Archive | August 2015

Paradigm shifts in the world of biology- evolution of proteins

At the moment the race is on to prove that the biochemical compounds got kick-started, not by earthly processes, but by organic molecules arriving on comets. I must admit I have my doubts as to the relative impact of cometary compounds compared to the contribution of Earth’s geological processes creating a complex mix of chemicals ready to create the “primordial soup” for life.  Of course biological structures are chemically based, and comply with both the laws of physics and chemistry (and maths) so far as one is aware anyhow (they seem to be able to slow down entropy).

The planet was synthesized as the solar system formed about 4.5 Ga, creating toxic conditions that prevented life from arising for another billion years or so, such as high levels of methane in the atmosphere.  There are Bacteria and other forms of life, including multicellular life, which form another Kingdom containing plants, animals and fungi, in which hominids are found. However, there is another Kingdom, that of the unicellular organisms Archaea which are ubiquitous on the planet. These and some forms of Bacteria do not photosynthesise, but utilise chemicals, and some of these are called chemotrophs whilst some are called Methanogens, because they utillise chemical substances to produce methane.

A lot of these are found in extreme environments, especially Archaea which tend to like toxic conditions. These types of Bacteria and Archaea are the ones that probably were the earliest ones when Earth was toxic. When comets were bringing in toxic organic molecules like formaldehyde. But after Earth stabilised as a whole rock, which was a good billion years earlier than when the first fossil unicellular organisms are found. So it took a billion years for the processes to occur that resulted in life, and one must ask what may be involved.  That life was therefore not the cyanobacteria, the unicellular organisms which by developing photosynthesis oxygenated the planet, making it possible for many lifeforms to develop by using the nascent oxygen of the atmosphere. Flamingos turn pink due to eating such “algae”- an erroneous term that should never be used in the context of cyanobacteria. Cyanobacteria which photosynthesized arose yet another billion years after the original unicellular organisms, c. 2.4 Ga.

There is a difference between methanogens which produce methane and other chemotrophs and the type of protocells which must have developed on the early Earth. It is clear the latter must have found a way to utilise the toxic compounds available. Thus I think that if people are looking for methanogens such as on Mars where the production of methane was sought as evidence of life, they may have it the wrong way around. What is needed is an organism that can somehow utilise toxic conditions and/or a toxic atmosphere, not ones that can produce it! Such organisms that may have existed for the first billion years of toxic Earth, surviving and feeding off what was available! Which wasn’t oxygen, since it took a further billion years after life evolved, for unicellular bacteria to figure out how to split the water molecule, and for them to learn to use the carbon dioxide in the atmosphere in photosynthesis.

Therefore one is looking at another kind of unicellular organism to start the Life show off.  The organism I suggest may have been anaerobic methanotrophs as there was no oxygen but a lot of methane in the early toxic Earth.  Wikipedia describes these on the page “Methanotroph” (https://en.wikipedia.org/wiki/Methanotroph), including references.  Excerpts have been repeated here for explanatory purposes, with some modification for further explanation:

(from Wikipedia): Methanotrophs oxidize methane by first initiating reduction of an oxygen atom to H2O2 and transformation of methane to CH3OH using methane monooxygenases (MMOs, enzymes) . Differences in the method of formaldehyde fixation and membrane structure divide the methanotrophs into several groups. Methane-oxidizing bacteria have been separated into four subgroups: two methane-assimilating bacteria (MAB) groups, the methanotrophs, and two autotrophic ammonia-oxidizing bacteria (AAOB). Investigations in marine environments revealed that methane can be oxidized anaerobically (Anaerobic Oxidation of Methane or AOM) by a consortia of methane-oxidizing Archaea and sulfate-reducing Bacteria. The exact mechanism of methane oxidation under anaerobic conditions is still a topic of debate but the most widely accepted theory is that the Archaea use the reversed methanogenesis pathway to produce carbon dioxide and another, unknown substance. Ettwig et al. found a bacterium oxidizes methane anaerobically without a partner, probably by utilizing the oxygen produced internally from the dismutation of nitric oxide into nitrogen and oxygen gas.
Wikipedia further describes this process in its page “Anaerobic oxidation of methane” (https://en.wikipedia.org/wiki/Anaerobic_oxidation_of_methane), excerpts from which are similarly provided:
(from Wikipedia): AOM occurs in anoxic marine and freshwater sediments. During AOM methane is oxidized with different terminal electron acceptors such as sulfate, nitrate, nitrite and metals. ANME stands for “anaerobic methanotroph”. Recently, ANME-2d is shown to be responsible for nitrate-driven AOM without a partner organism via reverse methanogenesis with nitrate as the terminal electron acceptor, using genes for nitrate reduction that have been laterally transferred from a bacterial donor. In 2010, omics analysis showed that nitrite reduction can be coupled to methane oxidation by a single Bacterial species, NC10, without the need for an Archaeal partner.

