Microbial Genetics, Viral Life Cycles, and Microbe-Host Symbiosis: Study Notes

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Microbial Genetics: Gene Transfer Mechanisms

Vertical vs. Horizontal Gene Transfer

Gene transfer in microorganisms occurs via two main mechanisms: vertical gene transfer and horizontal gene transfer.

Vertical gene transfer: Transmission of genetic material from parent to offspring during reproduction.
Horizontal gene transfer: Movement of genetic material between organisms other than by descent. This is a major driver of genetic diversity in prokaryotes.

Modes of Horizontal Gene Transfer

There are three primary modes of horizontal gene transfer in bacteria:

Transformation: Uptake of free DNA from the environment.
Conjugation: Direct transfer of DNA between two bacterial cells via cell-to-cell contact.
Transduction: Transfer of DNA mediated by bacteriophages (viruses that infect bacteria).

Transformation

Source of DNA: Free DNA fragments released from lysed cells into the environment.
Competency: Cells must be in a physiological state called "competent" to uptake DNA. This often requires specific conditions and molecular machinery (e.g., translocosome in Gram-positive bacteria).
Mechanism: DNA is imported and incorporated into the genome via homologous recombination, requiring sequence similarity (homology).
Amount of DNA transferred: Usually small fragments, less than 1% of the genome.
Example: Streptococcus pneumoniae can uptake DNA from related species, leading to genetic variation.

Conjugation

Source of DNA: DNA is transferred directly from donor to recipient cell, typically via a plasmid (e.g., F plasmid).
Competency: Donor cells must possess the fertility (F) plasmid to form a sex pilus; recipient cells lack the plasmid.
Mechanism: Plasmid is nicked, transferred through the pilus, and replicated in both cells.
Amount of DNA transferred: Can be large, often entire plasmids (tens of kilobases), sometimes chromosomal segments.
Payload: Plasmids often carry genes for antibiotic resistance, metal resistance, or other conditional traits.
Example: Transfer of antibiotic resistance genes among Escherichia coli populations.

Transduction

Source of DNA: DNA fragments from the host cell are accidentally packaged into phage capsids during viral replication.
Competency: Recipient cells must have the appropriate phage receptor for infection.
Mechanism: Phage injects DNA into recipient; homologous recombination incorporates DNA into the genome.
Amount of DNA transferred: Limited by the size of the phage capsid (up to tens of kilobases).
Example: Salmonella phages can transfer virulence genes between strains.

Generalized vs. Specialized Transduction

Generalized transduction: Any portion of the host genome can be transferred; occurs when phage packaging is random.
Specialized transduction: Only specific regions near the phage integration site are transferred; occurs with temperate phages that integrate into the host genome.
Limitation: Amount of DNA transferred is limited by capsid size.

Viral Life Cycles and Infection Mechanisms

Basic Steps of Viral Infection

Viruses infect host cells through a series of steps:

Attachment: Virus binds to specific receptors on the host cell surface.
Entry: Viral genome enters the host cell.
Eclipse period: No detectable virions outside the cell; viral genome is being replicated and expressed.
Rise period: New virions are assembled and released, often by cell lysis.

Lytic vs. Lysogenic Cycles

Lytic cycle: Virus takes over host machinery, replicates, assembles new virions, and lyses the cell.
Lysogenic cycle: Viral genome integrates into host chromosome and remains dormant; replicated passively as host divides.
Transition: Lysogenic viruses can re-enter the lytic cycle under certain conditions.

Stages of Lytic Infection

Attachment
Eclipse period: Viral genome is inside the cell; early mRNAs shut down host defenses, replicate viral genome, and produce proteins.
Rise period: Virions are assembled and released.

Viral Genome Types and Infection Mechanisms

DNA viruses: Must transcribe DNA to mRNA using host machinery.
+RNA viruses: Genome acts as mRNA; can be directly translated.
-RNA viruses: Genome is complementary to mRNA; must carry RNA-dependent RNA polymerase to synthesize mRNA.
Retroviruses: RNA genome is reverse-transcribed into DNA by reverse transcriptase, then integrated into host genome.

