OspTAC2 encodes a pentatricopeptide repeat protein and regulates rice chloroplast development

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.

Cryo-EM structures of the plant plastid-encoded RNA polymerase

Chloroplasts are green plastids in the cytoplasm of eukaryotic algae and plants responsible for photosynthesis. The plastid-encoded RNA polymerase (PEP) plays an essential role during chloroplast biogenesis from proplastids and functions as the predominant RNA polymerase in mature chloroplasts. The PEP-centered transcription apparatus comprises a bacterial-origin PEP core and more than a dozen eukaryotic-origin PEP-associated proteins (PAPs) encoded in the nucleus. Here, we determined the cryo-EM structures of Nicotiana tabacum (tobacco) PEP-PAP apoenzyme and PEP-PAP transcription elongation complexes at near-atomic resolutions. Our data show the PEP core adopts a typical fold as bacterial RNAP. Fifteen PAPs bind at the periphery of the PEP core, facilitate assembling the PEP-PAP supercomplex, protect the complex from oxidation damage, and likely couple gene transcription with RNA processing. Our results report the high-resolution architecture of the chloroplast transcription apparatus and provide the structural basis for the mechanistic and functional study of transcription regulation in chloroplasts.

Young Leaf White Stripe encodes a P-type PPR protein required for chloroplast development

Pentatricopeptide repeat (PPR) proteins function in post-transcriptional regulation of organellar gene expression. Although several PPR proteins are known to function in chloroplast development in rice (Oryza sativa), the detailed molecular functions of many PPR proteins remain unclear. Here, we characterized a rice young leaf white stripe (ylws) mutant, which has defective chloroplast development during early seedling growth. Map-based cloning revealed that YLWS encodes a novel P-type chloroplast-targeted PPR protein with 11 PPR motifs. Further expression analyses showed that many nuclear- and plastid-encoded genes in the ylws mutant were significantly changed at the RNA and protein levels. The ylws mutant was impaired in chloroplast ribosome biogenesis and chloroplast development under low-temperature conditions. The ylws mutation causes defects in the splicing of atpF, ndhA, rpl2, and rps12, and editing of ndhA, ndhB, and rps14 transcripts. YLWS directly binds to specific sites in the atpF, ndhA, and rpl2 pre-mRNAs. Our results suggest that YLWS participates in chloroplast RNA group II intron splicing and plays an important role in chloroplast development during early leaf development.

An Overview of Pentatricopeptide Repeat (PPR) Proteins in the Moss Physcomitrium patens and Their Role in Organellar Gene Expression

Pentatricopeptide repeat (PPR) proteins are one type of helical repeat protein that are widespread in eukaryotes. In particular, there are several hundred PPR members in flowering plants. The majority of PPR proteins are localized in the plastids and mitochondria, where they play a crucial role in various aspects of RNA metabolism at the post-transcriptional and translational steps during gene expression. Among the early land plants, the moss Physcomitrium (formerly Physcomitrella) patens has at least 107 PPR protein-encoding genes, but most of their functions remain unclear. To elucidate the functions of PPR proteins, a reverse-genetics approach has been applied to P. patens. To date, the molecular functions of 22 PPR proteins were identified as essential factors required for either mRNA processing and stabilization, RNA splicing, or RNA editing. This review examines the P. patens PPR gene family and their current functional characterization. Similarities and a diversity of functions of PPR proteins between P. patens and flowering plants and their roles in the post-transcriptional regulation of organellar gene expression are discussed.

Chloroplastic pentatricopeptide repeat proteins (PPR) in albino plantlets of Agave angustifolia Haw. reveal unexpected behavior

BACKGROUND

Pentatricopeptide repeat (PPR) proteins play an essential role in the post-transcriptional regulation of genes in plastid genomes. Although important advances have been made in understanding the functions of these genes, there is little information available on chloroplastic PPR genes in non-model plants and less in plants without chloroplasts. In the present study, a comprehensive and multifactorial bioinformatic strategy was applied to search for putative PPR genes in the foliar and meristematic tissues of green and albino plantlets of the non-model plant Agave angustifolia Haw.

