BIOL3060 #15 Bacterial and Viral Genetics

The Role of Bacteria and Viruses in Our World

Bacteria and viruses are everywhere, viruses infect all organisms and are the most abundant biological entities on earth

• Global Impact

  • Ocean bacteria produce 50% of earth’s oxygen

  • Remove 50% of atmospheric CO2

• agriculture

  • Pathogens of crops and animals

  • Provide nutrients like nitrogen and phosphorous to plants

• Human Health

  • Natural bacteria live in the mouth, gut, and skin, aiding digestion, immunity, and disease prevention

  • Many infectious diseases are caused y bacteria or viruses but can be controlled with antibiotics and vaccines

Bacteria and Viruses in Medicine and Genetics

• Medical and Industrial Importance:

  • bacteria produce drugs, hormones, food additives, and chemicals

  • viruses used in gene therapy to deliver healthy genes

• Genetic significance:

  • they have simple genetic systems = ideal for studying heredity and gene function

  • They share core genetic features with humans and other organisms

• Studies of bacterial and viral genetics have led to:

  • discovery of DNA as genetic material

  • Gene regulation models (ex. lac operon in E. coli that allows cells to digest lactose)

  • Tools for biotechnology and molecular biology

Advantages of Using Bacteria and Viruses for Genetic Studies

1. Reproduction is rapid

2. Many progeny can be produced

   1. 1 and 2 together allow lots of large generations in a short amount of time

3. Haploid genome allows all mutations to be expressed directly

4. Asexual reproduction simplifies the isolation of genetically pure strains

5. Growth in the laboratory is easy and requires little space

6. Genomes are small

7. Techniques are available for isolating and manipulating their genes

8. They have medical importance

9. They can be genetically engineered to rpoduce substances of commercial value

Diversity of Prokaryotes

Prokaryotes: unicellular organisms with a relatively simple cell structure. Prokaryotes include bacteria (eubacteria) and archaea

Two Main Groups:

• Archaea: unicellular organisms with prokaryotic cell structure that are found in all environments

• Eubacteria (Bacteria): most familiar bacterial species

Notes:

• DNA sequencing of uncultured bacteria has transformed our understanding of microbiology

• Bacteria and Archaea are genetically distinct from each other and bacteria/ eukaryotes are also genetically distinct

Bacterial Shapes and Sizes

• Bacteria exhibit a wide variety of shapes

  • Cocci (spherical)

  • Bacilli (rod-shaped)

  • Spirilla (helical)

• Size varies greatly: many are very very small but a few are visible to the naked eye

Bacterial Structures

Functional Diversity!

• Photosynthetic bacteria capture sunlight and produce oxygen

• Spore-forming bacteria survive extreme conditions

  • resistant to heat, cold, radiation, drought, chemicals, etc

• Stalks or filaments superficially resemble fungi

  • Stalks allow bacteria to anchor to surfaces, like rocks, plant roots, or sediments in aquatic environments, which allow them to stay in nutrient-rich environments

Bacterial Complexity

• Proteins like FtsZ help bacterial cell division, similar to eukaryotic tubulin in mitosis

• Bacteria have proteins that:

  • Condense DNA (Like histones in eukaryotes)

  • Maintain cell shape and cytoskeletal support

• Chromosome replication is coordinated with cell division, ensuring each daughter cell receives one copy of the genome (an exact copy)

NOTE: Bacteria have round DNA, don’t have the crossing over we’re used to, so the FtsZ ring helps separate bacteria (bacteria cannot just to cytokinesis)

Studying Bacteria Genetically

• Bacterial heredity is similar to other organisms, but:

  • they are haploid (only one copy of each gene)

  • cells are tiny, making phenotypes hard to observe directly

• Implication: scientists must use special lab techniques to study their genetics

• Key tool: Culture media: nutrient mixtures that allow bacteria to grow under controlled conditions

Growing and Analyzing Bacteria: Types of Media

• Minimal medium: only nutrients required by wild-type (prototrophic) bacteria

• Complete medium: includes all nutrients needed for growth, including supplements for mutants (auxotrophs)

