Maximum likelihood phylogenetic tree of Deg/HtrA proteases in selected plant species. Following plant species were investigated: Arabidopsis thaliana, Oryza sativa, Populus trichocarpa, Physcomitrella patens, Chlamydomonas reinhardtii, and the cyanobacterium Synechocystis sp. PCC6803. Phylogenetic tree labeled labeled with the new names as suggested by this study. Filled circles indicated a bootstrap support (100 replicates) of > 90%, empty circles indicate a bootstrap support of > 70%. Additionally, the domain arrangement representative for proteases from each group is indicated. Deg/HtrA proteases from clade I contain one protease domain (oval shapes) and one PDZ domain (diamonds), with the exception of Deg5 proteases, which possess a protease domain only. Proteases from clade II contain an additional PDZ domain, clade III gathers proteases with one active (oval shape) and one inactive (discontinous oval shape) protease domain and four PDZ domains, whereas enzymes from clade IV contain a single protease domain, which is shifted toward the C-terminus.