Last Universal Common Ancestor More Complex Than Previously Thought
ScienceDaily (Oct. 5, 2011) — Scientists call it LUCA, the Last Universal Common Ancestor, but they don't know much about this great-grandparent of all living things. Many believe LUCA was little more than a crude assemblage of molecular parts, a chemical soup out of which evolution gradually constructed more complex forms. Some scientists still debate whether it was even a cell.
What might have been in Earth's ancient 'chemical soup'? Scientists don't know much about LUCA, the Last Universal Common Ancestor, the great-grandparent of all living things. Many believe LUCA was little more than a crude assemblage of molecular parts, a chemical soup out of which evolution gradually constructed more complex forms. New evidence suggests that LUCA was a sophisticated organism, with a complex structure recognizable as a cell. (Credit: © Dave / Fotolia)
New evidence suggests that LUCA was a sophisticated organism after all, with a complex structure recognizable as a cell, researchers report. Their study appears in the journal Biology Direct.
The study builds on several years of research into a once-overlooked feature of microbial cells, a region with a high concentration of polyphosphate, a type of energy currency in cells. Researchers report that this polyphosphate storage site actually represents the first known universal organelle, a structure once thought to be absent from bacteria and their distantly related microbial cousins, the archaea. This organelle, the evidence indicates, is present in the three domains of life: bacteria, archaea and eukaryotes (plants, animals, fungi, algae and everything else).
The existence of an organelle in bacteria goes against the traditional definition of these organisms, said University of Illinois crop sciences professor Manfredo Seufferheld, who led the study.
"It was a dogma of microbiology that organelles weren't present in bacteria," he said. But in 2003 in a paper in the Journal of Biological Chemistry, Seufferheld and colleagues showed that the polyphosphate storage structure in bacteria (they analyzed an agrobacterium) was physically, chemically and functionally the same as an organelle called an acidocalcisome (uh-SID-oh-KAL-sih-zohm) found in many single-celled eukaryotes.
Their findings, the authors wrote, "suggest that acidocalcisomes arose before the prokaryotic (bacterial) and eukaryotic lineages diverged." The new study suggests that the origins of the organelle are even more ancient.
The study tracks the evolutionary history of a protein enzyme (called a vacuolar proton pyrophosphatase, or V-H+PPase) that is common in the acidocalcisomes of eukaryotic and bacterial cells. (Archaea also contain the enzyme and a structure with the same physical and chemical properties as an acidocalcisome, the researchers report.)
By comparing the sequences of the V-H+PPase genes from hundreds of organisms representing the three domains of life, the team constructed a "family tree" that showed how different versions of the enzyme in different organisms were related. That tree was similar in broad detail to the universal tree of life created from an analysis of hundreds of genes. This indicates, the researchers said, that the V-H+PPase enzyme and the acidocalcisome it serves are very ancient, dating back to the LUCA, before the three main branches of the tree of life appeared.
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Evolution of vacuolar proton pyrophosphatase domains and volutin granules: clues into the early evolutionary origin of the acidocalcisome
Manfredo J Seufferheld, Kyung Mo Kim, James Whitfield, Alejandro Valerio and Gustavo Caetano-Anolles
Biology Direct 2011, 6:50 doi:10.1186/1745-6150-6-50Published: 5 October 2011
Abstract (provisional)
Background
Volutin granules appear to be universally distributed and are morphologically and chemically identical to acidocalcisomes, which are electron-dense granular organelles rich in calcium and phosphate, whose functions include storage of phosphorus and various metal ions, metabolism of polyphosphate, maintenance of intracellular pH, osmoregulation and calcium homeostasis. Prokaryotes are thought to differ from eukaryotes in that they lack membrane-bounded organelles. However, it has been demonstrated that as in acidocalcisomes, the calcium and polyphosphate-rich intracellular "volutin granules (polyphosphate bodies)" in two bacterial species, Agrobacterium tumefaciens, and Rhodospirillum rubrum, are membrane bound and that the vacuolar proton-translocating pyrophosphatases (V-H+PPases) are present in their surrounding membranes. Volutin granules and acidocalcisomes have been found in organisms as diverse as bacteria and humans.
Results
Here, we show volutin granules also occur in Archaea and are, therefore, present in the three superkingdoms of life (Archaea, Bacteria and Eukarya). Molecular analyses of V-H+PPase pumps, which acidify the acidocalcisome lumen and are diagnostic proteins of the organelle, also reveal the presence of this enzyme in all three superkingdoms suggesting it is ancient and universal. Since V-H+PPase sequences contained limited phylogenetic signal to fully resolve the ancestral nodes of the tree, we investigated the divergence of protein domains in the V-H+PPase molecules. Using Protein family (Pfam) database, we found a domain in the protein, PF03030. The domain is shared by 31 species in Eukarya, 231 in Bacteria, and 17 in Archaea. The universal distribution of the V-H+PPase PF03030 domain, which is associated with the V-H+PPase function, suggests the domain and the enzyme were already present in the Last Universal Common Ancestor (LUCA).
Conclusions
The importance of the V-H+PPase function and the evolutionary dynamics of these domains support the early origin of the acidocalcisome organelle. In particular, the universality of volutin granules and presence of a functional V-H+PPase domain in the three superkingdoms of life reveals that the acidocalcisomes may have appeared earlier than the divergence of the superkingdoms. This result is remarkable and highlights the possibility that a high degree of cellular compartmentalization could already have been present in the LUCA.
Reviewers: This article was reviewed by Anthony Poole, Lakshminarayan Iyer and Daniel Kahn.
The complete article is available as a provisional PDF. The fully formatted PDF and HTML versions are in production.
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