Establishment of the chloroplast genetic system in rice during early leaf development and at low temperatures

OsPGL3A encodes a DYW-type pentatricopeptide repeat protein involved in chloroplast RNA processing and regulated chloroplast development

The chloroplast serves as the primary site of photosynthesis, and its development plays a crucial role in regulating plant growth and morphogenesis. The Pentatricopeptide Repeat Sequence (PPR) proteins constitute a vast protein family that function in the post-transcriptional modification of RNA within plant organelles. In this study, we characterized mutant of rice with pale green leaves (pgl3a). The chlorophyll content of pgl3a at the seedling stage was significantly reduced compared to the wild type (WT). Transmission electron microscopy (TEM) and quantitative PCR analysis revealed that pgl3a exhibited aberrant chloroplast development compared to the wild type (WT), accompanied by significant alterations in gene expression levels associated with chloroplast development and photosynthesis. The Mutmap analysis revealed that a single base deletionin the coding region of Os03g0136700 in pgl3a. By employing CRISPR/Cas9 mediated gene editing, two homozygous cr-pgl3a mutants were generated and exhibited a similar phenotype to pgl3a, thereby confirming that Os03g0136700 was responsible for pgl3a. Consequently, it was designated as OsPGL3A. OsPGL3A belongs to the DYW-type PPR protein family and is localized in chloroplasts. Furthermore, we demonstrated that the RNA editing efficiency of rps8-182 and rpoC2-4106, and the splicing efficiency of ycf3-1 were significantly decreased in pgl3a mutants compared to WT. Collectively, these results indicate that OsPGL3A plays a crucial role in chloroplast development by regulating the editing and splicing of chloroplast genes in rice.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-024-01468-7.

New perspectives on the molecular mechanisms of stress signalling by the nucleotide guanosine tetraphosphate (ppGpp), an emerging regulator of photosynthesis in plants and algae

The nucleotides guanosine tetraphosphate and guanosine pentaphosphate (together (p)ppGpp) are found in a wide range of prokaryotic and eukaryotic organisms where they are associated with stress signalling. In this review, we will discuss recent research highlighting the role of (p)ppGpp signalling as a conserved regulator of photosynthetic activity in the chloroplasts of plants and algae, and the latest discoveries that open up new perspectives on the emerging roles of (p)ppGpp in acclimation to environmental stress. We explore how rapid advances in the study of (p)ppGpp signalling in prokaryotes are now revealing large gaps in our understanding of the molecular mechanisms of signalling by (p)ppGpp and related nucleotides in plants and algae. Filling in these gaps is likely to lead to the discovery of conserved as well as new plant- and algal-specific (p)ppGpp signalling mechanisms that will offer new insights into the taming of the chloroplast and the regulation of stress tolerance.

Genetic mapping and molecular characterization of the delayed green gene dg in watermelon (Citrullus lanatus)

Leaf color mutants are common in higher plants that can be used as markers in crop breeding and are important tools in understanding regulatory mechanisms of chlorophyll biosynthesis and chloroplast development. Genetic analysis was performed by evaluating F₁, F₂ and BC₁ populations derived from two parental lines (Charleston gray with green leaf color and Houlv with delayed green leaf color), suggesting that a single recessive gene controls the delayed green leaf color. In this study, the delayed green mutant showed a conditional pale green leaf color at the early leaf development but turned to green as the leaf development progressed. Delayed green leaf plants showed reduced pigment content, photosynthetic, chlorophyll fluorescence parameters, and impaired chloroplast development compared with green leaf plants. The delayed green (dg) locus was mapped to 7.48 Mb on chromosome 3 through bulk segregant analysis approach, and the gene controlling delayed green leaf color was narrowed to 53.54 kb between SNP130 and SNP135 markers containing three candidate genes. Sequence alignment of the three genes indicated that there was a single SNP mutation (G/A) in the coding region of ClCG03G010030 in the Houlv parent, which causes an amino acid change from Arginine to Lysine. The ClCG03G010030 gene encoded FtsH extracellular protease protein family is involved in early delayed green leaf development. The expression level of ClCG03G010030 was significantly reduced in delayed green leaf plants than in green leaf plants. These results indicated that the ClCG03G010030 might control watermelon green leaf color and the single SNP variation in ClCG03G010030 may result in early delayed green leaf color development during evolutionary process.

Rice TCD8 Encoding a Multi-Domain GTPase Is Crucial for Chloroplast Development of Early Leaf Stage at Low Temperatures

The multi-domain GTPase (MnmE) is conservative from bacteria to human and participates in tRNA modified synthesis. However, our understanding of how the MnmE is involved in plant chloroplast development is scarce, let alone in rice. A novel rice mutant, thermo-sensitive chlorophyll-deficient mutant 8 (tcd8) was identified in this study, which apparently presented an albino phenotype at 20 °C but a normal green over 24 °C, coincided with chloroplast development and chlorophyll content. Map-based cloning and complementary test revealed the TCD8 encoded a multi-domain GTPase localized in chloroplasts. In addition, the disturbance of TCD8 suppressed the transcripts of certain chloroplast-related genes at low temperature, although the genes were recoverable to nearly normal levels at high temperature (32 °C), indicating that TCD8 governs chloroplast development at low temperature. The multi-domain GTPase gene in rice is first reported in this study, which endorses the importance in exploring chloroplast development in rice.

