Chromatin and regulatory differentiation between bundle sheath and mesophyll cells in maize

C₄ plants partition photosynthesis enzymes between the bundle sheath (BS) and the mesophyll (M) cells for the better delivery of CO₂ to RuBisCO and to reduce photorespiration. To better understand how C₄ photosynthesis is regulated at the transcriptional level, we performed RNA-seq, ATAC-seq, ChIP-seq and Bisulfite-seq (BS-seq) on BS and M cells isolated from maize leaves. By integrating differentially expressed genes with chromatin features, we found that chromatin accessibility coordinates with epigenetic features, especially H3K27me3 modification and CHH methylation, to regulate cell type-preferentially enriched gene expression. Not only the chromatin-accessible regions (ACRs) proximal to the genes (pACRs) but also the distal ACRs (dACRs) are determinants of cell type-preferentially enriched expression. We further identified cell type-preferentially enriched motifs, e.g. AAAG for BS cells and TGACC/T for M cells, and determined their corresponding transcription factors: DOFs and WRKYs. The complex interaction between cis and trans factors in the preferential expression of C₄ genes was also observed. Interestingly, cell type-preferentially enriched gene expression can be fine-tuned by the coordination of multiple chromatin features. Such coordination may be critical in ensuring the cell type-specific function of key C₄ genes. Based on the observed cell type-preferentially enriched expression pattern and coordinated chromatin features, we predicted a set of functionally unknown genes, e.g. Zm00001d042050 and Zm00001d040659, to be potential key C₄ genes. Our findings provide deep insight into the architectures associated with C₄ gene expression and could serve as a valuable resource to further identify the regulatory mechanisms present in C₄ species.

Autophagic degradation of the chloroplastic 2-phosphoglycolate phosphatase TaPGLP1 in wheat

KEY MESSAGE

TaPGLP1, a chloroplast stromal 2-phosphoglycolate phosphatase of wheat, is an ATG8-interacting protein and undergoes autophagic degradation in starvation-treated wheat mesophyll protoplasts. Selective autophagy in plants has been shown to target diverse cellular cargoes including whole chloroplasts (Chlorophagy) and several chloroplast components (Piecemeal chlorophagy). Most cargoes of selective autophagy are captured by the autophagic machinery through their direct or indirect interactions with the autophagy-essential factor ATG8. Here, we reported a new ATG8-interacting cargo of piecemeal chlorophagy, the wheat photorespiratory 2-phosphoglycolate phosphatase TaPGLP1. The TaPGLP1-mCherry fusions expressed in wheat protoplasts located in the chloroplast stroma. Strikingly, these fusions are translocated into newly formed chloroplast surface protrusions after a long time incubation of protoplasts in a nutrition-free solution. Visualization of co-expressed TaPGLP1-mCherry and the autophagy marker GFP-TaATG8a revealed physical associations of TaPGLP1-mCherry-accumulating chloroplast protrusions with autophagic structures, implying the delivery of TaPGLP1-mCherry fusions from chloroplasts to the autophagic machinery. TaPGLP1-mCherry fusions were also detected in the GFP-TaATG8a-labelled autophagic bodies undergoing degradation in the vacuoles, which suggested the autophagic degradation of TaPGLP1. This autophagic degradation of TaPGLP1 was further demonstrated by the enhanced stability of TaPGLP1-mCherry in protoplasts with impaired autophagy. Expression of TaPGLP1-mCherry in protoplasts stimulated an enhanced autophagy level probably adopted by cells to degrade the over-produced TaPGLP1-mCherry fusions. Results from gene silencing assays showed the requirement of ATG2s and ATG7s in the autophagic degradation of TaPGLP1. Additionally, TaPGLP1 was shown to interact with ATG8 family members. Collectively, our data suggest that autophagy mediates the degradation of the chloroplast stromal protein TaPGLP1 in starvation-treated mesophyll protoplasts.

