The proteolytic machinery of chloroplasts and mitochondria in Arabidopsis consists primarily of three families of ATPdependent proteases, Clp, Lon, and FtsH, and one family of ATP-independent proteases, DegP. However, the functional significance of the multiplicity of their genes is not clear. To test whether expression of specific isomers could be differently affected by growth conditions, we analyzed transcript abundance following short-term exposure to different environmental stimuli, using 70-mer oligonucleotide arrays. This analysis revealed variability in the response to high light and different temperatures within members of each family. Thirty out of the 41 tested genes were up-regulated in response to high light, including both chloroplast and mitochondrial isozymes, whereas only six and five genes responded to either high or low temperature, respectively. The extent of response was variable, ranging from 2-to 20-fold increase in the steady-state levels.Absolute transcript levels of the tested genes, compiled from one-channel arrays, were also variable. In general, transcripts encoding mitochondrial isozymes were accumulated to a lower level than chloroplastic ones. Within the FtsH family, transcript abundance of most genes correlated with the severity of mutant phenotypes in the relevant genes. This correlation was also evident at the protein level. Analysis of FtsH isozymes revealed that FtsH2 was the most abundant species, followed by FtsH5 and 8, with FtsH1 being accumulated to only 10% of FtsH2 level. These results suggest that, unlike previous expectations, the relative importance of different chloroplast protease isozymes, evidenced by mutant phenotypes at least in the FtsH family, is determined by their abundance, and not necessarily by different specific functions or specialized expression under certain conditions.The proteolytic machinery of chloroplasts and mitochondria is essential for controlling the quality and turnover of these organelles' proteins and, thus, is important for their proper function. In Arabidopsis, the proteolytic machinery of chloroplasts consists primarily of three families of ATP-dependent proteases, Clp, Lon, and FtsH, and one family of ATPindependent proteases, DegP (for review, see Adam and Clarke, 2002;Sokolenko et al., 2002). Homologous enzymes are found also in mitochondria (Sarria et al., 1998;Adam et al., 2001;Halperin et al., 2001b;Kolodziejczak et al., 2002). All these families have well-characterized homologs in Escherichia coli (for review, see Clarke, 1999;Adam, 2000). Clp is a Ser protease that separates its two essential functions in two different polypeptides: a small subunit, ClpP, containing the proteolytic active site, and a larger regulatory ATPase subunit, either ClpA or ClpX (for review, see Gottesman, 1996). Lon protease is an ATPdependent Ser protease in which the catalytic and ATPase domains reside in a single polypeptide (for review, see Gottesman, 1996). FtsH is the only essential ATP-dependent protease in E. coli. It is a membranebound metall...

FtsH is a membrane‐bound ATP‐dependent metalloprotease complex found in prokaryotes and organelles of eukaryotic cells. It consists of one or two trans‐membrane helices at its amino‐terminus, a highly conserved ATPase domain, which relates it to the AAA protein family, and a zinc‐binding domain towards its carboxy‐terminus that serves as the proteolytic site. Most bacteria contain a single FtsH gene, but the cyanobacterium Synechocystis has four. The Arabidopsis thaliana genome contains 12 genes encoding FtsH proteins, nine of them can be targeted to chloroplasts, whereas the other three are mitochondrial. Chloroplast FtsH protease is located in the thylakoid membrane, where it forms complexes, most likely hexamers, whose ATPase and proteolytic domains are exposed to the stroma. It is involved in the degradation of the D1 protein of photosystem II reaction centre during its repair from photoinhibition, as well as in the degradation of unassembled proteins in the thylakoid and the stroma. In Arabidopsis, FtsH2 is the most abundant isomer, followed by FtsH5, 8 and 1. This hierarchy is well reflected in the severity of the variegated phenotype of mutants in these genes.