STRIPE3, encoding a human dNTPase SAMHD1 homolog, regulates chloroplast development in rice

Chloroplast is an important organelle for photosynthesis and numerous essential metabolic processes, thus ensuring plant fitness or survival. Although many genes involved in chloroplast development have been identified, mechanisms underlying such development are not fully understood. Here, we isolated and characterized the stripe3 (st3) mutant which exhibited white-striped leaves with reduced chlorophyll content and abnormal chloroplast development during the seedling stage, but gradually produced nearly normal green leaves as it developed. Map-based cloning and transgenic tests demonstrated that a splicing mutation in ST3, encoding a human deoxynucleoside triphosphate triphosphohydrolase (dNTPase) SAMHD1 homolog, was responsible for st3 phenotypes. ST3 is highly expressed in the third leaf at three-leaf stage and expressed constitutively in root, stem, leaf, sheath, and panicle, and the encoded protein, OsSAMHD1, is localized to the cytoplasm. The st3 mutant showed more severe albino leaf phenotype under exogenous 1-mM dATP/dA, dCTP/dC, and dGTP/dG treatments compared with the control conditions, indicating that ST3 is involved in dNTP metabolism. This study reveals a gene associated with dNTP catabolism, and propose a model in which chloroplast development in rice is regulated by the dNTP pool, providing a potential application of these results to hybrid rice breeding.

Regulation of ppGpp Synthesis and Its Impact on Chloroplast Biogenesis during Early Leaf Development in Rice

Guanosine tetraphosphate (ppGpp) is known as an alarmone that mediates bacterial stress responses. In plants, ppGpp is synthesized in chloroplasts from GTP and ATP and functions as a regulator of chloroplast gene expression to affect photosynthesis and plant growth. This observation indicates that ppGpp metabolism is closely related to chloroplast function, but the regulation of ppGpp and its role in chloroplast differentiation are not well understood. In rice, ppGpp directly inhibits plastidial guanylate kinase (GKpm), a key enzyme in GTP biosynthesis. GKpm is highly expressed during early leaf development in rice, and the GKpm-deficient mutant, virescent-2 (v2), develops chloroplast-deficient chlorotic leaves under low-temperature conditions. To examine the relationship between GTP synthesis and ppGpp homeostasis, we generated transgenic rice plants over-expressing RSH3, a protein known to act as a ppGpp synthase. When RSH3 was overexpressed in v2, the leaf chlorosis was more severe. Although the RSH3 overexpression in the wild type caused no visible effects, pulse amplitude modulation fluorometer measurements indicated that photosynthetic rates were reduced in this line. This finding implies that the regulation of ppGpp synthesis in rice is involved in the maintenance of the GTP pool required to regulate plastid gene expression during early chloroplast biogenesis. We further investigated changes in the expressions of RelA/SpoT Homolog (RSH) genes encoding ppGpp synthases and hydrolases during the same period. Comparing the expression of these genes with the cellular ppGpp content suggests that the basal ppGpp level is determined by the antagonistic action of multiple RSH enzymatic activities during early leaf development in rice.

Mutation of the rice AN1-type zinc-finger protein gene ASL4 causes chloroplast development defects and seedling lethality

Plant zinc-finger proteins play a crucial role in biosynthesis and plant development. However, it is not known whether certain zinc-finger proteins play a role in rice chloroplast development. In this study, a novel rice zinc-finger protein mutant asl4 (albino seedling lethality4), which exhibits an albino lethal phenotype at the seedling stage, was used. Chlorophyll fluorescence analysis and TEM were used to investigate features of the asl4 mutant. The genetic behaviour and function of ASL4 gene were then analysed thorough map-based cloning, transgenic complement and subcellular localization. The albino lethal phenotype was caused by a single nucleotide (G*) deletion mutation on the exon of the ASL4 (LOC_Os09g21710) gene. The ASL4 gene encoded a novel zinc-finger protein containing two ZnF-AN1 domains, which was localized to the nucleocytoplasm. The ASL4 transcripts were highly expressed in all leaves but relatively less in other tissues, suggesting its tissue-specific expression. The transcript levels of associated genes for Chl biosynthesis, photosynthesis and chloroplast development were severely suppressed in asl4 mutants. In conclusion, the absence of ASL4 function caused a defect in chloroplast development and seedling lethality. This is the first published report on the importance of the ZnF-AN1 type zinc-finger protein gene in chloroplast development in rice.

CDE4 encodes a pentatricopeptide repeat protein involved in chloroplast RNA splicing and affects chloroplast development under low-temperature conditions in rice

Pentatricopeptide repeat (PPR) proteins play important roles in the post-transcriptional modification of organellar RNAs in plants. However, the function of most PPR proteins remains unknown. Here, we characterized the rice (Oryza sativa L.) chlorophyll deficient 4 (cde4) mutant which exhibits an albino phenotype during early leaf development, with decreased chlorophyll contents and abnormal chloroplasts at low-temperature (20°C). Positional cloning revealed that CDE4 encodes a P-type PPR protein localized in chloroplasts. In the cde4 mutant, plastid-encoded polymerase (PEP)-dependent transcript levels were significantly reduced, but transcript levels of nuclear-encoded genes were increased compared to wild-type plants at 20°C. CDE4 directly binds to the transcripts of the chloroplast genes rpl2, ndhA, and ndhB. Intron splicing of these transcripts was defective in the cde4 mutant at 20°C, but was normal at 32°C. Moreover, CDE4 interacts with the guanylate kinase VIRESCENT 2 (V2); overexpression of V2 enhanced CDE4 protein stability, thereby rescuing the cde4 phenotype at 20°C. Our results suggest that CDE4 participates in plastid RNA splicing and plays an important role in rice chloroplast development under low-temperature conditions.

