VAR2/AtFtsH2 and EVR2/BCM1/CBD1 synergistically regulate the accumulation of PSII reaction centre D1 protein during de-etiolation in Arabidopsis

Thylakoid FtsH complex participates in PSII repair cycle during high light-induced photoinhibition. The Arabidopsis yellow variegated2 (var2) mutants are defective in the VAR2/AtFtsH2 subunit of thylakoid FtsH complex. Taking advantage of the var2 leaf variegation phenotype, dissections of genetic enhancer loci have yielded novel paradigms in understanding functions of thylakoid FtsH complex. Here, we report the isolation of a new var2 enhancer, enhancer of variegation2-1 (evr2-1). We confirmed that EVR2 encodes a chloroplast protein that was known as BALANCE OF CHLOROPHYLL METABOLISM 1 (BCM1), or CHLOROPHYLL BIOSYNTHETIC DEFECT 1 (CBD1). We showed that EVR2/BCM1/CBD1 was involved in the oligomerization of photosystem I complexes. Genetic assays indicated that general defects in chlorophyll biosynthesis and the accumulation of photosynthetic complexes do not necessarily enhance var2 leaf variegation. In addition, we found that VAR2/AtFtsH2 is required for the accumulation of photosynthetic proteins during de-etiolation. Moreover, we identified PSII core proteins D1 and PsbC as potential EVR2-associated proteins using Co-IP/MS. Furthermore, the accumulation of D1 protein was greatly compromised in the var2-5 evr2-1 double mutant during de-etiolation. Together, our findings reveal a functional link between VAR2/AtFtsH2 and EVR2/BCM1/CBD1 in regulating chloroplast development and the accumulation of PSII reaction centre D1 protein during de-etiolation.

Cytological, Biochemical, and Transcriptomic Analyses of a Novel Yellow Leaf Variation in a Paphiopedilum (Orchidaceae) SCBG COP15

The genus Paphiopedilum, belonging to the Orchidaceae, has high ornamental value. Leaf variations can considerably improve the economic and horticultural value of the orchids. In the study, a yellow leaf mutant of a Paphiopedilum hybrid named P. SCBG COP15 was identified during the in vitro plant culture process; however, little is known about their molecular mechanisms. For this, RNA-seq libraries were created and used for the transcriptomic profiling of P. SCBG COP15 and the yellow mutant. The Chl a, Chl b, and carotenoid contents in the yellow leaves decreased by approximately 75.99%, 76.92%, and 56.83%, respectively, relative to the green leaves. Decreased chloroplasts per cell and abnormal chloroplast ultrastructure were observed by electron microscopic investigation in yellowing leaves; photosynthetic characteristics and Chl fluorescence parameters were also decreased in the mutant. Altogether, 34,492 unigenes were annotated by BLASTX; 1,835 DEGs were identified, consisting of 697 upregulated and 1138 downregulated DEGs. HEMA, CRD, CAO, and CHLE, involved in Chl biosynthesis, were predicted to be key genes responsible for leaf yellow coloration. Our findings provide an essential genetic resource for understanding the molecular mechanism of leaf color variation and breeding new varieties of Paphiopedilum with increased horticultural value.

The FtsHi Enzymes of Arabidopsis thaliana: Pseudo-Proteases with an Important Function

FtsH metalloproteases found in eubacteria, animals, and plants are well-known for their vital role in the maintenance and proteolysis of membrane proteins. Their location is restricted to organelles of endosymbiotic origin, the chloroplasts, and mitochondria. In the model organism Arabidopsis thaliana, there are 17 membrane-bound FtsH proteases containing an AAA+ (ATPase associated with various cellular activities) and a Zn2+ metalloprotease domain. However, in five of those, the zinc-binding motif HEXXH is either mutated (FtsHi1, 2, 4, 5) or completely missing (FtsHi3), rendering these enzymes presumably inactive in proteolysis. Still, homozygous null mutants of the pseudo-proteases FtsHi1, 2, 4, 5 are embryo-lethal. Homozygous ftshi3 or a weak point mutant in FTSHi1 are affected in overall plant growth and development. This review will focus on the findings concerning the FtsHi pseudo-proteases and their involvement in protein import, leading to consequences in embryogenesis, seed growth, chloroplast, and leaf development and oxidative stress management.