RESULTS

A total of 1581 PPR transcripts were identified, of which 282 were chloroplastic. Leaf tissue in the albino plantlets showed the highest levels of expression of chloroplastic PPRs. The search for hypothetical targets of 12 PPR sequences in the chloroplast genes of A. angustifolia revealed their action on transcripts related to ribosomes and translation, photosystems, ATP synthase, plastid-encoded RNA polymerase and RuBisCO.

CONCLUSIONS

Our results suggest that the expression of PPR genes depends on the state of cell differentiation and plastid development. In the case of the albino leaf tissue, which lacks functional chloroplasts, it is possible that anterograde and retrograde signaling networks are severely compromised, leading to a compensatory anterograde response characterized by an increase in the expression of PPR genes.

A cytosolic pentatricopeptide repeat protein is essential for tapetal plastid development by regulating OsGLK1 transcript levels in rice

Most plant pentatricopeptide repeat (PPR) proteins localize to and function inside plastids and mitochondria. However, the function of PPRs that only localize to the cytoplasm remains unknown. Here, we demonstrated that the rice (Oryza sativa) PPR protein CYTOPLASM-LOCALIZED PPR1 (OsCPPR1) contributes to pollen development and localizes to the cytoplasm. Knocking down OsCPPR1 led to abnormal plastid development in tapetal cells, prolonged tapetal programmed cell death (PCD) and tapetum degradation, and significantly reduced pollen fertility. Transcriptome analysis revealed that the transcript level of OsGOLDEN-LIKE1 (OsGLK1), which encodes a transcription factor that regulates plastid development and maintenance, was significantly higher in the OsCPPR1 knockdown plants compared to wild-type plants. We further determined that OsCPPR1 downregulates OsGLK1 transcription by directly binding to the single-stranded regions of OsGLK1 mRNAs. Overexpression of OsGLK1 resulted in abnormal tapetum and plastid development, similar to that seen in OsCPPR1 knockdown plants, and suppression of OsGLK1 partially restored pollen fertility in the OsCPPR1 knockdown plants. We therefore conclude that OsCPPR1 suppresses OsGLK1 in the regulation of plastid development and PCD in the tapetum. Our work revealed novel functions for a cytosolic PPR, demonstrating the diverse roles of PPRs in plants and identifying a new regulatory mechanism for regulating pollen development in rice.

CAF Proteins Help SOT1 Regulate the Stability of Chloroplast ndhA Transcripts

Protein-mediated RNA stabilization plays profound roles in chloroplast gene expression. Genetic studies have indicated that chloroplast ndhA transcripts, encoding a key subunit of the NADH dehydrogenase-like complex that mediates photosystem I cyclic electron transport and facilitates chlororespiration, are stabilized by PPR53 and its orthologs, but the underlying mechanisms are unclear. Here, we report that CHLOROPLAST RNA SPLICING 2 (CRS2)-ASSOCIATED FACTOR (CAF) proteins activate SUPPRESSOR OF THYLAKOID FORMATION 1 (SOT1), an ortholog of PPR53 in Arabidopsis thaliana, enhancing their affinity for the 5' ends of ndhA transcripts to stabilize these molecules while inhibiting the RNA endonuclease activity of the SOT1 C-terminal SMR domain. In addition, we established that SOT1 improves the splicing efficiency of ndhA by facilitating the association of CAF2 with the ndhA intron, which may be due to the SOT1-mediated stability of the ndhA transcripts. Our findings shed light on the importance of PPR protein interaction partners in moderating RNA metabolism.

