Lecture 4/5 - Microbial Genetics Flashcards
What is an immunogen?
Any antigen that can elicit an immune response
What is an epitope?
Part of the antigen that binds to the antigen receptors
Where do mutation occur in surface Ag’s of a pathogen?
Within the nucleic acids – DNA/RNA
What is the results of the a mutation within the surface antigens of a pathogen?
Change in the structural proteins
– or –
Enzymes responsible for it’s assembly
What is the direct impact of genetic mutations in a pathogen?
Host immune response
Where is the H antigen found?
Flagella
Where is the O antigen found?
LPS
What are three methods to which antigenic mutations occur?
Drift + Shift + Switching
What are the two subtypes of antigenic switching?
Phase variation
– and –
Gene conversion
What can undergo antigenic shift?
Bacteria + Viruses
What can undergo antigenic shift?
Viruses
What can undergo antigenic switching?
Bacteria + Protozoa + Fungi
What is the process of antigenic drift?
Overtime population accumulates point mutations.
Leads to proteins products being altered causing distinct new strains of the bacteria
Where does antigenic drift tend to occur on a flu virus?
H antigen
What are the two components of the flu virus envelope spikes?
Hemaglutttinin
– and –
Neuraminidase
What is hemagluttinin?
Glycoprotein spike which attaches to the host receptors
What is neuraminidase?
Enzyme on the glycoprotein spike that releases from virus from the host cell
What is the structure of the flu viruses genome?
8 segments of ssRNA
What is the example of antigenic shift seen in the flu virus, that is given in lecture?
Two different strains (ie. human + birds), populate the same cell and undergo reassortment. this creates a whole new subtype of flu virus.
What is so dangerous about antigenic shift in the flu virus?
Can easily cause a pandemic because no species has been exposed to it. therefore no one has built immunity, leading to quicker spread of the virus.
Which genomic mutation is responsible for why we need yearly flu vaccines?
Antigenic drift
What genomic mutation is responsible for why there are flu pandemics in the world?
Antigenic shift
What are two important things that a successful pathogen must do?
Multiply in host
– and –
Evade the immune system
What is the mechanism of phase variation, a type of antigenic switching?
The gene is always apart of the cell genes but not always apart of the phenotype, but it is turned on and off depending on the current environment
What does phase variation lead to?
Phenotypic variation and therefore surface antigen variation. Go from having no flagella to having one
How is phase variation regulated?
Inversion of DNA sequence via recombinase
What are the two important components of a bacterial gene?
Promoter + Coding sequence
What is another name for gene conversion, a method of antigenic switching?
Gene shuffling
What is the mechanism of gene conversion?
Recombination within a specific group of genes. The phenotype is always there but the bacteria can switch through types, like changing a shirt. Biological function remains the same
What pathogen causes relapsing fever?
Borrelia recurrenntis
Why does relapsing fever occur?
Gene conversion; switches through serotypes causing the immune system to stop being able to recognize it.
What is responsible for malaria?
Plasmodium falciparum
What method is used by malaria to evade the immune system?
Variable surface glycoproteins aka VSG; does this by avoiding splenic destruction by attaching to endothelium
What are mobile genetic elements?
Segments of DNA that encode for enzymes/proteins that mediate movement of DNA within the genome or between cells
What are the two groups of MGE?
Replicons
– and –
No replicons
What is the basic method of the replicon?
Replicate DNA/RNA independently of host cell chromosome
What is the basic method of cells that are not replicons?
Replicate DNA/RNA as part of cell chromosome or plasmid DNA
What is different about a bacteriophage compared to a plasmid genetically?
RNA + DNA (plasmids are DNA only)
What do plasmids tend to carry?
Non-essential genetic information
What do plasmids allow for in a bacteria?
Selective advantage, especially when an AB is present
What are R plasmids?
Resistance plasmids, carry 1+ genes for AB resistance
What is special about R plasmids?
They are not genera specific and can be shared amongst any bacteria for the most part
What are bacteriophages?
Bacteria viruses
What do bacteriophages do?
Inject DNA into bacteria and use the host machinery to copy it’s DNA. Then use the lytic or lysogenic cycle to break out of the bacteria
Can bacteriophages move amongst genera?
