Sponges: Chondroclada lampadglobus Size: up to 50 cm high with - - PowerPoint PPT Presentation

Sponges: Chondroclada lampadglobus

Size: up to 50 cm high with inflated spheres 3‐5 cm in diameter Distribu-on: East Pacific Rise (178S, 23°S, 13°N) Biology: rooted in sediments near vents or on pillow basalts but not near to the animals communiJes. Carnivorous mode of feeding

Abyssocladia sp. From Lau Back‐Arc Basin; also found on the East Pacific Rise(carnivorous, up to 40 mm high

Carnivorous sponge (Demospongiae) is 8‐10 cm high and found at 1000 m depth off of New Zealand along the Rim of Fire rooted on

• basalt. The lip‐shaped spicules covering the outside of the sponge are

like sJcky Velcro and catch prey such as crustaceans that brush against them. Without a mouth or stomach, the cells of the sponge stream towards the prey and engulf its flesh, each cell digesJng a Jny part of the prey

41st Saas‐Fee course from Planets to Life 3‐9 April 2011

Lecture 4: The “top down” approach to

understanding the origin of life – cont.

• Microbes in low nutrient environments

(oligotrophic environments)

• MulJcellular animal that grows in the absence
• f oxygen and in 36% brine

– The nature of the mitochondria and related

• rganelles
• Origin of life 1

Heterotrophic life in low nutrients –

• ligotrophic organisms
• The most common bacteria in the open ocean

and in remote lakes (alpine) grow on microgram levels of organic nutrients (this group of microbes are the reason we are interested in Lake Vostok as an analoque environment to icy moons with liquid oceans)

• There are other microbes that grow on CO, CH4

and just recently a microbe was isolated that grows on hydrocarbons in the absence of oxygen

Examples of oligotrophic bacteria

Caulobacter crescentus dividing into a stalk daughter cell (top) and a mo6le daughter cell with a flagellum (bo:om); Caulobacter and related

• rganisms grow in disJlled water

agached to walls of the container

SAR11 now named Pelagibacter ubique is stained with DNA stains. P. ubique is the most numerous bacterial species in the world esJmated to be 1028 cells. This bacterium grows on µM levels of organic compounds and is inhibited by high

• concentraJons. It can eat DMSO and has a

proteorhodopsin (derives some energy from light) Scale bar is 1µm

The first anaerobic metazoan

First – why do metazoans like oxygen? a) the mitochondria

Mitochondria structure: 1) Inner membrane 2) outer membrane 3) Crista (internal compartments) 4) Matrix (matrix contains hundreds of enzymes, ribosomes, the mitochondrial genome, and the TCA cycle)

Mitochondria

A mitochondrion (plural mitochondria) is an

• rganelle found in most eukaryoJc cells.

Mitochondria are someJmes described as "cellular power plants," because their primary funcJon is to convert organic materials into energy in the form of ATP via the process of oxidaJve phosphorylaJon. Usually a cell has hundreds or thousands of mitochondria, which can occupy up to 25 percent of the cell's cytoplasm.

Biochemistry textbooks depict mitochondria as oxygen‐dependent

• rganelles, but many mitochondria can produce ATP without any
• xygen. In fact, several other types of mitochondria exist and they
• ccur in highly diverse groups of eukaryotes‐ proJsts as well as

metazoans – and possess an ooen overlooked diversity of pathways to deal with the electrons resulJng from carbohydrate oxidaJon. These anaerobically funcJoning mitochondria produce ATP with the help of proton‐pumping electron transport, but they do not need

• xygen to do so. Recent advances in understanding of

mitochondrial biochemistry provide many surprises and furthermore, give insights into the evoluJonary history of ATP‐ producing organelles.

LocaJon of deep‐sea anoxic hypersaline lakes in the Eastern Mediterranean Sea

Brine pool in the Gulf of Mexico

Selected geochemical characteris-cs of the L’Atalante deep hypersaline anoxic basin

Depth 3499 m Brine layer depth 400 m Salinity 366 0/00 Temperature 14.3°C Hydrogen sulfide 2.9 mM Methane 0.52 mM Ammonium 3.0 mM

The phylum Loricifera

Light microcopy image of an undescribed species of Spinoloricus that is living in the anoxic L’Atalante basin in the Mediterranean Sea. Stained with Rose Bengal. Size bar is 50 µm

Lorucufera (laJn, Lorica, corset + ferre, to bear); small (100 µm‐1mm)marine sediment‐ dwelling animals with 22 described species in 8 genera and at least 100 more species not

• described. They agached themselves to
• sediments. The animals have a head, mouth

and digesJve system. There is no circulatory system, and a relaJvely large brain. They have spiny heads, separate sexes and have a larval stage.

