Tetrapyrrole-based drought stress signalling

Lead toxicity regulation via protein degradation and tetrapyrrole biosynthesis pathways in Brassica species: A comparative quantitative analysis of proteomic study

Understanding the heavy metals (HMs) tolerance mechanism is crucial for improving plant growth in metal-contaminated soil. In order to evaluate the lead (Pb) tolerance mechanism in Brassica species, a comparative proteomic study was used. Thirteen-day-old seedlings of B. juncea and B. napus were treated with different Pb(NO3)2 concentrations at 0, 3, 30, and 300 mg/L. Under 300 mg/L Pb(NO3)2 concentration, B. napus growth was significantly decreased, while B. juncea maintained normal growth similar to the control. The Pb accumulation was also higher in B. napus root and shoot compared to B. juncea. Gel-free proteomic analysis of roots revealed a total of 68 and 37 differentially abundant proteins (DAPs) in B. juncea and B. napus-specifically, after 300 mg/L Pb exposure. The majority of these proteins are associated with protein degradation, cellular respiration, and enzyme classification. The upregulated RPT2 and tetrapyrrole biosynthesis pathway-associated proteins maintain the cellular homeostasis and photosynthetic rate in B. juncea. Among the 55 common DAPs, S-adenosyl methionine and TCA cycle proteins were upregulated in B. juncea and down-regulated in B. napus after Pb exposure. Furthermore, higher oxidative stress also reduced the antioxidant enzyme activity in B. napus. The current finding suggests that B. juncea is more Pb tolerant than B. napus, possibly due to the upregulation of proteins involved in protein recycling, degradation, and tetrapyrrole biosynthesis pathway.

FsHemF is involved in the formation of yellow Forsythia leaves by regulating chlorophyll synthesis in response to light intensity

The leaves of Forsythia koreana 'Suwon Gold' are yellow under natural light condition and can revert to green when the light intensity is reduced. To understand the molecular mechanism of leaf color changes in response to light intensity, we compared the chlorophyll content and precursor content between yellow- and green-leaf Forsythia under shade and light-recovery conditions. We identified the conversion of coproporphyrin III (Coprogen III) to protoporphyrin IX (Proto IX) as the primary rate-limiting step of chlorophyll biosynthesis in yellow-leaf Forsythia. Further analysis of the activity of the enzymes that catalyze this step and the expression pattern of the chlorophyll biosynthesis-related genes under different light intensities revealed that the negatively regulated expression of FsHemF by light intensity was the major cause affecting the leaf color change in response to light intensity in yellow-leaf Forsythia. To further understand the cause of differential expression pattern of FsHemF in yellow- and green-leaf lines, we compared the coding sequence and promoter sequence of FsHemF between yellow- and green-leaf Forsythia. We found that one G-box light-responsive cis-element was absent in the promoter region of green-leaf lines. To investigate the functional role of FsHemF, we performed virus-induced gene silencing (VIGS) of FsHemF in green-leaf Forsythia, which leads to yellowing leaf veins, decreased chlorophyll b content, and inhibition of chlorophyll biosynthesis. The results will assist in elucidating the mechanism of yellow-leaf Forsythia in response to light intensity.

Chitosan-Magnesium Oxide Nanoparticles Improve Salinity Tolerance in Rice (Oryza sativa L.)

High-salinity (HS) stress is a global element restricting agricultural productivity. Rice is a significant food crop, but soil salinity has a detrimental impact on its yield and product quality. Nanoparticles (NPs) have been found as a mitigation method against different abiotic stresses, even HS stress. In this study, chitosan-magnesium oxide NPs (CMgO NPs) were used as a new method for rice plants to alleviate salt stress (200 mM NaCl). The results showed that 100 mg/L CMgO NPs greatly ameliorated salt stress by enhancing the root length by 37.47%, dry biomass by 32.86%, plant height by 35.20%, and tetrapyrrole biosynthesis in hydroponically cultured rice seedlings. The application of 100 mg/L CMgO NPs greatly alleviated salt-generated oxidative stress with induced activities of antioxidative enzymes, catalase by 67.21%, peroxidase by 88.01%, and superoxide dismutase by 81.19%, and decreased contents of malondialdehyde by 47.36% and H₂O₂ by 39.07% in rice leaves. The investigation of ion content in rice leaves revealed that rice treated with 100 mg/L CMgO NPs maintained a noticeably higher K⁺ level by 91.41% and a lower Na⁺ level by 64.49% and consequently a higher ratio of K⁺/Na⁺ than the control under HS stress. Moreover, the CMgO NPs supplement greatly enhanced the contents of free amino acids under salt stress in rice leaves. Therefore, our findings propose that CMgO NPs supplementation could mitigate the salt stress in rice seedlings.

