BIS2C_2020. Lecture 11 Viruses and gene transfer

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

Anna’s hummingbird

Male Carpenter Bee

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

!10: Pathogens and Parasites
!11: Viruses and Gene Transfer
!12: Mutualisms and Microbiomes
Lecture 11 Context

Lecture 11 Outline
• Background and Context
• Viruses
!Introduction to viruses
!Viral origins
!Viral diversity
• Gene transfer

Background: Lab Connections
• Lab 2: Lateral gene transfer

Background: Lecture 10 review

Lecture 10 Outline
• Parasites and Pathogens
!Symbioses
!Pathogen Examples
!Fighting Pathogens
!Resistance

Symbiosis
Symbiosis: an intimate association between at least two
organisms in which at least one of them benefits

Organism
Class of symbiosis A B
Mutualism + +
Symbiosis: Mutualism

Symbiosis: Commensalism
Organism
Mutualism + +
Commensalism + 0

Organism
Mutualism + +
Commensalism + 0
Parasitism + -
Symbiosis: Parasitism

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.

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

Lecture 10 Outline
• Pathogens and Parasites
!Symbiosis
!Pathogen Examples
!Fighting Pathogens
!Resistance

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

Incredible Diversity of Viruses

General viral life cycle
https://www.youtube.com/watch?v=uIut0oVWCEg

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.

Organism
Mutualism + +
Commensalism + 0
Parasitism + -
Most viruses are known to be parasitic, but some may be
mutualistic

Are
Viruses
Alive?

Are
Viruses
Alive?
! Noncellular
! Life history
humans
! Mutate and evolve
! Estimated to be > 10,000,000,000,000,000,000,000,000,000,000

Reasons
for
“No”
! Noncellular
! Life history
humans
! Mutate and evolve
! Estimated to be > 10,000,000,000,000,000,000,000,000,000,000

Reasons
for
“Yes”
! Noncellular
! Life history
humans
! Mutate and evolve
! Estimated to be > 10,000,000,000,000,000,000,000,000,000,000

! Noncellular
! Life history
humans
! Mutate and evolve
! Estimated to be > 10,000,000,000,000,000,000,000,000,000,000
I
Say
“Yes”

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

Four Main Hypothesis Regarding the Origin of Viruses
Bacteria Prok Archaea Eukaryotes
Four Main Hypothesis
Regarding the Origin of
Viruses.

Virus Origin Model 1: Separate Origins from Cellular Life
Viruses Bacteria Prok Archaea Eukaryotes
Model 1:
Separate origin from
cellular life

Virus Origin Model 2: Outgroup to Cellular Life
Model 2:
Outgroup to cellular life.

Model 3:
Reduced version of a parasitic cells
Virus Origin Model 3: Reduced Versions of Parasitic Cells

Model 4:
Escaped portions of cells
Virus Origin Model 4: Escaped Portion of Cells

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.

Diversity of viruses

Genome Structure Classification

RNA Retroviruses

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

RNA retroviruses Life Cycle

Retrotransposon Life Cycle
Retrotransposon
Transcription
Translation
Integrate
Proteins Bound to RNA
RNA Copied to
DNA by Reverse
Transcription

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

Positive sense single stranded RNA viruses

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

Coronaviruses: Sars-CoV2
https://www.youtube.com/watch?v=5DGwOJXSxqg

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

NextStrain - Rooted —- See https://nextstrain.org/ncov/

NextStrain - Unrooted

NextStrain Transmissions

NextStrain Time Lapse

Negative sense single stranded RNA viruses

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

Influenza virus
• 8 single stranded RNA
chromosomes
• Chromosomes can mix
between different flu
strains when simultaneous
infection occurs

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

Double stranded DNA viruses: phage

Double stranded DNA virus #1: phage T4
• Phage are DNA viruses
that infect bacteria and
archaea
• Used in phage therapy

Phage T4 Animation

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

Double stranded DNA viruses: Mimivirus

• 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

Didier Raoult’s Latest

Virus Origin Model 2: Outgroup to Cellular Life
Model 2:
Outgroup to cellular life.
Some have
proposed Mimivirus
is an outgroup to
cellular life

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

Gene Transfer Animations: Transduction and Conjugation

Transfer of Function Via Plasmids

Transfer of Function Via Plasmids
Exchange

Lateral Gene Transfer Complicates Phylogenetic Relationships

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

BIS2C_2020. Lecture 11 Viruses and gene transfer

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