Download 2 - ISDC

 41st Saas‐Fee course from Planets to Life 3‐9 April 2011
Lecture 2: The “top down” approach to understanding the origin of life – cont. •  Understanding the characterisFcs of the organisms close to the root of the tree –  Most are extremophiles (grow at high temperatures, high and low pH, high salt, etc) –  The origin of metabolism –  The “RNA” world –  The possible role of viruses in the origin of life –  The possible importance of “biofilms” in the early evoluFon of life CharacterisFc differences between the three domains of life: Archaea, Bacteria and Eukarya Characteristics*
Archaea
Bacteria Eukarya
Cells with membrane-bound
nucleus and other organelles
No
No
Yes
DNA circular1
Yes
Yes
No
Ribosome size
70S
70S
80S
Membrane lipids
Ether linked
Ester linked Ester linked
Cell walls
No PDG2
PDG
No
Histone proteins
Yes
No
Yes
Operons in DNA
Yes
Yes
No
Ribosome structure
distinct
distinct
Archaeal-like
Antibiotic sensitivity
No
Yes
No
Photosynthesis
No
Yes
Yes
Growth at temperatures >80°C
Yes
Yes
No
*There are many physiological characterisFcs that are found only in bacteria and archaea. 1There are some excepFons. 2PDG is pepFdoglycan; Archaea do not have PDG but do have at least 7 different cell surface layers (protein, lipid, etc) The endoplasmic reFculum is an interconnected network of tubules, vesicles and is involved in the synthesis of proteins, lipidss, sugar metabolism, etc Longitudinal secFon through the flagella area The kinetosome (basil body) that is the anchoring site for a flagellum Limits of Life and Limits of Diversity
•  Are their limits to evolutionary diversity of life as we
know it?
•  What environmental conditions limit where life can
exist?
What did Darwin have to say that is germane
to these questions?
Quotes from The Origin
of Species
In reference to natural selec.on: “I can see no limit
to this power, in slowly and
beautifully adapting each
form to the most complex
relations of life”
Darwin's most famous book, was published in 1859. Within 20 years it convinced most of the internaFonal scienFfic community that evoluFon was a fact. Darwin’s ending
paragraph: “…from so
simple a beginning endless
forms most beautiful and
most wonderful have been,
and are being evolved”
“I can see no limit to this power etc” The blobfish (Psychrolutes marcidus) is found at depths greater than 5000 m off the coast of Australia and Tasmania. To remain buoyant, the flesh of the blobfish is a gelaFnous mass with a density slightly less than water. This allows the fish to float above the sea floor without expending energy on swimming. The relaFve lack of muscle is not a disadvantage as it primarily swallows edible macer that floats by in front it (adult blobfish ~30 cm long). This crustacean invades a fishes mouth, devours its tongue, and takes the tongues place. It then acts like a tongue; the fish can use it to grip and swallow prey ‐ the parasite gets first dibs at the food. (From: Carl Zimmer, Parasite Rex, Simon & Schuster) “there are no limits” ‐ The water bear (Tardigrade) could easily survive on Mars and in the ice of Europa TarFgrades are between 0.05 and 1.2 mm in length, have feet with claws like bears and walk like bears. They are found everywhere including hot springs, in a 5m layer of solid ice, on the top of the Himalayas, stone walls etc but mostly live in moss. They could survive on Mars because: The water bear is capable of surviving for more than 12 years in a completely dry state called the “tun” state or in “cysts”. In the “tun”state they will survive in liquid helium, absolute alcohol or even ether and brine. Just add water and they come back to life ‐ just like instant coffee “gummy bear”
Dry form “tun” Asphyi.c state ‐O2 coming back to life with addi.on of water 41st Saas‐Fee course from Planets to Life 3‐9 April 2011
