Origin of Life

Theories and evidence for chemical biopoieses

In Search of the Simplest Cell

ORIGIN OF LIFE: IN SEARCH OF THE SIMPLEST CELL: "In investigating the origin of life and the simplest possible life forms, one needs to enquire about the composition and working of a minimal cell that has some form of metabolism, genetic replication from a template, and boundary (membrane) production."

Hypothesis: the origin of life in a hydrogel environment. : "A hypothesis is proposed that the first cell(s) on the Earth assembled in a hydrogel environment. Gel environments are capable of retaining water, oily hydrocarbons, solutes, and gas bubbles, and are capable of carrying out many functions, even in the absence of a membrane. Thus, the gel-like environment may have conferred distinct advantages for the assembly of the first cell(s)."
Trevors JT, Pollack GH. Prog Biophys Mol Biol. 2005 Sep;89(1):1-8. Hypothesis: the origin of life in a hydrogel environment.

Possible impact of a primordial oil slick on atmospheric and chemical evolution.: "Low molecular weight liquid hydrocarbons from various sources, could have formed an oil layer covering the primeval ocean (present already 4.0-4.4 x 10(9) yr ago), preventing water from evaporating into the atmosphere. Water from other sources, precipitated by cold traps at higher altitude in the atmosphere, becomes trapped in the ocean. In a thereby more dry and presumably reducing atmosphere (before 3.9 x 10(9) yr ago) even more hydrocarbons, as well as reactive molecules will form. An oil layer can possibly act as a dry solvent for reactions, where the reactive molecules can produce monomers and condensing agents. Monomers and eventual polymers formed could become strongly concentrated at the oil-water interface, favouring molecular interactions at high mobility and low dilution, without exposure to the destructive action of UV-light. Increased water leakiness of the oil layer due to accumulation of polar molecules within, would lead to photooxidation of liquid hydrocarbons, and subsequent emulsification at the oil-water interface, forming cellular structures. The atmosphere would then have lost its reducing character."
Nilson FP. Possible impact of a primordial oil slick on atmospheric and chemical evolution. Orig Life Evol Biosph. 2002 Jun;32(3):247-53.

Growth of organic microspherules in sugar-ammonia reactions : "Reaction of small sugars of less than four carbons with ammonia in water yielded organic microspherules generally less than ten microns in size. The time course of microspherule growth was examined for the D-erythrose-ammonia reaction that yielded microspherules attached to the glass walls of containers. Measurements were made of the elemental composition and infrared spectrum of the microspherule material. These viscose semi-solid microspherules are viewed as possible containers for prebiotic catalytic processes relevant to the origin of life."
Weber AL. Growth of organic microspherules in sugar-ammonia reactions. Orig Life Evol Biosph. 2005 Dec;35(6):523-36.

The possible origin of the first cell biosystem in the thermal subsurface environment of the earth. : "Bacteria are the simplest living biosystems or organisms that exhibit all the characteristics of life. As such, they are excellent models to examine the cell as the basic unit of life and the cell theory which states that all organisms are composed of one or more similar cells. In this article I examine the hypothesis that the primordial soup so often referred to in science was possibly an oil/water interface and/or emulsion in the Earth's, warm, anaerobic subsurface. This warm subsurface location, protected from surface radiation, could have been a favourable location for the assembly of the first bacterial cells on the Earth capable of growth and controlled division or the first biosystem."
Trevors JT. The possible origin of the first cell biosystem in the thermal subsurface environment of the earth. Riv Biol. 2004 Jan-Apr;97(1):79-90.

An archaeal antioxidant: characterization of a Dps-like protein from Sulfolobus solfataricus. : "Evolution of an oxygenic atmosphere required primordial life to accommodate the toxicity associated with reactive oxygen species. We have characterized an archaeal antioxidant from the hyperthermophilic acidophile Sulfolobus solfataricus. The amino acid sequence of this approximately 22-kDa protein shares little sequence similarity with proteins with known function. However, the protein shares high sequence similarity with hypothetical proteins in other archaeal and bacterial genomes. Nine of these hypothetical proteins form a monophyletic cluster within the broad superfamily of ferritin-like diiron-carboxylate proteins. Higher order structural predictions and image reconstructions indicate that the S. solfataricus protein is structurally related to a class of DNA-binding protein from starved cells (Dps). The recombinant protein self assembles into a hollow dodecameric protein cage having tetrahedral symmetry (SsDps). The outer shell diameter is approximately 10 nm, and the interior diameter is approximately 5 nm. Dps proteins have been shown to protect nucleic acids by physically shielding DNA against oxidative damage and by consuming constituents involved in Fenton chemistry. In vitro, the assembled archaeal protein efficiently uses H2O2 to oxidize Fe(II) to Fe(III) and stores the oxide as a mineral core on the interior surface of the protein cage. The ssdps gene is up-regulated in S. solfataricus cultures grown in iron-depleted media and upon H2O2 stress, but is not induced by other stresses. SsDps-mediated reduction of hydrogen peroxide and possible DNA-binding capabilities of this archaeal Dps protein are mechanisms by which S. solfataricus mitigates oxidative damage."
Wiedenheft B, Mosolf J, Willits D, Yeager M, Dryden KA, Young M, Douglas T. An archaeal antioxidant: characterization of a Dps-like protein from Sulfolobus solfataricus. Proc Natl Acad Sci U S A. 2005 Jul 26;102(30):10551-6. Epub 2005 Jul 15.Free Full Text article

