Micro chapter 7

Microbiology: An Introduction

Content from Chapter 13

Viruses: Structure and Replication

Subviral Agents

Process of Identifying Microbes – Infectious Agents

Thirteenth Edition

General Characteristics of Viruses

• Viruses are minuscule, acellular infectious agents.
• Composed of:
  • DNA or RNA: Genetic material can be either type.
  • Protein Coat: Encloses the nucleic acid.
• Lacking cellular components:
  • No ribosomes
  • No cytoplasmic membrane
  • No cytosol
  • No organelles
• Classified as obligatory intracellular parasites:
  • They must reside within the living host cells to multiply.
• Metabolic characteristics:
  • No ATP-generating mechanisms.
  • Cannot grow or respond to environmental stimuli.
• They recruit the host cell’s metabolic pathways to increase their own numbers.

Viruses – Infectious Agents

• Viruses are known to:
  • Cause various infections in humans, animals, plants, and bacteria.
  • Infect every known phylum of organisms.
  • Contribute significantly to diseases in industrialized societies.
• Host Range:
  • Defined as the spectrum of host cells that a virus can infect.
  • Determined by specific attachment sites on the host and cellular factors.
• Notable categories of viruses:
  • Bacteriophages: Viruses that specifically infect bacteria.
  • Generalist viruses: Capable of infecting many kinds of cells across various hosts.

Virus Size Comparison

• Example sizes of various viruses and host organisms:
  • Bacteriophage T4: 225 nm
  • Ebola virus: 800 x 10 nm
  • Poliovirus: 30 nm
  • Rhinovirus: 30 nm
  • Human red blood cell: 10,000 nm in diameter
  • E. coli bacterium: 3000 x 1000 nm

Viral Structure

Morphology

• Intracellular state:
  • Metabolically active; capsid removed.
  • Exists as nucleic acid only.
• Extracellular state:
  • Metabolically inert; termed virion (complete viral particle).
• Components:
  • Nucleic Acid: Can be either single-stranded or double-stranded; linear or circular.
  • Capsid: Protein coat made of subunits called capsomeres.
  • Envelope: Some viruses possess a lipid, protein, and carbohydrate outer layer.
  • Spikes: Glycoproteins extending from the surface of the virus used for attachment.

General Morphology of Viruses

• Virus shapes include:
  • Polyhedral viruses: Many-sided.
  • Helical viruses: Cylindrical form.
  • Complex viruses: Have intricate structures.
  • Categorization based on whether they are enveloped or non-enveloped.

Taxonomy of Viruses

• Virus classification:
  • No traditional biological kingdoms or phyla.
  • Orders of viruses end with -ales, families with -viridae, genera with -virus.
  • Viral species: Groups of viruses sharing the same genetic material and ecological niche (host).
  • Descriptive common names are used for species, and subspecies are designated by numerical identifiers.
  • Scientific names must be italicized (e.g., Tobacco mosaic virus).

Classification of DNA Viruses

• Categories based on structure and replication mechanism:
  • Double-stranded DNA: Utilizes DNA polymerase (BC Class I).
  • Groups: Adenoviridae (non-enveloped), Poxviridae, Herpesviridae (enveloped).
  • Double-stranded DNA: Uses reverse transcriptase (BC Class VII).
  • Groups: Hepadnaviridae (enveloped).
  • Single-stranded DNA (BC Class II): Non-enveloped, example: Parvoviridae.

Classification of RNA Viruses

• Divided into categories:
  • Double-stranded RNA: Non-enveloped (BC Class III).
  • Single-stranded RNA:
  • Positive Strand (BC Class IV): Can be non-enveloped or enveloped.
  • Negative Strand (BC Class V): Can have one or multiple strands.
  • Single-stranded RNA that produces DNA (BC Class VI): Utilizes reverse transcriptase.

Bacteriophages (Phages)

• Characteristics of bacteriophages:
  • Infect and replicate within bacteria and archaea.
  • Possess either DNA or RNA genomes.
  • Exhibit diversity in genome size (smallest has 4 genes; largest has hundreds).
  • Estimated to be about 10^31 phages on Earth, surpassing all other organisms combined.
  • Spread through environments, from seawater to biospheres.
  • Two reproductive cycles: Lytic and Lysogenic (rarely both).
  • Phage therapy: An alternative to traditional antimicrobial treatments.

Growing Bacteriophages in the Laboratory

• Viral growth methodology:
  • Must be grown in living cells; typically use bacteria.
  • Bacteriophages create plaques, which are clear zones observed on a bacterial lawn in agar.
  • Each plaque corresponds to a single infectious particle, quantified as plaque-forming units (PFU).

Multiplication of Bacteriophages

Replication Strategies

• Lytic replication:
  • Results in the destruction and lysis of the host cell (virulent phage).
  • Leads to a productive phage cycle, creating more virions.
• Lysogenic replication:
  • The infected host cell continues to reproduce for several generations before lysis.
  • Temperate phages involve latent cycles (non-productive).

Detailed Steps of the Lytic Cycle of T-Even Bacteriophages

1. Attachment/Adsorption: Phage attaches to host cell using tail fibers.
2. Penetration/Entry: Phage lysozyme opens the cell wall; the tail sheath contracts, injecting DNA.
3. Biosynthesis: Replication of phage DNA and synthesis of proteins occur (involves transcibing and translating).
4. Maturation/Assembly: Phage components are assembled.
5. Release: Phage lysozyme breaks the cell wall leading to lysis and release.

