The Archaea ancient

1
Chapter 20

• The Archaea- ancient
• 12-29-2009

2
Archaea

• highly diverse with respect to morphology,
  physiology, reproduction and ecology
• Spherical, rod-shaped, spiral, irregular or
  pleomorphic
• Single cells or aggregated filaments (up to 200
  mm)
• best known for growth in anaerobic, hyper-saline
  and high-temperature habitats
• also found in marine arctic temperature and
  tropical waters

3
Phylogenetic relationships

• Bergeys Manual
• Prokaryotes
• Archaea (Ch. 20)
• Bacteria (Ch. 21-24)

Figure 20.1
4
Cell Walls

• lack muramic acid and D-amino acids
• can be stained gram or gram- (Fig. 3.30)
• pseudomurein found in some methanogenic species
  (Fig. 3.31)
• peptidoglycan-like polymer L-amino acids with
  complex polysaccharides
• complex polysaccharides, proteins or
  glycoproteins found in some other species

5
Lipids and Membranes
C20 diethers

• Bacteria/Eucaryotes
• fatty acids attached to glycerol by ester
  linkages
• Archaea
• branched chain hydrocarbons attached to glycerol
  by ether linkages
• some have di-glycerol tetra-ethers

bilayer membrane
monolayer membrane
C40 tetraethers
Fig. 3.11
6
Genetics

• binary fission, budding, fragmentation
• Chromosomes (variation in G/C contents- 21 68)
• Smaller genomes comparing to eubacteria
• some have histones that bind DNA to form
  nucleosome-like structures
• 30 of genes (code for proteins involved in
  transcription, translation or DNA metabolism )
  shared with eukaryotes
• many genes (involved in metabolic pathways)
  shared only with bacteria
• evidence for lateral gene transfer

7
Molecular biology

• Eukaryotic type DNAP
• Bacterial type RNA (polygenic RNA)
• Eukaryotic type RNAP, promoter, and tRNA
• Ribosomes
• 70S (bacterial-like)
• shape variable, differing from both bacterial and
  eukaryotic ribosomes
• Eukaryotic type elF2 and SRP (signal recognition
  particle) for protein secretion

8
Carrying eukaryotic type promoter

• A TATA box
• for TBP (the TATA box binding protein)
• - BRE (transcription factor B responsive
  element) purine-rich region before the TATA box

Figure 20.2
9
Metabolism

• great variation
• organotrophy, autotrophy, and phototrophy
• Unique glucose catabolism, pathways for CO2
  fixation
• Some have the ability to synthesize methane

10
Taxonomy

• Two phyla
• Crenarchaeota spring
• the ancestor of the archaea?
• Euryarchaeota wide
• most are extremely thermophilic
• many are acidophilic and sulfur dependent

11
Phylum Crenarchaeota
Figure 20.5 (a)

• most are extremely thermophilic (70-80C)
• many are acidophiles (pH 2-3)
• many are sulfur-dependent (solfatara)
• as electron acceptor or as electron source
• almost all are strict anaerobes

• grow in geothermally heated water or soils that
  contain elemental sulfur

12
Two best studied Crenarchaeota

• Sulfolobus
• irregularly lobed, spherical shaped
• cell walls contain lipoproteins and carbohydrates
• Thermoproteus
• long thin rod, bent or branched
• Glycoprotein cell wall
• 70-97 C
• pH 2.5-6.5

Figure 20.7
13
Phylum Euryarchaeota (Table 20.1)

• informally divided into five major groups
• methanogens
• halobacteria
• require at least 1.5 M NaCl (8)
• H. halobium- bacteriorhodopsins for
  photosynthesis
• Thermoplasms
• lack cell wall and grow in coal mines
• optimal growth at 55-59oC (PH 1-2, even at PH 0)
• extremely thermophilic S0-metabolizers
• sulfate-reducers

