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Which was the origin, DNA, RNA or Protein?

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  1. Dec 22, 2011 #1
    Hello!

    I'm looking for information, articles and theories about which could have been the original molecule of life: DNA, RNA or protein.
    Most of what I've found is based on the RNA world theory (which I think is pretty well explained and sounds plausible), but I haven't found out any well-explained counter-theories for that.

    So now I'm wondering: are there any other plausible theories that that one? Is there any evidence, that proteins or DNA could have been the origin of life? Are there any scientific articles written about those? (Well, of course there must be, but I just haven't found them...)

    Any help would be really welcome and thank you already in advance! :)


    I'm a Finnish biology student, so pardon if there are any grammatical errors or stupid word choices :P
     
  2. jcsd
  3. Dec 22, 2011 #2
    For an overall view, wikipedia would be a good place to start.
    http://en.wikipedia.org/wiki/Abiogenesis

    It tells about many other models besides the RNA World Hypothesis and there are plenty of resources at the bottom of the page. Note however that there is no universally accepted theory on abiogenesis.
     
  4. Jan 4, 2012 #3
    RNA world hypothesis - Wikipedia, the free encyclopedia
    Modern metabolism as a palimpsest of the RNA world

    Though DNA is more chemically stable than RNA, it is nevertheless secondary. DNA nucleotides are made from RNA ones. First, some hydrogen is added to the ribose, chemically reducing its 2' -OH group to -H, making deoxyribose. Then, a methyl group is added to the uracil groups, making thymine groups.
    http://www.cliffsnotes.com/study_guide/Deoxynucleotide-Synthesis.topicArticleId-24594,articleId-24539.html [Broken]

    DNA also has only one function: containing master copies of genetic information. RNA has several functions, and because of its chemical similarity, DNA could easily fill in for RNA there.

    RNA has several functions: List of RNAs
    • Messenger RNA: carries genetic information from DNA master copies
    • Self-splicing: some messenger-RNA molecules can do that
    • Transfer RNA: for translating nucleotide triplets into amino acids for proteins
    • Ribosomal RNA: the most essential parts of ribosomes, protein-assembly complexes
    • Ribozymes: RNA can act as an enzyme. Ribosomal RNA can be interpreted as a ribozyme, and self-splicing is a ribozyme sort of activity
    • Gene-regulation RNA's
    • RNA primers in DNA replicases, enzymes for copying DNA
    RNA also appears in some enzyme cofactors:
    ATP, cyclic AMP, NAD, FAD, Coenzyme A, Vitamin B12

    The presence of RNA in several of these functions is rather odd when one considers the widespread use and versatility of protein enzymes and the chemical similarity of DNA. This suggests that their presence of RNA is a vestigial feature.

    Since the most important parts of the protein-synthesis mechanism are RNA, this means that proteins are also secondary.

    So we end up at the RNA world, one where RNA acted as both information storage and enzymes. Some enzymes had post-transcriptional modification of RNA bases, like in transfer RNA and some ribozymes, and some used add-on cofactors, like amino acids and porphyrins.


    While the RNA world has become widely accepted, it faces the problem of the origin of the RNA. It's difficult to make it using prebiotic-synthesis techniques. I've seen some speculation that ribose was not the first backbone molecule of informational molecules, that there was originally something other than the R in RNA. But beyond that it's hard to say.

    So we have a sequence:
    Prebiotic world
    ???
    RNA world
    Proteins added
    DNA added
     
    Last edited by a moderator: May 5, 2017
  5. Jan 5, 2012 #4

    Andy Resnick

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    Stuart Kauffman, in "The Origins of Order", has a very good discussion regarding DNA/RNA-first and protein-first theories.

    There is evidence supporting RNA-first (all life is based on DNA or RNA as a stable data storage form, RNA can autocatalyze) and evidence opposing RNA-first (so-called 'nude genes' do not appear to *both* replicate and synthesize proteins). Similarly, there is evidence supporting protein-first (peptides can be easily created in the absence of RNA) and evidence opposing (proteins cannot replicate).

    What Kaufmann shows is that if *both* short peptide sequences and RNA sequences are present, the combinatorics of their reactions leads to an autocatalytic set of reactions when the length of peptide sequence or RNA sequence is still very short- 7 or so monomers. In this model, self-reproducing autocatalytic polymer systems emerge fairly easily, and small additions to the polymer length allow exponentially more complexity to be encoded, which is a model for evolution.
     