Generalized Transduction by a Bacteriophage

1. Phage infects donor bacterial cell, producing new phage DNA and proteins.
2. Host bacterial chromosome breaks into fragments.
3. During phage assembly, fragments of bacterial DNA are occasionally packaged.
4. The new phage infects a recipient bacterial cell, transferring the bacterial DNA.
5. Recombination may produce a genetically distinct recombinant cell.

Bacteriophage Lambda (λ): The Lysogenic Cycle

• Lysogeny: Phage remains latent in the host cell.
• The viral DNA integrates into the host genome as prophage.
  • Prophage replication occurs along with host chromosome replication.
  • Phage conversion results in new properties of the host cell.

Specialized Transduction

1. Prophage exists in a host with specific genes.
2. The phage genome excises improperly and carries adjacent bacterial genes.
3. This phage infects a new host, transferring these genes.
4. The result can be a recombinant cell with new capabilities (e.g., metabolism of galactose).

Outcomes of Bacteriophage Multiplication

• Lytic Cycle: Causes blasting and death of the host.
• Lysogenic Cycle: Prophage incorporation alters the bacterium’s phenotype, e.g., Streptococcus pyogenes can produce a scarlet fever toxin.
• Transduction: Bacterial genes are altered or transferred via phage infections, enabling genetic evolution among bacterial populations.

Growing Animal Viruses in the Laboratory

• Techniques include:
  • Living animals.
  • Embryonated eggs: viruses injected; observed by embryo reaction.
  • Tissue/cell cultures: separated cells with enzymes; detection of cytopathic effects (CPE).

Viral Identification Techniques

• Detection methodologies include:
  • Cytopathic effects from viral infections.
  • Serological tests: e.g., Western blot, ELISAs.
  • Nucleic acid tests: e.g., PCR, RFLPs.

Multiplication of Animal Viruses – Introduction

• Follows general replication pathways similar to bacteriophages, but with differences:
  • Attachment through glycoprotein/spike orientation differs.
  • Entry varies for enveloped vs naked viruses.
  • Eukaryotic nature impacts biosynthesis location; lack of cell walls complicates release.

Steps of Multiplication of Animal Viruses

1. Attachment: Attachment utilizes various orientations via glycoproteins/spikes.
2. Penetration: Occurs via endocytosis or fusion (entire capsid enters, not just nucleic acid).
3. Uncoating: Capsid is released by viral or host enzymes.
4. Biosynthesis: RNA replication occurs in the cytoplasm, while DNA replicates in the nucleus.
5. Maturation: Assembling nucleic acid with capsid proteins (location varies by virus type).
6. Release mechanisms:
   • Budding: Expulsion of enveloped viruses.
   • Rupture/Lysis: Non-enveloped virus releases occur through host membrane rupture.
   • Exocytosis or host apoptosis can also contribute to the release.

The Biosynthesis and Maturation of DNA Viruses

• DNA viruses replicate within the nucleus:
  • Host cell enzymes power DNA replication.
  • Capsid is synthesized in the cytoplasm.
  • The assembly of virions occurs in the nucleus.
  • Release varies between naked viruses (cell lysis) and enveloped viruses (budding).

The Biosynthesis of RNA Viruses

• RNA viruses generally multiply in the cytoplasm:
  • Use RNA-dependent RNA polymerase for replication.
  • Capsid proteins synthesized in the cytoplasm with assembly occurring there too.
  • Naked RNA viruses are released by cell lysis; enveloped viruses by budding.

Biosynthesis of RNA Viruses That Use DNA

• Single-stranded RNA viruses utilize reverse transcriptase to generate DNA from RNA.
• Viral DNA integrates into host chromosomes as a provirus; remains permanently integrated unlike prophages.

Comparison of Bacteriophage and Animal Viral Multiplication

Subviral Agents

• Defined as smaller than viruses but possess some of their properties:
  • Satellites: Need a helper virus for propagation.
  • Defective interfering particles: Mutant viruses lacking necessary genomic components.
  • Viroids: Small, circular, single-stranded RNA that can act as ribozymes.
  • Prions: Infectious proteins causing neurodegenerative diseases.

Satellites

• Satellites require the presence of helper viruses:
  • Satellite virus: Nucleic acid genomes encoding capsid proteins from helper viruses.
  • Satellite RNA: Packaged by proteins encoded by the helper virus, but does not encode capsid proteins.
• Defective interfering particles inhibit normal viral replication and may be protective to host.

Viroids and Virusoids

• Viroids: Do not code for proteins; cause plant diseases like potato spindle tuber through RNA silencing.
• Virusoids: Like viroids but are encapsulated by a helper virus coat protein; do not encode proteins.

Prions

• Definition: Infectious proteins leading to brain degeneration through transmissible spongiform encephalopathies (TSEs).
• Transmission can occur through ingestion, transplants, or surgical instruments.
• Diseases caused by prions:
  • Share characteristics of long incubation periods and are invariably fatal.
• PrPC: Normal cellular prion protein; no disease risk.
• PrPSc: Abnormal prion form accumulating in neurons, resulting in cellular death.

Prion Infectious Mechanism

1. Normal PrP can be converted into the infectious prion form.
2. The infectious prion accumulates and disrupts cellular function leading to cell death.

Human Diseases Caused by Prions

Conclusion

These notes provide a comprehensive overview of the fundamental principles and classifications related to viruses, including their structure, replication mechanisms, and the implications of subviral agents, aiding in a deeper understanding of microbiology as it pertains to infectious agents.