BiS2C: Lecture 12: Acquiring Novelty

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016
Lecture 12:
Acquiring Novelty
BIS 002C
Biodiversity & the Tree of Life
Spring 2016
Prof. Jonathan Eisen
1

Office Hours and Midterm
• Eisen: Today ~2:15 - 3:15
• Moore: Today 4:00 - 5:00
• Review Session
!Sunday
!1001 Geidt Hall
!6:00 - 7:30 PM
2

Where we are going and where we have been
• Previous Lecture:
!11: Function
• Current Lecture:
!12: Novelty and Acquiring Functions
• Next Lecture:
!13: Human Microbiome
3

Thought Questions & Main Topics
• How do organisms get new functions?
• How can we classify the ways organisms
live together?
4

Key Concepts
• Lateral gene transfer
• Symbiosis
!Mutualism
!Commensalism
!Parasitism
• Phylogenetic applications
5

Origin of Novelty
6

Origin of Novelty
• Intrinsic (changes on the inside)
7

Origin of Novelty
• How do organisms get new functions
• Intrinsic (changes on the inside)
• Extrinsic (acquired from the outside)
8

Extrinsic Origin of Novelty
Extrinsic acquisition of novelty
• Sexual recombination
• Interactions w/ Other Organisms
9

10

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 11
Sexual Recombination
In eukaryotes, the variants produced by mutation can “recombine” via sex
meiosismeiosis
fertilization

12

Lateral gene transfer model
13
A CB D E F G
Note Slides Compared to
Those Used in Section A

A CB D E F G
Gene
Transfer

A CB D E F G
Suppose this
was EFG
Gene
Transfer

A CB D E F G
Suppose this
was EFG
Now D will
have 2 EFGs
EFG
transfer

A CB D E F G
EFG
transfer

A1 CA2 D1 E F G1D2B G2
EFG
transfer

Suppose we built
phylogenetic trees
with EFGs form
these species
EFG
transfer

EFG Set #1
‘Normal” EFGs from
D1, D2

EFG Set #1
Also any other non-
transferred genes

EFG Set #2
22
‘Transferred” EFGs for
D1, D2

All EFGs
23
A1 CA2 D1 E F G1D2B G2D1 D2
All EFGs

Clicker
24

Double Lateral Transfer of EFGs
If we built a tree of all the
EFGs in these organisms,
which of the following would
not be seen as a
monophyletic grouping?
A: D1, D2
B. D1, D2, E
C. D1, D2, B
D. G1, G2, F
E. A1, A2
EFG

A CA2 D1 E F G1D2B G2
not be seen as a
A: D1, D2
B. D1, D2, E
C. D1, D2, B
D. G1, G2, F
E. A1, A2
EFG

A CA2 D2 E F G1D2B G2D1 D1 B
not be seen as a
A: D1, D2
B. D1, D2, E
C. D1, D2, B
D. G1, G2, F
E. A1, A2

Antibiotic Resistance Can Transfer Between Species
• http://www.niaid.nih.gov/
SiteCollectionImages/topics/
antimicrobialresistance/3geneTransfer.gif
29

30

Symbioss
• Symbiosis is an intimate association between at least
two different organisms in which at least one of them
benefits
• Endosymbiosis is a symbiosis in which one of the
organisms live inside the cells of the other
32

Classes of symbiosis
Organism
Class of symbiosis A B
Mutualism + +
Commensalism + 0
Parasitism + -
33

Organism
Mutualism + +
Commensalism + 0
Parasitism + -
34

Mutualistic Symbioses of Bacteria in Eukaryotes
• Digestive
! Ruminants
! Cellulolytic insects
• Defensive
• Behavioral
! Squid light organs
• Autotrophic
! Photosynthetic (many)
! Chemosynthetic in deep sea
• Nutritional
! Aphids
! Nitrogen fixation in legumes
35

Mutualistic Symbioses of Bacteria in Eukaryotes
• Digestive
! Ruminants
! Cellulolytic insects
• Defensive
• Behavioral
! Squid light organs
• Autotrophic
! Photosynthetic (many)
! Chemosynthetic in deep sea
• Nutritional
! Aphids
! Nitrogen fixation in legumes
36
More When We Discuss PAF
(Plants, Animals, Fungi)

Organism
Mutualism + +
Commensalism + 0
Parasitism + -
37

Organism
Mutualism + +
Commensalism + 0
Parasitism + -
38
More in Lecture 13
The Human Microbiome