Heme oxygenase-independent bilin biosynthesis revealed by a hmox1 suppressor screening in Chlamydomonas reinhardtii

Bilins are open-chain tetrapyrroles synthesized in phototrophs by successive enzymic reactions catalyzed by heme oxygenases (HMOXs/HOs) and ferredoxin-dependent biliverdin reductases (FDBRs) that typically serve as chromophore cofactors for phytochromes and phycobiliproteins. Chlamydomonas reinhardtii lacks both phycobiliproteins and phytochromes. Nonetheless, the activity and stability of photosystem I (PSI) and the catalytic subunit of magnesium chelatase (MgCh) named CHLH1 are significantly reduced and phototropic growth is significantly attenuated in a hmox1 mutant that is deficient in bilin biosynthesis. Consistent with these findings, previous studies on hmox1 uncovered an essential role for bilins in chloroplast retrograde signaling, maintenance of a functional photosynthetic apparatus, and the direct regulation of chlorophyll biosynthesis. In this study, we generated and screened a collection of insertional mutants in a hmox1 genetic background for suppressor mutants with phototropic growth restored to rates observed in wild-type 4A+ C. reinhardtii cells. Here, we characterized a suppressor of hmox1 named ho1su1 with phototrophic growth rates and levels of CHLH1 and PSI proteins similar to 4A+. Tetrad analysis indicated that a plasmid insertion co-segregated with the suppressor phenotype of ho1su1. Results from TAIL-PCR and plasmid rescue experiments demonstrated that the plasmid insertion was located in exon 1 of the HMOX1 locus. Heterologous expression of the bilin-binding reporter Nostoc punctiforme NpF2164g5 in the chloroplast of ho1su1 indicated that bilin accumulated in the chloroplast of ho1su1 despite the absence of the HMOX1 protein. Collectively, our study reveals the presence of an alternative bilin biosynthetic pathway independent of HMOX1 in the chloroplasts of Chlamydomonas cells.

Flow cytometry and 5-ethynyl-2'-deoxyuridine (EdU) labeling to detect the cell cycle dynamics of Phaeodactylum tricornutum under light

Cell cycle studies in plants and algae are highly dependent on reliable methods for detecting cellular DNA replication. With its short growth cycle and ease of genetic transformation, Phaeodactylum tricornutum is an important model organism for the study of pennate diatoms. Here we explored two different methods to detect the cell cycle of P. tricornutum, one using SYBR-green I to via flow cytometry, and the other using EdU labeling to observe cell cycle changes under fluorescence microscopy. Both EdU labeling fluorescence microscopy and SYBR-green I staining flow cytometry accurately indicated that the cells of P. tricornutum enter the G2/M phase after 12 h of light exposure. The results indicate that SYBR Green I was an adequate detection method for nuclear DNA quantitation in cells of P. tricornutum using a flow cytometer and without RNase A treatment. In addition, EdU can be applied to P. tricornutum to reliably detect cell proliferation. Besides, Mg-ProtoIX was able to reverse the cell cycle division inhibition of P. tricornutum and allow the nuclear DNA replication to proceed normally. Taken together, the photoperiodic division time point was clearly identified, which sheds light on the regulation of cell division mechanism in P. tricornutum.

Variety-specific transcript accumulation during reproductive stage in drought-stressed rice

The divergence of natural stress tolerance mechanisms between species is an intriguing phenomenon. To study it in rice, a comparative transcriptome analysis was carried out in 'heading' stage tissue (flag leaf, panicles and roots) of Nagina 22 (N22; drought-tolerant) and IR64 (drought-sensitive) plants subjected to field drought. Interestingly, N22 showed almost double the number of differentially expressed genes (DEGs) than IR64. Many DEGs colocalized within drought-related QTLs responsible for grain yield and drought tolerance and also associated with drought tolerance and critical drought-related plant traits such as leaf rolling, trehalose content, sucrose and cellulose content. Besides, co-expression analysis of the DEGs revealed several 'hub' genes known to actively regulate drought stress response. Strikingly, 1366 DEGs, including 21 'hub' genes, showed a distinct opposite regulation in the two rice varieties under similar drought conditions. Annotation of these variety-specific DEGs (VS-DEGs) revealed that they are distributed in various biological pathways. Furthermore, 103 VS-DEGs were found to physically interact with over 1300 genes, including 32 that physically interact with other VS-DEGs as well. The promoter region of these genes has sequence variations among the two rice varieties, which might be in part responsible for their unique expression pattern.

Autophagy during drought: function, regulation, and potential application

Drought is a major challenge for agricultural production since it causes substantial yield reduction and economic loss. Autophagy is a subcellular degradation and recycling pathway that functions in plant development and responses to many stresses, including drought. In this review, we summarize the current understanding of the function of autophagy and how autophagy is upregulated during drought stress. Autophagy helps plants to survive drought stress, and the mechanistic basis for this is beginning to be elucidated. Autophagy can selectively degrade aquaporins to adjust water permeability, and also degrades excess heme and damaged proteins to reduce their toxicity. In addition, autophagy can degrade regulators or components of hormone signaling pathways to promote stress responses. During drought recovery, autophagy degrades drought-induced proteins to reset the cell status. Autophagy is activated by multiple mechanisms during drought stress. Several transcription factors are induced by drought to upregulate autophagy-related gene expression, and autophagy is also regulated post-translationally through protein modification and stability. Based on these observations, manipulation of autophagy activity may be a promising approach for conferring drought tolerance in plants.