Plasma membrane-localized SEM1 protein mediates sugar movement to sink rice tissues

The translocation of photosynthate carbohydrates, such as sucrose, is critical for plant growth and crop yield. Previous studies have revealed that sugar transporters, plasmodesmata and sieve plates act as important controllers in sucrose loading into and unloading from phloem in the vascular system. However, other pivotal steps for the regulation of sucrose movement remain largely elusive. In this study, characterization of two starch excesses in mesophyll (sem) mutants and dye and sucrose export assays were performed to provide insights into the regulatory networks that drive source-sink relations in rice. Map-based cloning identified two allelic mutations in a gene encoding a GLUCAN SYNTHASE-LIKE (GSL) protein, thus indicating a role for SEM1 in callose biosynthesis. Subcellular localization in rice showed that SEM1 localized to the plasma membrane. In situ expression analysis and GUS staining showed that SEM1 was mainly expressed in vascular phloem cells. Reduced sucrose transport was found in the sem1-1/1-2 mutant, which led to excessive starch accumulation in source leaves and inhibited photosynthesis. Paraffin section and transmission electron microscopy experiments revealed that less-developed vascular cells (VCs) in sem1-1/1-2 potentially disturbed sugar movement. Moreover, dye and sugar trafficking experiments revealed that aberrant VC development was the main reason for the pleiotropic phenotype of sem1-1/1-2. In total, efficient sucrose loading into the phloem benefits from an optional number of VCs with a large vacuole that could act as a buffer holding tank for sucrose passing from the vascular bundle sheath.

Limitation of C4 photosynthesis by low carbonic anhydrase activity increases with temperature but does not influence mesophyll CO2 conductance

The CO2-concentrating mechanism (CCM) in C4 plants is initiated by the uptake of bicarbonate (HCO3-) via phosphoenolpyruvate carboxylase (PEPC). Generation of HCO3- for PEPC is determined by the interaction between mesophyll CO2 conductance and the hydration of CO2 to HCO3- by carbonic anhydrase (CA). Genetic reduction of CA was previously shown not to limit C4 photosynthesis under ambient atmospheric partial pressures of CO2 (pCO2). However, CA activity varies widely across C4 species and it is unknown if there are specific environmental conditions (e.g. high temperature) where CA may limit HCO3- production for C4 photosynthesis. Additionally, CA activity has been suggested to influence mesophyll conductance, but this has not been experimentally tested. We hypothesize that CA activity can limit PEPC at high temperatures, particularly at low pCO2, but does not directly influence gm. Here we tested the influence of genetically reduced CA activity on photosynthesis and gm in the C4 plant Zea mays under a range of pCO2 and temperatures. Reduced CA activity limited HCO3- production for C4 photosynthesis at low pCO2 as temperatures increased, but did not influence mesophyll conductance. Therefore, high leaf CA activity may enhance C4 photosynthesis under high temperature when stomatal conductance restricts the availability of atmospheric CO2.

The α subunit of the heterotrimeric G protein regulates mesophyll CO2 conductance and drought tolerance in rice

Mesophyll conductance g_m determines CO₂ diffusion rates from mesophyll intercellular air spaces to the chloroplasts and is an important factor limiting photosynthesis. Increasing g_m in cultivated plants is a potential strategy to increase photosynthesis and intrinsic water use efficiency (WUE_i ). The anatomy of the leaf and metabolic factors such as aquaporins and carbonic anhydrases have been identified as important determinants of g_m . However, genes involved in the regulation and modulation of g_m remain largely unknown. In this work, we investigated the role of heterotrimeric G proteins in g_m and drought tolerance in rice d1 mutants, which harbor a null mutation in the Gα subunit gene, RGA1. d1 mutants in both cv Nipponbare and cv Taichung 65 exhibited increased g_m , fostering improvement in photosynthesis, WUE_i , and drought tolerance compared with wild-type. The increased surface area of mesophyll cells and chloroplasts exposed to intercellular airspaces and the reduced cell wall and chloroplast thickness in the d1 mutant are evident contributors to the increase in g_m . Our results indicate that manipulation of heterotrimeric G protein signaling has the potential to improve crop WUE_i and productivity under drought.

Coordination of leaf hydraulic, anatomical, and economical traits in tomato seedlings acclimation to long-term drought

BACKGROUND

Leaf hydraulic and economics traits are critical for balancing plant water and CO₂ exchange, and their relationship has been widely studied. Leaf anatomical traits determine the efficiency of CO₂ diffusion within mesophyll structure. However, it remains unclear whether leaf anatomical traits are associated with leaf hydraulic and economics traits acclimation to long-term drought.

