Bacteriophage basics Flashcards
How many genes are in the typical phages (dsDNA tailed)
50-250 genes
What must be required for a successful plaque assay?
Multiple rounds of phage infection and growth
Why do lytic phages generally form clear plaques?
They kill the bacteria
What does a phage have to be able to interact with in a host bacteria?
The host cellular machinery including the host transcription and translation systems
What happens to the phage genome in the lysogenic cycle?
It becomes stably maintained within the cell, even through many subsequent generations of cell division
How do bacteriophages replicate?
They require a bacterial host and take advantage of the host’s cellular machinery and redirecting it toward viral reproduction
What are some other less known structures of phages?
Single stranded DNA or RNA can can be enveloped with a lipid membrane, have one or than one chromosome, or have a variety of other configurations
Are bacteriophage particular to hosts? If so, how?
Yes, the host range can be a single bacteria strain or it can span multiple bacterial species or genera. However, there are few if any phages with a host range that spans different bacterial orders and the possibility of spanning different phyla is even less likely
When the bacterial host cell is lysed and the new virions are released. Part of the lytic cycle
Phase 6 - Cell lysis and phage release
How simple can it be for phages to alter their host ranges?
Sometimes a single base mutation in their genome is enough to alter their host range
How long does it take G. terrae to form a lawn in lab?
2-3 days
When prophage-encoded and expressed proteins alter the host cell surface in such a way that other phages are excluded from adsorption and DNA injection
Exclusion
When the phage chromosome circularizes inside the host cell. Part of the lytic cycle
Phase 2 - Phage DNA circularization
What is morphology?
The color, size, and shape. The characteristics that vary between species
What are virions?
Late-gene products that are the structural proteins that comprise the new phage particle. The new phages
What is a common mechanism used by prophages to ensure its stability?
Integrating into the host chromosome through a process known as homologous recombination
What is the estimated number of phage population?
10^31 particles
What are the main parts of a bacteria?
A flagellum, cell wall, cytoplasmic membrane, cytoplasm, capsule, pili, ribosomes, and bacterial DNA
What happens when a prophage is integrated in a lysogen (host cell)?
The prophage is replicated by the host DNA polymerases and passed to both daughter cells during normal cell division
What is it called when we provide bacteria a media to grow in without other bacteria?
culturing bacteria
What happens to the genes required for the lytic cycle in the lysogenic cycle?
They are repressed, rather than expressed
How many bacteria are generally in a colony?
generally 10^7-10^8 cells
What are the percentages of a phage entering the lytic and lysogenic cycles?
80-90 go to lytic and 10-20 go to lysogenic
What do G. terrae colonies look like?
orange, round, rough, and dry in texture
What are bacteriophages?
viruses that infect bacterial hosts and have properties shared by all viruses
What has recent evidence suggested is possibly the “normal” phage life cycle?
Lysogenic cycle
What is the structure of the majority of the phages?
Tailed viruses containing a double stranded DNA genomes (Caudovirales). The linear DNA is contained in a protein shell (head or capsid) which is attached to a tail
What are the best characterized systems for bacterial resistance to phages?
Restriction, abortive infection, and CRISPR
What are the two phage life cycles?
Lytic and lysogenic (temperate)
What are late-genes?
Following early gene expression, a new set of phage genes are expressed called late genes
What do rRNA do for bacteria?
construct models of their evolutionary relationships (phylogeny)
Who were the major contributors in discovering phages?
Frederick Twort and Felix D’Herrelle
How is the growth rate of bacteria measured?
Doubling time. It is a logarithmic function
What method did D’Herrelle develop that is still used today when discovering phages?
Plaque assay
At what phase of the phage cycle do cells enter the lytic or lysogenic cycle?
Phase 2 - Phage DNA circulariziation
When were phages first discovered?
1915-1917
What is the host bacteria used in lab?
Gordon terrae 3612
What is the most abundant “life form”?
Bacteriophage
What is the range of doubling time for bacteria?
15-20 minutes up to days/weeks
How does a lysogen resist infection?
constitutive expression of the immunity repressor protein from the prophage, its subsequent binding to the prophage DNA, and the repression of transcription of the lytic genes
All bacteria have differing what?
ribsomal RNA (rRNA) sequences
What are the 6 phases of the lytic cycle?
- ) Phage adsorption and DNA injection
- ) Phage DNA circularization
- ) Phage DNA replication
- ) Phage heads and tails production and more DNA replication
- ) DNA packaging and phage assembly
- ) Cell lysis and phage release
When a phage attaches and adsorbs to a host cell using its tail fibers and injects its linear chromosome into the bacterium. Part of the lytic cycle
Phase 1 - phage adsorption and DNA injection
Why do lysogenic phages generally form cloudy plaques?
They contain a mixture of dead bacteria and lysogens
What is G. terrae grown in in lab?
PYCa media at 30 degrees C
What is G. terrae?
a gram positive soil organism whose relatives are well equipped to break down hydrocarbons
What do all bacteria in a colony have in common?
They are all identical because they came from the same single cell
What is a key factor in determining if a phage can infect a bacterial host?
If the host includes a receptor in the cell wall a phage can recognize and adsorb to
What happens to some prophages that don’t integrate into the host genome?
It is established as a large extrachromosomal plasmid (DNA) that encode and express several partitioning proteins that ensure each daughter cell receives a copy of the prophage plasmid
What does CRISPR stand for
Clustered regularly-interspaced palindromic repeats
When the phage heads and tails are produced. Part of the lytic cycle
Phase 4 - Phage head and tail production/more DNA replication
What is a bacterial lawn?
When many bacterial cells are added to a media and cover the surface in one sheet rather than individual colonies
What is the cell that carries a prophage called?
Lysogen
How do we determine the host range of phages?
It must be determined experimentally because they change frequently
Can a lysogen carry multiple prophages?
Yes, they are integrated at different locations in the chromosome
Where did the bacteria come from in this lab?
An oil contaminated soil sample in China
How many cells are considered to be in a saturated culture?
2-4 x 10^9 cells/mL
What do all bacteria lack? And roughly how large are they?
They lack a nuclear membrane and other membrane-bound organelles. They are usually 1-5 microns across (a red blood cell is 8)
What types of plaques do lytic and lysogenic (temperate) phages form?
Lytic phages form clear plaques and lysogenic phages form cloudy plaques
What are lytic phages also know as?
Virulent phages
How do bacterial cells divide?
Binary fission
What is the range of genes phages can have?
A handful to more than 500
When the phage DNA is replicated. Part of the lytic cycle
Phase 3 - Phage DNA replication
When new virions are assembled. Part of the lytic cycle
Phase 5 - DNA packaging and phage assembly
How many genes are typically in a bacterial host?
Possibly 6000 or more
A single phage particle present within a lawn of bacteria (thin layer) growing in a Petri dish can propagate in the bacteria to form a clearing. It is created by the destruction of bacteria cells by phage
Plaque or plaque assay
What is the phage genome called within the cell?
Prophage
What is G. terrae often used for?
Bioremediation (breakdown of pollutants) and industrial biotechnology
The ability of a lysogen to resist infection from an invading phage by repressing the invaders lytic genes
Superinfection immunity
