Bacterial Genetics
Genetic material in bacteria ★★
The lecture opens with what is true of every organism: all organisms have DNA and RNA as genetic material, all use the same nucleotides, and all replicate, transcribe and translate DNA — the central dogma of molecular biology. What follows is what is peculiar to bacteria.
| Element | Detail |
|---|---|
| Chromosome — haploid | Most: a single circular DNA molecule. A few: two circular DNA molecules |
| Plasmid | An extrachromosomal genetic element capable of autonomous replication |
| Bacteriophage | A bacterial virus — see §2 |
One copy of every gene, and no second allele to mask it.
In a diploid organism a new mutation is usually hidden behind a working copy, and takes generations to be exposed to selection. In a haploid bacterium a mutation is expressed immediately — good or bad, it is judged in the next generation, which for E. coli is twenty minutes away.
Add the three horizontal transfer mechanisms of §4, which let a useful gene jump between organisms rather than waiting to be inherited, and you have the whole explanation of antibiotic resistance.
- What form is the bacterial chromosome? → Haploid; most have a single circular DNA molecule, a few have two
- Define a plasmid. → An extrachromosomal genetic element capable of autonomous replication
- Why does haploidy matter? → Every mutation is expressed at once — no second allele to mask it
Bacteriophages ★★★
A virus that infects a bacterium, often simply called a phage.
| By mode of propagation | Behaviour |
|---|---|
| Virulent phage | Produces new virions in the host bacterial cell, killing the host cell |
| Temperate phage | Enters a latent, non-lytic prophage state. Replication of its nucleic acid is linked to replication of host cell DNA |
Phage that has inserted into the bacterial chromosome.
A bacterium carrying a prophage. A physiologic signal can trigger a lytic cycle, resulting in death of the host cell and liberation of many copies of the phage.
The lecture names three aspects of phage biology with long-term impact: transduction — phage carrying additional genetic information from cell to cell; lysogeny — phage resident in the bacterial genome; and recombination between phages.
A prophage sitting in the chromosome is not inert. Its genes are transcribed along with the host's, and some of those genes are toxins.
This is lysogenic conversion, and it explains several diseases you will meet later in this subject:
• Diphtheria toxin is encoded by a prophage — a Corynebacterium diphtheriae without the phage causes no diphtheria.
• Botulinum toxin (types C and D) and the erythrogenic toxin of scarlet fever are the same story.
• Cholera toxin is carried by the CTXφ phage.
So the answer to “why is this strain pathogenic and that one not?” is, surprisingly often, “because a virus infected it.”
- Define a bacteriophage. → A virus that infects a bacterium
- Virulent vs temperate phage? → Virulent produces new virions and kills the host; temperate enters a latent non-lytic prophage state
- Define prophage. → Phage inserted into the bacterial chromosome
- Define lysogenic bacterium. → A bacterium carrying a prophage; a physiologic signal can trigger a lytic cycle, killing the host and releasing phage
- Name three aspects of phage biology with long-term impact. → Transduction, lysogeny, recombination between phages
- Give an example of lysogenic conversion. → Diphtheria toxin, cholera toxin and scarlet-fever erythrogenic toxin are all phage-encoded
Pathogenicity islands and transposons ★★
Specific genes for pathogenic determinants, often clustered together in the DNA and encoding virulence genes.
- Have a different G+C content from the rest of the genome
- Are closely linked on the chromosome to tRNA genes
- Are flanked by direct repeats
- Contain diverse genes important for pathogenesis — adhesins, invasins, exotoxins — as well as genes involved in genetic mobilisation
Every bacterial species has a characteristic G+C ratio across its genome. A block of DNA whose ratio does not match the rest of the chromosome did not evolve there — it arrived.
Add the other three features and the story is complete: flanked by direct repeats and linked to tRNA genes (classic insertion sites), and carrying its own mobilisation genes. A pathogenicity island is a package of virulence that was acquired horizontally and retains the scars of the delivery.
Which is the same insight as §4: virulence, like resistance, spreads sideways.
Genetic elements that contain several genes, including those necessary for their migration from one genetic locus to another.
| Insertion sequence (IS) elements | Detail |
|---|---|
| Size | Relatively short transposons, 0.75–2.0 kbp |
| Effect | Produce the majority of insertion mutations |
| Distribution | Carried by almost all bacteria, each species harbouring its own characteristic ones |
- Define a pathogenicity island. → Genes for pathogenic determinants, clustered in the DNA and encoding virulence genes
- Name its four features. → Different G+C content · closely linked to tRNA genes · flanked by direct repeats · diverse pathogenesis genes plus mobilisation genes
- Why does the G+C content matter? → It shows the block was acquired horizontally rather than evolved in place
- Define a transposon. → A genetic element containing several genes, including those needed for migration from one locus to another
- How big are IS elements, and what do they do? → 0.75–2.0 kbp; they produce most insertion mutations and are carried by almost all bacteria
Vertical versus horizontal gene transfer ★★★
| Definition | |
|---|---|
| Vertical gene transfer | Organisms replicate their genomes and provide copies to descendants — passing genes to descendants |
| Horizontal gene transfer | A donor contributes part of its genome to a recipient that is not a descendant |
| The three types of horizontal transfer | Mechanism | Section |
|---|---|---|
| Transformation | Uptake of “naked” DNA | §5 ⭐ |
| Transduction | By bacteriophages | §6 ⭐ |
| Conjugation | Bacterial cells come into direct contact with each other | §7 |
In virology and infectious disease — which is where the 2019 paper sets it — vertical transmission means transmission from mother to offspring: transplacental, during delivery, or via breast milk. HBV, HIV, rubella, CMV and Treponema pallidum are the examples. That term belongs to the Viral Infection unit.