The “top down” approach to understanding the origin of life •  Understanding the characterisFcs of the organisms close to the root of the tree –  Most are extremophiles (grow at high temperatures, high and low pH, high salt, etc) The Universal PhylogeneFc Tree: Origin of Life and EvoluFon ImplicaFons Universal Phylogenetic Tree
What does this tree tell us about the evolu8on of organisms? 1.  There are three domains of life 2.  All extant life arose from a common ancestor 3.  Bacteria and Archaea thought to be part of the same group of organisms (prokaryotes, Monera etc) are disFnctly different 7.  The Eukarya evolved from the archaea 8.  The deepest rooted organisms are thermophiles (hyperthermophiles) 11.  The proFsts are polyphyleFc (see diplomonads and ciliates) 12.  The cyanobacteria (the mother of all oxygen producing photosyntheFc oganisms) are not deeply rooted The microbial world, its limits and our search for life elsewhere EXTREMOPHILES – Organisms that live in the most extreme environmental condiFons (Temperature, salinity, pH, pressure, radiaFon, heavy metals, low water acFvity, and combinaFon of extremes) Important note: There is sFll much we don’t understand about Earth life and the limits of evoluFon of carbon‐based life to live under extreme condiFons EvoluFonary innovaFons observed in Earth organisms THERE IS STILL MUCH TO BE
DISCOVERED
•  During the past 10 years the Census of Marine
Life has discovered thousands of new species of
animals and plants
•  This is even more pronounced for marine
microorganisms and it is estimated that more
than 99% of the microbes in the ocean are
uncharacterized new species
The microbial world, its limits and our search for life elsewhere EXTREMOPHILES – Organisms that live in the most extreme environmental condiFons (Temperature, salinity, pH, pressure, radiaFon, heavy metals, low water acFvity, and combinaFon of extremes) Why study extremophiles? •  Limits of carbon‐based life •  Some extremophiles deeply rooted in global phylogeneFc trees (parFcularly thermophiles) •  The range of habitat condiFons for extremophiles may be analogous to environmental condiFons on other planets and moons •  Paleomicrobiology (metabolic history) and the changing environmental condiFons throughout Earth history •  “Top down” approaches to studying the origin of life Limits of Life Parameter
Extreme range on
Earth
Extreme level for growth
of organisms
Temperature
~-50 - >1200°C
Lowest Temperature -15°C
Highest Temperature - 122°C
Eukaryotes to 62°C ;metazoans to ~50°C
pH
Water activity
(Aw)
Radiation
0 - 14
Bacteria, Archaea and fungi at pH 0 - 13
Heavy metals
Depends on environments
Bacteria and algae grow in 2-5mM Cd,
and specific metals (>10mM) Zn, Ni etc
Pressure
<1 to ~1,100 atm
High diversity of bacteria, invertebrates
(subseafloor habitas possibly and fish in ocean trenches
to >6 km in the crust)
Distilled H2O to total dryness Highest salt - 35% NaCl (many microbes
and animals can survive desiccation)
Generally less than 1 kGy
Some microbes survive levels 10X
higher than found naturally on Earth
Limits: Some key environmental variables regulaFng life processes •  Temperature and Pressure: Together they determine the boundary condiFons for liquid water •  Salinity: relates to the availability of water and in combinaFon with pressure or low temperature can result in added stress to cells •  pH: in most cases organisms evolve mechanisms to maintain pH’s near neutrality inside the cell •  Organic solvents: destroys lipid membranes •  Other combina.ons: dryness, radiaFon, redox condiFons, heavy metals, etc in combinaFon with T, P, S, and pH What are the limits for C‐based life? Only temperature and availability of water limit Earth life Note: toxic levels of metals, radiaFon, etc can kill life Temperature range for microbial growth and survival: 1. 
2. 
3. 
4. 
5. 
6. 