Evidence that the L’Atlante Loricifera grow in the absence of oxygen

• Live stains
• Electron microscopy and con‐focal microscopy

– No mitochondria

• Biochemical analyses
• Isotope uptake (leucine)

No evidence of agached microbes – would be the case if the animals were dead

IncorporaJon of Cell‐Tracker Green CMFDA by loriciferans from the anoxic sediments of the L‐Atalante basin. Series of confocal laser microscipy images across different secJons of the body volume of the loriciferans. SecJons 1‐21 represent the progressive scanning of the loriciferans from the inner to the outer part of the body. (a) Cell‐ Tracker Green treated loriciferans, and (b) Loriciferans killed by freezing prior to Cell‐ Tracker Green treatment and used as the control (Danovaro et al., BMC Biol 2010)

Electron micrographs of the internal body of loriciferans from the deep hypersaline anoxic L’Atalante basin. Illustrated are (a) a hydrogenosome‐like organelle; (b) hydrogenosome‐like‐organelle with evidence of a marginal plate; (c) a field of hydrogenosome‐like

• rganelles; (d) the proximity between a possible

endosymbioJc prokaryote and hydrogenosome‐like

• rganelles; (e‐f) the presence of possible endosymbioJc
• prokaryotes. Scale bars, 0.2 µm; H is hydrogenosome; P

is possible endosymbioJc prokaryote; M is marginal plate

Mitochondria Hydrogenosomes Mitosomes

Hydrogenosome is a membrane‐enclosed organelle of some anaerobic ciliates, trichomonads and fungi. The hydrogenosome of the trichomonads contain prokaryotes and produce hydrogen, acetate, carbon dioxide and ATP by the combined acJons of puruvate:ferredoxin oxido‐reductase, hydrogenase, acetate;succinate VoA transferase and succinate thiokinase. Superoxide dismutase, malate dehydrogenase, ferredoxin, adenylate kinase and NADH:ferredoxin oxido‐reductase are also localized in the

• hydrogenosome. This organelle is believed to have evolved from anaerobic

archaea although this is not a segled issue.

Model of ATP‐synthesis in hydrogenosomes

Summary of “extreme” life

• Only high (max temp. unknown) low temperatures

(probably <‐20°C) and the absence of sufficient water, prevent growth of organisms

• Microbes can uJlize a wide range of inorganic and organic

compounds and elements as energy sources (with and without oxygen)

• Microbes have adapted to grow in ultra low levels of key
• rganic and inorganic nutrients
• MulJ‐cellular animals have been shown to grow at 50°C

and in the absence of oxygen (new findings)

• It is very likely that there are planetary bodies, and

parJcularly icy moons with oceans that can support Earth life – the quesJon is acquiring such life

It is very likely that there are planetary bodies, and parJcularly icy moons with oceans that can support Earth life – the quesJon is acquiring such life

41st Saas‐Fee course from Planets to Life 3‐9 April 2011 Lecture 4 ‐ Origin of Life and its Early EvoluJon on Earth

Outline

• Some history
• When and where did life originate?
• How did life originate?
• Would an understanding of the “when” and

“how” quesJons help constrain the seungs (where) for the origin of life?

• What did the earliest life look like?

The origin of life: A historical perspecJve

• Spontaneous generaJon: Organic life could and does

arise from inorganic mager (generally agributed to Anaximander (Milesian philosopher) in the 6th and 5th centuries before Christ.

• Aristotle (384‐322 BC) life arose from the 4 elements:

earth, air, fire and water. Since Aristotle denied that the universe, and the earth, had a beginning, life

• ccurs all of the Jme.
• The idea of spontaneous generaJon persisted into the

19th century with mulJple recipes for making life (wheat and wet rags in an open jar will produce mice in 21 days) – lots of recipes for making maggots and other animals that like putrafaceous

illustraJon of the Swan‐necked bogle used in Pasteur's experiments to disprove spontaneous generaJon

The end of “spontaneous generaJon” or not?