Moss PPR-SMR protein PpPPR_64 influences the expression of a psaA-psaB-rps14 gene cluster and processing of the 23S-4.5S rRNA precursor in chloroplasts

Moss PPR-SMR protein PpPPR_64 is a pTAC2 homolog but is functionally distinct from pTAC2. PpPPR_64 is required for psaA gene expression and its function may have evolved in mosses. The pentatricopeptide repeat (PPR) proteins are key regulatory factors responsible for the control of plant organellar gene expression. A small subset of PPR proteins possess a C-terminal small MutS-related (SMR) domain and have diverse roles in plant organellar biogenesis. However, the function of PPR-SMR proteins is not fully understood. Here, we report the function of PPR-SMR protein PpPPR_64 in the moss Physcomitrium patens. Phylogenetic analysis indicated that PpPPR_64 belongs to the same clade as the Arabidopsis PPR-SMR protein pTAC2. PpPPR_64 knockout (KO) mutants grew autotrophically but with reduced protonemata growth and the poor formation of photosystems' antenna complexes. Quantitative reverse transcription-polymerase chain reaction and RNA gel blot hybridization analyses revealed a significant reduction in transcript levels of the psaA-psaB-rps14 gene cluster but no alteration to transcript levels of most photosynthesis- and non-photosynthesis-related genes. In addition, RNA processing of 23S-4.5S rRNA precursor was impaired in the PpPPR_64 KO mutants. This suggests that PpPPR_64 is specifically involved in the expression level of the psaA-psaB-rps14 gene and in processing of the 23S-4.5S rRNA precursor. Our results indicate that PpPPR_64 is functionally distinct from pTAC2 and is a novel PPR-SMR protein required for proper chloroplast biogenesis in P. patens.

SSR marker-based genetic diversity analysis and SNP haplotyping of genes associating abiotic and biotic stress tolerance, rice growth and development and yield across 93 rice landraces

BACKGROUND

As rice is the staple food for more than half of the world's population, enhancing grain yield irrespective of the variable climatic conditions is indispensable. Many traditionally cultivated rice landraces are well adapted to severe environmental conditions and have high genetic diversity that could play an important role in crop improvement.

METHODS AND RESULTS

The present study revealed a high level of genetic diversity among the unexploited rice landraces cultivated by the farmers of Kerala. Twelve polymorphic markers detected a total of seventy- seven alleles with an average of 6.416 alleles per locus. Polymorphic Information Content (PIC) value ranged from 0.459 to 0.809, and to differentiate the rice genotypes, RM 242 was found to be the most appropriate marker with a high value of 0.809. The current study indicated that the rice landraces are highly diverse with higher values of the adequate number of alleles, PIC, and Shannon information index. Utilizing these informative SSR markers for future molecular characterization and population genetic studies in rice landraces are advisable. Haplotypes are sets of genomic regions within a chromosome inherited together, and haplotype-based breeding is a promising strategy for designing next-generation rice varieties. Here, haplotype analysis explored 270 haplotype blocks and 775 haplotypes from all the chromosomes of landraces under study. The number of SNPs in each haplotype block ranged from two to 28. Haplotypes of genes related to biotic and abiotic stress tolerance, yield-enhancing, and growth and development in rice landraces were also elucidated in the current study.

CONCLUSIONS

The present investigation revealed the genetic diversity of rice landraces and the haplotype analysis will open the way for genome-wide association studies, QTL identification, and marker-assisted selection in the unexplored rice landraces collected from Kerala.

Interspecific Hybrids Between Pelargonium × hortorum and Species From P. Section Ciconium Reveal Biparental Plastid Inheritance and Multi-Locus Cyto-Nuclear Incompatibility

The genetics underlying Cyto-Nuclear Incompatibility (CNI) was studied in Pelargonium interspecific hybrids. We created hybrids of 12 closely related crop wild relatives (CWR) with the ornamental P. × hortorum. Ten of the resulting 12 (F₁) interspecific hybrids segregate for chlorosis suggesting biparental plastid inheritance. The segregation ratios of the interspecific F₂ populations show nuclear interactions of one, two, or three nuclear genes regulating plastid function dependent on the parents. We further validated that biparental inheritance of plastids is common in section Ciconium, using diagnostic PCR primers. Our results pave the way for using the diverse species from section Ciconium, each with its own set of characteristics, as novel sources of desired breeding traits for P. × hortorum cultivars.

