Bacterial Genetics

This article should serve as a broad introduction to the genetics of bacteria and their viruses; links to other pages spread throughout the article will offer greater detail on various topics.

Bacteria (singular: bacterium) are a taxonomic domain of unicellular, prokaryotic organisms. They are one of the three domains of life, along with archaea and eukarya (eukaryotes). Like all prokaryotes, bacteria lack a nucleus and any membrane-bound organelles such as mitochondria, chloroplasts or endoplasmic reticulum; they also possess smaller ribosomes than eukaryotes. Bacteria exhibit wide metabolic diversity, ranging from photosynthetic species like the cyanobacteria to heterotrophs like E. coli that break down compounds existing in the environment for energy and a carbon source. Bacteria occupy a wide range of ecological niches, from the digestive tract of humans to hot water springs and radioactive waste. They may be harmless, beneficial (e.g. in the case of mutualistic bacteria living in the human gut) or destructive (pathogenic) to man.

The genome of a bacterium is usually found as a circular chromosome associated with histone-like proteins in a complex called the nucleoid. Like in eukaryotes, the DNA of bacteria is supercoiled in order for a large amount of genetic material to be stored in a small space. The supercoiling must be 'unwound' to enable transcription or replication of the DNA. The circular chromosome is usually found tethered to the plasma membrane of the bacterium and this is useful in molecular biology experiments as it means the bacterium can be lysed and centrifuged to isolate the DNA in a membrane pellet.

Transcription and translation in bacteria are coupled processes, meaning that they occur simultaneously rather than being compartmentalised in different parts of the cell as in eukaryotes. Bacterial genes rarely contain introns and often multiple genes are transcribed to a single mRNA (monocistronic mRNA) so that related proteins, for instance all the enzymes required for a metabolic pathway, can be synthesised together. Bacterial gene expression is generally negatively regulated: in other words, gene expression is by default 'turned on' and must be inhibited; while in eukaryotes it is positively regulated and is by default 'turned off' and must be activated when gene products are required. Transcription of all types of RNA is performed by the same RNA polymerase, although different sigma factors, which are themselves activated environmentally, direct the RNA polymerase to different genes.

Transcriptional termination in bacteria may be rho-independent or rho-dependent. In rho-independent termination, a palindromic G/C-rich hairpin loop forms in mRNA, causing RNA polymerase to stall. This is followed by a poly-U tract in the mRNA which destabilises the RNA-DNA duplex (a phenomenon known as attenuation). In rho-dependent termination, the G/C-hairpin loop is still present, but there is no poly-U tract. Instead there is a poly-C tract preceding the hairpin loop by about 70 nucleotides; an ATP-dependent helicase enzyme called rho binds to the poly-C tract (on the mRNA) and thereby destabilises the RNA-DNA duplex while RNA polymerase is stalled at the hairpin loop.

Often bacterial genes are arranged into clusters called operons, such as the lac operon, that are transcribed from a single promoter region. Sometimes bacterial genes may be clustered into regulons, which are groups of genes that are regulated by the same protein. An example of a regulon is the set of genes responsible for the SOS response in some bacteria.

Bacteria can take up exogenous DNA from their environment in a process called transformation. The resultant bacterium is a transformant. Some bacteria code for membrane proteins that are specifically designed for DNA uptake and transformation, while other species can be 'encouraged' to take up foreign DNA in the lab, for example by providing an environment high in calcium chloride (CaCl2 promotes DNA uptake). Genetic information may also be transferred into the bacterium by a virus; this phenomenon is called transduction. Because viruses may extract DNA from one host bacterium and take that DNA to their next host, viral transduction can be considered one, indirect, method of sexual gene transfer between bacteria. DNA can also be transferred directly between bacteria by conjugation. Conjugation occurs across a 'mating bridge' between two bacteria, providing those bacteria are attached by specialised structures called pili (long flagellum-like structures). DNA exchange in this way, between bacteria of the same generation, is called horizontal gene transfer. The sexual contact necessary for conjugation was realised in the results of experiments by Lederberg & Tatum, and in Davis's U-tube experiment.

Besides the main chromosome, bacteria may also contain extra-chromosomal circular strands of naked DNA (i.e. DNA that is not bound to proteins) called plasmids. Plasmids are usually smaller in size than the bacterial chromosome and have a very high rate of replication. For this reason, molecular biologists often genetically engineer plasmids to clone a useful gene (and its product) multiple times in a short period.