While there is a rich history of discussion of spontaneous generaJon in the 17th to 19th centuries, much of the ideas centered around the “abiogenesis” of animals. ScienJsts in the 17th century (Francisco Redi) and 18th century (Lazzaro Spallanzani and John Needham) performed experiments with open and closed containers showing that animals did not appear in the closed containers. The definiJve experiment was performed by Louis Pasteur in 1859.

The end of spontaneous generaJon ‐ or not?

• Did Pasteur prove that life can never come from

non‐living mager? What he did disprove was that “modern (thus highly evolved) living

• rganisms arose from non‐living stuff. This is very

different from the idea that the first primiJve life

• nce arose from non‐living, non‐organic material.
• Charles Darwin in ONLY the first ediJon of the

Origin of Species (1859) wrote: “I should infer from analogy that probably all of the organic beings which have ever lived on this earth have descended from some one primordial form, into which life was first breathed”

Charles Darwin (1809 – 1882) Darwin discussed the idea of a “warm ligle pond” where life would have started The first tree of life (Darwin, Origin of Species, 1859) A common ancestor to all life. Root?

The great tree of life from the Origin of Species, 1859 (Charles Darwin) Note branching and root.

The modern era of origin of life studies

• Haldane/Oparin (early 20th century): the idea

that life arose from organic material formed abioJcally from inorganic material (replicator molecule and metabolism)

• Stanley Miller in 1957 demonstrated that amino

acids could be synthesized from inorganic gases thought to dominate early atmosphere

• Sidney Fox (1950’s) could synthesize protein

spheres from amino acids and heat that showed some properJes of cells

• Thomas Cech in 1982 reported on his discovery
• f catalyJc RNA molecules (had both informaJon

and catalyJc acJvity) “The RNA world”

Haldane proposed that carbon dioxide, ammonia and water vapor made up the bulk of the ancient atmosphere. EnergeJc radiaJon would convert these gases to organic compounds; their accumulaJon into a hot “organic soup” from which sprung life. Independently, Oparin proposed a similar model with the organic compounds forming “coacervates” (colloidal organic droplets). Oparin and Haldane believed that the informaJon macromolecule was a protein. JBS Haldane (1892‐1964) was trained as a geneJcist. A.I.Oparin (1894 – 1980) was trained as an organic chemist

Oparin favored abioJc synthesis, in which an informaJon‐containing protein was the first step in life. By contrast, Haldane proposed that some form of metabolism was the first step. Today, the main debate

is sJll “replicator first” or “metabolism first”

The Miller and Urey Experiment ‐ 1953 and a sJmulant to the “PrebioJc Soup” model (Oparin and Haldane) Stanley Miller (1930 – 2007) The Miller and Urey experiment was the first to produce a variety of amino acids (building block of proteins) abioJcally using a spark discharge (mimic lightning) as the energy source with what was thought to be the early atmosphere, methane, ammonia, hydrogen and water .

Are paradigms shioing?

• The paradigm that life originated in an “organic

soup” dates to Darwin and promulgated by Haldane, Oparin and Miller and others and is sJll a popular idea

• The “soup” people also favor the “replicator”

first hypothesis

• During the past 20 years or so, a significant origin
• f life community has embraced the idea that

submarine hydrothermal vents were the seung for life’s origin. This group favors the “metabolism” first hypothesis.

Agempts to understand the origin of life

• Geung started: prerequisite condiJons for the origin and

maintenance of C‐based life

– Water, organic monomers, availability of key elements, catalyJc minerals, environmental condiJons, etc – Organic soup vs focused producJon of precursor and catalyJc organic compounds

• The “metabolism first”, the “replicator first” and the “pepJde first”

worlds ‐ Probably just one world

– “Top‐down” approaches show a glimmer of insight – RNA world and the origin of the geneJc code, ribosome, translaJon and transcripJon – RNA world transiJon to DNA world

• Matching seungs with different steps leading to life (Where did life

start? Does the “where” have dimensions in space and -me?

– Temporal/spaJal gradients probably required for all steps

Bottom Up Approaches

Top Down Approaches

(Infer from extant life)

a) Settings for the origin of life b) Ancient physiologies (T°C, ±O2 etc) c) “Ancient” metabolisms (autotrophy vs heterotrophy) d) Ribozymes and the RNA world and models for the origin of the code e) Early replicators: ribozymes, ancient viruses, minerals, etc f) Origin of catalytic proteins

Organic precursors

(multiple sources) Metabolic circuits

RNA world

Genetic code and protein synthesis

Encapsulation?

