The Rubisco Chaperone BSD2 May Regulate Chloroplast Coverage in Maize Bundle Sheath Cells

REDUCED CHLOROPLAST COVERAGE proteins are required for plastid proliferation and carotenoid accumulation in tomato

Increasing the amount of cellular space allocated to plastids will lead to increases in the quality and yield of crop plants. However, mechanisms that allocate cellular space to plastids remain poorly understood. To test whether the tomato (Solanum lycopersicum L.) REDUCED CHLOROPLAST COVERAGE (SlREC) gene products serve as central components of the mechanism that allocates cellular space to plastids and contribute to the quality of tomato fruit, we knocked out the 4-member SlREC gene family. We found that slrec mutants accumulated lower levels of chlorophyll in leaves and fruits, accumulated lower levels of carotenoids in flowers and fruits, allocated less cellular space to plastids in leaf mesophyll and fruit pericarp cells, and developed abnormal plastids in flowers and fruits. Fruits produced by slrec mutants initiated ripening later than wild type and produced abnormal levels of ethylene and abscisic acid (ABA). Metabolome and transcriptome analyses of slrec mutant fruits indicated that the SlREC gene products markedly influence plastid-related gene expression, primary and specialized metabolism, and the response to biotic stress. Our findings and previous work with distinct species indicate that REC proteins help allocate cellular space to plastids in diverse species and cell types and, thus, play a central role in allocating cellular space to plastids. Moreover, the SlREC proteins are required for the high-level accumulation of chlorophyll and carotenoids in diverse organs, including fruits, promote the development of plastids and influence fruit ripening by acting both upstream and downstream of ABA biosynthesis in a complex network.

Transgenic expression of Rubisco accumulation factor2 and Rubisco subunits increases photosynthesis and growth in maize

Carbon assimilation by Rubisco is often a limitation to photosynthesis and therefore plant productivity. We have previously shown that transgenic co-expression of the Rubisco large (LS) and small (SS) subunits along with an essential Rubisco accumulation factor, Raf1, leads to faster growth, increased photosynthesis, and enhanced chilling tolerance in maize (Zea mays). Maize also requires Rubisco accumulation factor2 (Raf2) for full accumulation of Rubisco. Here we have analyzed transgenic maize lines with increased expression of Raf2 or Raf2 plus LS and SS. We show that increasing Raf2 expression alone had minor effects on photosynthesis, whereas expressing Raf2 with Rubisco subunits led to increased Rubisco content, more rapid carbon assimilation, and greater plant height, most notably in plants at least 6 weeks of age. The magnitude of the effects was similar to what was observed previously for expression of Raf1 together with Rubisco subunits. Taken together, this suggests that increasing the amount of either assembly factor with Rubisco subunits can independently enhance Rubisco abundance and some aspects of plant performance. These results could also imply either synergy or a degree of functional redundancy for Raf1 and Raf2, the latter of whose precise role in Rubisco assembly is currently unknown.

C4 rice engineering, beyond installing a C4 cycle

C4 photosynthesis in higher plants is carried out by two distinct cell types: mesophyll cells and bundle sheath cells, as a result highly concentrated carbon dioxide is released surrounding RuBisCo in chloroplasts of bundle sheath cells and the photosynthetic efficiency is significantly higher than that of C3 plants. The evolution of the dual-cell C4 cycle involved complex modifications to leaf anatomy and cell ultra-structures. These include an increase in leaf venation, the formation of Kranz anatomy, changes in chloroplast morphology in bundle sheath cells, and increases in the density of plasmodesmata at interfaces between the bundle sheath and mesophyll cells. It is predicted that cereals will be in severe worldwide shortage at the mid-term of this century. Rice is a staple food that feeds more than half of the world's population. If rice can be engineered to perform C4 photosynthesis, it is estimated that rice yield will be increased by at least 50% due to enhanced photosynthesis. Thus, the Second Green Revolution has been launched on this principle by genetically installing C4 photosynthesis into C3 crops. The studies on molecular mechanisms underlying the changes in leaf morphoanatomy involved in C4 photosynthesis have made great progress in recent years. As there are plenty of reviews discussing the installment of the C4 cycle, we focus on the current progress and challenges posed to the research regarding leaf anatomy and cell ultra-structure modifications made towards the development of C4 rice.

