Friday, February 10, 2006

Evolution of the Immune system: MHC part II

Yesterday in part I, I discussed the possible function of a proto-MHC molecule as a method for a population of asexually reproducing organisms to maintain genetic diversity. Although this provides the basis for what sort of function a proto-MHC might have performed, it doesn't provide the answer as to exactly what mechanisms allowed for this change. In order to further understand the origins of the vertebrate immune system, it is now implicit to examine the current MHC class I system and its function. Then explore some of the research into the mechanisms that may have diversified and allowed for the adaption of such a molecule for the immune system.

As stated in part I, as a general rule there are two main classes of MHC that are important in aquired immunity in vertebrates namely class I and class II. For simplicity, I'm going to restrict the discussion to the MHC class I complex for the remainder of this post. MHC class I molecules load peptides that have been processed by intracellular proteases and present them on the surface of cells. This process occurs in nearly every cell in the body, with the exceptions of sperm cells and some neurons. As MHC class I molecules load peptides that have been derived from the proteins produced by the host and those produced by potential invaders such as viruses, this makes them critical in immune function for tolerisation of the effector cells that initiate immune responses.

The proteins involved in MHC class I presentation, called the endogenous pathway as it occurs in cells is shown in diagram 1 below, adapted from Danchin E. et al, the major histocompatibility complex origins (full sized image recommended!).

Here the process can clearly be seen starting with the processing of endogenous antigen by a cellular proteasome. This enzyme slices the protein up into a series of small peptide bits, that can then be processed further and fed into the endoplasmic reticulum (ER in the diagram) by the Transporter associated with Antigen Processing or TAP1 and TAP2. Inside the endoplasmic reticulum, the two MHC class I heavy chains are assembled with the help of proteins called molecular chaperones. These chaperones help to stabilise the protein while it is being assembled and prevent it from falling to pieces. Calnexin (Cnx in the diagram) is the classical chaperone involved early on with others following during the process. Once assembled, the peptides transported through into the ER are complexed with the MHC class I and then the entire assembly of the class I MHC+peptide are secreted onto the surface of the cell.

Overall this seems pretty complicated and it raises questions as to how such a complicated system arose to begin with. As with many questions in biology, the answers lie in the study of the past and the evolutionary history that all organisms share. The origin of this system can be traced back to two large duplication events in the genomes of two classes of organisms: the first during the split some 766 million years ago between the jawless fish such as lampreys and jawed fishes, which later gave rise to higher vertebrates (including us!). This first duplication event is not thought to have given rise to the adaptive immune system, instead a second duplication event some 528 million years ago in the last common ancestor of jawed vertebrates is likely to be where this system arose.

So what makes these large scale duplications so important when it comes to the evolution of the immune system? At least initially in most cases the duplicate is just performing the function of the original gene without much of a change in function, but due to the lesser impact of selection on the duplicate it is prone to building up mutations. In many cases, rather than perform a new function the gene is simply obliterated by the accumulation of mutations that render it inactive. Alternatively, the duplicate may be functional and diverge to freely take on a new function later down the line.

Even more dramatic is an event where an entire organisms genome becomes duplicated doubling the chromosome number. These large increases in genomic content (or ploidy) are actually fairly common in plants and fungi. Once these sorts of duplications occur, the spare genes are free to mutate and particularly can be "co-opted" or have their functions altered for their use in other systems. Generally, a protein can be co-opted without a 'shift' meaning the duplicated genes function is retained without much of an alteration. Alternatively, the gene can have its function altered (co-option with shift) and do something that it normally didn't do or even have a new function added.

Predictably, many of the genes that now function in the endogenous pathway for MHC class I presentation have their roots from these ancestral duplicated genes. For example, at the start of the entire pathway is a large multi-subunit protein called the proteasome. This enzyme is responsible for the chopping up of endogenous antigens into peptides suitable for loading into MHC class I molecules. It turns out that similar proteasomes in organisms such as the fruit fly Drosophila melanogasta and in yeast produce peptides that are similar to those loaded onto MHC molecules. It is probably quite likely that such a proteasome is an example of a protein that has been co-opted for a new function without a substantial shift in biochemical behaviour.

