6 Microbial Genetics

DNA replication

Bacterial genetic information is carried mainly on a chromosome, and many bacteria also contain plasmids: smaller DNA molecules that replicate separately. Before a cell divides, it must copy its DNA. Because bacteria can also acquire DNA from other cells or their surroundings, their genetic variation arises through both changes to existing DNA and the acquisition of new genetic material.

Copying the chromosome

In Semiconservative replication, each new double-stranded DNA molecule contains one original strand and one newly made strand. Replication commonly starts at one chromosomal origin and proceeds in both directions.

The two DNA strands run in opposite directions, but DNA polymerases extend a new strand only in the $5' \to 3'$ direction. This makes the leading strand continuous and the lagging strand discontinuous: the lagging strand is built in short Okazaki fragments that DNA ligase joins. Primase makes RNA primers, helicase opens the DNA, and topoisomerases relieve twisting ahead of the replication machinery. Proofreading and repair systems help limit copying errors.

Takeaway: Replication preserves genetic information by using each original strand as a template, while enzymes coordinate copying and error control.

From genes to products

Once DNA has been copied, cells use selected genes to make functional products. Gene expression includes transcription, which copies information from DNA into messenger RNA (mRNA), and translation, in which ribosomes read mRNA codons and assemble a polypeptide. Some genes produce functional RNA rather than a protein.

In bacteria, transcription and translation can occur at the same time because there is no nucleus separating DNA from ribosomes. Related genes are often organized into an Operon: shared regulatory DNA controls several genes, which are transcribed together into one mRNA. This organization can coordinate production of proteins involved in the same process.

Takeaway: DNA stores instructions; gene expression turns selected instructions into RNA or protein, and operons coordinate the expression of related genes.

Mutation and variation

A Mutation is a heritable change in DNA sequence. It can arise spontaneously, for example from a replication error or a chemical change in DNA, or be induced by mutagens such as certain chemicals and radiation.

A substitution changes one nucleotide. An insertion adds nucleotides, while a deletion removes them. An insertion or deletion in a protein-coding sequence can cause a frameshift when the number of nucleotides added or removed is not a multiple of three; this changes the downstream codons.

The effect depends on where the mutation occurs and how it affects gene activity. It may have no detectable effect, alter protein function, or change the amount of a gene product. Mutations do not arise because a bacterium needs a particular trait. Instead, when a variant improves reproduction in a particular environment, natural selection can increase its frequency. For example, antibiotic-resistant variants may survive antibiotic exposure better than susceptible cells.

Takeaway: Mutations generate heritable variation; the environment influences which variants become more common.

Regulating gene expression

Bacteria regulate gene expression in response to changing conditions and to avoid making unneeded products. Regulation can occur at several stages, but controlling transcription is common. Repressors reduce transcription by binding regulatory DNA, while activators increase transcription by helping RNA polymerase initiate it.

The E. coli lac operon responds to both lactose and glucose. When lactose is absent, the LacI repressor binds the operator and blocks transcription. When lactose is available, a lactose-derived inducer binds the repressor and reduces its ability to bind the operator. Expression is strongest when glucose is scarce: low glucose raises cyclic AMP, which binds the CAP activator and helps RNA polymerase transcribe the operon. The combined controls favor lactose use when lactose is present and glucose is limited.

The trp operon controls genes for tryptophan synthesis. When tryptophan is plentiful, it helps activate a repressor that shuts down transcription. When tryptophan is scarce, repression is relieved. In E. coli, attenuation adds another control point, allowing transcription to respond to tryptophan availability while transcription is underway.

Takeaway: Repressors and activators adjust transcription so bacterial gene activity can respond to nutrient availability.

Genetic exchange between bacteria

Horizontal gene transfer moves genetic information between bacterial cells rather than passing it from parent to offspring during cell division. The three classic mechanisms differ in how DNA reaches the recipient:

• Transformation occurs when a competent bacterial cell takes up free DNA from its surroundings. The DNA may integrate into the chromosome by recombination or, if it is a suitable plasmid, be maintained separately.

• Transduction occurs when a bacteriophage carries bacterial DNA from one cell to another. In generalized transduction, phage particles can carry different regions of the donor chromosome. In specialized transduction, a phage transfers genes near its integration site.

• Conjugation transfers DNA from a donor to a recipient through direct cell-to-cell contact, commonly involving a conjugative plasmid. Some plasmids can also mobilize chromosomal DNA.

Transferred DNA can be lost unless it replicates independently or becomes stably incorporated into the recipient’s genome. Recombination can integrate donor DNA into a related chromosome and create a new combination of alleles. Plasmids and other mobile DNA can carry traits such as antibiotic resistance, allowing those traits to spread among bacteria.

Takeaway: Transformation, transduction, and conjugation provide distinct routes for DNA transfer; plasmid replication or recombination can help preserve acquired genes.