Single-cell transcriptome reveals dominant subgenome expression and transcriptional response to heat stress in Chinese cabbage

BACKGROUND

Chinese cabbage (Brassica rapa ssp. pekinensis) experienced a whole-genome triplication event and thus has three subgenomes: least fractioned, medium fractioned, and most fractioned subgenome. Environmental changes affect leaf development, which in turn influence the yield. To improve the yield and resistance to different climate scenarios, a comprehensive understanding of leaf development is required including insights into the full diversity of cell types and transcriptional networks underlying their specificity.

RESULTS

Here, we generate the transcriptional landscape of Chinese cabbage leaf at single-cell resolution by performing single-cell RNA sequencing of 30,000 individual cells. We characterize seven major cell types with 19 transcriptionally distinct cell clusters based on the expression of the reported marker genes. We find that genes in the least fractioned subgenome are predominantly expressed compared with those in the medium and most fractioned subgenomes in different cell types. Moreover, we generate a single-cell transcriptional map of leaves in response to high temperature. We find that heat stress not only affects gene expression in a cell type-specific manner but also impacts subgenome dominance.

CONCLUSIONS

Our study highlights the transcriptional networks in different cell types and provides a better understanding of transcriptional regulation during leaf development and transcriptional response to heat stress in Chinese cabbage.

OBV (obscure vein), a C2H2 zinc finger transcription factor, positively regulates chloroplast development and bundle sheath extension formation in tomato (Solanum lycopersicum) leaf veins

Leaf veins play an important role in plant growth and development, and the bundle sheath (BS) is believed to greatly improve the photosynthetic efficiency of C₄ plants. The OBV mutation in tomato (Solanum lycopersicum) results in dark veins and has been used widely in processing tomato varieties. However, physiological performance has difficulty explaining fitness in production. In this study, we confirmed that this mutation was caused by both the increased chlorophyll content and the absence of bundle sheath extension (BSE) in the veins. Using genome-wide association analysis and map-based cloning, we revealed that OBV encoded a C₂H₂L domain class transcription factor. It was localized in the nucleus and presented cell type-specific gene expression in the leaf veins. Furthermore, we verified the gene function by generating CRISPR/Cas9 knockout and overexpression mutants of the tomato gene. RNA sequencing analysis revealed that OBV was involved in regulating chloroplast development and photosynthesis, which greatly supported the change in chlorophyll content by mutation. Taken together, these findings demonstrated that OBV affected the growth and development of tomato by regulating chloroplast development in leaf veins. This study also provides a solid foundation to further decipher the mechanism of BSEs and to understand the evolution of photosynthesis in land plants.

Changes in photosynthetic traits and their responses to increasing fertilization rates in soybean (Glycine max (L.) Merr.) during decades of genetic improvement

BACKROUND

Changes in photosynthetic traits (PTs) during the long-term genetic improvement of soybean (Glycine max (L.) Merr.) yield have been studied, but detailed information on whether PT responses to environmental stress have improved, and their correlations with seed yield, are still unknown. Our objectives were to describe the changes in soybean PTs - leaf area index (LAI), leaf chlorophyll content (Chl), net photosynthetic rate (PN ), stomatal conductance (gs ), and transpiration rate (E) - during decades of genetic improvement, and to detect whether the responses to increasing fertilizer application rates (FRs) of the PTs of 13 different soybean cultivars released in various decades differed.

