Table 2.
Proteases and peptidases in chloroplasts.
| Name | AGI | Features | Localization | Mutant phenotype | References |
|---|---|---|---|---|---|
| ATP-dependent proteases | |||||
| Clp | |||||
| ClpP1 | ATCG00670 | Clp complex core (R ring), chloroplast-encoded | Stroma | Essential, homoplasmic knockout not available | Shikanai et al., 2001; Kuroda and Maliga, 2003 |
| ClpP3 | AT1G66670 | Clp complex core (P ring), essential for early development | Stroma | Arrest at the cotyledon stage in autotrophic conditions | Kim et al., 2013a |
| ClpP4 | AT5G45390 | Clp complex core (P ring), essential for embryogenesis | Stroma | Embryo lethal | Zheng et al., 2006; Kim et al., 2013a |
| ClpP5 | AT1G02560 | Clp complex core (P ring), essential for embryogenesis | Stroma | Embryo lethal | Kim et al., 2009 |
| ClpP6 | AT1G11750 | Clp complex core (P ring), chloroplast biogenesis | Stroma | Knockdown lines show pale-green leaves at early developmental stages | Sjögren et al., 2006 |
| ClpR1 | AT1G49970 | Clp complex core (R ring), essential for early development | Stroma | Knockdown and point mutation lines show pale-green and retarded growth phenotype | Koussevitzky et al., 2007a; Kim et al., 2009 |
| ClpR2 | AT1G12410 | Clp complex core (R ring), essential for early development | Stroma | Arrest at the cotyledon stage in autotrophic conditions and death after several weeks | Kim et al., 2009 |
| ClpR3 | AT1G09130 | Clp complex core (R ring) | Stroma | Substitution of ClpR1 | Kim et al., 2009 |
| ClpR4 | AT4G17040 | Clp complex core (R ring), essential for early development | Stroma | Arrest at the cotyledon stage in autotrophic conditions and death after several weeks | Kim et al., 2009 |
| ClpT1 | AT4G25370 | Assembly and stabilization of Clp complex | – | No visible phenotypes (single mutant), delayed development and virescent leaves (double mutant) | Sjögren and Clarke, 2011; Kim et al., 2015 |
| ClpT2 | AT4G12060 | ||||
| ClpC1 | AT5G50920 | Molecular chaperone, leaf development | Stroma | Virescent leaves and retarded growth | Sjögren et al., 2004 |
| ClpC2 | AT3G48870 | Molecular chaperone | Stroma | Indistinguishable from the wild type | Park and Rodermel, 2004; Nishimura et al., 2013 |
| ClpD | AT5G51070 | Molecular chaperone | Stroma | Indistinguishable from the wild type, induced by abiotic stresses | Nakashima et al., 1997; Zheng et al., 2002; Nishimura et al., 2013 |
| ClpS | AT1G68660 | Adaptor subunit, substrate recognition and delivery | Stroma | Indistinguishable from the wild type; reduced accumulation of chlorophyll a and b under short-day conditions | Nishimura et al., 2013 |
| ClpF | AT2G03390 | Binding to ClpS, substrate recognition and delivery | Stroma | Indistinguishable from the wild type | Nishimura et al., 2015 |
| FtsH | |||||
| FtsH1 | AT1G50250 | Forming the thylakoid FtsH hexamer (type A), functioning in PSII repair | Thylakoid membrane | Indistinguishable from the wild type | Sakamoto et al., 2003 |
| FtsH2 | AT2G30950 | VAR2, forming the thylakoid FtsH hexamer (type B), functioning in PSII repair and PSI assembly | Thylakoid membrane | Variegated leaves and sensitivity to photoinhibition | Sakamoto et al., 2003; Kato et al., 2012; Järvi et al., 2016 |
| FtsH5 | AT5G42270 | VAR1, forming the thylakoid FtsH hexamer (type A), functioning in PSII repair and PSI assembly | Thylakoid membrane | Variegated leaves and sensitivity to photoinhibition | Sakamoto et al., 2002, 2003; Järvi et al., 2016 |
| FtsH8 | AT1G06430 | Forming the thylakoid FtsH hexamer (type B), functioning in PSII repair | Thylakoid membrane | Indistinguishable from the wild type | Sakamoto et al., 2003 |
| FtsH6 | AT5G15250 | Degradation of LHCB1and LHCB3 in darkness or high light treatment, thermomemory | Thylakoid membrane | Indistinguishable from the wild type, sensitive to heat stress | Sakamoto et al., 2003; Zelisko et al., 2005; Sedaghatmehr et al., 2016 |
| FtsH7 | AT3G47060 | – | IEM | Indistinguishable from the wild type | Wagner et al., 2011 |
| FtsH9 | AT5G58870 | – | IEM | Indistinguishable from the wild type | Wagner et al., 2011 |
| FtsH11 | AT5G53170 | TIC protein turnover, thermotolerance | IEM | Virescent leaves and retarded growth, sensitive to heat stress | Chen et al., 2006, 2018a; Adam et al., 2019 |
