Chloroplast and mitochondrial proteases in Arabidopsis. A proposed nomenclature

The identity and scope of chloroplast and mitochondrial proteases in higher plants has only started to become apparent in recent years. Biochemical an d molecular studies suggested the existence of Clp, FtsH, and DegP protease s in chloroplasts, and a Lon protease in mitochondria, although currently t he full extent of their role in organellar biogenesis and function remains poorly understood. Rapidly accumulating DNA sequence data, especially from Arabidopsis, has revealed that these proteolytic enzymes are found in plant cells in multiple isomeric forms. As a consequence, a systematic approach was taken to catalog all these isomers, to predict their intracellular loca tion and putative processing sites, and to propose a standard nomenclature to avoid confusion and facilitate scientific communication. For the Clp pro tease most of the ClpP isomers are found in chloroplasts, whereas one is mi tochondrial. Of the ATPase subunits, the one ClpD and two ClpC isomers are Located in chloroplasts, whereas both ClpX isomers are present in mitochond ria. Isomers of the Lon protease are predicted in both compartments, as are the different forms of FtsH protease. DegP, the least characterized protea se in plant cells, has the most number of isomers and they are predicted to localize in several cell compartments. These predictions, along with the p roposed nomenclature, will serve as a framework for future studies of all f our families of proteases and their individual isomers.