Table of Contents
Viral and bacterial genetics are especially important for genetic engineering because viruses and bacteria naturally move, modify, and copy DNA. Here we focus on a few key mechanisms and properties that are directly useful for genetic engineering.
Viral Genetics: How Viruses Handle Genetic Information
Types of Viral Genomes
Viruses have much simpler genetic material than cells, but it comes in several forms. The main distinctions:
- DNA viruses
- Genome is DNA.
- Can be:
- Double-stranded DNA (dsDNA), like many bacteriophages and herpesviruses.
- Single-stranded DNA (ssDNA), like parvoviruses.
- Often replicate using host DNA polymerases (or their own, in larger viruses).
- RNA viruses
- Genome is RNA.
- Can be:
- Single-stranded RNA (ssRNA)
- Positive-sense (+) RNA: functions directly as mRNA.
- Negative-sense (−) RNA: must first be copied into +RNA by an RNA-dependent RNA polymerase.
- Double-stranded RNA (dsRNA).
- Require virus-coded RNA-dependent RNA polymerases, because cells do not normally copy RNA from RNA templates.
- Retroviruses (special type of RNA virus)
- Have ssRNA genomes.
- Use reverse transcriptase to make a DNA copy of their RNA.
- That viral DNA is integrated into the host genome as a provirus.
These different genome types come with different enzymes (like reverse transcriptase) and strategies, which are widely used as tools in molecular biology.
Productive, Latent, and Lysogenic Infection
Viruses can interact with host cells in different ways that affect how viral genes are expressed and how the viral genome is handled:
- Lytic (productive) infection
- Virus takes over the host cell.
- Viral genome is quickly expressed, many new viruses are made.
- Cell usually bursts (lysis), releasing progeny viruses.
- Typical of many bacteriophages in their lytic cycle.
- Latent infection
- Viral genome persists in the cell with little or no expression.
- Can be maintained as:
- A separate circular DNA (episome).
- An integrated copy in the host genome.
- Under certain conditions, the virus can be reactivated and enter a lytic phase.
- Lysogeny (special case in bacteriophages)
- Seen in temperate phages (e.g., bacteriophage λ).
- Viral DNA integrates into the bacterial chromosome as a prophage.
- Prophage is replicated along with the bacterial chromosome.
- Under stress (e.g., DNA damage), the prophage can excise and enter the lytic cycle.
Lysogeny is especially important in genetic engineering because it shows that foreign DNA can be stably integrated into a host genome and later excised or expressed.
Genetic Variation in Viruses
Viruses evolve quickly. This rapid change is central to their use as research tools and to understanding their risks:
- High mutation rates in RNA viruses
- RNA-dependent RNA polymerases and reverse transcriptase are error-prone.
- Leads to quasispecies: a cloud of related viral genomes in one infection.
- Important for:
- Rapid adaptation (e.g., influenza, HIV).
- Emergence of drug resistance.
- Recombination and reassortment
- Recombination: exchange of genetic segments when two related viruses infect the same cell.
- Reassortment: in viruses with segmented genomes (e.g., influenza), entire RNA segments can be swapped between strains.
- These processes can create new combinations of viral genes very quickly.
For genetic engineering, the ability of viral genomes to recombine and insert into host DNA is harnessed, but also carefully controlled to reduce unwanted changes.
Bacteriophages and Transduction (Overview Only)
Bacteriophages (viruses that infect bacteria) are a model system in genetics. A key process is transduction:
- Phage infection can accidentally package bacterial DNA.
- This DNA can be transferred to another bacterium when the phage infects again.
- This is one of the natural routes for horizontal gene transfer in bacteria.
The details of transduction and specific phage vectors are treated elsewhere; here the important point is that phages naturally move DNA between bacteria, which inspired laboratory cloning and gene transfer techniques.
Bacterial Genetics: Organization and Mobility of DNA
Bacterial Chromosomes and Plasmids
Bacteria typically have:
- A single circular chromosome
- Contains essential genes.
- Highly compacted and organized into a “nucleoid” (but not membrane-bound like a nucleus).
- Replicates from a specific origin of replication (
oriC). - Plasmids
- Small, usually circular DNA molecules that replicate independently of the chromosome.
- Often carry accessory genes, such as:
- Antibiotic resistance.
- Toxin production.
- Metabolic pathways for unusual substrates.
- Can be present in one or many copies per cell.
- Many plasmids are conjugative: they encode the machinery to transfer themselves between cells.
Plasmids are the central workhorse of genetic engineering because they are easy to isolate, cut, modify, and reintroduce into bacteria.
Horizontal Gene Transfer in Bacteria
Unlike eukaryotes, bacteria frequently exchange genetic material outside of reproduction. Three main mechanisms:
1. Transformation
- Uptake of free DNA from the environment.
