Published in Plant Cell on June 12, 2009
Structural and metabolic transitions of C4 leaf development and differentiation defined by microscopy and quantitative proteomics in maize. Plant Cell (2010) 1.58
Rampant gene loss in the underground orchid Rhizanthella gardneri highlights evolutionary constraints on plastid genomes. Mol Biol Evol (2011) 1.56
Reconstruction of metabolic pathways, protein expression, and homeostasis machineries across maize bundle sheath and mesophyll chloroplasts: large-scale quantitative proteomics using the first maize genome assembly. Plant Physiol (2010) 1.51
Evolution of C4 photosynthesis in the genus Flaveria: how many and which genes does it take to make C4? Plant Cell (2011) 1.43
Identification of nuclear genes encoding chloroplast-localized proteins required for embryo development in Arabidopsis. Plant Physiol (2010) 1.32
Genetic dissection of chloroplast biogenesis and development: an overview. Plant Physiol (2011) 1.20
Cooperative D1 degradation in the photosystem II repair mediated by chloroplastic proteases in Arabidopsis. Plant Physiol (2012) 1.10
ClpS1 is a conserved substrate selector for the chloroplast Clp protease system in Arabidopsis. Plant Cell (2013) 1.09
Plastid proteomics in higher plants: current state and future goals. Plant Physiol (2011) 1.06
Identification of protein stability determinants in chloroplasts. Plant J (2010) 1.03
Discovery of a Unique Clp Component, ClpF, in Chloroplasts: A Proposed Binary ClpF-ClpS1 Adaptor Complex Functions in Substrate Recognition and Delivery. Plant Cell (2015) 1.00
APO1 promotes the splicing of chloroplast group II introns and harbors a plant-specific zinc-dependent RNA binding domain. Plant Cell (2011) 0.99
Chloroplast RH3 DEAD box RNA helicases in maize and Arabidopsis function in splicing of specific group II introns and affect chloroplast ribosome biogenesis. Plant Physiol (2012) 0.98
Subunit stoichiometry, evolution, and functional implications of an asymmetric plant plastid ClpP/R protease complex in Arabidopsis. Plant Cell (2011) 0.95
Arabidopsis chloroplast mini-ribonuclease III participates in rRNA maturation and intron recycling. Plant Cell (2015) 0.92
Assessing the metabolic impact of nitrogen availability using a compartmentalized maize leaf genome-scale model. Plant Physiol (2014) 0.92
A var2 leaf variegation suppressor locus, SUPPRESSOR OF VARIEGATION3, encodes a putative chloroplast translation elongation factor that is important for chloroplast development in the cold. BMC Plant Biol (2010) 0.91
Assembly of the chloroplast ATP-dependent Clp protease in Arabidopsis is regulated by the ClpT accessory proteins. Plant Cell (2011) 0.91
Indispensable Roles of Plastids in Arabidopsis thaliana Embryogenesis. Curr Genomics (2010) 0.91
Conditional Depletion of the Chlamydomonas Chloroplast ClpP Protease Activates Nuclear Genes Involved in Autophagy and Plastid Protein Quality Control. Plant Cell (2014) 0.91
A rice virescent-yellow leaf mutant reveals new insights into the role and assembly of plastid caseinolytic protease in higher plants. Plant Physiol (2013) 0.90
Arabidopsis J-protein J20 delivers the first enzyme of the plastidial isoprenoid pathway to protein quality control. Plant Cell (2013) 0.87
The FtsH protease heterocomplex in Arabidopsis: dispensability of type-B protease activity for proper chloroplast development. Plant Cell (2010) 0.87
PPR-SMRs: ancient proteins with enigmatic functions. RNA Biol (2013) 0.87
The chloroplast ribosomal protein L21 gene is essential for plastid development and embryogenesis in Arabidopsis. Planta (2011) 0.85
Analysis of essential Arabidopsis nuclear genes encoding plastid-targeted proteins. PLoS One (2013) 0.84
Structures, Functions, and Interactions of ClpT1 and ClpT2 in the Clp Protease System of Arabidopsis Chloroplasts. Plant Cell (2015) 0.83
The purification of the Chlamydomonas reinhardtii chloroplast ClpP complex: additional subunits and structural features. Plant Mol Biol (2012) 0.83
