Chapter 17 - The Simpler Genetic Systems of Viruses, Bacteria, and Archaea

17. General Properties of Viruses, Bacteria, and Archaea

• Viruses are simpler genetic systems, along with bacteria and archaea.

17.1 General Properties of Viruses

• Viruses are nonliving particles that require living cells to replicate.
• They are not composed of cells.
• They do not use energy, carry out metabolism, maintain homeostasis, or reproduce on their own.
• Viruses infect all types of organisms.
• Tobacco mosaic virus was the first virus discovered.
• Viruses are studied due to their ability to cause disease.
• A virus is a small infectious particle with nucleic acid enclosed in a protein coat.
• Over 4,000 different types of viruses have been studied.
• Viruses differ in their host range, structure, and genome composition.
• Host range is the number of species and cells a virus can infect.
• It may be broad (ex: 150 species) or narrow (a specific cell type).
• All viruses have a protein coat called a capsid, which varies in shape and complexity.
• Many viruses that infect animal cells have a viral envelope, a lipid bilayer derived from the host cell.
• The viral genome may be composed of DNA or RNA, may be single- or double-stranded, and may be linear or circular.
• Bacteriophages may have complex protein coats.

17.2 Viral Reproductive Cycles

• The viral reproductive cycle results in the production of new viruses, following 5 to 6 steps:
  • Attachment to the surface of the host cell.
  • Entry of the viral genome into the host cell.
  • Integration into host’s chromosomal DNA; occurs for some viruses that carry a gene that encodes integrase.
  • Synthesis of viral components as the host cell machinery synthesizes new copies of the viral genome and viral proteins.
  • Viral assembly occurs as synthesized components are assembled into new viruses.
  • Release of new viruses into the environment; phages lyse their host cell, and enveloped viruses bud from the host cell.
• Some bacteriophages may follow either a lytic or a lysogenic cycle.
• During the lytic cycle, new phages are made, and then the bacterial cell is lysed.
• During the lysogenic cycle, the integrated phage DNA, called prophage, is replicated along with the DNA of the host cell.
• During the lysogenic cycle, viruses integrate their genomes into a host chromosome; the resulting prophage/provirus can be latent (inactive) for a long time.
• Environmental conditions influence whether or not viral DNA is integrated into a host chromosome and how long the virus remains in the lysogenic cycle.
• The herpesvirus called varicella-zoster can switch from the latent form to the active form that produces new virus particles.
• The initial infection causes chickenpox; the virus can be latent for many years.
• If the virus becomes active again, it can cause shingles; the blisters follow the path of the neurons that carry the virus.
• Emerging viruses typically arise via mutations in pre-existing viruses.
• Emerging viruses have arisen recently and/or are likely to have a greater probability of causing infection.
• The coronavirus named severe acute respiratory coronavirus 2 (SARS-CoV-2) is a very recent example.
• This virus causes a respiratory infection called coronavirus disease 2019 (COVID-19).
• SARS-CoV-2 is believed to be derived from a coronavirus found in bats.
• SARS-CoV-2 is related to other coronaviruses, such as those causing Middle East respiratory syndrome (MERS-CoV) and severe acute respiratory syndrome (SARS-CoV).
• Other examples of emerging viruses include influenza virus, Zika virus, and HIV.
• New strains of influenza arise regularly, Zika virus has recently spread globally, and human immunodeficiency virus (HIV) has killed over 35 million people during recent decades.
• HIV is the causative agent of acquired immunodeficiency syndrome (AIDS).
• The virus destroys a type of white blood cell called a helper T cell, disabling many aspects of the immune system.
• Worldwide, approximately 38 million people are living with HIV.
• Antiviral drugs inhibit viral proliferation, although they cannot eliminate the virus from the body.
• One strategy is to develop drugs that specifically bind to viral proteins (without affecting normal cell function).
• Drugs that inhibit the viral reverse transcriptase and viral proteases have been developed.
• The HIV reverse transcriptase lacks a proofreading function and makes many more errors than DNA polymerase; these errors can contribute to mutant strains of HIV.
• Many patients are treated with a “cocktail” of 3 or more HIV drugs, making it less likely that a mutant strain will overcome all the inhibitory effects.