Meta-analysis of transcriptomic studies of cytokinin-treated rice roots defines a core set of cytokinin response genes

Cytokinins regulate diverse aspects of plant growth and development, primarily through modulation of gene expression. The cytokinin-responsive transcriptome has been thoroughly described in dicots, especially Arabidopsis, but much less so in monocots. Here, we present a meta-analysis of five different transcriptomic analyses of rice (Oryza sativa) roots treated with cytokinin, including three previously unpublished experiments. We developed a treatment method in which hormone is added to the media of rice seedlings grown in sterile hydroponic culture under a continuous airflow, which resulted in minimal perturbation of the seedlings, thus greatly reducing changes in gene expression in the absence of exogenous hormone. We defined a core set of 205 upregulated and 86 downregulated genes that were differentially expressed in at least three of the transcriptomic datasets. This core set includes genes encoding the type-A response regulators (RRs) and cytokinin oxidases/dehydrogenases, which have been shown to be primary cytokinin response genes. GO analysis revealed that the upregulated genes were enriched for terms related to cytokinin/hormone signaling and metabolism, while the downregulated genes were significantly enriched for genes encoding transporters. Variations of type-B RR binding motifs were significantly enriched in the promoters of the upregulated genes, as were binding sites for other potential partner transcription factors. The promoters of the downregulated genes were generally enriched for distinct cis-acting motifs and did not include the type-B RR binding motif. This analysis provides insight into the molecular mechanisms underlying cytokinin action in a monocot and provides a useful foundation for future studies of this hormone in rice and other cereals.

Physiological and Proteomic Signatures Reveal Mechanisms of Superior Drought Resilience in Pearl Millet Compared to Wheat

Presently, pearl millet and wheat are belonging to highly important cereal crops. Pearl millet, however, is an under-utilized crop, despite its superior resilience to drought and heat stress in contrast to wheat. To investigate this in more detail, we performed comparative physiological screening and large scale proteomics of drought stress responses in drought-tolerant and susceptible genotypes of pearl millet and wheat. These chosen genotypes are widely used in breeding and farming practices. The physiological responses demonstrated large differences in the regulation of root morphology and photosynthetic machinery, revealing a stay-green phenotype in pearl millet. Subsequent tissue-specific proteome analysis of leaves, roots and seeds led to the identification of 12,558 proteins in pearl millet and wheat under well-watered and stress conditions. To allow for this comparative proteome analysis and to provide a platform for future functional proteomics studies we performed a systematic phylogenetic analysis of all orthologues in pearl millet, wheat, foxtail millet, sorghum, barley, brachypodium, rice, maize, Arabidopsis, and soybean. In summary, we define (i) a stay-green proteome signature in the drought-tolerant pearl millet phenotype and (ii) differential senescence proteome signatures in contrasting wheat phenotypes not capable of coping with similar drought stress. These different responses have a significant effect on yield and grain filling processes reflected by the harvest index. Proteome signatures related to root morphology and seed yield demonstrated the unexpected intra- and interspecies-specific biochemical plasticity for stress adaptation for both pearl millet and wheat genotypes. These quantitative reference data provide tissue- and phenotype-specific marker proteins of stress defense mechanisms which are not predictable from the genome sequence itself and have potential value for marker-assisted breeding beyond genome assisted breeding.

The pigment binding behaviour of water-soluble chlorophyll protein (WSCP)

Water-soluble chlorophyll proteins (WSCPs) are homotetrameric proteins that bind four chlorophyll (Chl) molecules in identical binding sites, which makes WSCPs a good model to study protein-pigment interactions. In a previous study, we described preferential binding of Chl a or Chl b in various WSCP versions. Chl b binding is preferred when a hydrogen bond can be formed between the C7 formyl of the chlorin macrocycle and the protein, whereas Chl a is preferred when Chl b binding is sterically unfavorable. Here, we determined the binding affinities and kinetics of various WSCP versions not only for Chl a/b, but also for chlorophyllide (Chlide) a/b and pheophytin (Pheo) a/b. Altered KD values are responsible for the Chl a/b selectivity in WSCP whereas differences in the reaction kinetics are neglectable in explaining different Chl a/b preferences. WSCP binds both Chlide and Pheo with a lower affinity than Chl, which indicates the importance of the phytol chain and the central Mg2+ ion as interaction sites between WSCP and pigment. Pheophorbide (Pheoide), lacking both the phytol chain and the central Mg2+ ion, can only be bound as Pheoide b to a WSCP that has a higher affinity for Chl b than Chl a, which underlines the impact of the C7 formyl-protein interaction. Moreover, WSCP was able to bind protochlorophyllide and Mg-protoporphyrin IX, which suggests that neither the size of the π electron system of the macrocycle nor the presence of a fifth ring at the macrocycle notably affect the binding to WSCP. WSCP also binds heme to form a tetrameric complex, suggesting that heme is bound in the Chl-binding site.