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Two alternative views on the relationship of the major lineages (omitting viruses) based on phylogenies of Life on Earth (right - click to enlarge image).

The Cyanobacterial radiation within the Eubacteria consists of several lineages of phyletically (morphologically and genetically) related organisms. Several of these organisms show a striking resemblance to fossil counterparts (images). [R]

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Cyanobacteria abstracts

The bioenergetic role of dioxygen and the terminal oxidase(s) in cyanobacteria. : "Owing to the release of 13 largely or totally sequenced cyanobacterial genomes, it is now possible to critically assess and compare the most neglected aspect of cyanobacterial physiology, i.e., cyanobacterial respiration, also on the grounds of pure molecular biology (gene sequences). While there is little doubt that cyanobacteria (blue-green algae) do form the largest, most diversified and in both evolutionary and ecological respects most significant group of (micro)organisms on our earth, and that what renders our blue planet earth to what it is, viz. the O(2)-containing atmosphere, dates back to the oxygenic photosynthetic activity of primordial cyanobacteria about 3.2x10(9) years ago, there is still an amazing lack of knowledge on the second half of bioenergetic oxygen metabolism in cyanobacteria, on (aerobic) respiration. Thus, the purpose of this review is threefold: (1) to point out the unprecedented role of the cyanobacteria for maintaining the delicate steady state of our terrestrial biosphere and atmosphere through a major contribution to the poising of oxygenic photosynthesis against aerobic respiration ("the global biological oxygen cycle"); (2) to briefly highlight the membrane-bound electron-transport assemblies of respiration and photosynthesis in the unique two-membrane system of cyanobacteria (comprising cytoplasmic membrane and intracytoplasmic or thylakoid membranes, without obvious anastomoses between them); and (3) to critically compare the (deduced) amino acid sequences of the multitude of hypothetical terminal oxidases in the nine fully sequenced cyanobacterial species plus four additional species where at least the terminal oxidases were sequenced. These will then be compared with sequences of other proton-pumping haem-copper oxidases, with special emphasis on possible mechanisms of electron and proton transfer."

Paumann M, Regelsberger G, Obinger C, Peschek GA. The bioenergetic role of dioxygen and the terminal oxidase(s) in cyanobacteria. Biochim Biophys Acta. 2005 Apr-May;1707(2-3):231-53. Epub 2005 Jan 26.

Common freshwater cyanobacteria grow in 100% CO2. : "Cyanobacteria and similar organisms produced most of the oxygen found in Earth's atmosphere, which implies that early photosynthetic organisms would have lived in an atmosphere that was rich in CO2 and poor in O2. We investigated the tolerance of several cyanobacteria to very high (>20 kPa) concentrations of atmospheric CO2. Cultures of Synechococcus PCC7942, Synechocystis PCC7942, Plectonema boryanum, and Anabaena sp. were grown in liquid culture sparged with CO2-enriched air. All four strains grew when transferred from ambient CO2 to 20 kPa partial pressure of CO2 (pCO2), but none of them tolerated direct transfer to 40 kPa pCO2. Synechococcus and Anabaena survived 101 kPa (100%) pCO2 when pressure was gradually increased by 15 kPa per day, and Plectonema actively grew under these conditions. All four strains grew in an anoxic atmosphere of 5 kPa pCO2 in N2. Strains that were sensitive to high CO2 were also sensitive to low initial pH (pH 5-6). However, low pH in itself was not sufficient to prevent growth. Although mechanisms of damage and survival are still under investigation, we have shown that modern cyanobacteria can survive under Earth's primordial conditions and that cyanobacteria-like organisms could have flourished under conditions on early Mars, which probably had an atmosphere similar to early Earth's."
Thomas DJ, Sullivan SL, Price AL, Zimmerman SM. Common freshwater cyanobacteria grow in 100% CO2. Astrobiology. 2005 Feb;5(1):66-74.

