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Viruses and other infectious particles From: Encyclopedia of Life Science. Simply put, viruses are tiny packages of genetic material. Though they consist of biomolecules, they are acellular, and thus are not considered living organisms. Cells are enclosed within a biological membrane composed of a phospholipid bilayer, a structure that viruses do not possess. The simplest viruses contain only a fragment of genetic material surrounded by a coat of protein, and viral particles can be observed only with the assistance of an electron microscope. As obligate intracellular parasites, viruses can replicate only within a host cell. They lack the necessary molecular machinery and metabolites to reproduce on their own. Viruses are specific for the type of host they infect, and viruses are known that infect organisms across all the domains and kingdoms: animals, plants, fungi, protists, bacteria, and archaea. Some viruses harm their hosts or cause serious damage. Human viruses are responsible for numerous diseases including chicken pox, mumps, influenza, poliomyelitis, the common cold, andacquired immunodeficiency syndrome, to name a few. Certain types of viruses cause cancer in humans and other animals. Viral Structure and Classification

Most viruses are less than 2,000 angstroms wide, and some are 10 times smaller than that (one angstrom is 10–10 meter), barely larger than a small protein. All viruses possess some form of nucleic acid enclosed by a proteinaceous coating. Called a capsid, this outer covering protects the viral nucleic acid from harmful chemicals and enzymes and consists of regular repeating subunits called capsomers that often assemble into intricate geometric arrangements. Cylindrical viral capsids have rodshaped capsomers that form a hollow helix. Another common arrangement is the icosahedron, a three-dimensionsal, 20-sided structure with 12 corners. Viruses that have only a nucleocapsid (the nucleic acid and the surrounding protein capsid) are referred to as naked viruses. As the nucleocapsid of some viruses emerges from its host cell, it takes with it part of the host cell membrane, which persists


as an envelope. Specific glycoprotein molecules embedded in the envelope, also called spikes because they protrude, often play an important role in host cell recognition. Some viral particles have more complex structures, but all still possess a capsid with a nucleic acid core. Viral Particles

Enlarge Image Viral genomes consist of either deoxyribonucleic acid (DNA) or ribonucleic acid (RNA), can be double-stranded (ds) or singlestranded (ss), linear or circular, and may or may not be segmented into several pieces containing different viral genes. RNA viruses can be either positive-sense (+) or negative-sense (-), depending on whether the RNA genome directly encodes a polypeptide chain, or if the genome is complementary to the sequence that a ribosome reads. The


smallest viral genome, that ofhepatitis B, encodes only four genes, though many are much larger. (In comparison, the human genome encodes 30,000–40,000 genes.) Because viruses do not use their own molecular machinery to replicate, they only require the genes necessary to build and assemble new viral particles, or virions. Viral genomes may also encode certain proteins or enzymes that regulate the host cell's activity or that are required if the virus has a unique mode of replication. Numerous classification schemes exist for viruses, depending on various purposes. For example, a biologist might categorize viruses based on what type of organism they infect. A physician might group them according to the sort of disease they cause. In 2000 the International Committee on the Taxonomy of Viruses devised a scheme dependent on the configuration of the viral genomes. Though viruses do not belong in any kingdom, virologists grouped them into three main groups called orders, then into families (see the table Human Virus Families), genera, and species. One must remember, however, that these classifications are not based on the same criteria as living organisms, but rather on slight variations in different properties such as host range or antigenicity. Human Virus Families Family

Nucleic Acid

Envelope d

Important Genera

Parvoviridae

ss DNA

no

Dependovirus

Adenoviridae

linear ds DNA

no

Mastadenovirus

Papovaviridae

circular ds DNA

no

Papillomavirus (causes warts), Polyomavirus

Poxviridae

ds DNA

yes

Orthopoxvirus (causes smallpox), Molluscipox virus

Herpesviridae

ds DNA

yes

Simplexvirus (HHV-1 and 2), Varicellovirus (HHV-3), Lymphocryptoviru s (HHV-4), Cytomegalovirus(HHV-5), Roseol ovirus (HHV-6), HHV-7, Kaposi's sarcoma (HHV-8)

Hepadnaviridae ds DNA

yes

Hepadnavirus (causes hepatitis B)


Picornaviridae

ss (+) RNA no

Enterovirus, Rhinovirus, Hepatitis A

Calciviridae

ss (+) RNA no

Hepatitis E, Norwalk agent

Flaviviridae

ss (+) RNA yes

Flavivirus, Pestivirus, Hepatitis C virus

Nidovirales

ss (+) RNA yes

Coronavirus

Rhabdoviridae

ss (-) RNA yes

Vesiculovirus, Lyssavirus (causes rabies)

Filoviridae

ss (-) RNA yes

Filovirus (Ebola and Marburg)

Paramyxovirida ss (-) RNA yes e

Paramyxovirus (causes mumps)

Orthomyxovirid ss (-) RNA, yes ae segmented

Influenzavirus (causes the flu)

Bunyaviridae Retroviridae

Reoviridae

ss (-) RNA, yes segmented

Bunyavirus, Hantavirus

ss RNA, encodes reverse yes transcriptas e

Lentivirus (Human immunodeficiency virus, causes AIDS), Oncoviruses

ds RNA

Reovirus

no

Viral Life Cycles

Viruses cannot replicate unless they are inside of a host cell, thus the life cycle of a virus must begin with a virus seeking and entering a suitable host cell. Viruses are specific for the type of cell they can infect. Not only are they host specific, but some are tissue specific as well, meaning one that infects humans might be able to infect cells that line the respiratory tract but not liver cells. The first step of the viral life cycle is adsorption, during which a virion attaches to receptors on the exterior of the host cell membrane. This is the step that defines the host range and specificity of the virus because the interactions between the virus and molecules exposed on the host cell surface, usually glycoproteins, are specific. On naked viruses, components of the capsid perform this role, whereas in enveloped viruses, spikes embedded in the envelope bind to the host cell receptors.