Rice TSV2 encoding threonyl-tRNA synthetase is needed for early chloroplast development and seedling growth under cold stress

Threonyl-tRNA synthetase (ThrRS), one of the aminoacyl-tRNA synthetases (AARSs), plays a crucial role in protein synthesis. However, the AARS functions on rice chloroplast development and growth were not fully appraised. In this study, a thermo-sensitive virescent mutant tsv2, which showed albino phenotype and lethal after the 4-leaf stage at 20°C but recovered to normal when the temperatures rose, was identified and characterized. Map-based cloning and complementation tests showed that TSV2 encoded a chloroplast-located ThrRS protein in rice. The Lys-to-Arg mutation in the anticodon-binding domain hampered chloroplast development under cold stress, while the loss of function of the ThrRS core domain in TSV2 fatally led to seedling death regardless of growing temperatures. In addition, TSV2 had a specific expression in early leaves. Its disruption obviously resulted in the downregulation of certain genes associated with chlorophyll biosynthesis, photosynthesis, and chloroplast development at cold conditions. Our observations revealed that rice nuclear-encoded TSV2 plays an important role in chloroplast development at the early leaf stage under cold stress.

Comparative Multi-Omics of Tender Shoots from a Novel Evergrowing Tea Cultivar Provide Insight into the Winter Adaptation Mechanism

Tea (Camellia sinensis [L.] O. Kuntze) tree is a perennial plant in which winter dormancy is an important biological adaptation to environmental changes. We discovered and reported a novel tea tree cultivar that can generate tender shoots in winter several years ago, but the molecular mechanism for this unique phenotype remains unknown . Here, we conducted comparative transcriptomics, proteomics and metabolomics along with phytohormone quantitation between the winter and spring tender shoots to investigate the physiological basis and putative regulatory mechanisms of its evergrowing character during winter. Our multi-omics study has led to the following findings. Gibberellin (GA) levels and key enzymes for GA biosynthesis and the signal transduction pathway were increased in the winter shoots, causing the ABA/GA content ratio to decrease, which might play a key regulatory role in maintaining normal growth during winter. The abundance of proteins, genes and metabolites involved in energy metabolism was all increased in winter shoots, indicating that energy is critical for continuous growth under the relatively weak-light and low-temperature environment. Abiotic resistance-related proteins and free amino acids were also increased in abundance in the winter shoots, which possibly represents an adaptation response to winter conditions. These results allowed us to hypothesize a novel molecular mechanism of adaptation for this unique tender shoot evergrowing in winter.

Cold acclimation can specifically inhibit chlorophyll biosynthesis in young leaves of Pakchoi

BACKGROUND

Leaf color is an important trait in breeding of leafy vegetables. Y-05, a pakchoi (Brassica rapa ssp. chinensis) cultivar, displays yellow inner (YIN) and green outer leaves (GOU) after cold acclimation. However, the mechanism of this special phenotype remains elusive.

RESULTS

We assumed that the yellow leaf phenotype of Y-05 maybe caused by low chlorophyll content. Pigments measurements and transmission electron microscopy (TEM) analysis showed that the yellow phenotype is closely related with decreased chlorophyll content and undeveloped thylakoids in chloroplast. Transcriptomes and metabolomes sequencing were next performed on YIN and GOU. The transcriptomes data showed that 4887 differentially expressed genes (DEGs) between the YIN and GOU leaves were mostly enriched in the chloroplast- and chlorophyll-related categories, indicating that the chlorophyll biosynthesis is mainly affected during cold acclimation. Together with metabolomes data, the inhibition of chlorophyll biosynthesis is contributed by blocked 5-aminolevulinic acid (ALA) synthesis in yellow inner leaves, which is further verified by complementary and inhibitory experiments of ALA. Furthermore, we found that the blocked ALA is closely associated with increased BrFLU expression, which is indirectly altered by cold acclimation. In BrFLU-silenced pakchoi Y-05, cold-acclimated leaves still showed green phenotype and higher chlorophyll content compared with control, meaning silencing of BrFLU can rescue the leaf yellowing induced by cold acclimation.

CONCLUSIONS

Our findings suggested that cold acclimation can indirectly promote the expression of BrFLU in inner leaves of Y-05 to block ALA synthesis, resulting in decreased chlorophyll content and leaf yellowing. This study revealed the underlying mechanisms of leaves color change in cold-acclimated Y-05.

Quantification of guanosine triphosphate and tetraphosphate in plants and algae using stable isotope-labelled internal standards

Guanosine tetraphosphate (G4P) and guanosine pentaphosphate (G5P) are signalling nucleotides found in bacteria and photosynthetic eukaryotes that are implicated in a wide-range of processes including stress acclimation, developmental transitions and growth control. Measurements of G4P/G5P levels are essential for studying the diverse roles of these nucleotides. However, G4P/G5P quantification is particularly challenging in plants and algae due to lower cellular concentrations, compartmentalization and high metabolic complexity. Despite recent advances the speed and accuracy of G4P quantification in plants and algae can still be improved. Here, we report a new approach for rapid and accurate G4P quantification which relies on the use of synthesized stable isotope-labelled as internal standards. We anticipate that this approach will accelerate research into the function of G4P signaling in plants, algae and other organisms.

Chloroplast development at low temperature requires the pseudouridine synthase gene TCD3 in rice

Low temperature affects a broad spectrum of cellular components in plants, such as chloroplasts, as well as plant metabolism. On the other hand, pseudouridine (Ψ) synthases are required for the most abundant post-transcriptional modification of RNA in Escherichia coli. However, the role of rice Ψ synthases in regulating chloroplast development at low temperature remains elusive. In this study, we identified the rice thermo-sensitive chlorophyll-deficient (tcd3) mutant, which displays an albino phenotype before the 4-leaf stage and ultimately dies when grown at 20 °C, but can grow normally at 32 °C. Genetic analysis showed that the mutant trait is controlled by a single recessive nuclear gene (tcd3). Map-based cloning, complementation and knockout tests revealed that TCD3 encodes a chloroplast-localized Ψ synthase. TCD3 is a cold-induced gene that is mainly expressed in leaves. The disruption of TCD3 severely affected the transcript levels of various chloroplast-associated genes, as well as ribosomal genes involved in chloroplast rRNA assembly at low temperature (20 °C), whereas the transcript levels of these genes were normal at high temperature (32 °C). These results provide a first glimpse into the importance of rice Ψ synthase gene in chloroplast development at low temperatures.