Beneficial role of acetylcholine in chlorophyll metabolism and photosynthetic gas exchange in Nicotiana benthamiana seedlings under salinity stress

Acetylcholine (ACh) is believed to improve plant growth. However, regulation at biochemical and molecular levels is largely unknown. The present study investigated the impact of exogenously applied ACh (10 µm) on growth and chlorophyll metabolism in hydroponically grown Nicotiana benthamiana under salt stress (150 mm NaCl). Salinity reduced root hydraulic conductivity while ACh-treated seedlings exhibited a significant increase, resulting in increased relative water content. Salinity induced a reduction in chlorophyll biosynthetic intermediates, such as protoporphyrin-IX, Mg-photoporphyrin-IX and protochlorophyllide, which were significantly ameliorated in the presence of ACh. This influence of ACh on chlorophyll synthesis was confirmed by up-regulation of HEMA1, CHLH, CAO and POR genes. Gas exchange parameters, i.e. stomatal conductance, internal CO2 concentration and transpiration rate, increased with ACh, thereby alleviating the salinity effects on photosynthesis. In addition, the salinity-induced enhancement of lipid peroxidation declined after ACh treatment through modulation of the activity of the assayed antioxidant enzymes (superoxide dismutase and peroxidase). Importantly, ACh significantly reduced the uptake of Na and increased uptake of K, resulting in a decline in the Na/K ratio. Results of the present study indicate that ACh can be effective in ameliorating NaCl-induced osmotic stress, altering chlorophyll metabolism and thus photosynthesis by maintaining ion homeostasis, hydraulic conductivity and water balance.

Transcriptomic profiles of Dunaliella salina in response to hypersaline stress

Background

Dunaliella salina is a good model organism for studying salt stress. In order to have a global understanding of the expression profiles of Dunaliella salina in response to hypersaline stress, we performed quantitative transcriptomic analysis of Dunaliella salina under hypersaline stress (2.5 M NaCl) of different time duration by the second and third generation sequencing method.

Results

Functional enrichment of the up-regulated genes was used to analyze the expression profiles. The enrichment of photosynthesis was observed, accompanied by enrichments of carbon fixation, pigment biosynthetic process and heme biosynthetic process, which also imply the enhancement of photosynthesis. Genes responsible for starch hydrolysis and glycerol synthesis were significantly up-regulated. The enrichment of biosynthesis of unsaturated fatty acids implies the plasma membrane undergoes changes in desaturation pattern. The enrichment of endocytosis implies the degradation of plasma membrane and might help the synthesis of new glycerophospholipid with unsaturated fatty acids. Co-enrichments of protein synthesis and degradation imply a higher protein turnover rate. The enrichments of spliceosome and protein processing in endoplasmic reticulum imply the enhancement of regulations at post-transcriptional and post-translational level. No up-regulation of any Na⁺ or Cl⁻ channels or transporters was detected, which implies that the extra exclusion of the ions by membrane transporters is possibly not needed. Voltage gated Na⁺ and Cl⁻ channels, mechanosensitive ion channel are possible signal receptors of salt stress, and Ca²⁺ and MAP kinase pathways might play a role in signal transduction.

Conclusion

At global transcriptomic level, the response of Dunaliella salina to hypersaline stress is a systematic work, possibly involving enhancements of photosynthesis, carbon fixation, and heme biosynthetic process, acceleration of protein turnover, spliceosome, protein processing in endoplasmic reticulum, and endocytosis, as well as degradation of starch, synthesis of glycerol, membrane lipid desaturation. Altogether, the changes of these biological processes occurred at trancriptomic level will help understand how a new intracellular balance achieved in Dunaliella salina to adapt to hypersaline environment, which are worth being confirmed at the physiological levels.

Physiological and Proteomic Signatures Reveal Mechanisms of Superior Drought Resilience in Pearl Millet Compared to Wheat

Presently, pearl millet and wheat are belonging to highly important cereal crops. Pearl millet, however, is an under-utilized crop, despite its superior resilience to drought and heat stress in contrast to wheat. To investigate this in more detail, we performed comparative physiological screening and large scale proteomics of drought stress responses in drought-tolerant and susceptible genotypes of pearl millet and wheat. These chosen genotypes are widely used in breeding and farming practices. The physiological responses demonstrated large differences in the regulation of root morphology and photosynthetic machinery, revealing a stay-green phenotype in pearl millet. Subsequent tissue-specific proteome analysis of leaves, roots and seeds led to the identification of 12,558 proteins in pearl millet and wheat under well-watered and stress conditions. To allow for this comparative proteome analysis and to provide a platform for future functional proteomics studies we performed a systematic phylogenetic analysis of all orthologues in pearl millet, wheat, foxtail millet, sorghum, barley, brachypodium, rice, maize, Arabidopsis, and soybean. In summary, we define (i) a stay-green proteome signature in the drought-tolerant pearl millet phenotype and (ii) differential senescence proteome signatures in contrasting wheat phenotypes not capable of coping with similar drought stress. These different responses have a significant effect on yield and grain filling processes reflected by the harvest index. Proteome signatures related to root morphology and seed yield demonstrated the unexpected intra- and interspecies-specific biochemical plasticity for stress adaptation for both pearl millet and wheat genotypes. These quantitative reference data provide tissue- and phenotype-specific marker proteins of stress defense mechanisms which are not predictable from the genome sequence itself and have potential value for marker-assisted breeding beyond genome assisted breeding.