RESULTS

To address this knowledge gap, eight hydraulic traits, including stomatal and venation structures, four economics traits, including leaf dry mass per area (LMA) and the ratio between palisade and spongy mesophyll thickness (PT/ST), and four anatomical traits related to CO₂ diffusion were measured in tomato seedlings under the long-term drought conditions. Redundancy analysis indicated that the long-term drought decreased stomatal conductance (g_s) mainly due to a synchronized reduction in hydraulic structure such as leaf hydraulic conductance (K_leaf) and major vein width. Simultaneously, stomatal aperture on the adaxial surface and minor vein density (VD_minor) also contributed a lot to this reduction. The decreases in mesophyll thickness (T_mes) and chlorophyll surface area exposed to leaf intercellular air spaces (S_c/S) were primarily responsible for the decline of mesophyll conductance (g_m) thereby affecting photosynthesis. Drought increased leaf density (LD) thus limited CO₂ diffusion. In addition, LMA may not be important in regulating g_m in tomato under drought. Principal component analysis revealed that main anatomical traits such as T_mes and S_c/S were positively correlated to K_leaf, VD_minor and leaf thickness (LT), while negatively associated with PT/ST.

CONCLUSIONS

These findings indicated that leaf anatomy plays an important role in maintaining the balance between water supply and CO₂ diffusion responses to drought. There was a strong coordination between leaf hydraulic, anatomical, and economical traits in tomato seedlings acclimation to long-term drought.

Ribosome profiling elucidates differential gene expression in bundle sheath and mesophyll cells in maize

The efficiencies offered by C4 photosynthesis have motivated efforts to understand its biochemical, genetic, and developmental basis. Reactions underlying C4 traits in most C4 plants are partitioned between two cell types, bundle sheath (BS), and mesophyll (M) cells. RNA-seq has been used to catalog differential gene expression in BS and M cells in maize (Zea mays) and several other C4 species. However, the contribution of translational control to maintaining the distinct proteomes of BS and M cells has not been addressed. In this study, we used ribosome profiling and RNA-seq to describe translatomes, translational efficiencies, and microRNA abundance in BS- and M-enriched fractions of maize seedling leaves. A conservative interpretation of our data revealed 182 genes exhibiting cell type-dependent differences in translational efficiency, 31 of which encode proteins with core roles in C4 photosynthesis. Our results suggest that non-AUG start codons are used preferentially in upstream open reading frames of BS cells, revealed mRNA sequence motifs that correlate with cell type-dependent translation, and identified potential translational regulators that are differentially expressed. In addition, our data expand the set of genes known to be differentially expressed in BS and M cells, including genes encoding transcription factors and microRNAs. These data add to the resources for understanding the evolutionary and developmental basis of C4 photosynthesis and for its engineering into C3 crops.

Mesophyll conductance variability of rice aquaporin knockout lines at different growth stages and growing environments

The plasma membrane subfamily of aquaporins [plasma membrane intrinsic proteins (PIPs)], which facilitates the CO₂ diffusion across membranes, is proposed to play an important role in mesophyll conductance to CO₂ (g_m ), a major limiting factor of photosynthesis. However, recent studies implied no causal relationship between g_m and PIPs because they failed to repeat the previous observed differences in g_m between PIP knockout lines and their wild-type. The contrasting results on the role of PIPs in g_m were interpreted as the different growth conditions among studies, which has never been tested. Here, we assessed whether the differences in g_m between wild-type and PIP knockout lines, Ospip1;1, Ospip1;2 and Ospip2;1, varied with growth condition (field versus pot condition) and growth stages in rice. Under field conditions, no differences were observed in plant performance, photosynthetic rate (A) and g_m between PIP knockout lines and the wild-type. However, in agreement with previous studies, two out of three knockout lines showed significant declines in tiller number, plant height, A and g_m under pot conditions. Moreover, we found that the differences in A and g_m between PIP knockout lines and the wild-type varied with the growth stage of the plants. Our results showed that the differences in g_m between PIP knockout lines and wild-type were depending on the growth environments and stage of the plants, and further efforts are required to reveal the underlying mechanisms.

Mesophyll conductance, photoprotective process and optimal N partitioning are essential to the maintenance of photosynthesis at N deficient condition in a wheat yellow-green mutant (Triticum aestivum L.)