14
Methanogens

• Anaerobic environments rich in organic mater
• animal rumens, anaerobic sludge digesters, within
  anaerobic protozoa
• Ecological and practical importance
• important in wastewater treatment
• produce significant amounts of methane
• as clean burning fuel and energy source
• greenhouse gas (? global warming)
• can oxidize iron
• contributes to corrosion of iron pipes

Fig. 20.9
15
Methanogenesis

• produce methane, a clean burning fuel and an
  excellent energy source
• can be an ecological problem
• 10,000 billion tons of methane hydrate buried in
  the ocean floor? methane consuming microbes?
• Methanotrophs

16
Methanotrophs

• 100 species
• using fluorescent probe for specific DNA
  sequences
• Methane consuming Archaea surrounding by a layer
  of bacteria cooperate metabolically oxidized as
  much as 300 million tons of methane annually

Box 20.2
17
The Halobacteria

• extreme halophiles (Dead sea)
• require at least 1.5 M NaCl
• lt 1.5 M ? cell wall disintegrates
• growth optima 3-4 M NaCl
• aerobic, respiratory, chemoheterotrophs with
  complex nutritional requirements

Figure 20.12b
18
Halobacterium salinarium

• has unique type of photosynthesis
• not chlorophyll based
• uses modified cell membrane (purple membrane)
• contains bacteriorhodopsin
• absorption of light by bacteriorhodopsin drives
  proton transport for ATP synthesis

halorhodopsin
19
(Bacterio)rhodopsin

• widely distributed among prokaryotes
• trap light energy w/o chlorophyll
• found in marine bacterioplankton
• also found in cyanobacteria
• low O2 , high light intensity
• light-driven proton pump? pH gradient? ATP
  synthesis

Figure 20.13-The Photocycle of Bacteriorhodopsin
20
The Thermoplasms

• Thermoacidophiles (55-59C pH 1-2)
• grow in refuse piles of coal mines
• cell structure
• lack cell walls
• shape depends on temperature
• 59C irregular filament
• at lower temperatures spherical
• may be flagellated and motile

Figure 20.14
21
The Thermoplasms

• Extremely Thermophilic S0-Metabolizers
• Thermococcus and Pyrococcus
• motile by flagella
• optimum growth temperatures 88 100C
• strictly anaerobic reduce sulfur to sulfide
• Sulfate-reducing Archaea
• Archaeoglobus
• cell walls consist of glycoprotein subunits
• optimum 83C
• isolated from marine hydrothermal vents

22
Chapter 21

• Bacteria The
  Deinococci and Nonproteobacteria Gram Negatives

23
Aquificae and Thermotogae

• Hyperthermophiles
• belong to the Archaea with optimum growth
  temperatures above 85C
• Thermophilic bacteria
• Aquificae
• Thermotogae

Figure 21.1
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Phylum Aquificae

• the deepest (oldest) branch of Bacteria
• Aquifex pyrophilus
• gram-negative rod
• growth optimum of 85C and maximum of 95C
• microaerophilic
• chemolithoautotroph
• A. aeolicus
• genome 1/3 size of E. coli

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Phylum Thermotogae

• second deepest branch
• best studied Thermotoga
• hyperthermophiles
• optimum 80C maximum 90C
• grow in active geothermal areas
• marine hydrothermal vents and terrestrial
  solfataric springs
• horizontal gene transfer
• 24 of coding sequences are similar to archaeal
  genes
• 16 similarity to Aquifex

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Deinococcus-Thermus

• Deinococcus is best studied
• spherical or rod-shaped
• in pairs or tetrads
• G()/ no typical G() cell wall
• lacks teichoic acid
• layered with outer membrane
• L-ornithine in peptidoglycan
• plasma membrane has large amounts of palmitoleic
  acid

27
Deinococcus

• Mesophilic and aerobic
• extraordinarily resistant to desiccation and
  radiation

DNA toroid

• Deinococcus radiodurans
• can survive 3-5 million rad (100 rad can be
  lethal to human)
• two circular chromosomes, a megaplasmid, a small
  plasmid
• No novel DNA repair system?
• has most efficient RecA and numerous repeats
• different chromosomal structure
• accumulation of high level of Mn2