A DEAD-box RNA helicase TCD33 that confers chloroplast development in rice at seedling stage under cold stress

Cold stress is one of the most common unfavorable environmental factors affecting the growth, development, and survival of plants. The DEAD-box RNA helicases play important roles in all types of processes of RNA metabolism. However, the function of DEAD-box RNA helicase under cold stress is poorly explored in plants, especially in rice. This study reported the identification of a novel rice thermo-sensitive chlorophyll-deficient mutant, tcd33, which displayed an albino phenotype before the four-leaf stage, then withered and eventually died at 20 °C, while wild-type plants exhibited normal green coloration at 32 °C. The tcd33 seedlings also exhibited less chlorophyll contents and severe defects of chloroplast structure under 20 °C condition. Map-based cloning and complementation experiments suggested that TCD33 encodes a chloroplast-located DEAD-box RNA helicase protein. The transcript expression level of TCD33 indicated that the genes related to chlorophyll (Chl) biosynthesis, photosynthesis, and chloroplast development in tcd33 mutants were down-regulated at 20 °C, while the down-regulated genes were nearly recovered to or slightly higher than the WT level at 32 °C. Together, our results suggest that the cold-inducible TCD33 is essential for early chloroplast development and is important for cold-responsive gene regulation and cold tolerance in rice.

WSL6 encoding an Era-type GTP-binding protein is essential for chloroplast development in rice

Rice WSL6 is involved in chloroplast ribosome biogenesis and is essential for early chloroplast development. Construction of the genetic translation system is a prerequisite for chloroplast development in plants. However, the molecular mechanism underlying this process is largely unknown. Here, we isolated a white stripe leaf6 (wsl6) mutant in rice. The mutant seedlings displayed white-striped leaves that were more severe under low-temperature conditions. Transmission electron microscopy analysis showed that the wsl6 mutant was defective in early chloroplast development. Map-based cloning revealed that WSL6 encodes an Era-type guanosine-5'-triphosphate (GTP)-binding protein located in chloroplasts. Immunoblotting and quantitative real-time polymerase chain reaction (qRT-PCR) analyses demonstrated an absence of 70S ribosomes in wsl6 chloroplasts. Further research showed that WSL6 binds to the 16S ribosomal RNA (rRNA) subunit of chloroplast ribosome 30S. In summary, these results show that WSL6 is essential for chloroplast ribosome biogenesis during early chloroplast development in rice.

Mutation of the rice TCM12 gene encoding 2,3-bisphosphoglycerate-independent phosphoglycerate mutase affects chlorophyll synthesis, photosynthesis and chloroplast development at seedling stage at low temperatures

Glycolysis is a central metabolic pathway that provides energy and products of primary metabolites. 2,3-Biphosphoglycerate-independent phosphoglycerate mutase (iPGAM) is a key enzyme that catalyses the reversible interconversion of 3-phosphoglycerate (3-PGA) to 2-phosphoglycerate (2-PGA) in glycolysis. Low temperature is a common abiotic stress in rice production. However, the mechanism for rice iPGAM genes is not fully understood at low temperature. In this study, the rice mutant tcm12, with chlorosis, malformed chloroplasts and impaired photosynthesis, was grown at a low temperature (<20 °C) to the three-leaf stage, while the normal phenotype at 32 °C was used. Chlorophyll fluorescence analysis and transmission electron microscopy were used to examine features of the tcm12 mutant. The inheritance behaviour and function of TCM12 were then analysed thorough map-based cloning, transgenic complementation and subcellular localisation. The thermo-sensitive chlorosis phenotype was caused by a single nucleotide mutation (T→C) on the fifth exon of TCM12 (LOC_Os12g35040) encoding iPGAM, localised to both nucleus and membranes. In addition, TCM12 was constitutively expressed, and its disruption resulted in down-regulation of some genes associated with chlorophyll biosynthesis and photosynthesis at low temperatures (20 °C). This is the first report of the involvement of rice iPGAM gene in chlorophyll synthesis, photosynthesis and chloroplast development, providing new insights into the mechanisms underlying early growth of rice at low temperatures.

OsSIG2A is required for chloroplast development in rice (Oryza sativa L.) at low temperature by regulating plastid genes expression

The chloroplast is an essential photosynthetic apparatus that is more sensitive to low temperatures than other organelles. Sigma factors were revealed regulating specific gene expression for maintaining photosynthetic efficiency and adapting to physiological and environmental conditions. However, the regulatory mechanisms of SIG genes supporting chloroplast development under low temperature in rice have not yet been reported. Here, we uncovered the essential role of OsSIG2A in rice chloroplast development at low temperatures by a newly reported thermo-sensitive chlorophyll deficient 12 (tcd12) mutant, which exhibited albino leaves with decreased chlorophyll content and malformed chloroplasts at seedling stage under low temperature. OsSIG2A is a typical chloroplast-localised RNA polymerase sigma factor, and constitutively expresses in different rice tissues, especially for young leaves and stems. Moreover, the transcription level of both PEP- and NEP- dependent genes, which are necessary for chloroplast development at early leaf development stage, was greatly affected in the tcd12 mutant under low temperature. Taken together, our findings indicate that OsSIG2A is required for early chloroplast differentiation under low temperatures by regulating plastid genes expression.

