EUREKA_EUREKA

LUCA: The global mega-organism What is referred to as LUCA; the primary ancesteral gene pool that is present in every organism on the planet. LUCA consisted of three types of micro-organisms that eventually gave rise to animals and plants.

These are known as; bacteria, archaea and eukaryotes.

WORDS: Ian Sample ILLUSTRATIONS: Tommings

ONCE upon a time, 3 billion years ago, there lived a single organism called LUCA. It was enormous: a mega-organism like none seen since, it filled the planet’s oceans before splitting into three and giving birth to the ancestors of all living things on Earth today. This strange picture

is emerging from efforts to pin down the last universal common ancestor - not the first life that emerged on Earth but the life form that gave rise to all others.

The latest results suggest LUCA was the result of early life’s fight to survive, attempts at which

turned the ocean into a global genetic swap shop for hundreds of millions of years. Cells struggling to survive on their own exchanged useful parts with each other without competition - effectively creating a global mega-organism.

It was around 2.9 billion years ago that LUCA split into the three domains of life: the singlecelled bacteria and archaea, and the more complex eukaryotes that gave rise to animals and plants (see timeline). It’s hard to know what

E

Bacteria Bacteria are present in most habitats on Earth, growing in soil, acidic hot springs, radioactive waste, water, and deep in the Earth's crust, as well as in organic matter and the live bodies of plants and animals, providing outstanding examples of mutualism in the digestive tracts of humans, termites and cockroaches. There are typically 40 million bacterial cells in a gram of soil and a million bacterial cells in a millilitre of fresh water; in all, there are approximately five nonillion (5×1030) bacteria on Earth, forming a biomass that exceeds that of all plants and animals. Bacteria are vital in recycling nutrients, with many steps in nutrient cycles depending on these organisms, such as the fixation of nitrogen from the atmosphere and putrefaction. In the biological communities surrounding hydrothermal vents and cold seeps, bacteria provide the nutrients needed to sustain life by converting dissolved compounds such as hydrogen sulphide and methane. Most bacteria have not been characterised, and only about half of the phyla of bacteria have species that can be grown in the laboratory.

Modern Virosphere Archaea Initially, archaea were seen as extremophiles that lived in harsh environments, such as hot springs and salt lakes, but they have since been found in a broad range of habitats, including soils, oceans, marshlands and the human colon. Archaea are particularly numerous in the oceans, and the archaea in plankton may be one of the most abundant groups of organisms on the planet. Archaea are now recognized as a major part of Earth’s life and may play roles in both the carbon cycle and the nitrogen cycle. No clear examples of archaeal pathogens or parasites are known, but they are often mutualists or commensals. One example is the methanogens that inhabit the gut of humans and ruminants, where their vast numbers aid digestion.

Methanogens are used in biogas production and sewage treatment, and enzymes from extremophile archaea that can endure high temperatures and organic solvents are exploited in biotechnology.

Eukaryotes Cell division in eukaryotes is different from that in organisms without a nucleus (Prokaryote). It involves separating the duplicated chromosomes, through movements directed by microtubules. There are two types of division processes. In mitosis, one cell divides to produce two genetically identical cells. In meiosis, which is required in sexual reproduction, one diploid cell (having two instances of each chromosome, one from each parent) undergoes recombination of each pair of parental chromosomes, and then two stages of cell division, resulting in four haploid cells (gametes). Each gamete has just one complement of chromosomes, each a unique mix of the corresponding pair of parental chromosomes.

LUCA

A

Ancient Virosphere

B

A brief history of life Earth bombarded with meteorites carrying water and minerals.

Earliest chemical evidence of fossils recorded.

4.5

Earliest fossils of cells.

LUCA splits into ancestors of bacteria, eukaryotes and archaea.

First multicellular life appears.

3.4

0.0

Billion Years Ago 3.8

2.9

0.9

Present day.

structure, they could tell us what LUCA could do. “Structure is known to be conserved when sequences aren’t,” agrees Anthony Poole of the University of Canterbury in Christchurch, New Zealand, though he cautions that two very similar structures could conceivably have evolved independently after LUCA. To reconstruct the set of proteins LUCA could make, Caetano-Anollés searched a database of proteins from 420 modern organisms, looking for structures that were common to all. Of the happened before the split. Hardly any fossil structures he found, just 5 to 11 per cent were evidence remains from this time, and any genes universal, meaning they were conserved enough that date that far back are likely to have mutated to have originated in LUCA. beyond recognition.

