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RNG chains in bacterial transcription

Posted by star on 2018-10-24 18:58:13

    RNA polymerase is a highly processive macromolecular machine. Structural factors that help to maintain the transcription elongation complex as an intact unit when it is paused include: the sliding clamp that binds the DNA template in front of the core RNA polymerase; The RNA exit tunnel that holds the nascent RNA and the segment of nascent RNA that is held to the DNA template by hydrogen bonds. Specific mechanisms are required to release RNA polymerase from the TEC. Two transcription termination pathways, intrinsic termination and Rho-dependent termination, contribute about equally to this release in E. coli.
    The intrinsic termination pathway is so named because it takes advantage of the core RNA polymerase's intrinsic catalytic activity to terminate transcription. Although nucleotide sequences specifying intrinsic terminators are present on DNA, it is actually the nascent, RNA (and not DNA) that triggers the transcription termination response. Two sequence motifs on the nascent RNA strand are essential for intrinsic terminator function.
    The first motif, a G-C rich inverted repeat, allow the RNA to fold into a stem and loop structure that reaches to within seven to nine nucleotides of the 3'-end of the nascent RNA strand. Mutations that maintain the stable stem structure are usually tolerated. Those that decrease the stem structure's stability tend to reduce or eliminate termination. Multiple mutations within the stem region also may lead to loss of terminator activity even though the stem structure retains its stability. Therefore, secondary RNA structure is important in determining intrinsic terminator activity but nucleotide sequence within the stem also appears to make a contribution.
    The second motif, a run of eight to ten nucleotides that consists mostly of uridines, comes immediately after the stem and loop structure. Intrinsic terminators appear to act by first caus......

The transcriptional elongation complex

Posted by star on 2018-10-24 18:51:39

    As the initiation stage comes to an end, the flexible flap closes to generate a transcription elongation complex (TEC), consisting of core RNA polymerase, template DNA, and a growing RNA chain elongation involves a catalytic cycle in which:
1. The nucleoside triphosphate moves through the secondary channel to reach the binding site. The passage of nucleoside triphosphates through the secondary channel may limit the elongation rate because there is only a one in four chance that the correct nucleotide will move through the secondary channel and reach the binding site.
2. A pair of electrons on the 3'-hydroxyl at the growing end of the RNA strand displaces the pyrophosphate group from the NTP to form the 5' to 3' phosphodiester bond.
3. The core RNA polymerase moves one nucleotide downstream. RNA polymerase moves along the DNA template at about 30 nucleotides per second. The incoming nucleoside triphosphates provide sufficient energy to synthesize the phosphodiester bond and drive the RNA core polymerase one nucleotide downstream.
    The DNase footprint of the transcription elongation complex is about 35 bp shorter than that of the initiating complex. Nevertheless, transcription elongation complex is the more stable of the two complexes. Approximately 14 bp within the region protected from DNase are melted, forming a transcription bubble. The first eight nucleotides within this bubble are paired with the RNA chain.
    The transcription bubble size appears to remain the same during the elongation process as RNA polymerase moves downstream because double-stranded DNA opens in front of the bubble and re-forms behind it. Conventions for numbering nucleotides in the transcription elongation complex are as follows: The entry position for the incoming nucleotide is + 1 and nucleotides downstream from this position (nucleotides in front of moving RNA polymerase) are +2, +3, and so forth. The 3'-ter......