Cytological and Transcriptomic Analysis Provide Insights into the Formation of Variegated Leaves in Ilex × altaclerensis 'Belgica Aurea'

Ilex × altaclerensis 'Belgica Aurea' is an attractive ornamental plant bearing yellow-green variegated leaves. However, the mechanisms underlying the formation of leaf variegation in this species are still unclear. Here, the juvenile yellow leaves and mature variegated leaves of I. altaclerensis 'Belgica Aurea' were compared in terms of leaf structure, pigment content and transcriptomics. The results showed that no obvious differences in histology were noticed between yellow and variegated leaves, however, ruptured thylakoid membranes and altered ultrastructure of chloroplasts were found in yellow leaves (yellow) and yellow sectors of the variegated leaves (variegation). Moreover, the yellow leaves and the yellow sectors of variegated leaves had significantly lower chlorophyll compared to green sectors of the variegated leaves (green). In addition, transcriptomic sequencing identified 1675 differentially expressed genes (DEGs) among the three pairwise comparisons (yellow vs. green, variegation vs. green, yellow vs. variegation). Expression of magnesium-protoporphyrin IX monomethyl ester (MgPME) [oxidative] cyclase, monogalactosyldiacylglycerol (MGDG) synthase and digalactosyldiacylglycerol (DGDG) synthase were decreased in the yellow leaves. Altogether, chlorophyll deficiency might be the main factors driving the formation of leaf variegation in I.altaclerensis 'Belgica Aurea'.

The chloroplast metalloproteases VAR2 and EGY1 act synergistically to regulate chloroplast development in Arabidopsis

Chloroplast development and photosynthesis require the proper assembly and turnover of photosynthetic protein complexes. Chloroplasts harbor a repertoire of proteases to facilitate proteostasis and development. We have previously used an Arabidopsis leaf variegation mutant, yellow variegated2 (var2), defective in thylakoid FtsH protease complexes, as a tool to dissect the genetic regulation of chloroplast development. Here, we report a new genetic enhancer mutant of var2, enhancer of variegation3-1 (evr3-1). We confirm that EVR3 encodes a chloroplast metalloprotease, reported previously as ethylene-dependent gravitropism-deficient and yellow-green1 (EGY1)/ammonium overly sensitive1 (AMOS1). We observed that mutations in EVR3/EGY1/AMOS1 cause more severe leaf variegation in var2-5 and synthetic lethality in var2-4 Using a modified blue-native PAGE system, we reveal abnormal accumulations of photosystem I, photosystem II, and light-harvesting antenna complexes in EVR3/EGY1/AMOS1 mutants. Moreover, we discover distinct roles of VAR2 and EVR3/EGY1/AMOS1 in the turnover of photosystem II reaction center under high light stress. In summary, our findings indicate that two chloroplast metalloproteases, VAR2/AtFtsH2 and EVR3/EGY1/AMOS1, function coordinately to regulate chloroplast development and reveal new roles of EVR3/EGY1/AMOS1 in regulating chloroplast proteostasis in Arabidopsis.

Protective Role of Leaf Variegation in Pittosporum tobira under Low Temperature: Insights into the Physio-Biochemical and Molecular Mechanisms

Leaf variegation has been demonstrated to have adaptive functions such as cold tolerance. Pittosporum tobira is an ornamental plant with natural leaf variegated cultivars grown in temperate regions. Herein, we investigated the role of leaf variegation in low temperature responses by comparing variegated “Variegatum” and non-variegated “Green Pittosporum” cultivars. We found that leaf variegation is associated with impaired chloroplast development in the yellow sector, reduced chlorophyll content, strong accumulation of carotenoids and high levels of ROS. However, the photosynthetic efficiency was not obviously impaired in the variegated leaves. Also, leaf variegation plays low temperature protective function since “Variegatum” displayed strong and efficient ROS-scavenging enzymatic systems to buffer cold (10 °C)-induced damages. Transcriptome analysis under cold conditions revealed 309 differentially expressed genes between both cultivars. Distinctly, the strong cold response observed in “Variegatum” was essentially attributed to the up-regulation of HSP70/90 genes involved in cellular homeostasis; up-regulation of POD genes responsible for cell detoxification and up-regulation of FAD2 genes and subsequent down-regulation of GDSL genes leading to high accumulation of polyunsaturated fatty acids for cell membrane fluidity. Overall, our results indicated that leaf variegation is associated with changes in physiological, biochemical and molecular components playing low temperature protective function in P. tobira.