28
Photosynthetic Bacteria

• three G(-) photosynthetic bacteria
• Anoxygenic photosynthesis
• the purple bacteria
• the green bacteria
• use hydrogen sulfide (H2S), Sulfur (S), or
  hydrogen (H2) as electron source to reduce
  NAD(P) to NAD(P)H
• Oxygenic photosynthesis
• the cyanobacteria
• use H2O as an electron donor and generate O2
  during photosynthesis

29
Photosynthesis pigments
differences in absorption spectra
correlates with ecological distribution
Figure 21.4
30
Phylum Cyanobacteria
Typical G(-) cell wall

• the largest and most diverse group of
  photosynthesis bacteria
• Phycobilisome
• phycocyanin and phycoerythrin
• Vary greatly in shape and appearance

Figure 21.7 (a)
31
Oxygenic Photosynthetic Bacteria

• Unicellular rods or cocci
• Non-filamentous aggregates
• Filamentous

??
Figure 21.8
32
Motility of Cyanobacteria- lacking flagella

• Phototaxis- use gas vacuoles to position in
  optimum illumination in water
• Gliding motility (Box 21.1)- occurs on a solid
  surface
• Via cytoplasmic fibrils or filaments
• Swimming with unknown mechanism
• Synechococcus swim up to 25 mm/sec

33
Gliding motility

• present in many taxa
• fruiting and nonfruiting aerobic
  chemoheterotrophs, Cyanobacteria, green nonsulfur
  bacteria, and at least two gram-positive genera
• Mechanism unknown
• occurs when cells in contact with solid surface
• cells leave slime trail as glide along
• can be very rapid (150 mm600 mm/ min)
• motility often lost with age
• low nutrient levels usually stimulate gliding

34
Advantages of gliding motility

• enables cells to encounter insoluble nutrient
  sources and digest them with cell bound digestive
  enzymes
• works well in drier habitats (e.g., soil,
  sediments, and rotting wood)
• enables cells to position themselves optimally
  for light intensity, O2, H2S, temperature,
  etc.

35
Ecology of Cyanobacteria

• tolerant of environmental extremes
• thermophilic up to 75C
• can cause blooms in nutrient-rich ponds and lakes
• some produce toxins
• often form symbiotic relationships
• Lichens symbionts with protozoa and fungi
• nitrogen-fixing species with plants

Figure 21.11
An eutrophic pond
36
Genus Chlamydia

• nonmotile, coccoid, G(-) bacteria
• cell walls lack muramic acid and peptidoglycan
  (however, they are pencillin sensitive)
• very small genomes ( 1/3 of E. coli)
• obligate intracellular parasites
• extracellular elementary body (EB)
• intracellular reticulate body (RB initial body)
• energy parasite

37
Life cycle of Chlamydia
Figure 21.13b
38
Important pathogens

• C. trachomatis ?? and Trachoma
• the greatest single cause of blindness throughout
  the world
• Also causes nongonococcal urethritis (??), and
  other diseases in humans
• C. psittaci and Psittacosis ???
• causes psittacosis in humans and many other
  animals including parrots, turkeys, sheep, goat
  and cats
• C. pneumoniae
• common cause of human pneumonia
• associated with atherosclerosis

Fig. 38.22
39
Phylum Spirochaetes

• gram-negative bacteria
• slender, long with flexible helical shape
• creeping (crawling) motility
• axial filament

Figure 21.15 (a1) and (a2)
40
Complex of axial fibrils (periplasmic flagella)
Figure 21.15 (b)
41
Spirochete motility
current thought axial fibrils rotate,
causing corkscrew-shaped outer sheath to rotate
and move cell through surrounding liquid
Figure 21.16
42
Syphilis ??
38.4 The Italian disease, the French disease, or
the great pox

