Characterizing and Classifying Viruses, Viroids, and Prions 13 Characterizing and Classifying Viruses, Viroids, and Prions

Characteristics of Viruses Minuscule, acellular, infectious agent having either DNA or RNA Cause infections of humans, animals, plants, and bacteria Cause most of the diseases that plague the industrialized world Cannot carry out any metabolic pathway Neither grow nor respond to the environment Cannot reproduce independently Recruit the cell's metabolic pathways to increase their numbers No cytoplasmic membrane, cytosol, organelles Have extracellular and intracellular state

Characteristics of Viruses Extracellular state Called virion Protein coat (capsid) surrounding nucleic acid Nucleic acid and capsid also called nucleocapsid Some have phospholipid envelope Outermost layer provides protection and recognition sites for host cells Intracellular state Capsid removed Virus exists as nucleic acid

Capsid (sectioned to show interior) Nucleic acid (viral genome) Figure 13.1 Virions, complete virus particles, include a nucleic acid, a capsid, and in some cases, an envelope. Capsid (sectioned to show interior) Nucleic acid (viral genome)

Characteristics of Viruses Genetic Material of Viruses Show more variety in nature of their genomes than do cells Primary way scientists categorize and classify viruses May be DNA or RNA, but never both Can be dsDNA, ssDNA, dsRNA, ssRNA May be linear and segmented or single and circular Much smaller than genomes of cells

Partial genome Viral of E. coli genome Ruptured E. coli Figure 13.2 The relative sizes of genomes. Partial genome of E. coli Viral genome Ruptured E. coli

Characteristics of Viruses Hosts of Viruses Most viruses infect only particular host's cells Due to affinity of viral surface proteins for complementary proteins on host cell surface May be so specific they only infect particular kind of cell in a particular host Generalists infect many kinds of cells or many different hosts All types of organisms are susceptible to some virus

Figure 13.3 Some examples of plant, bacterial, and human hosts of viral infections.

E. coli (bacterium) (1000 nm x 3000 nm) Red blood cell Figure 13.4 Sizes of selected virions. E. coli (bacterium) (1000 nm x 3000 nm) Red blood cell (10,000 nm in diameter) Bacterial ribosomes (25 nm) Smallpox virus (200 nm x 300 nm) Poliovirus (30 nm) Bacteriophage T4 (50 nm x 225 nm) Bacteriophage MS2 (24 nm) Tobacco mosaic virus (15 nm x 300 nm)

Characteristics of Viruses Capsid Morphology Capsids Provide protection for viral nucleic acid Means of attachment to host's cells Composed of proteinaceous subunits called capsomeres Capsomere may be made of single or multiple types of proteins

Characteristics of Viruses Viral Shapes Viruses can be classified by virion shape Three basic types of viral shapes: Helical Polyhedral Complex

Enveloped capsid Fiber layer Cell's vesicle Figure 13.5 The shapes of virions. Enveloped capsid Fiber layer Cell's vesicle

Head Tail fibers Tail Base plate Figure 13.6 The complex shape of bacteriophage T4. Head Tail fibers Tail Base plate

Characteristics of Viruses The Viral Envelope Acquired from host cell during viral replication or release Envelope is portion of membrane system of host Composed of phospholipid bilayer and proteins Some proteins are virally coded glycoproteins (spikes) Envelope proteins and glycoproteins often play role in host recognition Enveloped viruses are more fragile than naked viruses

Enveloped virus with helical capsid Figure 13.7 Enveloped virion. Glycoproteins Helical capsid Matrix protein Envelope Enveloped virus with helical capsid

Table 13.1 The Novel Properties of Viruses

Classification of Viruses Virus classification based on: Type of nucleic acid Presence of an envelope Shape Size Viral genera have only been organized into families Relationship among viruses is not well understood by taxonomists

Table 13.2 Families of Human Viruses (1 of 2)

Table 13.2 Families of Human Viruses (2 of 2)

Viral Replication Dependent on hosts' organelles and enzymes to produce new virions Lytic replication Viral replication usually results in death and lysis of host cell Five stages of lytic replication cycle: Attachment Entry Synthesis Assembly Release

