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Thread: To the Origin of Life - the Early Evolution of Biosynthesis and Energy Metabolism

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    Administrator lpetrich's Avatar
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    To the Origin of Life - the Early Evolution of Biosynthesis and Energy Metabolism

    I'll be posting on some stuff I'd collected some years ago -- stuff that I'll be wanting to update wherever possible.

    Did DNA replication evolve twice independently? [Nucleic Acids Res. 1999] - PubMed - NCBI In Bacteria and Archaea (or Eubacteria and Archaebacteria) separately, with eukaryotes inheriting their DNA-replication system from Archaea.

    Modern mRNA proofreading and repair: clues that the last universal common ancestor possessed an RNA genome? [Mol Biol Evol. 2005] - PubMed - NCBI

    I've seen the theory that the LUCA (Last Universal Common Ancestor) had a heteroduplex genome, with DNA and RNA strands bound to each other. But the LUCA did have DNA, meaning that DNA had a pre-LUCA origin. DNA building blocks are built from RNA ones, first by chemically reducing the ribose parts to deoxyribose, then by adding a methyl group to uracil, making thymine. DNA without the second step is uracil-DNA.

    Also pre-LUCA is the protein-synthesis apparatus. It involves transcription from genomic DNA to messenger RNA, and translation from mRNA to proteins. This translation is done with the help of RNA-protein complexes called ribosomes, and the RNA in them seems to be their most essential part. The translation involves transfer RNA's, snippets of RNA where one end fits the mRNA, and the other end has an amino acid attached. Amino acids are the building blocks of proteins. Transfer RNA's are notable for having nucleobases that were modified after being transcribed from the genome, postttranscriptional modification. Some of these modified nucleobases make their tRNA's capable of matching onto more than one mRNA nucleobase, enabling one tRNA to match onto several different three-nucleotide "codons".

    So we see so far RNA, RNA, RNA, and more RNA. RNA can act as an enzyme, and some enzyme cofactors contain bits of RNA: Coenzymes as coribozymes. [Biochimie. 2002] - PubMed - NCBI, Modern metabolism as a palimpsest of the RNA world. [Proc Natl Acad Sci U S A. 1989] - PubMed - NCBI mention B vitamins B1 (thiamine), B2 (riboflavin), B3 (niacin), B5 (pantothenate), B6 (pyridoxal).

    The remaining B vitamins are B7 (biotin), B9 (folate), and B12 (cobalamin). Biotin likely emerged after proteins did, not in the RNA world. B12 has a porphyrin ring, and porphyrins likely date back to the RNA world, if not farther.

    Niacin's more formal name is nicotinic acid, and it occurs as nicotinamide adenine dinucleotide (NAD), a length-2 RNA snippet. The nicotinamide part looks suspiciously like some modified nucleobase.

    Another cofactor is ATP, adenosine triphosphate: (adenine) - (ribose) - (P) - (P) - (P) where the (P) is a phosphate ion. It is often used as an energy intermediate, and that energy resides in its phosphate-phosphate bonds. When used in that fashion, it gets reduced to adenosine diphosphate (2 phospates) or adenosine monophosphate (1 phosphate), and it gets rebuilt by adding phosphates to make ATP again.

    More and more and more RNA.

    Because of all that RNA, the RNA world has become a very widely accepted hypothesis.

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    Administrator lpetrich's Avatar
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    The RNA world hypothesis: the worst theory of the early evolution of life (except for all the others)a | Biology Direct | Full Text discusses some criticisms of that hypothesis.

    Like: RNA is too complex a molecule to have arisen prebiotically

    Its building blocks have the structure (phosphate) - (ribose) - (nucleobase) and they join together in a chain with structure
    (R) - (N)
    (P)
    (R) - (N)
    (P)
    (R) - (N)
    (P)

    Though one can make some nucleobases prebiotically, it's very hard to do so for ribose. I've seen theories that it was not the first backbone molecule, that it had predecessors like amino acids or polycyclic aromatic hydrocarbons.

    He also notes: RNA is inherently unstable. Catalysis is a relatively rare property of long RNA sequences only. The catalytic repertoire of RNA is too limited

    Proteins are also limited, even if not as much. That is why some enzymes include cofactors, including metal ions. Some cofactors are plausibly traced back to the RNA world, indicating that RNA enzymes had help, just as protein enzymes do.