Peanut genes encoding tetrapyrrole biosynthetic enzymes, AhHEMA1 and AhFC1, alleviating the salt stress in transgenic tobacco

Glutamyl-tRNA reductase1 (HEMA1) and ferrochelatase1 (FC1) are both expressed in response to salt stress in the biosynthetic pathway of tetrapyrroles. Peanut (Arachis hypogaea L.) HEMA1 and FC1 were isolated by RT-PCR. The amino acid sequence encoded by the two genes showed high similarity with that in other plant species. The AhFC1 fusion protein was verified to function in chloroplast using Arabidopsis mesophyll protoplast. Sense and wild-type (WT) tobaccos were used to further study the physiological effects of AhHEMA1 and AhFC1. Compared with WT, the Heme contents and germination rate were higher in AhFC1 overexpressing plants under salt stress. Meanwhile, overexpressing AhHEMA1 also led to higher ALA and chlorophyll contents and multiple physiological changes under salt stress, such as higher activities of superoxide dismutase (SOD) and ascorbate peroxidase (APX), lower contents of reactive oxygen species (ROS) and slighter membrane damage. In addition, the activities of CAT, POD and APX in the AhFC1 overexpressing plants were significantly higher than that in WT lines under salt stress, but the activity of SOD between the WT plants and the transgenic plants did not exhibit significant differences. These results suggested that, peanut can enhance resistance to salt stress by improving the biosynthesis of tetrapyrrole biosynthetic.

Milestones achieved in response to drought stress through reverse genetic approaches

Drought stress is the most important abiotic stress that constrains crop production and reduces yield drastically. The germplasm of most of the cultivated crops possesses numerous unknown drought stress tolerant genes. Moreover, there are many reports suggesting that the wild species of most of the modern cultivars have abiotic stress tolerant genes. Due to climate change and population booms, food security has become a global issue. To develop drought tolerant crop varieties knowledge of various genes involved in drought stress is required. Different reverse genetic approaches such as virus-induced gene silencing (VIGS), clustered regularly interspace short palindromic repeat (CRISPR), targeting induced local lesions in genomes (TILLING) and expressed sequence tags (ESTs) have been used extensively to study the functionality of different genes involved in response to drought stress. In this review, we described the contributions of different techniques of functional genomics in the study of drought tolerant genes.

Characterization of Ferredoxin-Dependent Biliverdin Reductase PCYA1 Reveals the Dual Function in Retrograde Bilin Biosynthesis and Interaction With Light-Dependent Protochlorophyllide Oxidoreductase LPOR in Chlamydomonas reinhardtii

Bilins are linear tetrapyrroles commonly used as chromophores of phycobiliproteins and phytochromes for light-harvesting or light-sensing in photosynthetic organisms. Many eukaryotic algae lack both phycobiliproteins and phytochromes, but retain the bilin biosynthetic enzymes including heme oxygenase (HO/HMOX) and ferredoxin-dependent biliverdin reductase (FDBR). Previous studies on Chlamydomonas reinhardtii heme oxygenase mutant (hmox1) have shown that bilins are not only essential retrograde signals to mitigate oxidative stress during diurnal dark-to-light transitions, they are also required for chlorophyll accumulation and maintenance of a functional photosynthetic apparatus in the light. However, the underlying mechanism of bilin-mediated regulation of chlorophyll biosynthesis is unclear. In this study, Chlamydomonas phycocyanobilin:ferredoxin oxidoreductase PCYA1 FDBR domain was found to specifically interact with the rate-limiting chlorophyll biosynthetic enzyme LPOR (light-dependent protochlorophyllide oxidoreductase). PCYA1 is partially associated with chloroplast envelope membrane, consistent with the observed export of bilin from chloroplast to cytosol by cytosolic expression of a bilin-binding reporter protein in Chlamydomonas. Both the pcya1-1 mutant with the carboxyl-terminal extension of PCYA1 eliminated and efficient knockdown of PCYA1 expression by artificial microRNA exhibited no significant impact on algal phototrophic growth and photosynthetic proteins accumulation, indicating that the conserved FDBR domain is sufficient and minimally required for bilin biosynthesis and functioning. Taken together, these studies provide novel insights into the regulatory role of PCYA1 in chlorophyll biosynthesis via interaction with key Chl biosynthetic enzyme.

5-aminolevulinic acid improves salt tolerance mediated by regulation of tetrapyrrole and proline metabolism in Brassica napus L. seedlings under NaCl stress

5-aminolevulinic acid (ALA), a key biosynthetic precursor of tetrapyrroles, is vital for plant growth and adaptation to stress environments. Although exogenous ALA could enhance photosynthesis and biomass accumulation in plants under stress conditions, the underlying physiological and molecular mechanisms governed by ALA in promoting salt tolerance in Brassica napus L. are not yet clearly understood. In the present study, exogenous ALA with the concentration of 30 mg L^-1 was applied to the leaves of B. napus seedlings subjected to 200 mM NaCl. The results showed that NaCl stress decreased the photosynthesis, biomass accumulation, and levels of chlorophyll and heme with the reduction of the concentrations of intermediates including ALA, protoporphyrin IX (Proto IX), Mg-Proto IX, and Pchlide in the tetrapyrrole (chlorophyll and heme) biosynthetic pathway. The transcript levels of genes encoding ALA-associated enzymes and genes encoding Mg-chelatase in the chlorophyll biosynthetic branch were down-regulated, while the expression levels of genes encoding Fe-chelatase in the heme branch were not significantly altered by NaCl stress. Foliar application with ALA enhanced the aboveground biomass, net photosynthetic rate, activities of antioxidant enzymes, accumulation of chlorophyll and heme, and concentrations of intermediates related to chlorophyll and heme biosynthesis in B. napus under 200 mM NaCl. The expression of most genes mentioned above remained constant in ALA-treated plants in comparison with non-ALA-treated plants under NaCl stress. Additionally, exogenous ALA synchronously induced the proline concentration and up-regulated the expression of genes P5CS and ProDH encoding proline metabolic enzymes in the NaCl treatment. These findings suggested that ALA improved salt tolerance through promoting the accumulation of chlorophyll and heme resulting from the increase of intermediate levels in the tetrapyrrole biosynthetic pathway, along with enhancing the proline accumulation in B. napus.

