Sunday, December 21, 2008

Nuclear evolution

Proteins of the nuclear pore share evolutionary origins with vesicle coat proteins, providing a fascinating glimpse into the origin of eukaryotes.

One of the great innovations of life, after its origin and after the establishment of DNA as the hereditary material, was the advent of the eukaryotic cell about 2 billion years ago. Eukaryotic cells have numerous internal structures like golgi, vesicles, cytoskeleton, mitochondria, a nucleus and sometimes chloroplasts, and have many other innovations like meiosis and very complex gene regulation. Their origin is believed to be from the union of a phagocytic bacterium with a mitochondrial precursor bacterium, but that is only a very crude picture, with very much unknown. Perhaps the proto-eukaryote was a rather cosmopolitan eater, incorporating quite a few innovations from other bacteria on its way to global hyperpower status.

The nuclear membrane has always been a source of mystery. A huge cellular compartment, pocked with large pores that block only large macromolecules, it completely disassembles during mitosis so that the cell can divide, then spontaneously reforms and resumes its functions. It separates transcription from translation, keeping the DNA inside, and allowing new RNAs to go through complex splicing, capping, and other modifications before they are transported out through the nuclear pores to the cytoplasm where ribosomes stand ready to translate their messages into protein.

The mechanism whereby nuclear pores control the passage of large molecules has recently been solved, and it is a fascinating story in itself- a novel phase of matter composed of phenylalanine (F) and glycine (G) protein residues that lets through nuclear-signal tagged proteins (with their own F-G regions) like knives through butter, but not other proteins without the magic tag, whether they be hydrophobic or hydrophilic.

Anyhow, the present paper is about the proteins that make up the structure of the nuclear pore- a huge (125 megaDalton; most proteins are in the 200 kiloDalton range) complex of proteins that makes the nuclear membrane look like a dimpled sponge, and manages the transport mentioned above. To do this, it has to hang on to the nuclear membrane, which is a membrane like any other in the cell. This paper presents an atomic structure of two of these pore proteins, Nup85 and Seh1, which form a complex with each other and, well, not much else is known about what they do, other than that if their genes are deleted, the pores are severely defective. So they have an important role in pore structure, of the ~30 or so different proteins that make up the pore complex.

This combined protein structure is a beautiful extended glob of Nup85 helices (blue and gold) whose end forms one blade of the Seh1 beta-propeller (green). It was already known that these proteins loosely resemble others of the nuclear pore, by detectable sequence similarity, and the structure is very similar indeed to the combination of pore proteins Nup145C and Sec13. Two lessons here- first, this is yet another instance of duplication and diversification of genes/information in evolution, which I explore further below, and second, that three-dimensional structures can reveal similarities that are minimal or absent in the one-dimensional protein sequence- also a common occurrence now that more structures are being solved. Such similarities arise from common ancestry, which can be so distant that each of the amino acids in the protein sequence may have changed, but in such a way that the overall structure remains roughly the same. Beta propeller structures like that of Seh1 are common in other areas of the cell, expecially in signalling and transcriptional control, since they are great platforms for interacting with other proteins.

This structure showed similarity to other and more distant proteins as well- those involved in vesicle formation of a type termed "clathrin-coated vesicles" like Sec31 (the name "Nup" comes from NUclear Pore, and "Sec" comes from SECretion, which is defective in "Sec" mutants). Vesicles are the tiny transport vehicles that ferry materials (like neurotransmitters in neurons, or insulin in pancreatic beta cells) from the golgi to the outside of the cell, and likewise ingest material from outside the cell by budding in from the outer membrane, powered, in part, by their clathrin coats, which contain Sec13 and Sec31.

On closer inspection of the literature, this relationship is not exactly news, since Sec13 was already known to function both in the nuclear pore and in vesicle secretion (though it is not nearly as essential to nuclear pore structure as is Nup85), yet all the same, the close structural relationship of multiple components of the nuclear pores and secretory vesicles was news to me and the special focus in this article- the first one to tie this story together so broadly. [Ed note: no, see Devos et al, for prior work, per comment received below. This includes the proposal that generic vesicle trafficking preceded nucleus formation.] These proteins interact by binding to each other end-to-end on the Nup85 end, and binding to other proteins on the other end (Seh1, in this case). The whole thing is very stiff, thanks to all the helical cross-members. These proteins do not directly contact the membrane, but use adapter proteins to interface with it.