Chloroplast Translation Elongation Factor EF-Tu/SVR11 Is Involved in var2-Mediated Leaf Variegation and Leaf Development in Arabidopsis

Chloroplasts are semiautonomous organelles, retaining their own genomes and gene expression apparatuses but controlled by nucleus genome encoded protein factors during evolution. To analyze the genetic regulatory network of FtsH-mediated chloroplast development in Arabidopsis, a set of suppressor mutants of yellow variegated (var2) have been identified. In this research, we reported the identification of another new var2 suppressor locus, SUPPRESSOR OF VARIEGATION11 (SVR11), which encodes a putative chloroplast-localized prokaryotic type translation elongation factor EF-Tu. SVR11 is likely essential to chloroplast development and plant survival. GUS activity reveals that SVR11 is abundant in the juvenile leaf tissue, lateral roots, and root tips. Interestingly, we found that SVR11 and SVR9 together regulate leaf development, including leaf margin development and cotyledon venation patterns. These findings reinforce the notion that chloroplast translation state triggers retrograde signals regulate not only chloroplast development but also leaf development.

Cscs encoding chorismate synthase is a candidate gene for leaf variegation mutation in cucumber

Variegation is a frequently observed genetic phenomenon in landscaping. In this study, an ethyl methanesulfonate induced variegated leaf (Csvl) mutant in cucumber (Cucumis sativus L.) was identified. The Csvl mutant displayed green-yellow-white variegation phenotype throughout the whole growth cycle, while the leaf of wild type plants was normal green. The photosynthetic pigment contents and photosynthetic parameters of Csvl was significantly lower than wild type. The cytology observation results showed that the mesophyll cells of Csvl mutant contained defective chloroplasts. Genetic analysis indicated that variegated leaf phenotype was monogenic recessive inheritance. MutMap and genotyping results revealed that Csa6G405290 (Cscs), encoding chorismate synthase, was the candidate gene for variegated leaf mutant in cucumber. The expression level of Cscs was similar between wild type and variegated leaf mutant leaves. Transcriptome profile analysis of leaves of Csvl mutant identified 183 candidate genes involved in variegated leaf development in cucumber, including genes that encode heat shock protein, zinc finger protein. Cscs may regulate variegated leaf in cucumber by interacting with these genes. In a word, these results revealed that Cscs might regulate the variegated leaf phenotype in cucumber.

The Rice Rolled Fine Striped (RFS) CHD3/Mi-2 Chromatin Remodeling Factor Epigenetically Regulates Genes Involved in Oxidative Stress Responses During Leaf Development

In rice (Oryza sativa), moderate leaf rolling increases photosynthetic competence and raises grain yield; therefore, this important agronomic trait has attracted much attention from plant biologists and breeders. However, the relevant molecular mechanism remains unclear. Here, we isolated and characterized Rolled Fine Striped (RFS), a key gene affecting rice leaf rolling, chloroplast development, and reactive oxygen species (ROS) scavenging. The rfs-1 gamma-ray allele and the rfs-2 T-DNA insertion allele of RFS failed to complement each other and their mutants had similar phenotypes, producing extremely incurved leaves due to defective development of vascular cells on the adaxial side. Map-based cloning showed that the rfs-1 mutant harbors a 9-bp deletion in a gene encoding a predicted CHD3/Mi-2 chromatin remodeling factor belonging to the SNF2-ATP-dependent chromatin remodeling family. RFS was expressed in various tissues and accumulated mainly in the vascular cells throughout leaf development. Furthermore, RFS deficiency resulted in a cell death phenotype that was caused by ROS accumulation in developing leaves. We found that expression of five ROS-scavenging genes [encoding catalase C, ascorbate peroxidase 8, a putative copper/zinc superoxide dismutase (SOD), a putative SOD, and peroxiredoxin IIE2] decreased in rfs-2 mutants. Western-blot and chromatin immunoprecipitation (ChIP) assays demonstrated that rfs-2 mutants have reduced H3K4me3 levels in ROS-related genes. Loss-of-function in RFS also led to multiple developmental defects, affecting pollen development, grain filling, and root development. Our results suggest that RFS is required for many aspects of plant development and its function is closely associated with epigenetic regulation of genes that modulate ROS homeostasis.

