Viruses: Lytic and Lysogenic Pathways

Objectives

By the end of this lesson you should be able to:

1. Define the term virus
2. Identify main factors contributing to the spread of viral diseases 
3. Identify type of viruses by shape
4. Define the term bacteriophage
5. Differentiate between the lytic and lysogenic cycles of viruses
6. Explain in detail, the molecular mechanisms involving lambda virus’s “decision” to take a lytic or lysogenic pathway

 A virus is an infectious particle. You probably already know that they are responsible for many diseases include some of the worst pandemics in history. They damage or kill cells by causing the release of hydrolytic enzymes from lysosomes or causing cells to produce toxins that lead to disease symptoms. How much damage a virus cause depends on how quickly the infected tissue can be regenerated by cell division. For example, people infected by the flu virus usually recover quickly because the lining of the respiratory tract can repair itself fast. In contrast, infection with the polio virus leads to permanent damage due to the slow progress of nerve cell repair. The symptoms associated with viral infection such as fevers and aches are due to the immune system’s inflammation response rather than due to cell death caused by virus.

Three processes contribute to the proliferation of viral diseases:

1. High rate of RNA mutation due to lack of mechanism to correct errors
2. Technological and social factors e.g., affordable travel, blood transfusions, sexual promiscuity, use of intravenous drugs, and commercial intrusion into previously remote forested areas
3. Spread of new viral disease from animals e.g. the H5N1 avian flu (Note: H5N1 identifies which form of viral surface proteins are present: hemagglutinin (H), and neuraminidase (N).

Structure of Viruses

Viruses are very simple, consisting mainly of a genetic material and a protein coat. Viruses are considered to be nonliving since they do not reproduce or carry out metabolic activities on their own. Instead, they rely totally on their hosts. Hence, they are obligate intracellular parasites. They infect their hosts within a narrow host range.

The smallest virus is smaller than a ribosome (less than 20 nm in diameter). There genome generally consists of a linear or circular molecule of nucleic acid which may be a single or double-stranded DNA or RNA. The number of genes in their genome ranges from 4 to about a thousand.  

The protein shell enclosing the genome of virus is called a capsid. These may take on different shapes depending on the type of virus.

Capsids are made up of protein subunits called capsomeres.

How Viruses Infect Cells 

A viral infection begins when a virus binds to a host cell via a receptor on the surface of the host. Depending on the type of virus, it either injects its genome inside the host or is taken in by the host via endocytosis. Once inside, it commands the genome of the host to make replicates of the virus. The host provides all the resources (ATP, ribosomes, tRNA, amino acids, etc.) needed to make components of the virus. After all the necessary components are made, they spontaneously assemble into new viruses. This process generally damages or destroys the host cell as the new viruses emerge to infect new cells.

Viruses that infect bacteria are called bacteriophages. We will now look at the interesting and complex operation of one of the most well-studied bacteriophages – lambda (λ).

Replicative Cycles of Lambda Phage

Lambda phage can replicate by two alternative mechanisms: (1) lytic, and the (2) lysogenic cycle. The lytic cycle involves replication of the virus, leading to host cell rupture and death. The lysogenic cycle is one in which the virus incorporates itself into the genome of the bacteria and remains there without immediately killing the bacteria. However, whenever the bacteria replicates, the viral genome is also replicated and passed on to the next generation of the bacteria. Phages that use only the lytic cycle are called virulent phages while the ones that use both, like the lambda phage, are called temperate phages.   

What determines which of these pathways are taken, is the amount of resources in the environment. If resources are abundant, the lytic cycle is preferred. This is because it will have access to enough nutrients to make copies of the virus. If resources are limited, the lysogenic pathway is taken. In this pathway, the virus remains as a prophage (integrated into the bacterial genome) until conditions improve – or get much worse.

The alternate states are controlled by a complex genetic switch consisting of DNA-binding regulatory proteins and a set of operator sites. The decision to go lysogenic or lytic rests heavily on four gene, i.e., cI, cII, cIII, and Cro. The cI gene encodes a repressor protein called the λ repressor that represses the lytic cycle and promotes the lysogenic cycle. The Cro gene encodes a repressor that represses the lysogenic cycle and hence promote the lytic cycle. When cI is on and Cro is off, the virus is in the lysogenic cycle. When cI is off and Cro is on, the cell is in the lytic cycle.

Therefore, λ repressor (pcI) and pCro are in competition. Which one prevails, determine the state of the switch. On infection of a cell such as E. coli, RNA polymerase initiates transcription at both the P_R and P_L promotors of lambda bacteriophage. From P_R, Cro is the first gene transcribed, and from P_L, N is the first gene transcribed.

As RNA polymerase transcribes from N to cIII, it encounters a secondary RNA structure that causes it to pause. The pause allows enough time to permit a rho protein to overtake the RNA polymerase and terminate transcription. Thus, the expression of downstream genes are prevented until they are needed. Consider for example, how ineffective it would be if genes responsible for expressing proteins that break open the cell where made before viral parts were properly assembled.

What happens however, when you do want those downstream genes to be expressed? For that to happen, pN serves is an anti-terminator that works by enabling RNA polymerase to continue transcribing through the secondary RNA structure. Thus, pN allow transcription of cIII and other genes to the left of N as well as cII and other genes to the right of Cro.

The cII gene encodes for a protein that binds P_RE, a site that promotes transcription leftward to activate the cI gene. Remember that cI encodes the λ repressor (pcI) which prevents the lytic cycle.

The cII protein (pcII) is unstable since it can be degraded by bacterial proteases. These proteases respond to environmental conditions. They are active when resources are abundant and less active when resources are scarce.

When resources are abundant, bacteria proteases degrade pcII leading to a fall in production of λ repressor. With less λ repressor to block the lytic cycle, the lytic cycle prevails. Furthermore, when the Cro protein (pCro) occupies OR₃ (not shown in diagram) it blocks P_RM and thus prevent transcription of cI and λ repressor. This causes the lytic cycle to continue.

When resources are scarce, there is less degradation of pcII. Since cII is more active, more λ repressor is produced. The λ repressor binds to OR₁, blocking transcription of genes in the lytic cycle. Thus, the lysogenic cycle prevails. The cII protein also activates the transcription of the int gene which transcribes a protein called integrase required for the integration of the lambda genome into the host.

Once the lysogenic stage has been established, it is generally stable. However, under certain conditions such as ultraviolet light, the host can produce a protein called pRecA that stimulates the cleavage of the λ repressor and thus switching the cycle to lytic.

Reference:

1. Griffiths AJF, Wessler SR, Carroll SB and Doebley J. 2012. Introduction to genetic analysis (10th edition). WH Freeman and Company. New York, NY.
2. Reece, J. B., & Campbell, N. A. (2011). Campbell biology. Boston: Benjamin Cummings / Pearson.