Early Light-Inducible Protein (ELIP) Can Enhance Resistance to Cold-Induced Photooxidative Stress in Chlamydomonas reinhardtii

Comparative transcriptome provides new insights into the molecular regulation of olive trees to chilling stress

Olive (Olea europaea L.), an economically important oil-producing crop, is sensitive to low temperature, which severely limits its productivity and geographical distribution. However, the underlying mechanism of cold tolerance in olive remains elusive. In this study, a chilling experiment (4 °C) on the living saplings of two olive cultivars revealed that O. europaea cv. Arbequina showed stronger cold tolerance with greater photosynthetic activity compared with O. europaea cv. Leccino. Transcriptome analyses revealed that early light-inducible protein 1 (ELIP1), the main regulator for chlorophyll synthesis, is dramatically induced to protect the photosynthesis at low temperatures. Furthermore, weighted gene co-expression network analysis, yeast one-hybrid and luciferase assays demonstrated that transcription factor bHLH66 serves as an important regulator of ELIP1 transcription by binding to the G-box motif in the promoter. Taken together, our research revealed a novel transcriptional module consisting of bHLH66-ELIP1 in the adaptation of olive trees to cold stress.

Assessing the role of the graphene family nanomaterials (GFNs: Graphene, GO, rGO) in modifying the toxicity potential and environmental risk of flame retardant, tetrabromobisphenol-A (TBBPA) in the marine microalgae Chlorella sp

In recent years, a growing concern has emerged regarding the environmental implications of flame retardants (FRs) like tetrabromobisphenol-A (TBBPA) and graphene family nanomaterials (GFNs), such as graphene, graphene oxide (GO), and reduced graphene oxide (rGO), on marine biota. Despite these substances' well-established individual toxicity profiles, there is a notable gap in understanding the physicochemical interactions within the binary mixtures and consequent changes in the toxicity potential. Therefore, our research focuses on elucidating the individual and combined toxicological impacts of TBBPA and GFNs on the marine alga Chlorella sp. Employing a suite of experimental methodologies, including Raman spectroscopy, contact angle measurements, electron microscopy, and chromatography, we examined the physicochemical interplay between the GFNs and TBBPA. The toxicity potentials of individual constituents and their binary combinations were assessed through growth inhibition assays, quantifying reactive oxygen species (ROS) generation and malondialdehyde (MDA) production, photosynthetic activity analyses, and various biochemical assays. The toxicity of TBBPA and graphene-based nanomaterials (GFNs) was examined individually and in combinations. Both pristine TBBPA and GFNs showed dose-dependent toxicity. While lower TBBPA concentrations exacerbated toxicity in binary mixtures, higher TBBPA levels reduced the toxic effects compared to pristine TBBPA treatments. The principal mechanism underlying toxicity was ROS generation, resulting in membrane damage and perturbation of photosynthetic parameters. Cluster heatmap and Pearson correlation were employed to assess correlations between the biological parameters. Finally, ecological risk assessment was undertaken to evaluate environmental impacts of the individual components and the mixture in the algae.

The UV-A Receptor CRY-DASH1 Up- and Downregulates Proteins Involved in Different Plastidial Pathways

Algae encode up to five different types of cryptochrome photoreceptors. So far, relatively little is known about the biological functions of the DASH (Drosophila, Arabidopsis, Synechocystis and Homo)-type cryptochromes. The green alga Chlamydomonas reinhardtii encodes two of them. CRY-DASH1 also called DCRY1 has its maximal absorption peak in the UV-A range. It is localized in the chloroplast and plays an important role in balancing the photosynthetic machinery. Here, we performed a comparative analysis of chloroplast proteins from wild type and a knockout mutant of CRY-DASH1 named cry-dash1mut, using label-free quantitative proteomics as well as immunoblotting. Our results show upregulation of enzymes involved in specific pathways in the mutant including key enzymes of chlorophyll and carotenoid biosynthesis consistent with increased levels of photosynthetic pigments in cry-dash1mut. There is also an increase in certain redox as well as photosystem I and II proteins, including D1. Strikingly, CRY-DASH1 is coregulated in a D1 deletion mutant, where its amount is increased. In contrast, key proteins of the central carbon metabolism, including glycolysis/gluconeogenesis, dark fermentation and the oxidative pentose phosphate pathway are downregulated in cry-dash1mut. Similarly, enzymes of histidine biosynthesis are downregulated in cry-dash1mut leading to a reduction in the amount of free histidine. Yet, transcripts encoding for several of these proteins are at a similar level in the wild type and cry-dash1mut or even opposite. We show that CRY-DASH1 can bind to RNA, taking the psbA RNA encoding D1 as target. These data suggest that CRY-DASH1 regulates plastidial metabolic pathways at the posttranscriptional level.

EPS-corona formation on graphene family nanomaterials (GO, rGO and graphene) and its role in mitigating their toxic effects in the marine alga Chlorella sp

GFNs have widespread applications but can harm marine systems due to excessive use and improper disposal. Algae-secreted EPS can mitigate nanomaterial harm, but their impact on GFN toxicity is understudied. Hence, in the present study, we investigated the toxicity of three GFNs, graphene oxide (GO), reduced graphene oxide (rGO), and graphene, in pristine and EPS-adsorbed forms in the marine alga Chlorella sp. At an environmentally relevant concentration of 1 mgL-1, all three GFNs induced considerable oxidative stress and impeded growth and photosynthetic activity of the algae. The order of the toxic potential followed GO > rGO > graphene. The various facets of adsorption of EPS (1:1 mixture of loosely bound, and tightly bound EPS) on GFNs were investigated through microscopy, surface chemical analyses, fluorescence quenching studies, and isotherm and kinetics studies. Amongst the pristine GFNs treated with algal cells, GO was found to exert the maximum negative effects on algal growth. Upon adsorption of EPS over the GFNs, a significant decline in growth inhibition was observed compared to the respective pristine forms which strongly correlated with reduced oxidative stress and enhanced photosynthetic parameters in the cells. The formation of a layer of eco-corona after interaction of GFNs with EPS possibly caused a barrier effect which in turn diminished their toxic potential. The findings from the present investigation offer valuable insights into the environmental toxicity of GFNs and show that the eco-corona formation may lessen the risk posed by these materials in the marine environment.