Viral Replication: Overview PLAY Viral Replication: Overview

cycle of bacteriophage Figure 13.8 The lytic replication cycle in bacteriophages. Attachment Bacteriophage genome Entry Tail sheath Outer membrane Peptidoglycan Cytoplasmic membrane Bacterial chromosome Entry Attachment Phage DNA Lytic replication cycle of bacteriophage Release Synthesis Phage proteins Assembly Assembly Base Tail Sheath DNA Capsid Mature head Tail fibers Mature virion

Number of infective virions in medium (log scale) Figure 13.9 Pattern of virion abundance in lytic cycle. 1000 Burst size 100 Number of infective virions in medium (log scale) 10 Release of virions by lysis Entry 1 Synthesis and assembly 5 10 15 20 25 30 35 Time (minutes) Attachment Burst time

Viral Replication: Virulent Bacteriophages PLAY Viral Replication: Virulent Bacteriophages

Viral Replication Lysogenic Replication of Bacteriophages Modified replication cycle Infected host cells grow and reproduce normally for generations before they lyse Temperate phages Prophages — inactive phages Lysogenic conversion Results when phages carry genes that alter phenotype of a bacterium

Figure 13.10 Bacteriophage lambda.

Figure 13.11 The lysogenic replication cycle in bacteriophages. Attachment Prophage in chromosome Entry Lambda phage Lytic cycle Lysogeny Synthesis Release Replication of chromosome and virus; cell division Assembly Induction Further replications and cell divisions

Viral Replication: Temperate Bacteriophages PLAY Viral Replication: Temperate Bacteriophages 28

Viral Replication Replication of Animal Viruses Same basic replication pathway as bacteriophages Differences result from Presence of envelope around some viruses Eukaryotic nature of animal cells Lack of cell wall in animal cells

Viral Replication Replication of Animal Viruses Attachment of Animal Viruses Chemical attraction between viral protein and cell receptor Animal viruses do not have tails or tail fibers Have glycoprotein spikes or other attachment molecules that mediate attachment

Figure 13.12 Three mechanisms of entry of animal viruses. Viral genome inside capsid Cytoplasmic membrane of host engulfs virus (endocytosis) Empty capsid Receptors on cytoplasmic membrane Viral genome Direct penetration Viral genome Viral glycoproteins Viral glycoproteins remain in cytoplasmic membrane Uncoating capsid Envelope Endocytosis Receptors on cytoplasmic membrane of host Viral genome Uncoating capsid Membrane fusion

Viral Replication Replication of Animal Viruses Synthesis of DNA Viruses of Animals Each type of animal virus requires different strategy depending on its nucleic acid DNA viruses often enter the nucleus RNA viruses often replicate in the cytoplasm Must consider How mRNA is synthesized What serves as template for nucleic acid replication

Viral Replication Replication of Animal Viruses Synthesis of DNA Viruses of Animals dsDNA viruses Similar to replication of cellular DNA Viral genome replicated in the nucleus Viral proteins are made in the cytoplasm Some exceptions Hepatitis B viruses replicate DNA from an RNA intermediary

Viral Replication Replication of Animal Viruses Synthesis of DNA Viruses of Animals ssDNA viruses Cells do not use ssDNA Parvoviruses have ssDNA genomes DNA strand folds back on itself to form dsDNA, which is replicated by cellular DNA polymerase Newly replicated strand is released as ssDNA

Viral Replication Replication of Animal Viruses Synthesis of RNA Viruses of Animals Synthesis of RNA viruses differs from DNA virus replication Positive-sense (+) viral RNA can act as mRNA Negative-sense (–) viral RNA cannot be directly translated

Viral Replication Replication of Animal Viruses Synthesis of RNA Viruses of Animals Four types of RNA viruses: +ssRNA Retroviruses –ssRNA dsRNA

