The only empirical way to deduce how life may have emerged is by taking the stance of assuming continuity of biology from its inception to the present day. 3 Building upon this conviction, we have assessed extant types of energy and carbon metabolism for their appropriateness to conditions probably pertaining in those settings of the Hadean planet that fulfil the thermodynamic requirements for life to come into being.
Wood–Ljungdahl (WL) pathways leading to acetyl CoA formation are excellent candidates for such primordial metabolism.
The universal nature of the Wood–Ljungdahl pathway: the touchstone of biology
(a) The molecular make-up of the C1-body branch in the Wood–Ljungdahl pathway is not conserved between aceto- and methanogens
As is evident from figure 1, the reactions forming the WL pathway of aceto- and methanogens are deceptively similar and, at first glance, appear to differ mainly by the detailed chemical nature of their C1-body (formyl, methenyl, methylene and methyl) carriers, tetrahydrofolate (H4F) in acetogens and tetrahydromethanopterin (H4MPT) in methanogens.
However, acetogenesis appears to be restricted to the bacterial domain, whereas methanogenesis is exclusively found in Archaea (figure 2). This has led to the proposal that it may have been the very diversification of an ancestral hybrid WL pathway into versions eventually yielding acetate or methane as end products (figure 1) that drove the divergence of the last universal common ancestor (LUCA) of all prokaryotes into a bacterial and an archaeal domain.
This is a not trivial problem that is hand-waved away by making a just so guess. Why should that divergence have arisen?
The supposed distribution of free-energy-conserving metabolisms within the prokaryotes.
Differently coloured regions refer to the presence of different chemical (and electrochemical) types of quinones (or complete absence thereof for the cases of the grey regions).
The grey regions can also be interpreted as gaps, which can only be inferred making things up. The divergence clearly falsifies the claim of common ancestry. It is much more reasonable to infer that each clade of bacterias and archaea was made individually, each according to its kind.
Searches of the genomes of acetogens for enzymes clearly homologous to those of the methanogenic C1-branch came up empty-handed with one notable exception, i.e. the initial step of CO2 reduction which is, in both cases, catalysed by a molybdo/tungstopterin enzyme from the complex iron–sulfur molybdoenzyme (CISM) superfamily. However, even these latter enzymes differ substantially with respect to subunit and cofactor composition. Apart from this reaction, all other subsequent reduction steps of C1-bodies seem to be catalysed by unrelated enzymes in aceto- and methanogens.
The result/evidence basically falsifies/refutes the claim of common ancestry within different bacterias, and also between archaea and bacterias.
This finding makes even clearer the above-mentioned fact that the C1-bodies methenyl, methylene and methyl are carried by dissimilar molecules, methanopterins in methanogens and folates in acetogens
Organic soup scenarios stipulate that sufficient quantities of organic molecules may have been produced in Miller–Urey-type reactions to allow heterotrophy as the ancestral system of biomass production. Apart from all the controversy concerning the soundness of the starting conditions for Miller–Urey experiments, it has in the recent past been argued that organic soup scenarios for the origin of life are severely at odds with the second law of thermodynamics. More recent approaches to life's emergence have consequently concentrated on autotrophic carbon fixation and assumed that one or more of the known extant autotrophic pathways can serve as at least a partial model of how it was first achieved.
However, at least six distinct autotrophic carbon fixation pathways have been elucidated during the past few decades.
That observation, of course, once again, is at odds with the claim of common ancestry.
This multiplicity of pathways inevitably raised the question as to which of these possibly functioned in emerging life. As detailed at the beginning of this article, the WL pathway found in the acetogens and the methanogens is presently favored owing to its simplicity, far-going reliance on inorganic cofactors and chemiosmotic potential-generating second nature.
I wonder why the reliance of inorganic cofactors is a plus for the proposed scenarios, in face of the enormous complexity to synthesize them.
If this is how life began fixing carbon, we are led to wonder why an ancestral WL pathway has not become life's one and only principle for biomass production.
True. And if a creator would not be excluded a priori, the question or answer would be: Because the creator invented and designed various pathways to get the feat done, and so, showing his inventive power !!
The multiplicity of autotrophic CO2-fixation pathways therefore indeed represents a major puzzle in current scenarios stipulating an autotrophic origin of life.
There is no puzzle for proponents of intelligent design, however.
The vast majority of present-day methanotrophs, however, use molecular oxygen to oxidize methane. This very fact probably represents the second major obstacle for counting methanotrophy in as a putative primordial energy metabolism.
