Lecture 25: Bacteriophages

bacteriophages are _____ that infect _____

viruses; bacteria

bacteriophages are the most abundant _____ on Earth

biological entity

biocteriophages affect most aspects of bacterial _____

life

what are the three main components that make up a bacteriophage particle?

head, tail, tail fibers

the bacteriophage head is where the phages _____ is stored

genome

the bacteriophage _____ is what injects the genome into the host cell

tail

the bacteriophage _____ are what recognizes the host surface

tail fibers

on individual bacteriophage particle is called a _____

virion

Bacteriophages are extremely _____

diverse

what are 6 ways that phage families can differ?

morphology, genome material, genome size, host range, gene content, lifestyle

True or False: ALL phages have a DNA based genome

FALSE: can have ssRNA!

the most COMMON phage genome type is _____

dsDNA

the genome size of phages can range from _____ to _____kb

3; 500

what are the two main “lifestyles of bacteriophages”?

lytic or temperate

list the steps of the lytic cycle in order?

adsorption, injection, replication, packaging, lysis

what is adsorption?

phage binding to surface of host

most known phages have _____ genomes, while most eukaryotic viruses have _____ genomes

DNA; RNA

why do phages lack lipid envelopes?

Bacteria have a cell wall → cannot fuse with the membrane as a method of entry, like eukaryotic viruses

phage genomes are usually _____ while eukaryotic viruses can be _____ (segmented vs. non segmented)

non segmented; segmented

it is important to note that because phages are incredibly divers, there are _____ to almost all the rules

exceptions

what are the 4 most common phage families?

myoviridae; siphoviridae; podoviridae; inoviridae

what family of phage does T4 belong to? Are these phages typically lytic or temperate

Myoviridae; lytic

Inovidiae are known as one of the only _____ phages

filamentous

what phage family has the LARGEST genome size?

myoviridae

which phage family does Lambda belong to? Are these phages typically lytic or temperate

siphoviridae; temperate

which phage family does T7 belong to? Are these phages typically lytic or temperate

podoviridae; lytic

bacteriophages occupy more or all of the _____ of bacteria

niches

what are the 3 main ways of detecting phages?

filtration and microscopy, lab isolation, DNA sequencing

filtration and microscopy stains the _____ of the phages which can be used to determine the _____ of viral particles

nucleic acids (genome); number

lab isolations are done from _____ that form on a lawn of bacterial cells

plaque

DNA sequencing, particularly _____, is used to sequencing all the _____ in a given sample

metagenomic; viral DNA

What are the ONLY bacteria type that are not subject to predation by phages?

cells living INSIDE other cells

True or False: Bacteriphages are NON-motile

TRUE!

how are phages able to move?

dispersal by water currents, animal carriage (feces), and aerosols

phages have no form of _____ because the particles are _____ until infection

locomotion; inert

the host range of a single phage is very _____

NARROW

many phages will only infect certain _____ within a bacterial _____

stains; species

some phages can infect more than one species, but it is very RARE to infect multiple _____

genera (ex. phage might be able to infect multiple types of pseudomonas species, but won’t be able to infect pseudomonas AND bacillus)

What determine the host compatibility of phages?

whether a phage can complete all aspects of its lifecycle

in the lysogenic pathway, phages will _____ their genome into the _____, rather than beginning _____ immediately upon infection

insert; host genome; replication

what is the integrated phage genome called?

prophage

what is the cell that is carrying a prophage called?

lysogen

if there is _____ or _____, the prophage will excise and begin the _____ pathway

stress; DNA damage; lytic

lysogen are _____ to infection of the _____ type of phage as their prophage

IMMUNE; SAME

_____ affects the lysis vs. lysogen decision

prey availability

if there is HIGH prey availability, the phage will likely undergo the _____ cycle'

lytic

if there is LOW prey availability, the page will likely undergo the _____ cycle

Lysogenic

why would low prey availability push the phage to do the lysogenic cycle?

no prey availability = no future cells for progeny to infect = dead end (better to wait around until more come)

Some phage are able to monitor the _____ signals to get info about the relative _____

host QS; prey availability (population density)

Alternatively, other phages will make their own _____ during _____, which implies prey _____

QS signal; lysogeny; unavailability

If the population around the lysogen are also lysogen, the prophage can sense their _____ molecule, which _____ them from starting the lytic pathway

own QS; prevents

Why would the prophage not want to do lysis when there are a lot of lysogen around?

the lysogen are immune! → will have no one to infect

a HIGH signal of prophage QS molecule indicates that there is _____ available prey