  6. Jan 5, 2012 #5
    Yes, it's possible to make "thermal proteins" or "proteinoids", but they don't help make other thermal proteins, and they don't transmit information about themselves to other thermal proteins. It's something like fire, which can reproduce itself, but which does not transmit information about itself in the process.

    Nucleic acids, however, can transmit information about themselves; each strand can serve as a template for another strand. When James Watson and Francis Crick discovered the double-helix structure of DNA, they noted that "It has not escaped our attention that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material." That was the template mechanism, which was later abundantly confirmed.

    The template mechanism for transmitting information is a very simple one, but has anyone ever succeeded in constructing a protein system that can do that? I don't know of anyone who has done so.


    An RNA world does not rule out thermal proteins or randomly-assembled ones. In fact, transfer and ribosomal RNA would be a RNA-world invention for making nonrandom proteins.
     
  7. Jan 5, 2012 #6

    atyy

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  8. Jan 5, 2012 #7
    There is an additional conundrum with RNA and proteins. Asymmetry. It's a conundrum because the wrong asymmetry can cause compatibility problems.

    With the exception of glycine, the "backbone" part of protein-forming atoms has an asymmetric carbon atom, one where all four molecular groups attached are in an antisymmetric configuration. There are two possible ones, which are mirror images.

    Code (Text):

          side chain
          |
    H2N - C - COOH
          |
          H

          H
          |
    H2N - C - COOH
          |
          side chain
     
    In glycine, the side chain is hydrogen, which is why it does not have that asymmetry.

    The origin of the asymmetry of protein-forming amino acids has been much argued over, and I wish to avoid that subject for now.


    Ribose is much worse. It has 4 asymmetric carbon atoms. Deoxyribose cuts that down to 3, but it's made from ribose, and it emerged after ribose did.

    If ribose did not emerge directly from prebiotic, but instead took over from some other backbone molecule, that would resolve this conundrum.
     
  9. Jan 9, 2012 #8

    Ryan_m_b

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  10. Jan 28, 2012 #9

    I went to this article and found this - 2nd paragraph -

    "Most amino acids, often called "the building blocks of life", can form via natural chemical reactions unrelated to life, as demonstrated in the Miller–Urey experiment and similar experiments that involved simulating some of the hypothetical conditions of the early Earth in a laboratory.[1] Other equally fundamental biochemicals, such as nucleotides and saccharides can arise in similar ways."

    Does anyone object to the use of "most"?

    I actually conducted a reduced form Miller - Urey in 1969 and find the use of "most" to be excessive.
     
  11. Jan 28, 2012 #10

    bobze

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    The "key" thing to note is the "and similar experiments". Most of life's amino acids do have a "natural synthesis" (or rather a effective way they could be synthesized naturally) worked out. PubMed is your friend :smile:
     
  12. Jan 30, 2012 #11
    Only some of the protein-forming amino acids are reasonably likely to be prebiotic. The rest may have been result of metabolic leakage. Furthermore, the prebiotic ones are more common in the last universal common ancestor (LUCA) of all present-day organisms. These ones are alanine, aspartate, glutamate, glycine, isoleucine, leucine, proline, serine, threonine, valine.

    Evolution of Amino Acid Frequencies in Proteins Over Deep Time: Inferred Order of Introduction of Amino Acids into the Genetic Code
    Results:
     
  13. Jan 30, 2012 #12
    The origin of RNA-to-protein translation involves the origin of the ribosome, a structure composed of RNA and protein that acts as a workbench for this process.

    The information source is strands of messenger RNA (mRNA), and the protein's future amino acids are attached to small snippets of RNA called transfer RNA (tRNA). The AA's are added by aminoacyl tRNA synthetase (aaRS) enzymes.

    At the ribosome, a tRNA with an AA gets selected whose "anticodon" region fits against a triplet of nucleotides (the "codon") in the mRNA at a certain spot. The AA gets attached to the growing protein chain, the AA-less tRNA gets ejected, and the mRNA gets advanced so its next triplet gets used for translation.


    In this complicated molecular machine, the RNA's are the central parts, and the proteins are assistants. So the ribosome likely started off as the RNA parts only and gradually acquired proteins.

    Origin and Evolution of the Ribosome
    George E. Fox
     
  14. Jan 31, 2012 #13
    I've found RNA Second Messengers and Riboswitches: Relics from the RNA World? by Ronald R. Breaker
    Seems like the RNA-world hypothesis is getting more and more into the mainstream of origin-of-life research.