    Although crystal structures provide a great deal of information about the way that RNA polymerase initiates transcription, additional types of experimental information are required to explain how the active center in RNA polymerase moves during abortive initiation and how the system acquires the energy needed for RNA polymerase to escape the promoter.
    Two experiments performed to examine how the active center moves during abortive transcription initiation appeared to provide contradictory observations. First, the observation that abortive initiation leads to the formation of RNA products up to-8-10 nucleotides in length suggests that the RNA polymerase active center moves relative to the DNA that it acts on. Yet in apparent contrast, DNA-footprinting experiments indicate that the enzyme does not move during abortive transcription because it protects the same up-stream DNA fragment before and after abortive RNA synthesis.
    Three models have been offered to reconcile these seemingly contradictory observations. The scrunching model proposes that DNA is pulled into the RNA polymerase holoenzyme as the DNA unwinds to form the open complex. The energy stored in the scrunched DNA is then used for promoter escape. The inchworm model proposes that the leading edge of RNA polymerase advances during the early stage of transcription initiation to allow the active center to move forward, while the other end of the enzyme remains anchored to the upstream DNA region. The energy stored in the stretched protein is used for promoter escape. Finally, the transient excursion model proposes transient cycles of forward enzyme motion during abortive RNA synthesis and backward enzyme movement after abortive transcript release with long intervals between cycles. The long interval times between cycles was postulated to explain the footprinting observations.
    Richard H. Ebright and coworkers performed ......

Crystal structure of core polymerase

Posted by star on 2018-10-19 00:50:46

    Although the core polymerase crystal structure provides considerable information about RNA polymerase structure, it provides no direct information about interactions that exist among core polymerase, σ factor, and DNA. Darst and coworkers addressed these and related structural issues by preparing crystals that contained the Trq holoenzyme bound ta a synthetic DNA with a fork-junction sequence (the junction between double-stranded DNA and single-stranded DNA in the transcription bubble).

    The DNA molecule they synthesized for this purpose has a double-stranded -35 box, a mostly open -10 box, and an extended -10 element. The crystal structure of the RNA polymerase holoenzyme· fork-junction DNA complex, which appears to resemble the open complex. The σ70 factor assumes a different conformation when bound to core polymerase. One notable change is the disruption of an interaction between subdomain 1. 1 and domain 4. This interaction prevents the free σ70 factor from binding DNA. In essence, negatively charged subdomain 1.1 acts as a DNA mimic, which competes with promoter DNA for the binding site on domain 4.

    Darst and coworkers have also determined the crystal structure for the Taq RNA polymerase holoenzyme without bound DNA and Shigeyuki Yokoyama and coworkers have done the same for the Thermus thermopbilus RNA polymerase holoenzyme. Thus, a considerable amount of structural information is now available for the core enzyme, the holoenzyme, and the holoenzyme · fork-junction DNA complex. Based on comparisons of these structures, it appears that the bulk of the enzyme consist......

The core RNA polymerase

Posted by star on 2018-10-18 18:52:22

    Seth Darst and coworkers reported the high-resolution crystal structure for the core RNA polymerase from the bacteria T aquaticus (Taq). The protein has a total of five subunits that are present in the stoichiometry α2 ββ'ω. Each subunit is homologous with its E. coli counterpart. The ω subunit, which is not always present in isolated E. coli core RNA polymerase, may help to assemble the core RNA polymerase but is not required for RNA synthesis. The structural design of the Taq core RNA polymerase, along with the organization of its subunits.

    As evident from the orientation presented, the core polymerase resembles a crab claw. One pincer is almost entirely β subunit and the other almost entirely β' subunit. An internal groove or channel with many internal structural features runs along the full length of the core polymerase between the pincers. The channel is sufficiently wide to allow double-stranded DNA to fit inside. The core RNA polymerase is about 15 nm long (from the tips of the claws to the back) and 11 nm wide.

    Other noteworthy features of the Taq core RNA polymerase include the following:

1. The N-terminal domain (NTD) of one α subunit forms significant contacts with the corresponding domain in the other α subunit allowing the two α subunits to form a dimer. The two NTDs also bind the β-and β'-subunits. However the arrangement is not symmetrical because the NTD of one α subunit, α1 binds the β subunit while the NTD of the other α subunit, α2 binds the β' subunit. No residue in either α subunit has access to the channel of the core RNA polymerase where catalysis occure.

2. The β-and β'-subunits binds , which account for about 60% of the core RNA polymerases mass, interact extensively with each other. The catalytic site is formed by one such interaction a......

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