OsCAF2 contains two CRM domains and is necessary for chloroplast development in rice

BACKGROUND

Chloroplasts play an important role in plant growth and development. The chloroplast genome contains approximately twenty group II introns that are spliced due to proteins encoded by nuclear genes. CAF2 is one of these splicing factors that has been shown to splice group IIB introns in maize and Arabidopsis thaliana. However, the research of the OsCAF2 gene in rice is very little, and the effects of OsCAF2 genes on chloroplasts development are not well characterized.

RESULTS

In this study, oscaf2 mutants were obtained by editing the OsCAF2 gene in the Nipponbare variety of rice. Phenotypic analysis showed that mutations to OsCAF2 led to albino leaves at the seeding stage that eventually caused plant death, and oscaf2 mutant plants had fewer chloroplasts and damaged chloroplast structure. We speculated that OsCAF2 might participate in the splicing of group IIA and IIB introns, which differs from its orthologs in A. thaliana and maize. Through yeast two-hybrid experiments, we found that the C-terminal region of OsCAF2 interacted with OsCRS2 and formed an OsCAF2-OsCRS2 complex. In addition, the N-terminal region of OsCAF2 interacted with itself to form homodimers.

CONCLUSION

Taken together, this study improved our understanding of the OsCAF2 protein, and revealed additional information about the molecular mechanism of OsCAF2 in regulating of chloroplast development in rice.

Source-sink modifications affect leaf senescence and grain mass in wheat as revealed by proteomic analysis

BACKGROUND

The grain yield of cereals is determined by the synergistic interaction between source activity and sink capacity. However, source-sink interactions are far from being fully understood. Therefore, a field experiment was performed in wheat to investigate the responses of flag leaves and grains to sink/source manipulations.

RESULTS

Half-degraining delayed but partial defoliation enhanced leaf senescence. Sink/source manipulations influenced the content of reactive oxygen species in the flag leaf and the concentration of phytohormones, including cytokinins, indoleacetic 3-acid and jasmonic acid, in the flag leaves (LDef) and grains (GDef) in defoliated plants and flag leaves (LDG) and grain (GDG) in de-grained plants. Isobaric tag for relative and absolute quantitation (iTRAQ)-based quantitative proteomic analysis indicated that at 16 days after manipulation, a total of 97 and 59 differentially expressed proteins (DEPs) from various functional categories were observed in the LDG and LDef groups, respectively, compared with the control, and 115 and 121 DEPs were observed in the GDG and GDef groups, respectively. The gene ontology annotation terms of the DEPs mainly included carbon fixation, hydrogen peroxide catabolic process, chloroplast and cytoplasm, oxidoreductase activity and glutamate synthase activity in the flag leaves of manipulated plants and organonitrogen compound metabolic process, cytoplasm, vacuolar membrane, CoA carboxylase activity, starch synthase activity and nutrient reservoir activity in the grains of manipulated plants. KEGG pathway enrichment analysis revealed that photosynthesis, carbon, nitrogen and pyruvate metabolism and glycolysis/gluconeogenesis were the processes most affected by sink/source manipulations. Sink/source manipulations affected the activities of amylase and proteinases and, ultimately, changed the mass per grain.

CONCLUSIONS

Manipulations to change the sink/source ratio affect hormone levels; hydrolytic enzyme activities; metabolism of carbon, nitrogen and other main compounds; stress resistance; and leaf senescence and thus influence grain mass.

OsSLC1 Encodes a Pentatricopeptide Repeat Protein Essential for Early Chloroplast Development and Seedling Survival

BACKGROUND

The large family of pentatricopeptide repeat (PPR) proteins is widely distributed among land plants. Such proteins play vital roles in intron splicing, RNA editing, RNA processing, RNA stability and RNA translation. However, only a small number of PPR genes have been identified in rice.