The major effect of nitrogen (N) deficiency is the inhibition on CO₂ assimilation regulated by light energy absorption, transport and conversion, as well as N allocation. In this study, a yellow-green wheat mutant (Jimai5265yg) and its wild type (Jimai5265, WT) were compared between 0 mM N (N₀) and 14 mM N (N₁₄) treatments using hydroponic experiments. The mutant exhibited higher photosynthetic efficiency (A_n) than WT despite low chlorophyll (Chl) content in non-stressed conditions. The photosynthetic advantages of the mutant were maintained under N deficient condition. The quantitative analysis of limitations to photosynthesis revealed that CO₂ diffusion associated with mesophyll conductance (g_m) was the dominant limitation. Relative easiness to gain CO₂ in the chloroplast contributed to the higher A_n of Jimai5265yg. N deficiency induced the photoinhibition of PSII, but the cyclic electron transport and photochemical activity of PSI was higher in Jimai5265yg compared to Jimai5265, which was a protective mechanism to avoid photodamage. Because of the sharp drop of A_n, N deficient seedlings had much lower photosynthetic N use efficiency (PNUE). However, N deficiency increased the relative content of photosynthetic N (N_psn) and decreased the relative content of storage N (N_store). The range of change in N partitioning induced by N deficiency was smaller for Jimai5265yg compared to WT. The less insensitive to N deficiency for the mutant in terms of photosynthetic property and N partitioning suggested that g_m, cyclic electron transport around PSI and more optimal N partitioning pattern is necessary to sustain photosynthesis under N deficient condition.

RNA-seq analysis of laser microdissected Arabidopsis thaliana leaf epidermis, mesophyll and vasculature defines tissue-specific transcriptional responses to multiple stress treatments

Acclimation of plants to adverse conditions requires the coordination of gene expression and signalling pathways between tissues and cell types. As the energy and carbon capturing organs, leaves are significantly affected by abiotic and biotic stresses. However, tissue- or cell type-specific analyses of stress responses have focussed on the Arabidopsis root. Here, we comparatively explore the transcriptomes of three leaf tissues (epidermis, mesophyll, vasculature) after induction of diverse stress pathways by chemical stimuli (antimycin A, 3-amino-1,2,4-triazole, methyl viologen, salicylic acid) and ultraviolet light in Arabidopsis using laser capture microdissection followed by RNA sequencing. Stimulation of stress pathways caused an overall reduction in the number of genes expressed in a tissue-specific manner, though a small subset gained or changed their tissue specificity. We find no evidence of a common stress response, with only a few genes consistently responsive to two or more treatments in the analysed tissues. However, differentially expressed genes overlap between tissues for individual treatments. A focussed analysis provided evidence for an interaction of auxin and ethylene that mediates retrograde signalling during mitochondrial dysfunction specifically in the epidermis, and a gene regulatory network defined the hierarchy of interactions. Taken together, we have generated an extensive reference dataset that will be valuable for future experiments analysing transcriptional responses on a tissue or single-cell level. Our results will enable the tailoring of the tissue-specific engineering of stress-tolerant plants.

The bundle sheath of rice is conditioned to play an active role in water transport as well as sulfur assimilation and jasmonic acid synthesis

Leaves comprise multiple cell types but our knowledge of the patterns of gene expression that underpin their functional specialization is fragmentary. Our understanding and ability to undertake the rational redesign of these cells is therefore limited. We aimed to identify genes associated with the incompletely understood bundle sheath of C₃ plants, which represents a key target associated with engineering traits such as C₄ photosynthesis into Oryza sativa (rice). To better understand the veins, bundle sheath and mesophyll cells of rice, we used laser capture microdissection followed by deep sequencing. Gene expression of the mesophyll is conditioned to allow coenzyme metabolism and redox homeostasis, as well as photosynthesis. In contrast, the bundle sheath is specialized in water transport, sulphur assimilation and jasmonic acid biosynthesis. Despite the small chloroplast compartment of bundle sheath cells, substantial photosynthesis gene expression was detected. These patterns of gene expression were not associated with the presence or absence of specific transcription factors in each cell type, but were instead associated with gradients in expression across the leaf. Comparative analysis with C₃ Arabidopsis identified a small gene set preferentially expressed in the bundle sheath cells of both species. This gene set included genes encoding transcription factors from 14 orthogroups and proteins allowing water transport, sulphate assimilation and jasmonic acid synthesis. The most parsimonious explanation for our findings is that bundle sheath cells from the last common ancestor of rice and Arabidopsis were specialized in this manner, and as the species diverged these patterns of gene expression have been maintained.

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.

