Download Lecture 02, origins and prokaryotes - Cal State LA

Classifying Life: Old Scheme
Whittaker’s “5 Kingdom” system
Kingdom
Monera
(all prokaryotes)
Kingdom
Protista
Kingdom
Fungi
Kingdom
Plantae
emphasized difference between
prokaryotes (bacteria) and
eukaryotes (cells with nuclei)
all eukaryotes that weren’t
plants, fungi or animals got
lumped into the catch-all group
“protists”
Kingdom
Animalia
the Tree of Life has 3 domains
BACTERIA
ARCHAEA
This classification
scheme emphasizes
differences between
3 main groups, based on
their phylogeny –
EUKARYA
2 domains of prokaryotes
Archaea
- also called “extreme-ophiles,” lovers of extreme conditions
- have chemically distinct plasma membranes
- have ribosomes similar to ours
Bacteria
- oldest fossils (3.4 billion yr) = bacteria
- live in more O2 -rich, “normal”
environments
- cell walls contain a unique material,
peptidoglycan
- include many disease-causing
pathogens
Bacteria on the head of a pin
Prokaryote Characteristics
Small cells, typically 1-5 mm
- more bacteria live in your
gut than the # of cells in
your whole body
see page 567 in text for
a full comparison of the
3 domains of life
protein
.
Campbell & Reece 2002
Prokaryote Characteristics
No organelles inside cell, no nucleus; move with tail-like flagellum
Circular chromosome with fewer genes than eukaryotes
(3,200 genes in E. coli, versus ~35,000 in humans)
Small circles of DNA termed plasmids, encoding antibiotic resistance
Cell
Prokaryote Reproduction
Asexual reproduction makes 2 exact copies (clones) of original cell
- bacteria can divide every 20 min to 3 hr
Genetic diversity is promoted by several mechanisms:
a) trading plasmids among cells (temporary)
b) exchanging portions of the chromosome during conjugation,
when DNA is sent down a hollow
tube (pilus) connecting 2 cells
 followed by recombination,
the permanent movement of genes
onto a new chromosome
sex pilus
Why care about prokaryotes?
They are highly abundant in number, and live everywhere
- half of all carbon and 90% of nitrogen + phosphorus
found in life is contained in prokaryotes
They have amazingly diverse metabolisms
- bacteria catalyze chemical transformations that affect our
atmosphere and global carbon and nitrogen cycles,
which in turn affect all life
Some bacteria are pathogens that can make people sick
Understanding Metabolism
Life is all about getting energy in some form from your environment,
and transforming it into another form your cells can use
In chemical systems, energy is stored in bonds between hydrogen
and other elements (holding hydrogens means you’re reduced)
Energy can be released by getting H and its electrons off, handing
them to some acceptor like oxygen (O2) which is electron-hungry
- donor loses its electrons  gets oxidized
2 H2O
electron donor,
gets oxidized
light
4 H· + O2
2 H2O
light energy gets
stored in ATP by
cellular enzymes
Understanding Metabolism
Photosynthesis:
light
CO2 + H2O
CH2O + O2
ripping H’s and their
electrons away from oxygen
is super hard; requires
energy from light
[1] CO2 is reduced to sugar, which has energy stored in it for later
[2] the gas CO2 has been fixed, meaning converted to a larger
solid molecule (out of thin air!) used for building cell walls
[3] the gas O2 is released as a waste product
Understanding Metabolism
Respiration:
CO2 + H2O
CH2O + O2
ripping H’s and their electrons away
from carbon just requires oxygen –
and the right cellular machinery to
achieve a controlled burn !
[1] sugar is oxidized to release its stored energy
[2] the gas CO2 is released into the atmosphere
Metabolic diversity - Prokaryotes
Carbon source (building blocks)
Energy
source
Autotrophy
fix CO2  -C-C-C-
Heterotrophy
eat things for -C-C-C-
light + H2O
cyanobacteria
Heliobacter
organic
molecules
(sugar)
Clostridium
reduced
inorganic
molecules
(CH4,H2S
Nitrosomonas
E. coli
Beggiatoa
Metabolic diversity - Eukaryotes
Carbon source (building blocks)
Autotrophy
fix CO2  -C-C-C-
Heterotrophy
eat things for -C-C-C-
protists, plants
light + H2O (photosynthesis)
Energy
source
organic
molecules
(sugar)
reduced
inorganic
molecules
(CH4,H2S
protists, animals, fungi
(respiration)
Chemo- versus photo-autotrophy
light
Cyanobacteria
CO2 + H2O
CH2O + O2
Sulfur bacteria
CO2 + H2S
CH2O + S2
Photo-autotrophy:
general formula
for sugar
Light is used to “pump up” low energy electrons from water or
hydrogen sulfide, rip them off, then jam them onto carbon
Chemo- versus photo-autotrophy
light
Cyanobacteria
CO2 + H2O
CH2O + O2
Sulfur bacteria
CO2 + H2S
CH2O + S2
Chemo-autotrophy:
Requires reduced inorganic compounds, which are normally absent
in oxygen-rich environments (why?...)