High Performance of Photosynthesis and Osmotic Adjustment Are Associated With Salt Tolerance Ability in Rice Carrying Drought Tolerance QTL: Physiological and Co-expression Network Analysis

Understanding specific biological processes involving in salt tolerance mechanisms is important for improving traits conferring tolerance to salinity, one of the most important abiotic stresses in plants. Under drought and salinity stresses, plants share overlapping responsive mechanisms such as physiological changes and activation of signaling molecules, which induce and transmit signals through regulator genes in a regulatory network. In this study, two near isogenic lines of rice carrying chromosome segments of drought tolerance QTL on chromosome 8 from IR68586-F2-CA-31 (DH103) in the genetic background of sensitive cultivar "Khao Dawk Mali 105; KDML105" (designated as CSSL8-94 and CSSL8-95) were used to investigate physiological responses to salt stress [namely growth, Na⁺/K⁺ ratio, water status, osmotic adjustment, photosynthetic parameters, electrolyte leakage (EL), malondialdehyde (MDA), proline and sugar accumulations], compared with the standard salt tolerant (Pokkali; PK) and their recurrent parent (KDML105) rice cultivars. Physiological examination indicated that both CSSLs showed superior salt-tolerant level to KDML105. Our results suggested that salt tolerance ability of these CSSL lines may be resulted from high performance photosynthesis, better osmotic adjustment, and less oxidative stress damage under salt conditions. Moreover, to explore new candidate genes that might take part in salt tolerance mechanisms, we performed co-expression network analysis for genes identified in the CSSL rice, and found that Os08g419090, the gene involved with tetrapyrrole and porphyrin biosynthetic process (chlorophyll biosynthetic process), Os08g43230 and Os08g43440 (encoded TraB family protein and cytochrome P450, respectively) might have unprecedented roles in salt stress tolerance.

Algal light sensing and photoacclimation in aquatic environments

Anoxygenic photosynthetic prokaryotes arose in ancient oceans ~3.5 billion years ago. The evolution of oxygenic photosynthesis by cyanobacteria followed soon after, enabling eukaryogenesis and the evolution of complex life. The Archaeplastida lineage dates back ~1.5 billion years to the domestication of a cyanobacterium. Eukaryotic algae have subsequently radiated throughout oceanic/freshwater/terrestrial environments, adopting distinctive morphological and developmental strategies for adaptation to diverse light environments. Descendants of the ancestral photosynthetic alga remain challenged by a typical diurnally fluctuating light supply ranging from ~0 to ~2000 μE m^-2  s^-1 . Such extreme changes in light intensity and variations in light quality have driven the evolution of novel photoreceptors, light-harvesting complexes and photoprotective mechanisms in photosynthetic eukaryotes. This minireview focuses on algal light sensors, highlighting the unexpected roles for linear tetrapyrroles (bilins) in the maintenance of functional chloroplasts in chlorophytes, sister species to streptophyte algae and land plants.

Altered gene expression by sedaxane increases PSII efficiency, photosynthesis and growth and improves tolerance to drought in wheat seedlings

Succinate dehydrogenase inhibitor (SDHI) fungicides have been shown to increase PSII efficiency and photosynthesis under drought stress in the absence of disease to enhance the biomass and yield of winter wheat. However, the molecular mechanism of improved photosynthetic efficiency observed in SDHI-treated wheat has not been previously elucidated. Here we used a combination of chlorophyll fluorescence, gas exchange and gene expression analysis, to aid our understanding of the basis of the physiological responses of wheat seedlings under drought conditions to sedaxane, a novel SDHI seed treatment. We show that sedaxane increased the efficiency of PSII photochemistry, reduced non-photochemical quenching and improved the photosynthesis and biomass in wheat correlating with systemic changes in the expression of genes involved in defense, chlorophyll synthesis and cell wall modification. We applied a coexpression network-based approach using differentially expressed genes of leaves, roots and pregerminated seeds from our wheat array datasets to identify the most important hub genes, with top ranked correlation (higher gene association value and z-score) involved in cell wall expansion and strengthening, wax and pigment biosynthesis and defense. The results indicate that sedaxane confers tolerant responses of wheat plants grown under drought conditions by redirecting metabolites from defense/stress responses towards growth and adaptive development.