Modified Clp protease complex in the ClpP3 null mutant and consequences for chloroplast development and function in Arabidopsis. Plant Physiol (2013) 0.82
Specific Hsp100 Chaperones Determine the Fate of the First Enzyme of the Plastidial Isoprenoid Pathway for Either Refolding or Degradation by the Stromal Clp Protease in Arabidopsis. PLoS Genet (2016) 0.80
FtsHi4 is essential for embryogenesis due to its influence on chloroplast development in Arabidopsis. PLoS One (2014) 0.77
A mutation in Arabidopsis seedling plastid development1 affects plastid differentiation in embryo-derived tissues during seedling growth. Plant Physiol (2010) 0.76
A Putative Chloroplast Thylakoid Metalloprotease VIRESCENT3 Regulates Chloroplast Development in Arabidopsis thaliana. J Biol Chem (2015) 0.75
Essential role of conserved DUF177A protein in plastid 23S rRNA accumulation and plant embryogenesis. J Exp Bot (2016) 0.75
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Accumulation of high contents of free amino acids in the leaves of Nicotiana benthamiana by the co-suppression of NbClpC1 and NbClpC2 genes. Plant Cell Rep (2014) 0.75
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Elucidation of the methylerythritol phosphate pathway for isoprenoid biosynthesis in bacteria and plastids. A metabolic milestone achieved through genomics. Plant Physiol (2002) 4.18
Correlation of relative abundance ratios derived from peptide ion chromatograms and spectrum counting for quantitative proteomic analysis using stable isotope labeling. Anal Chem (2005) 4.16
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FLU: a negative regulator of chlorophyll biosynthesis in Arabidopsis thaliana. Proc Natl Acad Sci U S A (2001) 2.89
ATP-dependent proteases of bacteria: recognition logic and operating principles. Trends Biochem Sci (2006) 2.86
Identification of genes required for embryo development in Arabidopsis. Plant Physiol (2004) 2.81
Biosynthesis of isoprenoids via the non-mevalonate pathway. Cell Mol Life Sci (2004) 2.68
The N-end rule pathway for regulated proteolysis: prokaryotic and eukaryotic strategies. Trends Cell Biol (2007) 2.64
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Diversity of the biosynthesis of the isoprene units. Nat Prod Rep (2003) 2.05
ClpP: a distinctive family of cylindrical energy-dependent serine proteases. FEBS Lett (2007) 1.83
Recent advances in the study of Clp, FtsH and other proteases located in chloroplasts. Curr Opin Plant Biol (2006) 1.75
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Galactolipid synthesis in chloroplast inner envelope is essential for proper thylakoid biogenesis, photosynthesis, and embryogenesis. Proc Natl Acad Sci U S A (2007) 1.60
Clp protease complexes from photosynthetic and non-photosynthetic plastids and mitochondria of plants, their predicted three-dimensional structures, and functional implications. J Biol Chem (2003) 1.59
Protein degradation machineries in plastids. Annu Rev Plant Biol (2006) 1.58
The plastid clpP1 protease gene is essential for plant development. Nature (2003) 1.50
The capacity of green oilseeds to utilize photosynthesis to drive biosynthetic processes. Plant Physiol (2004) 1.48
In vivo studies on the roles of Tic110, Tic40 and Hsp93 during chloroplast protein import. Plant J (2005) 1.47
Plastoglobules: versatile lipoprotein particles in plastids. Trends Plant Sci (2007) 1.44
A member of the Whirly family is a multifunctional RNA- and DNA-binding protein that is essential for chloroplast biogenesis. Nucleic Acids Res (2008) 1.41
Evidence for a role of ClpP in the degradation of the chloroplast cytochrome b(6)f complex. Plant Cell (2000) 1.37
Interorganellar communication. Curr Opin Plant Biol (2007) 1.36
The plastidial MEP pathway: unified nomenclature and resources. Trends Plant Sci (2008) 1.33