• Sexually transmitted disease (STD) caused by
  Treponema pallidum
• Congenital syphilis
• T. pallidum enters the body through mucous
  membranes or minor breaks or abrasions of the
  skin (chancre ??)
• Not very contagious
• 1/10 acquisition from a single exposure
• treated with penicillin G at the early stage

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(No Transcript)
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Lyme disease
Tick
Fig. 38.8 (b) and (c)

• A zoonotic disease (diseases transmitted from
  animals to humans) caused by tick-borne Borrelia
  burgdorferi
• Localized stage
• develops 1 week to 10 days, expanding,
  ring-shaped, skin lesion, flu-like symptoms
• Disseminated stage
• occurs weeks or months after infection
• neurological abnormalities, heart inflammation,
  and arthritis
• Late stage
• occurs years later, demyelination of neurons,
  behavioral changes, and symptoms resembling
  Alzheimers disease and multiple sclerosis

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Phylum Bacteroidetes 3 classes

• Bacteroides ????
• gram-negative rods of various shapes anaerobic
  chemoheterotrophs
• often found in oral cavity and intestinal tract
  of humans and other animals and the rumen of
  ruminants constitute up to 30 of bacteria from
  human feces
• Associated with organ diseases
• B. fragilis is a common pathogen found in
  abdominal, pelvic, pulmonary, and blood
  infections.
• Sphingobacteria
• often have sphingolipids in cell walls
• many motile by gliding motility
• Cytophaga
• play major role in mineralization of organic
  material
• degrade complex polysaccharides

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Chapter 22

• The Proteobacteria- 5 subgroups
• purple bacteria
• 123009

47
The phylum Proteobacteria
Ch. 23
Ch. 24
5 groups Phylogenetically related but vary
markedly in many aspects morphology, physiology
Ch. 22
Figure 22.1
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Class a-proteobacteria Most
are oligotrophic (growing at low nutrient level)
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Rickettsia- An obligate intracellular parasite

• No flagella
• Rod shaped, coccoid, or pleomorphic with typical
  gram-negative cell walls
• lack glycolytic pathway
• do not use glucose as energy source
• take up and use ATP and other materials from host
  cell
• important pathogens parasitic forms grow in
  vertebrate erythrocytes, macrophages, and
  vascular endothelial cells

50
Rocky mountain spotted fever

• A zoonotic disease caused by Rickettsia
  rickettsii
• Rickettsia prowazekii and Rickettsia typhi
  typhus fever
• transmitted by ticks, lice, flea
• transovarian passage

Figure 38.10
clinical manifestations - vasculitis and sudden
onset of headache, high fever, chills, and skin
rash - can destroy blood vessels in heart, lungs,
or kidneys, leading to death
51
Q Fever

• caused by Coxiella burnetii
• g-proteobacteria
• intracellular gram-negative bacterium
• proliferates in lungs (atypical pneumonia)
• Also a zoonotic disease transmitted by
• Animals infected by ticks
• Human infected by contaminated dust (inhalation)
• dried feces or urine, or unpasteurized milk
• occupational hazard among slaughterhouse workers,
  farmers, and veterinarians
• sunder onset of headache, malaiseand high
  fever.
• endocarditis (rarely but fatal), hepatitis

52
Common features

• rod-shaped, coccoid, or pleomorphic
• typical gram-negative cell walls
• no flagella
• very small
• Rickettsia 0.3 to 0.5 by 0.8 to 2.0 ?m
• Coxiella 0.2 to 0.4 by 0.4 to 1.0 ?m
• parasitic or mutualistic
• parasitic species grow in vertebrate
  erythrocytes, macrophages, and vascular
  endothelial cells
• also live in blood-sucking arthropods, which
  serve as vectors or primary hosts

53
Parasitic life styles

• Rickettsia
• enters host by phagocytosis
• ?
• escapes phagosome
• ?
• reproduces in cytoplasm
• ?
• host cell bursts

• Coxiella
• enters host by phagocytosis
• ?
• remains in phagosome
• ?
• reproduces in phagolysosome
• ?
• host cell bursts