RESULTS

All of the soybean PTs increased significantly along with the year in which each cultivar was released, under different FR treatments, indicating that PTs have improved during decades of genetic breeding. Medium FR (nitrogen) treatment (150 kg ha -1 ) increased PT values, to different extents, at all the investigated growth stages. Leaf area index, Chl, and PN of the old and middle cultivar groups at the full bloom (R2), full seed (R6), and beginning maturity (R7) stages decreased significantly under high FR treatment (300 kg ha-1 ) compared with the medium FR treatment. The former had no effect on any of the PTs of new cultivar group, or had promotive effects. Thus, the photosynthetic capacities of the new cultivars are more tolerant to high FR-related stress than older cultivars.

CONCLUSIONS

The photosynthetic capacities, and tolerance to high FR-related stress, of soybean cultivars that were released in different years improved after long-term genetic breeding. © 2021 Society of Chemical Industry.

The state of oligomerization of Rubisco controls the rate of synthesis of the Rubisco large subunit in Chlamydomonas reinhardtii

Ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) is present in all photosynthetic organisms and is a key enzyme for photosynthesis-driven life on Earth. Its most prominent form is a hetero-oligomer in which small subunits (SSU) stabilize the core of the enzyme built from large subunits (LSU), yielding, after a chaperone-assisted multistep assembly process, an LSU8SSU8 hexadecameric holoenzyme. Here we use Chlamydomonas reinhardtii and a combination of site-directed mutants to dissect the multistep biogenesis pathway of Rubisco in vivo. We identify assembly intermediates, in two of which LSU are associated with the RAF1 chaperone. Using genetic and biochemical approaches we further unravel a major regulation process during Rubisco biogenesis, in which LSU translation is controlled by its ability to assemble with the SSU, via the mechanism of control by epistasy of synthesis (CES). Altogether this leads us to propose a model whereby the last assembly intermediate, an LSU8-RAF1 complex, provides the platform for SSU binding to form the Rubisco enzyme, and when SSU is not available, converts to a key regulatory form that exerts negative feedback on the initiation of LSU translation.

Rubisco production in maize mesophyll cells through ectopic expression of subunits and chaperones

C4 plants, such as maize, strictly compartmentalize Rubisco to bundle sheath chloroplasts. The molecular basis for the restriction of Rubisco from the more abundant mesophyll chloroplasts is not fully understood. Mesophyll chloroplasts transcribe the Rubisco large subunit gene and, when normally quiescent transcription of the nuclear Rubisco small subunit gene family is overcome by ectopic expression, mesophyll chloroplasts still do not accumulate measurable Rubisco. Here we show that a combination of five ubiquitin promoter-driven nuclear transgenes expressed in maize leads to mesophyll accumulation of assembled Rubisco. These encode the Rubisco large and small subunits, Rubisco assembly factors 1 and 2, and the assembly factor Bundle sheath defective 2. In these plants, Rubisco large subunit accumulates in mesophyll cells, and appears to be assembled into a holoenzyme capable of binding the substrate analog CABP (carboxyarabinitol bisphosphate). Isotope discrimination assays suggest, however, that mesophyll Rubisco is not participating in carbon assimilation in these plants, most probably due to a lack of the substrate ribulose 1,5-bisphosphate and/or Rubisco activase. Overall, this work defines a minimal set of Rubisco assembly factors in planta and may help lead to methods of regulating the C4 pathway.

ZnJ6 Is a Thylakoid Membrane DnaJ-Like Chaperone with Oxidizing Activity in Chlamydomonas reinhardtii