Organism
Mutualism + +
Commensalism + 0
Parasitism + -
39

II. Some terms
• Pathogens are infectious agents that cause a disease
(can be considered a subclass of parasites)
• Pathogenicity = ability to enter a host and cause disease
• Virulence = degree of pathogenicity
• Note - not all parasites are pathogens but all pathogens
are parasites
!40

The Following is a Brief Tour
41

Spirochetes
• Gram-negative
• Motile
• Chemoheterotrophic
• Unique rotating, axial
filaments (modified
flagella)
• Many are pathogens:
!Syphilis
!Lyme disease
• Others free-living
42

Chlamydias
• Gram-negative
• Cocci or rod-shaped
• Extremely small
• Live only as parasites
inside cells of
eukaryotes & cause
various diseases
!Trachoma
!Multiple sexually
transmitted
diseases
!Pneumonia
43
C. trachomatis

High-GC Gram Positives (Actinobacteria)
• High G+C/A+T ratio in DNA
• Elaborate branching
• Some reproduce by forming
chains of spores at tips of
filaments
• Most antibiotics are from this
group
• Causative agents of many
diseases such as
tuberculosis and leprosy
• Many originally misclassified
as fungi
44

Low-GC Gram Positives (Firmicutes)
• Low G+C/A+T ratio in DNA
• Some produce endospores
which are resistant “seeds”
that germinate when
conditions are good
• Many agents of diseases
(e.g., anthrax, MRSA,
Streptococcus, botulism,
tetanus)
• Many of agricultural and
industrial use (e.g., Lactic
acid bacteria)
• Some (Mycoplasmas) have
no cell wall and are
extremely small
45
Mycoplasmas

Proteobacteria
• Gram-negative
• Escherichia coli: model
organism and human
gut commensal and
pathogen
• Mitochondria evolved
from this group
• Includes many human
and animal
pathogens: plague,
cholera, typhoid
46

Alveolates: Apicomplexans
• All parasitic
• Have a mass of organelles at one tip
—the apical complex that help the
parasite enter the host’s cells.
47
Apical complex • Plasmodium falciparum-
Malaria kills 700,000-2,000,000
people per year—75% of them
are African children

Alveolates: Ciliates
48
Movement in a ciliate from the gut of a termite
• All have numerous cilia, the structure
is identical to flagella.
• Most are heterotrophic; very diverse
group.
• Have complex body forms and two
types of nuclei.
• Some pathogens (e.g., Ick)

Stramenopiles: Oomcyetes
Phytophthora
Potato Late Blight
• Non-photosynthetic.
• Are absorptive heterotrophs
• Once were classed as fungi, but
are unrelated.
49
Sudden Oak Death

Excavates: Diplomonads and Parabisalids
• Unicellular
• Lack mitochondria and most are
anaerobic. This is a derived condition
• Giardia lamblia - a diplomonad - is a
human parasite
• Trichomonas vaginalis - parabasalid - STD
50

Excavates: Kinetoplastids
• Unicellular parasites with two flagella and a
single mitochondrion.
• Mitochondrion contains a kinetoplast -
structure with multiple, circular DNA
molecules
• Includes trypanosomes and agents of
chagas, sleeping sickness, Leishmaniasis
Trypanosoma sp.
mixed with blood cells
51

Excavates: Heteroloboseans
• Amoeboid body form.
• Naegleria can enter humans and
cause a fatal nervous system
disease - “brain eating”
• Some can transform between
amoeboid and flagellated stages.
52

• Not colonial; live as single cells
• Some secrete shells or glue sand
grains together to form a casing.
• Many pathogens
53
Amoebozoans: Loboseans

No archaeal pathogens
• Lots of types of pathogens
! Bacteria that infect eukaryotes
! Viruses that infect eukaryotes, archaea and
bacteria
! Eukaryotes that infect other eukaryotes
• No known archaeal pathogens of any organism
! No clear explanation of why
! If you discover one, you will become famous
(well, among scientists)
54

Case Study: Anthrax
55

Slide by Brian Moore for BIS2C at UC Davis Spring 2016

Anthrax letters - 9/18/2001
!57

Bacillus anthracis
• A member of the Firmicutes
(low GC Gram positive)
phylum
• Sporulates
• Animal and human pathogen
• Highly invasive
• “Weoponized” by multiple
countries
58

