Biotechnology and Microbiology Concepts

Viruses (virus means poison) can be viewed as genetic information—either DNA or RNA—contained within a protective protein coat. They are inert particles, which means they are incapable of metabolism, growth, or reproduction. When a viral genome enters a host cell, however, it can hijack the cell’s machinery, inducing the cell to produce more viral particles. In essence, viruses straddle the definition of life. Outside the host cell they are inactive, but inside a cell they direct activities that have a profound effect on that cell. So, although they are considered biological entities, they are not organisms.

Viruses that infect bacteria are called bacteriophages or simply phages (phage means to eat).

Viruses are obligate intracellular parasites; they require live organisms as hosts. They are too small to be seen with a light microscope and can be visualized only with the electron microscope.

Bacteriophages are easy to cultivate in the lab and serve as important models to understand the molecular biology of animal viruses. They are also important because they serve as a vehicle for horizontal gene transfer in bacteria (review transduction, Ch 8). In addition, they kill bacteria, thereby reducing bacterial populations in nature. Recently, the FDA has approved the use of species-specific preparations of bacteriophages for control of bacteria (including Escherichia coli O157:H7) during food production and storage.

Viruses tend to be about 10–100 times smaller than the cells they infect.

A viral particle (called a virion) consists of nucleic acid surrounded by a protein coat (called a capsid) which protects the nucleic acid from enzymes (like nucleases) in the environment.

Some viruses have an envelope—a lipid bilayer outside the capsid. These enveloped viruses obtain that bilayer from the host cell. Viruses that do not have an envelope are non-enveloped or naked viruses. In general, enveloped viruses are more susceptible to detergents because they damage the envelope, making the viruses non-infectious.

Viruses contain only a single type of nucleic acid, either RNA or DNA—but never both. We classify viruses as either RNA or DNA viruses. The genome may be linear or circular, either double-stranded or single-stranded.

Viruses have specific surface components that allow the virion to attach to specific receptor sites on cell membranes of host cells. Many animal viruses have protein structures called spikes that stick out from either the lipid bilayer of enveloped viruses or the capsid of non-enveloped viruses.

A virus generally is one of three different shapes: icosahedral, helical, or complex (e.g., phages).

The names of virus families all end in the suffix -viridae and are italicized. E.g., SARS-CoV-2, the species of coronavirus that causes Covid19 is in the family Coronaviridae. Each virus family contains numerous genera whose name ends in -virus. E.g., for SARS-CoV-2, the genus is Betacoronavirus. The species name for viruses is often the name of the disease the virus causes. E.g., for SARS-CoV-2, the full species name is Severe acute respiratory syndrome-related coronavirus 2.

Note that this system for the naming viruses is different from the naming of living organisms that we learned in Ch 1.

Informal terms are often used to refer to groups of animal viruses that are not taxonomically related but share critical characteristics, such as the primary route of transmission: a. Enteric (enteric = relating to intestines) viruses – transmitted via fecal-oral route b. Respiratory viruses – transmitted via respiratory route c. Zoonotic viruses – viruses that cause zoonoses, which are diseases transmitted from an animal to a human i. Arboviruses are arthropod (insect) borne, e.g., mosquitoes, ticks, and sandflies. Arthropods are biological vectors; when an infected arthropod takes a blood meal from an animal, it transmits the virus. Arbovirus diseases include West Nile encephalitis, yellow fever, and dengue fever.

The general strategies for phage replication are similar in concept to those of viruses that infect animal cells, and they result in two possible outcomes: (1) a productive infection, in which new viral particles are produced, and (2) a latent state, in which the viral genome remains dormant within the cell but is replicated along with the host cell genome. For a productive infection, some types of viruses kill their host, but others do not.

