@article{wollenberg_swaffield_2001, title={Evolution of proteasomal ATPases}, volume={18}, ISSN={["1537-1719"]}, DOI={10.1093/oxfordjournals.molbev.a003897}, abstractNote={In eukaryotic cells, the majority of proteins are degraded via the ATP-dependent ubiquitin/26S proteasome pathway. The proteasome is the proteolytic component of the pathway. It is a very large complex with a mass of around 2.5 MDa, consisting of at least 62 proteins encoded by 31 genes. The eukaryotic proteasome has evolved from a simpler archaebacterial form, similar in structure but containing only three different peptides. One of these peptides is an ATPase belonging to the AAA (Triple-A) family of ATPASES: Gene duplication and diversification has resulted in six paralogous ATPases being present in the eukaryotic proteasome. While sequence analysis studies clearly show that the six eukaryotic proteasomal ATPases have evolved from the single archaebacterial proteasomal ATPase, the deep node structures of the phylogenetic constructions lack resolution. Incorporating physical data to provide support for alternative phylogenetic hypotheses, we have constructed a model of a possible evolutionary history of the proteasomal ATPASES:}, number={6}, journal={MOLECULAR BIOLOGY AND EVOLUTION}, author={Wollenberg, K and Swaffield, JC}, year={2001}, month={Jun}, pages={962–974} }
 @article{swaffield_purugganan_1997, title={The evolution of the conserved ATPase domain (CAD): Reconstructing the history of an ancient protein module}, volume={45}, ISSN={["0022-2844"]}, DOI={10.1007/PL00006259}, abstractNote={The AAA proteins (ATPases Associated with a variety of cellular Activities) are found in eubacterial, archaebacterial, and eukaryotic species and participate in a large number of cellular processes, including protein degradation, vesicle fusion, cell cycle control, and cellular secretory processes. The AAA proteins are characterized by the presence of a 230 to 250-amino acid ATPase domain referred to as the Conserved ATPase Domain or CAD. Phylogenetic analysis of 133 CAD sequences from 38 species reveal that AAA CADs are organized into discrete groups that are related not only in structure but in cellular function. Evolutionary analyses also indicate that the CAD was present in the last common ancestor of eubacteria, archaebacteria, and eukaryotes. The eubacterial CADs are found in metalloproteases, while CAD-containing proteins in the archaebacterial and eukaryotic lineages appear to have diversified by a series of gene duplication events that lead to the establishment of different functional AAA proteins, including proteasomal regulatory, NSF/Sec, and Pas proteins. The phylogeny of the CADs provides the basis for establishing the patterns of evolutionary change that characterize the AAA proteins.}, number={5}, journal={JOURNAL OF MOLECULAR EVOLUTION}, author={Swaffield, JC and Purugganan, MD}, year={1997}, month={Nov}, pages={549–563} }