Electrons in the H-S bond require less energy to remove
Produces a different waste product
Global nutrient cycles
Because bacterial metabolisms are so diverse, almost any
compound can act as fuel or food for some prokaryote
- accounts for their ecological diversity....
One species’ waste product can be the (a) energy source,
or (b) electron acceptor, for another species
[1] Critical for cycling nutrients through different molecular forms
Denitrification
by bacteria +
archaea
Nitrification
by bacteria
Fixation by bacteria + archaea
Decomposition
by bacteria,
archaea, fungi
Nitrification
by bacteria
Microbial Ecosystems
One species’ waste product can be the (a) energy source,
or (b) electron acceptor, for another species
[2] “food chain” of species can co-exist by not competing for same
resources (i.e., not using the same molecule as food)
Different photo-autotrophs even catch different wavelengths of light
so they are not in competition
Important principle of ecology: species in direct competition
cannot co-exist for long, because one will out-compete the other
Microbial Ecosystems
To think about when setting up your Winogradsky columns in lab:
- What compounds are fuel (electron donors) and which ones
act as electron acceptors, becoming waste products?
- How do multiple bacterial species co-exist? What resources
does each use?
Domain Archaea
Genetically, closer to eukaryotes than Domain Bacteria is
“Extremophiles” live in environments that are inhospitable to most life
May yield clues to early life on earth, or life on other planets (?)
Halophiles – common in extremely salty environments
(e.g deserts, hot springs)
Thermophiles – Occur in very hot environments (some >100ºC)
(e.g. hot springs, undersea vents)
Anaerobes – occur in environments lacking oxygen
(e.g. methanogens in the termite hindgut, cow gut)
Thermophiles color the surface of this Nevada desert hot spring
Campbell & Reece 2005
Pyrococcus furiosus, source of polymerase used in PCR
Halophiles color the water of salt evaporation ponds in San Francisco Bay
Campbell & Reece 2005
Anaerobes – live in anaerobic (= anoxic, lacking oxygen) environments
(cow gut, termite hindgut)
some Archaea can use odd
chemicals like hydrogen gas
as fuel
electrons are transferred to
oxygen, releasing energy
produces methane, a potent
greenhouse gas
methane
4 H2 + CO2
oxidized
carbon
CH4 + 2 H2O
reduced
carbon
Not so extreme?..
in the ’90s, we discovered that tiny Archaea are very abundant
throughout the world’s oceans (100,000 cells per mL of seawater)
Comprised a third of the bacterio-plankton in the Antarctic
- constitute a huge fraction of the biomass in the cold, deep
waters of world’s oceans
- many cannot be grown in the lab, and are known only from
environmental DNA sequences
DeLong et al., 1994, High abundance of
Archaea in Antarctic marine picoplankton.
Nature 371:695-7
Prokaryote Phylogeny
last common
ancestor of all
members of
Domain Bacteria
All proteobacteria are
related to each other
(they all shared one
common ancestor)
Most bacterial phylogenies (= family trees) are based on comparing
the DNA base sequence of a ribosomal RNA gene called 16S
-
Domain Bacteria
Tend to grow in aerobic (oxygen-containing), less extreme environments
Cells surrounded by a cell wall made of material called peptidoglycan,
a mixture of peptides (short chains of amino acids) and sugars all
cross-linked together to make strong sheets
Have structurally distinct ribosomes, complexes of protein and RNA
that carry out protein synthesis in the cell
Have special enzymes to deal with copying the DNA of their
circular chromosomes
Antibiotic Targets
Antibiotics target these differences between our eukaryotic cells,
and the prokaryotic cells of pathogenic bacteria, to block...