Assembly of photosynthetic complexes is sensitive to changing light intensities, drought and pathogens, each of which induces a redox imbalance that requires the assistance of specific chaperones to maintain protein structure. Here we report a thylakoid membrane-associated DnaJ-like protein, ZnJ6 (Cre06.g251716.t1.2), in Chlamydomonas reinhardtii. The protein has four CXXCX(G)X(G) motifs that form two zinc fingers (ZFs). Site-directed mutagenesis (Cys > Ser) eliminates the ability to bind zinc. An intact ZF is required for ZnJ6 stability at elevated temperatures. Chaperone assays with recombinant ZnJ6 indicate that it has holding and oxidative activities. ZnJ6 is unable to reduce the disulfide bonds of insulin but prevents its aggregation in a reducing environment. It also assists in the reactivation of reduced denatured RNaseA, possibly by its oxidizing activity. ZnJ6 pull-down assays revealed interactions with oxidoreductases, photosynthetic proteins and proteases. In vivo experiments with a C. reinhardtii insertional mutant (∆ZnJ6) indicate enhanced tolerance to oxidative stress but increased sensitivity to heat and reducing conditions. Moreover, ∆ZnJ6 has reduced photosynthetic efficiency shown by the Chlorophyll fluorescence transient. Taken together, we identify a role for this thylakoid-associated DnaJ-like oxidizing chaperone that assists in the prevention of protein misfolding and aggregation, thus contributing to stress endurance, redox maintenance and photosynthetic balance.

How does nitrate regulate plant senescence?

Nitrogen is an essential macronutrient for plant growth and development and plays an important role in the whole life process of plants. Nitrogen is an important component of amino acids, chlorophyll, plant hormones and secondary metabolites. Nitrogen deficiency leads to early senescence in plants, which is accompanied by changes in gene expression, metabolism, growth, development, and physiological and biochemical traits, which ensures efficient nitrogen recycling and enhances the plant's tolerance to low nitrogen. Therefore, it is very important to understand the adaptation mechanisms of plants under nitrogen deficiency for the efficient utilization of nitrogen and gene regulation. With the popularization of molecular biology, bioinformatics and transgenic technology, the metabolic pathways of nitrogen-deficient plants have been verified, and important progress has been made. However, how the responses of plants to nitrogen deficiency affect the biological processes of the plants is not well understood. The current research also cannot completely explain how the metabolic pathways identified show other reactions or phenotypes through interactions or cascades after nitrogen inhibition. Nitrate is the main form of nitrogen absorption. In this review, we discuss the role of nitrate in plant senescence. Understanding how nitrate inhibition affects nitrate absorption, transport, and assimilation; chlorophyll synthesis; photosynthesis; anthocyanin synthesis; and plant hormone synthesis is key to sustainable agriculture.

Setaria viridis chlorotic and seedling-lethal mutants define critical functions for chloroplast gene expression

Deep insights into chloroplast biogenesis have been obtained by mutant analysis; however, in C₄ plants a relevant mutant collection has only been developed and exploited for maize. Here, we report the initial characterization of an ethyl methyl sulfonate-induced mutant population for the C₄ model Setaria viridis. Approximately 1000 M₂ families were screened for the segregation of pale-green seedlings in the M₃ generation, and a subset of these was identified to be deficient in post-transcriptional steps of chloroplast gene expression. Causative mutations were identified for three lines using deep sequencing-based bulked segregant analysis, and in one case confirmed by transgenic complementation. Using chloroplast RNA-sequencing and other molecular assays, we describe phenotypes of mutants deficient in PSRP7, a plastid-specific ribosomal protein, OTP86, an RNA editing factor, and cpPNP, the chloroplast isozyme of polynucleotide phosphorylase. The psrp mutant is globally defective in chloroplast translation, and has varying deficiencies in the accumulation of chloroplast-encoded proteins. The otp86 mutant, like its Arabidopsis counterpart, is specifically defective in editing of the rps14 mRNA; however, the conditional pale-green mutant phenotype contrasts with the normal growth of the Arabidopsis mutant. The pnp mutant exhibited multiple defects in 3' end maturation as well as other qualitative changes in the chloroplast RNA population. Overall, our collection opens the door to global analysis of photosynthesis and early seedling development in an emerging C₄ model.

