupted the binding between element B and AEP and its enhancer activity was significantly reduced, suggesting that AEP is essential for the transactivation of the wflAFP gene intron. The rat AEP is ubiquitously expressed in various tissues, and the flounder homolog is present as shown by genomic Southern analysis. The potential role of AEP in regulating the flounder AFP gene expression is discussed.

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Unraveling the role of helicases in transcription

Cited by 51 publications

References 78 publications

Unraveling DNA helicases

Unraveling DNA helicases

The Saccharomyces cerevisiae MER3 gene, encoding a novel helicase-like protein, is required for crossover control in meiosis

The rat ortholog of the presumptive flounder antifreeze enhancer‐binding protein is a helicase domain‐containing protein

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