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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.

    In the absence of cAMP· CRP, the lac promoter is quite weak because its-10 box differs significantly from the consensus sequence. A mutant lac promoter with a -10 box that has the consensus sequence does not re-quire cAMP · CRP for transcription activation. It therefore seems reasonable to propose that interactions between cAMp· CRP complex and RNA polymerase holoenzyme increase the holoenzyme's affinity for the lac promoter. Biochemical and genetic studies support this proposal.
    Thomas Steitz and coworkers determined the crystal structure for the cAMP· CRP complex bound to DNA. CRP consists of two chemically identical polypeptide chains of 209 amino acid residues. Each chain consists of an N-terminal domain and a C-terminal domain, which are connected by a hinge region containing four amino acids. The N-terminal domain consists of a series of antiparallel β-sheets that form a pocket for binding cAMP The C-terminal domain contains a helix-turn-helix motif that binds to DNA. In the absence of cAMP, CRP · DNA interactions are nonspecific and weak. However, the cAMP · CRP complex binds very tightly to a specific DNA sequence designated the activator site (AS). In the lac operon, the center of AS is 61. 5 bp upstream from the transcription start site. Many other bacterial operons are activated by cAMP · CRP (see below). Each of these operons also contains at least one AS. Comparing AS sequences reveals the following 22 bp consensus sequence with twofold symmetry.


    The most highly conserved nucleotides in AS are the two TGTGA motifs. Mutations that alter nucleotides in the TGTGA motifs lead to decreased lac operon transcription. Each CRP subunit binds to half of the AS. The interacti......

    The mechanism by which glucose inhibits β-galactosidase synthesis remained a complete mystery for about 20 years after Monod first observed the phenomenon. Richard S. Makman and Earl W. Sutherland found an important clue to the mystery in 1965 when they observed that the intracellular concentration of 3', 5'-cyclic adenylate or cAMP drops from about 10-4 M to 10-7 M when glucose is added to a growing culture of E.coli.
    Genetic studies confirmed cAMP's involvement in catabolite repression. Two mutant classes were isolated that could not synthesize lac enzymes when cultured in a medium containing lactose but no glucose. Class mutants regained the ability to synthesize lac enzymes when cAMP was added to the growth medium but class ‖ mutants did not.
    Subsequent studies showed that class I mutants have defects in adenylate cyclase, the enzyme that converts ATP to cAMP. The structural gene for adenylate cyclase, cya, maps at minute 85.98. Adenylate cyclase exists in an active form that is phospfborylated, (it contains an attached phosphate group) and an inactive form that is dephosphorylated. Class ‖ mutants have defects in a protein that binds cAMP. This protein, called the cAMP receptor protein (CRP) or the catabolite activator protein (CAP), is encoded by the crp gene, which maps at minute 75. 09. In vitro studies have shown that CRP and cAMP form a complex, denoted cAMP·CRP complex, which is needed to activate the lac system. The cAMP · CRP requirement is independent of the repression system since cya and crp mutants cannot make lac mRNA even if a lacI- or lacOc mutation is present. Thus, cAMP · CRP is a positive regulator or activator, in contrast to the repressor and the lac operon is independently regulated both positively and negatively.
    Based on the information presented above, it seems reasonable to propose that glucose somehow inhibits phospho......

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