LOW

a HIGH signal of HOST QS molecule indicates that there is _____ available prey

HIGH

what are three other phage lifestyles that are kind of abnormal?

non-integrating prophages, pseudolysogeny, non-lytic replication

non-integrating prophages will still do _____, but their genome asks more like a _____ without integrating into the host genome

lysogeny; plasmid

Pseudolysogeny occurs when the phage infects a _____ cell; the prophage will then _____ the lytic cycle while it waits for proper _____, after which it will _____

starving; pause; nutrients; resume lysis

non-lytic replication cycles don’t _____ the cell when they leave and this is also known as the “_____”

lyse; carrier state

What is an example of a page family that does a non-lytic replication cycle?

inoviridae (filamentous)

phages predation promote _____ of _____ systems in their bacterial hosts

evolution; defense

the _____ of phage infection drives evolution of anti-phage defenses

lethality

once a host develops bacterial defenses, phages often evolve _____

phage counter-defenses

What is the most common bacterial defense against phages?

restriction enzymes

What is the restriction enzyme system called?

restriction-modification

RM systems use _____ that recognize specific phage _____

restriction endonuclease; DNA sequences

RM endonuclease do _____ DNA _____ after recognizing it in the phage DNA

site-specific; cleavage

what is the name of the bacterial RM endonuclease?

EcoRI

The sites that endonuclease recognize in phages are very similar to _____ sequences

host

how does the bacterial RM endonuclease not accidentally cut their own DNA?

methylation

the host _____ its own DNA so that it’s not digested, this is called _____

modifies; self-non self descrimination

_____ methylates the RM enzyme sequences on the _____ genome

DNA methylase; HOST

the Phage DNA is NOT _____

methylated

methylation is accomplished by _____ that methylate _____ or _____ in the RM recognition site, which prevents DNA cleavage

methyltransferases; adenine; cytosine

phage genomes can sometimes become _____, which renders them restriction-_____

methylated; resistant

The progeny of an accidentally methylated phage will be _____ when they infect other hosts

resistant

If a methylated phage progeny infects a cell without a methylase protein, it’s progeny will _____ methylation and regain _____

LOSE; susceptibility

Phages can _____ restriction enzyme recognition sites from the phage genome or use _____ that are _____ to cleavage in order to overcome RM systems

Eliminate; modified nucleotides; resistant

T4 phages genome contain _____ instead of C which is very resistant to cleavage by RM systems

hydroxymethyl-cytosine

Phages can also express a _____ that inhibits restriction endonuclease

protein

The proteins expressed by phages that inhibit RM systems have many _____ that mimic the structure of _____. This causes the RM endonuclease to bind and get _____

negatively charged AA; DNA; plugged up

_____ of T7 phages and _____ of T4 phages are both used to inhibit restriction endonucleases

Ocr; Arn

both Ocr and Arn proteins _____ in surface charge, and bind to _____, preventing DNA cleavage

mimic DNA; restriction enzymes

What is the other main bacterial defense against phage infection?

CRISPR-Cas system

what does CRISPR stand for?

clustered regularly interspaced short palindromic repeats

what does Cas stand for?

CRISPR-associated genes

CRISPR functions were first defined by researchers optimizing _____ production

large-scale yogurt

what yogurt company first discovered CRISPR?

Danisco

Yogurt production involves milk fermentation by _____

Streptococcus thermophilus

if there is a contamination of the yogurt by _____, the entire batch is useless

phages

When looking at the genomes between phage resistant and susceptible isolates of S. thermophiles, the only thing that changed was the _____

CRISPR locus

CRISPR is the only form of _____ immunity in prokaryotes

adaptive

CRISPR begins when a phage infects a bacteria and a section of the DNA, called a _____ in removed from the phage genome and _____ into the _____

spacer; inserted; host CRISPR locus

the process of adding a new spacer is called _____

immunization

The CRISPR locus (with the new spacer) is _____ and produced a _____ that associates with _____ proteins

expressed; guideRNA; Cas

what is the guide RNA called?

crRNA

guide (cr)RNA binds to _____ which are expressed by the _____ genes

Cas nucelases; Cas

The guide RNA is used to _____ the cell. Once it finds a phage genome that matches the _____, the _____ will _____ the genome

surveil; spacer; Cas nucleases; cut

What is the process of using crRNA to detect and destroy phage DNA called?

Targeting

Immunization is the generation of _____, and targeting is using memory to _____

memory; destroy the virus

Because CRISPR is an _____ immune system, it can respond to a _____ viral population

adaptive; changing