Microbial growth at ‐15°C and up to at least 122°C Enzyme acFvity at low temperature depends on liquid solvent Salts and extracellular polysaccharides (EPS) can protect cells; some hyperthermophiles have >4M K at high temperatures Bacterial spores and vegetaFve cells have been observed from million year ice cores Anaerobes including methanogens (along with methane) in ice cores Anaerobic methane oxidizing archaea associated with methane hydrates Viable microbes observed at 250°C (122°C) Maximum growth T for eukaryotes (70°C) Maximum growth T for metazoans (~50°C) Enzyme acFvity in water/organic solvent mixture (Bragger et al., 2000) (Modified from Deming and Eiken, 2007) Temperature Classes of Microorganisms Hyperthermophile (Temp. OpFmum >80°C) – Early microbiology studies pioneered by Thomas Brock in the 1970’s Boulder Spring, Yellowstone NaFonal Park Octobus Springs, Yellowstone NaFonal Park (The site where Thermus aqua;cus was isolated. T aqua;cus provides the polymerize enxyme used in the Polymerase Chain ReacFon) Hydrothermal vents discovered 1977, black smokers, 1979 Juan deFuca Ridge – NE Pacific (2,500 m depth, 350°C hot fluid) Different Edifice Morphologies, Endeavour
Highest Temperature Organism on Earth from Finn (Mothra) Highest Temperature Organism on Earth from Finn 3 days growth 2 m 1.03 m 121°C organism grown under anaerobic condiFons with acetate, FeIII forms magneFte, doubles 24 hrs Kashefi et al., Science 2003 Pyrolobus fumarii* (Tmax = 113ºC, Topt= 106ºC, Tmin= 90ºC) FISH staining of vent chimney Red, Archaea; Green, Bacteria (Chris.an Jeanthon) TEM, P. fumarii cell (Reinhard Rachel) A Pyrodic8um species has been described (Science 301:934, 2001) that can grow up to 121ºC, and a strain of Methanopyrus kandleri has been shown to grow up to 122ºC (PNAS 105:10949, 2008) Even hyperthermophiles have parasites Nanoarchaeum 0.4 µm Red, Nanoarchaeum Green, Ignicoccus Photos by Reinhard Rachel Nanoarchaeum genome (PNAS 100:12984, 2003; J. Bacteriol. 190:1743, 2008) a. Circular, 0.49 Mbp–smallest genome of any species of Archaea. b. Contains no recognizable genes encoding biosyntheFc enzymes for amino acids, nucleoFdes, or coenzymes. c. Lacks genes encoding proteins for major catabolic pathways (e.g., glycolysis). d. Missing genes for some ATPase subunits. e. Most gene dense genome of any cell (99% of genes encode proteins). Hyperthermophiles: Overcoming the negaFve effects of high temperature Problems
Solutions
1. Protein Denaturation
Heat-stable proteins; heatshock proteins (chaperones)
2. DNA Denaturation
Reverse DNA gyrase;
introduces positive
supercoiling into the
chromosome, which raises
the melting point;
stabilizing proteins
3. Membrane Melting
Tetra-ether lipid monolayer
membranes; covalent bonds
adjoining membrane halves
resist membrane peeling
4. Low Solubility of O2 at High Temperatures
Diverse anaerobic energy
metabolisms; S0- and H2based metabolisms
Eukaryotes that live at high temperatures •  Upper temperature for growth of a single‐cell eukaryotes is 62°C (fungi) •  Upper temperature for growth of a metazoan is 50°C (polychaete worm from deep‐sea hydrothermal vents) Alvinella pompejana “Pompei worm” (A heat‐loving metazoan) Size: up to 150 mm Distribu.on: East Pacific Rise from 21°N to 23°S Biology: Dwells inside organic tubes in acFve chimney walls. Temperature growth range 20‐50°C but can tolerate exposure to temperatures >100°C; Feeds on bacteria; outer surface colonized by filamentous bacteria Inferno Palm worms – Axial Volcano Alvinella pompejana Worm Photograph of a video taken from DSRV Alvin in hydrothermal vents at 21°N, East Pacific Rise, showing an Alvinella pompejana worm standing on a substrate measured at 105°C. Sketch to clarify the posiFon of the worm and the temperature probe Nature 1992 Alvinella pompejana (East Pacific Rise) Scanning electron micrograph ‐ head size is 3 cm Cary