Lytic phages exit the host at the end of the infection cycle by lysing the cell. Lytic infections are productive infections because they result in the formation of new viral particles. E.g. T4 phage cycle: i. Attachment – On contact with host cells, a phage attaches to a receptor on the bacterial host cell wall surface. The receptor used by phages performs important functions for the bacterial cell—the phages merely exploit the protein receptors for their own use. Any cells that lack the receptors used by a particular phage are not susceptible to infection by that specific phage. ii. Genome Entry – Following entry, a bacteriophage injects its genome into the cell. T4 does this by degrading a small part of the bacterial cell wall, using an enzyme located in the tip of its tail. This enzyme, a lysozyme, is similar to the lysozyme found in tears, and degrades peptidoglycan. The tail then contracts and injects the phage DNA through the host’s cell wall and membrane, and into the cell. The capsid remains on the surface of the cell. iii. Synthesis of Phage Proteins and Genome – Within minutes, genes on the viral genome are expressed and translated by the infected cell’s own machinery (bacterial RNA polymerase and ribosomes). The phage-encoded proteins are made in a specific time sequence to control the course of infection. Early on, the phage directs the bacterial cell to synthesize proteins needed to initiate phage replication (e.g., a nuclease that degrades the host cell’s DNA is made). The phage genome is then replicated. Later, the phage directs the bacterial cell to synthesize structural components that make up the phage (e.g., the capsid and spike proteins). iv. Assembly – Once sufficient quantities of the phage genome and structural components are made, they assemble to produce new phage particles. v. Release – Late in infection, the phage-encoded lysozyme is produced. This enzyme digests the host cell from within, causing the cell to lyse, thereby releasing the phage. These phage particles then infect any adjacent cells in the environment.

Temperate phages have the option of either directing a lytic infection (productive infection) or incorporating their DNA into the host cell chromosome. The latter situation is called a lysogenic infection, and the infected cell is a lysogen. In a lysogenic infection, the phage DNA exists within the cell without causing damage. The integrated phage DNA, called a prophage, is replicated along with the host cell chromosome. When the cell divides, the prophage is passed on to the cell’s daughter cells. Later, the prophage can begin the process that leads to a lytic infection.

Once inside the bacterial cell, lambda phage DNA can direct either a lytic infection or integrate into the Escherichia coli chromosome (= lysogenic infection). The integration process uses a phage-encoded enzyme called integrase that inserts the phage DNA into the host cell chromosome. The integrated phage DNA, a prophage, replicates along with the host chromosome prior to cell division. Although the prophage can remain integrated indefinitely, it can also be excised from the host chromosome by a phage-encoded excisionase. When this happens, a lytic infection begins.

A phage-encoded protein, a repressor, blocks RNA polymerase and prevents expression of the gene required for excision, and is essential for maintaining the lysogenic state. If that repressor is destroyed or removed, a lytic cycle can begin.

Lysogenic conversion is a change in the phenotype of a lysogen as a consequence of the specific prophage it carries. E.g., only strains of Corynebacterium diphtheriae that are infected for a certain phage synthesize the toxin that causes diphtheria.

Review generalized transduction (Ch 8)

A tumor is excessive cell growth via mitosis (a type of cell division that creates two identical daughter cells in eukaryotes). Some tumors are benign, meaning they do not metastasize (spread) to other tissues. Other tumors are malignant (cancerous), meaning they have the potential to spread.

Thus, a tumor = excessive cell growth, and cancer = excessive cell growth AND capacity for metastasis.

Control of normal cell growth involves genes that stimulate cell growth, called proto-oncogenes, and others that inhibit cell growth, termed tumor suppressor genes. Expression of these genes is coordinated to regulate cell division and growth. Mutations that either enhance the expression of proto-oncogenes or reduce the expression of tumor suppressor genes are the most common cause of abnormal and/or uncontrolled growth. A single change in the DNA sequence of these regulatory genes is probably not enough to cause a tumor; rather multiple changes are required.

An oncogene is a proto-oncogene that has been mutated in a way that it promotes uncontrolled growth. Numerous events, including spontaneous and induced mutations, can lead to conversion of a host’s normal proto-oncogene into an oncogene, leading to tumor formation. In some cases, the change is associated with a viral infection. Viruses that insert their genome into the host cell’s chromosome may cause changes at the insertion site that convert a proto-oncogene into an oncogene. In addition, certain viruses can carry an oncogene.

Viruses that lead to tumor formation are called oncogenic viruses. Most tumors are not caused by oncogenic viruses, however, but by mutations in the host genes that regulate cell growth.

At least 15 human papillomaviruses (HPV) are associated with the development of cancers, possibly by interfering with the function of an important tumor suppressor gene product.

Prions are misfolded proteins that have the ability to transfer their misfolded shape onto normal variants of the same protein.

Prions are composed only of protein, which is reflected in the name (proteinaceous infectious agent). They have no nucleic acid. Prions are linked to slow and fatal human diseases like Creutzfeldt-Jakob disease and kuru, both of which are transmissible spongiform encephalopathies. In these diseases, misfolded proteins accumulate in nervous tissue. For unknown reasons, neurons die, and brain function deteriorates as the tissues develop holes.