Figure 13.13 Synthesis of proteins and genomes in animal RNA viruses. Receptors on cytoplasmic membrane of host Receptors on cytoplasmic membrane of host Receptors on cytoplasmic membrane of host –ssRNA virus +ssRNA virus dsRNA virus +ssRNA –ssRNA dsRNA Transcription by viral RNA polymerase Transcription by RNA-dependent RNA transcriptase Unwinding –ssRNA +ssRNA acts as template and as mRNA Complementary +ssRNA to act as template and as mRNA Translation of viral proteins; genome acts as mRNA Transcription by viral RNA polymerase to make complementary RNA strands Complementary –ssRNA to act as template Further transcription Further transcription Translation of viral proteins Copies of –ssRNA Translation of viral proteins Copies of +ssRNA Assembly Assembly Assembly Positive-sense ssRNA virus Negative-sense ssRNA virus Double-stranded RNA virus

Viral Replication Replication of Animal Viruses Synthesis of RNA Viruses of Animals Retroviruses Do not use their genomes as mRNA Use DNA intermediary transcribed by viral reverse transcriptase as template to produce viral genomes

Table 13.3 Synthesis Strategies of Animal Viruses

Viral Replication Replication of Animal Viruses Assembly and Release of Animal Viruses Most DNA viruses assemble in nucleus Most RNA viruses develop solely in cytoplasm Number of viruses produced depends on type of virus and size and initial health of host cell Enveloped viruses cause persistent infections Naked viruses are released by exocytosis or lysis

Enveloped virion Budding of enveloped virus Viral Cytoplasmic proteins Figure 13.14 The process of budding in enveloped viruses. Enveloped virion Budding of enveloped virus Viral proteins Cytoplasmic membrane of host Viral capsid

Number of infective virions in medium Figure 13.15 Pattern of virion abundance in persistent infections. Number of infective virions in medium Synthesis and assembly Release of virions Entry Time Attachment

Viral Replication: Animal Viruses PLAY Viral Replication: Animal Viruses

Viral Replication Replication of Animal Viruses Latency of Animal Viruses When animal viruses remain dormant in host cells Viruses are called latent viruses or proviruses May be prolonged for years with no viral activity Incorporation of provirus into host DNA is permanent

Table 13.4 A Comparison of Bacteriophage and Animal Virus Replication

The Role of Viruses in Cancer Cell division is under strict genetic control Genes dictate that some cells can no longer divide at all Cells that can divide are prevented from unlimited division Genes for cell division "turned off" or genes inhibiting division "turned on" Neoplasia Uncontrolled cell division in multicellular animal Mass of neoplastic cells is tumor Benign versus malignant tumors Malignant tumors also called cancers Metastasis occurs when tumors spread

The Role of Viruses in Cancer Protooncogenes promote cell growth and division Uncontrolled activation of oncogenes can lead to cancer Environmental factors that contribute to the activation of oncogenes: Ultraviolet light Radiation Carcinogens Viruses

Virus inserts promoter Virus inserts into repressor gene Figure 13.16 The oncogene theory of the induction of cancer in humans. Normal state: DNA Protooncogene Gene for repressor Represses mRNA Repressor Result: No cancer First "hit": Virus inserts promoter DNA Oncogene Gene for repressor Represses mRNA Repressor Result: Still no cancer Second "hit": Virus inserts into repressor gene DNA Oncogene No repressor protein because gene is segmented mRNA Protein Causes cell division Result: Cancer

The Role of Viruses in Cancer Viruses cause 20–25% of human cancers Some carry copies of oncogenes as part of their genomes Some promote oncogenes already present in host Some interfere with tumor repression Specific viruses are known to cause some human cancers: Burkitt's lymphoma Hodgkin's disease Kaposi's sarcoma Cervical cancer

Culturing Viruses in the Laboratory Viruses cannot grow in standard microbiological media Cultured inside host cells Three types of media for culturing viruses: Media consisting of mature organisms Embryonated eggs Cell cultures

Culturing Viruses in the Laboratory Culturing Viruses in Mature Organisms Culturing Viruses in Bacteria Phages grown in bacteria in liquid cultures or on agar plates Lysis of bacteria produces plaques Allows estimation of phage numbers by plaque assay

Bacterial lawn Viral plaques Figure 13.17 Viral plaques in a lawn of bacterial growth on the surface of an agar plate. Bacterial lawn Viral plaques