    The universal ancestor was a thermophile or a hyperthermophile.[Gene. 2001] - PubMed - NCBI
    The universal ancestor and the ancestor of bacteria were hyperthermophiles. [J Mol Evol. 2003] - PubMed - NCBI
    The universal ancestor was a thermophile or a hyperthermophile: tests and further evidence. [J Theor Biol. 2003] - PubMed - NCBI
    Di Giulio M

    The Last Universal Common Ancestor (LUCA) and the ancestors for domains Bacteria and Archaea (LBCA and LACA) are all (hyper)thermophiles. However, the Last Eukaryotic Common Ancestor (LECA) was a mesophile, preferring temperatures that we'd consider "normal".

    The universal ancestor and the ancestors of Archaea and Bacteria were anaerobes whereas the ancestor of the Eukarya domain was an aerobe. [J Evol Biol. 2007] - PubMed - NCBI
    Di Giulio M

    His (her?) method was to correlate proteins' amino-acid content with their organisms' temperature and oxygen tolerances. He then estimated the temperature and oxygen tolerances of reconstructed ancestral proteins.

    These results are consistent with speculations about origin in hydrothermal vents and the like. The LUCA, LBCA, and LACA would thus not be very distant from the original organism. These results are also consistent with atmosphere oxygenation being the result of O2-releasing photosynthesis. Organisms that lived before that photosynthesis had evolved would have to have been anaerobes. That necessarily includes the ancestors of cyanobacteria or blue-green algae, the first O2-releasers. Those ancestors include the LBCA and the LUCA but not the LACA, so it's interesting that the LACA was also anaerobic.
     
  15. Jan 31, 2012 #14
    The LECA, however, is a latecomer, originating after the atmosphere got oxygenated. That was about 2.5 billion years ago, the Great Oxygenation Event. It was a hybrid organism, containing a mishmash of genes from several organisms. The informational systems are largely from Archaea, and the metabolic ones largely from Bacteria.

    The LECA had mitochondria, which are descended from some alpha-proteobacterium that an ancestor of the LECA had "eaten". Mitochondria use O2, consistent with the LECA being O2-tolerant. Mitochondrion-less present-day protists have lots of evidence of former mitochondria:
    Genetic evidence for a mitochondriate ancestry in the 'amitochondriate' flagellate Trimastix pyriformis. [PLoS One. 2008] - PubMed - NCBI
    Mitochondrion-related organelles in eukaryotic protists. [Annu Rev Microbiol. 2010] - PubMed - NCBI

    Chloroplasts are descended from some cyanobacterium that some early protist had "eaten", but that protist was not the LECA, but some descendant. Some protists later "ate" other photosynthetic protists, producing an endosymbiosis Russian-doll effect.

    The LECA also had a well-defined cell nucleus, complete with Nuclear Pore Complexes, as can be determined by comparing NPC proteins.
    Evolution: functional evolution of nuclear structure. [J Cell Biol. 2011] - PubMed - NCBI
    Evolution of the karyopherin-β family of nucleocytoplasmic transport factors; ancient origins and continued specialization. [PLoS One. 2011] - PubMed - NCBI
    Evidence for a shared nuclear pore complex architecture that is conserved from the last common eukaryotic ancestor. [Mol Cell Proteomics. 2009] - PubMed - NCBI
    Comparative genomic evidence for a complete nuclear pore complex in the last eukaryotic common ancestor. [PLoS One. 2010] - PubMed - NCBI
     
  16. Jan 31, 2012 #15

    Ygggdrasil

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    It's worth noting that the ancestral sequence reconstruction methods used by Di Giulio to infer the thermostability of ancient proteins are far from perfect, rely on many untested (an in some cases incorrect) assumptions, and suffer from many biases. For example, some have suggested that these methods tend to overestimate the thermostability of ancient proteins, putting into question the main conclusions of the studies you cite above. You can read one such study below:

    Williams PD, Pollock DD, Blackburne BP, Goldstein RA (2006) Assessing the Accuracy of Ancestral Protein Reconstruction Methods. PLoS Comput Biol 2(6): e69. doi:10.1371/journal.pcbi.0020069
     
  17. Feb 7, 2012 #16
    Wow, thanks a lot for all your replies!
    It's been interesting to read (or at least skim) the articles you have linked and see all the different aspects and results :)
    Thank you once more!
     
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