Upregulation of bundle sheath electron transport capacity under limiting light in C4 Setaria viridis

C₄ photosynthesis is a biochemical pathway that operates across mesophyll and bundle sheath (BS) cells to increase CO₂ concentration at the site of CO₂ fixation. C₄ plants benefit from high irradiance but their efficiency decreases under shade, causing a loss of productivity in crop canopies. We investigated shade acclimation responses of Setaria viridis, a model monocot of NADP-dependent malic enzyme subtype, focussing on cell-specific electron transport capacity. Plants grown under low light (LL) maintained CO₂ assimilation rates similar to high light plants but had an increased chlorophyll and light-harvesting-protein content, predominantly in BS cells. Photosystem II (PSII) protein abundance, oxygen-evolving activity and the PSII/PSI ratio were enhanced in LL BS cells, indicating a higher capacity for linear electron flow. Abundances of PSI, ATP synthase, Cytochrome b₆ f and the chloroplast NAD(P)H dehydrogenase complex, which constitute the BS cyclic electron flow machinery, were also increased in LL plants. A decline in PEP carboxylase activity in mesophyll cells and a consequent shortage of reducing power in BS chloroplasts were associated with a more oxidised plastoquinone pool in LL plants and the formation of PSII - light-harvesting complex II supercomplexes with an increased oxygen evolution rate. Our results suggest that the supramolecular composition of PSII in BS cells is adjusted according to the redox state of the plastoquinone pool. This discovery contributes to the understanding of the acclimation of PSII activity in C₄ plants and will support the development of strategies for crop improvement, including the engineering of C₄ photosynthesis into C₃ plants.

Live imaging of microtubule organization, cell expansion, and intercellular space formation in Arabidopsis leaf spongy mesophyll cells

Leaf spongy mesophyll cells form an interconnected network of branched cells and intercellular spaces to maximize the surface area available for light capture and photosynthetic gas exchange. To investigate the morphogenetic events leading to cell separation and branching in Arabidopsis thaliana, we used mesophyll-specific promoters to facilitate imaging of mesophyll cell shape and microtubule (MT) organization over multiple spatiotemporal scales without interference from the overlying epidermal cells. We show that cells enlarge by selective expansion of cell wall regions in contact with intercellular spaces. Cell-cell contacts remain relatively fixed in size, forming the termini of interconnecting branches. Surprisingly, classic schizogeny (de-adhesion of neighboring cells) is relatively infrequent, being related to the local topology of cell junctions during early expansion. Intercellular spaces cue the position of stable MT bundles, which in turn promote efficient dilation of intercellular spaces and cell branching. Our data provide insights into mesophyll morphogenesis and MT organization and lay the groundwork for future investigations.

Targeted knockdown of ribulose-1, 5-bisphosphate carboxylase-oxygenase in rice mesophyll cells

We generated antisense constructs targeting two of the five Rubisco small subunit genes (OsRBCS2 and 4) which account for between 30-40 % of the RBCS transcript abundance in leaf blades. The constructs were driven by a maize phosphoenolpyruvate carboxylase (PEPC) promoter known to have enriched expression in mesophyll cells (MCs). In the resulting lines leaf, Rubisco protein content was reduced by between 30-50 % and CO₂ assimilation rate was limited under photorespiratory and non-photorespiratory conditions. A relationship between Rubisco protein content and CO₂ assimilation rate was found. This was associated with a significant reduction in dry biomass accumulation and grain yield of between 37-70%. In addition to serving as a resource for reducing Rubisco accumulation in a cell-preferential manner, these lines allow us to characterize gene function and isoform specific suppression on photosynthesis and growth. Our results suggest that the knockdown of multiple genes is required to completely reduce Rubisco accumulation in MCs.

Potential importance of malate diffusion in the response of maize photosynthesis to heterogeneous light

It is well known that the photosynthetic performance of a leaf is highly dependent on the systemic regulation from distal parts within a plant under light heterogeneity. However, there are few studies focusing on C₄-specific processes. In the present study, two cultivars of maize (Zea mays L.), 'Rongyu 1210' (RY) and 'Zhongdan 808' (ZD), were treated with heterogeneous light (HL). The net photosynthetic rate (P_n) of newly developed leaves was found to increase in HL-treated RY, while it decreased in HL-treated ZD. Result also showed a negative correlation between the P_n and the content of malate, a key metabolite in C₄ photosynthesis, in these two cultivars. In HL-treated ZD, malate content increased with a decline in the abundance of NADP-malic enzyme (EC 1.1.1.40), suggesting that less malate was decarboxylated. Moreover, a restriction of malate diffusion is proposed in HL-treated ZD, since the interface length between mesophyll cells (MC) and bundle sheath cells (BSC) decreased. In contrast, malate diffusion and subsequent decarboxylation in HL-treated RY should be stimulated, due to an increase in the abundance of NADP-malate dehydrogenase (EC 1.1.1.82) and a decline in the content of malate. In this case, malate diffusion from MC to BSC should be systemically stimulated, thereby facilitating C₄ photosynthesis of a maize leaf in heterogeneous light. While if it is systemically restricted, C₄ photosynthesis would be suppressed.