Enveloped Animal Viruses

Enlarge Image After adsorption, either the entire viral particle or its nucleic acid must penetrate into the host cell. In some cases, the complete viral particle enters by endocytosis, an invagination of the cell membrane that results in the virion being enclosed in a membrane-bound vesicle within the host cell cytoplasm. Digestive enzymes break down the membrane and the viral envelope, leaving the nucleic acid floating freely in the cytoplasm. Another mechanism for penetration involves fusion of a viral envelope with the host cell membrane, so that only the nucleocapsid enters into the host cell. An uncoating step follows the entry of the nucleocapsid, and also results in free nucleic acid. The next step—the synthesis of new nucleic acid, capsomers, and spikes—is the most complex and variable between viruses. The specific


sequence of steps largely depends on the form of the viral nucleic acid. In general, viruses with a DNA genome must travel to the nucleus for transcription of the viral genes and replication of the nucleic acid, whereas RNA viruses complete these processes in the cytoplasm. If the virus contains a (+) strand of RNA, then a ribosome can immediately dock onto the RNA transcript and initiate translation, or the synthesis of viral proteins. Viral RNA that is (-) must first direct the synthesis of a complementary strand, which serves as the transcript for translation by ribosomes. Some viruses package enzymes that can synthesize a (+) RNA strand from a (-) RNA strand in their capsid, and the enzyme is released into the host cell along with the RNA. In either case, synthesis can occur only if a supply of ribonucleotides is available. The host cell provides these. When (+) RNA is present, host ribosomes will begin translation using amino acids and energy in the form of ATP, also supplied by the host cell. Polypeptides necessary for building capsomers, spikes, and other unique viral protein accumulate. Following the synthesis stage, assembly of the viral capsids occurs, and then nucleic acid is packaged into the protein shells. For enveloped viruses, spikes are inserted into the cell membrane as assembly takes place. The nucleocapsids become coated as they push their way through the membrane to the cell's exterior during budding, or exocytosis. Nonenveloped viruses are released into the environment when the cell bursts open, or lyses. The host cell dies immediately when it ruptures, but host cells infected with enveloped viruses eventually die as well from the virus interfering with cellular processes or physical damage to cellular structures. Thousands of newly released virions seek new host cells to infect, and the cycle begins again. Bacteriophages, viruses that infect bacterial cells, exhibit a slightly different life cycle. Scientists know most about the T-even bacteriophages (phages) that infect Escherichia coli. Their structure is complex, consisting of an icosahedral head that contains the DNA, a collar, a cylindrical sheath ending in a base plate surrounded by tail pins, and long tail fibers. Like animal viruses, the first step of the bacteriophage life cycle is adsorption, mediated by specific interactions between the phage and receptors on the bacterial cell surface. The sheath contracts, bringing the head closer to the bacterial cell body, and the virus injects the DNA through the cell membrane. After


penetration, the virus can enter the lytic phase or the lysogenic phase. If the former occurs, the virus replicates using the bacterial enzymes and metabolites and then assembles new viral particles. A single cell can hold up to 200 new viral particles before it lyses—hence the name "lytic cycle." The released phage can then infect other nearby host cells. Temperate phages enter lysogeny rather than the synthesis stage following penetration. During lysogeny, the viral DNA becomes incorporated into the bacterial genome and can remain latent, or inactive, meaning viral replication does not occur. While the virus exists as a prophage, the bacterial cell replicates the viral DNA along with its own, making numerous copies that end up in all the daughter cells produced by binary fission. Induction is the conversion of a lysogenic cell into a virus-replicating factory. In a process that is not completely understood, the viral DNA pops out of the bacterial chromosome and enters the lytic phase. Other Infectious Particles

Prions and viroids are other acellular, subviral forms of infectious agents. Prions are small, proteinaceous, infectious particles that are not associated with any nucleic acid and cause scrapie in sheep and other spongiform encephalopathies of animals and humans. Spongiform encephalopathies are rare, progressive, fatal diseases that cause the brain tissue to become porous and spongy. One example, CreutzfeldtJakob disease, causes premature dementia and loss of muscular coordination. Bovine spongiform encephalopathy, also known as mad cow disease, is similar in nature. Also caused by a prion, this disease can be transmitted from animals to human by eating contaminated meat. Though prions are obviously medically important, they also pose an interesting biological problem—how can a piece of protein replicate itself without any nucleic acid component? All life-forms possess DNA that encodes all the information necessary for that organism to carry out the functions of life. Prions conspicuously lack this macromolecule. After a prion enters a host cell, the protein converts normal proteins that are already present into prions by causing them to refold in a different way. As more of the proteins refold in the prion fashion, conversion of normal to abnormal proteins occurs more rapidly until the cell becomes clogged with the prions, a situation that interferes with


normal cell function and eventually cell death. When a cell dies, the prions it contained are released and can infect neighboring cells, causing the infection to spread. Viroids are viruslike agents composed only of circular ss RNA, less than 400 nucleotides long, that is not encapsidated by protein or other type of coating. They are known to infect agriculturally important plants such as tomatoes, cucumbers, coconuts, potatoes, and citrus trees. Satellites are subviral agents that require coinfection with another virus, called a helper virus, to replicate. When the satellite encodes for the capsid proteins, it is called a satellite virus.


Viruses and other infectious particles