Growing and Analyzing Bacteria: Growth Methods

• Broth culture: liquid medium in sterile test tubes

• Agar plates: solid medium poured into Petri dishes

Growing and Analyzing Bacteria: Plating

• Spread bacteria on agar → each cell grows into a colony (genetically identical)

• Colonies allow scientists to isolate pure strains and count individual bacteria

Studying Bacterial Phenotypes

• Microbiological study bacterial phenotypes: traots that can be onserved or detected chemically

• Colony appearance: color, shape, texture

• Observing phenotypes helps identify mutant strains for further genetic study

  • phenotypes can be difficult to tell apart

  • only works if phenotypes are visible to the human eye

Auxotrophs

Auxotrophs are mutant bacteria that have lost the ability to make a specific compound that they need to live, so much acquire that nutrient from environment

Comparison with wild-type (prototrophs)

• Wild-type bacteria: can grow on minimal medium because they make all necessary nutrients

• Auxotrophs: require supplemented medium to provide missing nutrients

Allows scientists to identify missing genes and study metabolic pathways

Auxotroph Example: Detecting Leucine Auxotrophs

1. Spread bacteria on medium containing leucine → both wild-type (leu+) and mutant (leu-) grow

2. Use replica plating to transfer colonies to:

   1. Plate with leucine (supplemented medium)

   2. Plate without leucine (selective medium)

3. Compare growth:

   1. leu+ bacteria grow on both plates

   2. leu- mutant grow only on supplemented medium

4. Colonies that grow only in the supplemented medium are leucine auxotrophs and can be cultured for further study

Modern Genomic Methods in Bacterial Research

Genomic methods: isolate and analyze DNA sequences from bacteria

• Key advantage: can study bacteria that cannot be grown in the lab

• Insights gained from genomics:

  • Bacterial diversity: discover new species and strains

  • Bacterial evolution: track how bacteria change over time

  • Gene organization: see how genes are arranged on the chromosome

  • Gene function: understand what different genes do

• Complements traditional methods like colony observation and replica plating, giving a more complete picture of bacteria genetics

The Bacterial Genome

• bacteria are unicellular and lack a nuclear membrane

• most bacterial genomes are single, circular chromsomes of double-stranded DNA

  • Example: E. coli: 4.6 million base pairs

• some bacteria have multiple chromsomes

  • vibrio cholerae: 2 circular chromosomes

  • rhiobium meliloti: 3 chromosomes

• rare cases have linear chromosomes

• protein-coding DNA

  • 90% of bacterial DNA encodes proteins (E. coli)

  • Only 1% of human DNA encodes proteins

Vibrio cholerae

• two circular chromosomes are double-stranded DNA loops

• each chromosomes carries different sets of genes, which together provide all the information the bacterium needs to survive and cause disease (cholerae)

• having multiple chromosomes can allow for specialization of gene functions and faster adaptations

• each chromosome may carry distinct functions, for example: one for essential metabolic functions, another for symbiosis with plants, and another for accessory functions

Plasmids

Small, usually circular DNA molecule that is distinct from the bacterial chromosome

• Plasmids replicate independently of the bacterial chromosome

Can be single-copy or multiple-copy per cell (even if only have 1 chromosome, can have many plasmids)

• Not essential for survival, but can:

  • promote gene transfer between bacteria

  • carry antibiotic resistance genes

  • aid in genetic engineering

Plasmid Replication

• replication begins at the origin of replication (ori)

• DNA strands separate, and replication proceeds around the circle

• results in two daughter plasmids, each with one new and one old DNA strand

Episomes

Episomes: plasmid cpable of replicating freely and able to integrate into a bacterial chromosome

• like retroviruses, episomes can integrate their DNA into the host genome

• however, episomes are bacterial DNA, note viral RNA, and don’t need reverse transcriptase (unless engineered in labs)

• both systems show how DNA can move between “extra” DNA elements and chromosomes

Episomes

Example: R Plasmid (Resistance Plasmid)