Recent research has just changed the ball-game for how life developed on Earth.  Forsythe et al. (described in Science Daily as  “Finding the origins of life in a drying puddle http://www.sciencedaily.com/releases/2015/07/150720094522.htm  July 20, 2015; link to 2015 paper below) produced polypeptides in wetting and drying conditions, with the likelihood being that proteins evolved on terrestrial Earth and not in the oceans as previously envisaged.  This confirmed to me the importance of the role evaporation in life’s evolution.

Although it is very interesting that a puddle containing the necessary ingredients may have been available for evaporative and hydrating processes to work on, creating polypeptides and later complex proteins in terrestrial zones, that does not per se mean that life itself i.e. the initial protocell, arose terrestrially.  Life may still have arisen in the oceans, but this would necessitate the “puddles” being nearby to an ocean, so that coastal inundation could have swept the new proteins into the ocean.  There they then would have to have replicated to become abundant enough to reach locations where life formed, e.g. deepsea vents, indicating that RNA may have preceded life. If however the process of polypeptide formation leading to proteins led to life on land, then RNA may have arisen at an early stage after it did so.

These timelines, processes and organisms have implications for how these processes may occur on other planets.  It is interesting to speculate that on other planets somewhere in the Universe, the conditions (gases etc.) may not be entirely chemically produced. They could, from our knowledge of life on Earth, involve the production of oxygen for an advanced evolutionary atmosphere, and the production of carbon dioxide from methane for an earlier, toxic one.  All that is needed for the production of proteins is apparently a puddle undergoing drying and wetting.   But I am a skeptic unfortunately about the prospects of there being life on any other planet!

All this leads me to speculate as to what happened next.  I mean in the puddle.  Previously I had thought that a membrane may have begun, which was the precursor to the cell wall, by a water or water-metallic membrane forming between two rocks, eventually closing around like a bubble.  This could have occurred at the vents for example.  However if proteins evolved in puddles, whether on the coast or inland, the next step for complex proteins might have been protective mechanisms.  From drying out that is, or from inundation for that matter.  To avoid evaporative damage or solar UV damage, proteins may have evolved protective structures.  These may initially have been in the form of simple lipid structures, and lipids are hydrophobic so keep water out, but may also prevent leachiing of water and nutrients.  So if the team of researchers can form proteins in the puddle it might be interesting to see what happens if they add a few lipids to the mix.

Either way it seems to me that coastal environments are favored, particularly those in which metallic elements are readily available, such as the volcanic salt lakes of eastern Africa.  If one follows up the anaerobic methanotroph theory, elements were definitely needed for bacteria, and may have been for some protein development earlier.  For example see the excellent review by Hanson and Hanson in the references below for the importance of copper to methanotrophs.  Previously I thought that such evaporative lakes may have been the site of eukaryote (multicellular) evolution, however it now appears that marine conditions may not necessarily have been involved for evolution of prokaryotes before them.

However fossil evidence of early bacteria indicate that the marine environment is indeed likely to have been the site for evolution of life and its radiation.  This presents a conundrum as newly evolved proteins in puddles must get from land to sea, inferring coastal inundation processes.  And they must be capable of replication, inferring the evolution of RNA replicative processes prior to the evolution of life.

REFERENCES

Forsythe, Jay G. et al. (2015): “Ester-Mediated Amide Bond Formation Driven by Wet-Dry Cycles: A Possible Path to Polypeptides on the Prebiotic Earth”; Angewandte Chemie International Edition (early version online: http://onlinelibrary.wiley.com/doi/10.1002/anie.201503792/abstract).

References given by Wikipedia worth following up:
Ettwig, K. F.; Butler, M. K.; Le Paslier, D.; Pelletier, E.; Mangenot, S.; Kuypers, M. M. M.; Schreiber, F.; Dutilh, B. E.; Zedelius, J.; De Beer, D.; Gloerich, J.; Wessels, H. J. C. T.; Van Alen, T.; Luesken, F.; Wu, M. L.; Van De Pas-Schoonen, K. T.; Op Den Camp, H. J. M.; Janssen-Megens, E. M.; Francoijs, K. J.; Stunnenberg, H.; Weissenbach, J.; Jetten, M. S. M.; Strous, M. (2010). “Nitrite-driven anaerobic methane oxidation by oxygenic bacteria”. Nature 464 (7288): 543–548. doi:10.1038/nature08883.
Hanson, R. S. and Hanson, T. E. (1996). “Methanotrophic bacteria”. Microbiological reviews 60 (2): 439–471.

Haroon, M.F., Hu, S., Shi, Y., Imelfort, M., Keller, J., Hugenholtz, P., et al. (2013) Anaerobic oxidation of methane coupled to nitrate reduction in a novel archaeal lineage. Nature 500: 567–570.

Reimann, Joachim; Jetten, Mike S.M.; Keltjens, Jan T. (2015). “Chapter 7, Section 4 Enzymes in Nitrite-driven Methane Oxidation”. In Peter M.H. Kroneck and Martha E. Sosa Torres. Sustaining Life on Planet Earth: Metalloenzymes Mastering Dioxygen and Other Chewy Gases. Metal Ions in Life Sciences 15. Springer. pp. 281–302. doi:10.1007/978-3-319-12415-5_7