DNA life

From Shen & Buick 2005

CO2, CO

Bogom‐up approaches to origin of life studies: Five broad topics

1) Sources or organic precursors to life and chirality selection of d- and l-isomers 2) Synthesis of biopolymers 3) Metabolism versus “replicator” as the first step leading to cells 4) The origin of nucleic acids, the genetic code, and the evolution of the “central dogma” and the first evolving entity 5) Settings for the different steps (still unknown) in the origin of life and how settings can affect the

• utcomes in 1, 2 and 3

The pathway leading to life (Earth)

• 1. FormaJon and concentraJon of organic precursor

compounds and organic catalysts

• 2. CondensaJon and polymerizaJon
• 3. ??? RNA, protein, protometabolism
• 4. ??? The geneJc code, ribosomes etc
• 5. “Unity of biochemistry”: selecJon of the figest genes,

biochemistry etc before the separaJon of the three domains of life

• 6. TransiJon from RNA to DNA
• 7. The three domains of life

– The origin of eukaryotes

A living en-ty?

Loca-on, loca-on, loca-on

Linked?

SPACE ATMOSPHERE

LIGHTNING IDP’S, COMETS, METEORITES, SHOCK SYNTHESIS UV CATALYSIS

OCEAN CRUST PHOTOREDUCTION OF CARBON

HYDROTHERMAL ORGANIC SYNTHESIS

REDUCED INORGANIC SPECIES

SOURCES OF ORGANIC CARBON ON THE PREBIOTIC EARTH ‐ Includes many of the organic building blocks of life

Peridotite-hosted hydrothermal vent

magma

From Schopf,2002

The Building Blocks – The first experiment

Urey, Miller 1953 – from Schopf, 2002 & Smith, Szathmary,1995

Organic Chemistry of Carbonaceous Meteorites

COMPOUNDS CM OCCURRENCE BIOLOGY

Biochemical Building Blocks

Amino acids

Fatty acids Glycerol Phosphate Purines Pyrimidines Ribose Phosphate + + + +

Others

Alcohols

Aldehydes Amides Amines Carboxylic acids Hydrocarbons Ketones Phosphonic acids Sulfonic acids Sulfides

Membranes Nucleic acids

+ + ‐ +

Proteins

+ + + + + + + + + +

SyntheJc organic reacJons potenJally occurring

• n the early Earth
• Gas phase reacJons

– Reduced gases (H2, CH4, NH3, H2) + energy (heat, electric discharge, UV etc) → Cyanide (HCN) and formaldehyde

• ReacJons producing water‐soluble products

– HCN → purines (e.g. adenine) – HCHO → simple sugars (glyceraldehyde, glucose) – HCN + HCHO → amino acids (Strecker synthesis)

• ReacJons producing water insoluble products (hydrocarbon

derivaJves)

– CO, H2 + heat, iron catalyst → hydrocarbons and amphiphiles (long‐chain fagy acids, alcohols) (Fisher‐Tropsch reacJons)

• PolymerizaJon reacJons (least undestood)

– Amino acids + dry heat → pepJde bonds (protein‐like polymers) – Glyceraldehyde → polyglyceric acid – Purines, pyrimidines, sugar, phosphate → nucleic acids

In addiJon, the are a variety of minerals that catalyze reacJon involving the reducJon of CO2 into a variety of organic compounds

Cairns‐Smith Clay Model for the origin of life Clay crystals

Crystal growth and “mutaJon”

Condense organic compounds (clays as templates and reacJve surfaces)“organic takeover”

Macromolecules Cells Crystal growth occurs by addiJon of units

• f the kink edge of a conJnuous ramp

spiraling around the central core InformaJon stored in crystals as a group of crystal “defects” that can be replicated through cleavage and crystal growth

Examples of possible reac-ons involving pyrite based on pyrite having a ca-onic surface in which a variety of anionic reac-ons are possible. The example in (A) is the adsorp-on of glyceraldehyde‐3‐phoshate to the surface followed by polymeriza-on. (B) Par-cipa-on of pyrite in a reac-on that can drive and otherwise energe-cally unfavorable reac-on. For example, the reduc-on of CO2 by H2 has a posi-ve Gibbs free energy reac-on. However, if CO2 reduc-on is linked to the pyrite reac-on the synthesis of formic acid is energe-cally favorable

