Transcript 2/27/12 Bacterial Evolution

16.1 Formation and Early History of Earth
• The Earth is ~4.5 billion years old
• First evidence for microbial life can be found
in rocks ~3.86 billion years old (Figure 16.1)
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16.1 Formation and Early History of Earth
• Stromatolites
– Fossilized microbial mats consisting of layers of
filamentous prokaryotes and trapped sediment
– Found in rocks 3.5 billion years old or younger
– Comparisons of ancient and modern
stromatolites
• Anoxygenic phototrophic filamentous bacteria
formed ancient stromatolites
• Oxygenic phototrophic cyanobacteria dominate
modern stromatolites
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Figure 16.1
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16.2 Origin of Cellular Life
• Early Earth was anoxic and much hotter than
present day
• First biochemical compounds were made by
abiotic systems that set the stage for the
origin of life
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16.2 Origin of Cellular Life
• Surface origin hypothesis
– The first membrane-enclosed, self-replicating
cells arose out of primordial soup rich in
organic and inorganic compounds in ponds on
Earth’s surface
– Dramatic temperature fluctuations and mixing
from meteor impacts, dust clouds, and storms
argue against this hypothesis
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16.2 Origin of Cellular Life
• Subsurface origin hypothesis (Figure 16.4)
– Life originated at hydrothermal springs on ocean
floor
• Conditions would have been more stable
• Steady and abundant supply of energy (e.g., H2
and H2S) may have been available at these sites
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Figure 16.4
Evolutionary
events
Early
Bacteria
Early
Archaea
(0.3 to 0.5 billion years)
Time
Dispersal to
other habitats
Diversification
of molecular
biology, lipids,
and cell wall
structure
LUCA
Mound:
precipitates of clay,
metal sulfides, silica,
and carbonates
DNA
Ocean water
RNA and
proteins
(20°C, containing
metals, CO2 and
PO42)
RNA life
Flow of substances
up through mound
Prebiotic
chemistry
Amino
acids
Nitrogen
bases
Sugars
Ocean crust
Nutrients in hot
hydrothermal water
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16.2 Origin of Cellular Life
• Prebiotic chemistry of early Earth set stage for
self-replicating systems
• First self-replicating systems may have been
RNA-based (RNA world theory)
– RNA can bind small molecules (e.g., ATP,
other nucleotides)
– RNA has catalytic activity; may have catalyzed
its own synthesis
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16.2 Origin of Cellular Life
• DNA, a more stable molecule, eventually
became the genetic repository
• Three-part systems (DNA, RNA, and protein)
evolved and became universal among cells
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16.2 Origin of Cellular Life
• Other Important Steps in Emergence of
Cellular Life
– Buildup of lipids
– Synthesis of phospholipid membrane vesicles
that enclosed the cell’s biochemical and
replication machinery
• May have been similar to montmorillonite clay
vesicles
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Figure 16.5
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16.2 Origin of Cellular Life
• Last universal common ancestor (LUCA)
– Population of early cells from which cellular
life may have diverged into ancestors of
modern-day Bacteria and Archaea
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16.2 Origin of Cellular Life
• As early Earth was anoxic, energy-generating
metabolism of primitive cells was exclusively
anaerobic and likely chemolithotrophic
(autotrophic; Figure 16.6)
– Obtained carbon from CO2
– Obtained energy from H2; likely generated by
H2S reacting with H2S or UV light (Figure 16.7)
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Figure 16.7
Alternative source of H2
Primitive
ATPase
Primitive
hydrogenase
Cytoplasmic
membrane
S0 reductase
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Out
In
16.3 Microbial Diversification
• ~2.7 billion years ago, cyanobacteria developed
a photosystem that could use H2O instead of
H2S, generating O2
• By 2.4 billion years ago, O2 concentrations raised
to 1 part per million; initiation of the Great
Oxidation Event
• O2 could not accumulate until it reacted with
abundant reduced materials in the oceans (e.g.,
FeS, FeS2)
– Banded iron formations: laminated sedimentary
rocks; prominent feature in geological record
(Figure 16.8)
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16.3 Microbial Diversification
• Consequence of O2 for the evolution of life
– Formation of ozone layer that provides a
barrier against UV radiation
• Without this ozone shield, life would only have
continued beneath ocean surface and in
protected terrestrial environments
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16.3 Microbial Diversification
• Molecular evidence suggests ancestors of
Bacteria and Archaea diverged ~4 billion
years ago
• As lineages diverged, distinct metabolisms
developed
• Development of oxygenic photosynthesis
dramatically changed course of evolution
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16.4 Endosymbiotic Origin of Eukaryotes