Culturing Viruses in the Laboratory Culturing Viruses in Mature Organisms Culturing viruses in Plants and Animals Numerous plants and animals have been used to culture viruses Laboratory animals can be difficult and expensive to maintain Ethical concerns

Culturing Viruses in the Laboratory Culturing Viruses in Embryonated Chicken Eggs Inexpensive Among the largest of cells Free of contaminating microbes Contain a nourishing yolk Fertilized chicken eggs are often used Embryonic tissues provide ideal site for growing viruses Some vaccines prepared in chicken cultures

Injection into chorioallantoic membrane Injection into chorioallantois Figure 13.18 Inoculation sites for the culture of viruses in embryonated chicken eggs. Injection into chorioallantoic membrane Injection into chorioallantois Injection into embryo Injection into amnion Injection into yolk sac

Culturing Viruses in the Laboratory Culturing Viruses in Cell (Tissue) Culture Cells isolated from an organism and grown on a medium or in a broth Cell cultures sometimes inaccurately called tissue cultures Two types of cell cultures: Diploid cell cultures Continuous cell cultures

Figure 13.19 An example of cell culture.

Are Viruses Alive? Some consider them complex pathogenic chemicals Others consider them to be the least complex living entities Use sophisticated methods to invade cells Have the ability to take control of their host cell Are able to replicate themselves Evolve over time

Other Parasitic Particles: Viroids and Prions Characteristics of Viroids Extremely small, circular pieces of ssRNA that are infectious and pathogenic in plants Similar to RNA viruses, but lack capsid Viroid RNA does not code for proteins Viroid RNA adheres to complementary plant RNA Plant enzyme degrades the dsRNA Results in a disease state

Genome of bacteriophage T7 Figure 13.20 The RNA strand of the small potato spindle tuber viroid (PSTV). Genome of bacteriophage T7 PSTV

Figure 13.21 One effect of viroids on plants.

Other Parasitic Particles: Viroids and Prions Characteristics of Prions Proteinaceous infectious agents Cellular PrP Made by all mammals Normal, functional structure has α-helices Prion PrP Disease-causing form has β-sheets Prion PrP causes cellular PrP to refold into prion PrP

Prions: Overview PLAY Prions: Overview

Cellular PrP (c-PrP) Prion PrP (p-PrP) Figure 13.22 The two stable, three-dimensional forms of prion protein (PrP). Cellular PrP (c-PrP) Prion PrP (p-PrP)

Figure 13.23 Templating action of prions. p-PrP Cell makes c-PrP, which is inserted into cytoplasmic membrane. p-PrP may infect the brain or may be produced by an altered c-PrP gene (not shown). Prion protein (p-PrP) reacts with c-PrP on the cell surface. p-PrP converts c-PrP to p-PrP. The new p-PrP converts more c-PrP.

Spongiform encephalopathy brain Figure 13.24 Brain tissue. Normal brain tissue Spongiform encephalopathy brain

Prions: Characteristics PLAY Prions: Characteristics

Other Parasitic Particles: Viroids and Prions Characteristics of Prions Prion diseases Spongiform encephalopathies Large vacuoles form in brain Characteristic spongy appearance BSE, scrapie, kuru, CWD, vCJD Transmitted by ingestion, transplantation, or contact of mucous membranes with infected tissues No standard treatment for any prion disease

Other Parasitic Particles: Viroids and Prions Characteristics of Prions Normal sterilization procedures do not deactivate prions Prions destroyed by incineration or autoclaving in concentrated sodium hydroxide European Union recently approved use of enzymes to remove prions from medical equipment

Prions: Diseases PLAY Prions: Diseases

Table 13.5 Comparison of Viruses, Viroids, and Prions to Bacterial Cells

Micro Matters In the Micro Matters video in chapter 13, Dave's uncle has pneumonia. Dave and his classmates research pathogens that can cause pneumonia. Pneumonia is an infection of the lungs. Pneumonia can be caused by bacteria, fungi, and viruses. Bacterial pneumonia can often be treated with antibiotics. Fungal and viral pneumonia have fewer specific treatment options.