The tomato WV gene encoding a thioredoxin protein is essential for chloroplast development at low temperature and high light intensity

BACKGROUND

Chloroplast biogenesis, a complex process in higher plants, is the key to photoautotrophic growth in plants. White virescent (wv) mutants have been used to unfold the molecular mechanisms underlying the regulation of chloroplast development and chloroplast gene expression in plants. However, most of genes controlling white virescent phenotype still remain unknown.

RESULTS

In this study, we identified a temperature- and light intensity-sensitive mutant, named as wv. The content of chlorophyll was dramatically decreased in the immature leaves of wv mutant under the conditions of low temperature and high-light intensity. TEM observation showed that the chloroplasts in the young leaves of wv mutant lacked an organized thylakoid membrane, whereas crescent-shaped chloroplasts with well-developed stromal and stacked grana thylakoids in the mature leaves were developed. Immunoblot analyses suggested that proteins of photosynthetic complexes were decreased substantially in wv mutants. Based on map-based cloning and transgenic analysis, we determined that the wv phenotype was caused by single base mutation in the first intron of WV gene, which encoded a thioredoxin protein with 365 amino acids. qRT-PCR analysis revealed that the expression of WV gene was significantly down-regulated in wv mutant. In addition, knockdown of WV gene through RNAi also resulted in white virescent young leaves, suggesting that the mutation possibly blocks the differentiation of chloroplasts through inhibiting the expression of WV gene. Furthermore, the expression of WV peaked in apical buds and gradually decreased along with the developmental stage, which was consistent with the wv mutant phenotype. Expression analysis of chloroplast-encoded genes by qRT-PCR showed that the wv mutation affected the expression pattern of chloroplast-encoded PEP dependent genes.

CONCLUSION

Our results suggested that wv mutant was sensitive to low temperature and light intensity. WV gene was essential for chloroplast differentiation. A single base mutation in the first intron resulted in down-regulation of WV gene expression, which inhibited the expression of chloroplast-encoded genes, thereby blocking chloroplast formation and chlorophyll synthesis.

Rice albino 1, encoding a glycyl-tRNA synthetase, is involved in chloroplast development and establishment of the plastidic ribosome system in rice

The chloroplast is an important organelle that performs photosynthesis as well as biosynthesis and storage of many metabolites. Aminoacyl-tRNA synthetases (aaRSs) are key enzymes in protein synthesis. However, the relationship between chloroplast development and aaRSs still remains unclear. In this study, we isolated a rice albino 1 (ra1) mutant through methane sulfonate (EMS) mutagenesis of rice japonica cultivar Ningjing 4 (Oryza sativa L.), which displayed albinic leaves in seedling stage due to abnormal chloroplast development. Compared with wild type (WT), ra1 showed significantly decreased levels of chlorophylls (Chl) and carotenoids (Car) in 2-week-old seedlings, which also showed obvious plastidic structural defects including abnormal thylakoid membrane structures and more osmiophilic particles. These defects caused albino phenotypes in seedlings. Map-based cloning revealed that RA1 gene encodes a glycyl-tRNA synthetase (GlyRS), which was confirmed by genetic complementation and knockout by Crispr/Cas9 technology. Sequence analysis showed that a single base mutation (T to A) occurred in the sixth exon of RA1 and resulted in a change from Isoleucine (Ile) to Lysine (Lys). Real-time PCR analyses showed that RA1 expression levels were constitutive in most tissues, but most abundant in the leaves and stems. By transient expression in Nicotiana benthamiana, we found that RA1 protein was localized in the chloroplast. Expression levels of chlorophyll biosynthesis and plastid development related genes were disordered in the ra1 mutant. RNA analysis revealed biogenesis of chloroplast rRNAs was abnormal in ra1. Meanwhile, western blotting showed that synthesis of proteins associated with plastid development was significantly repressed. These results suggest that RA1 is involved in early chloroplast development and establishment of the plastidic ribosome system in rice.

Comparative Proteomic Analysis Reveals That Chlorophyll Metabolism Contributes to Leaf Color Changes in Wucai ( Brassica campestris L.) Responding to Cold Acclimation

Chlorophyll is a vital photosynthetic pigment that plays a key role in plant development, participating in light energy capture and energy conversion. In this study, a novel wucai ( Brassica campestris L.) germplasm with green outer leaves and yellow inner leaves at the adult stage (W7-2) was used to examine chlorophyll metabolism response to cold acclimation. A green leaf wucai genotype without leaf color changes named W7-1 was selected as the control to evaluate the chlorophyll metabolism changes of W7-2. Compared to W7-1, the contents of chlorophyll a (Chl a) and chlorophyll b (Chl b) in W7-2 were significantly reduced at five developmental stages (13, 21, 29, 37, and 45 days after planting (DAP)). An iTRAQ-based quantitative proteomic analysis was carried out at 21 and 29 DAP according to the leaf color changes in both of genotypes. 1409 proteins were identified, while 218 of them displayed differential accumulations between W7-2 and W7-1 during the two developmental stages. The differentially expressed proteins (DEPs) mainly assigned to chlorophyll biosynthesis, photosynthesis, carbohydrate metabolism, ribosome metabolism and posttranslational modification. Among these DEPs, NADPH-protochlorophyllide oxidoreductase (PORB) and Mg-protoporphyrin IX chelatase 1 (CHLI1) were the key enzymes participating in chlorophyll (Chl) biosynthesis, which was down-regulated at 21 DAP and up-regulated at 29 DAP in W7-2 compared with W7-1, respectively. The expression analysis of genes of three subunits of Mg-chelatase ( CHLI1, CHLD, and CHLH), Genomes Uncoupled 4 ( GUN4), and Thioredoxin ( TRX3) associated with chlorophyll metabolism also displayed significant down-regulation in W7-2. In particular, PORB showed significant up-regulation in W7-2, significantly affecting chlorophyll biosynthesis. Additionally, differences in chlorophyll metabolism between W7-2 and W7-1 were in terms of altered photosynthesis, carbohydrate, and energy metabolism. We found that the transcription levels of most photosynthesis proteins showed significantly lower levels, and the genes expression level, associated with carbohydrate and energy metabolism, were lower in W7-2 than in W7-1. Therefore, the present study results help understand the physiological and molecular mechanisms underlying leaf coloring responding to cold acclimation.