RESULTS

In this study, we raised a mutant from tissue-culture-derived plants of Oryza sativa subsp. japonica 'Zhonghua 11', which exhibited a lethal chlorosis phenotype from germination to the third-leaf stage. The mutant was designated seedling-lethal chlorosis 1 (slc1). The slc1 mutant leaves showed extremely low contents of photosynthetic pigments and abnormal chloroplast development, and were severely defective in photosynthesis. Map-based cloning of OsSLC1 revealed that a single base (G) deletion was detected in the first exon of Os06g0710800 in the slc1 mutant, which caused a premature stop codon. Knockout and complementation experiments further confirmed that OsSLC1 is responsible for the seedling-lethal chlorosis phenotype in the slc1 mutant. OsSLC1 was preferentially expressed in green leaves, and encoded a chloroplast-localized PPR protein harboring 12 PPR motifs. Loss-of-function of OsSLC1 affected the intron splicing of multiple group II introns, and especially precluded the intron splicing of rps16, and resulted in significant increase in the transcript levels of 3 chloroplast ribosomal RNAs and 16 chloroplast development-related and photosynthesis-related genes, and in significant reduction in the transcript levels of 1 chloroplast ribosomal RNAs and 2 chloroplast development-related and photosynthesis-related genes.

CONCLUSION

We characterized a novel chloroplast-localized PPR protein, OsSLC1, which plays a vital role in the intron splicing of multiple group II introns, especially the rps16 intron, and is essential for early chloroplast development and seedling survival in rice.

Disruption of ζ-Carotene Desaturase Protein ALE1 Leads to Chloroplast Developmental Defects and Seedling Lethality

ζ-carotene desaturase (ZDS) is a key enzyme in carotenoid biosynthesis and plays an important role in plant photosynthesis. We characterized an albino leaf-color mutant obtained from ethyl methanesulfonate treatment: albino and seedling lethality 1 (ale1). The material contains a chloroplast thylakoid defect where photosynthetic pigments declined and reactive oxygen species accumulated resulting in ale1 death within 3 weeks. Positional cloning and sequencing revealed that there was a single base substitution in ALE1, which encoded a ZDS involved in carotenoid biosynthesis. RNAi and complementation tests confirmed the identity of ALE1. Subcellular localization showed that the ALE1 protein is localized in the chloroplast. Expression analysis indicated that the genes involved in chlorophyll and carotenoid biosynthesis were downregulated. We conclude that ALE1 plays an important role in chloroplast and plant growth in rice.

The nuclear-localized PPR protein OsNPPR1 is important for mitochondrial function and endosperm development in rice

Pentatricopeptide repeat (PPR) proteins constitute one of the largest protein families in land plants. Recent studies revealed the functions of PPR proteins in organellar RNA metabolism and plant development, but the functions of most PPR proteins, especially PPRs localized in the nucleus, remain largely unknown. Here, we report the isolation and characterization of a rice mutant named floury and growth retardation1 (fgr1). fgr1 showed floury endosperm with loosely arranged starch grains, decreased starch and amylose contents, and retarded seedling growth. Map-based cloning showed that the mutant phenotype was caused by a single nucleotide substitution in the coding region of Os08g0290000. This gene encodes a nuclear-localized PPR protein, which we named OsNPPR1, that affected mitochondrial function. In vitro SELEX and RNA-EMSAs showed that OsNPPR1 was an RNA protein that bound to the CUCAC motif. Moreover, a number of retained intron (RI) events were detected in fgr1. Thus, OsNPPR1 was involved in regulation of mitochondrial development and/or functions that are important for endosperm development. Our results provide novel insights into coordinated interaction between nuclear-localized PPR proteins and mitochondrial function.

