L3: Bacterial Genetics Flashcards
What makes mobile genetic elements and gene transfer important to medicine? 3
- Antibiotic resistance genes that encode drug modifying enzymes, efflux systems, alternate antibiotic targets, or metabolic enzymes are located on MGE’s
- Virulence factors are on MGE’s
- Gene transfer occurs between all bacterial species
What is a virulence factor?
genes that contribute to the ability of bacterial species to cause disease
How is gene transfer in bacteria described?
highly promiscuous
What allows for the emergence of pathogens not previously recognized and re-emergence of pathogens once thought vanquished?
transfer of antibiotic resistance genes and virulence factors
What is a core genome?
genes common to all individuals of a species
What is a pan genome?
genes sporadically present in a species but may be shared with other species
What is transformation?
A form of gene transfer involving programmed uptake of naked DNA from the environment
What does transformation require?
host homologous recombination system
What does transformation mainly transfer?
only gene fragments
What is transduction?
A form of gene transfer mediated by bacterial viruses (bacteriophage)
(Genes hitchhike on phage)
Is transduction generalized or specialized?
Either or
What is conjugation?
A form of gene transfer requiring direct cell-to-cell contact and exchange of intact genetic elements
Which of the three is the broadest host range form of gene transfer?
Conjugation
Does conjugation require recombination?
No
What is a bacteriophage?
Bacterial viruses that depend on a host cell for replication then exit the cell to infect other host cells
What is a plasmid?
Self-replicating genetic elements maintained separately from the chromosome that cannot exist independently from a host cell.
What is a transposon?
Non-replicating genetic elements capable of “hopping” or transposing from one position on the genome to another.
What is a genomic island?
Clusters of related genes variably present in strains of the same species and associated with bacteriophage-like genes and properties
What are ICE elements?
mobile genetic elements that combine features of bacteriophage, plasmids, and transposons and may include genomic islands
What are integrons?
specialized antibiotic resistance cassette accumulation system
How is it possible to detect penicillin resistant S. pneumoniae, especially high level resistance?
step-wise selection at progressively higher penicillin dosages.
Comparison of the PBP gene sequences from sensitive and resistant strains of bacteria reveal what?
What are these known as?
resistant genes contain blocks of sequence similar to oral Streptococci superimposed on a framework of S. pneumoniae sequence
Mosaic genes
S. pneumoniae is also capable of natural competence, what does this mean?
Ability to take up naked DNA from the environment
Steps of competence? (4)
- Binding of dsDNA
- Uptake of ssDNA
- Recombination into chromosome
- Gene replacement
Naturally competent bacteria are always able to do what two things?
In response to what?
- Undergo transformation
- Undergo a developmental program
Response to stress to form sub-population of competent cells
What is artificial competence?
Exposure of cells to various chemical treatments in a lab
Besides expressing genes required for DNA uptake, what else can competent bacteria do? (3)
- Secrete chemicals that induce lysis of non-competent neighbors
- Undergo periodic spontaneous lytic cycles
- Secrete DNA through pores
What are some of the medically important competent bacteria? 4
Neisseria gonorrhoeae, Neisseria meningitides, Haemophilus influenzae, Helicobacteri pylori.
What are the advantages of transformation? (2)
- Any DNA can be acquired using it
2. If the DNA isn’t useful, you can break it down for good
Three disadvantages of transformation?
- The recipient must encode the program required for competence
- Acquired DNA must be somewhat similar to be homologously recombined (limited host range)
- Transferred DNA must escape DNases in the environment until it contacts a competent cell
What is another method of making mosaic genes besides transformation?
Generalized transduction
What happens in generalized transduction? 2
- In the lytic pathway, the bacteriophage makes a mistake and packages host DNA in the bacteriophage capsid instead of bacteriophage DNA
- This host DNA is then carried passively with the phage head and injected into next host cell it contacts
Why is generalized transduction named so?
Since each fragment of host DNA has equal probability of being packaged, its called generalized transduction
What are the steps of the bacteriophage life cycle. 5
- Bacterial cell undergoes viral attachment and injections of DNA
- Bacteriophage Viral protein and DNA synthesis occur
- Destruction of bacterial chromosome
- Packaging and assembling of complete viruses
- cell lysis releasing many bacteriophage particles
Advantages of generalized transduction? 3
- Any DNA can be acquired
- DNA is protected in phage head
- No special program required by recipient
Disadvantages of generalized transduction? 2
- Bacteriophage have very limited host ranges
2. Homologous recombination is required to integrate the DNA into recipient genome.
How does a cholera bacteria gain the toxin gene?
Lysogenic conversion
What does lysogenic conversion require? (2)
- Bacteriophage is capable of lysogenic lifestyle
2. Toxin gene is part of the bacteriophage genome, always traveling with it
What are steps of lysogenic pathway?
- Bacterial cell encounters bacteriophage and viral attachment and injection of DNA occurs
- Viral integration into chromosome
- Lysogenic cell prophage occurs
- Continued cell division
5A: Bacteriophage stably replicates with bacterial chromosome
5B: Prophage induction occurs and lytic pathway begins
So what process explains where the toxic cholera gene came from in the first place?
Specialized transduction
What is specialized transduction?
When a prophage excies to begin its lytic cycle it makes an error and carries adjacent chromosome with it becoming a permanent part of phage genome.
Cholera toxin comes from what family of toxins?
Binary or A-B toxins
E. Coli has what phage?
What gene product?
What clinical manifestation?
Lambda phage
Shigalike toxin
Hemorrhagic diarrhea
Clostridium botulinum has what phage?