- Bacteria that can naturally do this are called competent.
- Steps:
- Double-stranded DNA binds to the bacterial surface.
- One strand may be degraded; the other is transported into the cell.
- Incoming DNA can recombine with the chromosome if there is sufficient sequence similarity (homologous recombination), or persist as a plasmid if it has its own origin of replication.
In genetic engineering, transformation is mimicked artificially by making bacteria chemically competent or electrocompetent, enabling them to take up plasmid DNA prepared in the lab.
2. Conjugation
- Direct cell-to-cell transfer of DNA through physical contact.
- Frequently mediated by F plasmids (fertility plasmids) and related elements.
- Key features:
- Donor cell (F⁺): carries a conjugative plasmid with genes for a pilus and transfer machinery.
- Recipient cell (F⁻): lacks this plasmid.
- A mating bridge forms; a single DNA strand of the plasmid is transferred and then replicated in both cells.
- Variants:
- F plasmid remaining independent: converts F⁻ recipients into F⁺ donors.
- Hfr (high frequency recombination) strains: F plasmid integrated into the chromosome; can transfer chromosomal genes into a recipient.
Conjugation shows how large DNA fragments can be transferred in nature. In biotechnology, conjugative plasmids and engineered “suicide plasmids” are used to move genes between bacterial strains or into environmental bacteria.
3. Transduction (Bacteriophage-Mediated Transfer)
- DNA transfer is mediated by bacteriophages.
- In generalized transduction, random fragments of bacterial DNA are mistakenly packaged into phage heads.
- In specialized transduction, only specific bacterial genes near a prophage integration site are transferred when the prophage excises imprecisely.
- Transduced DNA can recombine with the recipient’s chromosome.
Transduction has been used as a genetic mapping tool and, in modified form, as a controlled gene delivery system.
Mobile Genetic Elements
Bacterial genomes are not static. Several mobile elements can move within and between DNA molecules:
Insertion Sequences (IS Elements)
- Small DNA segments that encode a transposase enzyme and short terminal repeats.
- Can insert into new sites in the genome.
- Often disrupt genes or regulatory regions where they insert.
Transposons
- Larger mobile elements that often carry one or more additional genes (e.g., antibiotic resistance).
- Also mobilized by transposase.
- Can jump:
- Between plasmids.
- Between plasmid and chromosome.
- Between different locations on the chromosome.
Transposons are important in genetic engineering both as a problem (spreading resistance genes) and as a tool (designed transposons for random mutagenesis).
Integrons (Conceptual Introduction)
- Genetic platforms that can capture, express, and rearrange gene cassettes.
- Often associated with antibiotic resistance gene clusters.
- Involve a site-specific recombinase and a recombination site structure.
Integrons illustrate how bacteria can rapidly assemble multi-resistance regions, which is a major concern for clinical microbiology and biotechnology safety.
Regulation of Bacterial Gene Expression (Briefly in Context)
For genetic engineering, two aspects of bacterial gene regulation are especially relevant:
- Promoters and operators
- Promoters are DNA sequences where RNA polymerase binds to start transcription.
- Operators and regulatory sequences control whether the promoter is active.
- Genetic engineering uses synthetic promoters and regulatory systems (e.g., inducible promoters activated by lactose analogues or other small molecules) to turn gene expression on or off.
- Operons
- Groups of genes transcribed together under control of a single promoter.
- Allow co-regulation of functionally related genes.
- Many engineered constructs mimic this design to express several proteins from a single control region.
The natural regulatory architecture of bacteria (promoters, operators, operons) is reused and simplified in engineered plasmids.
Why These Aspects Matter for Genetic Engineering
Several features of viral and bacterial genetics directly underlie modern genetic engineering methods:
- Plasmids as vectors
- Modified natural plasmids are used to carry foreign genes into bacteria.
- Antibiotic resistance genes on plasmids serve as selectable markers to identify transformed cells.
- Viral integration and packaging
- Viral strategies (integration, high-level expression, efficient packaging) are adapted to build viral vectors for delivering genes into eukaryotic cells.
- Reverse transcriptase from retroviruses is used in the lab to convert RNA to DNA (e.g., for cDNA synthesis).
- Horizontal gene transfer mechanisms
- Transformation, conjugation, and transduction are harnessed or mimicked to move genetic constructs between organisms or between laboratory strains.
- Mobile elements
- Transposons and related systems are used to:
- Insert genes into new chromosomal locations.
- Create random mutations for functional studies.
Understanding these selected aspects of viral and bacterial genetics provides the conceptual basis for the experimental methods and applications discussed in later sections on genetic engineering tools and techniques.