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Due to neofunctionalization, a single fold can be identified in multiple proteins that have distinct molecular functions. Depending on the time that has passed since gene duplication and the number of mutations, the sequence similarity between functionally divergent proteins can be relatively high, eroding the value of sequence similarity as the sole tool for accurately annotating the function of uncharacterized homologs. Here, we combine bioinformatic approaches with targeted experimentation to reveal a large multifunctional family of putative enzymatic and nonenzymatic proteins involved in heme metabolism. This family (homolog of HugZ (HOZ)) is embedded in the "FMN-binding split barrel" superfamily and contains separate groups of proteins from prokaryotes, plants, and algae, which bind heme and either catalyze its degradation or function as nonenzymatic heme sensors. In prokaryotes these proteins are often involved in iron assimilation, whereas several plant and algal homologs are predicted to degrade heme in the plastid or regulate heme biosynthesis. In the plant Arabidopsis thaliana, which contains two HOZ subfamilies that can degrade heme in vitro (HOZ1 and HOZ2), disruption of AtHOZ1 (AT3G03890) or AtHOZ2A (AT1G51560) causes developmental delays, pointing to important biological roles in the plastid. In the tree Populus trichocarpa, a recent duplication event of a HOZ1 ancestor has resulted in localization of a paralog to the cytosol. Structural characterization of this cytosolic paralog and comparison to published homologous structures suggests conservation of heme-binding sites. This study unifies our understanding of the sequence-structure-function relationships within this multilineage family of heme-binding proteins and presents new molecular players in plant and bacterial heme metabolism.

Ultrastructural changes and visual symptoms resulting from nutritional disorders involving boron, manganese, iron, zinc, copper, molybdenum, and nickel depend on the species of the plant, and are unknown in passion fruit plants (Passiflora edulis Sims). A hydroponic experiment evaluated the symptoms of nickel addition and micronutrient deficiency in passion fruit seedlings "BRS Gigante Amarelo" and determined the micronutrient contents in leaf and root tissue, root development, ultrastructural changes (leaf tissue deformations) and dry matter accumulation when visual symptoms were observed. Results showed that the order of manifestation of deficiencies was Fe > Mn > Zn > Cu > Mo > B. Nickel toxicity appeared 40 days after the experiment was started, presenting chlorosis in the new leaves followed by general yellowing and some white parts. Boron omission of resulted in deformations in the leaf limbus and loss of apical dominance, showing deformation of the growth points. Mn omission caused reduction of growth and generalized chlorosis of young leaves with a thick reticulum. Iron omission of resulted in internerval chlorosis with a fine lattice appearance. Omission of zinc and copper resulted in deformation and elongation of the leaves, reducing height and root development. Molybdenum omission caused chlorosis in the older leaves, which was observed to spread over time. Iron was the nutrient that most reflected symptoms of deficiency by the formation of root hairs. The findings of this research suggest that the knowledgement of plant micronutrients status permits an understanding of the physiological responses of passion fruit plants to crop fertilization. [ABSTRACT FROM AUTHOR]

Key message: Foliar-applied Zn onCatharanthus roseusenhanced production of vindoline, the main impediment precursor for costly anticancer bisindoles. A leaf-abundant CrZIPwas characterized for likely role in modulating vindoline metabolism. The leaf-localized Catharanthus roseus alkaloid, vindoline, is the major impediment precursor in the production of scanty and expensive anticancer bisindoles, vinblastine and vincristine. Earlier studies have hinted toward the role of micronutrients in its accumulation. Here, the effect of various micronutrients on the leaf vindoline content was analyzed. Foliar application of zinc (Zn, 100 ppm) was found to be most effective for enhancing the vindoline content. Comparison of leaf samples of Zn-treated and control plants was performed using paired-end transcriptome sequencing and promising candidates among the differentially expressed genes were identified. A zinc-regulated, iron-regulated transporter-like proteins (ZIP) family member, which was found to be upregulated in Zn-treated samples, was taken up for functional characterization. Complementation of the zrt1/zrt2 yeast mutant (ZHY3) by CrZIP suggested that it encodes a functional Zn transporter. VIGS and transient overexpression of CrZIP in C. roseus showed a direct relationship between its expression and vindoline content. GFP fusion-based subcellular localization indicated chloroplast localization of CrZIP. Previously, vindoline biosynthesis has been reported to be dependent on intact chloroplasts. The chloroplast localization of CrZIP and its direct relationship with vindoline content in this study identifies the possible role of CrZIP, in modulating zinc-induced vindoline accumulation in the plant.Highlights: Foliar-applied Zn was most effective for enhancing vindoline content in C. roseus. RNA-seq unveiled the gene network involved in response to foliar Zn application. Leaf-abundant CrZIP, upregulated by Zn, could functionally transport Zn into yeast. Its VIGS/overexpression in C. roseus showed direct relation with vindoline content. Its chloroplast localization hints to role in effecting Zn-induced vindoline level. [ABSTRACT FROM AUTHOR]

Background: Acquiring representative bacterial 16S rRNA gene community profiles in plant microbiome studies can be challenging due to the excessive co-amplification of host chloroplast and mitochondrial rRNA gene sequences that reduce counts of plant-associated bacterial sequences. Peptide Nucleic Acid (PNA) clamps prevent this by blocking PCR primer binding or binding within the amplified region of non-target DNA to stop the function of DNA polymerase. Here, we applied a universal chloroplast (p)PNA clamp and a newly designed mitochondria (m)PNA clamp to minimise host chloroplast and mitochondria amplification in 16S rRNA gene amplicon profiles of leaf, bark and root tissue of two oak species (Quercus robur and Q. petraea). Results: Adding PNA clamps to PCR led to an overall reduction of host chloroplast and mitochondrial 16S rRNA gene sequences of 79%, 46% and 99% in leaf, bark and root tissues, respectively. This resulted in an average increase in bacterial sequencing reads of 72%, 35%, and 17% in leaf, bark, and root tissue, respectively. Moreover, the bacterial diversity in the leaf and bark increased, with the number of ASVs rising by 105 in the leaf samples and 218 in the bark samples, respectively. In root tissues, where host oak chloroplast and mitochondria contamination were low, alpha and beta diversity did not change, suggesting the PNA clamps did not bias the bacterial community. Conclusion: In conclusion, this study shows that PNA clamps can effectively reduce host chloroplast and mitochondria PCR amplification and improve assessment of the detected bacterial diversity in Quercus petraea and Quercus robur bacterial 16S rRNA gene sequencing studies. [ABSTRACT FROM AUTHOR]

To enhance plant biomass production under low nitrogen conditions, we employed a method to artificially and temporarily accumulate the bacterial second messenger, guanosine tetraphosphate (ppGpp), to modify plastidial or mitochondrial metabolism. Specifically, we fused a chloroplast or mitochondrial transit-peptide to the N-terminus of the bacterial ppGpp synthase YjbM, which was conditionally expressed by an estrogen-inducible promoter in Arabidopsis. The resulting recombinant Arabidopsis plants exhibited estrogen-dependent ppGpp accumulation in chloroplasts or mitochondria and showed reduced fresh weight compared to wild type (WT) plants when grown on agar-solidified plates containing a certain amount of estrogen. This finding aligns with the previous study indicating that plastidial ppGpp levels can influence plant biomass production. When the recombinant plants were grown in the soil with estrogen and low nitrogen-containing water at specific time intervals, they exhibited greater fresh weight than WT plants. These results suggest that the conditional accumulation of ppGpp in not only chloroplasts, but also in mitochondria can lead to improved plant biomass production in soil with low nitrogen applications. [ABSTRACT FROM AUTHOR]

