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CHAPTER 28
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Prokaryotes
Chapter 28
The First Cells
• Microfossils are fossilized forms of
microscopic life
– Oldest are 3.5 billion years old
– Seem to resemble present-day prokaryotes
3
• Stromatolites
are mats of
cyanobacterial
cells that trap
mineral deposits
– Oldest are 2.7
billion years old
– Modern forms
are also known
4
• Living things are selective in the carbon
isotopes used
– Living things incorporate carbon-12
– Higher level of carbon-12 than nonliving
things
• Isotopic analysis of carbon-12 in fossils
suggests that carbon fixation was active
as much as 3.8 BYA
5
• Biomarkers
– Organic molecules of biological origin
– Proven difficult to find
– Hydrocarbons derived from fatty acid tails of
lipids were found in ancient rocks
• Indicates that cyanobacteria are at least 2.7 billion
years old
– Possible origin of life pushed back beyond 3.5
BYA
6
Prokaryotic Diversity
• Oldest, structurally simplest, and most
abundant forms of life
• Abundant for over a billion years before
eukaryotes
• Less than 10% of species are known
• Fall into 2 domains
– Bacteria (also called Eubacteria)
– Archaea (formerly called Archaebacteria)
• Many archaeans are extremophiles
7
• Unicellularity
– Most are single-celled
– Amy stick together to form associations
– Some can form complex biofilms
• Cell size
– Size varies tremendously
– Most are less than 1 mm in diameter
• Chromosome
– Single circular double-stranded DNA
– Found in the nucleoid region of cell
– Often have plasmids
• Cell division
– Most divide by binary fission
8
• Genetic recombination
– Occurs through horizontal gene transfer
– NOT a form of reproduction
• Internal compartmentalization
– No membrane-bounded organelles
– No internal compartment
– Ribosomes differ from eukaryotic form
• Flagella
– Simple in structure
– Different from eukaryotic flagella
• Metabolic diversity
– Oxygenic and anoxygenic photosynthesis
– Chemolithotrophic
9
Bacteria vs. Archaea
• Plasma membrane
– All prokaryotes have a plasma membrane
– Bacterial lipids are unbranched
• Use ester bonds
– Archaean membranes are formed on glycerol
skeleton with ether linkages (not ester)
• Hydrocarbons may be branched or have rings
• Tetraether polymer allows extremophiles to
withstand high temperatures
10
11
• Cell wall
– All prokaryotes have cell walls
– Bacteria have peptidoglycan
– Archaea lack peptidoglycan
• DNA replication
– Both have single replication origin
– Archaeal DNA replication is more similar to
that of eukaryotes
• Gene Expression
– Archaeal transcription and translation are
more similar to those of eukaryotes
12
Early Classification
Characteristics
• Relied on staining characteristics and
observable phenotypes
1. Photosynthetic or nonphotosynthetic
2. Motile or nonmotile
3. Unicellular, colony-forming, or
filamentous
4. Formation of spores or division by
transverse binary fission
5. Importance as human pathogens or not
13
Molecular Classification
1. Amino acid sequences of key proteins
2. Percent guanine–cytosine content
3. Nucleic acid hybridization
– Closely related species will have more base
pairing
4. Gene and RNA sequencing
– Especially rRNA
5. Whole-genome sequencing
14
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Domain
Bacteria
Domain
Archaea
Domain
Eukarya
Common ancestor
15
• Based on these molecular data, several
prokaryotic groupings have been proposed
• Bergey’s Manual of Systematic
Bacteriology, 2nd edition
– 3 of 5 volumes completed
• Large scale sequencing of random
samples indicates vast majority of bacteria
have never been cultured or studied in
detail
16
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Euryarchaeota
Aquificae
Bacilli
Actinobacteria
Spirochaetes
1 µm
1.37 µm
Archaea differ greatly
from bacteria.
Although both are
prokaryotes, archaeal
cell walls lack
peptidoglycan; plasma
membranes are made
of different kinds of
lipids than bacterial
plasma membranes;
RNA and ribosomal
proteins are more like
eukaryotes than
bacteria. Mostly
anaerobic. Examples
include Methanococcus,
Thermoproteus,
Halobacterium.