et al., Nature 391:545‐546 (1998) There is an ongoing “discussion” as to the upper temperature for growth of the Alvinella worms that live on acFve sulfide structures. This report by Cary and colleagues demonstrated that the rear part of the tube where Alvinella pompejana resides reaches temperatures close to 80°C. Some of the biochemistry data on these worms indicate that 40‐50°C may be the hocest temperature for these animals.It is clear, however, that Alvinella can survive exposure to temperatures approaching 100°C. Science 312:231 (2006) Schema.c of the thermal gradient aquarium. Chamber consisted of : (A) aluminum reinforcement plate; (B) clear polycarbonate window; (C) PEEK ouwlow tubing; (D) holes drilled into the block to within 2.5 mm of the slot containing animals for inserFon of temperature probe; (E) )‐ring face seal; (F) slot to contain animals; (G)PEEK inflow tubing; and (H) an anodized aluminum block with a slot to contain animals. DistribuFon of P. sulfincola and P. palmiformis worms in temperature‐gradient experiments. Worms were uniformly dispersed within the aquaria before establishing the temperature gradient. (A to C) Plots of P. sulfincola distribuFons over Fme within a 20° to 61°C gradient; N = 5, 9 and 4 individuals, respecFvely. (D) Plot of P. palmformis distribuFons over Fme within a 20° to 55°C gradient; N = 8 individuals. Scale Worm (Polychaete) living on the edge Juan deFuca Ridge NE Pacific (320°C fluid) (Deming, 2009)!
Psychrophiles •  Lowest temperature for growth ‐12°C, acFve metabolism <‐22°C. •  Evidence for survival at temperatures as low as ‐80°C (liquid nitrogen) •  Spores found in ice cores that are >1 million years old Psychrophiles: Tempmax < 20ºC Marine sea ice Polaromonas Topt = +4ºC ←Photos by Jim Staley→ Losest temperature for growth: Psychromonas ingrahami Topt= +4°C, Tmin= –12°C, Tmax= +10°C Cultured phage‐bacterial host systems acFve at –1°C Middelboe et al., 2002 (seawater) Borriss et al., 2003 (sea ice) Wells and Deming, 2006 (both) 3 µm Colwellia psychrerythraea strain 34H 3 µm 3 µm (Borriss et al., 2003) (Wells and Deming, 2006) Problems and Solutions: Psychrophiles Problems!
Solutions!
Prevent ice-crystal formation and cell
death!
Live in a briny habitat, produce
compatible solutes and/or
exopolysaccharides (EPS) !
Enable protein activity: enzymes must
maintain significant catalytic
activity at low temperature!
Make more flexible proteins
(higher α-helix; lower βsheet content)!
Make more polar and less
hydrophobic proteins, with
fewer weak bonds (ionic,
hydrogen)!
Maintain membrane function: the
organism must maintain
significant levels of nutrient
transport at low temperature!
Make lipids with greater content
of short-chained, branched,
and unsaturated fatty acids!
“I can see no limit to this power etc” (Darwin referring to natural selecFon” The Antarc;c ice‐fish (Channichthyidae) are the only known vertebrates without hemoglobin. Consequently, their blood is transparent. Their metabolism relies on the oxygen dissolved in the liquid blood and is absorbed directly through the skin from the water. This works because of the increased solubility of oxygen in cold water and is an adaptaFon to life at temperatures that are less than 0°C (icefish size 25 cm long) (Wikipedia) Summary – Temperature and life •  To date, the lowest temperature for growth is ‐12°C and the maximum temperature for growth is 122°C •  Low temperature microbes (psychrophiles) do not have ancient lineages –  Spore‐forming psychrophilic bacteria are of concern regarding planetary protecFon issues to icy planetary bodies •  High temperature microbes (hyperthermophiles) have ancient lineages –  Hyperthermophiles are of interest regarding the origin of life and the origin of metabolism and eukaryotes –  The highest temperature for growth of a eukaryote is >60°C lower than the maximum temperature for a microbe