L10 - Predators of Bacteria 2 Flashcards
What type of phage is T7, and what is its genome structure?
T7 is a lytic phage with a linear dsDNA genome (not circular). The genome consists of genes that are activated at different stages of infection.
How are T7 phage genes organized and what are their functions?
T7 phage genes are numbered based on when they are switched on:
Early genes: Involved in entering the host cytoplasm and controlling host machinery.
Mid genes: Responsible for DNA replication.
Late genes: Involved in virus structure and assembly.
How does T7 phage infect E. coli and what is the process of genome injection?
T7 phage recognizes the LPS receptor on E. coli using its tail fibers. The tail retracts, and the genome enters the bacterial cell through a syringe mechanism. The entire genome is injected over 6-12 minutes.
What happens when gene 0.3 of T7 phage is expressed?
Gene 0.3 produces an anti-restriction enzyme that prevents the host’s nucleases and restriction enzymes from degrading the phage genome, using the host RNA polymerase.
What is the role of gene 0.7 in the T7 phage infection process?
Gene 0.7 produces a protein kinase that phosphorylates E. coli RNA polymerase, shutting down the host’s machinery and allowing the phage to take control.
How does the T7 phage begin to rapidly transcribe its genome?
Gene 1 of T7 phage encodes its own RNA polymerase, which is faster than the host’s RNA polymerase, allowing the phage to transcribe its genome and express its genes at an accelerated rate.
What happens when mid gene 5 is transcribed during T7 infection?
When gene 5 is transcribed, E. coli’s machinery is completely shut down, and the cell transforms into a phage factory, solely producing phage components.
How does replication begin in T7 phage, and what is the role of gene product 4?
Replication begins at two sites, stabilized by gene product 4 (GP4), which has helicase activity. GP4 also makes short primers through its primase activity, enabling DNA synthesis on the lagging strand.
What is the role of GP2.5 in T7 phage replication?
GP2.5, a single-stranded binding protein (yellow), wraps around GP4 and coordinates the replication process, stabilizing the single-stranded DNA.
How does the T7 phage genome form concatamers during replication?
Double-stranded DNA is synthesized with terminal redundancy (TR regions), forming sticky ends (ssDNA) that hybridize to create concatamers, long DNA molecules that can be cut into individual genomes.
What is morphogenesis in T7 phage, and how is it related to concatamers?
Morphogenesis occurs when the concatamers are cleaved into fragments, and each fragment is packaged into a phage head, ensuring each new virion contains one complete genome.
What is the structure and genome of M13 phage, and how does it infect E. coli?
M13 is a filamentous phage with a circular ssDNA genome. It infects E. coli by binding to the F pilus, inserting its genome into the host cytoplasm.
Why is the infecting strand of M13 phage not directly used for DNA replication?
The infecting strand is a positive DNA molecule and cannot serve as a template for replication, so it must first be converted into double-stranded DNA (dsDNA) using host machinery.
What roles do proteins P2, P5, and P10 play in the replication and assembly of M13 phage?
P2 is responsible for rolling-circle replication and cyclization of the genome.
P5 accumulates in the cytoplasm and turns off viral protein translation once a critical threshold is reached to avoid detection by the host.
P10 counteracts P2’s nicking activity, regulating the process.
How does M13 phage synthesis control the production of viral particles?
After enough DNA is synthesized, P5 turns off protein production to avoid detection, while P10 accumulates to balance the process. Coat proteins are synthesized at the correct time, and viral particles are secreted through the cell membrane.
How is M13 phage used in laboratory applications?
M13 can be engineered to carry genes of interest by inserting them into the phage genome. The phage particles produced will carry these genes, making M13 a useful tool for genetic research.
What is the structure and infection process of lambda phage?
Lambda phage is a dsDNA head-and-tail phage with a linear genome that has sticky ends. During infection, the genome can circularize into a dsDNA molecule, resembling a plasmid.
How does lambda phage behave in lytic vs. lysogenic cycles?
In the lytic cycle, the genome remains circular, and phage replication occurs. In the lysogenic cycle, the genome integrates into the host chromosome and remains dormant.
What is the regulatory center of lambda phage, and what happens there?
The regulatory center, also known as the immunity region, is where replication and transcription begin, controlling the phage’s behavior as a viral particle.
How does lambda phage integrate into the E. coli chromosome during lysogeny?
The lambda phage genome integrates into the host chromosome through homologous recombination at identical O regions (POP primer site for the phage and BOB primer site for the host), facilitated by the integrase enzyme.
What happens during the excision of lambda phage from the host chromosome?
Excision requires integrase and Xis enzymes, resulting in the creation of two new att sites: att left and att right, which facilitate the release of the phage genome.
How are transcription and regulation of lambda phage controlled?
Transcription begins at the Pl (early left operon) and Pr (early right operon), producing N protein, which leads to long transcripts. The balance of proteins C1 and Cro determines whether the phage enters the lytic or lysogenic cycle.
What roles do C1 and Cro play in regulating lambda phage’s lytic and lysogenic cycles?
C1 promotes lysogeny by turning on transcription of maintenance proteins (e.g., C2), while Cro promotes the lytic cycle by inhibiting C1 and turning off maintenance proteins, leading to phage replication and cell lysis.
What is the classical bistable genetic switch in lambda phage?
The classical bistable genetic switch is the interaction between C1 and Cro proteins. The concentration of each protein determines whether the phage enters the lytic cycle (Cro dominance) or lysogenic cycle (C1 dominance).
How do C2 and C3 proteins influence the lysogenic cycle?
C2 and C3 proteins suppress late gene transcription (involved in the lytic cycle) by binding to promoters Pre and Paq, ensuring the phage remains integrated into the host chromosome and preventing lytic replication.
How does lambda phage exit the host and enter the lytic cycle?
When the host experiences stress (e.g., DNA damage triggering the SOS response), C2 and C3 are degraded by host proteases, disrupting repression of late genes. This leads to excision, allowing the phage to enter the lytic cycle.
How does the presence of Cro influence the lambda phage cycle?
Cro binds to operators near the promoter for maintenance (PRM), turning off C1 production and favoring the lytic cycle. High Cro levels promote late gene transcription, leading to the assembly of viral particles and cell lysis.
What happens during the lysogenic cycle of lambda phage?
During lysogeny, the phage genome integrates into the host chromosome, maintained by proteins like C1, C2, and C3. The phage remains dormant until external stress or signals trigger excision and the shift to the lytic cycle.
How can phages be controlled?
- extracellular modulators: nucleases, proteases, ion chelating molecules, receptor availability
- intracelllar modulators: restriction enzymes, immunity systems (crispr), super-infection immunity
What are some other predators of bacteria
- bdellovibrio bacteriovorus and BALOS
- vampirococcus
- daptobacter
What are bdellovibrio bacteriovorus and BALOs? how does it predate bacteria?
gram negative and it preys on other gram negative bacteria.
- fagella helps it ot find its host = chemotaxis
- binds to host
- penetrates into cell (periplasm), loses its motility and estabilishes its niche to extract nutrient from host
- giant cell separated individual cells and then leaves
What is vampirococcus and how does it prey on bacteria
it is gram negative and it preys on chromatium spp. freshwater sulphur bacteria. - finds host by chemotaxis
- they dont invade bacterial cells but uses type 4 secretion system to release toxins into the cell
- sucks out all the nutrients and makes more copies of themselves outside the host
What is daptobacter and how does it prey on bacteria
it is gram negative and preys on chromatium spp. freshwater sulphur bacteria. it goes into cytoplasm and uses all nutrients to divide by binary fission
