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General Transcription Factors: Basal Transcription

Posted by star on 2018-11-27 18:09:34

    RNA polymerase II requires the assistance of protein factors to bind to the core promoter. This requirement was first demonstrated by studying specific initiation at the major late promoter of adenovirus DNA, which controls highly expressed genes for structural proteins in the virus particle. RNA polymerase II cannot catalyze specific initiation at this promoter but gains the ability to do so when a soluble cell-free extract from human KB cells (cells derived from an oral epidermoid carcinoma) is added to it. In 1979, Robert G. Roeder and coworkers used classical protein fractionation techniques to isolate protein factors from the KB cell extract that assist RNA polymerase II. These protein factors, or general transcription factors (GTFs) as they are now known, were named TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIIH. The first two letters, TF, indicate the protein is a general transcription factor; the Roman numeral II signifies the factor supports RNA polymerase II transcription; and the final letter was assigned based on the protein fractionation scheme rather than on protein function. (The letters C and G are missing because later studies showed that the proteins originally assigned these letters afe not transcription factors for RNA polymerase II.) Subsequent studies by Roeder and other investigators demonstrated that these general transcription factors are present in all eukaryotes from yeast to humans. Moreover, archaea have similar general transcription factors. Counterparts in other eukaryotes serve the same functions.

E. coli regulates r-protein synthesis

Posted by star on 2018-11-19 22:17:58

    A gene dosage experiment also shows that the synthesis of ribosomal proteins (r-proteins) is not regulated at the transcriptional level. The genes encoding the 52 r-proteins are organized into 20 operons. Addition of an appropriate plasmid can increase the number of copies of one of these operons in a cell, say, tenfold. This would increase the rate of synthesis of the corresponding mRNA tenfold, but the rate of production of r-proteins encoded in the mRNA remains that observed with one copy of the operon. Thus, the amount of the r-proteins that is synthesized is not proportional to the amount of the mRNA encoding them, so clearly translation and not transcription is being limited.

    An understanding of the mode of translational regulation came from in vitro translation experirnents. In these experiments, a single species of r-protein mRNA was translated and the inhibitory effect of each r-protein encoded in the mRNA was tested. It was observed that translation of each mRNA could be inhibited by the addition of one(a particular one) of the encoded r-proteins. Further analysis showed that the translational repression is a result of binding of that r-protein to a base sequence near the site at which ribosomes initially bind to mRNA. A variant of the in vitro experiment completes the story, namely, the addition of the particular rRNA (5S, 18S, or 23S) to which the r-protein binds in the ribosome prevents translational re-pression. A base sequence analysis of the mRNAs and the rRNA shows a similar sequence and a common stem-and-loop structure in the binding sites of each RNA molecule for a particular r-protein. Thus, competition exists between rRNA and r-protein mRNA for a particular r-protein. Binding studies show that each repressing r-protein species binds preferentially to the rRNA; thus, as long as rRNA is available for ribosome production, r-proteins will bind to rRNA and synthesis of r-proteins will continue. Studies with......

Bacterial mRNA molecules are rapidly degraded

Posted by star on 2018-11-18 22:25:52

    Intracellular mRNA content depends on the rate at which mRNA is degraded as well as the rate at which it is synthesized. The typical E.coli mRNA molecule has a half-life of about two to three minuteS. However, some mRNA half-lives are about 30 minutes while others are as short as a few seconds. Bacteria derive an important advantage from rapid mRNA degradation. If mRNA molecules were stable, newly synthesized mRNA molecules would have to compete with preexisting mRNA molecules for the protein synthetic machinery. Such competition would limit the cell's ability to synthesize proteins that are needed to respond to physiological changes. Rapid mRNA degradation frees the protein synthetic machinery to translate the newly formed mRNA molecules, which are formed in response to the cell's changing physiological requirements.
    Bacteria use several enzymes to degrade mRNA. These enzymes can be divided into two major classes, polynucleotide phosphorylases and ribonucleases (RNases). A polynucleotide phosphorylase de-grades RNA by adding phosphate groups to phosophodiester bonds to form nucleoside diphosphates. Phosphorolytic cleavage begins at the 3’-end and continues sequentially in a 3’→5’ direction. RNases cleave phosphodiester bonds to produce RNA fragments, while exoribonucleases cut phosphodiester bonds in a sequential fashion starting at the 3’-end and moving 3’→5’ to produce nucleoside monophosphates. To date, no bacterial degradation enzyme has been found that catalyzes sequential RNA cleavage in a 5’→ 3’ direction. In contrast, bacteria do have exonucleases that remove nucleotides from DNA in a 5’→ 3’ direction. Although the study of mRNA degradation is still in its infancy, the involvement of certain enzymes in this process is well documented. We now examine a few of these enzymes and explore their role in mRNA degradation.

Control of the lysogenic pathway

Posted by star on 2018-11-18 18:02:35

    The gene expression cascade leading to the lysogenic pathway also starts with divergent transcription initiated from the PL and PR promoters. However, the accumulation of the CII regulator prevents the expression of the lytic regulators. The CII regulator is a tetramer. Each of the four monomers has a helix-turn-helix motif. However, only two of these motifs bind to DNA. The function of the other two motifs is not known.
    The CII regulator activates transcription initiated from PRE, PI, and PaQ. Activation of PRE leads to rapid CI regulator synthesis. The CI regulator that accumulates in response to this activation binds to OL and OR and represses transcription from the early promoters PL and PR. The structure of the CI regulator protein and its interaction with operator DNA is described below. The intracellular concentration of the CI regulator that accumulates in response to the activation at PRE is 10 to 20 times higher than that present in an established λ lysogen. The initial high concentration of the CI regulator probably ensures that all infecting phage DNA becomes repressed. Activation from P1, stimulates transcription of the int gene. The product of this gene, integrase, is needed to insert λ DNA into the host chromosome to form the prophage. The PaQ promoter is located within the Q gene. Therefore, the CII regulator inhibits transcription of the Q gene when it binds to this promoter. Furthermore, the PaQ transcript appears to function as an antisense RNA that inhibits the translation of the Q transcript. As should now be clear the CII protein is very important for establishing lysogeny. An ATP-dependent host protein called FtsH can prevent the infected cell from entering the lysogenic pathway by cleaving CII. The CIII protein prevents this from ha......

cAMP · CRP activates more than 100 operons

Posted by star on 2018-11-13 22:03:45

    Enzymes responsible for the catabolism of many other organic molecules, including galactose, arabinose, sorbitol, and glycerol, are synthesized by inducible operons. Each of these operons cannot be induced if glucose is present. These are called catabolite-sensitive operons. A network of operons that is under the control of a single regulatory protein such as cAMP · CRP is called a modulon.
    A simple genetic experiment shows that cAMP · CRP participates in the regulation of many operons. A single spontaneous mutation in a gene for the catabolism of a sugar such as lactose, galactose, arabinose, or maltose arises with a frequency of roughly 10-6. A double mutation, lac-mal-, would arise at a frequency of 10-12, which for all practical purposes cannot be measured. However double mutants that are phenotypically Lac- Mal- or Gal- Ara- do arise at a measurable frequency. These apparent double mutants are not the result of mutations in the two sugar operons but always turn out to be crp- or cya-. Furthermore, if a Lac- Mal- mutant appears as a result of a single mutation, the protein products of the other catabolite-sensitive operons are also not synthesized. Biochemical experiments with a few of these catabolite-sensitive operons indicate that binding of cAMP · CRP occurs in the promoter region in each of these systems.

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