Archaeplastida , a group of photosynthetic organisms with primary plastids, consists of green algae (plus land plants), red algae, and glaucophytes. In contrast to green and red algae, information on lipids and lipid biosynthesis is still incomplete in the glaucophytes. The chloroplast is the site of photosynthesis and fatty acid synthesis in all photosynthetic organisms known to date. However, the genomic data of the glaucophyte Cyanophora paradoxa indicated the lack of acetyl-CoA carboxylase and most components of fatty acid synthase in the chloroplast. Instead, multifunctional fatty acid synthase and acetyl-CoA carboxylase are likely to reside in the cytosol. To examine this hypothesis, we measured fatty acid synthesis in isolated chloroplasts and whole cells using stable isotope labeling. The chloroplasts had very low fatty acid synthesis activity, if any. Most processes of fatty acid synthesis, including elongation and desaturation, must be performed within the cytosol, and the fatty acids imported into the chloroplasts are assembled into the chloroplast lipids by the enzymes common to other algae and plants. Cyanophora paradoxa is a rare organism in which fatty acid synthesis and photosynthesis are not tightly linked. This could question the common origin of these two biosynthetic processes in Archaeplastida. [ABSTRACT FROM AUTHOR]

Overwintering evergreen trees in boreal regions continuously convert absorbed light energy into heat through a process known as sustained thermal dissipation. To better understand this mechanism, this study examined the alterations in the photosynthetic apparatus and transcriptomes of yew (Taxus cuspidata) leaves throughout the year, comparing sun-exposed and shaded leaves. The Y (II) parameter, conventionally used to estimate the quantum yield of photosystem II (PSII), indicated the occurrence of temperature-dependent thermal dissipation during winter. On the other hand, the levels of photosystem subunits, including the D1 subunit of the PSII reaction center, remained relatively stable year-round, indicating that typical photoinhibition is unlikely to occur. Time-resolved chlorophyll fluorescence analysis revealed that heat dissipation at the PSII antenna is prominent in winter. Winter transcriptomes are notably characterized by a predominance of Elip transcripts encoding early light-induced protein (ELIP), which constitute 20% of the total transcripts, as deduced from RNA-seq analysis. Furthermore, ELIP protein concentration increased to nearly half that of the major light-harvesting complexes. The predicted structure of ELIP includes potential chlorophyll a and carotenoid binding sites. These findings, taken together with a previous report showing ELIP capacity for energy dissipation, lead to a re-evaluation of its significant role in sustained thermal dissipation. [ABSTRACT FROM AUTHOR]

Key message: Auxin stimulates chloroplast division by upregulating the expression of genes involved in chloroplast division and influencing the positioning of chloroplast division rings. Chloroplasts divide by binary fission, forming a ring complex at the division site. Auxin, particularly indole acetic acid (IAA), significantly influences various aspects of plant growth. However, the impact of auxin on chloroplast division remains unclear. In this study, different concentrations of exogenous IAA were applied to wild Arabidopsis thaliana. The results showed that the number and size differences of chloroplasts in the cells of Arabidopsis thaliana treated with high concentrations of IAA increased compared to untreated plants. Further investigation revealed that high concentrations of IAA affected the expression of chloroplast division genes and the formation of division rings. In chloroplast division mutants, the effect of IAA on promoting chloroplast division is impaired. Defects of IAA synthetic gene also lead to a reduced effect of IAA on chloroplast division. Our findings demonstrate that auxin influences chloroplast division by regulating the expressions of chloroplast division genes and affecting the localization of division rings. These results are significant for further exploring the relationship between auxin and chloroplast division. [ABSTRACT FROM AUTHOR]

Chloroplasts, distinctive subcellular organelles found exclusively in plant species, contain three membranes: the outer, inner, and thylakoid membranes. They also have three soluble compartments: the intermembrane space, stroma, and thylakoid lumen. Accordingly, delicate sorting mechanisms are required to ensure proper protein targeting to these sub-chloroplast compartments. Except for most outer membrane proteins, chloroplast interior proteins possess N-terminal cleavable transit peptides as primary import signals. After the cleavage of transit peptides, which occurs during or after import into chloroplasts, the inner and thylakoid membrane proteins, as well as stromal and thylakoid luminal proteins, are further sorted based on additional targeting signals. In this review, we aim to recapitulate the mechanisms by which proteins are targeted to chloroplasts and subsequently sorted into sub-chloroplast compartments, with a focus on the design principles of sorting signals present in chloroplast proteins. [ABSTRACT FROM AUTHOR]

Summary Tomato fruit ripening is a complex developmental process that is important for fruit quality and shelf life. Many factors, including ethylene and several key transcription factors, have been shown to play important roles in the regulation of tomato fruit ripening. However, our understanding of the regulation of tomato fruit ripening is still limited. Here, we describe mut26, an EMS‐induced tomato (Solanum lycopersicum) mutant that exhibits chlorophyll‐deficient phenotypes in various organs, including fruits. Genetic mapping and functional analyses revealed that a single‐nucleotide substitution and a corresponding Pro398–>Ser mis‐sense mutation in SlChlH (GENOMES UNCOUPLED 5, GUN5), which encodes the H subunit of magnesium chelatase, are responsible for the defects in the mut26 strain. Transcript analyses towards the expression of many SlPhANGs revealed that mut26 is defective in plastid retrograde signalling during tomato fruit ripening initiation, namely the transition from mature green to breaker stage. mut26 exhibits delayed progression of fruit ripening characterized by reduced fruit ethylene emission, increased fruit firmness, reduced carotenoid content and delayed plastid conversion from chloroplast to chromoplast. Given that fruit ripening requires signalling from plastids to nucleus, these data support the hypothesis that GUN5‐mediated plastid retrograde signalling promotes tomato fruit ripening. We further showed that the delayed fruit ripening of mut26 is not likely caused by reduced chlorophyll content. Taken together, we identified a new function of SlChlH in the promotion of tomato fruit ripening and ethylene biosynthesis, suggesting that GUN5‐mediated plastid retrograde signalling plays a promotive role in tomato fruit ripening. [ABSTRACT FROM AUTHOR]

Stress on the Endoplasmic reticulum (ER) can severely disrupt cellular function by impairing protein folding and post-translational modifications, thereby leading to the accumulation of poor-quality proteins. However, research on its impact on photosynthesis remains limited. In this study, we investigated the impact of ER stress on the photosynthetic efficiency of Chlamydomonas reinhardtii using pharmacological inducers, tunicamycin (TM) and brefeldin A (BFA), which specifically target the ER. Our measurements of photosynthetic parameters showed that these ER stress-inducing compounds caused a significant decline in photosynthetic efficiency. A proteomic analysis confirmed that TM and BFA effectively induce ER stress, as evidenced by the upregulation of ER stress-related proteins. Furthermore, we observed a widespread downregulation of photosynthesis-related proteins, which is consistent with the results obtained from our measurements of photosynthetic parameters. These findings suggest that the stress on ER has a profound impact on chloroplast function, disrupting photosynthetic processes. This study highlights the critical interdependence between the ER and chloroplasts, and it underscores the broader implications of ER stress on the cellular metabolism and energy efficiency of photosynthetic organisms. [ABSTRACT FROM AUTHOR]

