Exploring the Physical World

Which Came First?

An experiment in recreating primordial proteins solves a long-standing riddle

• TAGS: Proteins, Evolution, Biochemistry, Enzymes

Tawfik Slider
The characteristic (HhH)2 fold and its binding to the minor groove of a modern DNA molecule. How did the first ones form?

REHOVOT, ISRAEL—June 22, 2020—What did the very first proteins – those that appeared on Earth around 3.7 billion years ago – look like? Prof. Dan Tawfik of the Weizmann Institute of Science and Prof. Norman Metanis of the Hebrew University of Jerusalem have reconstructed protein sequences that may well resemble those ancestors of modern proteins, and their research suggests a way that these primitive proteins could have progressed to forming living cells. Their findings were published in the Proceedings of the National Academy of Sciences (PNAS).

The proteins encoded in a cell’s genetic material are the screws, springs, and cogs of a living cell – all of its moving parts. But the first proteins, it is assumed, appeared well before cells and, thus, before life as we know it. Modern proteins are made of 20 different amino acids, all of them essential to protein-building, and all arranged in the form of a polymer – a long, chain-like molecule – in which the placement of each amino acid is crucial to the protein’s function.

Tawfik, Dan 4
Prof. Dan Tawfik

But there is a paradox in thinking about how the earliest proteins arose: the amino acids needed to make proteins are themselves produced by other proteins – enzymes. It’s a chicken-and-egg kind of question, and it has only been partially answered until now.

Scientists believe that the very first true proteins materialized from shorter protein segments called peptides. The peptides would have been sticky assemblies of the amino acids that were spontaneously created in the primeval chemical soup; the short peptides would then have bound to one another, over time producing a protein capable of some sort of action. The spontaneous generation of amino acids was demonstrated in 1952, in the famous experiment by Miller and Urey, in which they replicated the conditions thought to exist on Earth prior to life and added the kinds of energy that could come from lightning or volcanoes. Showing that amino acids could, under the right conditions, form without help from enzymes or any other mechanism in a living organism suggested that amino acids were the “egg” that preceded the enzyme “chicken.”

Tawfik 2
Ornithine to arginine in a simple chemical reaction

Prof. Tawfik, who is in the Institute’s Department of Biomolecular Sciences, says that is all well and good, “but one vital type of amino acid has been missing from that experiment and every experiment that followed in its wake: amino acids like arginine and lysine that carry a positive electric charge.” These amino acids are particularly important to modern proteins, as they interact with DNA and RNA, both of which carry net negative charges. RNA is today presumed to be the original molecule that could both carry information and make copies of itself, so contact with positively charged amino acids would theoretically be necessary for further steps in the development of living cells to occur.

There was, however, one positively charged amino acid that appeared in the Miller-Urey experiments: ornithine. This amino acid is today found as an intermediate step in arginine production, but is not, itself, used to build proteins. The research team asked: What if ornithine was the missing amino acid in those ancestral proteins? They designed an original experiment to test this hypothesis.

The scientists began with a relatively simple protein from a family that binds to DNA and RNA, applying phylogenetic methods (in which information on the historical relationships of lineages is used to test evolutionary hypotheses) to infer the sequence of the ancestral protein. This protein would have been rich in positive charges, with 14 of the 64 amino acids being either arginine or lysine. Next, the scientists created synthetic proteins in which ornithine replaced these as the positive charge carrier.

Tawfik 3
Proteins with primitive arginine-based proteins (right) might have been capable of self-assembly and phase separation to create cell-like droplets

The ornithine-based proteins did bind to DNA, but weakly. Prof. Metanis’ lab, however, found that simple chemical reactions could convert ornithine to arginine – and these chemical reactions occurred under conditions assumed to be prevalent on Earth at the time the first proteins would have appeared. As more and more of the ornithine was converted to arginine, the proteins came to resemble modern proteins, and to bind to DNA in a way that was stronger and more selective.

The scientists also discovered that, in the presence of RNA, the ancient form of the peptide engaged in phase separation (like drops of oil in water) – a step that can then lead to self-assembly and “departmentalization.” And this, says Prof. Tawfik, suggests that such proteins, together with RNA, could form proto-cells from which true living cells might have evolved.

Prof. Dan Tawfik is the incumbent of the Nella and Leon Benoziyo Professorial Chair.

