Bacterial Genetics (Brewer) - 4/25/16 Flashcards
Describe 3 characteristics of bacterial populations.
- Clonal - all descendants of a cell are genetically identical (in absence of genetic mutation)
- Large - >10^11 bacteria/gram of intestinal contents
- Corollary: rare genetic events have a substantial probability of occurrence
Describe Penicillin resistance in Neisseria gonorrhoeae (2 modes of genetic change).
- Mutations accumulate with use of drug
- Acquisition of a gene from another source: plasmid-based gene encodes enzyme that hydrolyzes penicillin - no inhibition at clinically achievable concentrations (bad news because then penicillin is essentially a worthless antibiotic… pharmaceuticals have to keep tweaking drugs in response to bacterial sensitivity)
Describe 4 characteristics of bacterial genomes.
- Typically single circular DNA molecule = bacterial “chromosome”
- Few species have multiple or linear chromosomes
- Large cells may have >1 copy of chromosome
- All copies are normally identical
How does genome size reflect life-style (whether or not bacteria can survive outside a host or whether it is absolutely essential to have a host)?
E. coli - 4700 genes [makes all required compounds from glucose, multiplies outside host]
Haemophilus - 1743 genes [obligate parasite, requires many small molecules]
Mycoplasma - 470 genes [no cell wall, requires nearly all small molecules]
What are the accessory genetic elements common in bacteria?
- Plasmids
- Mostly circular DNA
- Many types
- Size and copies/cell vary (the larger the plasmid, the fewer the copies there tend to be inside the cell)
- Easy to detect [lyse cells so plasmid DNA escapes, chromosome stays inside cell –> separate plasmids by size w/ gel electrophoresis –> detect plasmid DNA using ethidium bromide –> non-fluorescent in solution but intensely fluorescent when bound to DNA] - Viruses [=bacteriophages, “eaters of bacteria”]
- Genetic parasites, inject genomes into bacterial cell, use its machinery for their replication
- Type 1: Virulent (or lytic) bacteriophages release progeny by lysis of cell
- Type 2: Temperate bacteriophages insert genomes into bacterial chromosome, replicate as part of it –> Integrated viral genome = provirus or prophage –> Later, provirus can excise from chromosome, replicate, lyse cell - Insertion Sequences and Transposons
Insertion Sequence:
- Can move from one location to another in DNA
- Contain ONLY the machinery for their own movement
- Gene for transposase - enzyme that catalyzes movement
- Inverted repeats at termini - recognized by transposase
Transposon:
- Resemble IS but contain genes unrelated to transposition (antibiotic-resistance genes frequently form part of transposons)
- Pathogenicity Islands
- Appear to be very large transposons
- Contain up to 50-100 genes
- May contain a ‘complete kit’ of virulence genes: Non-pathogen + PI = pathogen
- Most pathogenic strains contain multiple PI
How do accessory genetic elements replicate?
- Chromosomes, plasmids, and viruses have sites for initiation of DNA synthesis (molecules with such sites = replicons)
- Replicons also have sites for partition of replicated DNA –> daughter cells
- IS, TS, PI are NOT replicons b/c of their extreme simplicity - only replicate when integrated into one*
How can non-viral genes become incorporated into a provirus?
- Expression of most genes in provirus blocked by provirus-encoded repressor
- Non-viral genes can become incorporated into provirus
- If escape repression, expressed from provirus
- Virulence genes [especially toxins] often found in proviruses
What is an inverted repeat?
A sequence of nucleotides that is the reverse complement of another sequence located farther downstream
What are the three steps in the evolution of a transposon?
- IS inserts near antibiotic-resistance gene
- Second copy of IS inserts on other side (transposase can now act to move both IS’s and DNA between them)
- Damage or loss of internal inverted repeats locks structure together
How is the movement of IS and Tn catalyzed?
Catalyzed by transposases that recognize their terminal repeats
NOTE: similar enzymes catalyze 1) integration of HIV genome into human DNA and V/D/J splicing in assembly of Ig/TCR genes
What are the two modes of transposition?
- Cut and Paste (IS moved from donor to recipient)
- Replicative (IS is in both donor and recipient)
- Some TN encode a ‘Resolvase’ that separates the fused circles
Why are virulence genes and genes for antibiotic resistance often found in plasmids and viruses?
- Plasmids and viruses have mechanisms for transfer of DNA between bacterial cells (of same or different species)
- Chromosomes do not get moved by itself… get moved by plasmids/viruses only by accident
- Transposons can move chromosomal genes to plasmids/viruses –> enable rapid spread within and between bacterial populations
Describe the three mechanisms by which DNA transfer occurs between bacterial cells.
Transformation: DNA released by lysis of one cell, taken up by another.
Conjugation: DNA transfer by direct cell-to-cell contact; requires participation of a conjugative plasmid*
- Plasmid encodes all biochemical functions required for DNA transfer
- Usually only plasmid DNA transferred via conjugation bridge
- One way transfer = highly efficient
- Best-studied conjugative plasmid: F-plasmid or F-factor of E. coli
Transduction: Transfer via virus
- Bacterial DNA packaged into virus particle; transferred to another cell on infection
Contrast transfer of F-plasmid with the transfer of chromosomal DNA by the F-plasmid
Transfer of F-plasmid:
Conjugation bridge breaks –> recipient cell contains linear fragment –> transferred DNA re-circularized
Transfer of chromosomal DNA by F-plasmid:
Step 1. Insertion of F into bacterial chromosome; chromsome with integrated F behaves as giant plasmid in conjugation
Step 2. Chromosomal DNA (gray) transferred as well as plasmid DNA (green); bridge usually breaks before entire chromosome is transferred
What are R-Factors?
F-like plasmids with multiple antibiotic-resistance genes
R-Factors = most common cause for multi-drug resistance to bacteria
(Transposon is composed by a transposon which is composed by a transposition… each with resistance genes)
I.e. TB
