Insane in the (Outer) membrane

Okay, this is weird, even by Archaeal standards. That’s like saying that an outfit is eccentric, even by Lady Gaga standards. But this recent discovery about the structure of an unusual Archaeal cell is just a bit much: it takes one of the most basic features of cell structure and turns it inside out.

The Archaea are a group of organisms with small cells that are superficially similar to Bacteria. However, the genetic and biochemical differences between Bacteria and Archaea are as great as the differences between Bacteria and us, the Eukaryotes. Archaea have earned a reputation as oddballs. Many are “extremophiles,” living in environments with paint-peeling pH or scalding temperatures or pickling concentrations of brine. But in spite of all the differences between the Eukaryotes, Bacteria and Archaea, we are all descended from a common pool of ancestors, which accounts for our similarities: we all have inherited the same genetic coding and decoding system, and use similar mechanisms for getting energy.


This may look like a picture of Hoover Dam, but it’s actually a graphic explaining how almost every cell gets energy. There’s too much water upstream of the dam; there’s not enough water downstream of the dam. If you let water go through the dam, energy is released that you can use to do work—in this case, turn electrical generators. The system keeps recharging itself, as energy from the environment (the sun) does the work of lifting water back up into the atmosphere, eventually filling the river that feeds the dam.

This is how cells make energy. The cell’s membrane acts as a dam. Outside the cell, there are too many positive ions, while inside the cell there aren’t enough. If the cell lets positive ions in, energy is released that can do work. In this case, the energy drives a protein called ATPase that sits in the membrane. ATPase makes ATP, the chemical that powers just about everything in the cell. The cell keeps recharging itself by taking energy from the environment (sunlight or food) to push positive ions back out of the cell and “refilling” the reservoir (the outside of the cell).

The power from this “energized” membrane is used not only to make ATP, but also to move stuff into and out of the cell. There are a few cells that make ATP by a different mechanism, fermentation; but they still use much of their ATP to energize their membranes. An energized membrane is one of the hallmarks of any living cell, Bacterial, Eukaryotic, or Archaeal.
This universal mechanism for storing energy shows up in the architecture of every cell. In Bacteria, it’s like so:

The inner membrane is the energized membrane, where the ATPase is found. The ATP that is produced diffuses into the cell, where it is used to copy DNA and make proteins and power all the essential work of the cell. The space between the inner and outer membranes is small, less than 20% of the cell’s volume; it has a relatively high concentration of positive ions, and no ATP is found there.

Eukaryotes have mitochondria to make most of their ATP. The mitochondrion is actually evolved from bacteria that took up residence in the Eukaryotic cell, so we see basically the same arrangement of membranes and ATPase. The only difference is that special pores move ATP out of the mitochondrion and into the rest of the cell:



Archaeal cells are pretty much the same as Bacterial cells, except there’s no outer membrane. In every case, Bacterial, Eukaryotic, or Archaeal, the inner membrane is the energized membrane—the cell’s Hoover Dam.



Researchers led by Harald Huber of Regensberg, Germany, have been patiently studying the Archaean Ignicoccus hospitalis. This organism was found growing in near-boiling water at a geothermal vent in the Midatlantic Ridge, but it has been domesticated and grown in the laboratory in a mixture of hydrogen, elemental sulfur, and carbon dioxide at a temperature of 90 degrees Celsius. This passes for normal behavior in Archaea. The first surprise came in 2002 when Huber’s group used an electron microscope to examine these cells. What we’re looking at here is a very thin slice of a cell.


Now this is weird. There are clearly two membranes, and no cell wall. Bacteria generally have two membranes, but the Archea? No. And the space between the inner and outer membranes? HUGE! It’s 75% of the cell’s volume! In the Bacteria, that compartment is at most 20% of the cell’s volume. All the business of the cell—all the DNA, all the gene expression, all the synthesis of macromolecules and so on—goes on in the darker region, inside what we’ll call the inner membrane.

This bizarre structure raises questions. Since Ignicoccus’ structure resembles that of a Bacterium, Huber's group assumed it would be organized like a Bacterium, with an energized inner membrane. But why would so much of the cell—all that space between the membranes—not get any energy? So, they decided to look for ATPase. Since ATPase is too small to show up even in an electron microscope, they used a chemical trick to “tag” each molecule of ATPase with a little blob of gold. This shows up as a little black dot under an electron microscope. Here’s what they found; each black dot is a molecule of ATPase with a gold-tagged antibody stuck to it:


This picture makes as much sense to me as this:

I think that Huber’s group thought the same, so they checked and re-checked their result by a couple of completely different methods. The result was confirmed, and is baffling. The outer membrane is full of ATPase; the space between the membranes must get plenty of ATP. But all the DNA, all the gene expression, all the protein synthesis—all the stuff that consumes ATP—is going on inside the inner membrane. Nothing like a normal Archaeal cell, and nothing like a normal Bacterial cell.

The last page of the article describing this discovery is basically a long list of questions raised by this weird structure. Some of these questions are mechanical: if all the DNA and gene expression machinery is inside the inner membrane, how does ATP get through the inner membrane? What goes on in the space between membranes? Is the inner membrane energized? Even more puzzling are the evolutionary questions raised by Ignicoccus’ structure and the location of its ATPase. Ignicoccus is the only cell we know—perhaps in the entire world—with an energized outer membrane. Since all the other Archaea have just one membrane, it’s likely that Ignicoccus evolved from something with just one membrane. How did that happen? Is the outer membrane the recent addition—and if so, how did ATPase end up there? Is the inner membrane the recent addition—and if so, how did it evolve a mechanism to import ATP?

On the one hand, this discovery is not terribly significant; Ignicoccus is a niche player in a highly restricted environment, and it has no close relatives. On the other hand, it raises a lot of big questions about how such a freakish cell could evolve. These questions are relevant to us. A leading hypothesis for the origin of Eukaryotic cells posits that an Archaeal cell engulfed a bacterial cell; the Bacterium became the mitochondrion, while the Archaeal DNA was protected by an internal membrane. Huber notes that an Archaeal cell similar to Ignicoccus could be our great-great-to-the-gazillion-grandaddy.

Ulf Küpera, Carolin Meyerb, Volker Müllerc, Reinhard Rachelb, and Harald Hubera (2009). Energized outer membrane and spatial separation of metabolic processes in the hyperthermophilic Archaeon Ignicoccus hospitalis. PNAS 107:7, 3152-3156.

REINHARD RACHEL, IRITH WYSCHKONY, SABINE RIEHL and HARALD HUBER (2001). The ultrastructure of Ignicoccus: Evidence for a novel outer membrane and for intracellular vesicle budding in an archaeon. Archaea 1, 9-18.