Unit 4: Genetic Flow and Its Role in Microbial Evolution and Adaptation

Vocabulary practice flashcards covering horizontal gene transfer mechanisms (transformation, transduction, conjugation), homologous recombination, antibiotic targets, resistance mechanisms, persistence, and biotechnology tools from Unit 4.

Horizontal Gene Transfer (HGT)

The transfer of genetic material from one cell to another non-vertically between organisms that are not direct descendants, allowing bacteria to rapidly acquire new characteristics and fueling metabolic diversity.

Transformation

A mechanism of horizontal gene transfer in which free donor DNA released from one lysed cell is taken up and incorporated into the genome of a recipient cell, effecting genetic change.

Transduction

A mechanism of horizontal gene transfer where host bacterial DNA transfer from one cell to another is mediated by a bacteriophage virus.

Conjugation

A mechanism of horizontal gene transfer requiring direct cell-to-cell contact and a conjugative plasmid in the donor cell to transfer plasmid-encoded DNA unidirectionally to a recipient cell.

Homologous Recombination

The physical exchange of DNA sequences between two homologous genetic elements from different sources sharing nearly identical base sequences.

Heteroduplex

A hybrid double-stranded region of DNA formed during homologous recombination wherein each complementary strand originates from a different parental chromosome.

Splice

An outcome of homologous recombination resolution in which genetic material is fully exchanged between two DNA molecules, producing a complete crossover.

Patch

An outcome of homologous recombination resolution where only small localized patches of DNA are exchanged without a complete crossover.

Competence

The physiological capacity of a bacterial cell to take up free environmental DNA and be transformed, mediated by specialized membrane-associated binding proteins, autolysins, and nucleases.

RecA Protein

A bacterial recombination protein that binds single-stranded DNA and promotes homologous base pairing and strand invasion into a recipient chromosome.

F Plasmid

A circular conjugative episome of $99{,}159\,\text{bp}$ in Escherichia coli that carries genes regulating DNA replication, insertion sequences (IS), and a tra region encoding sex pilus synthesis and type IV secretion.

oriT (Origin of Transfer)

The specialized DNA sequence on a conjugative plasmid where rolling circle replication and single-stranded transfer to a recipient cell are initiated.

tra Region

A region of the F plasmid containing genes that encode transfer functions, mating pair formation, sex pilus synthesis, and the type IV secretion system.

TraI

An enzyme encoded by the tra operon of the F plasmid that possesses both single-strand nicking and helicase activities to unwind DNA for conjugative transfer.

Episome

A plasmid, such as the F plasmid, capable of integrating reversibly into the bacterial host chromosome.

Hfr Strain (High Frequency of Recombination)

A bacterial donor strain possessing an F plasmid integrated into its host chromosome via homologous recombination between insertion sequences (IS), capable of mobilizing host chromosomal genes during conjugation.

Lytic Cycle

A viral reproductive cycle wherein a bacteriophage takes over host machinery, synthesizes new virions, and causes enzymatic destruction and lysis of the infected bacterial cell.

Lysogenic Cycle

A viral life cycle characterized by the integration of bacteriophage nucleic acid into the host bacterium genome, where it replicates silently as a prophage alongside the host chromosome.

Temperate Phage

A bacteriophage that has the ability to undergo either the lytic or lysogenic developmental pathway.

Prophage

The dormant state of a temperate bacteriophage genome integrated stably within the chromosome of a bacterial host.

Lysogen

A bacterial host cell carrying a prophage integrated within its chromosome, possessing the capacity to enter the lytic cycle under inductive stress.

Generalized Transduction

A process occurring during lytic viral growth where packaging enzymes accidentally package random pieces of host bacterial chromosomal DNA into the virion head instead of viral DNA, forming defective transducing particles.

Transducing Particle

A defective phage capsid containing accidental fragments of bacterial host DNA rather than viral genome, capable of gene injection but unable to establish a viral infection.

Specialized Transduction

A transduction process mediated by temperate phages in which improper prophage excision transfers specific adjacent host chromosomal genes along with phage DNA at high efficiency.

Lambda Phage

A temperate bacteriophage of Escherichia coli that integrates adjacent to the galactose operon and can carry out specialized transduction of galactose catabolism genes upon incorrect excision.

