Chloroplast Biogenesis Is Regulated by Direct Action of the Ubiquitin-Proteasome System

Chloroplast Rescued by Ubiquitin The ubiquitin proteasome system is important in the regulation of many nucleocytosolic processes. However, its regulatory reach was not thought to extend to the chloroplast. Using a forward-genetic screen in Arabidopsis, Ling et al. (p. 655; see the Perspective by Kessler) identified a ubiquitin E3 ligase, termed SP1, embedded in the chloroplast outer envelope membrane. SP1 was found to target components of the chloroplast protein import machinery for degradation by the ubiquitin proteasome and was important for changes in chloroplast biogenesis. Protein degradation helps to coordinate the growth of chloroplasts with that of the whole plant. Development of chloroplasts and other plastids depends on the import of thousands of nucleus-encoded proteins from the cytosol. Import is initiated by TOC (translocon at the outer envelope of chloroplasts) complexes in the plastid outer membrane that incorporate multiple, client-specific receptors. Modulation of import is thought to control the plastid’s proteome, developmental fate, and functions. Using forward genetics, we identified Arabidopsis SP1, which encodes a RING-type ubiquitin E3 ligase of the chloroplast outer membrane. The SP1 protein associated with TOC complexes and mediated ubiquitination of TOC components, promoting their degradation. Mutant sp1 plants performed developmental transitions that involve plastid proteome changes inefficiently, indicating a requirement for reorganization of the TOC machinery. Thus, the ubiquitin-proteasome system acts on plastids to control their development.

[1]  H. Leyser,et al.  Characterisation of three shoot apical meristem mutants of Arabidopsis thaliana , 1992 .

[2]  J. Ashby.  References and Notes , 1999 .

[3]  T. Inaba,et al.  Arabidopsis Tic110 Is Essential for the Assembly and Function of the Protein Import Machinery of Plastidsw⃞ , 2005, The Plant Cell Online.

[4]  Kentaro Inoue,et al.  OEP80, an essential protein paralogous to the chloroplast protein translocation channel Toc75, exists as a 70-kD protein in the Arabidopsis thaliana chloroplast outer envelope , 2011, Plant Molecular Biology.

[5]  J. Froehlich.  Studying Arabidopsis envelope protein localization and topology using thermolysin and trypsin proteases. , 2011, Methods in molecular biology.

[6]  P. Masson,et al.  A Role for the TOC Complex in Arabidopsis Root Gravitropism1[W][OA] , 2009, Plant Physiology.

[7]  C. Crews,et al.  The ubiquitin‐proteasome pathway and proteasome inhibitors , 2001, Medicinal research reviews.

[8]  Z. Zhai,et al.  GIDE is a mitochondrial E3 ubiquitin ligase that induces apoptosis and slows growth , 2008, Cell Research.

[9]  K. Keegstra,et al.  A method for isolating a high yield of Arabidopsis chloroplasts capable of efficient import of precursor proteins. , 2001, The Plant journal : for cell and molecular biology.

[10]  Paul Jarvis,et al.  Use of a SPAD-502 meter to measure leaf chlorophyll concentration in Arabidopsis thaliana , 2011, Photosynthesis Research.

[11]  S. Fang,et al.  The AAA-ATPase p97 is essential for outer mitochondrial membrane protein turnover , 2011, Molecular biology of the cell.

[12]  N. Hofmann,et al.  Chloroplast outer membrane protein targeting and insertion. , 2005, Trends in plant science.

[13]  Dong Wook Lee,et al.  Heat Shock Protein Cognate 70-4 and an E3 Ubiquitin Ligase, CHIP, Mediate Plastid-Destined Precursor Degradation through the Ubiquitin-26S Proteasome System in Arabidopsis[C][W] , 2009, The Plant Cell Online.

[14]  J. Chory,et al.  An Arabidopsis mutant defective in the plastid general protein import apparatus. , 1998, Science.

[15]  A. Matouschek,et al.  Substrate selection by the proteasome during degradation of protein complexes , 2008, Nature chemical biology.

[16]  Jill Herschleb,et al.  Functional Analysis of the RING-Type Ubiquitin Ligase Family of Arabidopsis1[w] , 2005, Plant Physiology.

