Monday, December 17, 2012

Principles of life exemplified (again): cell membrane domains

Principles of life
As regular readers know, one of the core ideas we present in our book, The Mermaid's Tale, is that there is a basic set of principles that explain life in the short term (development), the long and extremely long term (evolution) and the simultaneous (ecosystems).  These principles are being used implicitly or explicitly in biology labs around the world as researchers design and interpret their experiments because they derive from everything we know about life.  That they work everywhere and at all time scales isn't our invention, we just happened to have drawn up the list.  (We've blogged about this before, e.g citing examples of the principles in action.)

We think the list is important because we feel that it is far too widely assumed, even if just tacitly or subliminally, that the only theory about variation in life is the Darwinian theory of competitively based evolution.   This is not to assert that natural selection is unimportant, but we do think that it is far less important or pervasive than the kinds of relationships and properties we have tried to enumerate--indeed, without these coming first, there wouldn't be anything for selection to select for.  One hundred and fifty years of discoveries since Darwin have given us much broader insight into how life works, which we think our list exemplifies.

The principles as we formulate them (annotated here, and of course in our book):
1. Inheritance with memory
2. Modularity
3. Sequestration
4. Coding and interaction
5. Contingency
6. Chance
7. Adaptability
8. Cooperation
This comes up again today because of a paper in the December 7 issue of Cell which illustrates exactly our point about these principles -- they are all around us, and can be used to predict and interpret the kinds of findings in biology that are made all the time.  The paper, "General Protein Diffusion Barriers Create Compartments within Bacterial Cells," Schlimpert et al., describes modularity in the cell membrane of prokaryotes, single-celled organisms without a nucleus, which is similar to that already known in eukaryotes.

In eukaryotes, things that stick off the cellular membrane, like cilia or neuronal axons, 'know' what and where to be because of proteins that are partitioned non-uniformly into specific domains on the plasma membrane through specialized barriers that pick and choose what can pass through.  Schlimpert et al. describe the "protein-mediated membrane diffusion barrier" in the stalked bacterium, Caulobacter crescentus, which, ultimately is "critical for cellular fitness because [such barrier structures] minimize the effective cell volume, allowing faster adaptation to environmental changes that require de novo synthesis of envelope proteins."

Caulobacter have two forms of daughter cell.  'Swarmer' cell with flagellum for moving; 'Stalked' cell, with adhesive organelle, for adhering to surfaces. Swarmer cells soon differentiate into stalked cells (Wikipedia).
Like eukaryotes, prokaryotes also segregate proteins in the cytoplasm, the interior of the cell, into specialized "micrcompartments."  This is important, because different kinds of functions and reactions need their own local environmental conditions (e.g., pH, particular proteins or other molecules), without interference from other stuff in the cell.  So they do share this local organizing principle, but that prokaryotes also had protein-mediated diffusion barriers that determined the organization of the membrane was not previously known. Schlimbert et al. demonstrate this by showing that the stalk-cell body boundary behaves differently from the rest of the cell membrane, as molecules that are allowed to diffuse through the rest of the membrane cannot pass through this boundary.  The work is described in much detail in the paper, but for our purposes here, these are the important points:
Unlike in eukaryotic cells, these diffusion barriers not only laterally compartmentalize cellular membranes but also limit the free diffusion of soluble proteins, thereby providing a significant fitness advantage. Diffusion barrier formation in Caulobacter therefore represents a thus far unrecognized mechanism to optimize the growth of a prokaryote by restricting protein mobility within the cell.
Principles in action
This one very specific example of a microorganism in action illustrates very nicely some of the basic principles we've proposed. In particular, modularity, sequestration and adaptability.  If one were to have hypothesized ahead of time how prokaryotic membranes were organized, the idea that they were composed of specialized domains -- modules -- would have been an obvious first guess, and not just because that's how eukaryotic cell membranes are organized but because that's how all of life is organized.  And, modularity goes hand-in-hand with sequestration, but sequestration that isn't complete because some communication between the inside and the outside of the cell is essential.

Schlimpert et al. write that the presence of the cell membrane domains allows "faster adaptation to environmental changes that require de novo synthesis of envelope proteins."  Again, no surprise that adaptability is enhanced by membrane modularity, as adaptability is one of the most important traits that organisms have evolved, and probably one of the earliest because it's so ubiquitous.

As for the rest of our list of principles, they are simply inherent in the mechanics of life, and so of course in Caulobacter. Inheritance with memory is so basic that it's a given in terms of how organisms reproduce; memory being embodied in DNA.  Coding and interaction are fundamental to how all genes are expressed, and how receptors receive signal and so on, and because life is a 4 dimensional process, contingency is equally inherent; every step of development and of maintaining homeostasis or reproducing depends on what has come before.  Life also is inherently random and dependent upon cooperation; among genes, cellular organelles, micro compartments and so on.

So, again, a simple set of principles predicts and explains a tiny piece of life, because all of life shares a common ancestor; descent with modification for the last 3.5 billion years has given us the incredible diversity of life we see around us, but it hasn't changed the fundamentals.

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