Same words, two subjects. Read the paper carefully before answering.
- Vertical vs horizontal gene transfer? → Vertical: to descendants at replication. Horizontal: donor to a non-descendant recipient
- Name the three types of horizontal transfer. → Transformation (naked DNA), transduction (by phage), conjugation (direct contact)
- What does 'vertical transmission' mean in the 2019 paper? → Mother-to-offspring transmission of infection — transplacental, at delivery, or via breast milk
⭐ Transformation ★★★
The form of gene transfer and recombination in bacteria in which a piece of free DNA is taken up by a bacterial cell and integrated into the recipient genome.
For the fourth mark, add that the recipient must be competent — able to take up DNA — and name the classical experiment: Griffith's 1928 pneumococcal experiment, in which heat-killed smooth (encapsulated) Streptococcus pneumoniae transformed live rough strains into virulent smooth ones. That experiment is the historical proof that DNA is the genetic material, and it is the reason transformation is the first mechanism taught.
- Define transformation. → Gene transfer in which free DNA is taken up by a bacterial cell and integrated into the recipient genome
- What must the recipient be? → Competent
- Which classical experiment demonstrated it? → Griffith's pneumococcal experiment — heat-killed smooth strains transformed rough strains into virulent ones
⭐ Transduction ★★★
The form of gene transfer and recombination between bacteria via a bacteriophage.
| Type | How it works |
|---|---|
| Generalised transduction | Any fragment of host DNA may be packaged into a phage head by mistake during lytic assembly, and delivered to the next cell. Any gene can be transferred |
| Specialised transduction | A prophage excises imprecisely from the chromosome, carrying the adjacent host genes with it. Only genes flanking the integration site are transferred |
For full marks, name and distinguish the two types: generalised transduction, in which any fragment of host DNA may be mis-packaged into a phage head during lytic assembly, so any gene can be transferred; and specialised transduction, in which a prophage excises imprecisely and carries only the host genes adjacent to its integration site.
Add the clinical point if there is room: transduction transfers antibiotic-resistance genes — notably staphylococcal penicillinase.
The distinction is entirely about when the mistake happens.
Generalised — the error is at packaging. The phage is chopping up host DNA and stuffing heads; occasionally it stuffs a host fragment instead of its own genome. Any fragment is as likely as any other, so any gene can go. General.
Specialised — the error is at excision. A prophage sitting at one fixed site cuts itself out sloppily and takes its neighbours. Only the neighbours can go, so it is limited to specific genes. Specialised.
Generalised needs a virulent (lytic) cycle; specialised needs a temperate phage — which is why §2 comes before this section.
- Define transduction. → Gene transfer and recombination between bacteria via a bacteriophage
- Name the two types. → Generalised and specialised
- Generalised transduction — what and when? → Mis-packaging of any host DNA fragment into a phage head during lytic assembly; any gene may transfer
- Specialised transduction — what and when? → Imprecise excision of a prophage, carrying adjacent host genes only
- Which requires a temperate phage? → Specialised transduction
Conjugation ★★★
The form of gene transfer and recombination in bacteria that requires direct cell-to-cell contact — often via a sex pilus.
The sex pilus is encoded by the fertility (F) plasmid. A cell carrying the F plasmid is the donor; a cell without it is the recipient.
Of the three mechanisms, this is the one that keeps hospital microbiologists awake.
Transformation needs free DNA in the environment and a competent recipient. Transduction needs a phage with the right host range. Conjugation needs only that two cells touch — and in a gut, or on a catheter, or in a biofilm, cells touch constantly.
Worse, R plasmids typically carry several resistance genes together. One conjugation event can therefore convert a susceptible organism into a multi-resistant one in a single step — and it works between species. That is why an antibiotic used against one organism can select resistance in a completely different one sharing the same patient.
- Define conjugation. → Gene transfer and recombination requiring direct cell-to-cell contact, often via a sex pilus
- What encodes the sex pilus? → The fertility (F) plasmid
- Why is conjugation the most clinically important? → It needs only cell contact, and R plasmids carry several resistance genes at once, transferable between species
Revision
The lecture's own summary slide
- Definitions: phage, prophage, transformation, conjugation, transduction, lysogenic bacterium
- Genetic materials in bacteria
- Three forms of genetic recombination in bacteria
⭐ The three mechanisms side by side — the answer to any comparison question
| Transformation | Transduction | Conjugation | |
|---|---|---|---|
| Vehicle | Free “naked” DNA | Bacteriophage | Sex pilus |
| Contact needed? | No | No | Yes — direct cell to cell |
| Requirement | A competent recipient | A phage of the right host range | The F plasmid in the donor |
| Subtypes | — | Generalised (mis-packaging, any gene) · specialised (imprecise excision, adjacent genes) | — |
| Set in | 2020 Section I ⭐ | 2019 Section I ⭐ | Named on the summary slide |
- Define transduction for 4 marks. → Transfer of bacterial DNA from donor to recipient by a bacteriophage; generalised (mis-packaging, any gene) and specialised (imprecise prophage excision, adjacent genes only)
- Define transformation for 4 marks. → Uptake of free DNA by a competent bacterial cell and integration into its genome; Griffith's pneumococcal experiment
- Define conjugation. → Gene transfer requiring direct cell contact via a sex pilus encoded by the F plasmid
- Define prophage and lysogenic bacterium. → Prophage: phage inserted into the bacterial chromosome. Lysogenic bacterium: one carrying a prophage, in which a physiologic signal can trigger lysis
- Name the genetic materials of a bacterium. → A haploid, usually single circular chromosome; plasmids; bacteriophages