Summary There is an increasing demand to boost photosynthesis in rice to increase yield potential. Chloroplasts are the site of photosynthesis, and increasing their number and size is a potential route to elevate photosynthetic activity. Notably, bundle sheath cells do not make a significant contribution to overall carbon fixation in rice, and thus, various attempts are being made to increase chloroplast content specifically in this cell type. In this study, we developed and applied a deep learning tool, Chloro‐Count, and used it to quantify chloroplast dimensions in bundle sheath cells of OsHAP3H gain‐ and loss‐of‐function mutants in rice. Loss of OsHAP3H increased chloroplast occupancy in bundle sheath cells by 50%. When grown in the field, mutants exhibited increased numbers of tillers and panicles. The implementation of Chloro‐Count enabled precise quantification of chloroplasts in loss‐ and gain‐of‐function OsHAP3H mutants and facilitated a comparison between 2D and 3D quantification methods. Collectively, our observations revealed that a mechanism operates in bundle sheath cells to restrict chloroplast occupancy as cell dimensions increase. That mechanism is unperturbed in Oshap3H mutants but loss of OsHAP3H function leads to an increase in chloroplast numbers. The use of Chloro‐Count also revealed that 2D quantification is compromised by the positioning of chloroplasts within the cell. [ABSTRACT FROM AUTHOR]

Introduction: The Arabidopsis abc1k1/pgr6 (Activity of BC1 complex/proton regulation 6) mutant is characterized by photosynthetic and conditional developmental phenotypes triggered by stressful red as well as high light. The Arabidopsis ABC1-like kinases belong to the atypical kinase family and contain conserved ATP-binding and hydrolysis motifs, but their physiological requirement has never been investigated. Methods: By mutation to asparagine, we demonstrate that the highly conserved active site aspartate residue within ATP-binding motif VIIb is required for the physiological functions of ABC1K1. Results: Complementation of the abc1k1 knock out mutant with ABC1K1 D400N, failed to restore the wildtype phenotype. Discussion: These results provide in vivo evidence for a critical role of the active site aspartate residue (D400) of ABC1K1. [ABSTRACT FROM AUTHOR]

The chloroplast and mitochondrion are semi-autonomous organelles that play essential roles in cell function. These two organelles are embellished with prokaryotic remnants and contain many new features emerging from the co-evolution of organelles and the nucleus. A typical plant chloroplast or mitochondrion genome encodes less than 100 genes, and the regulation of these genesˈ expression is remarkably complex. The regulation of chloroplast and mitochondrion gene expression can be achieved at multiple levels during development and in response to environmental cues, in which, RNA metabolism, including: RNA transcription, processing, translation, and degradation, plays an important role. RNA metabolism in plant chloroplasts and mitochondria combines bacterial-like traits with novel features evolved in the host cell and is regulated by a large number of nucleus-encoded proteins. Among these, pentatricopeptide repeat (PPR) proteins are deeply involved in multiple aspects of the RNA metabolism of organellar genes. Research over the past decades has revealed new insights into different RNA metabolic events in plant organelles, such as the composition of chloroplast and mitochondrion RNA editosomes. We summarize and discuss the most recent knowledge and biotechnological implications of various RNA metabolism processes in plant chloroplasts and mitochondria, with a focus on the nucleus-encoded factors supporting them, to gain a deeper understanding of the function and evolution of these two organelles in plant cells. Furthermore, a better understanding of the role of nucleus-encoded factors in chloroplast and mitochondrion RNA metabolism will motivate future studies on manipulating the plant gene expression machinery with engineered nucleus-encoded factors. [ABSTRACT FROM AUTHOR]

Tobacco is a special commercial crop that prefers potassium but not chlorine, and excessive chloride (Cl–) accumulation can cause toxicity. Here, we revealed that the structural characteristics of chloroplasts in tobacco leaves were significantly destroyed under high Cl– salinity, but not mitochondria. Large differences in leaf structure, MDA content, and antioxidant enzyme activities were observed for the treatment with highest chloride accumulation at the 14th day. Moreover, RNA-seq analysis of tobacco leaves exposed to high Cl– salinity revealed global changes in gene transcription levels. A total of 1360 DEGs involved in cell wall, lipid, starch, and secondary metabolism processes were unevenly distributed on chromosomes, and were mainly enriched for starch and sucrose metabolism, phenylpropanoid biosynthesis, ribosome and ribosome biogenesis, protein processing in the endoplasmic reticulum, and plant hormone signal transduction pathways. Overall, our study provides valuable insights for further research on the mechanism underlying Cl– salinity and salt-tolerant tobacco development. [ABSTRACT FROM AUTHOR]

Microsatellites, or simple sequence repeats (SSRs), are repetitive DNA sequences typically composed of 1–6 nucleotides. These repetitive sequences are found in almost all genomes, including chloroplasts and mitochondria, and are widely distributed throughout the genomes. Microsatellites are highly polymorphic, and their length may differ from species to species. Consequently, microsatellites are widely used as molecular markers and play pivotal roles in various biological research. However, comprehensive information about the length variation of microsatellites in various organellar genome sequences is not available. Therefore, to provide mined information and explore the variability in the length of microsatellites across species, we developed a comprehensive resource named pSATdb 2.0 (polymorphic microSATellites database; ). This upgraded version of its predecessor pSATdb provides comprehensive information on the frequency and distribution of 348,894 microsatellites identified in organellar genome sequences. These sequences originate from 15,681 organisms spanning 3252 genera within Metazoa and Viridiplantae. Remarkably, pSATdb 2.0 is the only database that offers information on common and polymorphic microsatellites detected between organisms, along with unique microsatellites specific to each genus. Furthermore, this database features unrestricted access and includes pioneer functionalities such as Advanced Search, BLAST, and JBrowse, which facilitate user-specific microsatellite search and its visualization within the database. The pSATdb holds immense potential for the research community to support diverse studies, including genetic diversity, genetic mapping, marker-assisted selection, and comparative population investigations. [ABSTRACT FROM AUTHOR]

Gyrinops versteegii and Aquilaria malaccensis are two important species of the Aquilarieae tribe. The main problem of this tribe is the challenge of species identification that is strongly dependent on the presence of flowers and fruit, which are not always available. The availability of whole genome information is expected to address the problems of species identification. This research aims to construct and compare the chloroplast and mitochondrial genomes of G. versteegii and A. malaccensis from short-read data using the NOVOplasty and GetOrganelle assembler. The chloroplast genome assembly revealed a full-length quadripartite circular structure with sizes of 174.814 bp (G. versteegii) and 174.821-174.822 bp (A. malaccensis), with highly conserved gene and organization. Meanwhile, the mitochondrial genome is multipartite with a size of 400.012 bp (G. versteegii) and 400.000 bp (A. malaccensis), with highly variable genes and organization due to the presence of gene cluster repeats. The LSC/IR/SCC region borders and phylogenetic analysis in chloroplasts indicate variations between the genomes of these two species. The investigation of nucleotide diversity in the chloroplast genome revealed that the trnL-rpl32 region had the highest nucleotide diversity (Pi = 0.03). This information will be useful in the future for a variety of downstream analyses. [ABSTRACT FROM AUTHOR]