Thus there is a common, if distantly related, structural motif used in at least two places in the cell. A sort of stiff structural spanning member with tinker toy-like ends used as scaffolds for membranes. In one case (the secretion system) it helps form small vesicles that dynamically bud into and out of the outer membrane. In the other case, we can guess with some confidence (following the authors) that these proteins hold onto the membrane of the nuclear envelope, anchoring the rest of the nuclear pore. Indeed, the authors develop a quite detailed model of how 16 copies of Nup85+Seh1, combined with various numbers of the Nup85 homologs Nup84, Nup145C, Nic96, combined with a few other proteins, could account for the entire inner barrel scaffold of the nuclear pore.

It is apparent that useful innovations do not go unrewarded in evolution, and may generate a diversity of offspring in the form of related proteins that originate from accidental copies of the first version, diversifying and specializing over time. There are many other cases like this, such as the 851 copies of olfactory receptor genes in humans (many defunct), or the 800 plus genes encoding GPCR signalling proteins in humans, or the 700-odd zinc finger DNA-binding regulatory proteins, to name a few of the most prolific.

The set of innovations that led to eukaryotes involved a great deal of membrane management, with several eventual compartments involving assembly, growth, targetting and transit of materials, disassembly, signalling about status, etc. If one structural motif could be used for the basic task of holding on to membranes with a consistent yet reversable shape, it was likely to be used for many such tasks before gene duplication allowed specialization to occur. This also indicates that certain internal membrane systems like the nucleus, endoplasmic reticulum, and golgi/vesicle systems did not arise from separate symbiotic incorporations of other bacteria, unlike the mitochondrion, which does not use Sec31/Nup85-like proteins, as far as I can determine, while having a variety of its own membrane proteins, some traceable to its own bacterial ancestor.

PS- One may ask whether this work addresses the question of which came first- trafficking vesicles or nuclei. No, it doesn't, since it only ties these structures (or at least key parts of them) into a common genealogy. There are a couple of ways to look for answers, though. One is to compare more constituents of these structures, especially those that are specific to each. These may have histories that tie them to other cellular milestones that can give relative timings. For instance, nuclei have lamin proteins and outer pore proteins that may be derived from other cell constituents that are more recent, indicating that the fully elaborated nucleus came later than the simpler vesicles. Unfortunately, this approach is unlikely to give definitive answers, since so much uncertainty attaches to what parts of an organelle were developed when, and which were originally the most important ones.

Another way is to look for existing organisms that have one or the other organelle- either vesicles without nuclei, or the reverse. So little is known about microorganisms that this is not a vain quest. There have been eukaryotic protists found without mitochondria, for instance, which were thought to be primitive and argue for the late incorporation of the endosymbiont. Later, however, these parasites (like Giardia) were found to have numerous mitochondrial genes in their nuclear genomes and have other molecular abnormalities, indicating that they previously had mitochondria which they lost in the mean time, being able to survive without them in food-rich host tissues. Since the history of life is a wildly diversifying bush rather than a ladder, there are many organisms that retain primitive states and are doing quite well, thank you ... like the amazingly vast diversity of bacteria, the proto-chordate sea quirt, the proto-vertebrate hagfish, the platypus, etc.

My speculative bet is that, the proto-eukaryote being putatively a phagocytic amoeba-like organism, having an endocytic and exocytic vesicle system would have been a good bet to be an early feature, with elaboration of nuclei happening later as the rewards of doing extra regulatory steps of RNA maturation, or just protecting the DNA from the occasional loose food item, prompted the gradual segregation of DNA into a nucleus using pre-existing cell components.

1 comment:

  1. This wasn't the first article on this at all - See Devos et al, PLoS Biol, 2004; Devos et al, PNAS, 2006. The idea is called the "protocoatomer hypothesis".