• Endosymbiosis
– Well-supported hypothesis for origin of
eukaryotic cells
– Contends that mitochondria and chloroplasts
arose from symbiotic association of
prokaryotes within another type of cell
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16.5 The Evolutionary Process
• Mutations
– Changes in the nucleotide sequence of an
organism’s genome
– Occur because of errors in replication, UV
radiation, and other factors
– Adaptative mutations improve fitness of an
organism, increasing its survival
• Other genetic changes include gene duplication,
horizontal gene transfer, and gene loss
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16.6 Evolutionary Analysis: Theoretical
Aspects
• Phylogeny
– Evolutionary history of a group of organisms
– Inferred indirectly from nucleotide sequence data
• Molecular clocks (chronometers)
– Certain genes and proteins that are measures of
evolutionary change
– Major assumptions of this approach are that
nucleotide changes occur at a constant rate, are
generally neutral, and are random
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16.6 Evolutionary Analysis: Theoretical
Aspects
• The most widely used molecular clocks are small
subunit ribosomal RNA (SSU rRNA) genes
– Found in all domains of life
• 16S rRNA in prokaryotes and 18S rRNA in
eukaryotes
– Functionally constant
– Sufficiently conserved (change slowly)
– Sufficient length
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Figure 16.11
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16.6 Evolutionary Analysis: Theoretical
Aspects
• Carl Woese
– Pioneered the use of SSU rRNA for phylogenetic
studies in 1970s
– Established the presence of three domains of life:
• Bacteria, Archaea, and Eukarya
– Provided a unified phylogenetic framework for
Bacteria
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16.6 Evolutionary Analysis: Theoretical
Aspects
• The Ribosomal Database Project (RDP)
– A large collection of rRNA sequences
• Currently contains >409,000 sequences
– Provides a variety of analytical programs
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16.7 Evolutionary Analysis: Analytical
Methods
• Comparative rRNA sequencing is a routine
procedure that involves the following
(Figure 16.12):
– Amplification of the gene encoding SSU rRNA
– Sequencing of the amplified gene
– Analysis of sequence in reference to other
sequences
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Figure 16.12
Isolate DNA
16 S gene
Amplify 16S
gene by PCR
Run on agarose
gel; check for
correct size
Kilobases 1
3.0–
2
3
4
5
2.0–
1.5–
1.0–
0.5–
Sequence
A C G G T
Align sequences;
generate tree
Ancestral
cell
Distinct
species
Distinct
species
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Figure 16.16
PROKARYOTES
EUKARYOTES
Archaea
Bacteria
Eukarya
Animals
Entamoebae
Green nonsulfur
bacteria
Euryarchaeota
Methanosarcina
Mitochondrion
Proteobacteria
Chloroplast
Grampositive
bacteria
Methano-
Crenarchaeota bacterium
Thermoproteus
Pyrodictium
Fungi
Extreme
halophiles
Plants
Ciliates
Thermoplasma
Thermococcus
Cyanobacteria
Flavobacteria
Methanococcus
Slime
molds
Marine
Crenarchaeota
Pyrolobus
Flagellates
Methanopyrus
Trichomonads
Thermotoga
Thermodesulfobacterium
Microsporidia
Aquifex
LUCA
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Diplomonads
(Giardia)
16.8 Microbial Phylogeny
• Domain Bacteria
– Contains at least 80 major evolutionary groups
(phyla)
– Many groups defined from environmental
sequences alone—i.e., there are no cultured
representatives
– Many groups are phenotypically diverse—i.e.,
physiology and phylogeny not necessarily
linked
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16.8 Microbial Phylogeny
• Eukaryotic organelles originated within Bacteria
– Mitochondria arose from Proteobacteria
– Chloroplasts arose from the cyanobacteria
• Domain Archaea consists of two major groups:
– Crenarchaeota
– Euryarchaeota
• Each of the three domains of life can be
characterized by various phenotypic properties
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16.10 Phenotypic Analysis
• Bacterial taxonomy incorporates multiple
methods for identification and description of
new species
• The polyphasic approach to taxonomy uses
three methods:
1. Phenotypic analysis
2. Genotypic analysis
3. Phylogenetic analysis
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16.10 Phenotypic Analysis
• Phenotypic analysis examines the
morphological, metabolic, physiological, and
chemical characters of the cell
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16.11 Genotypic Analysis
• Several methods of genotypic analysis are
available:
–
–
–
–
DNA–DNA hybridization
DNA profiling
Multilocus sequence typing (MLST)
GC ratio
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16.11 Genotypic Analysis
• DNA–DNA hybridization
– Genomes of two organisms are hybridized to
examine proportion of similarities in their gene
sequences (Figure 16.20)
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Figure 16.20
Organisms to Organism 1
be compared:
Organism 2
Genomic DNA
Genomic DNA
DNA
Shear and label (– P )
preparation
Shear DNA
Heat to
form
single
strands
Hybridization
experiment: Mix DNA, adding unlabeled DNA in excess:
11
Hybridized DNA