Independent introductions and admixtures have contributed to adaptation of European maize and its American counterparts

Through the local selection of landraces, humans have guided the adaptation of crops to a vast range of climatic and ecological conditions. This is particularly true of maize, which was domesticated in a restricted area of Mexico but now displays one of the broadest cultivated ranges worldwide. Here, we sequenced 67 genomes with an average sequencing depth of 18x to document routes of introduction, admixture and selective history of European maize and its American counterparts. To avoid the confounding effects of recent breeding, we targeted germplasm (lines) directly derived from landraces. Among our lines, we discovered 22,294,769 SNPs and between 0.9% to 4.1% residual heterozygosity. Using a segmentation method, we identified 6,978 segments of unexpectedly high rate of heterozygosity. These segments point to genes potentially involved in inbreeding depression, and to a lesser extent to the presence of structural variants. Genetic structuring and inferences of historical splits revealed 5 genetic groups and two independent European introductions, with modest bottleneck signatures. Our results further revealed admixtures between distinct sources that have contributed to the establishment of 3 groups at intermediate latitudes in North America and Europe. We combined differentiation- and diversity-based statistics to identify both genes and gene networks displaying strong signals of selection. These include genes/gene networks involved in flowering time, drought and cold tolerance, plant defense and starch properties. Overall, our results provide novel insights into the evolutionary history of European maize and highlight a major role of admixture in environmental adaptation, paralleling recent findings in humans.

Organellar Gene Expression and Acclimation of Plants to Environmental Stress

Organelles produce ATP and a variety of vital metabolites, and are indispensable for plant development. While most of their original gene complements have been transferred to the nucleus in the course of evolution, they retain their own genomes and gene-expression machineries. Hence, organellar function requires tight coordination between organellar gene expression (OGE) and nuclear gene expression (NGE). OGE requires various nucleus-encoded proteins that regulate transcription, splicing, trimming, editing, and translation of organellar RNAs, which necessitates nucleus-to-organelle (anterograde) communication. Conversely, changes in OGE trigger retrograde signaling that modulates NGE in accordance with the current status of the organelle. Changes in OGE occur naturally in response to developmental and environmental changes, and can be artificially induced by inhibitors such as lincomycin or mutations that perturb OGE. Focusing on the model plant Arabidopsis thaliana and its plastids, we review here recent findings which suggest that perturbations of OGE homeostasis regularly result in the activation of acclimation and tolerance responses, presumably via retrograde signaling.

Comparative proteomic analysis reveals the positive effect of exogenous spermidine on photosynthesis and salinity tolerance in cucumber seedlings

Our results based on proteomics data and physiological alterations proposed the putative mechanism of exogenous Spd enhanced salinity tolerance in cucumber seedlings. Current studies showed that exogenous spermidine (Spd) could alleviate harmful effects of salinity. It is important to increase our understanding of the beneficial physiological responses of exogenous Spd treatment, and to determine the molecular responses underlying these responses. Here, we combined a physiological analysis with iTRAQ-based comparative proteomics of cucumber (Cucumis sativus L.) leaves, treated with 0.1 mM exogenous Spd, 75 mM NaCl and/or exogenous Spd. A total of 221 differentially expressed proteins were found and involved in 30 metabolic pathways, such as photosynthesis, carbohydrate metabolism, amino acid metabolism, stress response, signal transduction and antioxidant. Based on functional classification of the differentially expressed proteins and the physiological responses, we found cucumber seedlings treated with Spd under salt stress had higher photosynthesis efficiency, upregulated tetrapyrrole synthesis, stronger ROS scavenging ability and more protein biosynthesis activity than NaCl treatment, suggesting that these pathways may promote salt tolerance under high salinity. This study provided insights into how exogenous Spd protects photosynthesis and enhances salt tolerance in cucumber seedlings.

Transcriptome analysis revealed the drought-responsive genes in Tibetan hulless barley

Background

Hulless barley, also called naked barley, is an important cereal crop worldwide, serving as a healthy food both for human consumption and animal feed. Nevertheless, it often suffered from drought stress during its growth and development, resulting in a drastic reduction in barley yields. Therefore, study on molecular mechanism of hulless barley drought-tolerance is very important for increasing barley production. To investigate molecular mechanism of barley drought-resistance, this study examined co-regulated mRNAs that show a change in expression pattern under early well water, later water deficit and finally water recovery treatments, and to identify mRNAs specific to water limiting conditions.

Results

Total of 853 differentially expressed genes (DEGs) were detected and categorized into nine clusters, in which VI and VIII were apparently up-regulated under low relative soil moisture content (RSMC) level. The majority of genes in these two clusters was relevant to abiotic stress responses in abscisic acid (ABA) dependent and independent signaling pathway, including NCED, PYR/PYL/RCAR, SnRK2, ABF, MYB/MYC, AP2/ERF family, LEA and DHN. In contrast, genes within clusters II and IV were generally down-regulated under water stress; cluster IX genes were up-regulated during water recovery response to both low and high RSMC levels. Genes in implicated in tetrapyrrole binding, photosystem and photosynthetic membrane were the most affected in cluster IX.

Conclusion

Taken together, our findings indicate that the responses of hulless barley to drought stress shows differences in the pathways and genes activated. Furthermore, all these genes displayed different sensitivities to soil water deficit and might be profitable for future drought tolerance improvement in barley and other crops.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2685-3) contains supplementary material, which is available to authorized users.