    Then some stuff on the possible origin of ribosomes as protein enzymes for replicating RNA. I find it very unconvincing, since it is very hard to make a protein replicator. But with nucleic acids, replication is almost trivially easy -- a nucleic-acid strand can be used as a template for making a copy of itself. Watson and Crick themselves noticed that when they worked out the structure of DNA: "It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material."

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    Administrator lpetrich's Avatar
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    The physiology and habitat of the last universal common ancestor | Nature Microbiology
    The concept of a last universal common ancestor of all cells (LUCA, or the progenote) is central to the study of early evolution and life's origin, yet information about how and where LUCA lived is lacking. We investigated all clusters and phylogenetic trees for 6.1 million protein coding genes from sequenced prokaryotic genomes in order to reconstruct the microbial ecology of LUCA. Among 286,514 protein clusters, we identified 355 protein families (∼0.1%) that trace to LUCA by phylogenetic criteria. Because these proteins are not universally distributed, they can shed light on LUCA's physiology. Their functions, properties and prosthetic groups depict LUCA as anaerobic, CO2-fixing, H2-dependent with a Wood–Ljungdahl pathway, N2-fixing and thermophilic. LUCA's biochemistry was replete with FeS clusters and radical reaction mechanisms. Its cofactors reveal dependence upon transition metals, flavins, S-adenosyl methionine, coenzyme A, ferredoxin, molybdopterin, corrins and selenium. Its genetic code required nucleoside modifications and S-adenosyl methionine-dependent methylations. The 355 phylogenies identify clostridia and methanogens, whose modern lifestyles resemble that of LUCA, as basal among their respective domains. LUCA inhabited a geochemically active environment rich in H2, CO2 and iron. The data support the theory of an autotrophic origin of life involving the Wood–Ljungdahl pathway in a hydrothermal setting.
    There is a lot to unpack here.
    • Anaerobic: the LUCA did not use oxygen or release that gas, and that gas was likely poisonous to it.
    • CO2-fixing: it got its biological-molecule carbon from CO2.
    • H2-dependent: it lived off of hydrogen gas.
    • Wood-Ljungdahl pathway: it takes CO2 and H2 and makes acetic acid: CH3COOH -- did the LUCA piss vinegar?
    • N2-fixing: it got its biological-molecule nitrogen from N2.
    • Thermophilic: it liked high temperatures, like 80 C.
    • FeS clusters: iron-sulfur clusters in its enzymes
    • Transition metals: vanadium, manganese, iron, cobalt, copper, zinc, molybdenum, ...
    • Flavins: riboflavin (vitamin B2) with RNA building blocks and proteins. Involved in electron-transfer metabolism.
    • S-adenosyl methionine: the amino acid methionine with a RNA building block. Involved in the transfer of methyl: CH3- groups.
    • Coenzyme A: the amino acid cysteine and pantothenic acid (vitamin B5) along with a RNA building block. Involved with acetic acid.
    • Ferredoxin: an enzyme with iron-sulfur clusters that is involved in electron-transfer metabolism.
    • Molybdopterin: a carrier of molybdenum that is much like folic acid (vitamin B9)
    • Corrins: porphyrin-like rings that are in vitamin B12.
    • Selenium: a sulfur-like element that sometimes substitutes for sulfur.

    It also did modification of RNA nucleobases, such as what is in transfer RNA's.

    So all in all, it was a rather complicated organism, and there is evidence that it had a lot of evolution behind it.

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    Administrator lpetrich's Avatar
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    The Emergence and Early Evolution of Biological Carbon-Fixation by authors Madeline C. Weiss, Filipa L. Sousa, Natalia Mrnjavac, Sinje Neukirchen, Mayo Roettger, Shijulal Nelson-Sathi & William F. Martin.

    That paper's authors propose that the LUCA had not one, but two carbon-fixation pathways, two ways of capturing CO2: the Wood-Ljungdahl pathway and the citric-acid cycle. That latter one is also called the tricarboxylic acid cycle and the Krebs cycles. The W-L pathway makes methyl groups and acetic acid, while the citric-acid cycle produces starter molecules for several amino acids.