By looking at their function, he concludes that That isn’t an insuperable obstacle to painting LUCA had enzymes to break down and extract LUCA’s portrait, says Gustavo Caetanoenergy from nutrients, and some protein-making Anollés of the University of Illinois at UrbanaChampaign. While the sequence of genes changes equipment, but it lacked the enzymes for making and reading DNA molecules. quickly, the three-dimensional structure of the proteins they code for is more resistant to the test This is in line with unpublished work by of time. So if all organisms today make a protein Wolfgang Nitschke of the Mediterranean Institute of Microbiology in Marseille, France. He with the same overall structure, he says, it’s a reconstructed the history good bet that the structure was of enzymes crucial to metabolism and found present in LUCA. He calls such structures that LUCA could use both nitrate and carbon as living fossils, and points out that since the energy sources. Nitschke presented his work at function of a protein is highly dependent on its

the UCL Symposium on the Origin of Life in London on 11 November.

If LUCA was made of cells it must have had membranes, and Armen Mulkidjanian of the University of Osnabrück in Germany thinks he knows what kind. He traced the history of membrane proteins and concluded that LUCA could only make simple isoprenoid membranes, which were leaky compared with more modern designs (Proceedings of the International Moscow Conference on Computational Molecular Biology, 2011, p 92).

LUCA probably also had an organelle, a cell compartment with a specific function. Organelles were thought to be the preserve of eukaryotes, but in 2003 researchers found an organelle called the acidocalcisome in bacteria. CaetanoAnollés has now found that tiny granules in some archaea are also acidocalcisomes, or at least their precursors. That means acidocalcisomes are found in all three domains of life, and date back to LUCA. So LUCA had a rich metabolism that used different food sources, and it had internal organelles. So far, so familiar. But its genetics are

a different story altogether. For starters, LUCA may not have used DNA. Poole has studied the history of enzymes called ribonucleotide reductases, which create the building blocks of DNA, and found no evidence that LUCA had them. Instead, it may have used RNA: many biologists think RNA came first because it can store information and control chemical reactions (New Scientist, 13 August, p 32).

The crucial point is that LUCA was a “progenote”, with poor control over the proteins that it made, says Massimo Di Giulio of the Institute of Genetics and Biophysics in Naples, Italy. Progenotes can make proteins using genes as a template, but the process is so error-prone that the proteins can be quite unlike what the gene specified. Both Di Giulio and Caetano- Anollés have found evidence that systems that make protein synthesis accurate appear long after LUCA. “LUCA was a clumsy guy trying to solve the complexities of living on primitive Earth,” says Caetano-Anollés.

He thinks that in order to cope, the early cells must have shared their genes and proteins with each other. New and useful molecules would

have been passed from cell to cell without competition, and eventually gone global. Any cells that dropped out of the swap shop were doomed. “It was more important to keep the living system in place than to compete with other systems,” says Caetano-Anollés. He says the free exchange and lack of competition mean this living primordial ocean essentially functioned as a single mega-organism.

“There is a solid argument in favour of sharing genes, enzymes and metabolites,” says Mulkidjanian. Remnants of this geneswapping system are seen in communities of microorganisms that can only survive in mixed communities. And LUCA’s leaky membranes would have made it easier for cells to share.

“It’s a plausible idea,” agrees Eric Alm of the Massachusetts Institute of Technology. But he says he “honestly can’t tell” if it is true.

Only when some of the cells evolved ways of producing everything they needed could the mega-organism have broken apart. We don’t know why this happened, but it appears to have coincided with the appearance of oxygen in the atmosphere, around 2.9 billion years ago.

