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BIS2C_2020. Lecture 11 Viruses and gene transfer

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BIS2C_2020. Lecture 11.

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BIS2C_2020. Lecture 11 Viruses and gene transfer

  1. 1. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 BIS2C Biodiversity & the Tree of Life Spring 2020 Lecture 11: Viruses and Gene Transfer Prof. Jonathan Eisen
  2. 2. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Anna’s hummingbird
  3. 3. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Male Carpenter Bee
  4. 4. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Learning Goals • Understand general features of viruses • Understand the evidence for and against the idea that viruses are alive • Be able to explain the models for the origins of viruses and give examples of which viruses appear to fit with these models • Provide examples of different kinds of viruses and some of their features • Be able to compare and contrast lateral gene transfer and sexual reproduction
  5. 5. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 !10: Pathogens and Parasites !11: Viruses and Gene Transfer !12: Mutualisms and Microbiomes Lecture 11 Context
  6. 6. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Lecture 11 Outline • Background and Context • Viruses !Introduction to viruses !Viral origins !Viral diversity • Gene transfer
  7. 7. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Lecture 11 Outline • Background and Context • Viruses !Introduction to viruses !Viral origins !Viral diversity • Gene transfer
  8. 8. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Background: Lab Connections • Lab 2: Lateral gene transfer
  9. 9. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Background: Lecture 10 review
  10. 10. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Lecture 10 Outline • Background and Context • Parasites and Pathogens !Symbioses !Pathogen Examples !Fighting Pathogens !Resistance
  11. 11. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Symbiosis Symbiosis: an intimate association between at least two organisms in which at least one of them benefits
  12. 12. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Organism Class of symbiosis A B Mutualism + + Symbiosis: Mutualism Symbiosis: an intimate association between at least two organisms in which at least one of them benefits
  13. 13. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Symbiosis: Commensalism Organism Class of symbiosis A B Mutualism + + Commensalism + 0 Symbiosis: an intimate association between at least two organisms in which at least one of them benefits
  14. 14. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Organism Class of symbiosis A B Mutualism + + Commensalism + 0 Parasitism + - Symbiosis: an intimate association between at least two organisms in which at least one of them benefits Symbiosis: Parasitism
  15. 15. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Parasitism: an intimate association between at least two different organisms in which one of them benefits and one of them is negatively affected. Host: the organism that is harmed. Parasite: the organism that benefits. Pathogen: infectious agent that causes a disease. This is a major subclass of parasites. Symbiosis: Parasitism
  16. 16. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Pathogen Examples • What follows is a tour • For this tour you need to know for underlined and bolded diseases: !which are caused by bacteria !which are caused by “prokaryotic archaea” !which are caused eukaryotes !which are caused by viruses • For the ones caused by bacteria, you need to know: !which are caused by Gram-positives !which are caused by Gram-negatives
  17. 17. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Lecture 10 Outline • Background and Context • Pathogens and Parasites !Symbiosis !Pathogen Examples !Fighting Pathogens !Resistance
  18. 18. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Approach 4: Attack the pathogen • Antibiotics, also known as antibacterials: inhibit or kill bacteria • Antifungals: inhibit or kill fungi • Antivirals: inhibit or kill viruses • Some are broad in their targets and some are narrower
  19. 19. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Lecture 10 Outline • Background and Context • Pathogens and Parasites !Symbiosis !Pathogen Examples !Fighting Pathogens !Resistance
  20. 20. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Lecture 11 Outline • Background and Context • Viruses !Introduction to viruses !Viral origins !Viral diversity • Gene transfer
  21. 21. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Lecture 11 Outline • Background and Context • Viruses !Introduction to viruses !Viral origins !Viral diversity • Gene transfer
  22. 22. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Incredible Diversity of Viruses
  23. 23. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 General viral life cycle https://www.youtube.com/watch?v=uIut0oVWCEg
  24. 24. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Some Key Features of Viruses
  25. 25. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Some Key Features of Viruses ! Noncellular ! Packaged into virion made up of: ! Genome (RNA or DNA) ! Protective coat (capsid) ! Sometimes additional coatings such as a lipid envelope ! Life history ! Obligately symbiotic and intracellular ! Replicate but only with assistance from host ! Causative agents of 1000s of known diseases including 100s in humans ! Mutate and evolve ! Infectious via virions/virus particles ! No metabolism themselves ! Estimated to be > 10,000,000,000,000,000,000,000,000,000,000 (10^31) virions on earth.
  26. 26. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Organism Class of symbiosis A B Mutualism + + Commensalism + 0 Parasitism + - Most viruses are known to be parasitic, but some may be mutualistic Symbiosis: Parasitism
  27. 27. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Some Key Features of Viruses Are Viruses Alive?
  28. 28. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Some Key Features of Viruses Are Viruses Alive? ! Noncellular ! Packaged into virion made up of: ! Genome (RNA or DNA) ! Protective coat (capsid) ! Sometimes additional coatings such as a lipid envelope ! Life history ! Obligately symbiotic and intracellular ! Replicate but only with assistance from host ! Causative agents of 1000s of known diseases including 100s in humans ! Mutate and evolve ! Infectious via virions/virus particles ! No metabolism themselves ! Estimated to be > 10,000,000,000,000,000,000,000,000,000,000 (10^31) virions on earth.