A low CO2-responsive mutant of Setaria viridis reveals that reduced carbonic anhydrase limits C4 photosynthesis

In C4 species, β-carbonic anhydrase (CA), localized to the cytosol of the mesophyll cells, accelerates the interconversion of CO2 to HCO3-, the substrate used by phosphoenolpyruvate carboxylase (PEPC) in the first step of C4 photosynthesis. Here we describe the identification and characterization of low CO2-responsive mutant 1 (lcr1) isolated from an N-nitroso-N-methylurea- (NMU) treated Setaria viridis mutant population. Forward genetic investigation revealed that the mutated gene Sevir.5G247800 of lcr1 possessed a single nucleotide transition from cytosine to thymine in a β-CA gene causing an amino acid change from leucine to phenylalanine. This resulted in severe reduction in growth and photosynthesis in the mutant. Both the CO2 compensation point and carbon isotope discrimination values of the mutant were significantly increased. Growth of the mutants was stunted when grown under ambient pCO2 but recovered at elevated pCO2. Further bioinformatics analyses revealed that the mutation has led to functional changes in one of the conserved residues of the protein, situated near the catalytic site. CA transcript accumulation in the mutant was 80% lower, CA protein accumulation 30% lower, and CA activity ~98% lower compared with the wild type. Changes in the abundance of other primary C4 pathway enzymes were observed; accumulation of PEPC protein was significantly increased and accumulation of malate dehydrogenase and malic enzyme decreased. The reduction of CA protein activity and abundance in lcr1 restricts the supply of bicarbonate to PEPC, limiting C4 photosynthesis and growth. This study establishes Sevir.5G247800 as the major CA allele in Setaria for C4 photosynthesis and provides important insights into the function of CA in C4 photosynthesis that would be required to generate a rice plant with a functional C4 biochemical pathway.

Subcellular Localization of Acyl-CoA: Lysophosphatidylethanolamine Acyltransferases (LPEATs) and the Effects of Knocking-Out and Overexpression of Their Genes on Autophagy Markers Level and Life Span of A. thaliana

Arabidopsis thaliana possesses two acyl-CoA:lysophosphatidylethanolamine acyltransferases, LPEAT1 and LPEAT2, which are encoded by At1g80950 and At2g45670 genes, respectively. Both single lpeat2 mutant and double lpeat1 lpeat2 mutant plants exhibit a variety of conspicuous phenotypes, including dwarfed growth. Confocal microscopic analysis of tobacco suspension-cultured cells transiently transformed with green fluorescent protein-tagged versions of LPEAT1 or LPEAT2 revealed that LPEAT1 is localized to the endoplasmic reticulum (ER), whereas LPEAT2 is localized to both Golgi and late endosomes. Considering that the primary product of the reaction catalyzed by LPEATs is phosphatidylethanolamine, which is known to be covalently conjugated with autophagy-related protein ATG8 during a key step of the formation of autophagosomes, we investigated the requirements for LPEATs to engage in autophagic activity in Arabidopsis. Knocking out of either or both LPEAT genes led to enhanced accumulation of the autophagic adaptor protein NBR1 and decreased levels of both ATG8a mRNA and total ATG8 protein. Moreover, we detected significantly fewer membrane objects in the vacuoles of lpeat1 lpeat2 double mutant mesophyll cells than in vacuoles of control plants. However, contrary to what has been reported on autophagy deficient plants, the lpeat mutants displayed a prolonged life span compared to wild type, including delayed senescence.