Regardless of the cause, life on Earth was never

Anollés of the University of Illinois at UrbanaChampaign. While the sequence of genes changes quickly, the three-dimensional structure of the proteins they code for is more resistant to the test of time. So if all organisms today make a protein with the same overall structure, he says, it’s a good bet that the structure was present in LUCA. He calls such structures living fossils, and points out that since the function of a protein is highly dependent on its structure, they could tell us what LUCA could do. “Structure is known to be conserved when sequences aren’t,” agrees Anthony Poole of the University of Canterbury in Christchurch, New Zealand, though he cautions that two very similar structures could conceivably have evolved independently after LUCA. To reconstruct the set of proteins LUCA could

make, Caetano-Anollés searched a database of proteins from 420 modern organisms, looking for structures that were common to all. Of the structures he found, just 5 to 11 per cent were universal, meaning they were conserved enough to have originated in LUCA. By looking at their function, he concludes that LUCA had enzymes to break down and extract energy from nutrients, and some protein-making equipment, but it lacked the enzymes for making and reading DNA molecules.

This is in line with unpublished work by Wolfgang Nitschke of the Mediterranean Institute of Microbiology in Marseille, France. He reconstructed the history of enzymes crucial to metabolism and found that LUCA could use both nitrate and carbon as energy sources. Nitschke presented his work at the UCL Symposium on the Origin of Life in London on 11 November.

If LUCA was made of cells it must have had membranes, and Armen Mulkidjanian of the

A brief history of life

University of Osnabrück in Germany thinks he knows what kind. He traced the history of membrane proteins and concluded that LUCA could only make simple isoprenoid membranes, which were leaky compared with more modern designs (Proceedings of the International Moscow Conference on Computational Molecular Biology, 2011, p 92).

LUCA probably also had an organelle, a cell compartment with a specific function. Organelles were thought to be the preserve of eukaryotes, but in 2003 researchers found an organelle called the acidocalcisome in bacteria. CaetanoAnollés has now found that tiny granules in some archaea are also acidocalcisomes, or at least their precursors. That means acidocalcisomes are found in all three domains of life, and date back to LUCA. So LUCA had a rich metabolism that used different food sources, and it had internal organelles. So far, so familiar. But its genetics are a different story altogether. For starters, LUCA may not have used DNA. Poole has studied the history of enzymes called ribonucleotide reductases, which create the building blocks of

DNA, and found no evidence that LUCA had them. Instead, it may have used RNA: many biologists think RNA came first because it can store information and control chemical reactions (New Scientist, 13 August, p 32).

The crucial point is that LUCA was a “progenote”, with poor control over the proteins that it made, says Massimo Di Giulio of the Institute of Genetics and Biophysics in Naples, Italy. Progenotes can make proteins using genes as a template, but the process is so error-prone that the proteins can be quite unlike what the gene specified. Both Di Giulio and Caetano- Anollés have found evidence that systems that make protein synthesis accurate appear long after LUCA. “LUCA was a clumsy guy trying to solve the complexities of living on primitive Earth,” says Caetano-Anollés.

He thinks that in order to cope, the early cells must have shared their genes and proteins with

Earth bombarded with meteorites carrying water and minerals.

each other. New and useful molecules would have been passed from cell to cell without competition, and eventually gone global. Any cells that dropped out of the swap shop were doomed. “It was more important to keep the living system in place than to compete with other systems,” says Caetano-Anollés. He says the free exchange and lack of competition mean this living primordial ocean essentially functioned as a single mega-organism.

“There is a solid argument in favour of sharing genes, enzymes and metabolites,” says Mulkidjanian. Remnants of this geneswapping system are seen in communities of microorganisms that can only survive in mixed communities. And LUCA’s leaky membranes would have made it easier for cells to share.

“It’s a plausible idea,” agrees Eric Alm of the Massachusetts Institute of Technology. But he says he “honestly can’t tell” if it is true.

Only when some of the cells evolved ways of producing everything they needed could the

mega-organism have broken apart. We don’t know why this happened, but it appears to have coincided with the appearance of oxygen in the atmosphere, around 2.9 billion years ago.

Regardless of the cause, life on Earth was never the same again

Earliest chemical evidence of fossils recorded.

Earliest fossils of cells.

LUCA splits into ancestors of bacteria, eukaryotes and archaea.

First multicellular life appears.

Present day.

