4-Billion-Year-Old Fossil Protein Resurrected

First time accepted submitter Zoë Mintz writes "Researchers have 'resurrected' a 4-billion-year-old Precambrian protein and found they resembled those that existed when life began, proving that protein structures have the ability to remain constant over extended periods of time."

Comments

Sorta

[dnadoc]

They took present-day versions of the protein in living organisms, used a computer to interpolate a hypothetical common ancestor, then 'found' sequence homology - but people already knew the sequence was highly conserved, it's evident in modern organisms. There were no "fossils" involved. And conserved sequences make for poor molecular clocks, so who knows if it was 4 billion years ago.

Re:Sorta

[Samantha Wright]

The key is that because thioredoxins are found in all of the kingdoms, and are so conserved, the authors are assuming this is what the thioredoxin in the LUCA looked like. Even if the molecular clock isn't accurate over this one protein because of masked mutations, the number's most likely sound. (To one significant figure, anyway, since the LUCA is held to be 3.5 to 3.8 gya.)

Re:Sorta

[c0lo]

Better source

A team of scientists from Columbia University, Georgia Institute of Technology and the University of Granada in Spain have successfully reconstructed active enzymes from four-billion-year-old extinct organisms.
[...]
In their study, published in the journal Nature Structural & Molecular Biology, the researchers used vast amounts of genetic data to computationally reconstruct the genes of extinct species, a technique known as ancestral sequence reconstruction. The researchers then went a step further and synthesized the proteins encoded by these genes. They focused their efforts on a specific protein, thioredoxin, which is a vital enzyme found in all living cells.

Re:Sorta

[bzipitidoo]

(LUCA = Last Universal Common Ancestor.)

I read a lot of conflicting info about the early Earth. Is the end of the Hadean Eon and beginning of the Archean supposed to be when life began? Or is some other event supposed to divide the two eons, like perhaps the emergence of conditions hospitable to life? I've read that it is 3.8 gya or 4.0 gya. Why not say 3.9+/-0.1 gya? Obviously 4 was picked for being a very round number, but settling on a single number however round seems a bad idea. Makes it sound like we're more certain of those dates than we really are.

Much of our knowledge is sketchy and speculative. No one really says whether the first life forms might be considered bacteria, or archaea. The archaean domain is still new to science. Was only in the late 1970s that archaea were recognized as being different enough to qualify as a separate domain and not part of the domain of bacteria. Then there are fun ideas like the RNA world hypothesis. There's the idea that life could have started and died several times before achieving permanence. Panspermia is another notion.

Re:Sorta

[Samantha Wright]

The LUCA dates range from 3.5 to 4 gya, so it's even broader than that. Different estimates come from different sources and with different precision, though, so it's not quite right to give a single symmetrical error measurement. I'd personally vote for saying 3.8 +0.2/-0.3 gya. In the case of this article, however, they chose 4 exactly because of their molecular clock predictions.

The article doesn't clarify between the Archean and Hadean periods, however, and it's probably bad to equate the LUCA with the beginning of life because we have pretty strong evidence that the LUCA was already a very well-developed organism, with a complete central dogma, hundreds of enzymes, and a preference for potassium ions over sodium ones. Wikipedia cites several science journalism pieces that argue for a Palaeoarchaean LUCA.

As for what the LUCA actually looked like, I would say somewhere between Archaea and Bacteria, but defying both categories. Archaeans have a number of later innovations that definitely disqualify them from being good representatives, since they can do sophisticated chromatin modelling (folding DNA to make gene transcription more efficient) and have a unique membrane composition (which I personally like to imagine may be evidence of multiple abiogenesis events, but that's a bit of an uninformed theory.) Bacteria, on the other hand, are known to have a tendency towards simplifying their genomes. If anything the bias seems to be toward Bacteria as the root; no one has recently proposed that Archaeans pre-date Bacteria.

Re:Alive

[Anonymous Coward]

No it isn't. I'm a scientist and we use the word resurrected too. We are talking about molecular resurrection, not whole organism resurrection. The scientific community re-purposes common words to mean different specific scientific things all the time. We use the word resurrection to mean that we made an ancient protein in the lab, and the protein still has it's original function. There is a big difference between just making a predicted ancestral protein in the lab, and having it actually work the same way it used to. The protein needs to fold correctly and be in the correct environment.

For more details of the previous use of this word, google "Ribosomal Paleontology and Resurrection".

Re:"resembled those that existed when life began"

[Samantha Wright]

With protein sequence evolution it's a little more controlled: the modifications occur more-or-less randomly, and there are almost no cases where a letter (residue) is replaced throughout the entire vocabulary (proteome) due to phonological shifts. As a result, if you have enough datapoints to work from, like with the thioredoxins, it's simply a matter of picking the version most commonly agreed upon by all of the branches. In that sense, it's more like textual criticism than historical linguistics, particularly since you can also use the requirement of "it has to be well-formed language" (i.e. a working protein) to weed out obviously bad combinations of changes.

For some reason, that bewilders a lot of reasonably scientifically-minded people.

Re: Alive

[Anonymous Coward]

Ever heard of weather being hellish, or the flight being a torture, a meal being an orgasm in the mouth, a person being an asspain or buttmad? Lauguage is strange thing, and as they say: time flies like an arrow, fruit flies like a banana.

Re:Alive

[fellip_nectar]

Our chief weapon is surprise...surprise and fear...fear and surprise.... Our two weapons are fear and surprise...and ruthless efficiency.... Our *three* weapons are fear, surprise, and ruthless efficiency...and an almost fanatical devotion to the Pope.... Our *four*...no... *Amongst* our weapons.... Amongst our weaponry...are such elements as fear, surprise.... I'll come in again.

Re:Alive

[Anonymous Coward]

They traced back the mutations of every thioredoxin variation to a common ancestor 4bn years ago. If you have three close species: A, B, C. The three share a variation of a protein which is exactly the same at nucleotid level except for one site, lets say: A: CGCGTA, B: CGTGTA, C: CGCGTA. You know, because of the rest of the genome, that A and B had a common ancestor 2 million years ago, and that common ancestor had a common ancestor with C 3 million years ago. Chances are that the original protein was CGCGTA. In this case, the reconstructed protein is the same as the A and C proteins, but given enough species you can use this kind of reconstruction techniques to figure out how the ancient version of a specific protein looked like.