Organic reac-on on pyrite surfaces under hydrothermal condi-ons (Wächterhäuser, 1988, 1998)

Pyrite

Wächterhäuser Model Pyrite Organic synthesis and condensaJon “surface metabolites” InformaJon Macromolecules CELLS Russell Model 1990’s FeS membranes (bubbles formed from a mix of acidic seawater and alkaline hydrothermal fluid) Organic synthesis (ΔEh across membrane) Metabolic pathway CondensaJon reacJons InformaJon macromolecules CELLS

Models for the origin of life in vent environments

Hypotheses

– “Sparseness” , from soup to a few nuts (Morowitz, Smith and Copley) – “protometabolic networks” that produce high concentrations of “key” organic compounds and not an “organic soup”, is a necessary “first step” leading to life – The origin of the “RNA world” required a “protometabolic network” – The genetic code and protein synthesis evolved in the “RNA world” – DNA world: large genomes and free-living cells

How to get high concentraJons of useful organic compounds?

• Specific synthesis – requires catalysts

(minerals)

Mineral surfaces that may be involved in the origin of life (Modified from Deamer, 2007)

Mineral Surface Properties Lava minerals Si, O, Fe Major mineral surface on early Earth Apatite Ca, PO4

2-

Primary phosphate mineral Clays Si, Al, O Can organize organics into films and catalyze polymerization reactions Pyrite FeS2 Source of reducing power Calcite CaCO3 Chiral surfaces; concentrate

• rganics such nucleotides from

models Quartz SiO2 Chiral surfaces Ultramafic minerals Fe, Mg Generate hydrogen and organic compounds from CO2 Borate minerals B Catalyze the synthesis of ribose Elemental composiJon

Mineral Needs

• Catalyze metabolic networks that involve

the reducJon of CO2 to organic compounds.

• There is a need to idenJfy the catalyJc

ability of other minerals under different T/ pH condiJons (minerals that mimic known enzyme groups: oxidoreductases, transferases, hydrolases, lyases, isomerases and ligases)

We can accomplish this by looking at minerals that contain the metals that are present in different minerals and examine their cataly-c ac-vity under the environmental condi-ons that they can form and remain stable

The BIG gap

• We know how to synthesize many of the
• rganic compounds required by life but we

know ligle about how to incorporate these compounds into “useful” macromolecules

• While it is generally believed that RNA

preceded DNA, we don’t know it can be synthesized under “environmental condiJons” and not in the laboratory

The “Molecular Biologists Dream” ‐ a scenario for the origin of the RNA world

The Scenario:

First, forma-on of precursors to nucleic acids on Earth or elsewhere and accumula-on on Earth Next, nucleoJdes were formed from prebioJc bases, sugars and phosphates and accumulated in some “special” environment. Next, a mineral catalyst such as a mineral like clays then catalyzed the forma-on of long single‐stranded polynucleo-des some of which were converted to complementary double strands by template‐directed synthesis ‐ this resulted in a “library” of double‐stranded RNA on the primi-ve Earth Next, among the double‐stranded RNAs there is at least one that on melJng yields a single‐stranded ribozyme capable of copying itself and its complementary RNA ‐ this would eventually lead to an exponenJally growing populaJon subjected to Darwinian evoluJon

CondensaJon reacJons and the formaJon of macromolecules

• PolymerizaJon on clays – proteins and nucleic acids
• Not known how to make a self‐replicaJng RNA

molecule or catalyJc proteins

• Lipids can self assemble into membrane‐like structures

– Very interesJng studies

The big ques-on is how to get high concentra-ons

• f the precursor compounds (either formed in

situ or concentrated from dilute solu-ons)? This ques-on is crucial in the arguments for and against the “metabolism first” vs the “replicator first” ideas.

Hypothesis: Mineral catalysis provided high concentraJons of organic compounds important for the synthesis of macromolecules and high‐ energy compounds, such as acetyl‐CoA, through “protometabolic” networks that involved mulJple minerals. Metal‐sulfur cluster proteins are relics of this early form of catalysis.

Those favoring “metabolism first” scenarios are divided between the reducJve acetyl‐CoA pathway and the reducJve TCA cycle – both involve CO2 fixaJon. An alkaline seung (serpenJnizaJon) provides a proton motor force for generaJng energy for reacJons.