The Aquificae
represent the deepest
or oldest branch of
bacteria. Aquifex
pyrophilus is a rodshaped hyperthermophile with a
temperature optimum
at 85°C; a chemoautotroph, it oxidizes
hydrogen or sulfur.
Several other related
phyla are also
thermophiles.
23.80 µm
Gram-positive
bacteria. Largely solitary;
many form endospores.
Responsible for many
significant human
diseases, including
anthrax (Bacillus
anthracis); botulism
(Clostridium botulinum);
and other common
diseases
(staphylococcus,
streptococcus).
22.15 µm
Some gram-positive
bacteria form
branching filaments
and some produce
spores; often mistaken
for fungi. Produce
many commonly used
antibiotics, including
streptomycin and
tetracycline. One of
the most common types
of soil bacteria; also
common in dental
plaque. Streptomyces,
Actinomyces.
Thermophiles
Crenarchaeota
Euryarchaeota
Aquificae
Thermotogae
Chloroflexi
Gram-positive bacteria
DeinococcusThermus
Low G/C (Firmicutes)
Bacilli
Archaea
25.96 µm
Long, coil-shaped
cells that stain gramnegative. Common in
aquatic
environments.
Rotation of internal
filaments produces a
corkscrew
movement. Some
spirochetes such as
Treponema pallidum
(syphilis) and
Borrelia burgdorferi
(Lyme disease) are
significant human
pathogens.
Clostridium
High G/C
Actinobacteria
Bacteria
17
a: © SPL/Photo Researchers, Inc.; b; © Dr. R. Rachel and Prof. Dr. K. O. Stetten, University of Regensburg, Lehrstuhl fuer Mikrobiologie, Regensburg, Germany;
c: © Andrew Syred/SPL/Photo Researchers, Inc.; d: © Microfi ield Scientifi c Ltd/SPL/Photo Researchers, Inc.; e: © Alfred Paseika/SPL/Photo Researchers, Inc.
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Cyanobacteria
Beta
Gamma
Delta
25.04 µm
10.57 µm
Cyanobacteria are a
form of photosynthetic
bacterium common in
both marine and
freshwater environments. Deeply
pigmented; often
responsible for “blooms”
in polluted waters.
Both colonial and
solitary forms are
common. Some
filamentous forms have
cells specialized for
nitrogen fixation.
A nutritionally diverse
group that includes
soil bacteria like the
lithotroph
Nitrosomonas that
recycle nitrogen
within ecosystems by
oxidizing the
ammonium ion
(NH4+). Other members
are heterotrophs and
photoheterotrophs.
Gammas are a
diverse group including
photosynthetic sulfur
bacteria, pathogens,
like Legionella, and
the enteric bacteria
that inhabit animal
intestines. Enterics
include Escherichia
coli, Salmonella (food
poisoning), and
Vibrio cholerae
(cholera).
Pseudomonas are a
common form of soil
bacteria, responsible
for many plant
diseases, and are
important opportunistic
pathogens.
Photosynthetic
Spirochaetes
Cyanobacteria
Chlorobi
750 µm
The cells of
myxobacteria exhibit
gliding motility by
secreting slimy
polysaccharides over
which masses of cells
glide; when the soil
dries out, cells
aggregate to form
upright multicellular
colonies called
fruiting bodies. Other
delta bacteria are
solitary predators that
attack other bacteria
(Bdellovibrio) and
bacteria used in
bioremediation
(Geobacter).