  29. 29. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Some Key Features of Viruses Reasons for “No” ! Noncellular ! Packaged into virion made up of: ! Genome (RNA or DNA) ! Protective coat (capsid) ! Sometimes additional coatings such as a lipid envelope ! Life history ! Obligately symbiotic and intracellular ! Replicate but only with assistance from host ! Causative agents of 1000s of known diseases including 100s in humans ! Mutate and evolve ! Infectious via virions/virus particles ! No metabolism themselves ! Estimated to be > 10,000,000,000,000,000,000,000,000,000,000 (10^31) virions on earth.
  30. 30. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Some Key Features of Viruses Reasons for “Yes” ! Noncellular ! Packaged into virion made up of: ! Genome (RNA or DNA) ! Protective coat (capsid) ! Sometimes additional coatings such as a lipid envelope ! Life history ! Obligately symbiotic and intracellular ! Replicate but only with assistance from host ! Causative agents of 1000s of known diseases including 100s in humans ! Mutate and evolve ! Infectious via virions/virus particles ! No metabolism themselves ! Estimated to be > 10,000,000,000,000,000,000,000,000,000,000 (10^31) virions on earth.
  31. 31. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Some Key Features of Viruses ! Noncellular ! Packaged into virion made up of: ! Genome (RNA or DNA) ! Protective coat (capsid) ! Sometimes additional coatings such as a lipid envelope ! Life history ! Obligately symbiotic and intracellular ! Replicate but only with assistance from host ! Causative agents of 1000s of known diseases including 100s in humans ! Mutate and evolve ! Infectious via virions/virus particles ! No metabolism themselves ! Estimated to be > 10,000,000,000,000,000,000,000,000,000,000 (10^31) virions on earth. I Say “Yes”
  32. 32. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Lecture 11 Outline • Background and Context • Viruses !Introduction to viruses !Viral origins !Viral diversity • Gene transfer
  33. 33. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Woese Tree of Life rRNA rRNArRNA ACUGC ACCUAU CGUUCG ACUCC AGCUAU CGAUCG ACCCC AGCUCU CGCUCG Taxa Characters S ACUGCACCUAUCGUUCG R ACUCCACCUAUCGUUCG E ACUCCAGCUAUCGAUCG F ACUCCAGGUAUCGAUCG C ACCCCAGCUCUCGCUCG W ACCCCAGCUCUGGCUCG Taxa Characters S ACUGCACCUAUCGUUCG E ACUCCAGCUAUCGAUCG C ACCCCAGCUCUCGCUCG EukaryotesBacteria ?????Archaebacteria
  34. 34. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Four Main Hypothesis Regarding the Origin of Viruses Bacteria Prok Archaea Eukaryotes Four Main Hypothesis Regarding the Origin of Viruses.
  35. 35. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Virus Origin Model 1: Separate Origins from Cellular Life Viruses Bacteria Prok Archaea Eukaryotes Model 1: Separate origin from cellular life
  36. 36. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Viruses Bacteria Prok Archaea Eukaryotes Virus Origin Model 2: Outgroup to Cellular Life Model 2: Outgroup to cellular life.
  37. 37. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Bacteria Prok Archaea Eukaryotes Model 3: Reduced version of a parasitic cells Virus Origin Model 3: Reduced Versions of Parasitic Cells
  38. 38. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Bacteria Prok Archaea Eukaryotes Model 3: Reduced version of a parasitic cells Virus Origin Model 3: Reduced Versions of Parasitic Cells
  39. 39. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Bacteria Prok Archaea Eukaryotes Model 3: Reduced version of a parasitic cells Virus Origin Model 3: Reduced Versions of Parasitic Cells
  40. 40. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Bacteria Prok Archaea Eukaryotes Model 3: Reduced version of a parasitic cells Virus Origin Model 3: Reduced Versions of Parasitic Cells
  41. 41. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Bacteria Prok Archaea Eukaryotes Model 4: Escaped portions of cells Virus Origin Model 4: Escaped Portion of Cells
  42. 42. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Bacteria Prok Archaea Eukaryotes Model 4: Escaped portions of cells Virus Origin Model 4: Escaped Portion of Cells
  43. 43. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Bacteria Prok Archaea Eukaryotes Model 4: Escaped portions of cells Virus Origin Model 4: Escaped Portion of Cells
  44. 44. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Bacteria Prok Archaea Eukaryotes Model 4: Escaped portions of cells Virus Origin Model 4: Escaped Portion of Cells
  45. 45. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Probably a Little of Each of Models 2-4 • Viruses likely have many different origins overall • Models 2-4 from previous slides each have some support (outgroup, reduced parasite, escaped portion of cell). • Model for a completely separate origin not well supported.
