Scientists identify fragments of proteins that already existed billions of years ago

December 28, 2015
The first folded proteins seem to have originated from an ancestral set of peptides. Credit: MPI for Developmental Biology/ Vikram Alva

Proteins and languages share many similarities – both, for instance, yield their meaning through a proper arrangement of basic building blocks. Andrei Lupas, Director at the Max Planck Institute for Developmental Biology in Germany, and his team apply computational methods to reconstruct primordial building blocks by comparative studies of modern proteins. The same approach is used in linguistics to reconstruct ancient vocabularies through the comparison of modern languages. In a recent study the scientists report the identification of 40 ancestral, peptidic fragments, which possibly represent the observable remnants of a time when the first proteins were created, more than 3.5 billion years ago.

Proteins are integral of all life, from bacteria to humans. In our bodies, they are essential for all chemical processes: they form our nails, hair, bones, and muscles, they help digest the food we eat, and they defend us form pathogenic bacteria and viruses. "Life can be viewed as substantially resulting from the chemical activity of proteins", says Lupas, Director of the Department of Protein Evolution at the Max Planck Institute for Developmental Biology. He and his collaborators are particularly interested in understanding how these complex biomolecules originated. Today we know that proteins are primarily built through the combinatorial assembly of only a few thousand modular units, termed domains. It is however unclear how these modular units themselves emerged.

The scientists investigated the hypothesis that the first protein domains arose by fusion and piecemeal growth from an ancestral set of simple peptides, which themselves emerged in an RNA-based pre-cellular life, around 3.5 billion years ago.

In a systematic analysis of modern proteins, they were able to identify 40 peptidic fragments that occur in seemingly unrelated proteins, yet bear striking resemblance in their sequences and structures. Based on their widespread occurrence in the most ancient proteins (e.g., ribosomal proteins) and on their involvement in basal functions (e.g., RNA-binding, DNA-binding), the authors propose that these fragments are the observable remnants of a primordial RNA-peptide world, a precursor form of the DNA-based life we know today.

In the future, the contribution of these fragments to the formation of protein structure will have to be investigated experimentally, opening new avenues to optimize existing proteins and design new ones, not yet seen in nature. "If we elucidate this process, we should be able to create new forms", concludes Lupas, with exciting applications to biotechnology.

Explore further: Protein evolution follows a modular principle

More information: Vikram Alva et al. A vocabulary of ancient peptides at the origin of folded proteins, eLife (2015). DOI: 10.7554/eLife.09410

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katesisco
1 / 5 (13) Dec 28, 2015
well, this may be evidence of that homeopathic succession was able to initiate atomic integration at the onset. This 'teleportation' of 'matter' is exactly what that ---using water to be the sender and receiver of matter being recreated via low frequency sound.
antialias_physorg
5 / 5 (15) Dec 28, 2015
well, this may be evidence of that homeopathic succession was able to initiate atomic integration at the onset. This 'teleportation' of 'matter' is exactly what that ---using water to be the sender and receiver of matter being recreated via low frequency sound.

Erm..whut? Did you just grab a few 'sciency' words and plug them in a sentence and expect it to come out as a coherent statement? Really?
Torbjorn_Larsson_OM
5 / 5 (10) Dec 28, 2015
Yet another passed test for evolution, digging down below the last universal ancestor based on phylogeny.

Gupta (among others) elucidated how eukaryotes was an archea that pretty much hybridized with a bacteria. Cateano-Anolles have elucidated protein evolution along the RNA to DNA universal ancestor lineage. And now we are looking at the stage where an RNA/RNA genetic/enzymatic cell evolved into an RNA/protein one, "from an ancestral set of peptides active as co-factors in RNA-dependent replication and catalysis".

[tbctd]
Torbjorn_Larsson_OM
5 / 5 (9) Dec 28, 2015
[ctd]

Indeed browsing the paper the set is "enriched for iron-sulfur- and nucleic acid-binding ... they predate the emergence of hydrophobic contacts as a driving force for protein folding and that their open structures reflect the association with an RNA scaffold". The former is consistent with the oldest identified cellular functionality, and they note that 6 of Caetano-Anolles's oldest folds contain at least one of the 40 fragments indicating the evolutionary overlap.

This is an excellent complement to Petrov et al latest foray into ribosome evolution, which goes even deeper and elucidate the evolution of the production of these short co-factors, at first random, later encoded. [ http://www.pnas.o...abstract ] Both results agree that iterative (even repetitive) accretion was the early base for functional evolution, i.e. massive variation.

@aa_po: =D Certainly looks that way! "The Way Of The Crank", shows at six and midnight.
venus666
1 / 5 (7) Dec 28, 2015
It is known that protein plays a vital role in living forms and no person can live without
protein. So many people want to get enough protein to make sure that their body can run
normally. rotein is the basis of all the
living forms and the important part of organism. It is also the main materials of renewal
and repair human tissues. Hair, skin,bone,muscle, brain and blood are made of proteins. So
protein is significant to people's growth and development. http://www.creati...vice.htm
Whydening Gyre
5 / 5 (6) Dec 29, 2015
It is known that protein plays a vital role in living forms and no person can live without
protein. So many people want to get enough protein to make sure that their body can run
normally. rotein is the basis of all the
living forms and the important part of organism. It is also the main materials of renewal
and repair human tissues. Hair, skin,bone,muscle, brain and blood are made of proteins. So
protein is significant to people's growth and development. http://www.creati...vice.htm

Wow... is JVK starting a new biz?
And AA - it's just the D-Wave learning to be creative...:)
AGreatWhopper
3.8 / 5 (10) Jan 01, 2016
JVK is a retired lab tech. He's not starting anything but yawns wherever he can post without being deleted. He seems to think that painting petri dishes makes him an expert on RNA. lol It's kind of like the guy that changes the tires on an airliner deciding that lift isn't what keeps airplanes in the air and coming up with a brain damaged theory of atmospheric electromagnetism to explain the mechanics.
Whydening Gyre
5 / 5 (5) Jan 01, 2016
JVK is a retired lab tech. He's not starting anything but yawns wherever he can post without being deleted. He seems to think that painting petri dishes makes him an expert on RNA. lol It's kind of like the guy that changes the tires on an airliner deciding that lift isn't what keeps airplanes in the air and coming up with a brain damaged theory of atmospheric electromagnetism to explain the mechanics.

My comment was sarcasm. Seems someone else (the Venus666 person) is taking to "gobbledy-gook"ing science to sell a product, so was joking that JVK must have a acquired a new "Norm De Plume"...
viko_mx
1 / 5 (3) Jan 02, 2016
Let some supporter of the theory of evolution explain haw can be made proteins by random events in he external environment?

In the living cells the process of protein synthesis is complex multi stage precisely synchronized endothermic process, which is assisted of several dozens of other complex proteins and molecular machines from the beginning to the and. Proteins which were not successfully synthesized according to the genetic information laid down in the genes are disrupted by specific enzymes. The living cells do not tolerate unknown proteins and destroy them.
So how the effect of this highly complex programmed process in the living cell can be achieved by random events?

At all if the life can relate on chance, why the living cells relies on such complex synchronized processes to maintain their stasis and vital functions.
Torbjorn_Larsson_OM
5 / 5 (2) Jan 06, 2016
If viko the troll had asked a question that wasn't already answered by the article and elaborated in full by me (re key results and key players, if not references) he could have evoked a longer response.

Nits: Biology has no specific "supporters", emergence wasn't random and modern protein production, especially protein folding, isn't entirely deterministic.

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