[17]  R. P. Jarvis,et al.  Rapid isolation of Arabidopsis chloroplasts and their use for in vitro protein import assays. , 2011, Methods in molecular biology.

[18]  Kentaro Inoue,et al.  A Molecular-Genetic Study of the Arabidopsis Toc75 Gene Family1 , 2005, Plant Physiology.

[19]  Dayong Li,et al.  Arabidopsis DAL1 and DAL2, two RING finger proteins homologous to Drosophila DIAP1, are involved in regulation of programmed cell death , 2010, Plant Cell Reports.

[20]  P. Jarvis,et al.  Unusual nucleotide‐binding properties of the chloroplast protein import receptor, atToc33 , 2003, FEBS letters.

[21]  Akio Matsuda,et al.  Genome-Wide and Functional Annotation of Human E3 Ubiquitin Ligases Identifies MULAN, a Mitochondrial E3 that Regulates the Organelle's Dynamics and Signaling , 2008, PloS one.

[22]  C. Camilleri,et al.  The Arabidopsis thaliana cDNAs coding for eIF4E and eIF(iso)4E are not functionally equivalent for yeast complementation and are differentially expressed during plant development. , 1998, The Plant journal : for cell and molecular biology.

[23]  E. López-Juez,et al.  Plastids unleashed: their development and their integration in plant development. , 2005, The International journal of developmental biology.

[24]  F. Kessler,et al.  Nucleotide binding and dimerization at the chloroplast pre-protein import receptor, atToc33, are not essential in vivo but do increase import efficiency. , 2010, The Plant journal : for cell and molecular biology.

[25]  A. Barbrook,et al.  A role for SENSITIVE TO FREEZING2 in protecting chloroplasts against freeze-induced damage in Arabidopsis. , 2008, The Plant journal : for cell and molecular biology.

[26]  Wilhelm Gruissem,et al.  Proteome Dynamics during Plastid Differentiation in Rice1[W] , 2006, Plant Physiology.

[27]  M. Glickman,et al.  Ubiquitin-proteasome system and mitochondria - reciprocity. , 2011, Biochimica et biophysica acta.

[28]  Joachim Kurth,et al.  The Arabidopsis ppi1 Mutant Is Specifically Defective in the Expression, Chloroplast Import, and Accumulation of Photosynthetic Proteins Online version contains Web-only data. Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.012955. , 2003, The Plant Cell Online.

[29]  M. Pagano,et al.  Experimental tests to definitively determine ubiquitylation of a substrate. , 2005, Methods in enzymology.

[30]  H. McBride,et al.  MAPL is a new mitochondrial SUMO E3 ligase that regulates mitochondrial fission , 2009, EMBO reports.

[31]  G. Martin,et al.  A Bacterial Inhibitor of Host Programmed Cell Death Defenses Is an E3 Ubiquitin Ligase , 2006, Science.

[32]  M. Kuntz,et al.  Characteristics of the tomato chromoplast revealed by proteomic analysis. , 2010, Journal of experimental botany.

[33]  Lan-Ying Lee,et al.  Tape-Arabidopsis Sandwich - a simpler Arabidopsis protoplast isolation method , 2009, Plant Methods.

[34]  M. Schmid,et al.  Genome-Wide Insertional Mutagenesis of Arabidopsis thaliana , 2003, Science.

[35]  D. Logan,et al.  Mitochondria-targeted GFP highlights the heterogeneity of mitochondrial shape, size and movement within living plant cells. , 2000, Journal of experimental botany.

[36]  P. He,et al.  Direct Ubiquitination of Pattern Recognition Receptor FLS2 Attenuates Plant Innate Immunity , 2011, Science.

[37]  Hsou-min Li,et al.  Determining the location of an Arabidopsis chloroplast protein using in vitro import followed by fractionation and alkaline extraction. , 2011, Methods in molecular biology.

[38]  F. Kessler,et al.  The Function and Diversity of Plastid Protein Import Pathways: A Multilane GTPase Highway into Plastids , 2006, Traffic.

[39]  R. Deshaies,et al.  RING domain E3 ubiquitin ligases. , 2009, Annual review of biochemistry.

[40]  K. Lilley,et al.  In Vivo Analyses of the Roles of Essential Omp85-Related Proteins in the Chloroplast Outer Envelope Membrane1[W][OA] , 2011, Plant Physiology.