• An R plasmid is a plasmid that carries genes for antibiotic resistance

• Like other episomes it can exist independently in the bacteria cytoplasm or integrate into the bacteria chromosome

• r-determinants

  • these are genes that confer resistance to various antibiotics and toxic substances

  • ‘in the image, the resistance genes are labeled Tc^R: resistance to tetrocycline

• RTF segment (Resistance Tranfer Factor)

  • this segment contains genes necessary for plasmid replication and transfer between bacteria

Gene Exchange in Bacteria

• genetic exchange in common in bacteria and contributes to evolution

• all mechanisms involve:

  • DNA transfer

  • recombination with the recipient chromosome

• Three mechanisms:

  • Transformation: uptake of DNA from the environment

  • Transduction: DNA transfer via bacteriophages (viruses)

  • Conjugation: direct transfer from donor to recipient

Transformation

• Bacterium takes up naked DNA from the surrounding medium

• Transferred DNA can recombine with the bacterial chromosome

• Can create recombinant bacteria with new traits

• Transformation frequency varies among species; lab techniques can increase uptake

Famous Bacterial Transformation Experiment

• Frederick Griffith (1879-1941) was a British bacteriologist who is famous for his classic experiment in 1928 demonstrating bacterial transformation

  • S strain: smooth, virulent (causes disease)

  • R strain: rough, non-virulent (does not cause disease)

• He killed S strain bacteria by heat and mixed them with live R strain bacteria

• Some R strain bacteria “transformed” and became virulent S strain, causing those mice to die

Transduction

• bacteriophage infects a donor bacterium, accidentally packaging bacterial DNA → take up some bacterial DNA

• bacterial chromosome is sometimes partially broken down to make nucleotides for replicating viral DNA

• Virus infects a new bacterium, delivering recombinant DNA

• Recombination can creat recipient bacteria with new genes

• Host range limits transduction to same or closely related species

Transduction in Salmonella Example

P22 Phage in Salmonella

• Organism: Salmonella enterica (bacterium)

• Virus: P22 bacteriophage

• Process:

  • P22 infect a donor Salmonella cell

  • During viral replication, some bacterial DNa fragments are accidentally packaged into new viral particles

  • The donor DNA can join with the recipient’s DNA creating a recombinant bacterium with new traits

Key Concept:

• Bacteriophages act as vectors for gene transfer

• Transduction can transfer genes for traits such as toxin production or antibiotic resistance

Transduction v. Reserve Transcription

Transduction

• a bacteriophage (virus that infects bacteria) transfers DNA from one bacterium to another

• Steps:

  • virus infects a donor bacterium

  • virus accidentally packages bacterial DNA into its capsid

  • Virus infects a new bacterium and delivers the DNA

  • the transferred DNA can recombine with the recipient’s chromosome

• Key point: DNA moves via a virus; no RNA or reverse transcription is involved

Reverse Transcription

• involved copy RNA into DNA using the enzyme reverse transcriptase

• typical in retroviruses (ex. HIV)

• viral RNA is converted into DNA, which can then integrate into the host genome

• Key point: RNA → DNA, not just DNA transfer

Conjugation

• requires cell-to-cell contact; a cytoplasmic bridge (pilus) forms

• DNA transferred: plasmid or part of the chromosome from donor → recipient

• after transfer, crossing over may occur, creating a recombinant chromosome

• directionality: DNA moves only from donor → recipient (no reciprocal exchange, so donor does not get anything new)

• Note: not all bacteria can do this, need the F Factor to form a pilus (bridge)

Bacterial Conjugation and the F Factor

• The F Factor (fertility factor) is a plasmid episome found in some E. coli and other bacteria that carries genes that allow a bacterium to conjugate

• F+ cells (with the F factor): can donate DNA to F- cells (without F factor)

• During conjugation: the F plasmid is copied and transferred to the recipient cell, making it F+ and capable of donating DNA to others

• Importance of F factor:

  • enables horizontal gene transfer, spreading genes like antibiotic resistance

  • can integrate into the chromosome (Hfr), transferring chromosomal genes to the recipient

  • helps map bacterial genes and study gene function