The chloroplast clpP gene, encoding a proteolytic subunit of ATP-dependent protease, is indispensable for chloroplast development in tobacco. Plant Cell Physiol (2001) 1.32
Identification of a 350-kDa ClpP protease complex with 10 different Clp isoforms in chloroplasts of Arabidopsis thaliana. J Biol Chem (2001) 1.30
A stromal Hsp100 protein is required for normal chloroplast development and function in Arabidopsis. Plant Physiol (2004) 1.29
RNR1, a 3'-5' exoribonuclease belonging to the RNR superfamily, catalyzes 3' maturation of chloroplast ribosomal RNAs in Arabidopsis thaliana. Nucleic Acids Res (2005) 1.28
Large scale comparative proteomics of a chloroplast Clp protease mutant reveals folding stress, altered protein homeostasis, and feedback regulation of metabolism. Mol Cell Proteomics (2009) 1.27
Molecular physiological analysis of the two plastidic ATP/ADP transporters from Arabidopsis. Plant Physiol (2004) 1.24
Mutants for photosystem I subunit D of Arabidopsis thaliana: effects on photosynthesis, photosystem I stability and expression of nuclear genes for chloroplast functions. Plant J (2004) 1.23
The Arabidopsis embryo mutant schlepperless has a defect in the chaperonin-60alpha gene. Plant Physiol (2001) 1.20
Distinctive types of ATP-dependent Clp proteases in cyanobacteria. J Biol Chem (2007) 1.20
Structural and functional insights into the chloroplast ATP-dependent Clp protease in Arabidopsis. Plant Cell (2006) 1.20
Plastid lysophosphatidyl acyltransferase is essential for embryo development in Arabidopsis. Plant Physiol (2004) 1.19
An essential role of a TatC homologue of a Delta pH- dependent protein transporter in thylakoid membrane formation during chloroplast development in Arabidopsis thaliana. Proc Natl Acad Sci U S A (2001) 1.19
PNPase activity determines the efficiency of mRNA 3'-end processing, the degradation of tRNA and the extent of polyadenylation in chloroplasts. EMBO J (2002) 1.18
Crystal structure at 1.9A of E. coli ClpP with a peptide covalently bound at the active site. J Struct Biol (2006) 1.17
Inactivation of the clpC1 gene encoding a chloroplast Hsp100 molecular chaperone causes growth retardation, leaf chlorosis, lower photosynthetic activity, and a specific reduction in photosystem content. Plant Physiol (2004) 1.17
Further in vivo studies on the role of the molecular chaperone, Hsp93, in plastid protein import. Plant J (2007) 1.16
Loss of plastidic lysophosphatidic acid acyltransferase causes embryo-lethality in Arabidopsis. Plant Cell Physiol (2004) 1.13
Mutations in ClpC2/Hsp100 suppress the requirement for FtsH in thylakoid membrane biogenesis. Proc Natl Acad Sci U S A (2004) 1.12
Downregulation of ClpR2 leads to reduced accumulation of the ClpPRS protease complex and defects in chloroplast biogenesis in Arabidopsis. Plant Cell (2006) 1.12
Mutations in SUPPRESSOR OF VARIEGATION1, a factor required for normal chloroplast translation, suppress var2-mediated leaf variegation in Arabidopsis. Plant Cell (2008) 1.12
The light sensitivity of ATP synthase mutants of Chlamydomonas reinhardtii. Plant Physiol (2001) 1.10
AtNAP7 is a plastidic SufC-like ATP-binding cassette/ATPase essential for Arabidopsis embryogenesis. Proc Natl Acad Sci U S A (2004) 1.09
Inactivation of the chloroplast ATP synthase gamma subunit results in high non-photochemical fluorescence quenching and altered nuclear gene expression in Arabidopsis thaliana. J Biol Chem (2003) 1.08
Quantitative proteomics of a chloroplast SRP54 sorting mutant and its genetic interactions with CLPC1 in Arabidopsis. Plant Physiol (2008) 1.07
Chloroplast ribosome release factor 1 (AtcpRF1) is essential for chloroplast development. Plant Mol Biol (2007) 1.06
An Arabidopsis thaliana virescent mutant reveals a role for ClpR1 in plastid development. Plant Mol Biol (2006) 1.06
A nuclear-encoded ClpP subunit of the chloroplast ATP-dependent Clp protease is essential for early development in Arabidopsis thaliana. Planta (2006) 1.02