WSL5, a pentatricopeptide repeat protein, is essential for chloroplast biogenesis in rice under cold stress

Chloroplasts play an essential role in plant growth and development, and cold conditions affect chloroplast development. Although many genes or regulators involved in chloroplast biogenesis and development have been isolated and characterized, many other components affecting chloroplast biogenesis under cold conditions have not been characterized. Here, we report the functional characterization of a white stripe leaf 5 (wsl5) mutant in rice. The mutant develops white-striped leaves during early leaf development and is albinic when planted under cold stress. Genetic and molecular analysis revealed that WSL5 encodes a novel chloroplast-targeted pentatricopeptide repeat protein. RNA sequencing analysis showed that expression of nuclear-encoded photosynthetic genes in the mutant was significantly repressed, and expression of many chloroplast-encoded genes was also significantly changed. Notably, the wsl5 mutation causes defects in editing of rpl2 and atpA, and splicing of rpl2 and rps12. wsl5 was impaired in chloroplast ribosome biogenesis under cold stress. We propose that the WSL5 allele is required for normal chloroplast development in maintaining retrograde signaling from plastids to the nucleus under cold stress.

Green magic: regulation of the chloroplast stress response by (p)ppGpp in plants and algae

The hyperphosphorylated nucleotides guanosine pentaphosphate and tetraphosphate [together referred to as (p)ppGpp, or 'magic spot'] orchestrate a signalling cascade in bacteria that controls growth under optimal conditions and in response to environmental stress. (p)ppGpp is also found in the chloroplasts of plants and algae where it has also been shown to accumulate in response to abiotic stress. Recent studies suggest that (p)ppGpp is a potent inhibitor of chloroplast gene expression in vivo, and is a significant regulator of chloroplast function that can influence both the growth and the development of plants. However, little is currently known about how (p)ppGpp is wired into eukaryotic signalling pathways, or how it may act to enhance fitness when plants or algae are exposed to environmental stress. This review discusses our current understanding of (p)ppGpp metabolism and its extent in plants and algae, and how (p)ppGpp signalling may be an important factor that is capable of influencing growth and stress acclimation in this major group of organisms.

OsNOA1 functions in a threshold-dependent manner to regulate chloroplast proteins in rice at lower temperatures

BACKGROUND

Although decreased protein expressions have been observed in NOA1 (Nitric Oxide Associated protein 1) deficient plants, the molecular mechanisms of how NOA1 regulates protein metabolism remain poorly understood. In this study, we have used a global comparative proteomic approach for both OsNOA1 suppression and overexpression transgenic lines under two different temperatures, in combination with physiological and biochemical analyses to explore the regulatory mechanisms of OsNOA1 in rice.

RESULTS

In OsNOA1-silenced or highly overexpressed rice, considerably different expression patterns of both chlorophyll and Rubisco as well as distinct phenotypes were observed between the growth temperatures at 22 °C and 30 °C. These observations led us to hypothesize there appears a narrow abundance threshold for OsNOA1 to function properly at lower temperatures, while higher temperatures seem to partially compensate for the changes of OsNOA1 abundance. Quantitative proteomic analyses revealed higher temperatures could restore 90% of the suppressed proteins to normal levels, whereas almost all of the remaining suppressed proteins were chloroplast ribosomal proteins. Additionally, our data showed 90% of the suppressed proteins in both types of transgenic plants at lower temperatures were located in the chloroplast, suggesting a primary effect of OsNOA1 on chloroplast proteins. Transcript analyses, along with in vitro pull-down experiments further demonstrated OsNOA1 is associated with the function of chloroplast ribosomes.

CONCLUSIONS

Our results suggest OsNOA1 functions in a threshold-dependent manner for regulation of chloroplast proteins at lower temperatures, which may be mediated by interactions between OsNOA1 and chloroplast ribosomes.

White Leaf and Panicle 2, encoding a PEP-associated protein, is required for chloroplast biogenesis under heat stress in rice

The plastid-encoded RNA polymerase (PEP) plays an important role in the transcription machinery of mature chloroplasts, yet details of its function remain elusive in rice. Here, we identified a novel PEP-associated protein (PAP), WLP2, based on its two allelic white leaf and panicle mutants, wlp2s and wlp2w. The two mutants were albino lethal at high temperatures and showed decreased chlorophyll accumulation, abnormal chloroplast ultrastructure, and attenuated photosynthetic activity. Map-based cloning suggested that WLP2 encodes a putative pfkB-type carbohydrate kinase family protein, which is homologous to fructokinase-like 1 (AtFLN1) in Arabidopsis. WLP2 is mainly expressed in green tissues and its protein localizes in chloroplasts. Expression levels of PEP-encoded genes, chloroplast development genes and photosynthesis-related genes were compromised in wlp2 mutants, indicating that WLP2 is essential for normal chloroplast biogenesis. Moreover, WLP2 and its paralog OsFLN2 can physically interact with thioredoxin OsTRXz to form a TRX-FLN regulatory module, which not only regulates transcription of the PEP-encoded genes but also maintains the redox balance in chloroplasts under heat stress. Furthermore, the wlp2w mutant gene represents a potential advantage in enhancing seed purity and high-throughput breeding. Our results strongly indicate that WLP2 protects chloroplast development from heat stress via a TRX-FLN regulatory module in rice.