| FtsH12 | AT1G79560 | Protein import, early chloroplast development | IEM | Embryo lethal | Wagner et al., 2011; Schreier et al., 2018; Shingo et al., 2018; Mielke et al., 2021 |
| Lon | |||||
| Lon1 | AT5G26860 | Removal of damaged proteins, organelle biogenesis | Chloroplast and mitochondria | Shorter root and stem, smaller leaves, and retarded growth | Rigas et al., 2009; Daras et al., 2014 |
| Lon4 | AT3G05790 | Removal of damaged proteins, drought tolerance | Thylakoid, dual-localized to mitochondria | Sensitivity to drought stress | Ostersetzer et al., 2007; Li et al., 2010 |
| ATP-independent proteases | |||||
| Deg | |||||
| Deg1 | AT3G27925 | Cleaving the lumen transmembrane loop of D1, PSII repair | Lumenal side of thylakoid membrane | Early flowering; fewer, thinner, and pale-green leaves; sensitivity to photoinhibition | Kapri-Pardes et al., 2007; Kley et al., 2011 |
| Deg2 | AT2G47940 | Degradation of LHCB6, chaperone-like activity, possibly cleaving the stroma transmembrane loop of D1 | Stromal side of thylakoid membrane | Indistinguishable from the wild type | Huesgen et al., 2006; Lucinski et al., 2011a; Sun et al., 2012 |
| Deg5 | AT4G18370 | Degradation of PsbF and synergistic function in the degradation of D1 (cleaving the lumenal transmembrane loop of D1) with Deg8 | Lumenal side of thylakoid membrane | Slightly reduced growth rate | Sun et al., 2007; Lucinski et al., 2011b |
| Deg7 | AT3G03380 | PSII (D1, D2, CP43, and CP47) repair, possibly cleaving the stromal transmembrane loop of D1 | Stromal side of thylakoid membrane | Indistinguishable from the wild type | Sun et al., 2010 |
| Deg8 | AT5G39830 | Synergistic function in the degradation of D1 (cleaving the lumenal transmembrane loop of D1) with Deg5 | Lumenal side of thylakoid membrane | Slightly reduced growth rate | Sun et al., 2007 |
| Peptidases | |||||
| SPP | AT5G42390 | TP cleavage of newly imported proteins | Stroma | Embryo lethal | Trösch and Jarvis, 2011 |
| PreP1 | AT3G19170 | Degradation of peptides with length of 10–65 amino acids | Stroma | Very weak chlorotic phenotype for prep1 mutant, no visible phenotypes for prep2 mutant, virescent leaves with reduced thylakoid grana stacks for prep1 prep2 double mutant | Nilsson Cederholm et al., 2009 |
| PreP2 | AT1G49630 | ||||
| OOP | AT5G65620 | Degradation of peptides with length of 8–23 amino acids | Stroma | Indistinguishable from the wild type, may be involved in salicylic acid signaling | Kmiec et al., 2013; Moreau et al., 2013 |
| Plsp1/TPP | AT3G24590 | Degradation of TT in the lumen and maturation of TOC75 | Thylakoid membrane and envelope | Albino and death before development of complete true leaves | Inoue et al., 2005; Shipman and Inoue, 2009; Shipman-Roston et al., 2010 |
| Others | |||||
| CtpA | AT4G17740 | C-terminal processing of D1 | Lumen | Essential for autotrophic growth and chloroplast development | Che et al., 2013 |
| EGY1 | AT5G35220 | Metalloprotease activity, chloroplast development | Thylakoid membrane | Pigmentation deficiency | Chen et al., 2005 |
| EGY2 | AT5G05740 | Metalloprotease activity, hypocotyl elongation, regulation of chloroplast gene expression | Thylakoid membrane | Shorter hypocotyls and larger rosette leaves at flowering time | Chen et al., 2012; Adamiec et al., 2018 |
| SppA | AT1G73990 | High light acclimation | Thylakoid membrane | Indistinguishable from the wild type, sensitive to high light stress | Wetzel et al., 2009 |
| NANA | AT3G12700 | Aspartyl protease, regulates carbohydrate metabolism, starch accumulation | Chloroplast | Shorter hypocotyl and roots at seedling stages, dwarf phenotypes in soil | Paparelli et al., 2012 |
| CND41 | AT5G10770 | Aspartyl protease, DNA binding, degradation of Rubisco holoproteins during leaf senescence | Stroma | Tobacco antisense lines show delayed-senescence phenotype in nitrogen-depleted conditions | Nakano et al., 1997; Kato et al., 2004 |
| CGEP | AT2G47390 | Glutamyl peptidase, may be involved in starch metabolism | Stroma | Indistinguishable from the wild type, genetically interacts with Clp mutants | Bhuiyan et al., 2020 |