Arabidopsis thaliana mutants reveal a role for CSP41a and CSP41b, two ribosome-associated endonucleases, in chloroplast ribosomal RNA metabolism. Plant Mol Biol (2008) 1.02
Identification of new protein substrates for the chloroplast ATP-dependent Clp protease supports its constitutive role in Arabidopsis. Biochem J (2009) 1.01
SsTypA1, a chloroplast-specific TypA/BipA-type GTPase from the halophytic plant Suaeda salsa, plays a role in oxidative stress tolerance. Plant Cell Environ (2008) 1.00
An Arabidopsis chloroplast-targeted Hsp101 homologue, APG6, has an essential role in chloroplast development as well as heat-stress response. Plant J (2006) 0.98
Ribosomal RNA processing and an RNase R family member in chloroplasts of Arabidopsis. Plant Mol Biol (2004) 0.96
Clp protease controls chlorophyll b synthesis by regulating the level of chlorophyllide a oxygenase. Plant J (2007) 0.96
Plants need their vitamins too. Curr Opin Plant Biol (2007) 0.95
The nuclear-encoded chlorophyll-binding photosystem II-S protein is stable in the absence of pigments. J Biol Chem (1995) 0.93
The chloroplast ClpP complex in Chlamydomonas reinhardtii contains an unusual high molecular mass subunit with a large apical domain. FEBS J (2005) 0.88
Alterations in photosynthesis in Arabidopsis lacking IMMUTANS, a chloroplast terminal oxidase. Photosynth Res (2007) 0.88
Altered expression of the Arabidopsis ortholog of DCL affects normal plant development. Planta (2004) 0.87
Isolation of chloroplast proteins from Arabidopsis thaliana for proteome analysis. Methods Mol Biol (2007) 0.82
Loss of the N-terminal domain of chlorophyllide a oxygenase induces photodamage during greening of Arabidopsis seedlings. BMC Plant Biol (2008) 0.78
Sorting signals, N-terminal modifications and abundance of the chloroplast proteome. PLoS One (2008) 3.41
A set of consensus mammalian mediator subunits identified by multidimensional protein identification technology. Mol Cell (2004) 3.34
Central functions of the lumenal and peripheral thylakoid proteome of Arabidopsis determined by experimentation and genome-wide prediction. Plant Cell (2002) 2.48
Protein profiling of plastoglobules in chloroplasts and chromoplasts. A surprising site for differential accumulation of metabolic enzymes. Plant Physiol (2006) 2.45
In-depth analysis of the thylakoid membrane proteome of Arabidopsis thaliana chloroplasts: new proteins, new functions, and a plastid proteome database. Plant Cell (2004) 2.33
PPDB, the Plant Proteomics Database at Cornell. Nucleic Acids Res (2008) 2.29
Consequences of membrane protein overexpression in Escherichia coli. Mol Cell Proteomics (2007) 2.11
Tuning Escherichia coli for membrane protein overexpression. Proc Natl Acad Sci U S A (2008) 2.11
The oligomeric stromal proteome of Arabidopsis thaliana chloroplasts. Mol Cell Proteomics (2005) 2.01
Recent advances in the study of Clp, FtsH and other proteases located in chloroplasts. Curr Opin Plant Biol (2006) 1.75
Functional differentiation of bundle sheath and mesophyll maize chloroplasts determined by comparative proteomics. Plant Cell (2005) 1.73
Consequences of C4 differentiation for chloroplast membrane proteomes in maize mesophyll and bundle sheath cells. Mol Cell Proteomics (2008) 1.70
MASCP Gator: an aggregation portal for the visualization of Arabidopsis proteomics data. Plant Physiol (2010) 1.59
Clp protease complexes from photosynthetic and non-photosynthetic plastids and mitochondria of plants, their predicted three-dimensional structures, and functional implications. J Biol Chem (2003) 1.59
Structural and metabolic transitions of C4 leaf development and differentiation defined by microscopy and quantitative proteomics in maize. Plant Cell (2010) 1.58
Reconstruction of metabolic pathways, protein expression, and homeostasis machineries across maize bundle sheath and mesophyll chloroplasts: large-scale quantitative proteomics using the first maize genome assembly. Plant Physiol (2010) 1.51