    The Wood–Ljungdahl pathway:

    The first part uses a relative of folic acid, tetrahydrofolate:
    CO2 + 2H+ + 2e + ATP + H2O -> HCOOH + ADP + Pi (free phosphate ion)

    e = electron, and in LUCA-ish organisms and the LUCA itself, it comes from hydrogen gas.

    The THF itself starts off as -NH HN- (I won't try to draw the rest of the molecule)
    -NH HN-
    HCOOH ->, -> H2O
    -N-CHO HN-
    H+ ->, -> H2O
    -N-CH=N(+)-
    H+ + 2e ->
    -N-CH2-N-
    2H+ + 2e ->
    -NH CH3-N-

    This methyl group: CH3- is then handled by various other enzymes and coenzymes. For biosynthesis, it is attached to other molecules. But in methanogens, it gets a final 2H+ + 2e and becomes methane.

    The second part of the W-L pathway:
    CO2 + 2H+ + 2e -> CO + H2O
    CH3-X + CO + CoA-SH -> CoA-S-(C=O)-CH3 + H-X
    Thus making acetyl coenzyme A. The acetyl part may then be used for additional biosynthesis tasks, or else released as acetic acid by adding water.

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    Administrator lpetrich's Avatar
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    Here is the Citric acid cycle. Biochemists often like to use -ate instead of -ic acid in the names of acids. Thus, acetate instead of acetic acid.

    Citrate: COOH-CH2-(HO)C(COOH)-CH2-COOH
    CoA-SH (coenzyme A) ->, -> H2O + CH3-CO-S-CoA (acetyl coenzyme A)
    Oxaloacetate: COOH-CH2-CO-COOH
    2H+ + 2e ->
    Malate: COOH-CH2-HCOH-COOH
    -> H2O
    Fumarate: COOH-CH=CH-COOH
    2H+ + 2e ->
    Succinate: COOH-CH2-CH2-COOH
    CoA-SH ->, -> H2O
    Succinyl CoA: COOH-CH2-CH2-CO-S-CoA
    CO2 + 2H+ + 2e ->, -> H2O + CoA-SH
    Alpha-ketoglutarate: COOH-CH2-CH2-CO-COOH
    2H+ + 2e + CO2 ->
    Isocitrate: COOH-CH2-(H)C(COOH)-HCOH-COOH
    (rearranged)
    Citrate: COOH-CH2-(HO)C(COOH)-CH2-COOH

    As one can tell, both the W-L pathway and the citric acid cycle consume electrons and CO2 molecules and make acetic acid.

    The citric-acid cycle supplies raw materials for making several protein-forming amino acids. Here are the ones with the simplest pathways for making them (somewhat simplified):

    Oxaloacetate: COOH-CH2-CO-COOH
    -NH2 ->
    Aspartate: COOH-CH2-CH(-NH2)-COOH
    -NH2 ->
    Asparagine: NH2-CO-CH2-CH(-NH2)-COOH

    Alpha-ketoglutarate: COOH-CH2-CH2-CO-COOH
    -NH2 ->
    Glutamate: COOH-CH2-CH2-CH(-NH2)-COOH
    -NH2 ->
    Glutamine: NH2-CO-CH2-CH2-CH(-NH2)-COOH

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    Fair dinkum thinkum bilby's Avatar
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    Quote Originally Posted by lpetrich View Post
    Here is the Citric acid cycle. Biochemists often like to use -ate instead of -ic acid in the names of acids. Thus, acetate instead of acetic acid.
    That's a reasonable position to take in the context of biochemistry, which mostly occurs in highly impure aqueous solutions where multiple anions (and cations) are present. When the cation is the important group, as is invariably the case when discussing acids (H+ being the most common and least interesting of the possible anions in an acid solution, by definition), and several anions are present in solution (most biological contexts have plenty of K+, Na+ and often Mg2+ and Ca2+ present as well as the ubiquitous H+), there is no good reason to specify the anion, and the use of the '-ic acid' suffix might be taken as implying that it is specifically and exclusively H+.

    Biochemists and organic chemists have a habit of ignoring H+ ions, and even covalently bonded H, as it is just assumed to be there by default if no other group or anion is specified.