12
Hybridized DNA
Results and
interpretation:
Same
species
100
75
Same genus,
but different Different
genera
species
50
25
Percent hybridization
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0
11
12
100%
25%
Same strain
(control)
1 and 2 are likely
different genera
16.11 Genotypic Analysis
• DNA–DNA hybridization
– Provides rough index of similarity between two
organisms
– Useful complement to SSU rRNA gene
sequencing
– Useful for differentiating very similar organisms
– Hybridization values of 70% or higher suggest
strains belong to the same species
• Values of at least 25% suggest same genus
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16.11 Genotypic Analysis
• Multilocus sequence typing (MLST)
– Method in which several different
“housekeeping genes” from an organism are
sequenced (Figure 16.22)
– Has sufficient resolving power to distinguish
between very closely related strains
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Figure 16.22
Linkage Distance
Allele analysis
New isolate or
clinical sample
Isolate DNA
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Amplify 6–7
target genes
Sequence
Compare with
other strains
and generate
tree
0.6
0.4
0.2
0
Strains
1–5
New strain
Strain 6
Strain 7
16.11 Genotypic Analysis
• GC ratios
– Percentage of guanine plus cytosine in an
organism’s genomic DNA
– Vary from 20 to 80% among Bacteria and
Archaea
– Generally accepted that if GC ratios of two
strains differ by ~5% they are unlikely to be
closely related
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16.12 The Species Concept in
Microbiology
• No universally accepted concept of species for
prokaryotes
• Current definition of prokaryotic species
– Collection of strains sharing a high degree of
similarity in several independent traits
• Most important traits include 70% or greater
DNA–DNA hybridization and 97% or greater
16S rRNA gene sequence identity
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16.12 The Species Concept in
Microbiology
• Biological species concept not meaningful as
prokayotes are haploid and do not undergo
sexual reproduction
• Genealogical species concept is an alternative
– Prokaryotic species is a group of strains that,
based on DNA sequences of multiple genes,
cluster closely with others phylogenetically and
are distinct from other groups of strains
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16.12 The Species Concept in
Microbiology
• Phylogenetic analysis
– 16S rRNA gene sequences are useful in
taxonomy; serve as “gold standard” for the
identification and description of new species
• Proposed that a bacterium should be
considered a new species if its 16S rRNA gene
sequence differs by more than 3% from any
named strain, and a new genus if it differs by
more than 5%
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16.12 The Species Concept in
Microbiology
• Phylogenetic analysis (cont’d)
– The lack of divergence of the 16S rRNA gene
limits its effectiveness in discriminating between
bacteria at the species level; thus, a multigene
approach can be used
– Multigene sequence analysis is similar to MLST,
but uses complete sequences and comparisons
are made using cladistic methods (Figure 16.24)
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Figure 16.24
Multigene Tree
16S rRNA Gene Tree
Photobacterium damselae
50 changes
Photobacterium leiognathi
Photobacterium mandapamensis
FS-2.1
FS-4.2
FS-3.1
FS-5.1
FS-2.2
Photobacterium
phosphoreum
ATCC 11040T
FS-5.2
Photobacterium angustum
Photobacterium phosphoreum
Photobacterium iliopiscarium
ATCC 51761
NCIMB 13476
NCIMB 13478
NCIMB 13481
Photobacterium
iliopiscarium
ATCC 51760T
Photobacterium kishitanii
chubb.1.1
ckamo.3.1
canat.1.2
hstri.1.1
calba.1.1
BAA-1194T
apros.2.1
ckamo.1.1
vlong.3.1
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Photobacterium
kishitanii
16.12 The Species Concept in
Microbiology
• Phylogenetic analysis (cont’d)
• Whole-genome sequence analyses are
becoming more common
– Genome structure: size and number of
chromosomes, GC ratio, etc.
– Gene content
– Gene order
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16.12 The Species Concept in
Microbiology
• This model is based solely on the assumption
of vertical gene flow
• New genetic capabilities can also arise by
horizontal gene transfer; the extent among
bacteria is variable
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16.12 The Species Concept in
Microbiology
• No firm estimate on the number of prokaryotic
species
• Nearly 7,000 species of Bacteria and Archaea
are presently known
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16.13 Classification and Nomenclature
• Classification
– Organization of organisms into progressively
more inclusive groups on the basis of either
phenotypic similarity or evolutionary
relationship
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16.13 Classification and Nomenclature
• Prokaryotes are given descriptive genus
names and species epithets following the
binomial system of nomenclature used
throughout biology
• Assignment of names for species and higher
groups of prokaryotes is regulated by the
International Code of Nomenclature of
Bacteria
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