Members each domain are either single cells or multicellular organisms. Members of eukaryota are either single cells or multicellular, but in all cases the cells have a complex structure, with a nucleus and a variety of membrane-enclosed organelles. Although bacteria and archaea are superficially similar to each other, with very little internal structure, their differing molecular biology justifies putting them in separate domains.
Until recently, it was thought that neither bacteria nor archaea contain any membrane-enclosed organelles. (Indeed it’s now generally thought (endosymbiotic theory) that many or most organelles originated as primitive bacteria or archaea that became symbiotically incorporated in more complex eukaryotic cells.)
Not long ago structures were found in some bacteria that closely resemble organelles (acidocalcisomes) that store phosphates and related chemicals in eukaryotes. Now very similar structures have been found in some archaea. The presence of versions of the same basic structure in all three domains suggest that the common ancestor of the three also had some degree of complexity, instead of the simplicity that had been supposed.
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.
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).
So, what is it, exactly, that the researchers have found?
The acidocalcisomes of eukaryotes are membrane-enclosed organelles that have been known for some time. They are rich in calcium and polyphosphate, chemicals involved in energy transfer, and are 100 nm to 200 nm in diameter. And they’ve been found in cells as diverse as algae and human blood platelets. The corresponding structures in bacteria are called volutin granules. These have now been found in some archaea as well.
A key enzyme type, vacuolar proton-translocating pyrophosphatases (V-H+PPases), occurs in volutin granules as well as acidocalcisomes. Molecular analysis of the corresponding enzymes has identified a subunit that occurs in a number of species of bacteria, archaea, and eukaryota. The presence of the similar enzymes and subunits in each of the three domains is evidence that they had a common ancestor.
The abstract of the research article gives the details:
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.
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).