Mutations in the Arabidopsis AtMRS2-11/AtMGT10/VAR5 Gene Cause Leaf Reticulation

In higher plants, the development of functional chloroplasts is essential for photosynthesis and many other physiological processes. With a long-term goal of elucidating the genetic regulation of chloroplast development, we identified two allelic leaf variegation mutants, variegated5-1 (var5-1) and var5-2. Both mutants showed a distinct leaf reticulation phenotype of yellow paraveinal regions and green interveinal regions, and the leaf reticulation phenotype correlated with photosynthetic defects. Through the identification of mutation sites in the two mutant alleles and the molecular complementation, we confirmed that VAR5 encodes a CorA family of Mg²⁺ transporters also known as AtMRS2-11/AtMGT10. Using protoplast transient expression and biochemical fractionation assays, we demonstrated that AtMRS2-11/AtMGT10/VAR5 likely localizes to the chloroplast envelope. Moreover, we established that AtMRS2-11/AtMGT10/VAR5 forms large molecular weight complexes in the chloroplast and the sizes of these complexes clearly exceed those of their bacterial counterparts, suggesting the compositions of CorA Mg²⁺ transporter complex is different between the chloroplast and bacteria. Our findings indicate that AtMRS2-11/AtMGT10/VAR5 plays an important role in the tissue specific regulation of chloroplast development.

Plastid signals and the bundle sheath: mesophyll development in reticulate mutants

The development of a plant leaf is a meticulously orchestrated sequence of events producing a complex organ comprising diverse cell types. The reticulate class of leaf variegation mutants displays contrasting pigmentation between veins and interveinal regions due to specific aberrations in the development of mesophyll cells. Thus, the reticulate mutants offer a potent tool to investigate cell-type-specific developmental processes. The discovery that most mutants are affected in plastid-localized, metabolic pathways that are strongly expressed in vasculature-associated tissues implicates a crucial role for the bundle sheath and their chloroplasts in proper development of the mesophyll cells. Here, we review the reticulate mutants and their phenotypic characteristics, with a focus on those in Arabidopsis thaliana. Two alternative models have been put forward to explain the relationship between plastid metabolism and mesophyll cell development, which we call here the supply and the signaling hypotheses. We critically assess these proposed models and discuss their implications for leaf development and bundle sheath function in C3 species. The characterization of the reticulate mutants supports the significance of plastid retrograde signaling in cell development and highlights the significance of the bundle sheath in C3 photosynthesis.

Proteomic evidence for genetic epistasis: ClpR4 mutations switch leaf variegation to virescence in Arabidopsis

Chloroplast development in plants is regulated by a series of coordinated biological processes. In this work, a genetic suppressor screen for the leaf variegation phenotype of the thylakoid formation 1 (thf1) mutant combined with a proteomic assay was employed to elucidate this complicated network. We identified a mutation in ClpR4, named clpR4-3, which leads to leaf virescence and also rescues the var2 variegation. Proteomic analysis showed that the chloroplast proteome of clpR4-3 thf1 is dominantly controlled by clpR4-3, providing molecular mechanisms that cause genetic epistasis of clpR4-3 to thf1. Classification of the proteins significantly mis-regulated in the mutants revealed that those functioning in the expression of plastid genes are oppositely regulated while proteins functioning in antioxidative stress, protein folding, and starch metabolism are changed in the same direction between thf1 and clpR4-3. The levels of FtsHs including FtsH2/VAR2, FtsH8, and FtsH5/VAR1 are greatly reduced in thf1 compared with those in the wild type, but are higher in clpR4-3 thf1 than in thf1. Quantitative PCR analysis revealed that FtsH expression in clpR4-3 thf1 is regulated post-transcriptionally. In addition, a number of ribosomal proteins are less expressed in the clpR4-3 proteome, which is in line with the reduced levels of rRNAs in clpR4-3. Furthermore, knocking out PRPL11, one of the most downregulated proteins in the clpR4-3 thf1 proteome, rescues the leaf variegation phenotype of the thf1 and var2 mutants. These results provide insights into molecular mechanisms by which the virescent clpR4-3 mutation suppresses leaf variegation of thf1 and var2.