Existence of potent in vitro regeneration system is a prerequisite for efficient genetic transformation and functional genomics of crop plants. In this study, two contrasting cultivars differencing in their in vitro regeneration efficiency were identified. Tissue culture friendly cultivar Golden Promise (GP) and tissue culture resistant DWRB91(D91) were selected as contrasting cultivars to investigate the molecular basis of regeneration efficiency through multiomics analysis. Transcriptomics analysis revealed 1487 differentially expressed genes (DEGs), in which 795 DEGs were upregulated and 692 DEGs were downregulated in the GP-D91 transcriptome. Genes encoding proteins localized in chloroplast and involved in ROS generation were upregulated in the embryogenic calli of GP. Moreover, proteome analysis by LC-MS/MS revealed 3062 protein groups and 16,989 peptide groups, out of these 1586 protein groups were differentially expressed proteins (DEPs). Eventually, GC-MS based metabolomics analysis revealed the higher activity of plastids and alterations in key metabolic processes such as sugar metabolism, fatty acid biosynthesis, and secondary metabolism. TEM analysis also revealed differential plastid development. Higher accumulation of sugars, amino acids and metabolites corresponding to lignin biosynthesis were observed in GP as compared to D91. A comprehensive examination of gene expression, protein profiling and metabolite patterns unveiled a significant increase in the genes encompassing various functions, such as ion homeostasis, chlorophyll metabolic process, ROS regulation, and the secondary metabolic pathway. [ABSTRACT FROM AUTHOR]

Leaf color affects the efficiency of photosynthesis, and leaf color mutants are important genetic materials for studying the mechanisms of photosynthesis, chlorophyll biosynthesis, and chloroplast development in rice. In this study, a white-striped leaf mutant, wst1, was obtained from the mutant population of the indica restorer line 'Chuanhui 907' (R907) when treated with 60Co-γ radiation. Compared to the wild-type, the wst1 mutant showed normal leaf color before tillering and white stripes on the leaf and leaf sheaths after tillering. The chlorophyll and carotenoid contents were significantly reduced, and the thylakoids of chloroplasts developed abnormalities in wst1 plants in the tillering stage. The results of agronomic trait analysis showed that the number of effective panicles, plant height, seed setting rate, and 1000-grain weight of the wst1 mutant were significantly lower than those of the wild-type. Genetic analysis revealed that the phenotype of the wst1 mutant is controlled by a pair of recessive nuclear genes. The candidate gene was mapped to a 72 kb region between the InDel markers M6 and M12 on the short arm of chromosome 1 using molecular marker linkage analysis. Candidate genes were sequenced on the interval, and a G base was replaced by A at the 6972nd position on the 16th exon of LOC_Os01g01920, which encoded a previously reported protein containing the HD domain, WSF3/WFSL1, leading to alternative splicing, causing a 104 bp deletion in the coding region, and resulting in mistranslation after the 490 amino acid of the encoded protein translation in wst1. RT-qPCR analysis showed that the expression levels of most genes related to chlorophyll synthesis and chloroplast development were significantly altered in wst1 plants. Our study identified a novel allele of wsf3 and wfsl1 mutant and provided a new genetic resource and theoretical basis for further understanding of the molecular mechanism of WST1 gene regulation of white-striped leaves in rice. [ABSTRACT FROM AUTHOR]

Crop yields must drastically increase to meet the demands of a rapidly increasing global population. One current option being investigated is the augmentation of photosynthetic capacity by incorporating the C4 photosynthetic pathway into C3 crops such as rice to significantly increase production. Crops with improved photosynthetic mechanisms would make better use of the solar radiation that can be converted into yield. This will help to boost grain yield, reduce water loss, and increase nitrogen use efficiency, particularly in hot and dry conditions. Identifying and manipulating the genes required to install C4 photosynthesis in rice is a big challenge. However, the international C4 rice collaboration, is formed to test the possibility of incorporating the C4 mechanism into rice. This article summarizes the parameters that must be changed in rice in order for the C4 pathway to be successfully introduced. It also examines the biochemistry, physiology, molecular biology, and synthetic biology approaches between the C3 and C4 photosynthetic processes. [ABSTRACT FROM AUTHOR]

This study aimed to explore the mechanism by which Zn retards Fe toxicity by analyzing the morphological, photosynthetic, and chloroplast physiological parameters of wheat seedlings treated with either single or combined Zn and Fe. Different behavior of the seedlings was observed under untreated and treated conditions. The most discriminating quantitative traits were associated with leaf area, biomass dry mass and fresh mass, net photosynthetic rate, intercellular CO2 concentration, stomatal conductance, transpiration rate of seedlings, Hill reaction, Mg2+-ATPase and Ca2+-ATPase activities, malondialdehyde and O2*- contents, and glutathione reductase, ascorbate peroxidase, peroxidase, and superoxide dismutase activities and their gene expression in the seedling chloroplast. The obtained findings suggest the important function of an appropriate Zn concentration in preventing Fe toxicity. Therefore, a thorough evaluation of the effects of Zn on Fe-stressed plant growth is beneficial for sustainable agriculture.

Phalaenopsis deliciosa (Rchb. f.), an ornamental orchid known for vibrant flowers, has a 148,090 bp chloroplast genome with 36.78% GC content. It includes an 85,241 bp large single-copy (LSC) region, an 11,649 bp small single-copy (SSC) region, and two 13,800 bp inverted repeats (IRs), encoding 122 genes (76 protein-coding, 38 tRNA, and 8 rRNA). This genome data refines the Phalaenopsis gene database and supports research on phylogeny and molecular breeding.

Summary: Sessile plants harness mitochondria and chloroplasts to sense and adapt to diverse environmental stimuli. These complex processes involve the generation of pivotal signaling molecules, including reactive oxygen species (ROS), phytohormones, volatiles, and diverse metabolites. Furthermore, the specific modulation of chloroplast proteins, through activation or deactivation, significantly enhances the plant's capacity to engage with its dynamic surroundings. While existing reviews have extensively covered the role of plastidial retrograde modules in developmental and light signaling, our focus lies in investigating how chloroplasts leverage photosynthetic ROS to navigate environmental fluctuations and counteract oxidative stress, thereby sustaining primary metabolism. Unraveling the nuanced interplay between photosynthetic ROS and plant stress responses holds promise for uncovering new insights that could reinforce stress resistance and optimize net photosynthesis rates. This exploration aspires to pave the way for innovative strategies to enhance plant resilience and agricultural productivity amidst changing environmental conditions. [ABSTRACT FROM AUTHOR]

Summary: Climate change not only leads to higher air temperatures but also increases the vapour pressure deficit (VPD) of the air. Understanding the direct effect of VPD on leaf gas exchange is crucial for precise modelling of stomatal functioning.We conducted combined leaf gas exchange and online isotope discrimination measurements on four common European tree species across a VPD range of 0.8–3.6 kPa, while maintaining constant temperatures without soil water limitation. In addition to applying the standard assumption of saturated vapour pressure inside leaves (ei), we inferred ei from oxygen isotope discrimination of CO2 and water vapour.ei desaturated progressively with increasing VPD, consistently across species, resulting in an intercellular relative humidity as low as 0.73 ± 0.11 at the highest tested VPD. Assuming saturation of ei overestimated the extent of reductions in stomatal conductance and CO2 mole fraction inside leaves in response to increasing VPD compared with calculations that accounted for unsaturation. In addition, a significant decrease in mesophyll conductance with increasing VPD only occurred when the unsaturation of ei was considered.We suggest that the possibility of unsaturated ei should not be overlooked in measurements related to leaf gas exchange and in stomatal models, especially at high VPD. [ABSTRACT FROM AUTHOR]