A Systematic View Exploring the Role of Chloroplasts in Plant Abiotic Stress Responses

Chloroplasts are intracellular semiautonomous organelles central to photosynthesis and are essential for plant growth and yield. The significance of the function of chloroplast-related genes in response to climate change has not been well studied in crops. In the present study, the initial focus was on genes that were predicted to be located in the chloroplast genome in rice, a model crop plant, with genes either preferentially expressed in the leaf or ubiquitously expressed in all organs. The characteristics were analyzed by Gene Ontology (GO) enrichment and MapMan functional classification tools. It was then identified that 110 GO terms (45 for leaf expression and 65 for ubiquitous expression) and 1,695 genes mapped to MapMan overviews were strongly associated with chloroplasts. In particular, the MapMan cellular response overview revealed a close association between heat stress response and chloroplast-related genes in rice. Moreover, features of these genes in response to abiotic stress were analyzed using a large-scale publicly available transcript dataset. Consequently, the expression of 215 genes was found to be upregulated in response to high temperature stress. Conversely, genes that responded to other stresses were extremely limited. In other words, chloroplast-related genes were found to affect abiotic stress response mainly through high temperature response, with little effect on response to drought and salinity stress. These results suggest that genes involved in diurnal rhythm in the leaves participate in the reaction to recognize temperature changes in the environment. Furthermore, the predicted protein–protein interaction network analysis associated with high temperature stress is expected to provide a very important basis for the study of molecular mechanisms by which chloroplasts will respond to future climate changes.

Genome-wide association mapping of leaf mass traits in a Vietnamese rice landrace panel

Leaf traits are often strongly correlated with yield, which poses a major challenge in rice breeding. In the present study, using a panel of Vietnamese rice landraces genotyped with 21,623 single-nucleotide polymorphism markers, a genome-wide association study (GWAS) was conducted for several leaf traits during the vegetative stage. Vietnamese landraces are often poorly represented in panels used for GWAS, even though they are adapted to contrasting agrosystems and can contain original, valuable genetic determinants. A panel of 180 rice varieties was grown in pots for four weeks with three replicates under nethouse conditions. Different leaf traits were measured on the second fully expanded leaf of the main tiller, which often plays a major role in determining the photosynthetic capacity of the plant. The leaf fresh weight, turgid weight and dry weight were measured; then, from these measurements, the relative tissue weight and leaf dry matter percentage were computed. The leaf dry matter percentage can be considered a proxy for the photosynthetic efficiency per unit leaf area, which contributes to yield. By a GWAS, thirteen QTLs associated with these leaf traits were identified. Eleven QTLs were identified for fresh weight, eleven for turgid weight, one for dry weight, one for relative tissue weight and one for leaf dry matter percentage. Eleven QTLs presented associations with several traits, suggesting that these traits share common genetic determinants, while one QTL was specific to leaf dry matter percentage and one QTL was specific to relative tissue weight. Interestingly, some of these QTLs colocalize with leaf- or yield-related QTLs previously identified using other material. Several genes within these QTLs with a known function in leaf development or physiology are reviewed.

The Enigmatic Roles of PPR-SMR Proteins in Plants

The pentatricopeptide repeat (PPR) protein family, with more than 400 members, is one of the largest and most diverse protein families in land plants. A small subset of PPR proteins contain a C-terminal small MutS-related (SMR) domain. Although there are relatively few PPR-SMR proteins, they play essential roles in embryo development, chloroplast biogenesis and gene expression, and plastid-to-nucleus retrograde signaling. Here, recent advances in understanding the roles of PPR-SMR proteins and the SMR domain based on a combination of genetic, biochemical, and physiological analyses are described. In addition, the potential of the PPR-SMR protein SOT1 to serve as a tool for RNA manipulation is highlighted.

Transcriptional Profile Corroborates that bml Mutant Plays likely Role in Premature Leaf Senescence of Rice (Oryza sativa L.)

Leaf senescence is the last period of leaf growth and a dynamic procedure associated with its death. The adaptability of the plants to changing environments occurs thanks to leaf senescence. Hence, transcriptional profiling is important to figure out the exact mechanisms of inducing leaf senescence in a particular crop, such as rice. From this perspective, leaf samples of two different rice genotypes, the brown midrib leaf (bml) mutant and its wild type (WT) were sampled for transcriptional profiling to identify differentially-expressed genes (DEGs). We identified 2670 DEGs, among which 1657 genes were up- and 1013 genes were down-regulated. These DEGs were enriched in binding and catalytic activity, followed by the single organism process and metabolic process through gene ontology (GO), while the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that the DEGs were related to the plant hormone signal transduction and photosynthetic pathway enrichment. The expression pattern and the clustering of DEGs revealed that the WRKY and NAC family, as well as zinc finger transcription factors, had greater effects on early-senescence of leaf compared to other transcription factors. These findings will help to elucidate the precise functional role of bml rice mutant in the early-leaf senescence.