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Modern stromatolites -- living fossils

Stromatolites in Shark Bay, Western Australia -- exposed (left) and submerged (right).

This extensive field of relict organisms was discovered in 1956. More examples occur in other locations on the ancient shield of western Australia. Map. Western Australia boasts some of the oldest known examples of stromatolites (3.45 billion years old), occurring as fossils in the Pilbara region between Marble Bar and Port Hedland. More recently, stromatolite colonies have been discovered in locations such as the Bahamas, the Indian Ocean, Yellowstone National Park, and Poza Azul lake at Cuatro Cienegas, Mexico.
At low (left) and higher tides (right).

The water of Hamelin Pool within Shark Bay is twice as saline as typical sea-water because of rapid evaporation from the shallow water, and because a bar across the bay's entrance reduces mixing with normal brine. This hypersaline water is inhospitable to marine animals, which which otherwise would feed on the bacteria that construct stromatolites. As a result stromatolites can grow undisturbed in Shark Bay. Most stromatolites are extremely slow growing. Those in Hamelin Pool grow at a maximum of .3mm a year. This means that those that are up to a metre high are several thousands of years old. More images of stromatolites of Hamelin Pool (Shark Bay) / stromatolites displaying weathering / partly submerged / partly exposed

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Structure of stromatolites

Stromatolites grow slowly – layer upon layer – as mats of cyanobacteria grow atop older layers. Because this process still occurs today, paleontologists were able to determine the origin of carbonaceous material in fossilized laminated domes found widely around the globe.

Bacterial photosynthesis depletes carbon dioxide in the surrounding water, initiating precipitation of calcium carbonate. Layers of CaCO3 precipitate over the growing mat of bacterial filaments. This mineral, together with grains of sediment precipitating from the water, is trapped within a sticky layer of mucilage that surrounds the bacterial colonies. The cyanobacteria continued to grow upwards through this sediment to form a new layer. As this process occurs over and over again, layers of sediment are created.

Hamelin Pool in Shark Bay in western Australia is well known for the stromatolite "turfs" rising along its beaches. Meter-high stromatolites in the northern Bahamas are alternately buried and exhumed by carbonate sand bodies in an area of active bedform migration. Marooned Mexican stromatolites in Poza Azul lake at Cuatro Cienegas, Mexico, are of interest to NASA scientists who believe that these calcified clumps of primitive bacteria lurking in cactus-ringed lagoons could provide important clues in their search for extraterrestrial life. Images: diagram of stromatolites in dolomite block / fossil showing columnar structure / cylindrical structure / fossil showing striations / diagram of stromatolite morphology / stromatolite types /

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Fossilized stromatolites

Ancient fossilized strata of stomatolites at Steep Rock Iron Mine Steep Rock Stromatolites, Canada (right)

Originating over 3 billion years ago, stromatolites are the oldest known fossils. Fossilized stromatolites were laid down by colonial structures built by photosynthesizing cyanobacteria and other microbes. The cyanobacteria, also called blue-green algae, were likely responsible for the creation of earth's oxygen atmosphere. These organisms are prokaryotic – cells lacking a cellular nucleus – and thrived in warm aquatic environments, building reefs much as coral does today. Domed columns are typical, and the fossilized structures were quite extensive. Cyanobacteria were the dominant lifeform on Earth for over 2 billion years.

Today they are nearly extinct, living a precarious existence in only a few localities worldwide – the most famous location is Shark Bay in Western Australia. Domed columns are typical, and the fossilized structures were quite extensive.
Close-up of Precambrian stromatolites of the 1.3 Ga Siyeh Formation in Glacier National Park (left).
NW Ontario, Canada contains the Archean Steep Rock carbonate platform, noted as one of the best-exposed and preserved platforms of this age on the planet. Stromatolite in ferruginous chert-carbonate unit, Kakabeka Falls Carbonate Chert Picture

"The centres of many stromatolites in the Siyeh Formation are concave downward rather than domed upward, as if they have collapsed. This may, indeed, have happened. The region lay close to the edge of the continent, where frequent earthquakes would have shaken the stromatolites, perhaps damaging them in this way." Source

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Stromatolite fossils

The fine details of fossilized stromatolites, together with chemical profiles and observation of modern stromatolites, reveal their origin in the slow accretion of minerals associated with cyanobacteria.

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. . . origin of site 10/06/06