No, they are genera specific.
What are the three mechanisms that bacteria user to exchange DNA among bacteria?
Transformation - Conjugation - Transduction
In general, what is transformation in regards to genetic exchange?
Incorporation of exogenous (aka naked DNA) into cytoplasm (via plasmid) or chromosome
In general, what is conjugation?
Mating leading to exchange of genetic information from one bacterium to another
In general, what is transduction?
Transfer of bacterial DNA from one bacterium to another via bacteriophage
How is naked DNA, from transformation, incoporated into the genome of the receiving bacteria?
Homologous recombination + Nonhomologous recombination
When does invitro competence normally develop in bacteria?
During the log phase of cell culture
What does naturally competent mean?
Process of natural transformation, meaning the cells have the ability to undergo this process. Which is not common
When does recombination of DNA occur in a bacteria?
When cell takes up new DNA and it does not have a bacterial origin
What happens if the DNA is rejected in transformation?
Restriction enzymes cut it up
What does homologous recombination require?
Sequence similarity between donor and recipient
What does homologous recombination use to be successful?
Recombination gene products (aka Rec proteins)
What are the two mechanisms by which nonhomologous recombination can occur?
Random or Site Directed
What occurs with random nonhomologous recombination?
Gene is randomly inserted, recombined with host DNA. Can lead to distruption of the genetic makeup of that bacteria. Especially if it is placed within a promoter or coding sequence of a gene
What is it call when there is a failed attempt at non-homologous recombination with random insertion?
Null mutaiton
How is the site-directed nonhomologous recombination done?
Has a specific sequence - “CATGCAC”
No REC proteins are needed
What is the end result of nonhomologous recombination?
Addition NOT replacement of chromosomal DNA
What is the most common method of genetic exchange?
Conjugation
What is the pro of conjugation?
Can occur between bacteria of the same species or different ones; depends on the plasma type involved
What occurs with conjugation?
One way transfer between donor and recipient bacteria
What directs Conjugation?
Genes on the plasmid DNA
What type of plasmid carry information for plasmid mobilization?
Conjugative plasmids
What can also be carried on conjugative plasmids?
Bacteriocins + AB resistance
What genes are important for the conjugative process?
Transfer of plasmid (making the recipient a donor)
Ability to make sex pilus
Initiate plasmid DNA synthesis
What system is needed to carry out the DNA transfer in conjugation?
T4SS - Type IV secretory system
What bacteria has T4SS been ID’ed in?
Gram-negative, but similar system found in Gram-positive.
What designates whether a bacteria is the donor or the recipient?
F+ = donor = male F- = recipient = female
What is a conjugant cell?
When F+ and F- are attached
What determines what mating type a cell is?
Presence of F plasmid
What is the result of plasmid transfer?
Plasmid moved as linear ssDNA
– and –
Rolling circle replication
What is rolling circle replication?
Produces dsDNA plasmid in recipient AND DONOR cell
Where does mobilization being in rolling circle replication of a plasmid?
Plasmid-encoded protein causing single-stranded, site-specific cleavage at oriT
What initiates rolling circle replication?
Nick
What is responsible for directing the linear strand of plasmid?
T4SS - In Gram-negative bacteria
What is the steps in rolling circle replication?
Transfer of ssDNA + Recircularize/Replication = dsDNA
What is an antigen?
Any molecule that can be bound by antibody, T cell receptor, or MHC
How does gram-positive conjugation occur?
Adhesion molecules on surface of the donor cells
NO SEX pilus
What occurs with high frequency recombination?
Before conjugation begins - F plasmid intergrats into IS/Tn within host chromosome
How does the F plasmid during Hfr intergrate itself within the host chormosome?
Via nonhomologous recombination
What is the definition of a Hfr cell?
Host cell with integrated F plasmid
What is an episome?
A replicon that can exist either seperate from the host cell chromosome or as part of the chromosome
What does Tn stand for?
Transposon
What is IS stand for?
Insertion sequence
What is an integrated plasmid?
Plasmid that has been integrated into the host cell chromosome
What is the order of chromosome transfer when a Hfr cell is involved?