[41]  J. Chory,et al.  An Intracellular Signal Transduction Pathway between the Chloroplast and Nucleus Is Involved in De-Etiolation , 1996, Plant physiology.

[42]  P. Jarvis,et al.  A simple method for isolating import‐competent Arabidopsis chloroplasts , 2002, FEBS letters.

[43]  B. Burla,et al.  Pheophytin Pheophorbide Hydrolase (Pheophytinase) Is Involved in Chlorophyll Breakdown during Leaf Senescence in Arabidopsis[W][OA] , 2009, The Plant Cell Online.

[44]  W. Frommer,et al.  ARAMEMNON, a Novel Database for Arabidopsis Integral Membrane Proteins1 , 2003, Plant Physiology.

[45]  O. Maudoux,et al.  Single Point Mutations Distributed in 10 Soluble and Membrane Regions of the Nicotiana plumbaginifolia Plasma Membrane PMA2 H+-ATPase Activate the Enzyme and Modify the Structure of the C-terminal Region* , 1998, The Journal of Biological Chemistry.

[46]  Hsou-min Li,et al.  Protein transport into chloroplasts. , 2010, Annual review of plant biology.

[47]  J. Thompson,et al.  CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. , 1994, Nucleic acids research.

[48]  Matthew D. Smith,et al.  Members of the Toc159 import receptor family represent distinct pathways for protein targeting to plastids. , 2004, Molecular biology of the cell.

[49]  R. Vierstra.  The ubiquitin–26S proteasome system at the nexus of plant biology , 2009, Nature Reviews Molecular Cell Biology.

[50]  C. Koncz,et al.  In vivo studies on the roles of Tic110, Tic40 and Hsp93 during chloroplast protein import. , 2004, The Plant journal : for cell and molecular biology.

[51]  P. Hilson,et al.  Modular cloning in plant cells. , 2005, Trends in plant science.

[52]  M. Neff,et al.  Web-based primer design for single nucleotide polymorphism analysis. , 2002, Trends in genetics : TIG.

[53]  K. Keegstra,et al.  An outer envelope membrane component of the plastid protein import apparatus plays an essential role in Arabidopsis. , 2004, The Plant journal : for cell and molecular biology.

[54]  P. Jarvis,et al.  Functional Similarity between the Chloroplast Translocon Component, Tic40, and the Human Co-chaperone, Hsp70-interacting Protein (Hip)* , 2007, Journal of Biological Chemistry.

[55]  Jörg Bauer,et al.  The major protein import receptor of plastids is essential for chloroplast biogenesis , 2000, Nature.

[56]  P. Jarvis.  Targeting of nucleus-encoded proteins to chloroplasts in plants. , 2008, The New phytologist.

[57]  Hsou-min Li,et al.  Stromal Hsp70 Is Important for Protein Translocation into Pea and Arabidopsis Chloroplasts[C][W][OA] , 2010, Plant Cell.

[58]  G. Murtaza,et al.  Molecular and genetic analyses of Tic20 homologues in Arabidopsis thaliana chloroplasts. , 2011, The Plant journal : for cell and molecular biology.

[59]  G. Shen,et al.  The E3 ligase AtCHIP ubiquitylates FtsH1, a component of the chloroplast FtsH protease, and affects protein degradation in chloroplasts. , 2007, The Plant journal : for cell and molecular biology.

[60]  Metodi Metodiev,et al.  Thioredoxin-mediated reversible dissociation of a stromal multiprotein complex in response to changes in light availability , 2008, Proceedings of the National Academy of Sciences.

[61]  K. Keegstra,et al.  Stable association of chloroplastic precursors with protein translocation complexes that contain proteins from both envelope membranes and a stromal Hsp100 molecular chaperone , 1997, The EMBO journal.

[62]  Hai Huang,et al.  The Proteolytic Function of the Arabidopsis 26S Proteasome Is Required for Specifying Leaf Adaxial Identity[W][OA] , 2006, The Plant Cell Online.

[63]  P. Jarvis,et al.  Further in vivo studies on the role of the molecular chaperone, Hsp93, in plastid protein import. , 2007, The Plant journal : for cell and molecular biology.