The regulation of gene expression is crucial for maintaining cellular activities and responding to environmental stimuli. RNA molecules are central to this regulatory network, influencing transcription, post-transcriptional processing, and translation. Recent advancements have expanded our understanding of RNA modifications beyond the nucleus, highlighting their impact on chloroplast function and photosynthesis efficiency. Chloroplasts, essential for photosynthesis, rely on precise genetic regulation to adapt to environmental changes. RNA modifications, such as methylation and pseudouridylation, are critical in regulating chloroplast RNA stability, processing, and translation. This review summarizes current knowledge of how RNA modifications affect chloroplast function and photosynthesis. It discusses the roles of specific RNA modifications occurring in chloroplast RNA, including N6-methyladenosine (m6A), 5-methylcytosine (m5C), and pseudouridylation, as well as the enzymes which are known to be involved in these processes. This review also explores extrachloroplastic RNA modifications that influence chloroplast function, emphasizing the importance of m6A and m5C modifications and their associated enzymes. [ABSTRACT FROM AUTHOR]

Jujube (Ziziphus jujuba Mill.), renowned for its nutritional value and health benefits, is believed to have originated in the middle and lower reaches of the Yellow River in China, where it underwent domestication from wild jujube. Nonetheless, the evolutionary trajectory and species differentiation between wild jujube and cultivated jujube still require further elucidation. The chloroplast genome (plastome), characterized by its relatively lower mutation rate compared to the nuclear genome, serves as an excellent model for evolutionary and comparative genomic research. In this study, we analyzed 326 nonredundant plastomes, encompassing 133 jujube cultivars and 193 wild jujube genotypes distributed throughout China. Noteworthy variations in the large single copy region primarily account for the size differences among these plastomes, impacting the evolution from wild jujube to cultivated varieties. Horizontal gene transfer (HGT) unveiled a unique chloroplast‐to‐nucleus transfer event, with transferred fragments predominantly influencing the evolution of the nuclear genome while leaving the plastome relatively unaffected. Population genetics analysis revealed two distinct evolutionary pathways from wild jujube to cultivated jujube: one driven by natural selection with minimal human interference, and the other resulting from human domestication and cultivation. Molecular dating, based on phylogenetic analysis, supported the likelihood that wild jujube and cultivated jujube fall within the same taxonomic category, Z. jujuba. In summary, our study comprehensively examined jujube plastome structures and HGT events, simultaneously contributing novel insights into the intricate processes that govern the evolution and domestication of jujube species. [ABSTRACT FROM AUTHOR]

Leaf traits are known as indicative of species functional properties in angiosperms. Fern fronds are little studied in this concern, especially ex situ. We studied leaf mesophyll structure, pigments and gas exchange in four fern species grown in a glasshouse—Sphaeropteris cooperi (terrestrial tree fern), Phlebodium aureum (semi‐epiphytic herbaceous), Asplenium australasicum (epiphytic shrubby) and Platycerium bifurcatum (epiphytic herbaceous). Saturated assimilation rate (Asat) decreased and intrinsic water use efficiency (iWUE) increased from a terrestrial tree fern to epiphytic ferns. Asat positively correlated with chloroplast number (Nchl/A) and their surface area per leaf area (Achl/A). iWUE negatively related to Nchl/A and chlorophyll/carotenoid ratio. Most differences between species were found in the mesophyll thickness (MT) and mesophyll cell volume (Vcell) with the smallest values in S. cooperi and the largest ones in P. bifurcatum. We found that photosynthetic limitations in ferns were related to the chloroplast photosynthetic activity rather than to Nchl/A or pigment content which did not differ from most angiosperms. Epiphytic ferns showed larger values of Vcell per cell and per chloroplast compared to angiosperms and tree ferns. We concluded that an increase in MT and Vcell in the studied ferns was not associated with photosynthetic performance, but was related to volumetric cytoplasm–chloroplast ratio meaningful to light absorption and the water‐storage function of fern fronds. [ABSTRACT FROM AUTHOR]

SUMMARY: Arabidopsis uracil phosphoribosyltransferase (UPP) is an essential enzyme and plants lacking this enzyme are strongly compromised in chloroplast function. Our analysis of UPP amiRNA mutants has confirmed that this vital function is crucial to establish a fully functional photosynthesis as the RIESKE iron sulfur protein (PetC) is almost absent, leading to a block in photosynthetic electron transport. Interestingly, this function appears to be unrelated to nucleotide homeostasis since nucleotide levels were not altered in the studied mutants. Transcriptomics and proteomic analysis showed that protein homeostasis but not gene expression is most likely responsible for this observation and high light provoked an upregulation of protease levels, including thylakoid filamentation temperature‐sensitive 1, 5 (FtsH), caseinolytic protease proteolytic subunit 1 (ClpP1), and processing peptidases, as well as components of the chloroplast protein import machinery in UPP amiRNA lines. Strongly reduced PetC amounts were not only detected by immunoblot from mature plants but in addition in a de‐etiolation experiment with young seedlings and are causing reduced high light‐induced non‐photochemical quenching Φ(NPQ) but increased unregulated energy dissipation Φ(NO). This impaired photosynthesis results in an inability to induce flavonoid biosynthesis. In addition, the levels of the osmoprotectants raffinose, proline, and fumarate were found to be reduced. In sum, our work suggests that UPP assists in stabilization PetC during import, processing or targeting to the thylakoid membrane, or protects it against proteolytic degradation. Significance Statement: The moonlighting enzyme uracil phosphoribosyltransferase from Arabidopsis is an essential protein. By in‐depth analysis of knockdown mutants, we observed disrupted chloroplast proteostasis, characterized by altered amounts of proteins in the categories protein import, processing, folding, and degradation, accompanied by massively reduced amounts of the PetC (Rieske) subunit of the cytochrome b6/f complex. [ABSTRACT FROM AUTHOR]

Key message: The N-terminal transmembrane domain of LPAT1 crosses the inner membrane placing the N terminus in the intermembrane space and the C-terminal enzymatic domain in the stroma. Galactolipids mono- and di-galactosyl diacylglycerol are the major and vital lipids of photosynthetic membranes. They are synthesized by five enzymes hosted at different sub-chloroplast locations. However, localization and topology of the second-acting enzyme, lysophosphatidic acid acyltransferase 1 (LPAT1), which acylates the sn-2 position of glycerol-3-phosphate (G3P) to produce phosphatidic acid (PA), remain unclear. It is not known whether LPAT1 is located at the outer or the inner envelope membrane and whether its enzymatic domain faces the cytosol, the intermembrane space, or the stroma. Even the size of mature LPAT1 in chloroplasts is not known. More information is essential for understanding the pathways of metabolite flow and for future engineering endeavors to modify glycerolipid biosynthesis. We used LPAT1 preproteins translated in vitro for import assays to determine the precise size of the mature protein and found that the LPAT1 transit peptide is at least 85 residues in length, substantially longer than previously predicted. A construct comprising LPAT1 fused to the Venus fluorescent protein and driven by the LPAT1 promoter was used to complement an Arabidopsis lpat1 knockout mutant. To determine the sub-chloroplast location and topology of LPAT1, we performed protease treatment and alkaline extraction using chloroplasts containing in vitro-imported LPAT1 and chloroplasts isolated from LPAT1-Venus-complemented transgenic plants. We show that LPAT1 traverses the inner membrane via an N-terminal transmembrane domain, with its N terminus protruding into the intermembrane space and the C-terminal enzymatic domain residing in the stroma, hence displaying a different membrane topology from its bacterial homolog, PlsC. [ABSTRACT FROM AUTHOR]