First 1/2 of the F plasmid + Chromosome + Second 1/2 of F plasmid
Why is there a chance that conjugation with a Hfr cell might be incomplete?
Cellular connection is fragile and the DNA is long, may break before finished.
What is the highest probable ending to conjugation involving a Hfr cell?
Transfer of the first 1/2 of the F plasmid and a portion of the adhacent chromosome. Meaning the F- cell does not become an Hfr cell
What occurs with full transfer of the Hfr genome?
Conversion of the F- cell to the Hfr cell
What mediates the process of transduction?
Bacterial viruses aka bacteriophages
What is the basic process of genetic transfer in regards to transduction?
Phage picks up fragments of bDNA and packages them into virions (phage particles). bDNA is then delivered to infected cell
What happens to the bDNA once a bacteriophage introduces it to the infected cell?
Incorporated into bacterial genome via homologous recombination
What are the three structural components of a bacteriophage?
Capsid + Tail + Nucleic acid core
What are the two mechanisms for escape from the host cell that virulent phages use?
Lytic or/and Lysogenic
What are the basic steps that occur in the lytic cycle?
Attaches/Absorption Injection/Penetration Replication Assembly Lysis (once enough are made)
What is the key to generalized transduction?
The Lytic Cycle
What is still present during the phage assembly of the lytic cycle?
bDNA
What happens when a viral capsid is packed with bDNA?
becomes a Defective phage and can only attach to a new host cell and inject bDNA, where recombination with host chromosome is carried out
Why does a viral capsid sometimes get bDNA?
Doesn’t know the difference between bDNA or vDNA
What is important about the lytic cycle, in regards to what it involves?
Virulent phages, but if accidentally pick up bacteria this changes
What is lysogeny?
Integration of vDNA into bDNA/chromosome
How is lysogeny carried out?
via nonhomologous recombination
What is formed because of lysogeny?
Latent prophage
What is the result of lysogenic conversion?
Bacterial cell becomes lysogen
What becomes of a latent prophage?
Replication of this viral DNA with the bacterial host DNA so all the daughter cells carry it
What can happen to the latent prophage?
If stress occurs (ie. UV light, temp, nutrients etc.) lytic cycle can be activated. If the prophage has a virulent gene this will then make the bacteria a pathogen.
What were three examples of pathogenic lysogens in the lecture?
Hemorrhagic diarrhea
Botulism
Diphtheria
What is specialized transduction?
Very rare but during stress-induced lytic cycle prophage is incorrectly excised from bDNA and now has segments of bDNA + vDNA.
What is a defective phage?
Machinery packs capsids with vDNA + bDNA
Lytic cycle releases these and they are spread via nonhomologous recombination
What are not replicons?
IS + Tn + PAI
What does PAI stand for?
Pathogenicity Island
What is the simplest form of MGE?
Insertion sequence
What does an IS contain?
Inverted repeats on ends
Transposase gene for integration into replicon w/ no additional coding
How is an IS inserted?
Via nonhomologous method into a specific sequence - creates direct repeats upon insertion
Where does a Tn transfer?
transfers DNA within a cell from one position to another
chromosome to plasmid
plasmid to plasmid
What is the structure of a Tn?
2 insertion sequences + central region
What is contained on the central region of a Tn?
AB resistance + toxin genes
What can be the results of the nonhomologous recombination with a Tn?
Can insert into an inactive gene on chromosome or plasmid and aid bacteria in being more virulent or resistant
or can insert into a essential protein and cause cell death
What is a PAI?
unusual clusters of genes, that insert tRNA or tRNA-like genes into bacterial chormosome
What do PAI encode for?
Virulence factors such as toxins + AB resistance
How is a PAI inserted into the genome?
Nonhomologous recombination
Why are PAI’s unstable?
Different %G+C that parent DNA - implies foreign source to DNA
Overtime breaks down, lost from genome
Not seen in nonpathogenic forms of species
What is clinically important to remember about PAI’s?
Can cause different pathogens even if the bacteria are from the same species
What is structure is adding to the spread of AB resistance?
Integron
What is an integron?
Genetic element that allows for efficient capture and expression of exogenous genes
