Antibiotics That Affect Replication and DNA Structure
Antibiotics are substances that block the growth of cells. Many antibiotics are naturally synthesized chemical compounds made by soil microorganisms, especially actinomycetes, that may help them compete with other soil microorganisms. There are also other ideas as to why bacteria make antibiotics, including for their use in intercellular communication, especially in highly organized structures like biofilms. Many antibiotics specifically block DNA replication or change the structure of DNA. Because some parts of the replication machinery have remained relatively unchanged throughout evolution, many of these antibiotics work against essentially all types of bacteria. Some even work against eukaryotic cells and so are used as antifungal agents and in antitumor chemotherapy.
Antibiotics That Block Precursor Synthesis
As discussed above, DNA is polymerized from the deoxynucleoside triphosphates. Any antibiotic that blocks the synthesis of these deoxynucleotide precursors will block DNA replication.
Inhibition of dihydrofolate reductase
Some of the most important precursor synthesis blockers are antibiotics that inhibit the enzyme dihydrofolate reductase. One such compound, trimethoprim, works very effectively in bacteria, and the antitumor drug methotrexate (amethopterin) inhibits the dihydrofolate reductase of eukaryotes. Methotrexate is used as an antitumor agent, among other uses such as in the treatment of inflammatory arthritis.
Antibiotics like trimethoprim that inhibit dihydrofolate reductase kill the cell by depleting it of tetrahydrofolate, which is needed for many biosynthetic reactions. This inhibition is overcome, however, if the cell lacks the enzyme thymidylate synthetase, which synthesizes dTMP; therefore, most mutants that are resistant to trimethoprim have mutations that inactivate the thyA thymidylate synthetase gene. The reason is apparent from the pathway for dTMP synthesis shown in Figure 1.5. Thymidylate synthetase is solely responsible for converting tetrahydrofolate to dihydrofolate when it transfers a methyl group from tetrahydrofolate to dUMP to make dTMP. The dihydrofolate reductase is the only enzyme in the cell that can restore the tetrahydrofolate needed for other biosynthetic reactions. However, if the cell lacks thymidylate synthetase, there is no need for a dihydrofolate reductase to restore tetrahydrofolate. Therefore, inhibition of dihydrofolate reductase by trimethoprim has no effect, thus making thyA mutant cells resistant to the antibiotic. Of course, if the cell lacks a thymidylate synthetase, it cannot make its own dTMP from dUMP and must be provided with thymidine in the medium so that it can replicate its DNA.
There is more than one mechanism by which cells can achieve trimethoprim resistance. They can have an altered dihydrofolate reductase to which trimethoprim cannot bind, or they can have more copies of the gene so that they make more enzyme than there is trimethoprim to inhibit it. Some plasmids and transposons carry genes for resistance to trimethoprim. These genes encode dihydrofolate reductases that are much less sensitive to trimethoprim and so can act even in the presence of high concentrations of the antibiotic.
Inhibition of ribonucleotide reductase
The antibiotic hydroxyurea inhibits the enzyme ribonucleotide reductase, which is required for the synthesis of all four precursors of DNA synthesis (Figure 1.5). The ribonucleotide reductase catalyzes the synthesis of the deoxynucleoside diphosphates dCDP, dGDP, dADP, and dUDP from the ribonucleoside diphosphates, an essential step in deoxynucleoside triphosphate synthesis. Mutants resistant to hydroxyurea have an altered ribonucleotide reductase.
Competition with deoxyuridine monophosphate
5-Fluorodeoxyuridine and the related 5-fluorouracil have monophosphate forms resembling dUMP, the substrate for thymidylate synthetase. By competing with the natural substrate for this enzyme, they inhibit the synthesis of deoxythymidine monophosphate. Mutants resistant to these compounds have an altered thymidylate synthetase. These are useful antibiotics for the treatment of fungal, as well as bacterial, infections.
Antibiotics That Block Polymerization of Deoxynucleotides
The polymerization of deoxynucleotide precursors into DNA would also seem to be a tempting target for antibiotics. However, there seem to be surprisingly few antibiotics that directly block this process. Most antibiotics that block polymerization do so indirectly, by binding to DNA or by mimicking the deoxynucleotides and causing chain termination, rather than by inhibiting the DNA polymerase itself.
Deoxynucleotide precursor mimics
Dideoxynucleotides are similar to the normal deoxynucleotide precursors, except that they lack a hydroxyl group on the 3′
Cross-linking
Mitomycin C blocks DNA synthesis by cross-linking the guanine bases in DNA to each other. Sometimes the cross-linked bases are in opposing strands. If the two strands are attached to each other, they cannot be separated during replication. Even one cross-link in DNA that is not repaired prevents replication of the chromosome. This antibiotic is also a useful antitumor drug, probably for the same reason. DNA cross-linking also affects RNA transcription.
Antibiotics That Affect DNA Structure
Acridine dyes
The acridine dyes include