MicroRNA expression profile in bovine mammary gland parenchyma infected by coagulase-positive or coagulase-negative staphylococci

MicroRNAs (miRNAs) are short, non-coding RNAs, 21-23 nucleotides in length which are known to regulate biological processes that greatly impact immune system activity. The aim of the study was to compare the miRNA expression in non-infected (H) mammary gland parenchyma samples with that of glands infected with coagulase-positive staphylococci (CoPS) or coagulase-negative staphylococci (CoNS) using next-generation sequencing. The miRNA profile of the parenchyma was found to change during mastitis, with its profile depending on the type of pathogen. Comparing the CoPS and H groups, 256 known and 260 potentially new miRNAs were identified, including 32 that were differentially expressed (p ≤ 0.05), of which 27 were upregulated and 5 downregulated. Comparing the CoNS and H groups, 242 known and 171 new unique miRNAs were identified: 10 were upregulated (p ≤ 0.05), and 2 downregulated (p ≤ 0.05). In addition, comparing CoPS with H and CoNS with H, 5 Kyoto Encyclopedia of Genes and Genomes pathways were identified; in both comparisons, differentially-expressed miRNAs were associated with the bacterial invasion of epithelial cells and focal adhesion pathways. Four gene ontology terms were identified in each comparison, with 2 being common to both immune system processes and signal transduction. Our results indicate that miRNAs, especially miR-99 and miR-182, play an essential role in the epigenetic regulation of a range of cellular processes, including immunological systems bacterial growth in dendritic cells and disease pathogenesis (miR-99), DNA repair and tumor progression (miR-182).

Can hydraulic design explain patterns of leaf water isotopic enrichment in C3 plants?

H₂ ¹⁸ O enrichment develops when leaves transpire, but an accurate generalized mechanistic model has proven elusive. We hypothesized that leaf hydraulic architecture may affect the degree to which gradients in H₂ ¹⁸ O develop within leaves, influencing bulk leaf stable oxygen isotope enrichment (Δ_L ) and the degree to which the Péclet effect is relevant in leaves. Leaf hydraulic design predicted the relevance of a Péclet effect to Δ_L in 19 of the 21 species tested. Leaves with well-developed hydraulic connections between the vascular tissue and the epidermal cells through bundle sheath extensions and clear distinctions between palisade and spongy mesophyll layers (while the mesophyll is hydraulically disconnected) may have velocities of the transpiration stream such that gradients in H₂ ¹⁸ O develop and are expressed in the mesophyll. In contrast, in leaves where the vascular tissue is hydraulically disconnected from the epidermal layers, or where all mesophyll cells are well connected to the transpiration stream, velocities within the liquid transport pathways may be low enough that gradients in H₂ ¹⁸ O are very small. Prior knowledge of leaf hydraulic design allows informed selection of the appropriate Δ_L modelling framework.

Specific leaf area is modulated by nitrogen via changes in primary metabolism and parenchymal thickness in pepper

Nitrogen promotes changes in SLA through metabolism and anatomical traits in Capsicum plants. Specific leaf area (SLA) is a key trait influencing light interception and light use efficiency that often impacts plant growth and production. SLA is a key trait explaining growth variations of plant species under different environments. Both light and nitrogen (N) supply are important determinants of SLA. To better understand the effect of irradiance level and N on SLA in Capsicum chinense, we evaluated primary metabolites and morphological traits of two commercial cultivars (Biquinho and Habanero) in response to changes in both parameters. Both genotypes showed increased SLA with shading, and a decrease in SLA in response to increased N supply, however, with Habanero showing a stable SLA in the range of N deficiency to sufficient N doses. Correlation analyses indicated that decreased SLA in response to higher N supply was mediated by altered amino acids, protein, and starch levels, influencing leaf density. Moreover, in the range of moderate N deficiency to N sufficiency, both genotypes exhibited differences in SLA response, with Biquinho and Habanero displaying alterations on palisade and spongy parenchyma, respectively. Altogether, the results suggest that SLA responses to N supply are modulated by the balance between certain metabolites content and genotype-dependent changes in the parenchyma cells influencing leaf thickness and density.

Effect of light on the rearrangements of PSI super-and megacomplexes in the non-appressed thylakoid domains of maize mesophyll chloroplasts

We demonstrated the existence of PSI-LHCI-LHCII-Lhcb4 supercomplexes and PSI-LHCI-PSII-LHCII megacomplexes in the stroma lamellae and grana margins of maize mesophyll chloroplasts; these complexes consist of different LHCII trimers and monomer antenna proteins per PSI photocentre. These complexes are formed in both low (LL) and high (HL) light growth conditions, but with different contents. We attempted to identify the components and structure of these complexes in maize chloroplasts isolated from the leaves of low and high light-grown plants after darkness and transition to far red (FR) light of high intensity. Exposition of plants from high and low light growth condition on FR light induces different rearrangements in the composition of super- and megacomplexes. During FR light exposure, in plants from LL, the PSI-LHCI-LHCII-Lhcb4 supercomplex dissociates into free LHCII-Lhcb4 and PSI-LHCI complexes, and these complexes associate with the PSII monomer. This process occurs differently in plants from HL. Exposition to FR light causes dissociation of both PSI-LHCI-LHCII-Lhcb4 supercomplexes and PSI-PSII megacomplexes. These results suggest a different function of super- and megacomplex organization than the classic state transitions model, which assumes that the movement of LHCII trimers in the thylakoid membraneis considered as a mechanism for balancing light absorption between the two photosystems in light stress. The behavior of the complexes described in this article does not seem to be well explained by this model, i.e., it does not seem likely that the primary purpose of these megacomplexes dynamics is to balance excitation pressure. Rather, as stated in this article, it seems to indicate a role of these complexes for PSI in excitation quenching and for PSII in turnover.