Exploring the Physical World

Which Came First?

An experiment in recreating primordial proteins solves a long-standing riddle

• TAGS: Proteins , Evolution , Biochemistry , Enzymes

Tawfik Slider
The characteristic (HhH)2 fold and its binding to the minor groove of a modern DNA molecule. How did the first ones form?

REHOVOT, ISRAEL—June 22, 2020—What did the very first proteins – those that appeared on Earth around 3.7 billion years ago – look like? Prof. Dan Tawfik of the Weizmann Institute of Science and Prof. Norman Metanis of the Hebrew University of Jerusalem have reconstructed protein sequences that may well resemble those ancestors of modern proteins, and their research suggests a way that these primitive proteins could have progressed to forming living cells. Their findings were published in the Proceedings of the National Academy of Sciences (PNAS).

The proteins encoded in a cell’s genetic material are the screws, springs, and cogs of a living cell – all of its moving parts. But the first proteins, it is assumed, appeared well before cells and, thus, before life as we know it. Modern proteins are made of 20 different amino acids, all of them essential to protein-building, and all arranged in the form of a polymer – a long, chain-like molecule – in which the placement of each amino acid is crucial to the protein’s function.

Tawfik, Dan 4
Prof. Dan Tawfik

But there is a paradox in thinking about how the earliest proteins arose: the amino acids needed to make proteins are themselves produced by other proteins – enzymes. It’s a chicken-and-egg kind of question, and it has only been partially answered until now.

Scientists believe that the very first true proteins materialized from shorter protein segments called peptides. The peptides would have been sticky assemblies of the amino acids that were spontaneously created in the primeval chemical soup; the short peptides would then have bound to one another, over time producing a protein capable of some sort of action. The spontaneous generation of amino acids was demonstrated in 1952, in the famous experiment by Miller and Urey, in which they replicated the conditions thought to exist on Earth prior to life and added the kinds of energy that could come from lightning or volcanoes. Showing that amino acids could, under the right conditions, form without help from enzymes or any other mechanism in a living organism suggested that amino acids were the “egg” that preceded the enzyme “chicken.”

Tawfik 2
Ornithine to arginine in a simple chemical reaction

Prof. Tawfik, who is in the Institute’s Department of Biomolecular Sciences, says that is all well and good, “but one vital type of amino acid has been missing from that experiment and every experiment that followed in its wake: amino acids like arginine and lysine that carry a positive electric charge.” These amino acids are particularly important to modern proteins, as they interact with DNA and RNA, both of which carry net negative charges. RNA is today presumed to be the original molecule that could both carry information and make copies of itself, so contact with positively charged amino acids would theoretically be necessary for further steps in the development of living cells to occur.

There was, however, one positively charged amino acid that appeared in the Miller-Urey experiments: ornithine. This amino acid is today found as an intermediate step in arginine production, but is not, itself, used to build proteins. The research team asked: What if ornithine was the missing amino acid in those ancestral proteins? They designed an original experiment to test this hypothesis.

The scientists began with a relatively simple protein from a family that binds to DNA and RNA, applying phylogenetic methods (in which information on the historical relationships of lineages is used to test evolutionary hypotheses) to infer the sequence of the ancestral protein. This protein would have been rich in positive charges, with 14 of the 64 amino acids being either arginine or lysine. Next, the scientists created synthetic proteins in which ornithine replaced these as the positive charge carrier.

Tawfik 3
Proteins with primitive arginine-based proteins (right) might have been capable of self-assembly and phase separation to create cell-like droplets

The ornithine-based proteins did bind to DNA, but weakly. Prof. Metanis’ lab, however, found that simple chemical reactions could convert ornithine to arginine – and these chemical reactions occurred under conditions assumed to be prevalent on Earth at the time the first proteins would have appeared. As more and more of the ornithine was converted to arginine, the proteins came to resemble modern proteins, and to bind to DNA in a way that was stronger and more selective.

The scientists also discovered that, in the presence of RNA, the ancient form of the peptide engaged in phase separation (like drops of oil in water) – a step that can then lead to self-assembly and “departmentalization.” And this, says Prof. Tawfik, suggests that such proteins, together with RNA, could form proto-cells from which true living cells might have evolved.

Prof. Dan Tawfik is the incumbent of the Nella and Leon Benoziyo Professorial Chair.