Central Dogma
Sandra: “Got that central dogma in me”
DNA Structure
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Single Circular Chromosome (prokaryotic DNA structure, typically seen in bacteria and archaea)
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In contrast to eukaryotic cells (which have multiple linear chromosomes), prokaryotes feature a more streamlined and efficient genome architecture with fewer regulatory elements.
Horizontal Gene Transfer (HGT)
- The process by which organisms transfer genetic material between one another, outside of traditional reproduction (vertical transmission).
- Plays a critical role in bacterial evolution, contributing to the spread of antibiotic resistance, virulence factors, and metabolic pathways.
1. Vertical Transmission
- Genes are passed from parent to offspring through standard reproduction.
2. Horizontal Transmission
- Genes are transferred between organisms, potentially across species barriers.
Mechanisms of Horizontal Transmission:
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Conjugation: Transfer via sex pilus
- [GOOD] for bacteria
- A direct cell-to-cell contact is established, allowing the exchange of plasmids (extrachromosomal DNA).
- F-plasmid: Contains genes necessary for the formation of the sex pilus.
- Important for spreading antibiotic resistance genes.
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Transduction: Transfer via bacteriophages (viruses that infect bacteria)
- [BAD] for bacteria
- Bacteriophages can accidentally package bacterial DNA and transfer it to other bacteria during infection.
- There are two types:
- Generalized Transduction: Random bacterial DNA is packaged into the viral particle.
- Specialized Transduction: Only specific bacterial genes adjacent to the viral integration site are transferred.
- This can introduce foreign DNA that disrupts bacterial function or integrates into the host genome, potentially altering behavior or killing the bacteria.
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Transformation: Uptake of naked DNA (often plasmids) from the environment
- [GOOD] for bacteria
- Bacteria take up DNA fragments or plasmids from their surroundings and incorporate them into their genome.
- Natural competence (ability to uptake DNA) varies across species. In lab settings, methods to induce competence include:
- Heat shock: Involves exposing bacteria to cold followed by rapid warming, opening pores in the membrane to allow DNA uptake.
- Electroporation: Uses electric pulses to create temporary pores in the membrane for plasmid insertion.
- Application: Transformation is widely used in genetic engineering to introduce desired traits or genes into bacterial hosts.
Evolutionary Conundrum
- Horizontal gene transfer challenges the traditional view of evolution as a tree-like structure of descent from a common ancestor. Instead, HGT presents a more networked model of evolution with genes shared between unrelated organisms.
- HGT is particularly prominent in prokaryotes, allowing rapid adaptation to changing environments (e.g., antibiotic pressure). This complicates the evolutionary tree and forces reconsideration of how traits spread across populations.
The Restriction-Modification (RM) System
The Immune System of Bacteria
- Bacteria have evolved sophisticated systems to defend themselves against foreign DNA, particularly from bacteriophages (viruses that infect bacteria).
Components:
- Restriction Enzymes (REase)
- These enzymes cut DNA at specific recognition sites (motifs) that are usually palindromic (e.g., 5’-GAATTC-3’).
- They serve as a defense mechanism by cleaving foreign DNA (such as bacteriophage DNA), preventing infection.
- Many restriction enzymes are named after the bacteria from which they were isolated (e.g., EcoRI from E. coli).
- Methyltransferases (MTase)
- Methylate the host’s own DNA at the same recognition sites targeted by restriction enzymes.
- Methylation acts as a protective “mark,” preventing the host’s restriction enzymes from cutting its own DNA.
- This system of paired restriction enzymes and methyltransferases ensures foreign DNA is destroyed while the host genome remains intact.
Stealth-by-Engineering
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Some engineered bacterial strains can evade detection by restriction enzymes through a process termed “Stealth-by-Engineering.”
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This is particularly useful in synthetic biology, where scientists want to insert foreign DNA into bacteria without triggering the RM system.
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Methods to evade RM systems include:
- Methylation of foreign DNA: Before introducing the DNA into bacteria, scientists can methylate it to mimic the host’s natural DNA.
- Synthetic redesign of DNA motifs: Using advanced DNA synthesis platforms (such as PacBio and Twist Bioscience), specific restriction sites are modified or removed, preventing cleavage by restriction enzymes. This allows for safe integration of engineered genes into bacterial genomes.
- Codon optimization: In stealth engineering, scientists optimize codon usage (changing DNA sequences without altering the protein) to make the inserted genes resemble the host’s native DNA.
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Invisible Engineering:
- This concept involves using genetic engineering techniques to modify bacteria in ways that avoid detection by their immune-like RM systems.
- By manipulating methylation patterns and restriction enzyme recognition sites, researchers can “cloak” foreign DNA, rendering it invisible to bacterial defenses.
- This has significant applications in biotechnology, including gene therapy, vaccine development, and the production of pharmaceuticals.
Example: Engineered bacterial strains designed to produce therapeutic compounds or break down pollutants without triggering their own RM defenses.
DNOVO Synthesis
- DNOVO refers to de novo (from scratch) DNA synthesis, enabling precise construction of genetic sequences without the need for a template.
- Twist Bioscience and other companies offer custom DNA synthesis services, allowing scientists to design and create novel genes, pathways, or even entire genomes tailored to specific functions.
- Applications:
- Production of synthetic biology products: biofuels, pharmaceuticals, and enzymes.
- Creation of genetically modified organisms (GMOs) with improved traits (e.g., drought resistance in plants).
- Development of personalized medicine: custom therapies based on individual genetic profiles.
- Applications:
Invisible Engineering and the Future
- Invisible engineering is part of a broader trend in synthetic biology, where organisms are modified in subtle ways to achieve desired outcomes while avoiding detection by natural systems (such as immune responses or environmental stressors).
- As technologies like CRISPR-Cas9 and long-read sequencing (PacBio) continue to improve, the potential for more sophisticated and stealthy genetic modifications grows.
- Ethical concerns arise as the ability to engineer life forms becomes more advanced, raising questions about how far humanity should go in manipulating the genetic code.
Key Future Areas:
- Gene Therapy: Using engineered viruses to introduce therapeutic genes into human cells without triggering immune rejection.
- Bioremediation: Engineering bacteria that can detoxify pollutants without being attacked by native bacterial communities.
- Agriculture: Developing crop plants with enhanced traits (yield, resistance to pests) that do not suffer from horizontal gene transfer risks or environmental interference.
This extended version includes additional details and context, especially about invisible engineering and its applications in synthetic biology. It also integrates relevant examples to make the content clearer and more insightful.