Anthrax forensics
• Question - How do you figure out where the
Anthrax in the letters came from?
• Answer came from phylogenetics
!60

Anthrax Diversity
Figure 3. Worldwide distribution of B. anthracis clonal lineages:Phylogenetic and geographic relationships
among 1,033 B. anthracis isolates.
doi:10.1371/journal.pone.0000461.g002
!61

VNTR Tree by Paul Keim et al
Figure 2. UPGMA dendrogram of VNTR data from worldwide B. anthracis isolates: Fifteen VNTR loci and
UPGMA cluster analysis were used to establish genetic relationships among the 1,033 B. anthracis isolates.!62

• The “AMES”
strain of
anthrax
• Used in labs
throughout
world

Case Study: Viruses and the Tree of Life
66

Viruses
Viruses are obligate parasites of other organisms and
cannot live on their own
67

Viral Diversity

Phage
69
A double-stranded DNA virus: Bacteriophage
T4. Viruses that infect bacteria are referred to
as bacteriophage (or simply phage). T4
attaches leglike fibers to the outside of its host
cell and injects its DNA into the cytoplasm
through its “tail” (pink structure in this
rendition).
A double-stranded DNA mimivirus: This
Acanthamoeba polyphaga mimivirus (APMV) has
the largest diameter of all known viruses and a
genome larger than some prokaryote genomes. It
is named for its host, an amoeba. Cutaway view.
150 nm60 nm
• Phage are DNA
viruses that infect
bacteria and
archaea
• Phage therapy
involves using
phage to attack
bacterial infections
• Repopularize w/
spread of
antibiotic
resistance

CRISPR is an Adaptive Immune System for Bacteria/Archaea
71
doi:10.1016/j.biochi.2015.03.025
2015 Breakthrough Prize
Jennifer Doudna
Emmanuelle Charpentier

Mimivirus
72
A double-stranded DNA virus: Bacteriophage
T4. Viruses that infect bacteria are referred to
as bacteriophage (or simply phage). T4
attaches leglike fibers to the outside of its host
cell and injects its DNA into the cytoplasm
through its “tail” (pink structure in this
rendition).
A double-stranded DNA mimivirus: This
Acanthamoeba polyphaga mimivirus (APMV) has
the largest diameter of all known viruses and a
genome larger than some prokaryote genomes. It
is named for its host, an amoeba. Cutaway view.
150 nm60 nm
• Mimivirus is a
DNA virus w/ giant
genome
• It is infected by its
own viruses
• Incredibly diverse
functional content

Mimiviruses Genomes Similar in Size to Those of Many Parasitic
73

Where do viruses sit on the tree of life?
Viruses are obligate parasites of other organisms and
74

Bacteria Archaea Eukaryotes
Virus Evolution Model 1: The Fourth Domain
Viruses

Bacteria Archaea Eukaryotes
Virus Evolution Model 2: Separate Origin
Viruses

Bacteria Archaea EukaryotesViruses Viruses
Virus Evolution Model 3: From Within Other Groups

Probably a Little of Each
79

Where do viruses sit on the tree of life?
• Viruses are obligate parasites of other organisms and
• Three main theories about viruses and where they sit on
the tree of life
• 1. Viruses are relics from a pre-cellular world
• 2. Viruses are escaped portions of cellular organisms
• 3. Viruses are extremely derived and reduced cellular
organisms
80

Case Study: Influenza Virus
81

Influenza virus
!82
A negative-sense single-stranded RNA
virus: Influenza virus H5N1, the “bird flu”
virus. Surface view.
A positive-sense single-stranded RNA
virus: Coronavirus of a type thought to be
responsible for severe acute respiratory
syndrome (SARS). Surface view.
50 nm50 nm
• “Influenza” – term dates
from 15th century Italy when
epidemics were attributed to
the influence of the stars
• Negative strand RNA
viruses
• 8 single strand
chromosomes
• Two key proteins for
antigenicity
! H = Hemagglutanin
! N = Neuraminadase

Flu Phylogeny
PLoS Currents Influenza.
2009 Sep 3:RRN1031. 83
Different segments of
the flu genome can
have very different
histories

Flu Recombination
84

Recent work of Prof. Brian Moore …
85
Viruses 2015, 7, 3310-3328; doi:10.3390/v7062773

BiS2C: Lecture 12: Acquiring Novelty

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