Proteobacteria
Beta
Gamma
Alpha–
Rickettsia
Epsilon–
Helicobacter
Delta
18
f: © Dr. Robert Calentine/Visuals Unlimited; g: © Science VU/S. Watson/Visuals Unlimited; h: © Dennis Kunkel Microscopy, Inc.;
i: © Prof. Dr. Hans Reichenbach, Helmholtz Centre for Infection Research, Braunschweig
Prokaryotic Cell Structure
• 3 basic shapes
– Bacillus – Rod-shaped
– Coccus – Spherical
– Spirillum – Helical-shaped
19
• Cell wall
– Peptidoglycan forms a rigid network
• Maintains shape
• Withstands hypotonic environments
• Archaea have a similar molecule
– Gram stain
• Gram-positive bacteria have a thicker
peptidoglycan wall and stain a purple color
• Gram-negative bacteria contain less peptidoglycan
and do not retain the purple-colored dye – retain
counterstain and look pink
20
21
• Gram positive bacteria
– Thick, complex network of peptidoglycan
– Also contains lipoteichoic and teichoic acid
• Gram negative bacteria
– Thin layer of peptidoglycan
– Second outer membrane with lipopolysaccharide
– Resistant to many antibiotics
22
• S-layer
– Rigid paracrystalline layer found in some
bacteria and archaea
– Outside of peptidoglycan or outer membrane
layers in gram-negative and gram-positive
bacteria
– Diverse functions – often involves adhesion
• Capsule
– Gelatinous layer found in some bacteria
– Aids in attachment
– Protects from the immune system
23
• Flagella
– Slender, rigid, helical structures
– Composed of the protein flagellin
– Involved in locomotion – spins like propeller
• Pili
– Short, hairlike structures
– Found in gram-negative bacteria
– Aid in attachment and conjugation
24
25
• Endospores
– Develop a thick wall around their genome and
a small portion of the cytoplasm
– When exposed to environmental stress
– Highly resistant to environmental stress
• Especially heat
– When conditions improve can germinate and
return to normal cell division
– Bacteria causing tetanus, botulism, and
anthrax
26
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a.
0.47µm
b.
0.86µm
a: © Science VU/S. W. Watson/Visuals Unlimited; b: © Norma J. Lang/Biological Photo Service
• Internal membrane
– Invaginated regions of plasma membrane
– Function in respiration or photosynthesis
27
• Nucleoid region
– Contains the single, circular chromosome
– May also contain plasmids
• Ribosomes
– Smaller than those of eukaryotes
– Differ in protein and RNA content
– Targeted by some antibiotics
28
Prokaryotic Genetics
• Prokaryotes do not reproduce sexually
• 3 types of horizontal gene transfer
– Conjugation – cell-to-cell contact
– Transduction – by bacteriophages
– Transformation – from the environment
• All 3 processes also observed in archaea
29
Conjugation
• Plasmids may encode
advantageous info
– Are not required for normal
function
• In E. coli, conjugation is
based on the presence of
the F plasmid (fertility
factor)
– F+ cells contain the plasmid
– F- cells do not
30
cell produces F pilus that connects it to F cell
•
• Transfer of F plasmid occurs through
conjugation bridge
• F plasmid copied through rolling circle
replication
• The end result is two F+ cells
F+
31
• The F plasmid can integrate into the bacterial
chromosome
– Events similar to crossing over in eukaryotes
– Homologous recombination
• Hfr cell (high frequency of recombination)
– F plasmid integrated into chromosome
– Replicated every time host divides
• The F plasmid can also excise itself by reversing
the integration process
– An inaccurate excision may occur picking up some
chromosomal DNA – F′ plasmid
32
33
Transduction
• Generalized transduction
– Virtually any gene can be transferred
– Occurs via accidents in the lytic cycle
– Viruses package bacterial DNA and transfer it
in a subsequent infection
• Specialized transduction
– Occurs via accidents in the lysogenic cycle
– Imprecise excision of prophage DNA
– Only a few host genes can be transferred
34
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Infection with Phage
Phage adheres to cell.
Phage DNA is injected in to cell. Phage DNA is replicated and
host DNA is degraded.
Phage particles are packaged
with DNA and are released.
Infection with Transducing Phage
Cell contains DNA from donor.
DNA is incorporated by
homologous recombination.
Phage injects a piece of
chromosomal DNA.
Transducing phage
adheres to cell.
