Phage phenotype refers to the morphology, biochemistry and behaviour of viruses that infects and replicates within bacteria and archaea.

1. DR. VIBHA KHANNA
ASSO. PROF. (BOTANY)
S.P.C. GOVERNMENT COLLEGE
AJMER (RAJASTHAN)

2. CYTOGENETICS
• BLOCK 3: PHAGE BIOLOGY
• PRESENTATION 2:
PHAGE PHENOTYPES
Bacteriophage, also known as a phage, is a virus that
infects and replicates within bacteria and archaea.
Phenotype is all the characteristics displayed by an
organism which includes morphology, biochemistry,
behaviour etc.

3. Phages: An Introduction
• Bacteriophages (or phages for short) are viruses that infect bacteria.
• Like any virus, they are obligatory parasites, requiring the host
cellular machinery to reproduce.
• Thousands of varieties of phages exist, each of which may infect
only one type or a few types of bacteria or archaea.
• Like all viruses, phages are simple organisms that consist of a core
of genetic material (nucleic acid) surrounded by a protein capsid.
• The nucleic acid may be either DNA or RNA and may be double-
stranded or single-stranded.
• The shape of viruses is closely related to their genome, and a large
genome indicates a large capsid and therefore a more complex
organisation.
• There are three basic structural forms of phage:
– an icosahedral (20-sided) head with a tail,
– an icosahedral head without a tail, and
– a filamentous form.

4. Phages: An Introduction
• Phages are found in a variety of morphologies:
– filamentous phages,
– phages with a lipid-containing envelope and
– phages with lipids in the particle shell
• They have a genome, either DNA or RNA, which can be
single or double stranded, and contain information on
– the proteins that constitute the particles,
– additional proteins that are responsible for switching cell
molecular metabolism in favour of viruses and,
– the information on the self-assembly process.
• The genome can be one or multipartite and is located
inside the phage capsid.

5. Phages: An Introduction
• Infection begins by attachment of the phage particle to its
host cell through specific recognition of a receptor on the
host surface, followed by delivery of the phage nucleic
acids into the infected cell.
• Once inside the bacterium, the phage takes over the
bacterial cell, hijacks its cellular components and shuts
down its defense mechanisms.
• Phage genes are expressed, and the phage genome is
replicated and eventually packed into self-assembled phage
particles.
• At the end of the lytic infection cycle, progeny phage
particles emerge from the cell in a process that usually
involves cell lysis by phage proteins.

6. Types of Phages: On The Basis Of
Construction

7. Types of Phages: On The Basis of Life-cycle
Phages are categorized into two types.
• Virulent phages cannot become prophages; they are
always lytic.
• Temperate phages can integrate into the
bacterial chromosomes as prophages, allowing the host
cells to survive in the lysogenic state.
A lysogenic bacteria, or lysogen, is resistant to subsequent
infection, because an “immunity” is conferred by the
presence of the prophage.
Prophages occasionally exit the bacterial chromosome and
enter the lytic cycle.
(The word lysogenic means “lysis causing” as the property
of self-immunity, but ability to lyse other genotypes was
the way that this condition was first identified.)

8. Studying Phages
Phages are so small that they are visible only under the electron
microscope.
The phage phenotypes are studied on the basis of the visible manifestation
of infected bacteria by taking advantage of several phage characters.
• Plaque morphology is a phage character that can be analyzed: When a
phage infects a single bacterial cell, a sequence of events in the infectious
cycle, leads to the release of progeny phages from the lysed cell. After lysis,
the progeny phages infect neighboring bacteria, and these bacteria, too, lyse
and reinfect. This reinfection results in an exponential increase in the
number of lysed cells.
Within hours, after the start of an experiment of this type, the effects are
visible to the naked eye as a clear area, or ‘plaque’, on the opaque “lawn” of
bacteria growing on the surface of a plate of solid medium. Such plaques can
be large or small, fuzzy or sharp, and so forth, depending on the phage type.
• Host range is another phage character that we can analyze
genetically, because phages may differ in the types of bacterial strains that
they can infect and lyse. For example, certain strains of bacteria are immune
to attachment or injection by specific phages.

9. Classification
• Virus classification is based on characteristics such as
– morphology,
– type of nucleic acid,
– replication mode,
– host organism and
– type of disease.
• The International Committee on Taxonomy of Viruses
(ICTV) has produced an ordered system for classifying
viruses (https://talk.ictvonline.org/taxonomy/).
• Phages are classified in a number of virus families;
some examples include Inoviridae, Microviridae,
Rudiviridae, and Tectiviridae.

10. The Tailed Phages
• The most studied group
of phages is the tailed
phages
(order Caudovirales)
which are classified by
the type of tail;
– Siphoviridae have a long
non-contractile tail,
– Podoviridae have a short
non-contractile tail and
– Myoviridae have a
complex contractile tail

11. Structural Organization of Phages
• Phages may have different shapes and sizes. The
most studied group is that of tailed phages with a
dsDNA genome, and it also represents the largest
group.
• The tailed phages have three major components:
– a capsid where the genome is packed,
– a tail that serves as a pipe during infection to secure
transfer of genome into host cell and
– a special adhesive system (adsorption apparatus) at
the very end of the tail that will recognise the host cell
and penetrate its wall.

12. Protein Components of the Phage-capsid
• The functional phage is a result of a multistep process that starts with all
the necessary proteins produced by the host cell after infection.
• The proteins include : capsid, portal, tail, scaffolding, terminase, etc.
• The capsids of the dsDNA phages often have fivefold or icosahedral
symmetries, which are broken at one of the fivefold axes by the head-to-
tail interface (HTI), which is a multi-protein complex (connector).
• The main component of the HTI is a dodecameric ‘portal protein’ (PP)
within the capsid. The PP represents the DNA-packaging part of the
capsid.
• The HTI also includes oligomeric rings of head completion proteins that
play dual roles: (1) making an additional interface to molecules of ATP
which provide energy for DNA packaging and (2) then connecting the
portal protein and the tail.
• Some HTIs also serve as valves that close the exit channel preventing
leakage of genome from the capsid but opening as soon as the phage is
attached to the host cell.