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    Administrator lpetrich's Avatar
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    These amino groups come from nitrogen fixation, and it uses an enzyme called Nitrogenase. It essentially does
    N2 + 6H+ + 6e -> 2NH3

    Nitrogen fixation does not work well in oxygen, and some organisms have ways of protecting their N2 fixation from O2. Some cyanobacteria live in strands, with their cells being like beads on a string, and some of them may become "heterocysts", cells specialized for nitrogen fixation. To avoid poisoning their N2 fixation with O2, they depend on their neighbors for photosynthesis.

    There are two possible pathways for reducing nitrogen to ammonia: distal and alternating. M is the metal ion that the nitrogen is attached to.
    The M is some metal ion. A triple bond I will denote with a #: N#N

    Distal:
    M-N#N
    M-N=NH
    M=N-NH2
    M=N-NH3+
    M#N + -NH3+
    M=NH
    M-NH2
    M-NH3+
    M + -NH3+

    Alternating:
    M-N#N
    M-N=NH
    M-NH=NH
    M-NH-NH2
    M-NH2-NH2
    M-NH2-NH3+
    M-NH2 + -NH3+

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    Administrator lpetrich's Avatar
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    Evolution of the first metabolic cycles by Günter Wächtershäuser (1990): He proposed that the reductive citric-acid cycle is prebiotic. I've found Uncertainty of Prebiotic Scenarios: The Case of the Non-Enzymatic Reverse Tricarboxylic Acid Cycle | Scientific Reports "Reverse" meaning in the reductive direction. "Our results suggest that a) rTCA cycle belongs to a degenerate optimum of auto-catalytic cycles, and b) the set of targets for investigations of the origin of the common metabolic core should be significantly extended." -- meaning that it is likely one of several similar sorts of cycles that could have emerged prebiotically.


    Porphyrins are rings of rings that are found in various places. With what metal ions are in their centers:
    • Cobalt ion: vitamin B12
    • Iron ion: heme -- in cytochromes, hemoglobin, ...
    • Magnesium ion: chlorophyll

    I looked at the structure of a version of vitamin B12, Cyanocobalamin, and I found a RNA building block in it. So it likely goes back to the RNA world. I've also found:

    Possible origin for porphin derivatives in prebiotic chemistry--a computational study. [Orig Life Evol Biosph. 2005] - PubMed - NCBI
    Prebiotic Porphyrin Genesis: Porphyrins from Electric Discharge in Methane, Ammonia, and Water Vapor -- PNAS
    So porphyrins may be prebiotic.

    Their biosynthesis occurs by two pathways: C5 and Shemin. The Shemin one is only in alpha-proteobacteria and nonphotosynthetic eukaryotes; the C5 one is in everything else. So the Shemin one was likely invented by some early alpha-proteobacterium and incorporated into eukaryotes with the ancestor of the mitochondria. The C5 one was returned to eukaryotedom by the cyanobacterium that became the ancestor of the chloroplasts.


    Terpenes, or terpenoids or isoprenoids more generally, are polymers of isoprene:
    CH2 = C (-CH3) = CH2

    They are present in a variety of places across all three domains, and they may date back to the RNA world: cell-membrane lipids in Archaea, chlorophyll, carotenoids, and quinones in Bacteria, and the raw material for steroids in Eukarya. They get their name from turpentine, something produced by conifer trees.

    Isoprenoid biosynthesis: The evolution of two ancient and distinct pathways across genomes | PNAS Those are pathways for making isoprene. Archaea mostly use the mevalonate (MVA) pathway and Bacteria the deoxyxylulose 5-phosphate (DXP) pathway.

    Eukaryotes are a mixture. Animals and fungi use the MVA pathway, while plants and algae have both. In "higher" plants, MVA is used for steroids, with DXP for all other terpenoids. The DXP rather evidently came with the chloroplasts, though not with the mitochondria.

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    Contributor DrZoidberg's Avatar
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    It could have evolved independently lots of times. Nature has a way of destroying evidence

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    Mazzie Daius fromderinside's Avatar
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    Circling back is so fun to do. Wonder if it has anything to do with cyclicity of such as weather.

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