  46. 46. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Lecture 11 Outline • Background and Context • Viruses !Introduction to viruses !Viral origins !Viral diversity • Gene transfer
  47. 47. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Diversity of viruses
  48. 48. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Genome Structure Classification
  49. 49. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Diversity of viruses
  50. 50. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 RNA Retroviruses
  51. 51. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 RNA retroviruses • Genomes of single stranded RNA • After infection, RNA genome is copied into DNA which is then inserted into genome • Inserted DNA known as “provirus”. • Example: HIV
  52. 52. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 RNA retroviruses Life Cycle
  53. 53. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Retrotransposon Life Cycle Retrotransposon Transcription Translation Integrate Proteins Bound to RNA RNA Copied to DNA by Reverse Transcription
  54. 54. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Transcription Translation Proteins Bound to RNA RNA Copied to DNA by Reverse Transcription Integrate Retrotransposon Add a Few Steps And This is a Retrovirus Add Protein Coat Export From Cell Bind Receptor Release Package Spread Retrotransposon vs. Retrovirus Life Cycles
  55. 55. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Bacteria Prok Archaea Eukaryotes Model 4: Escaped portions of cells Virus Origin Model 4: Escaped Portion of Cells
  56. 56. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Positive sense single stranded RNA viruses
  57. 57. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Single strand RNA virus: Positive Sense • Positive sense refers to having an RNA genome than can be directly translated into proteins • Examples: causes of hepatitis, polio, common cold, COVID19
  58. 58. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Coronaviruses: Sars-CoV2 https://www.youtube.com/watch?v=5DGwOJXSxqg
  59. 59. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 SARS-CoV-2 • Member of the Coronavirus group • Related to the viruses that cause SARS, MERS, and infections in a variety of mammals • Causes COVID-19 disease • 1000s of genomes sequenced • Current theory suggests it came from bats into human population
  60. 60. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 NextStrain - Rooted —- See https://nextstrain.org/ncov/
  61. 61. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 NextStrain - Unrooted
  62. 62. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 NextStrain Transmissions
  63. 63. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 NextStrain Time Lapse
  64. 64. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Negative sense single stranded RNA viruses
  65. 65. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Single strand RNA virus: Negative Sense • Negative sense refers to the RNA genome needing to 1st copied into opposite mRNA before it is translated into proteins • Example: influenza virus
  66. 66. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Influenza virus • 8 single stranded RNA chromosomes • Chromosomes can mix between different flu strains when simultaneous infection occurs
  67. 67. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 1918 Flu Epidemic • 1918 Influenza pandemic • > 50 million people died • Caused by major shift in the surface of the flu virus such that it was no longer recognized by most people’s immune system • Thought to have occurred when flu from pigs crossed over into human population
  68. 68. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Double stranded DNA viruses: phage
  69. 69. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Double stranded DNA virus #1: phage T4 • Phage are DNA viruses that infect bacteria and archaea • Used in phage therapy
  70. 70. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Phage T4 Animation
  71. 71. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 CRISPR is an Adaptive Immune System for Bacteria/Archaea 2015 Breakthrough Prize Jennifer Doudna Emmanuelle Charpentier • CRISPR is a technique used for rapid and simple genetic engineering • Make use of enzymes that bacteria use to protect themselves from phage infections
  72. 72. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Double stranded DNA viruses: Mimivirus
  73. 73. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 • Mimivirus is a DNA virus w/ giant genome • Genome larger than that of many bacteria • Capsid larger than many bacterial cells • It is infected by its own viruses • Complex functional content including genes for metabolism, translation, and more. Double stranded DNA virus #2: mimivirus Co-Discovered by Didier Raoult
  74. 74. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Didier Raoult’s Latest
  75. 75. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Viruses Bacteria Prok Archaea Eukaryotes Virus Origin Model 2: Outgroup to Cellular Life Model 2: Outgroup to cellular life. Some have proposed Mimivirus is an outgroup to cellular life
  76. 76. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Bacteria Prok Archaea Eukaryotes Model 3: Reduced version of a parasitic cells Virus Origin Model 3: Reduced Versions of Parasitic Cells More likely Mimivirus is a reduced version of a parasitic cell
  77. 77. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Lecture 11 Outline • Background and Context • Viruses !Introduction to viruses !Viral origins !Viral diversity • Gene transfer
  78. 78. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Gene Transfer Animations: Transduction and Conjugation
  79. 79. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Transfer of Function Via Plasmids
  80. 80. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Transfer of Function Via Plasmids Exchange
  81. 81. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Transfer of Function Via Plasmids Exchange
  82. 82. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Lateral Gene Transfer Complicates Phylogenetic Relationships
  83. 83. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Lateral gene transfer (LGT) vs Sexual Recombination • Direction !Sexual recombination is bidirectional with DNA from two parental lineages mixing !LGT is unidirectional with DNA moving from one organism to another. • Amount of genome !LGT involves usually small portions of a genome !Sexual recombination involves whole genomes. • Relatedness !LGT can occur across vast evolutionary distances (but most common among close relatives). !Sexual recombination usually within species but sometimes more distant relatives
  84. 84. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Lecture 11 Outline • Background and Context • Viruses !Introduction to viruses !Viral origins !Viral diversity • Gene transfer
  85. 85. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 !10: Pathogens and Parasites !11: Viruses and Gene Transfer !12: Mutualisms and Microbiomes Lecture 11 Context

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