35
Transformation
• Natural transformation
– Occurs in many bacterial species, including
Streptococcus which was studied by Griffith
– DNA that is released from a dead cell is
picked up by another live cell
– Encoded by bacterial chromosome
• Not an accident of plasmid or phage biology
36
• Artificial transformation
– Some species do not naturally undergo
transformation
– Accomplished in the lab
– Used to transform E. coli for molecular cloning
37
• R (resistance) plasmids
– Encode antibiotic resistance genes
– Acquire genes through transposable elements
– Important factor in appearance of antibiotic
resistant strains of Staphylococcus aureus
• Virulence plasmids or transduction
– Encode genes for pathogenic traits
– Enterobacteriaceae
– E. coli O157:H7 strain
38
• Mutations can arise spontaneously in
bacteria as with any organism
– Radiation and chemicals increase likelihood
• Auxotrophs are nutritional mutants
– Studied using replica plating
• Mutations (and plasmids) can spread
rapidly in a population
– Methicilin-resistant Staphylococcus aureus
(MRSA)
– Vancomycin-resistant Staphylococcus aureus
(VRSA)
39
Prokaryotic Metabolism
• Acquisition of Carbon
– Autotrophs – from inorganic CO2
• Photoautotrophs – energy from Sun
• Chemolithoautotrophs – energy from oxidizing
inorganic substances
– Heterotrophs – from organic molecules
• Photoheterotrophs – light as energy source but
obtain organic carbon made by other organisms
• Chemoheterotroph – both carbon atoms and
energy from organic molecules
– Humans are also an example
40
• Type III secretion system
– Found in many gram-negative bacteria
– Molecular syringe to inject virulence proteins
into host cell cytoplasm
– Yersinia pestis (bubonic plague), Salmonella,
Shigella
41
Human Bacterial Disease
• In the early 20th century, infectious
diseases killed 20% of children before the
age of five
– Sanitation and antibiotics considerably
improved the situation
• In recent years, however, many bacterial
diseases have appeared and reappeared
42
Tuberculosis (TB)
•
•
•
•
•
Scourge for thousands of years
Mycobacterium tuberculosis
Afflicts the respiratory system
Thwarts immune system
Easily transferred from person to person
through the air
• Mutidrug-resistant (MDR) strains are very
alarming
43
• Dental caries (tooth decay)
– Plaque consists of bacterial biofilms
– Streptococcus sobrinus ferments sugar to
lactic acid
– Tooth enamel degenerates
• Peptic ulcers
– Helicobacter pylori is the main cause
– Treated with antibiotics
44
Sexually transmitted diseases (STDs)
• Gonorrhea
– One of the most prevalent communicable
diseases in North America.
– Neisseria gonorrhoeae
– Transmitted through exchange of body fluids
– Can pass from mom to baby via birth canal
• Chlamydia
– Chlamydia trachomatis
– “Silent STD” – incidence has skyrocketed
– Can cause PID and heart disease
45
• Syphilis
– Treponema pallidum
– Transmitted through sex or contact with open
chancre
– Can pass from mom to baby via birth canal
– Four distinct stages
• Primary – Chancre – highly infectious
• Secondary – Rash – infectious
• Tertiary – Latency – no longer infectious but
attacking internal organs
• Quaternary – Damage now evident
46
47
Beneficial Prokaryotes
• Decomposers release a dead organism’s
atoms to the environment
• Fixation
– Photosynthesizers fix carbon into sugars
• Ancient cyanobacteria added oxygen to air
– Nitrogen fixers reduce N2 to NH3 (ammonia)
• Anabaena in aquatic environments
• Rhizobium in soil
48
• Symbiosis refers to the ecological
relationship between different species that
live in direct contact with each other
– Mutualism – both parties benefit
• Nitrogen-fixing bacteria on plant roots
• Cellulase-producing bacteria in animals
– Commensalism – one organism benefits and
the other is unaffected
– Parasitism – one organism benefits and the
other is harmed
49
• Bacteria are used in genetic engineering
– “Biofactories” that produce various chemicals,
including insulin and antibiotics
• Bacteria are used for bioremediation
– Remove pollutants from water, air, and soil
– Biostimulation – adds nutrients to encourage
growth of naturally occurring microbes
• Exxon Valdez oil spill
50