Genetic interactions reveal that specific defects of chloroplast translation are associated with the suppression of var2-mediated leaf variegation

Arabidopsis thaliana L. yellow variegated (var2) mutant is defective in a chloroplast FtsH family metalloprotease, AtFtsH2/VAR2, and displays an intriguing green and white leaf variegation. This unique var2-mediated leaf variegation offers a simple yet powerful tool for dissecting the genetic regulation of chloroplast development. Here, we report the isolation and characterization of a new var2 suppressor gene, SUPPRESSOR OF VARIEGATION8 (SVR8), which encodes a putative chloroplast ribosomal large subunit protein, L24. Mutations in SVR8 suppress var2 leaf variegation at ambient temperature and partially suppress the cold-induced chlorosis phenotype of var2. Loss of SVR8 causes unique chloroplast rRNA processing defects, particularly the 23S-4.5S dicistronic precursor. The recovery of the major abnormal processing site in svr8 23S-4.5S precursor indicate that it does not lie in the same position where SVR8/L24 binds on the ribosome. Surprisingly, we found that the loss of a chloroplast ribosomal small subunit protein, S21, results in aberrant chloroplast rRNA processing but not suppression of var2 variegation. These findings suggest that the disruption of specific aspects of chloroplast translation, rather than a general impairment in chloroplast translation, suppress var2 variegation and the existence of complex genetic interactions in chloroplast development.

Effects of chloroplast dysfunction on mitochondria: white sectors in variegated leaves have higher mitochondrial DNA levels and lower dark respiration rates than green sectors

Co-ordination between plastids and mitochondria is so essential that there should be extensive inter-organellar crosstalk during development of plant cells. Indeed, chloroplast dysfunction in white leaves of plastid ribosome-deficient mutant barley, albostrians, is reportedly accompanied by increases in the levels of mitochondrial DNA and mitochondrial transcripts, suggesting that (i) developmental/physiological status of plastids (or heterotrophic growth condition of albino leaves) can affect the status of mitochondrial genome, and (ii) the function of the affected mitochondria may also be up-regulated accordingly. However, functional aspects of the mitochondria affected by chloroplast dysfunction have not yet been examined in detail. Here, we examined the effects of chloroplast dysfunction on mitochondrial DNA level and dark respiration rate, by comparing white and green sectors within individual variegated leaves, using 12 ornamental plants as experimental materials. The pattern of leaf variegation differed from species to species, suggesting that different mechanisms were involved in the formation of white sectors in different species. Quantitative hybridization analysis revealed that mitochondrial DNA levels were generally higher in white sectors than in green sectors. In spite of the elevated mitochondrial DNA levels, however, dark respiration rates in white sectors were generally lower than those in green sectors. Several possible mechanisms for elevation of mitochondrial DNA level and suppression of dark respiration rates in white sectors are discussed.

RecA maintains the integrity of chloroplast DNA molecules in Arabidopsis

Although our understanding of mechanisms of DNA repair in bacteria and eukaryotic nuclei continues to improve, almost nothing is known about the DNA repair process in plant organelles, especially chloroplasts. Since the RecA protein functions in DNA repair for bacteria, an analogous function may exist for chloroplasts. The effects on chloroplast DNA (cpDNA) structure of two nuclear-encoded, chloroplast-targeted homologues of RecA in Arabidopsis were examined. A homozygous T-DNA insertion mutation in one of these genes (cpRecA) resulted in altered structural forms of cpDNA molecules and a reduced amount of cpDNA, while a similar mutation in the other gene (DRT100) had no effect. Double mutants exhibited a similar phenotype to cprecA single mutants. The cprecA mutants also exhibited an increased amount of single-stranded cpDNA, consistent with impaired RecA function. After four generations, the cprecA mutant plants showed signs of reduced chloroplast function: variegation and necrosis. Double-stranded breaks in cpDNA of wild-type plants caused by ciprofloxacin (an inhibitor of Escherichia coli gyrase, a type II topoisomerase) led to an alteration of cpDNA structure that was similar to that seen in cprecA mutants. It is concluded that the process by which damaged DNA is repaired in bacteria has been retained in their endosymbiotic descendent, the chloroplast.