Chapter 17
Lecture Outline
Origins and Evolution
Overview
Origins of life
 Models of early life
 Microbial taxonomy
 Microbial divergence and phylogeny
 Horizontal gene transfer
 Symbiosis and the origin of mitochondria
and chloroplasts

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Origins of Life



Early geological evidence of life
3.4 billion years ago
Stromatolites

Mass of sedimentary layers of limestone (calcium carbonate)
produced by marine microbial communities over many years
Cyanobacteria Stromatolite
3.4 billion years old stromatolite
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Requirements of Life

Essential elements
 C,



H, N, O, Mg, Ca, Na, K, Fe
Available on early Earth
No free O2 in atmosphere
Temperature
 Between

boiling and freezing points of water
Source of energy
 Reduced
minerals
 Sunlight
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Evidence of Life
Stromatolites
 Isotope ratios

 Limestone
depleted of
13C (microbes rather fix
12CO )
2

Microfossils
 Filamentous
Prokaryotes
 Cyanobacteria
 Algae
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Early Metabolism
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Models for Early Life: Prebiotic Soup

Small organic molecules
arise abiotically
 Fundamental
biochemicals
of life arose spontaneously
through condensation of
reduced inorganic
molecules
 Created by lightning

Can replicate in laboratory
 Found
on other planets
 Lipids spontaneously
organize into micelles
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Models for Early Life: Metabolist Model

FeS catalyzes fixation of
carbon
 Self-sustaining
reaction

Electron transport still
uses FeS centers
 Creates

pyruvate
Central to glycolysis, TCA
cycle, fermentation,
nitrogen assimilation,
amino acid synthesis
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Models for Early Life: The RNA World

RNA performed all the informational
and catalytic roles of today’s DNA and
proteins





Only 4 different “letters”
Adenine arises spontaneously from
ammonia and carbon dioxide
Precursor to DNA
Used as genome by some viruses
Has catalytic activity (ribozymes)



Splices introns
Regulates gene expression
Synthesizes proteins


RNA performs major functions of the
ribosome
Precursor of proteins?

Remnants may persist as nucleotide
cofactors
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Taxonomy


Taxonomy is the description and organization of
life forms into classes (taxa).
Taxonomy includes
 Classification
 Recognition of different classes of life
 Nomenclature
 Naming of different classes
 Identification
 Recognition of the class of a given microbe isolated in pure
culture
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Taxonomic Classification of Species

Traditionally based on hierarchy of ranks

Long studied organisms tend to have many
ranks
 Recent isolates have few
 Ultimate designation of a type of organism is
species (Genus species)


Fundamental basis of modern taxonomy is
DNA sequence similarity
Nongenetic classifications for practical
purposes

Phenotypic categories



E.g. pigmentation, cell shape, etc
Useful for identification from clinical or field
sample
Ecological categories

Environmental niche


Includes host as niche for pathogens
Disease categories


Type of disease caused
Host system affected
13
-ales
-aceae
Species of same genus are closely related.
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Defining a Prokaryotic Species




Eukaryotes: Failure to interbreed distinguishes
two species
Prokaryotes reproduce asexually
Horizontal (= lateral) gene transfer among even
distantly related prokaryotes
Prokaryotic species are defined by ≥ 70% DNA
genomic sequence similarity, ≥ 97% ribosomal
small subunit sequence similarity.
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References for Taxonomy




Official rules for naming species are determined by
International Committee on Systematics of Prokaryotes.
Official species recognition upon publication in the
International Journal of Systematic and Evolutionary
Microbiology
All accepted taxonomic categories are compiled in
Bergey’s Manual of Determinative Bacteriology
Up-to-date taxonomy of prokaryotes and eukaryotes
maintained on-line at NCBI
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Identification of Species

DNA-based methods (phylogeny)
 Sequencing

part of the genetic sequence
Phenotypic traits
 Dichotomous key

Series of yes/no decisions successively narrows down the
possible category of species
 Probabilistic


indicator
Battery of biochemical tests performed simultaneously
Predefined data base is required
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Example for
Dichotomous Key
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Taxonomic Identification Based on
Probabilistic Indicator

Use metabolic, morphologic properties
 Reflect
genetic background
 Growth substrates
 Biochemical structure


Cell envelope—Gram stain
Rapid pathogen identification
 Multiple

color tests
Results scored to give most probable species
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Example for Probabilistic Indicator
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Simplified Indicator Table
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Microbial Divergence and
Phylogeny