Global Dynamic Molecular Profiling of Stomatal Lineage Cell Development by Single-Cell RNA Sequencing

The regulation of stomatal lineage cell development has been extensively investigated. However, a comprehensive characterization of this biological process based on single-cell transcriptome analysis has not yet been reported. In this study, we performed RNA sequencing on 12 844 individual cells from the cotyledons of 5-day-old Arabidopsis seedlings. We identified 11 cell clusters corresponding mostly to cells at specific stomatal developmental stages using a series of marker genes. Comparative analysis of genes with the highest variable expression among these cell clusters revealed transcriptional networks that regulate development from meristemoid mother cells to guard mother cells. Examination of the developmental dynamics of marker genes via pseudo-time analysis revealed potential interactions between these genes. Collectively, our study opens the door for understanding how the identified novel marker genes participate in the regulation of stomatal lineage cell development.

Cytological evidence of BSD2 functioning in both chloroplast division and dimorphic chloroplast formation in maize leaves

BACKGROUND

Maize bsd2 (bundle sheath defective2) is a classical C4 mutant with defective C4 photosynthesis, accompanied with reduced accumulation of Rubisco (ribulose bisphosphate carboxylase oxygenase) and aberrant mature chloroplast morphology in the bundle sheath (BS) cells. However, as a hypothetical chloroplast chaperone, the effects of BSD2 on C4 chloroplast development have not been fully examined yet, which precludes a full appreciation of BSD2 function in C4 photosynthesis. The aims of our study are to find out the role ofBSD2 in regulating chloroplasts development in maize leaves, and to add new insights into our understanding of C4 biology.

RESULTS

We found that at the chloroplast maturation stage, the thylakoid membranes of chloroplasts in the BS and mesophyll (M) cells became significantly looser, and the granaof chloroplasts in the M cells became thinner stacking in the bsd2 mutant when compared with the wildtype plant. Moreover, at the early chloroplast development stage, the number of dividing chloroplasts and the chloroplast division rate are both reduced in the bsd2 mutant, compared with wild type. Quantitative reverse transcriptase-PCR analysis revealed that the expression of both thylakoid formation-related genesand chloroplast division-related genes is significantly reduced in the bsd2 mutants. Further, we showed that BSD2 interacts physically with the large submit of Rubisco (LS) in Bimolecular Fluorescence Complementation assay.

CONCLUSIONS

Our combined results suggest that BSD2 plays an essential role in regulating the division and differentiation of the dimorphic BS and M chloroplasts, and that it acts at a post-transcriptional level to regulate LS stability or assembly of Rubisco.

BSD2 is a Rubisco-specific assembly chaperone, forms intermediary hetero-oligomeric complexes, and is nonlimiting to growth in tobacco

The folding and assembly of Rubisco large and small subunits into L8 S8 holoenzyme in chloroplasts involves many auxiliary factors, including the chaperone BSD2. Here we identify apparent intermediary Rubisco-BSD2 assembly complexes in the model C3 plant tobacco. We show BSD2 and Rubisco content decrease in tandem with leaf age with approximately half of the BSD2 in young leaves (~70 nmol BSD2 protomer.m2 ) stably integrated in putative intermediary Rubisco complexes that account for <0.2% of the L8 S8 pool. RNAi-silencing BSD2 production in transplastomic tobacco producing bacterial L2 Rubisco had no effect on leaf photosynthesis, cell ultrastructure, or plant growth. Genetic crossing the same RNAi-bsd2 alleles into wild-type tobacco however impaired L8 S8 Rubisco production and plant growth, indicating the only critical function of BSD2 is in Rubisco biogenesis. Agrobacterium mediated transient expression of tobacco, Arabidopsis, or maize BSD2 reinstated Rubisco biogenesis in BSD2-silenced tobacco. Overexpressing BSD2 in tobacco chloroplasts however did not alter Rubisco content, activation status, leaf photosynthesis rate, or plant growth in the field or in the glasshouse at 20°C or 35°C. Our findings indicate BSD2 functions exclusively in Rubisco biogenesis, can efficiently facilitate heterologous plant Rubisco assembly, and is produced in amounts nonlimiting to tobacco growth.