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Human fibroblast filled with Rickettsia
prowazekii
Figure 22.4 (a)
Coxiella burnetti growing within
fibroblast vacuole
Figure 22.4 (c)
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Caulobacter

• often adhere to other microorganisms
• long prosthecae ? nutrient uptake

Prostheca By which they attach to solid
substrate and adhere to each other to form a
rosette of cells
Figure 22.8
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Genus Rhizobium

• gram-negative, motile rods
• often contain poly-b-hydroxybutyrate (PHB)
  granules
• become pleomorphic under adverse conditions
• grow symbiotically as nitrogen-fixing bacteroids
  (? ammonium) within root nodule cells of legumes

Fig. 22.9
In Alfalfa root
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Genus Agrobacterium
Figure 22.10

• Not stimulating root nodule formation or fixing
  nitrogen
• transform infected plant cells (crown, roots, and
  stems) into autonomously proliferating tumors
• Agrobacterium tumefaciens
• causes crown gall disease by means of
  tumor-inducing (Ti) plasmid

Crown gall (??)
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Gene Exchange between domains
- the Ti plasmid -

• Transfer the T-DNA to plant and lower fungi
• Can also mobilize other plasmid with correct mob
  sequence to plant cells
• A vector used for gene modification in plant
  (transgenic plant)

59
Nitrifying bacteria- Nitrification

• conversion of ammonia to nitrate
• ammonia? nitrite? nitrate
• Nitrosomonas ammonia to nitrite
• b-proteobacteria (Table 22.2)
• Nitrobacter nitrite to nitrate
• a-proteobacteria (Table 22.2)
• Fate of nitrate
• easily used by plants
• Rapidly lost from soil through leaching or
  denitrification? N2

60
Brucellosis- undulant fever

• A zoonotic disease caused by Brucella spp.
  (a-proteobacteria, Brucellaceae Fig. 22.2)
• Notification of the Public Health LRN (Laboratory
  Response Network) is required
• A select agent as biocrime
• Humans are generally infected by
• ingestion of contaminated food (milk products
  mothers breast milk or water, inhalation, via
  skin wound, direct person-to-person (rare)
• Acute form flu-like symptom undulant form
  undulant fever, arthritis, and testicular
  inflammation, neurologic symptom may occur
  chronic form chronic fatigue, depression, and
  arthritis

61
Six bacteria used as biocrimes

zoonotic
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Class b-proteobacteria
63
Order Burkholderiales

• Most species use poly-b-hydroxybutyrate (PHB) as
  carbon source
• Burkholderia cepacia
• degrades gt 100 organic molecules
• very active in recycling organic material
• plant and human pathogen (nosocomial pathogen)
• a particular problem for cystic fibrosis
  patients
• B. mallei and Glanders (???)
• A zoonosis (horses are likely nonhuman
  reservoirs) by skin contact or inhalation
• A potent bio-weapon

64
Six bacteria used as biocrimes

zoonotic
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Bordetella pertussis and pertussis

• Non-motile encapsulated species
• causes whooping cough by pertussis toxin (PT)
• An AB toxin (A action or activity B binding)
• DPT vaccine and DaPT vaccine (acellular
  pertussis )

66
Nitrogen Fixation by
Burkholderia and Ralstonia

• both form symbiotic associations with legumes
• both have nodulation genes (nod)
• suggesting a common genetic origin with rhizobia
• genetic information may have been obtained
  through lateral gene transfer

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Genus Neisseria

• nonmotile, gram-negative cocci
• most often occur in pairs
• may have capsules and fimbriae
• inhabitants of mucous membranes of mammals
• some human pathogens
• Neisseria gonorrhoeae gonorrhea ??
• Pelivic inflammatory disease (PID)
• A major cause of sterility and ectopic
  pregnancies
• Neisseria meningitidis meningitis ??????
• most disease causing strains- A, B, C, Y and
  W-135 (Table 38.2)
• vaccination

Fig. 38.18
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• Happy New Year !!!
• New year resolution..