Screening a transposon‐mutagenized soybean population led to the discovery of a recessively inherited chlorotic phenotype. This "y24" phenotype results in smaller stature, weaker stems, and a smaller root system. Genome sequencing identified 15 candidate genes with mutations likely to result in a loss of function. Amplicon sequencing of a segregating population was then used to narrow the list to a single candidate mutation, a single‐base change in Glyma.07G102300 that disrupts splicing of the second intron. Single cell transcriptomic profiling indicates that this gene is expressed primarily in mesophyll cells, and RNA sequencing data indicate that it is upregulated in germinating seedlings by cold stress. Previous studies have shown that mutations to Os05g34040, the rice ortholog of Glyma.07G102300, produced a chlorotic phenotype that was more pronounced in cool temperatures. Growing soybean y24 mutants at lower temperatures also resulted in a more severe phenotype. In addition, transgenic expression of wild‐type Glyma.07G102300 in the knockout mutant of the Arabidopsis ortholog At4930720 rescues the chlorotic phenotype, further supporting the hypothesis that the mutation in Glyma.07G102300 is causal of the y24 phenotype. The variant analysis strategy used to identify the genes underlying this phenotype provides a template for the study of other soybean mutants. [ABSTRACT FROM AUTHOR]

Thylakoid membranes in chloroplasts and cyanobacteria harbor the multisubunit protein complexes that catalyze the light reactions of photosynthesis. In plant chloroplasts, the thylakoid membrane system comprises a highly organized network with several subcompartments that differ in composition and morphology: grana stacks, unstacked stromal lamellae, and grana margins at the interface between stacked and unstacked regions. The localization of components of the photosynthetic apparatus among these subcompartments has been well characterized. However, less is known about the localization of proteins involved in the biogenesis and repair of the photosynthetic apparatus, the partitioning of proteins between two recently resolved components of the traditional margin fraction (refined margins and curvature), and the effects of light on these features. In this study, we analyzed the partitioning of numerous thylakoid biogenesis and repair factors among grana, curvature, refined margin, and stromal lamellae fractions of Arabidopsis thylakoid membranes, comparing the results from illuminated and dark‐adapted plants. Several proteins previously shown to localize to a margin fraction partitioned in varying ways among the resolved curvature and refined margin fractions. For example, the ALB3 insertase and FtsH protease involved in photosystem II (PSII) repair were concentrated in the refined margin fraction, whereas TAT translocon subunits and proteins involved in early steps in photosystem assembly were concentrated in the curvature fraction. By contrast, two photosystem assembly factors that facilitate late assembly steps were depleted from the curvature fraction. The enrichment of the PSII subunit OE23/PsbP in the curvature fraction set it apart from other PSII subunits, supporting the previous conjecture that OE23/PsbP assists in PSII biogenesis and/or repair. The PSII assembly factor PAM68 partitioned differently among thylakoid fractions from dark‐adapted plants and illuminated plants and was the only analyzed protein to convincingly do so. These results demonstrate an unanticipated spatial heterogeneity of photosystem biogenesis and repair functions in thylakoid membranes and reveal the curvature fraction to be a focal point of early photosystem biogenesis. [ABSTRACT FROM AUTHOR]

Phalaenopsis deliciosa (Rchb. f.), an ornamental orchid known for vibrant flowers, has a 148,090 bp chloroplast genome with 36.78% GC content. It includes an 85,241 bp large single-copy (LSC) region, an 11,649 bp small single-copy (SSC) region, and two 13,800 bp inverted repeats (IRs), encoding 122 genes (76 protein-coding, 38 tRNA, and 8 rRNA). This genome data refines the Phalaenopsis gene database and supports research on phylogeny and molecular breeding. [ABSTRACT FROM AUTHOR]

Photosynthetic eukaryotes have metabolic pathways that occur in distinct subcellular compartments. However, because metabolites synthesized in one compartment, including fixed carbon compounds and reductant generated by photosynthetic electron flows, may be integral to processes in other compartments, the cells must efficiently move metabolites among the different compartments. This review examines the various photosynthetic electron flows used to generate ATP and fixed carbon and the trafficking of metabolites in the green alga Chlamydomomas reinhardtii; information on other algae and plants is provided to add depth and nuance to the discussion. We emphasized the trafficking of metabolites across the envelope membranes of the two energy powerhouse organelles of the cell, the chloroplast and mitochondrion, the nature and roles of the major mobile metabolites that move among these compartments, and the specific or presumed transporters involved in that trafficking. These transporters include sugar-phosphate (sugar-P)/inorganic phosphate (Pi) transporters and dicarboxylate transporters, although, in many cases, we know little about the substrate specificities of these transporters, how their activities are regulated/coordinated, compensatory responses among transporters when specific transporters are compromised, associations between transporters and other cellular proteins, and the possibilities for forming specific 'megacomplexes' involving interactions between enzymes of central metabolism with specific transport proteins. Finally, we discuss metabolite trafficking associated with specific biological processes that occur under various environmental conditions to help to maintain the cell's fitness. These processes include C4 metabolism in plants and the carbon concentrating mechanism, photorespiration, and fermentation metabolism in algae. [ABSTRACT FROM AUTHOR]

The genus Macadamia in the Proteaceae family includes four species native to Australia. Two of the four species, M. integrifolia and M. tetraphylla, have recently been utilized to generate domesticated macadamia varieties, grown for their edible nuts. To explore diversity in macadamia genetic resources, a total of 166 wild genotypes, representing all four species, were sequenced. The four species were clearly distinguished as four separate clades in a phylogenetic analysis of the nuclear genome (based upon concatenated nuclear gene CDS and SNPs). The two larger species (M. integrifolia and M. tetraphylla) formed a clade, that had diverged from a clade including the smaller species (M. ternifolia and M. jansenii). The greatest diversity in nuclear and chloroplast genomes was found in the more widely distributed M. integrifolia while the rare M. jansenii showed little diversity. The chloroplast phylogeny revealed a much more complex evolutionary history. Multiple chloroplast capture events have resulted in chloroplast genome clades, including genotypes from different species. This suggests extensive reticulate evolution in Macadamia despite the emergence of the four distinct species that are supported by the analysis of their nuclear genomes. The chloroplast genomes showed strong associations with geographical distribution reflecting limited maternal gene movement in these species that have large seeds. The nuclear genomes showed lesser geographical differences, probably reflecting the longer distance pollen movement. This improved understanding of the distribution of diversity in Macadamia will aid in the conservation of these rare species now found in highly fragmented rainforest remnants. [ABSTRACT FROM AUTHOR]

SUMMARY: The casein kinase II (CK2) complex consists of catalytic (α) and regulatory (β) subunits and is highly conserved throughout eukaryotes. Plant CK2 plays critical roles in multiple physiological processes; however, its function in plant immunity remains obscure. In this study, we demonstrated that the unique chloroplast‐localized CK2 α subunit (CPCK2) is a negative regulator of Arabidopsis thaliana innate immunity. cpck2 mutants displayed enhanced resistance against the fungal pathogen powdery mildew, Golovinomyces cichoracearum and the virulent bacterial pathogen, Pseudomonas syringae pv. tomato (Pto) DC3000. Moreover, the cpck2‐1 mutant accumulated higher salicylic acid (SA) levels and mutations that disabled SA biosynthesis or signaling inhibited cpck2‐1‐mediated disease resistance. CPCK2 interacted with the chloroplast‐localized carbonic anhydrase (CA), SA‐binding protein 3 (SABP3), which was required for cpck2‐mediated immunity. Significantly, CPCK2 phosphorylated SABP3, which promoted S‐nitrosylation of this enzyme. It has previously been established that S‐nitrosylation of SABP3 reduces both its SA binding function and its CA activity, which compromises the immune‐related function of SABP3. Taken together, our results establish CPCK2 as a negative regulator of SA accumulation and associated immunity. Importantly, our findings unveil a mechanism by which CPCK2 negatively regulates plant immunity by promoting S‐nitrosylation of SABP3 through phosphorylation, which provides the first example in plants of S‐nitrosylation being promoted by cognate phosphorylation. Significance Statement: CPCK2, a chloroplast‐localized casein kinase II α subunit, plays a negative role in plant innate immunity. CPCK2 directly interacted with and phosphorylated SA‐binding protein 3 (SABP3) to enhance the S‐nitrosylation status of SABP3, implying a potential mechanism by which CPCK2 negatively regulates plant immunity by promoting S‐nitrosylation of SABP3 through phosphorylation, which is the first example in plants of S‐nitrosylation being promoted by cognate phosphorylation. [ABSTRACT FROM AUTHOR]