PALE-GREEN LEAF12 Encodes a Novel Pentatricopeptide Repeat Protein Required for Chloroplast Development and 16S rRNA Processing in Rice

Pentatricopeptide repeat (PPR) proteins regulate organellar gene expression in plants, through their involvement in organellar RNA metabolism. In rice (Oryza sativa), 477 genes are predicted to encode PPR proteins; however, the majority of their functions remain unknown. In this study, we identified and characterized a rice mutant, pale-green leaf12 (pgl12); at the seedling stage, pgl12 mutants had yellow-green leaves, which gradually turned pale green as the plants grew. The pgl12 mutant had significantly reduced Chl contents and increased sensitivity to changes in temperature. A genetic analysis revealed that the pgl12 mutation is recessive and located within a single nuclear gene. Map-based cloning of PGL12, including a transgenic complementation test, confirmed the presence of a base substitution (C to T), generating a stop codon, within LOC_Os12g10184 in the pgl12 mutant. LOC_Os12g10184 encodes a novel PLS-type PPR protein containing 17 PPR motifs and targeted to the chloroplasts. A quantitative real-time PCR analysis showed that PGL12 was expressed in various tissues, especially the leaves. We also showed that the transcript levels of several nuclear- and plastid-encoded genes associated with chloroplast development and photosynthesis were significantly altered in pgl12 mutants. The mutant exhibited defects in the 16S rRNA processing and splicing of the plastid transcript ndhA. Our results indicate that PGL12 is a new PLS-type PPR protein required for proper chloroplast development and 16S rRNA processing in rice.

Abiotic Stresses Intervene with ABA Signaling to Induce Destructive Metabolic Pathways Leading to Death: Premature Leaf Senescence in Plants

Abiotic stresses trigger premature leaf senescence by affecting some endogenous factors, which is an important limitation for plant growth and grain yield. Among these endogenous factors that regulate leaf senescence, abscisic acid (ABA) works as a link between the oxidase damage of cellular structure and signal molecules responding to abiotic stress during leaf senescence. Considering the importance of ABA, we collect the latest findings related to ABA biosynthesis, ABA signaling, and its inhibitory effect on chloroplast structure destruction, chlorophyll (Chl) degradation, and photosynthesis reduction. Post-translational changes in leaf senescence end with the exhaustion of nutrients, yellowing of leaves, and death of senescent tissues. In this article, we review the literature on the ABA-inducing leaf senescence mechanism in rice and Arabidopsis starting from ABA synthesis, transport, signaling receptors, and catabolism. We also predict the future outcomes of investigations related to other plants. Before changes in translation occur, ABA signaling that mediates the expression of NYC, bZIP, and WRKY transcription factors (TFs) has been investigated to explain the inducing effect on senescence-associated genes. Various factors related to calcium signaling, reactive oxygen species (ROS) production, and protein degradation are elaborated, and research gaps and potential prospects are presented. Examples of gene mutation conferring the delay or induction of leaf senescence are also described, and they may be helpful in understanding the inhibitory effect of abiotic stresses and effective measures to tolerate, minimize, or resist their inducing effect on leaf senescence.

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.

Transcriptome Analysis of a Premature Leaf Senescence Mutant of Common Wheat (Triticum aestivum L.)