Comparing the effects of different exogenous hormone combinations on seed-derived callus induction in Nicotiana tabacum

Callus from Nicotiana tabacum is used as a model in plant developmental research. We tested several phytohormone (Indoleacetic acid - IAA; 2,4-Dichlorophenoxyacetic acid - 2,4-D; kinetin - KIN; 6-Benzylaminopurine - BAP) combinations to compare different approaches to callus induction directly from the seeds of Nicotiana tabacum. Callus formation was observed up to 4 weeks after sowing and the most effective were 0.5 mg/L of 2,4-D with 0.25 mg/L of BAP and 2 mg/L 2,4-D with 1 mg/L of BAP. The calli were green, photosynthetically active and after 6 weeks of growth, no stress symptoms (estimated on the basis of fluorescence of chlorophyll a in photosystem II) were noticed.

Phototropin- and photosynthesis-dependent mitochondrial positioning in Arabidopsis thaliana mesophyll cells

Mitochondria are frequently observed in the vicinity of chloroplasts in photosynthesizing cells, and this association is considered necessary for their metabolic interactions. We previously reported that, in leaf palisade cells of Arabidopsis thaliana, mitochondria exhibit blue-light-dependent redistribution together with chloroplasts, which conduct accumulation and avoidance responses under the control of blue-light receptor phototropins. In this study, precise motility analyses by fluorescent microscopy revealed that the individual mitochondria in palisade cells, labeled with green fluorescent protein, exhibit typical stop-and-go movement. When exposed to blue light, the velocity of moving mitochondria increased in 30 min, whereas after 4 h, the frequency of stoppage of mitochondrial movement markedly increased. Using different mutant plants, we concluded that the presence of both phototropin1 and phototropin2 is necessary for the early acceleration of mitochondrial movement. On the contrary, the late enhancement of stoppage of mitochondrial movement occurs only in the presence of phototropin2 and only when intact photosynthesis takes place. A plasma-membrane ghost assay suggested that the stopped mitochondria are firmly adhered to chloroplasts. These results indicate that the physical interaction between mitochondria and chloroplasts is cooperatively mediated by phototropin2- and photosynthesis-dependent signals. The present study might add novel regulatory mechanism for light-dependent plant organelle interactions.

Integrated Framework of the Immune-Defense Transcriptional Signatures in the Arabidopsis Shoot Apical Meristem

The growing tips of plants grow sterile; therefore, disease-free plants can be generated from them. How plants safeguard growing apices from pathogen infection is still a mystery. The shoot apical meristem (SAM) is one of the three stem cells niches that give rise to the above ground plant organs. This is very well explored; however, how signaling networks orchestrate immune responses against pathogen infections in the SAM remains unclear. To reconstruct a transcriptional framework of the differentially expressed genes (DEGs) pertaining to various SAM cellular populations, we acquired large-scale transcriptome datasets from the public repository Gene Expression Omnibus (GEO). We identify here distinct sets of genes for various SAM cellular populations that are enriched in immune functions, such as immune defense, pathogen infection, biotic stress, and response to salicylic acid and jasmonic acid and their biosynthetic pathways in the SAM. We further linked those immune genes to their respective proteins and identify interactions among them by mapping a transcriptome-guided SAM-interactome. Furthermore, we compared stem-cells regulated transcriptome with innate immune responses in plants showing transcriptional separation among their DEGs in Arabidopsis. Besides unleashing a repertoire of immune-related genes in the SAM, our analysis provides a SAM-interactome that will help the community in designing functional experiments to study the specific defense dynamics of the SAM-cellular populations. Moreover, our study promotes the essence of large-scale omics data re-analysis, allowing a fresh look at the SAM-cellular transcriptome repurposing data-sets for new questions.