4.5

3.4

0.0

Billion Years Ago 3.8

2.9

0.9

Anollés of the University of Illinois at Urbana-Champaign. While the sequence of genes changes quickly, the three-dimensional structure of the proteins they code for is more resistant to the test of time. So if all organisms today make a protein with the same overall structure, he says, it’s a good bet that the structure was present in LUCA. He calls such structures living fossils, and points out that since the function of a protein is highly dependent on its structure, they could tell us what LUCA could do. “Structure is known to be conserved when sequences aren’t,” agrees Anthony Poole of the University of Canterbury in Christchurch, New Zealand, though he cautions that two very similar structures could conceivably have evolved independently after LUCA. To reconstruct the set of proteins LUCA could make, CaetanoAnollés searched a database of proteins from 420 modern organisms, looking for structures that were common to all. Of the structures he found, just 5 to 11 per cent were universal, meaning they were conserved enough to have originated in LUCA. By looking at their function, he concludes that LUCA had enzymes to break down and extract energy from nutrients, and some protein-making equipment, but it lacked the enzymes for making and reading DNA molecules.

This is in line with unpublished work by Wolfgang Nitschke of the Mediterranean Institute of Microbiology in Marseille, France. He reconstructed the history of enzymes crucial to metabolism and found that LUCA could use both nitrate and carbon as energy sources.

Nitschke presented his work at the UCL Symposium on the Origin of Life in London on 11 November.

If LUCA was made of cells it must have had membranes, and Armen Mulkidjanian of the University of Osnabrück in Germany thinks he knows what kind. He traced the history of membrane proteins and concluded that LUCA could only make simple isoprenoid membranes, which were leaky compared with more modern designs (Proceedings of the International Moscow Conference on Computational Molecular Biology, 2011, p 92).

LUCA probably also had an organelle, a cell compartment with a specific function. Organelles were thought to be the preserve of eukaryotes, but in 2003 researchers found an organelle called the acidocalcisome in bacteria. CaetanoAnollés has now found that tiny granules in some archaea are also acidocalcisomes, or at least their precursors. That means acidocalcisomes are found in all three domains of life, and date back to LUCA. So LUCA had a rich metabolism that used different food sources, and it had internal organelles. So far, so familiar. But its genetics are

A brief history of life Earth bombarded with meteorites carrying water and minerals.

a different story altogether. For starters, LUCA may not have used DNA. Poole has studied the history of enzymes called ribonucleotide reductases, which create the building blocks of DNA, and found no evidence that LUCA had them. Instead, it may have used RNA: many biologists think RNA came first because it can store information and control chemical reactions (New Scientist, 13 August, p 32).

The crucial point is that LUCA was a “progenote”, with poor control over the proteins that it made, says Massimo Di Giulio of the Institute of Genetics and Biophysics in Naples, Italy. Progenotes can make proteins using genes as a template, but the process is so error-prone that the proteins can be quite unlike what the gene specified. Both Di Giulio and Caetano- Anollés have found evidence that systems that make protein synthesis accurate appear long after LUCA. “LUCA was a clumsy guy trying to solve the complexities of living on primitive Earth,” says Caetano-Anollés.

He thinks that in order to cope, the early cells must have shared their genes and proteins with

Earliest chemical evidence of fossils recorded.

Earliest fossils of cells.

LUCA splits into ancestors of bacteria, eukaryotes and archaea.

First multicellular life appears.

Present day.

4.5

each other. New and useful molecules would have been passed from cell to cell without competition, and eventually gone global. Any cells that dropped out of the swap shop were doomed. “It was more important to keep the living system in place than to compete with other systems,” says Caetano-Anollés. He says the free exchange and lack of competition mean this living primordial ocean essentially functioned as a single mega-organism.

“There is a solid argument in favour of sharing genes, enzymes and metabolites,” says Mulkidjanian. Remnants of this geneswapping system are seen in communities of microorganisms that can only survive in mixed communities. And LUCA’s leaky membranes would have made it easier for cells to share.

“It’s a plausible idea,” agrees Eric Alm of the Massachusetts Institute of Technology. But he

3.4

0.0

Billion Years Ago 3.8

says he “honestly can’t tell” if it is true.

Only when some of the cells evolved ways of producing everything they needed could the mega-organism have broken apart. We don’t know why this happened, but it appears to have coincided with the appearance of oxygen in the atmosphere, around 2.9 billion years ago.

Regardless of the cause, life on Earth was never the same again

2.9

0.9

A brief history of life Earth bombarded with meteorites carrying water and minerals.

Earliest chemical evidence of fossils recorded.

Earliest fossils of cells.