Pyrenoids are subcompartments of algal chloroplasts that increase the efficiency of Rubisco-driven CO 2 fixation. Diatoms fix up to 20% of global CO 2 , but their pyrenoids remain poorly characterized. Here, we used in vivo photo-crosslinking to identify pyrenoid shell (PyShell) proteins, which we localized to the pyrenoid periphery of model pennate and centric diatoms, Phaeodactylum tricornutum and Thalassiosira pseudonana. In situ cryo-electron tomography revealed that pyrenoids of both diatom species are encased in a lattice-like protein sheath. Single-particle cryo-EM yielded a 2.4-Å-resolution structure of an in vitro TpPyShell1 lattice, which showed how protein subunits interlock. T. pseudonana TpPyShell1/2 knockout mutants had no PyShell sheath, altered pyrenoid morphology, and a high-CO 2 requiring phenotype, with reduced photosynthetic efficiency and impaired growth under standard atmospheric conditions. The structure and function of the diatom PyShell provide a molecular view of how CO 2 is assimilated in the ocean, a critical ecosystem undergoing rapid change. [Display omitted] • Identification of the PyShell, a protein sheath that surrounds diatom pyrenoids • Multiscale imaging of PyShell lattices from in situ architecture to in vitro structure • PyShell knockout disrupts pyrenoid morphology and function, impairing cell growth • The PyShell is widely conserved, enabling much of the ocean's CO 2 fixation Identification and characterization of a protein lattice around the pyrenoid compartments of diatoms reveals that these prolific marine algae evolved a distinct pyrenoid architecture to promote Rubisco's CO 2 -fixing activity. [ABSTRACT FROM AUTHOR]

The existence of an efficient inducible transgene expression system is a valuable tool in recombinant protein production. The synthetic theophylline-responsive riboswitch (theo.RS) can be replaced in the 5 ′ untranslated region of an mRNA and control the translation of downstream gene in chloroplasts in response to the binding with a ligand molecule, theophylline. One of the drawbacks associated with the efficiency of the theo.RS is the leak in the RS structure allowing undesired background translation when the switch is expected to be off. The purpose of this study was to detect the factors causing the leak of the theo.RS in the off mode, using molecular dynamics (MD) simulations the appropriate balancing of the simulation system, using the necessary commands, a 40 ns simulation was conducted. Analysis of the solvent-accessible surface area for both ribosome-binding site (RBS) regions indicated that nucleotide 79 of the theo.RS, a guanine, had the highest surface exposure to ribosome access. These results were verified with the study of hydrogen bonding of RBS regions with the RNA structure. Therefore, redesigning the RBS regions and avoiding the unmasked nucleotide(s) in the structure may improve the tightness of theo.RS in off mode resulting in the efficient inhibition of translation. [ABSTRACT FROM AUTHOR]

SUMMARY: The intracellular localization of the florigen FLOWERING LOCUS T (FT) is important for its long‐distance transport toward the shoot apical meristem. However, the mechanisms regulating the FT localization remain poorly understood. Here, we discovered that in Arabidopsis thaliana, the chloroplast‐localized protein THYLAKOID FORMATION 1 (THF1) physically interacts with FT, sequestering FT in the outer chloroplast envelope. Loss of THF1 function led to temperature‐insensitive flowering, resulting in early flowering, especially under low ambient temperatures. THF1 mainly acts in the leaf vasculature and shoot apex to prevent flowering. Mutation of CONSTANS or FT completely suppressed the early flowering of thf1‐1 mutants. FT and THF1 interact via their anion binding pocket and coiled‐coil domain (CCD), respectively. Deletion of the CCD in THF1 by gene editing caused temperature‐insensitive early flowering similar to that observed in the thf1‐1 mutant. FT levels in the outer chloroplast envelope decreased in the thf1‐1 mutant, suggesting that THF1 is important for sequestering FT. Furthermore, THF1 protein levels decreased in seedlings grown at high ambient temperature, suggesting an explanation for its role in plant responses to ambient temperature. A thf1‐1 phosphatidylglycerolphosphate synthase 1 (pgp1) double mutant exhibited additive acceleration of flowering at 23 and 16°C, compared to the single mutants, indicating that THF1 and phosphatidylglycerol (PG) act as independent but synergistic regulators of temperature‐responsive flowering. Collectively, our results provide an understanding of the genetic pathway involving THF1 and its role in temperature‐responsive flowering and reveal a previously unappreciated additive interplay between THF1 and PG in temperature‐responsive flowering. Significance Statement: In this study, the interaction between Arabidopsis florigen FLOWERING LOCUS T (FT) and the chloroplast‐localized protein THYLAKOID FORMATION 1 (THF1) is unveiled. THF1 sequesters FT within the chloroplast envelope, particularly under low ambient temperature conditions, modulating temperature‐responsive flowering in Arabidopsis. [ABSTRACT FROM AUTHOR]

Ctenium has about 20 species distributed in Africa, Arabia, and the Neotropics, with no species occurring on more than one continent. Its relationship with the morphologically similar Kampochloa is still unclear and has not been investigated. In this study, we performed phylogenomic analyses using 71 protein‐coding genes of 24 newly sequenced plastomes, of 13 species of Ctenium and 1 species of Kampochloa to understand their biogeography and the phylogenetic and evolutionary relationships between these two genera and within Ctenium. Our results support two major clades of Ctenium: the Neotropics and Old‐World clades. Kampochloa is shown to be a close relative of the genus Ctenium, and their morphological similarities support this. Divergence time estimation analyses show that Kampochloa and Ctenium diverged around 7.99 Ma, and might have originated in the late Miocene during the rapid expansion of C4 grasslands. With this evidence from morphology and phylogenomic data, we propose the inclusion of the previously unplaced Kampochloa into the subtribe Cteniinae. [ABSTRACT FROM AUTHOR]

This study aimed to explore the mechanism by which Zn retards Fe toxicity by analyzing the morphological, photosynthetic, and chloroplast physiological parameters of wheat seedlings treated with either single or combined Zn and Fe. Different behavior of the seedlings was observed under untreated and treated conditions. The most discriminating quantitative traits were associated with leaf area, biomass dry mass and fresh mass, net photosynthetic rate, intercellular CO2 concentration, stomatal conductance, transpiration rate of seedlings, Hill reaction, Mg2+-ATPase and Ca2+-ATPase activities, malondialdehyde and O2 contents, and glutathione reductase, ascorbate peroxidase, peroxidase, and superoxide dismutase activities and their gene expression in the seedling chloroplast. The obtained findings suggest the important function of an appropriate Zn concentration in preventing Fe toxicity. Therefore, a thorough evaluation of the effects of Zn on Fe-stressed plant growth is beneficial for sustainable agriculture. [ABSTRACT FROM AUTHOR]•– contents, and glutathione reductase, ascorbate peroxidase, peroxidase, and superoxide dismutase activities and their gene expression in the seedling chloroplast. The obtained findings suggest the important function of an appropriate Zn concentration in preventing Fe toxicity. Therefore, a thorough evaluation of the effects of Zn on Fe-stressed plant growth is beneficial for sustainable agriculture. [ABSTRACT FROM AUTHOR]