Plasmids may be classified by function. For example, some plasmids are fertility (F) plasmids. F plasmids code for their own transfer to another bacterium by conjugation (see above). Bacteria that have an F plasmid are called F+ individuals (donor bacteria) while those without the plasmid are called F- individuals (recipient bacteria). Although it is common for F plasmids to be transmitted between individuals, the transfer of chromosomal DNA in this way is rare. Occasionally, F plasmids may be incorporated into the main bacterial chromosome by genetic recombination at sites called IS elements. This creates HFr (high frequency recombination) strains. Because the genes on the encoporated F plasmid code for conjugal transfer, when these genes are spliced into the main bacterial chromosome, the entire chromosome may be transferred by conjugation to a recipient bacterium. When an F plasmid is donated from a HFr strain to a F- individual, the F- individual becomes a merozygote because it lacks some F genes (i.e. the ones that weren't incorporated into the bacterial chromosome). Reversal of the recombination in HFr strains can occur; however often some F genes remain spliced into the main chromosome. Bacteria where this has occurred are called F' (verbalised F prime) individuals.

Another type of plasmid is the resistance (R) plasmid which carries genes for resistance against environmental toxins, including antibiotics. Antibiotic resistance develops quickly in bacterial populations because the R plasmid may be exchanged between individuals by conjugation, enabling all bacteria close in proximity to express the resistance genes.

Bacteria reproduce asexually by binary fission; there is no instance of mitosis or meiosis in the process of bacterial cell division. This means that offspring are clones of their parents. The transfer of genetic information from parent to offspring in bacteria is called vertical gene transfer. Like all living organisms, bacterial genes are prone to recombination and mutation, driving the evolution of genomes and phenotypes. Natural selection may act on bacterial colonies; for instance, by selecting for those bacteria with mutations that make them resistant to antibiotics.

Viruses that infect bacteria are called bacteriophages (or simply phages). Bacteriophages have two cycles of 'behaviour': the lysogenic and lytic cycles. In the lytic cycle, the phage genome is incorporated into the bacterium and viral proteins are synthesised using the host bacterium's protein synthesis machinery. Once new phages have been made and assembled, the progeny break out of (lyse) the bacterial cell in search of new hosts, killing it in the process.

In the lysogenic cycle, a phage is incorporated into the bacterial host (the host is called a lysogen), but there is no detrimental effect to that host. The viral genome simply exists within the bacterial genome without being expressed. This is because during lysogeny, repressor molecules are made which inhibit the onset of the lytic cycle. Lysogenic integration into the host genome is DNA sequence-specific, involving enzymes that are site-specific recombinases.

Super-infection by phages is a phenomenon where two viral genomes invade and lyse a bacterial cell. This is not possible where one of the phages is lysogenic, because the lysogen's repressor molecules act on its genome and any other phage genomes that enter the cell, preventing onset of the lytic cycle in any of those genomes.

Because viruses carry genetic information into bacteria, they are useful as vectors in genetic engineering. Often the genes responsible for the lysogenic cycle are replaced by the target gene, and the recombinant phage is then introduced to bacteria on a petri dish. Because the engineered phages are only capable of the lytic cycle, we can tell which bacteria have been transformed by which bacteria have been lysed. Lysed bacteria appear as opaque plaques on a petri dish.

Another human use of bacteriophages is to kill pathogenic bacteria. As bacterial populations develop antibiotic resistance, bacteriophage therapy has been considered an alternative method for curing bacterial disease. This is because, unlike artifically produced antibiotics, phages are capable of co-evolution with the bacteria as they develop resistance, so that the phage can 'self-modify' (i.e. via mutation and negative frequency-dependent selection) to overcome newly acquired levels of resistance in the bacteria.

The bacterial defence against invading phage genomes is the synthesis of restriction endonuclease enzymes.These enzymes recognise and destroy certain DNA sequences, notably those of the invading phage, before the foreign genome can be incorporated into the bacterial cell. There are many types of restriction enzymes, and these types act on the DNA molecule in different ways. Certain types, notably type 2 restriction enzymes, are useful in many processes of genetic engineering. Restriction enzymes have been isolated from many species of bacteria and the nomenclature of the isolated enzyme depends on the species it was isolated from, the strain of that species and the order in which it has been isolated. For instance, the famous restriction enzyme, ECOR1, was isolated from E. coli Strain R and was the first of its kind to be isolated.