TSV, a putative plastidic oxidoreductase, protects rice chloroplasts from cold stress during development by interacting with plastidic thioredoxin Z

Rice is vulnerable to cold stress. Seedlings are very sensitive to cold stress and this harms global rice production. The effects of cold on chloroplast development are well known, but little is known about the underlying molecular mechanisms. Here, we isolated a temperature-sensitive virescent (tsv) mutant that is extremely sensitive to cold stress. It displayed defective chloroplasts, decreased chlorophyll and zero survivorship under cold stress. We isolated and identified TSV by map-based cloning and rescue experiments, combined with genetic, cytological and molecular biological analyses. We found that TSV, a putative plastidic oxidoreductase, is a new type of virescent protein. A mutation in tsv causes premature termination of the gene product. The activity of plastid-encoded RNA polymerase (PEP) and the expression of genes participating in chlorophyll synthesis were severely reduced in the tsv mutant under cold stress, but not at normal temperatures. TSV expression was induced by low temperatures. Strikingly, TSV interacted with OsTrxZ (a subunit of PEP in chloroplasts) and enhanced OsTrxZ stability under low temperatures. We demonstrated that TSV protects rice chloroplasts from cold stress by interacting with OsTrxZ. These results provide novel insights into ways in which rice chloroplast development and chlorophyll synthesis are protected by TSV under cold stress.

Lethal albinic seedling, encoding a threonyl-tRNA synthetase, is involved in development of plastid protein synthesis system in rice

An albinic rice is caused by mutation of threonyl-tRNA synthetase, which is essential for plant development by stabilizing of NEP and PEP gene expressions and chloroplast protein synthesis. Chloroplast biogenesis and development depend on complex genetic mechanisms. Apart from their function in translation, aminoacyl-tRNA synthetases (aaRSs) play additional role in gene expression regulation, RNA splicing, and cytokine activity. However, their detailed functions in plant development are still poorly understood. We isolated a lethal albinic seedling (las) mutant in rice. Physiological and ultrastructural analysis of las mutant plants revealed weak chlorophyll fluorescence, negligible chlorophyll accumulation, and defective thylakoid membrane development. By map based cloning we determined that the LAS allele gene encodes threonyl-tRNA synthetase (ThrRS). LAS was constitutively expressed with relatively high level in leaves. NEP-dependent gene transcripts accumulated in the developing chloroplasts, while PEP-dependent transcripts were reduced in the las mutant. This result indicated that PEP activity was impaired. Chloroplast-encoded protein levels were sharply reduced in the las mutant. Biogenesis of chloroplast rRNAs (16S and 23S rRNA) was arrested, leading to impaired translation and protein synthesis. Together, our findings indicated that LAS is essential not only for chloroplast development by stabilizing the NEP and PEP gene expression, but also for protein synthesis and construction of the ribosome system in rice chloroplasts.

The rice TCD11 encoding plastid ribosomal protein S6 is essential for chloroplast development at low temperature

Plastid ribosome proteins (PRPs) are important components for chloroplast biogenesis and early chloroplast development. Although it has been known that chloroplast ribosomes are similar to bacterial ones, the precise molecular function of ribosomal proteins remains to be elucidated in rice. Here, we identified a novel rice mutant, designated tcd11 (thermo-sensitive chlorophyll-deficient mutant 11), characterized by the albino phenotype until it died at 20°C, while displaying normal phenotype at 32°C. The alteration of leaf color in tcd11 mutants was aligned with chlorophyll (Chl) content and chloroplast development. The map-based cloning and molecular complementation showed that TCD11 encodes the ribosomal small subunit protein S6 in chloroplasts (RPS6). TCD11 was abundantly expressed in leaves, suggesting its different expressions in tissues. In addition, the disruption of TCD11 greatly reduced the transcript levels of certain chloroplasts-associated genes and prevented the assembly of ribosome in chloroplasts at low temperature (20°C), whereas they recovered to nearly normal levels at high temperature (32°C). Thus, our data indicate that TCD11 plays an important role in chloroplast development at low temperature. Upon our knowledge, the observations from this study provide a first glimpse into the importance of RPS6 function in rice chloroplast development.

A naturally occurring conditional albino mutant in rice caused by defects in the plastid-localized OsABCI8 transporter

A wide range of molecules are transported across membranes by the ATP binding cassette (ABC) transporters. Plants possess a collection of ABC proteins bearing similarities to the components of prokaryotic multi subunit ABC transporters, designed as ABC group I. However the functions of most of them are not well understood. Here, we characterized a naturally occurring rice mutant that exhibited albino phenotype under continuous rainy days in the field, but gradually recovered to normal green after the rainy season. Molecular and genetic analyses revealed that the phenotypes were caused by a mutation in the OsABCI8 that encoded a member of the ABCI family. Subcellular localization demonstrated that OsABCI8 is a chloroplast ABC transporter. Expression of OsABCI8 is significantly enhanced in rainy days compared to sunny days. Besides defects in chloroplast development and chlorophyll biosynthesis, the mutant phenotype is accompanied by a higher accumulation of iron, suggesting that OsABCI8 is involved in iron transportation and/or homeostasis in rice. Our results demonstrate that OsABCI8 represents a conserved ABCI protein involved in transition metals transportation and/or homeostasis and suggest an important role of the plastid-localized OsABCI8 for chloroplast development.