What gene product?
What clinical manifestation?
Clostridial phage
Botulinum toxin
Botulism = Food poisoning
Corynebacterium diphtheriae has what phage?
What gene product?
What clinical manifestation?
Corynephage beta
Diphtheria toxin
Diphtheria
Strep pyogenes has what phage?
What gene product?
What clinical manifestation?
T12
Erythogenic toxin
Scarlet fever
Advantages of specialized transduction? 3
- DNA is protected from DNases in the phage head
- No special program required by the recipient
- Homologous recombination is not required because the DNA is part of the phage
Disadvantages of specialized transduction? 3
- Gene transfer limited by history of phage and its adjacent genes
- Bacteriophage must be able to infect both donor and recipient strain which limits host range
- High risk and phage might kill it
Do virulence genes appear randomnly in the chromosome? Why or why not?
No appearing in clusters at specific sites called islands
Can different pathogenicity islands be integrated together?
Yes, frequently different clusters of virulence genes will be integrated at the same site in different but related pathogens
What genes are typically in pathogenicity islands?
genes commonly used by bacteriophage for lysogenic insertion but no other phage genes
Can pathogenicity islands be mobilized by the phage?
Yes
What does the GC content of pathogenicity islands suggest?
foreign acquisition
The first vancomycin resistant S. aureus was found with what other two strains?
- Vancomycin sensitive Staph aureus
2. Vancomycin resistant Enterococcus faecalis
What are bacterial plasmids?
Genetic elements that are replicated and inherited independently from the bacterial chromosome
What four things do bacterial plasmids encode that are important to their action?
- own origin of replication
- own initiator protein
- negative regulatory circuit (cop) that keeps the copy number within prescribed limits
- own mechanisms to ensure proper distribution to daughter cells to ensure stable inheritance
How much does the size vary of a bacterial plasmid?
2000 to 100s of thousands of BP’s
Do plasmids have genes for resistance and virulence?
Sometimes yes
Why do plasmids encode their own negative regulatory circuit?
How does each copy number vary between plasmids?
prevents plasmids from becoming a burden on their host
Each plasmid has its own characteristic copy number
Do smaller or larger plasmids have more copy numbers?
Smaller
What is conjugation?
What type of process is it?
mechanism of gene transfer that requires direct cell-to-cell contact between donor and recipient cells, sometimes called bacterial mating
replicative process, both donor and recipient end up with a copy of the plasmid
What does conjugation require?
numerous plasmid-encoded genes called tra (short for transfer) genes encoding proteins that perform two separate functions
Two types of transfer genes in conjugation?
Mpf: Mating Pair Formation genes
Dtr: DNA transfer and replication genes
Mating pair formation genes encode what?
What else in some cases?
a pore that will cross the donor and recipient walls and membrane
a specialized appendage or protein (sex pilus or aggregation substance) that facilitates cell contact
DNA transfer and replication genes encode what? 3
- Enzyme that nicks one strand of the plasmid
- Another enzyme that transports the nicked strand to the pore
- Another set of enzymes facilitates replication of a replacement strand in the donor and second strand in the recipient.
What are transposons?
Discrete segments of DNA that are able to “jump” or transpose from one site in the genome to another.
What do transposons encode?
Function of this?
transposase
recognizes the ends of the transposon, cut them from their initial location and catalyze their movement to a new location
What are the simplest transposons?
What do they contain? (2)
Insertion sequences
Transposase
Recognition sites
What are composite transposons?
Two insertion sequences flanking a gene that will mobilize that gene is the transposase recognizes the outside ends of the insertion sequences.
What are the two most important things for dissemination of antibiotic resistance genes?
- Conjugative plasmids
2. Transposons
Are virulence factors located on plasmids?
Yes
What family of bacteria is the most famous case of virulence factors on plasmids?
Bacillus cereus
How do the three species of B. cereus vary?
- B. cereus = Harmless
- B. thuringiensis (carries plasmids for crystal forming toxins that kills insects and used in Bt corn.)
- B. anthracis (two plasmids: 1 = Capsule that protects bacterium from immune system. 2 = Encodes anthrax toxin)
How had a person with B. cereus gotten infected with anthrax like disease?
Why didn’t it need the capsule genes?
The strain had acquired the anthrax toxin-encoding plasmid from B. anthracis.
Made its own distinct capsule
Can transposons carry virulence factors?
Yes, toxic shock syndrome from S. aureus
Advantages of conjugation? (4)
- DNA protected from DNases through transfer method
- No special program or receptor is required by the recipient cell (everything is in the plasmid)
- Homologous recombination is not required
- conjugation is highly promiscuous
What happens in crown gall?
Piece of bacterial DNA is transferred to plant DNA to induce tumors (conjugation)
Disadvantages of conjugation?
- Plasmid replication is somewhat host restricted.
- Delivery of transposons may not require plasmid replication
- Some plasmids encode replication systems that allow replication in a variety of hosts broad host range plasmids.
- Genes transferred by conjugation islimited to genes associated with the plasmid.
Can conjugative plasmids accumulate transposons?
Yes
Conjugative plasmids can mobilize non-conjugative plasmids in the same cell if what?
Provide the Mpf systems that these plasmisd lack.
How are Hfr strains integrated into chromosome?
Conjugative plasmids can integrate into the chromosome and begin the conjugative process while attached to the chromosome, carrying bordering DNA along into the recipient which can the be integrated into the chromosome.
What is the most important mechanism of gene transfer in nature?
Conjugation