Ectopic expression of ORANGE promotes carotenoid accumulation and fruit development in tomato

Carotenoids are critically important to plants and humans. The ORANGE (OR) gene is a key regulator for carotenoid accumulation, but its physiological roles in crops remain elusive. In this study, we generated transgenic tomato ectopically overexpressing the Arabidopsis wild-type OR (AtOR^WT ) and a 'golden SNP'-containing OR (AtOR^His ). We found that AtOR^His initiated chromoplast formation in very young fruit and stimulated carotenoid accumulation at all fruit developmental stages, uncoupled from other ripening activities. The elevated levels of carotenoids in the AtOR lines were distributed in the same subplastidial fractions as in wild-type tomato, indicating an adaptive response of plastids to sequester the increased carotenoids. Microscopic analysis revealed that the plastid sizes were increased in both AtOR^WT and AtOR^His lines at early fruit developmental stages. Moreover, AtOR overexpression promoted early flowering, fruit set and seed production. Ethylene production and the expression of ripening-associated genes were also significantly increased in the AtOR transgenic fruit at ripening stages. RNA-Seq transcriptomic profiling highlighted the primary effects of OR overexpression on the genes in the processes related to RNA, protein and signalling in tomato fruit. Taken together, these results expand our understanding of OR in mediating carotenoid accumulation in plants and suggest additional roles of OR in affecting plastid size as well as flower and fruit development, thus making OR a target gene not only for nutritional biofortification of agricultural products but also for alteration of horticultural traits.

Overexpression of Rubisco subunits with RAF1 increases Rubisco content in maize

Rubisco catalyses a rate-limiting step in photosynthesis and has long been a target for improvement due to its slow turnover rate. An alternative to modifying catalytic properties of Rubisco is to increase its abundance within C₄ plant chloroplasts, which might increase activity and confer a higher carbon assimilation rate. Here, we overexpress the Rubisco large (LS) and small (SS) subunits with the Rubisco assembly chaperone RUBISCO ASSEMBLY FACTOR 1 (RAF1). While overexpression of LS and/or SS had no discernable impact on Rubisco content, addition of RAF1 overexpression resulted in a >30% increase in Rubisco content. Gas exchange showed a 15% increase in CO₂ assimilation (A_SAT) in UBI-LSSS-RAF1 transgenic plants, which correlated with increased fresh weight and in vitro V_cmax calculations. The divergence of Rubisco content and assimilation could be accounted for by the Rubisco activation state, which decreased up to 23%, suggesting that Rubisco activase may be limiting V_cmax, and impinging on the realization of photosynthetic potential from increased Rubisco content.

Complex Chaperone Dependence of Rubisco Biogenesis

Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco), a ∼530 kDa complex of 8 large (RbcL) and 8 small subunits (RbcS), mediates the fixation of atmospheric CO₂ into usable sugars during photosynthesis. Despite its fundamental role, Rubisco is a remarkably inefficient enzyme and thus is produced by plants in huge amounts. It has long been a key target for bioengineering with the goal to increase crop yields. However, such efforts have been hampered by the complex requirement of Rubisco biogenesis for molecular chaperones. Recent studies have identified an array of auxiliary factors needed for the folding and assembly of the Rubisco subunits. The folding of plant RbcL subunits is mediated by the cylindrical chloroplast chaperonin, Cpn60, and its cofactor Cpn20. Folded RbcL requires a number of additional Rubisco specific assembly chaperones, including RbcX, Rubisco accumulation factors 1 (Raf1) and 2 (Raf2), and the Bundle sheath defective-2 (BSD2), to mediate the assembly of the RbcL₈ intermediate complex. Incorporation of the RbcS and displacement of the assembly factors generates the active holoenzyme. An Escherichia coli strain expressing the chloroplast chaperonin and auxiliary factors now allows the expression of functional plant Rubisco, paving the way for Rubisco engineering by large scale mutagenesis. Here, we review our current understanding on how these chaperones cooperate to produce one of the most important enzymes in nature.