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The Archaea ancient

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Title: 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
24
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

25
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

26
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

43
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44
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

45
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

46
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
48
Class a-proteobacteria Most
are oligotrophic (growing at low nutrient level)
49
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

54
Human fibroblast filled with Rickettsia
prowazekii
Figure 22.4 (a)
Coxiella burnetti growing within
fibroblast vacuole
Figure 22.4 (c)
55
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
56
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
57
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 (??)
58
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
62
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
65
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

67
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
68
  • Happy New Year !!!
  • New year resolution..
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