WHITE STRIPE LEAF4 Encodes a Novel P-Type PPR Protein Required for Chloroplast Biogenesis during Early Leaf Development

Pentatricopeptide repeat (PPR) proteins comprise a large family in higher plants and perform diverse functions in organellar RNA metabolism. Despite the rice genome encodes 477 PRR proteins, the regulatory effects of PRR proteins on chloroplast development remains unknown. In this study, we report the functional characterization of the rice white stripe leaf4 (wsl4) mutant. The wsl4 mutant develops white-striped leaves during early leaf development, characterized by decreased chlorophyll content and malformed chloroplasts. Positional cloning of the WSL4 gene, together with complementation and RNA-interference tests, reveal that it encodes a novel P-family PPR protein with 12 PPR motifs, and is localized to chloroplast nucleoids. Quantitative RT-PCR analyses demonstrate that WSL4 is a low temperature response gene abundantly expressed in young leaves. Further expression analyses show that many nuclear- and plastid-encoded genes in the wsl4 mutant are significantly affected at the RNA and protein levels. Notably, the wsl4 mutant causes defects in the splicing of atpF, ndhA, rpl2, and rps12. Our findings identify WSL4 as a novel P-family PPR protein essential for chloroplast RNA group II intron splicing during early leaf development in rice.

The Rice TCM5 Gene Encoding a Novel Deg Protease Protein is Essential for Chloroplast Development under High Temperatures

BACKGROUND

High temperature affects a broad spectrum of cellular components and metabolism in plants. The Deg/HtrA family of ATP-independent serine endopeptidases is present in nearly all organisms. Deg proteases are required for the survival of Escherichia coli at high temperatures. However, it is still unclear whether rice Deg proteases are required for chloroplast development under high temperatures.

RESULTS

In this study, we reported the first rice deg mutant tcm5 (thermo-sensitive chlorophyll-deficient mutant 5) that has an albino phenotype, defective chloroplasts and could not survive after the 4-5 leaf seedling stage when grown at high temperature (32 °C). However, when grown at low temperatures (20 °C), tcm5 has a normal phenotype. Map-based cloning showed that TCM5 encoding a chloroplast-targeted Deg protease protein. The TCM5 transcripts were highly expressed in all green tissues and undetectable in other tissues, showing the tissue-specific expression. In tcm5 mutants grown at high temperatures, the transcript levels of certain genes associated with chloroplast development especially PSII-associated genes were severely affected, but recovered to normal levels at low temperatures. These results showed important role of TCM5 for chloroplast development under high temperatures.

CONCLUSIONS

The TCM5 encodes chloroplast-targeted Deg protease protein which is important for chloroplast development and the maintenance of PSII function and its disruption would lead to a defective chloroplast and affected expression levels of genes associated with chloroplast development and photosynthesis at early rice seedling stage under high temperatures.

The Rice Pentatricopeptide Repeat Gene TCD10 is Needed for Chloroplast Development under Cold Stress

BACKGROUND

Chloroplast plays a vital role in plant development and growth. The pentatricopeptide repeat (PPR) gene family is one of the largest gene families in plants. In addition, cold stress affects a broad spectrum of cellular components, e.g. chloroplast, and metabolism in plants. However, the regulatory mechanism for rice PPR genes on chloroplast development still remains elusive under cold stress.

RESULT

In this paper, we characterized a new rice PPR gene mutant tcd10 (thermo-sensitive chlorophyll-deficient mutant 10) that exhibits the albino phenotype, malformed chloroplast and could not survive after the 5-leaf stage when grown at 20 °C, but does the normal phenotype at 32 °C. Map-based cloning, followed by RNA interference and CRISPR/Cas9 genome editing techniques, revealed that TCD10 encoding a novel PPR protein, mainly localized to the chloroplasts, with 27 PPR motifs, is responsible for the mutant phenotype. In addition, TCD10 is specific expression in tissues. The disruption of TCD10 resulted in an evidently reduced expression of chloroplast-associated genes under cold stress (20 °C), whereas they did recovered to normal levels at high temperature (32 °C). These results showed an important role of TCD10 for chloroplast development under cold stress.

CONCLUSIONS

The TCD10 encodes a novel rice PPR protein, mainly located in chloroplasts, which is important for chloroplast development, growth and the maintenance of photosynthetic electron transport and its disorder would lead to an aberrant chloroplast and abnormal expressions in these genes for chloroplast development and photosynthesis in rice under cold stress.

Temperature-sensitive albino gene TCD5, encoding a monooxygenase, affects chloroplast development at low temperatures

Chloroplasts are essential for photosynthesis and play critical roles in plant development. In this study, we characterized the temperature-sensitive chlorophyll-deficient rice mutant tcd5, which develops albino leaves at low temperatures (20 °C) and normal green leaves at high temperatures (32 °C). The development of chloroplasts and etioplasts is impaired in tcd5 plants at 20 °C, and the temperature-sensitive period for the albino phenotype is the P4 stage of leaf development. The development of thylakoid membranes is arrested at the mid-P4 stage in tcd5 plants at 20 °C. We performed positional cloning of TCD5 and then complementation and knock-down experiments, and the results showed that the transcript LOC_Os05g34040.1 from the LOC_Os05g34040 gene corresponded to the tcd5 phenotype. TCD5 encodes a conserved plastid-targeted monooxygenase family protein which has not been previously reported associated with a temperature-sensitive albino phenotype in plants. TCD5 is abundantly expressed in young leaves and immature spikes, and low temperatures increased this expression. The transcription of some genes involved in plastid transcription/translation and photosynthesis varied in the tcd5 mutant. Although the phenotype and temperature dependence of the TCD5 orthologous mutant phenotype were different in rice and Arabidopsis, OsTCD5 could rescue the phenotype of the Arabidopsis mutant, suggesting that TCD5 function is conserved between monocots and dicots.