Formation of low mass protostars and their circumstellar disks
BIS2C_2020. Lecture 11 Viruses and gene transfer
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. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Anna’s hummingbird
3. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Male Carpenter Bee
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. 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. 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. 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. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Background: Lab Connections
• Lab 2: Lateral gene transfer
9. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Background: Lecture 10 review
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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Incredible Diversity of Viruses
23. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
General viral life cycle
https://www.youtube.com/watch?v=uIut0oVWCEg
24. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Some Key Features of Viruses
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. 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. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Some Key Features of Viruses
Are
Viruses
Alive?
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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Diversity of viruses
48. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Genome Structure Classification
49. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Diversity of viruses
50. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
RNA Retroviruses
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. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
RNA retroviruses Life Cycle
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. 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. 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. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Positive sense single stranded RNA viruses
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. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Coronaviruses: Sars-CoV2
https://www.youtube.com/watch?v=5DGwOJXSxqg
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. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
NextStrain - Rooted —- See https://nextstrain.org/ncov/
61. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
NextStrain - Unrooted
62. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
NextStrain Transmissions
63. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
NextStrain Time Lapse
64. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Negative sense single stranded RNA viruses
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. 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. 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. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Double stranded DNA viruses: phage
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. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Phage T4 Animation
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. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Double stranded DNA viruses: Mimivirus
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. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Didier Raoult’s Latest
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. 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. 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. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Gene Transfer Animations: Transduction and Conjugation
79. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Transfer of Function Via Plasmids
80. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Transfer of Function Via Plasmids
Exchange
81. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Transfer of Function Via Plasmids
Exchange
82. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Lateral Gene Transfer Complicates Phylogenetic Relationships
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. 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. 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