Denton: Evolution, A Theory in Crisis, page 249
We now know not only of the existence of a break between the living and non-living world, but also that it represents the most dramatic and fundamental of all the discontinuities of nature. Between a living cell and the most highly ordered non-biological system, such as a crystal or a snowflake, there is a chasm as vast and absolute as it is possible to conceive.
Only 355 clusters preserve domain monophyly a These 355 proteins were probably present in LUCA and thus provide a glimpse of LUCA’s genome.
LUCA had 30–100 proteins for ribosomes and translation. LUCA’s genes encode 19 proteins involved in ribosome biogenesis and eight aminoacyl tRNA synthetases, which are also essential for the genetic code to work 2
LUCA lived from gasses. For carbon assimilation, LUCA used the simplest and most ancient of the six known pathways of CO2 fixation, called the acetyl–CoA (or Wood–Ljungdahl) pathway which is increasingly central for our concepts on early evolution because of its chemical simplicity 1 Carbon monoxide (CO) is synthesized by carbon monoxide dehydrogenase (CODH) The methyl and carbonyl moieties are condensed to an enzyme-bound acetyl group that is removed from a metal cluster in acetyl–CoA synthase (ACS) as an energy-rich thioester. Thioesters harbor chemically reactive bonds that play a crucial role in energy metabolism and in metabolism in general, both modern and ancient.
Life is about harnessing energy. Thioesters b are chemically reactive—they forge direct links between carbon metabolism and energy metabolism (ATP synthesis) as they give rise to acetyl phosphate, the possible precursor of ATP in evolution as a currency of high-energy bonds
Many RNA-modifying enzymes trace to LUCA, particularly the enzymes that modify tRNA. Several of those enzymes are methyltransferases (many SAM dependent), and they remind us that, before the genetic code arose, the four main RNA bases could hardly have been in great supply in pure form because there were no genes or enzymes, only chemical reactions. Spontaneous synthesis of bases in a real early Earth environment like a hydrothermal vent, an environment that lacks the control of a modern laboratory , is not likely to generate the four main bases in pure form. Many side products will accumulate, including chemically modified bases .
Chemical modifications in the tRNA anticodon are essential for codon–anticodon interactions to work. Modifications of the rRNA are concentrated around the peptidyl transferase site and are also essential for tRNA ribosome interactions. It is possible ( how does the author know ?? ) that the genetic code itself arose in the same chemically reactive environment where LUCA arose and that modified bases in tRNA carry the chemical imprint of that environment. New laboratory syntheses of RNA molecules in the origin of life context now also include investigations of modified bases , as it is becoming increasingly clear that these are crucial components at the very earliest phases of molecular and biological evolution.
a In cladistics, a monophyletic group, or clade, is a group of organisms that consists of all the descendants of a common ancestor (or more precisely ancestral population). Monophyletic groups are typically characterised by shared derived characteristics (synapomorphies), which distinguish organisms in the clade from other organisms.
b In chemistry thioesters are compounds with the functional group R–S–CO–R'. They are the product of esterification between a carboxylic acid and a thiol. In biochemistry, the best-known thioesters are derivatives of coenzyme A, e.g., acetyl-CoA. Thioesters are common intermediates in many biosynthetic reactions, including the formation and degradation of fatty acids and mevalonate, precursor to steroids.
Thioesters and the origin of lifeAs posited in a "Thioester World", thioesters are possible precursors to life. As de Duve explains:
It is revealing that thioesters are obligatory intermediates in several key processes in which ATP is either used or regenerated. Thioesters are involved in the synthesis of all esters, including those found in complex lipids. They also participate in the synthesis of a number of other cellular components, including peptides, fatty acids, sterols, terpenes, porphyrins, and others. In addition, thioesters are formed as key intermediates in several particularly ancient processes that result in the assembly of ATP. In both these instances, the thioester is closer than ATP to the process that uses or yields energy. In other words, thioesters could have actually played the role of ATP in a "thioester world" initially devoid of ATP. Eventually, [these] thioesters could have served to usher in ATP through its ability to support the formation of bonds between phosphate groups.
However, due to the high free energy change of thioester's hydrolysis and correspondingly their low equilibrium constants, it is unlikely that these compounds could have accumulated abiotically to any significant extent especially in hydrothermal vent conditions
Last edited by Admin on Fri Feb 14, 2020 6:22 pm; edited 8 times in total