Megadalton complexes in the chloroplast stroma of Arabidopsis thaliana characterized by size exclusion chromatography, mass spectrometry, and hierarchical clustering. Mol Cell Proteomics (2010) 1.50
New functions of the thylakoid membrane proteome of Arabidopsis thaliana revealed by a simple, fast, and versatile fractionation strategy. J Biol Chem (2004) 1.49
Nucleoid-enriched proteomes in developing plastids and chloroplasts from maize leaves: a new conceptual framework for nucleoid functions. Plant Physiol (2011) 1.49
Plastoglobules: versatile lipoprotein particles in plastids. Trends Plant Sci (2007) 1.44
A member of the Whirly family is a multifunctional RNA- and DNA-binding protein that is essential for chloroplast biogenesis. Nucleic Acids Res (2008) 1.41
Expression of tetanus toxin Fragment C in tobacco chloroplasts. Nucleic Acids Res (2003) 1.40
A ribonuclease III domain protein functions in group II intron splicing in maize chloroplasts. Plant Cell (2007) 1.34
Retracted The pathogen-inducible nitric oxide synthase (iNOS) in plants is a variant of the P protein of the glycine decarboxylase complex. Cell (2003) 1.33
RIP1, a member of an Arabidopsis protein family, interacts with the protein RARE1 and broadly affects RNA editing. Proc Natl Acad Sci U S A (2012) 1.32
Large-scale label-free quantitative proteomics of the pea aphid-Buchnera symbiosis. Mol Cell Proteomics (2011) 1.29
Stepwise deamidation of ribonuclease A at five sites determined by top down mass spectrometry. Biochemistry (2006) 1.28
Large scale comparative proteomics of a chloroplast Clp protease mutant reveals folding stress, altered protein homeostasis, and feedback regulation of metabolism. Mol Cell Proteomics (2009) 1.27
A new approach for plant proteomics: characterization of chloroplast proteins of Arabidopsis thaliana by top-down mass spectrometry. Mol Cell Proteomics (2003) 1.24
The functional network of the Arabidopsis plastoglobule proteome based on quantitative proteomics and genome-wide coexpression analysis. Plant Physiol (2012) 1.23
A plant-specific RNA-binding domain revealed through analysis of chloroplast group II intron splicing. Proc Natl Acad Sci U S A (2009) 1.19
An ortholog of the Ro autoantigen functions in 23S rRNA maturation in D. radiodurans. Genes Dev (2007) 1.17
High light response of the thylakoid proteome in arabidopsis wild type and the ascorbate-deficient mutant vtc2-2. A comparative proteomics study. Plant Physiol (2006) 1.16
Cell-type-specific differentiation of chloroplasts in C4 plants. Trends Plant Sci (2009) 1.14
Downregulation of ClpR2 leads to reduced accumulation of the ClpPRS protease complex and defects in chloroplast biogenesis in Arabidopsis. Plant Cell (2006) 1.12
The Clp protease system; a central component of the chloroplast protease network. Biochim Biophys Acta (2010) 1.11
Analysis of curated and predicted plastid subproteomes of Arabidopsis. Subcellular compartmentalization leads to distinctive proteome properties. Plant Physiol (2004) 1.09
ClpS1 is a conserved substrate selector for the chloroplast Clp protease system in Arabidopsis. Plant Cell (2013) 1.09
A comprehensive analysis of the 14-3-3 interactome in barley leaves using a complementary proteomics and two-hybrid approach. Plant Physiol (2006) 1.09
Quantitative proteomics of a chloroplast SRP54 sorting mutant and its genetic interactions with CLPC1 in Arabidopsis. Plant Physiol (2008) 1.07
Arabidopsis thaliana deficient in two chloroplast ascorbate peroxidases shows accelerated light-induced necrosis when levels of cellular ascorbate are low. Plant Mol Biol (2007) 1.06
Construction of plastid reference proteomes for maize and Arabidopsis and evaluation of their orthologous relationships; the concept of orthoproteomics. J Proteome Res (2012) 1.03
Deregulation of maize C4 photosynthetic development in a mesophyll cell-defective mutant. Plant Physiol (2008) 1.00