17.3 Genetic Properties of Bacteria and Archaea

• The genome of most prokaryotes consists of a single chromosome.
• Prokaryotic chromosomes are usually circular and are composed of DNA and proteins.
• Cells may have multiple copies of the single chromosome.
• Each chromosome is tightly packed within a nucleoid region.
• Usually only a few million base pairs long.
• Typically contain a few thousand genes; most genes encode proteins.
• Typically have a single origin of replication site that organizes the initiation of DNA replication.
• Bacterial cells are small; a typical bacterial chromosome must be compacted about 1,000-fold to fit inside the cell.
• Unlike eukaryotic DNA, bacterial DNA is not wound around histone proteins; instead, compaction involves the formation of loops and DNA supercoiling.
• Loop domains are formed through interaction with nucleoid-associated proteins (DNA-binding proteins); enzymes called topoisomerases twist the DNA and control the degree of supercoiling.
• The structure of the archaeal chromosome varies across species (some resemble bacteria, others resemble eukaryotes).
• Some archaeal species have bacteria-like nucleoid-associated proteins, and their chromosome is organized like in bacteria.
• Other species produce eukaryotic-like histone proteins, and their chromosome is wrapped around histone proteins to form nucleosomes and organized into loop domains.
• In addition to chromosomal DNA, prokaryotic cells commonly contain plasmids that exist separately from the main chromosome.
• Plasmids occur naturally in many strains of bacteria, archaea, and some eukaryotic cells (ex: yeast).
• Vary in size; may contain a few genes to several dozen genes.
• Have their own origin of replication and replicate independently.
• The number of copies of the plasmid per cell varies from a few to ~100.
• Plasmids are not usually necessary for survival, but they can provide growth advantages.
• Most plasmids fall into 5 categories:
  • Resistance plasmids (R factors) contain genes that confer resistance against antibiotics and other toxins.
  • Degradative plasmids enable digestion and utilization of an unusual substance.
  • Col-plasmids encode colicins, proteins that kill other bacteria.
  • Virulence plasmids turn a bacterium into a pathogenic strain.
  • Fertility plasmids (F factors) allow bacteria to transfer genes to each other.
• Most bacteria and archaea rapidly produce new cells through a cell division process called binary fission.
• Some species, such as E. coli, can divide every 20-30 minutes.
• When placed on a solid growth medium, an E. coli cell and its daughter cells undergo repeated cell divisions and form a group of genetically identical cells called a bacterial colony.
• A single cell can produce a visible colony of 10 to 100 million cells in less than a day!
• Cell division of most bacterial species occurs by a process called binary fission.
• DNA replication produces 2 identical copies of the chromosome.
• The plasma membrane is drawn inward, and a new cell wall is formed, separating the 2 daughter cells.
• Unless a mutation occurs, daughter cells are genetically identical to the mother cell; binary fission is a process of asexual reproduction.
• Plasmids are replicated independently and are distributed into daughter cells during binary fission.

17.4 Gene Transfer Between Prokaryotic Cells

• Although prokaryotes reproduce asexually, they exhibit genetic diversity.
• Mutations and gene transfer are sources of diversity.
• Gene transfer occurs in three different ways: conjugation, transformation, and transduction.
• Strains are lineages of the same species that have genetic differences (ex: an antibiotic-resistant strain of E. coli and an antibiotic-sensitive strain of E. coli).
• In the early 1950s, it was discovered that certain bacterial strains could donate genetic material during conjugation.
• Donor strains contain a fertility plasmid that can be transferred to a recipient strain.
• F+ cells have the fertility plasmid, and F- cells do not.
• The plasmid contains genes required for conjugation and may also carry genes that confer a growth advantage.
• Sex pili are made by F+ cells and specifically bind to F- cells.
• In contrast to conjugation, bacterial transformation does not require direct contact between cells.
• Living bacterial cells import a strand of DNA (typically derived from a dead bacterium).
• Frederick Griffith first discovered this process in 1928 while working with strains of S. pneumoniae.
• Only competent cells with competence factors are capable of transformation.
• Competence factors facilitate binding, uptake, and incorporation of DNA.
• On rare occasions, a phage may pick up a piece of DNA from the bacterial chromosome.
• When the phage infects another bacterium, it transfers this segment into the chromosome of its new host.
• Transduction usually occurs because of an error in the lytic cycle; host DNA is accidentally enclosed as phage coat proteins are assembled.
• Horizontal gene transfer refers to any process in which an organism incorporates genetic material from another organism without being the offspring of that organism.
• Conjugation, transformation, and transduction are examples of horizontal gene transfer.
• Roughly 17% of genes in E. coli and Salmonella typhimurium have been acquired by horizontal transfer during the past 100 million years.
• The medical relevance of horizontal gene transfer is profound.
• Many antibiotic-resistant strains of bacteria acquire resistance through horizontal gene transfer.