13. Protein Components of the Phage-tail
• The phage tail is the structural component of the phage
that is essential during infection.
• Its ‘adsorption apparatus’ located on the distal end of the
tail recognizes a receptor, or the envelope chemistry, of the
host cell and ensures genome delivery to the cell
cytoplasm.
• In Myoviridae and Siphoviridae, the tail is composed of a
series of stacked rings with the host recognition device
being located at the end of the tail.
• In Podoviridae the adsorption apparatus is bound
immediately to the HTI. The adsorption apparatus is
surrounded in many phages by fibrils that ensure a tight
connection to the host cell.

14. Structural Organization of Phages
Capsid: (Procapsid + genetic material )
Connectors {head-to-tail interface (HTI)} : a portal protein
complex (PP) + head completion proteins
Tail: tail proteins (TPs) + tape measure protein (TMP) + tail
terminator protein (TrP)
Adsorption apparatus: base plate; tail fibrils
Envelope: lipid membranes (with receptor binding and fusogen
proteins) {*Present in only 3 families of phages}

15. Self-assembly Pathway of Phages
• Multiple copies of the capsid/scaffold complex bind the
portal protein to form the procapsid;
• then, the scaffold proteins are ejected, and DNA is
packaged into the procapsid, which expands to the size of
the mature capsid.
• The head completion proteins (the stopper and the
adaptor) are bound to the portal complex preventing DNA
leakage.
• Next, decoration proteins bind to the capsid, and
• the tail, assembled separately or after DNA packaging, is
attached; thus, the final infectious phage is produced.
• The preassembled tail attaches in Myoviridae and
Siphoviridae, while in Podoviridae the tail assembles at the
stopper.

16. Self-assembly Pathway of Phages

17. Phage Life Cycles.
• The lytic life cycle is where phages infect and rapidly kill their infected host
cells. This assists in shaping bacterial population dynamics and may also
assist in their long term evolution via generalized transduction.
• The lysogenic life cycle in contrast, is where phages instead of directly
killing their hosts, integrate into their host genome, or exist as plasmids
within their host cell. This lysogenic life cycle can be stable for thousands
of generations and the bacteriophage may alter the phenotype of the
bacterium by expressing genes that are not expressed in the usual course
of infection in a process known as lysogenic conversion.
• In pseudolysogeny a bacteriophage enters a cell but neither co-opts cell-
replication machinery nor integrates stably into the host genome.
Pseudolysogeny occurs when a host cell encounters unfavourable growth
conditions and appears to play an important role in phage survival by
enabling the preservation of the phage genome until host growth
conditions have become advantageous again.
• In chronic infection new phage particles are produced continuously over
long periods of time but without apparent cell killing.

18. Phage Life Cycles.

19. Host–phage Interactions
• Lytic infection. Lytic or virulent phage redirect the host
metabolism toward the production of new phage which are
released as the host cell lyses.
• Lysogenic infection. Phage nucleic acid material of the
temperate or lysogenic phage remains dormant within the
host as prophage. Prophage are replicated along with the
host until the lytic cycle is induced.
• Chronic infection. Infected host cells constantly release
phage progeny by budding or extrusion without lysing the
host cell.
• Pseudolysogenic infection. Phage multiply in only a
fraction of the infected host cells. Also known as the phage-
carrier state.

20. Bacteriophages: An Overview
• Bacteriophages are viruses that infect bacteria.
• The term was derived from "bacteria" and phagein (Greek), meaning "to
devour"
• They are a major agent of horizontal gene transfer between bacteria.
• The phage particle consists of the phage genome packaged in a capsid. The
capsid is a container made up of phage proteins.
• Phages have several different types of infectious cycles, two of which are the
lytic and the lysogenic life cycles.
– During a lytic infection, a phage infects a bacterium and takes over its
machinery to replicate itself and produce new phage particles. In the
course of replication and release of the new phage particles, the host
bacterium is lysed, and thus killed. Phages that can only carry out this
type of infection are called lytic or virulent phages.
– Phages can also carry out a lysogenic infection in which the phage
inserts its genome into the bacterial genome. Once inserted, the phage
genome then remains in the bacterial genome until it receives an
environmental signal, causing it to excise itself from the bacterial
genome, replicate, and produce viral particles. Phages that set up a
lysogenic infection are referred to as lysogenic or temperate phages.

21. Bacteriophages: An Overview
• Transduction, is a classical method of ‘horizontal gene
transfer’. The process, can occur as a result of a lytic or
lysogenic infection.
• During either type of life cycle, phages may acquire genes not
originally part of their genome, i.e., non-phage genes.
– During the lytic life cycle, a piece of bacterial DNA may be packaged into
the phage particle in place of the phage genome. The resulting particle is
no longer capable of replicating itself, but is capable of infecting a new
bacterium. When the phage particle infects a new bacterium, the
packaged DNA from the original host bacterium is introduced into the
new bacterium. Sometimes that DNA integrates into the new
bacterium’s genome.
– Transduction can also occur as part of a lysogenic life cycle. When a
lysogenic phage genome integrated into a bacterial genome starts
replication again, the bacterial DNA that is adjacent to the phage
genome may also be excised. Such bacterial DNA becomes part of the
phage genome and is packaged into the phage particle. When the phage
infects a new bacterium, it introduces the original host bacterium’s DNA
into the new bacterium.