Conveniently, phylogenetic studies (Clark M.S. et al) conducted on the three main catalytic proteins in the immunoproteasome, PSMB8, PSMB9 and PSMB10 replace the functionally similar ones in the normal proteasome PSMB5, PSMB6 and PSMB7. This indicates they have arisen from a duplication of three similar ancestral proteins after the seperation of the jawed and jawless vertebrate lineages. As would be expected, both the cellular proteasome and the immunoproteasome produce peptides that can be loaded onto MHC molecules. The original more ancestral like catalytic unit (PSMB5, PSMB6 and PSMB7) has more or less been co-opted without any alteration in behaviour. Additionally, in the immunoproteasome the PSMB8, PSMB9 and PSMB10 subunits have mutated and become more specialised, producing more specific peptides for loading onto MHC.

Another example of a protein co-opted for use in the endogenous pathway for MHC expression are proteins called molecular chaperones. Calnexin, which is involved with the complete assembly of the final MHC complex by stablising the two heavy chain is already present in eukaryotic cells. In its specific case, the gene has been duplicated twice with calnexin maintaining its original function and the duplicate calmegin, has been completely altered in function for a role in the function of sperm. This example again emphasises the importance that duplications followed by co-option and mutation of the spare gene play in the evolution of complex systems.

The TAP1/TAP2 transporters that are responsible for moving peptides into the endoplasmic reticulum are also the result of ancestral gene duplications. Three genes involved in peptide transport, TAP1/TAP2 and another protein ABCB9, belong to the adenosine triphosphate-binding cassette (ABC) family. These proteins are again all related from a single common ancestral gene that was duplicated and diversified sometime after the jawed/jawless vertebrate split. In evidence of this, phylogenetic studies have found orthologs of ABCB9 in the lamprey genome but not for TAP1 or TAP2.

Possibly the most compelling evidence for the evolution of the MHC from ancestral duplication events followed by co-option of the newly derived genes comes from the genomic structure of the MHC regions. The clustering of genes involved in the MHC pathways, the the previously mentioned MHC I, MHC II and MHC III regions maps similarly to a primitive 'proto-MHC' like region in amphioxus. Most interestingly, it was discovered through these analyses that the MHC class I region genes were translocated fairly recently from the ancestral location in the mammalian lineage, which is not the norm in other jawed invertebrates. This discovery led to the hypothesis that the ancestral proto-MHC like region has existed before the split between protosomes and deuterosomes some 800 million years ago. Considering the bloc duplications of the MHC region, scientists were able to determine that this hypothesis was correct. A proto-MHC region has been present in the common ancestor of protosomes and deuterosomes, giving more clues as to the origins of the vertebrate immune system.

Although this post has ended up a little long, the details given here are only scratching the surface of the large and fascinating field of research surrounding the origins of the immune system. In summary, the current MHC region is the product of multiple duplication events in several proteins localised around a pro-MHC like region existing since the protosome/deuterosome split. Additionally, many of the genes critical for immune function have been duplicated from other ancestral genes and then co-opted for new functions involving immunity. The concluding part of this series tommorow will further examine the environmental selection factors that maintain such an unusally diverse range of MHC alleles.


Danchin E.G., V. Vitiello, A. Vienne, O. Richard, P. Gouret, M.F. McDermott and P. Pontarotti (2004). The major histocompatibility complex origins. Immunological reviews, 198:216-232.

Danchin E.G., L. Abi-Rachel, A. Gilles and P. Pontarroti (2003). Conservation of the MHC region throughout evolution. Immunogenetics, 55:141-148.

Phylogenetic analysis of the proteasome subunits.

Clark M.S., P. Pontarroti, A. Gilles, A. Kelly and G. Elgar (2000). Identification and characterisation of a beta proteasome subunit cluster in the Japanese pufferfish (Fugu rubripes). The Journal of Immunology, 165:4446-4452.

Papers and a good textbook article on gene duplications

McLysaght A., K. Hokamp and K.H. Wolfe (2002). Extensive genomic duplication during early chordate evolution. Nature Genetics, 31:200-204

Gu X., Y. Wang and J. Gu (2002). Age distrubution of human gene families shows significant roles of both large- and small-scale duplications in vertebrate evolution. Nature Genetics, 31:205-209

Alberts B., A. Johnson, J. Lewis, M. Raff, K. Roberts and P. Walter (2002). Molecular Biology of the Cell 4th edition. Garland Science Taylor and Francis Group, pages 40-41;459-462.