Evolution of the Snf2 family

None of 293 scanned archaeal or bacterial genomes contains a protein classified in any of the eukaryotic subfamilies (Flaus et al, 1996). All Snf2-related proteins in these genomes belong to the SSO1653 subfamily and the more distant rapA group. Conversely, these two groups are likely to be specific to microbial organisms because the only two members identified in eukaryotes, SSO1653 member detected in X tropicalis and a rapA member in Leishmania genomes, appear to be false positives.

Members of the SSO1653 subfamily or rapA group are present in over two thirds of complete microbial genomes. This broad yet incomplete distribution suggests they perform non-essential functions that are sufficiently advantageous to maintain their prevalence.

Although proteins in the rapA group are outside the strict definition of the Snf2 family because they lack several features common to all true subfamilies, the SSO1653 subfamily carries all the Snf2 family sequence and structural hallmarks shared by the eukaryotic subfamilies.

SSO1653 subfamily members are present in both bacteria and archaea, but they are not ubiquitous in archaeal genomes despite the presence of transcription, replication and repair mechanisms with significant similarity to those of eukaryotes 1, 2.

There is also no obvious linkage between the presence of histone-like proteins and SSO1653 subfamily members in archaeal genomes. Furthermore, the SSO1653 subfamily falls in a grouping with the eukaryotic ERCC6 and Mot1 subfamilies, both of whose biochemical role appears not to involve chromatin directly.

In contrast to the limited archaeal and bacterial distribution of Snf2 family proteins, the early branching Giardia lamblia and the minimal Encephalozooan cuniculi genomes both encode 6 different Snf2 family genes falling into subfamilies represented across eukarya, several of which have clear linkage to chromatin transactions.

It is therefore possible that the SSO1653 subfamily represents an ancestral Snf2-like form from which the eukaryotic subfamilies radiated. Such expansion of the Snf2 family early in eukaryote evolution 3 could have been coincident with the development of high density nucleosomal packaging 4.

references
1: Bartlett, M. S. (2005). Determinants of transcription initiation by archaeal RNA polymerase. Curr Opin Microbiol. PubMed
2: Kelman, Z. and M. F. White (2005). Archaeal DNA replication and repair. Curr Opin Microbiol. PubMed
3: Eisen, J. A., K. S. Sweder, et al. (1995). Evolution of the SNF2 family of proteins: subfamilies with distinct sequences and functions. Nucleic Acids Res 23(14): 2715-23. PubMed
4: Minsky, A., R. Ghirlando, et al. (1997). Nucleosomes: a solution to a crowded intracellular environment? J Theor Biol 188(3): 379-85. PubMed