APO1 promotes the splicing of chloroplast group II introns and harbors a plant-specific zinc-dependent RNA binding domain. Plant Cell (2011) 0.99
Correlation of mRNA and protein abundance in the developing maize leaf. Plant J (2014) 0.98
Chloroplast RH3 DEAD box RNA helicases in maize and Arabidopsis function in splicing of specific group II introns and affect chloroplast ribosome biogenesis. Plant Physiol (2012) 0.98
ABC1K atypical kinases in plants: filling the organellar kinase void. Trends Plant Sci (2012) 0.96
Subunit stoichiometry, evolution, and functional implications of an asymmetric plant plastid ClpP/R protease complex in Arabidopsis. Plant Cell (2011) 0.95
A mammalian mediator subunit that shares properties with Saccharomyces cerevisiae mediator subunit Cse2. J Biol Chem (2003) 0.94
Effects of SecE depletion on the inner and outer membrane proteomes of Escherichia coli. J Bacteriol (2008) 0.94
Loss of plastoglobule kinases ABC1K1 and ABC1K3 causes conditional degreening, modified prenyl-lipids, and recruitment of the jasmonic acid pathway. Plant Cell (2013) 0.94
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Time to articulate a vision for the future of plant proteomics - A global perspective: An initiative for establishing the International Plant Proteomics Organization (INPPO). Proteomics (2011) 0.91
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The role of transitory starch in C(3), CAM, and C(4) metabolism and opportunities for engineering leaf starch accumulation. J Exp Bot (2011) 0.90
The workflow for quantitative proteome analysis of chloroplast development and differentiation, chloroplast mutants, and protein interactions by spectral counting. Methods Mol Biol (2011) 0.89
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The Clp protease system is required for copper ion-dependent turnover of the PAA2/HMA8 copper transporter in chloroplasts. New Phytol (2014) 0.87
The combined use of photoaffinity labeling and surface plasmon resonance-based technology identifies multiple salicylic acid-binding proteins. Plant J (2012) 0.87
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Characterization of the consequences of YidC depletion on the inner membrane proteome of E. coli using 2D blue native/SDS-PAGE. J Mol Biol (2011) 0.86
Immobilization of the first dimension in 2D blue native/SDS-PAGE allows the relative quantification of membrane proteomes. Methods (2008) 0.85
A bayesian mixture model for comparative spectral count data in shotgun proteomics. Mol Cell Proteomics (2011) 0.84
Constitutive expression of pea Lhcb 1-2 in tobacco affects plant development, morphology and photosynthetic capacity. Plant Mol Biol (2004) 0.84
The purification of the Chlamydomonas reinhardtii chloroplast ClpP complex: additional subunits and structural features. Plant Mol Biol (2012) 0.83
Salicylic Acid Inhibits the Replication of Tomato bushy stunt virus by Directly Targeting a Host Component in the Replication Complex. Mol Plant Microbe Interact (2015) 0.82
Consequences of depletion of the signal recognition particle in Escherichia coli. J Biol Chem (2010) 0.82
Modified Clp protease complex in the ClpP3 null mutant and consequences for chloroplast development and function in Arabidopsis. Plant Physiol (2013) 0.82
The menD and menE homologs code for 2-succinyl-6-hydroxyl-2,4-cyclohexadiene-1-carboxylate synthase and O-succinylbenzoic acid-CoA synthase in the phylloquinone biosynthetic pathway of Synechocystis sp. PCC 6803. Biochim Biophys Acta (2003) 0.82
Modeling of the P700+ charge recombination kinetics with phylloquinone and plastoquinone-9 in the A1 site of photosystem I. Biophys J (2002) 0.81
The pathogen-inducible nitric oxide synthase (iNOS) in plants is a variant of the P protein of the glycine decarboxylase complex. Cell (2004) 0.80
Correction: Structure, function, and substrates of Clp AAA+ protease systems in cyanobacteria, plastids, and apicoplasts: A comparative analysis. J Biol Chem (2022) 0.75