Unifying assumption of modern biology is
genetic relatedness, or molecular phylogeny.
Phylogeny generates a series of branching or
related groups called clades.
 Divergence

of related organisms
Each clade is a monophyletic group, a group of
species that share a common ancestor not
shared by any other species outside of the
clade.
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Divergence through Mutation and
Natural Selection

Random mutations


Mutation naturally occurs at each division
One mistake in a million base pairs


Natural selection


Very rare mutations are favorable
Allow better survival of cell


Faster growth, higher reproduction rate
Or allow cell to attack competitors


Higher if a mutagen is present
Antibiotics made by bacteria
Reductive (degenerative) evolution


In the absence of selective pressure
Loss or mutation of DNA encoding unselected traits
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Molecular Clocks

Assume mutations accumulate steadily



Sequence differences are proportional to number of
generations since divergence
Best to compare conserved sequences that are not
under selective pressure


Constant rate per generation
Gene for small subunit rRNA
Adjustments to rate

Conservation of sequences needed for function
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The Molecular Clock



Acquisition of new random mutations in each round of
DNA replication
Note: in vivo only 1 base/ 1 million per generation)
Most widely used genes are genes encoding the smallsubunit rRNA
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Small-subunit ribosomal RNA of
Streptomyces coelicolor Y00411

Blue shaded
connections indicate
sites of intramolecular
base pairing between
distant parts of the
RNA.
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Problems with Trees

Need distant outgroup to provide root
 Determines

which species is source
Lengths of branches differ
 Mutations
accumulate at different rates
Generation time differs
 Ability to tolerate, correct mutations differs
 Can be difficult to calibrate to time in years

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Divergence of Three Domains of Life
Discovered by Carl Woese
 Used small subunit rRNA phylogeny
 No root can be established since no
outgroup exists (to our knowledge)

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Microbial Phylogeny

3 Domains
 Archaea
 Bacteria
 Eukaryotes
?
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Horizontal Gene Transfer

Acquisition of DNA from another cell
 In
eukaryotes not as common as vertical
transfer

DNA passed from parent to child
 More
frequent in microbes
Plasmid transfer
 Transposable elements
 Bacteriophages

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Horizontal Gene Transfer

Complicates determination of phylogeny
 Many
genes derived from other species
 “Informational” genes usually not transferred

Interact with many cellular components
 “Operational”
genes transferred
Function independently of other cell
components
 Bring added functions to recipient
 Confer selective advantage

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Symbiosis and the Origin of
Mitochondria and Chloroplasts
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Symbiosis


Symbiosis is a major engine of evolution
Intimate association of two unrelated species
 Mutualism:
both partners benefit
 Parasitism: one partner benefits while harming the
other

Interacting organisms coevolve
 Rhizobium
and mutualist plant hosts
 Parasites and hosts

Parasites lose functions provided by hosts
Nematode worm Brugya malayi
Antibiotics can help
treat the disease!
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Wolbachia bacteria
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Endosymbionts

Many organisms live inside another
 Intestinal

flora
Some live intracellularly
 Paramecium
and
Chlorella
Paramecium shields algae
 Algae provide nutrients
 Paramecium can digest algae if necessary

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Mitochondria and Chloroplasts
Evolved from endosymbionts
 Organelles were bacteria

 Own
circular genome
 Double membrane
 Electron transport components
 Behave like endosymbiotic
organisms
Reproduce independently
 Lost functions to host

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Mitochondria and Chloroplasts

Chloroplast: cyanobacterium
 Photosynthesis
components similar
 rRNA similarities

Mitochondria: Rickettsia (Alpha
Proteobacterium)
 Electron
transport components
 rRNA similarities
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Concept Quiz
The first living organisms on earth likely
were most similar to which of the following
groups of present-day organisms?
Cyanobacteria
b. Archaea
c. Algae
d. Protozoa
a.
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Concept Quiz
What is the difference between a rooted and
an unrooted phylogenetic tree?
The presence of an outgroup
b. Variation in length of generations
c. Variation in mutation rate
a.
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Concept Quiz
Which of the following statements about
the endosymbiont theory is incorrect?
Mitochondrial and chloroplast DNA is
similar to that of bacteria
b. Mitochondria and chloroplasts
reproduce together with the nucleus
c. Mitochondria and chloroplasts provide
functions not encoded in nuclear DNA.
a.
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