Chloroplast Retrograde Regulation of Heat Stress Responses in Plants

It is well known that intracellular signaling from chloroplast to nucleus plays a vital role in stress responses to survive environmental perturbations. The chloroplasts were proposed as sensors to heat stress since components of the photosynthetic apparatus housed in the chloroplast are the major targets of thermal damage in plants. Thus, communicating subcellular perturbations to the nucleus is critical during exposure to extreme environmental conditions such as heat stress. By coordinating expression of stress specific nuclear genes essential for adaptive responses to hostile environment, plants optimize different cell functions and activate acclimation responses through retrograde signaling pathways. The efficient communication between plastids and the nucleus is highly required for such diverse metabolic and biosynthetic functions during adaptation processes to environmental stresses. In recent years, several putative retrograde signals released from plastids that regulate nuclear genes have been identified and signaling pathways have been proposed. In this review, we provide an update on retrograde signals derived from tetrapyrroles, carotenoids, reactive oxygen species (ROS) and organellar gene expression (OGE) in the context of heat stress responses and address their roles in retrograde regulation of heat-responsive gene expression, systemic acquired acclimation, and cellular coordination in plants.

Chloroplast Retrograde Regulation of Heat Stress Responses in Plants

It is well known that intracellular signaling from chloroplast to nucleus plays a vital role in stress responses to survive environmental perturbations. The chloroplasts were proposed as sensors to heat stress since components of the photosynthetic apparatus housed in the chloroplast are the major targets of thermal damage in plants. Thus, communicating subcellular perturbations to the nucleus is critical during exposure to extreme environmental conditions such as heat stress. By coordinating expression of stress specific nuclear genes essential for adaptive responses to hostile environment, plants optimize different cell functions and activate acclimation responses through retrograde signaling pathways. The efficient communication between plastids and the nucleus is highly required for such diverse metabolic and biosynthetic functions during adaptation processes to environmental stresses. In recent years, several putative retrograde signals released from plastids that regulate nuclear genes have been identified and signaling pathways have been proposed. In this review, we provide an update on retrograde signals derived from tetrapyrroles, carotenoids, reactive oxygen species (ROS) and organellar gene expression (OGE) in the context of heat stress responses and address their roles in retrograde regulation of heat-responsive gene expression, systemic acquired acclimation, and cellular coordination in plants.

Arabidopsis HY1-Modulated Stomatal Movement: An Integrative Hub Is Functionally Associated with ABI4 in Dehydration-Induced ABA Responsiveness

Heme oxygenase (HO; EC 1.14.99.3) has recently been proposed as a novel component in mediating wide ranges of the plant adaptive signaling processes. However, the physiological significance and molecular basis underlying Arabidopsis (Arabidopsis thaliana) HO1 (HY1) functioning in drought tolerance remained unclear. Here, we report that mutation of HY1 promoted, but overexpression of this gene impaired, Arabidopsis drought tolerance. This was attributed to the abscisic acid (ABA)-hypersensitive or -hyposensitive phenotypes, with the regulation of stomatal closure in particular. However, comparative transcriptomic profile analysis showed that the induction of numerous ABA/stress-dependent genes in dehydrated wild-type plants was differentially impaired in the hy1 mutant. In agreement, ABA-induced ABSCISIC ACID-INSENSITIVE4 (ABI4) transcript accumulation was strengthened in the hy1 mutant. Genetic analysis further identified that the hy1-associated ABA hypersensitivity and drought tolerance were arrested in the abi4 background. Moreover, the promotion of ABA-triggered up-regulation of RbohD abundance and reactive oxygen species (ROS) levels in the hy1 mutant was almost fully blocked by the mutation of ABI4, suggesting that the HY1-ABI4 signaling in the wild type involved in stomatal closure was dependent on the RbohD-derived ROS production. However, hy1-promoted stomatal closure was not affected by a nitric oxide scavenger. Correspondingly, ABA-insensitive behaviors in rbohD stomata were not affected by either the mutation of HY1 or its ectopic expression in the rbohD background, both of which responded significantly to exogenous ROS. These data indicate that HY1 functioned negatively and acted upstream of ABI4 in drought signaling, which was casually dependent on the RbohD-derived ROS in the regulation of stomatal closure.

Tetrapyrrole Signaling in Plants

Tetrapyrroles make critical contributions to a number of important processes in diverse organisms. In plants, tetrapyrroles are essential for light signaling, the detoxification of reactive oxygen species, the assimilation of nitrate and sulfate, respiration, photosynthesis, and programed cell death. The misregulation of tetrapyrrole metabolism can produce toxic reactive oxygen species. Thus, it is not surprising that tetrapyrrole metabolism is strictly regulated and that tetrapyrrole metabolism affects signaling mechanisms that regulate gene expression. In plants and algae, tetrapyrroles are synthesized in plastids and were some of the first plastid signals demonstrated to regulate nuclear gene expression. In plants, the mechanism of tetrapyrrole-dependent plastid-to-nucleus signaling remains poorly understood. Additionally, some of experiments that tested ideas for possible signaling mechanisms appeared to produce conflicting data. In some instances, these conflicts are potentially explained by different experimental conditions. Although the biological function of tetrapyrrole signaling is poorly understood, there is compelling evidence that this signaling is significant. Specifically, this signaling appears to affect the accumulation of starch and may promote abiotic stress tolerance. Tetrapyrrole-dependent plastid-to-nucleus signaling interacts with a distinct plastid-to-nucleus signaling mechanism that depends on GENOMES UNCUOPLED1 (GUN1). GUN1 contributes to a variety of processes, such as chloroplast biogenesis, the circadian rhythm, abiotic stress tolerance, and development. Thus, the contribution of tetrapyrrole signaling to plant function is potentially broader than we currently appreciate. In this review, I discuss these aspects of tetrapyrrole signaling.