(1) Cell wall biosynthesis – penicillin, vancomycin
- block synthesis of peptidoglycan cell wall, without which
cells pop when saltiness of surrounding fluid changes
(2) Protein synthesis – erythromycin, tetracycline, streptomycin
- jam the bacterial ribosome
(3) DNA replication – Cipro
- inhibit enzyme that uncoils DNA after replication of the
circular bacterial chromosome
-
Bacterial cell wall composition
Gram-positive
- no membrane covering
peptidoglycan wall
cell
wall
plasma membrane
Gram-negative
- outer membrane covers
peptidoglycan wall
cell
wall
plasma membrane
Cells stained with purple dye, washed, then stained with red dye
- the peptidoglycan wall traps the purple dye in Gram-positives
- the outer membrane repels the purple dye, but gets stained red
Gram-positive
- no membrane covering
peptidoglycan wall
cell
wall
plasma membrane
Gram-negative
- outer membrane covers
peptidoglycan wall
cell
wall
plasma membrane
Two Gram-positive groups
Actinobacteria
- many chain-forming soil bacteria
- soil bacterium Streptomyces is
source of 500 antibiotics
- a few pathogens: tuberculosis, leprosy
Firmicutes
- many dangerous pathogens, some of which form resting spores
Bacillus anthracis (anthrax)
Clostridium botulinum (botulism)
Staphylococcus sp. (staph)
Streptococcus sp. (strep)
Antibiotic Resistance
INTRODUCTION
1943
APPEARANCE
OF RESISTANCE
1946
Streptomycin
1945
1959
Tetracycline
1948
1953
Erythromycin
1952
1988
Vancomycin
1956
1988
Methicillin
1960
1961
Ampicillin
1961
1973
Cephalosporins
1964
late 1960’s
DRUG
Penicillin
Antibiotic Resistance
Antibiotics were introduced as therapeutic agents against bacterial
disease starting in 1943
- Major classes of antibiotics attained widespread use by 1960’s
Infectious bacteria still a major health concern, especially in hospitals
- Post-operation infections by Staphylococcus aureus remain a
critical problem for surgery patients
In 1952, most Staph infections succumbed to penicillin
- By late 1960’s, Staph was resistant; next treated with methicillin
- By 1980’s, methicillin-resistance was widespread
- In 1990’s, vancomycin became “drug of last resort”
- vancomycin resistance is common in bacteria other than Staph…
and resistant Staph reported in late 90’s
Ecology of drug resistance
Most antibiotics are natural products isolated from other microbes
- Fungi (penicillins)
- Soil bacteria of genus Streptomyces (erythromycin, streptomycin,
tetracycline, vancomycin)
Only 1 class of antibiotic is totally synthetic (Ciprofloxacin)
Antibiotics are an ancient weapon used in chemical warfare between
microbes; resistance is a natural defense
Over-use of antibiotics = selection favoring resistant individuals
- nukes their competition
- resistance genes accumulate on plasmids, get swapped by
bacteria like baseball cards
Cyanobacteria
- photo-autotrophs responsible for our O2-rich atmosphere
- fill the surface waters of the oceans
CO2 + H2O  CH2O + O2
Share an ancestor with chloroplasts
Nitrogen-fixers
N2  reduced organic
gas
nitrogen compounds
Filamentous: form chains of cells
Proteobacteria
Alpha proteobacteria
Includes Rhizobium which colonizes plant roots and
fixes N2 which helps plants to grow
Share an ancestor with mitochondria of eukaryotes!
Beta proteobacteria
Includes Nitrosomas; aids nitrogen cycling in soil
Ammonium  nitrite
NH4+
NO2-
Proteobacteria
Gamma proteobacteria
Salmonella spp. (food poisoning)
Vibrio cholerae (cholera)
Escherichia coli (human intestinal fauna)
yellow sulfur granules
Include Chromatium spp., “sulfur bacteria”
CO2 + 2H2S  CH2O + H2O + 2S
Epsilon proteobacteria
Mostly pathogenic
Campylobacter sp. (blood poisoning)
Helicobacter sp. (stomach ulcers)
Chlamydia
- Gram-negative pathogens
- parasites that live only inside host cells
- cause blindness, STD’s
Spirochaetes
- free-living or pathogenic
- swim by spiraling through fluid
Treponema pallidum (syphilis)
Borrelia burgdorferi (Lyme’s disease)