Phage Conversion

An alteration in the phenotype of a host bacterial cell caused by lysogenization with a temperate prophage, such as conferring viral immunity or introducing toxin production.

Corynebacteriophage b

A temperate bacteriophage carrying the tox gene that converts non-toxin-producing strains of Corynebacterium diphtheriae into pathogenic diphtheria toxin-producing strains.

Antibiotics

Antimicrobial substances naturally produced by microorganisms (primarily certain bacteria and fungi) that kill or inhibit the growth of bacteria by targeting essential molecular processes.

Quinolones

A class of synthetic antibacterial agents that target DNA gyrase in Gram-negative bacteria and topoisomerase IV in Gram-positive bacteria, inhibiting DNA unwinding and replication.

Rifampin

An antibiotic that prevents RNA transcription by directly binding and blocking bacterial RNA polymerase.

Puromycin

An antibiotic mimicking the $3'$ end of a tRNA that binds to the ribosomal A site, resulting in premature polypeptide chain termination.

Aminoglycosides

Antibiotics (such as streptomycin) that bind the 16S rRNA component of the bacterial 30S ribosomal subunit, causing mRNA misreading and error-filled protein accumulation.

Daptomycin

A cyclic lipopeptide antibiotic produced by Streptomyces that binds to phosphatidylglycerol residues in bacterial cytoplasmic membranes, forming pores and depolarizing the membrane.

\beta-Lactams

A class of antibiotics, including penicillin and cephalosporins, that inhibit bacterial cell wall synthesis by blocking transpeptidation catalyzed by penicillin-binding proteins.

Vancomycin

A glycopeptide antibiotic that binds peptidoglycan precursors in Gram-positive bacteria, preventing the formation of peptide interbridges during cell wall construction.

Bacitracin

A topical antibiotic that halts peptidoglycan synthesis by binding to the precursor transport system, creating gaps in the cell wall that lead to lysis.

\beta-Lactamase

A bacterial resistance enzyme that hydrolyzes and cleaves the core \beta-lactam ring structure, rendering penicillins inactive.

Efflux Pumps

Transmembrane transport systems that export antibiotics out of the bacterial cell, lowering intracellular drug concentrations and enabling survival at high external doses.

AcrAB-TolC

A well-characterized multidrug efflux system in Escherichia coli that pumps out multiple antibiotic classes, including rifampicin, chloramphenicol, and fluoroquinolones.

MecA

An alternative penicillin-binding protein encoded on a chromosomal island in methicillin-resistant Staphylococcus aureus (MRSA) that is not inhibited by \beta-lactams.

Persistence

A transient, non-heritable state where a small subpopulation of genetically identical bacteria becomes dormant and tolerant to lethal concentrations of multiple antibiotics.

Toxin-Antitoxin (TA) Module

A small genetic system comprising a stable toxin that halts cellular translation and a labile antitoxin that neutralizes the toxin under normal growth conditions.

HipA

A toxin in the HipAB module of Escherichia coli that phosphorylates GltX (glutamyl-tRNA synthetase), leading to uncharged tRNA accumulation, (p)ppGpp production, and dormancy.

HipB

The unstable antitoxin of the HipAB module that binds and inactivates the HipA toxin and autorepresses transcription at the hipBA promoter.

Phenotypic Heterogeneity

Cell-to-cell variations in gene expression, metabolite levels, or protein content that arise spontaneously within an isogenic, clonal bacterial population.

Complementation

The restoration of a wild-type phenotype in a mutant cell by the introduction of a functional wild-type copy of the defective gene on a plasmid or viral vector.

Chemical Competence

An artificial procedure where bacterial cells (such as Escherichia coli) are treated with high \text{Ca}^{2+} concentrations followed by a heat shock at $42^{\circ}\text{C}$ for $30\,\text{sec}$ to facilitate uptake of double-stranded DNA.

Electroporation

A laboratory method that exposes cells to high-voltage electric pulses (e.g., $15\,\text{kV/cm}$, $5\,\mu\text{sec}$) to permeabilize the cell envelope for DNA uptake.

endA1

A genetic mutation engineered into laboratory cloning strains like Escherichia coli DH5\alpha that inactivates an intracellular endonuclease that degrades foreign plasmids.