LUCA splits into ancestors of bacteria, eukaryotes and archaea.

First multicellular life appears.

Present day.

Anollés of the University of Illinois at Urbana-Champaign.

While the sequence of genes changes quickly, the threedimensional structure of the proteins they code for is more resistant to the test of time. So if all organisms today make a protein with the same overall structure, he says, it’s a good bet that the structure was present in LUCA. He calls such structures living fossils, and points out that since the function of a protein is highly dependent on its structure, they could tell us what LUCA could do. “Structure is known to be conserved when sequences aren’t,” agrees Anthony Poole of the University of Canterbury in Christchurch, New Zealand, though he cautions that two very similar structures could conceivably have evolved independently after LUCA. To reconstruct the set of proteins LUCA could make, CaetanoAnollés searched a database of proteins from 420 modern organisms, looking for structures that were common to all. Of the structures he found, just 5 to 11 per cent were universal, meaning they were conserved enough to have originated in LUCA. By looking at their function, he concludes that LUCA had enzymes to break down and extract energy from nutrients, and some protein-making equipment, but it lacked the enzymes for making and reading DNA molecules.

This is in line with unpublished work by Wolfgang Nitschke of the Mediterranean Institute of Microbiology in Marseille, France.

He reconstructed the history of enzymes crucial to metabolism and found that LUCA could

use both nitrate and carbon as energy sources.

Nitschke presented his work at the UCL Symposium on the Origin of Life in London on 11 November.

If LUCA was made of cells it must have had membranes, and Armen Mulkidjanian of the University of Osnabrück in Germany thinks he knows what kind. He traced the history of membrane proteins and concluded that LUCA could only make simple isoprenoid membranes, which were leaky compared with more modern designs (Proceedings of the International Moscow Conference on Computational Molecular Biology, 2011, p 92).

LUCA probably also had an organelle, a cell compartment with a specific function. Organelles were thought to be the preserve of eukaryotes, but in 2003 researchers found an organelle called the acidocalcisome in bacteria. CaetanoAnollés has now found that tiny granules in some archaea are also acidocalcisomes, or at least their precursors. That means acidocalcisomes are found in all three domains of life, and date back to LUCA. So LUCA had a rich metabolism that used different food sources, and it had internal organelles. So far, so familiar. But its genetics are

a different story altogether. For starters, LUCA may not have used DNA. Poole has studied the history of enzymes called ribonucleotide reductases, which create the building blocks of DNA, and found no evidence that LUCA had them. Instead, it may have used RNA: many biologists think RNA came first because it can store information and control chemical reactions (New Scientist, 13 August, p 32).

The crucial point is that LUCA was a “progenote”, with poor control over the proteins that it made, says Massimo Di Giulio of the Institute of Genetics and Biophysics in Naples, Italy. Progenotes can make proteins using genes as a template, but the process is so error-prone that the proteins can be quite unlike what the gene specified. Both Di Giulio and CaetanoAnollés have found evidence that systems that make protein synthesis accurate appear long after LUCA. “LUCA was a clumsy guy trying to solve the complexities of living on primitive Earth,” says Caetano-Anollés.

He thinks that in order to cope, the early cells must have shared their genes and proteins with each other. New and useful molecules would have been passed from cell to cell without competition, and eventually gone global. Any cells that dropped out of the swap shop were

“LUCA was a clumsy guy trying to solve the complexities of living on primitive Earth”

doomed. “It was more important to keep the living system in place than to compete with other systems,” says Caetano-Anollés. He says the free exchange and lack of competition mean this living primordial ocean essentially functioned as a single mega-organism.

“There is a solid argument in favour of sharing genes, enzymes and metabolites,” says Mulkidjanian. Remnants of this geneswapping system are seen in communities of microorganisms that can only survive in mixed communities. And LUCA’s leaky membranes would have made it easier for cells to share.

“It’s a plausible idea,” agrees Eric Alm of the Massachusetts Institute of Technology. But he says he “honestly can’t tell” if it is true.

Only when some of the cells evolved ways of producing everything they needed could the mega-organism have broken apart. We don’t know why this happened, but it appears to have coincided with the appearance of oxygen in the atmosphere, around 2.9 billion years ago.

Regardless of the cause, life on Earth was never the same again