Plastid-encoded RNA polymerase (PEP) is a bacterial-type multisubunit RNA polymerase responsible for the majority of transcription in chloroplasts. PEP consists of four core subunits, which are orthologs of their cyanobacterial counterparts. In Arabidopsis thaliana, PEP is expected to interact with 14 PEP-associated proteins (PAPs), which serve as peripheral subunits of the RNA polymerase. The exact contributions of PAPs to PEP function are still poorly understood. We used ptChIP-seq to show that PAP1 (also known as pTAC3), a peripheral subunit of PEP, binds to the same genomic loci as RpoB, a core subunit of PEP. The pap1 mutant shows a complete loss of RpoB binding to DNA throughout the genome, indicating that PAP1 is necessary for RpoB binding to DNA. A similar loss of RpoB binding to DNA is observed in a mutant defective in PAP7 (also known as pTAC14), another peripheral PEP subunit. We propose that PAPs are required for the recruitment of core PEP subunits to DNA.Key Message: The peripheral subunits of plastid-encoded RNA polymerase play a crucial role in recruiting the core PEP subunits to DNA in Arabidopsis chloroplasts. [ABSTRACT FROM AUTHOR]

Taraxacum kok-saghyz Rodin (TKS) is a recognized alternative source of natural rubber comparable to the rubber tree. The geranylgeranyl pyrophosphate synthase (GGPS) catalyzed the synthesis of geranylgeranyl pyrophosphate (GGPP), which is an important enzyme in the secondary metabolism pathway. In this study, we present the first analysis of the GGPS gene family in TKS, where a total of seven TkGGPS family members were identified. Their core motifs, conserved structural domains, gene structures, and cis-acting elements were described. In addition, two phylogenetic trees were constructed based on the Neighbor-Joining and Maximum-Likelihood methods, and the TkGGPSs were highly conserved and exhibited good collinearity with the other species. Transcriptome data showed that seven TkGGPS gene members were expressed in all the 12 tissues measured, and TkGGPS1, TkGGPS3, and TkGGPS6 were highly expressed in latex, suggesting that they may be associated with natural rubber synthesis. Meanwhile, quantitative real-time PCR (qRT-PCR) showed that the expression levels of the TkGGPS genes were regulated by the ethylene and methyl jasmonate (MeJA) pathways. Subcellular localization results indicated that all the TkGGPS proteins were also located in chloroplasts involved in photosynthesis in plants. This study will provide valuable insights into the selection of candidate genes for molecular breeding and natural rubber biosynthesis in TKS. [ABSTRACT FROM AUTHOR]

In the chloroplast, the 54 kDa subunit of the signal recognition particle (cpSRP54) is involved in the post-translational transport of the light-harvesting chlorophyll a / b -binding proteins (LHCPs) and the co-translational transport of plastid-encoded subunits of the photosynthetic complexes to the thylakoid membrane. It forms a high-affinity complex with plastid-specific cpSRP43 for post-translational transport, while a ribosome-associated pool coordinates its co-translational function. CpSRP54 constitutes a conserved multidomain protein, comprising a GTPase (NG) and a methionine-rich (M) domain linked by a flexible region. It is further characterized by a plastid-specific C-terminal tail region containing the cpSRP43-binding motif. To characterize the physiological role of the various regions of cpSRP54 in thylakoid membrane protein transport, we generated Arabidopsis cpSRP54 knockout (ffc1-2) lines producing truncated cpSRP54 variants or a GTPase point mutation variant. Phenotypic characterization of the complementation lines demonstrated that the C-terminal tail region of cpSRP54 plays an important role exclusively in post-translational LHCP transport. Furthermore, we show that the GTPase activity of cpSRP54 plays an essential role in the transport pathways for both nuclear as well as plastid-encoded proteins. In addition, our data revealed that plants expressing cpSRP54 without the C-terminal region exhibit a strongly increased accumulation of a photosystem I assembly intermediate. [ABSTRACT FROM AUTHOR]

Summary: Chloroplasts play a crucial role in plant defense against pathogens, making them primary targets for pathogen effectors that suppress host immunity. This study characterizes the Plasmopara viticola CRN‐like effector, PvCRN20, which interacts with DEG5 in the cytoplasm but not with its interacting protein, DEG8, which is located in the chloroplast.By transiently overexpressing in tobacco leaves, we show that PvCRN20 could inhibit INF1‐ and Bax‐triggered cell death. Constitutive expression of PvCRN20 suppresses the accumulation of reactive oxygen species (ROS) and promotes pathogen colonization. PvCRN20 reduces DEG5 entry into chloroplasts, thereby disrupting DEG5 and DEG8 interactions in chloroplasts.Overexpression of VvDEG5 and VvDEG8 induces ROS accumulation and enhances grapevine resistance to P. viticola, whereas knockout of VvDEG8 represses ROS production and promotes P. viticola colonization. Consistently, ectopic expression of VvDEG5 and VvDEG8 in tobacco promotes chloroplast‐derived ROS accumulation, whereas co‐expression of PvCRN20 counteracted this promotion by VvDEG5. Therefore, DEG5 is essential for the virulence function of PvCRN20. Although PvCRN20 is located in both the nucleus and cytoplasm, only cytoplasmic PvCRN20 suppresses plant immunity and promotes pathogen infection.Our results reveal that PvCRN20 dampens plant defenses by repressing the chloroplast import of DEG5, thus reducing host ROS accumulation and facilitating pathogen colonization. [ABSTRACT FROM AUTHOR]

SUMMARY: The protein levels of chloroplast photosynthetic genes and genes related to the chloroplast genetic apparatus vary to adapt to different conditions. However, the underlying mechanisms governing these variations remain unclear. The chloroplast intron Maturase K is encoded within the trnK intron and has been suggested to be required for splicing several group IIA introns, including the trnK intron. In this study, we used RNA immunoprecipitation followed by high‐throughput sequencing (RIP‐Seq) to identify MatK's preference for binding to group IIA intron domains I and VI within target transcripts. Importantly, these domains are crucial for splice site selection, and we discovered alternative 5′‐splice sites in three MatK target introns. The resulting alternative trnK lariat structure showed increased accumulation during heat acclimation. The cognate codon of tRNA‐K(UUU) is highly enriched in mRNAs encoding ribosomal proteins and a trnK‐matK over‐expressor exhibited elevated levels of the spliced tRNA‐K(UUU). Ribosome profiling analysis of the overexpressor revealed a significant up‐shift in the translation of ribosomal proteins compared to photosynthetic genes. Our findings suggest the existence of a novel regulatory mechanism linked to the abundance of tRNA‐K(UUU), enabling the differential expression of functional chloroplast gene groups. Significance Statement: This study uncovers a regulatory mechanism involving the chloroplast intron Maturase K (MatK), highlighting its role in preventing alternative 5′‐splice site selection of group IIA introns. Our findings suggest furthermore that MatK modulates tRNA‐K(UUU) abundance, which leads to differential translation of chloroplast ribosomal and photosynthetic genes, particularly during heat acclimation. [ABSTRACT FROM AUTHOR]