Prepackaged Enzymes in Viral Capsids

DNA viruses: Usually do not require prepackaged enzymes.
+RNA viruses: Do not require prepackaged enzymes.
-RNA viruses: Require RNA-dependent RNA polymerase.
Retroviruses: Require reverse transcriptase.

Viral Genome Size

DNA viruses: Typically have larger genomes than RNA viruses.
RNA viruses: Smaller genomes; higher mutation rates.
Retroviruses: Intermediate genome size; high mutation rates.

Viral Evolution: Antigenic Drift and Shift

Mechanisms of Viral Evolution

Antigenic drift: Gradual accumulation of mutations during replication; analogous to vertical gene transfer.
Antigenic shift: Abrupt reassortment of genome segments when a cell is co-infected by multiple viruses; analogous to horizontal gene transfer.

Influenza Virus Example

Influenza virus has 8 RNA segments; co-infection can lead to reassortment and new viral strains.
Antigenic shift produces novel combinations (e.g., H1N1, H3N2).
Antigenic drift changes surface proteins, complicating vaccine development.

Characterizing Viruses, Viroids, and Prions

Definitions and Differences

Virus: Infectious agent with nucleic acid (DNA or RNA) and protein coat; can infect all domains of life.
Virion: The extracellular, infectious form of a virus.
Viroid: Infectious agent composed only of a short strand of circular RNA; lacks protein coat; infects plants.
Prion: Infectious protein; lacks nucleic acid; causes neurodegenerative diseases (e.g., Creutzfeldt-Jakob disease).

Microbe-Host Symbiosis and Microbiomes

Symbiosis in Microbiology

Symbiosis: Long-term association between two species.
Mutualism: Both partners benefit.
Parasitism: One partner benefits at the expense of the other.
Commensalism: One partner benefits, the other is unaffected.

Microbiome and Human Health

Microbiome: The collection of microorganisms living in and on the human body.
Acquisition: Microbiome is acquired from the environment, birth, and diet.
Antibiotics: Broad-spectrum antibiotics can disrupt the microbiome, leading to health issues.

Opportunistic Pathogens

Definition: Microbes that are normally harmless but can cause disease under certain conditions (e.g., immunosuppression, entry into sterile sites).
Example: Staphylococcus aureus is benign on skin but can cause infection if introduced into the bloodstream.

Endosymbiosis

Definition: Symbiotic relationship where one organism lives inside another.
Example: Mitochondria and chloroplasts in eukaryotic cells are endosymbionts, derived from ancestral bacteria.
Characteristics: Endosymbionts lose genes required for free-living; cannot survive outside host cell.

Summary Table: Gene Transfer Mechanisms

Mechanism	Source of DNA	Vector	Competency Requirement	Amount of DNA Transferred
Transformation	Free DNA from environment	None (direct uptake)	Competent cell state	Small fragments (<1% genome)
Conjugation	Donor cell (plasmid/chromosome)	Sex pilus (F plasmid)	F+ donor, F- recipient	Large (entire plasmid, sometimes chromosomal)
Transduction	Host cell DNA	Bacteriophage	Phage receptor on recipient	Limited by capsid size (up to tens of kb)

Summary Table: Virus, Virion, Viroid, Prion

Agent	Nucleic Acid	Protein Coat	Infects
Virus	Yes (DNA or RNA)	Yes	All domains of life
Virion	Yes	Yes	Extracellular form
Viroid	Yes (RNA only)	No	Plants
Prion	No	Yes (misfolded protein)	Animals (esp. mammals)

Key Equations and Terms

Homologous recombination: Incorporation of DNA with sequence similarity into the genome.
Reverse transcriptase: Enzyme catalyzing
RNA-dependent RNA polymerase: Enzyme catalyzing
Central dogma:

Additional info: Academic context was added to clarify mechanisms, provide examples, and summarize key concepts for exam preparation.