Leaf senescence is an important agronomic trait that affects both crop yield and quality. In this study, we characterized a premature leaf senescence mutant of wheat (Triticum aestivum L.) obtained by ethylmethane sulfonate (EMS) mutagenesis, named m68. Genetic analysis showed that the leaf senescence phenotype of m68 is controlled by a single recessive nuclear gene. We compared the transcriptome of wheat leaves between the wild type (WT) and the m68 mutant at four time points. Differentially expressed gene (DEG) analysis revealed many genes that were closely related to senescence genes. Gene Ontology (GO) enrichment analysis suggested that transcription factors and protein transport genes might function in the beginning of leaf senescence, while genes that were associated with chlorophyll and carbon metabolism might function in the later stage. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that the genes that are involved in plant hormone signal transduction were significantly enriched. Through expression pattern clustering of DEGs, we identified 1012 genes that were induced during senescence, and we found that the WRKY family and zinc finger transcription factors might be more important than other transcription factors in the early stage of leaf senescence. These results will not only support further gene cloning and functional analysis of m68, but also facilitate the study of leaf senescence in wheat.

FRUCTOKINASE-LIKE PROTEIN 1 interacts with TRXz to regulate chloroplast development in rice

Chloroplast genes are transcribed by the plastid-encoded RNA polymerase (PEP) or nucleus-encoded RNA polymerase. FRUCTOKINASE-LIKE PROTEINS (FLNs) are phosphofructokinase-B (PfkB)-type carbohydrate kinases that act as part of the PEP complex; however, the molecular mechanisms underlying FLN activity in rice remain elusive. Previously, we identified and characterized a heat-stress sensitive albino (hsa1) mutant in rice. Map-based cloning revealed that HSA1 encodes a putative OsFLN2. Here, we further demonstrated that knockdown or knockout of the OsFLN1, a close homolog of HSA1/OsFLN2, considerably inhibits chloroplast biogenesis and the fln1 knockout mutants, created by clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associate protein 9, exhibit severe albino phenotype and seedling lethality. Moreover, OsFLN1 localizes to the chloroplast. Yeast two-hybrid, pull-down and bimolecular fluorescence complementation experiments revealed that OsFLN1 and HSA1/OsFLN2 interact with THIOREDOXINZ (OsTRXz) to regulate chloroplast development. In agreement with this, knockout of OsTRXz resulted in a similar albino and seedling lethality phenotype to that of the fln1 mutants. Quantitative reverse transcription polymerase chain reaction and immunoblot analysis revealed that the transcription and translation of PEP-dependent genes were strongly inhibited in fln1 and trxz mutants, indicating that loss of OsFLN1, HSA1/OsFLN2, or OsTRXz function perturbs the stability of the transcriptionally active chromosome complex and PEP activity. These results show that OsFLN1 and HSA1/OsFLN2 contribute to chloroplast biogenesis and plant growth.

The newly identified heat-stress sensitive albino 1 gene affects chloroplast development in rice

High temperature, a major abiotic stress, significantly affects the yield and quality of crops in many parts of the world. Components of the photosynthetic apparatus are highly susceptible to thermal damage. Although the responses to acute heat stress have been studied intensively, the mechanisms that regulate chloroplast development under heat stress remain obscure, especially in crop plants. Here, we cloned and characterized the gene responsible for the heat-sensitive albino1 (hsa1) mutation in rice (Oryza sativa). The hsa1 mutant harbors a recessive mutation in a gene encoding fructokinase-like protein2 (FLN2); the mutation causes a premature stop codon and results in a severe albino phenotype, with defects in early chloroplast development. The color of hsa1 mutant plants gradually changed from albino to green at later stages of development at various temperatures and chloroplast biogenesis was strongly delayed at high temperature (32 °C). HSA1 expression was strongly reduced in hsa1 plants compared to wild type (WT). HSA1 localizes to the chloroplast and regulates chloroplast development. An HSA1 deletion mutant induced by CRISPR/Cas9 was heat sensitive but had a faster greening phenotype than the original hsa1 allele at all temperatures. RNA and protein levels of plastid-encoded RNA polymerase-dependent plastid genes were markedly reduced in hsa1 plants compared to WT. These results demonstrated that HSA1 plays important roles in chloroplast development at early stages, and functions in protecting chloroplasts under heat stress at later stages in rice.

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.