Combined genomic and transcriptomic analysis reveals the contribution of tandem duplication genes to low-temperature adaptation in perennial ryegrass

Perennial ryegrass (Lolium perenne L.) is an agronomically important cool-season grass species that is widely used as forage for ruminant animal production and cultivated in temperate regions for the establishment of lawns. However, the underlying genetic mechanism of the response of L. perenne to low temperature is still unclear. In the present study, we performed a comprehensive study and identified 3,770 tandem duplication genes (TDGs) in L. perenne, and evolutionary analysis revealed that L. perenne might have undergone a duplication event approximately 7.69 Mya. GO and KEGG pathway functional analyses revealed that these TDGs were mainly enriched in photosynthesis, hormone-mediated signaling pathways and responses to various stresses, suggesting that TDGs contribute to the environmental adaptability of L. perenne. In addition, the expression profile analysis revealed that the expression levels of TDGs were highly conserved and significantly lower than those of all genes in different tissues, while the frequency of differentially expressed genes (DEGs) from TDGs was much higher than that of DEGs from all genes in response to low-temperature stress. Finally, in-depth analysis of the important and expanded gene family indicated that the members of the ELIP subfamily could rapidly respond to low temperature and persistently maintain higher expression levels during all low temperature stress time points, suggesting that ELIPs most likely mediate low temperature responses and help to facilitate adaptation to low temperature in L. perenne. Our results provide evidence for the genetic underpinning of low-temperature adaptation and valuable resources for practical application and genetic improvement for stress resistance in L. perenne.

Transcriptomic and co-expression network analyses on diverse wheat landraces identifies candidate master regulators of the response to early drought

Introduction

Over four billion people around the world rely on bread wheat (Triticum aestivum L.) as a major constituent of their diet. The changing climate, however, threatens the food security of these people, with periods of intense drought stress already causing widespread wheat yield losses. Much of the research into the wheat drought response has centred on the response to drought events later in development, during anthesis or grain filling. But as the timing of periods of drought stress become increasingly unpredictable, a more complete understanding of the response to drought during early development is also needed.

Methods

Here, we utilized the YoGI landrace panel to identify 10,199 genes which were differentially expressed under early drought stress, before weighted gene co-expression network analysis (WGCNA) was used to construct a co-expression network and identify hub genes in modules particularly associated with the early drought response.

Results

Of these hub genes, two stood out as novel candidate master regulators of the early drought response - one as an activator (TaDHN4-D1; TraesCS5D02G379200) and the other as a repressor (uncharacterised gene; TraesCS3D02G361500).

Discussion

As well as appearing to coordinate the transcriptional early drought response, we propose that these hub genes may be able to regulate the physiological early drought response due to potential control over the expression of members of gene families well-known for their involvement in the drought response in many plant species, namely dehydrins and aquaporins, as well as other genes seemingly involved in key processes such as, stomatal opening, stomatal closing, stomatal morphogenesis and stress hormone signalling.

Adaptive protein evolution through length variation of short tandem repeats in Arabidopsis

Intrinsically disordered protein regions are of high importance for biotic and abiotic stress responses in plants. Tracts of identical amino acids accumulate in these regions and can vary in length over generations because of expansions and retractions of short tandem repeats at the genomic level. However, little attention has been paid to what extent length variation is shaped by natural selection. By environmental association analysis on 2514 length variable tracts in 770 whole-genome sequenced Arabidopsis thaliana, we show that length variation in glutamine and asparagine amino acid homopolymers, as well as in interaction hotspots, correlate with local bioclimatic habitat. We determined experimentally that the promoter activity of a light-stress gene depended on polyglutamine length variants in a disordered transcription factor. Our results show that length variations affect protein function and are likely adaptive. Length variants modulating protein function at a global genomic scale has implications for understanding protein evolution and eco-evolutionary biology.

Foliar application of putrescine, salicylic acid, and ascorbic acid mitigates frost stress damage in Vitis vinifera cv. ̒Giziluzum̕

BACKGROUND

Cold stress is an effective factor in reducing production and injuring fruit trees. Various materials, such as salicylic acid, ascorbic acid, and putrescine, are used to alleviate the damage of abiotic stress.

RESULTS

The effect of different treatments of putrescine, salicylic acid, and ascorbic acid on alleviating the damage of frost stress (- 3 °C) to grapes 'Giziluzum' was investigated. Frost stress increased the amount of H₂O₂, MDA, proline, and MSI. On the other hand, it decreased the concentration of chlorophyll and carotenoids in the leaves. Putrescine, salicylic acid and ascorbic acid significantly increased the activities of catalase, guaiacol peroxidase, ascorbate peroxidase, and superoxide dismutase under frost stress. Following frost stress, the grapes treated with putrescine, salicylic acid, and ascorbic acid showed higher levels of DHA, AsA, and AsA/DHA than the untreated grapes. Our results showed that the treatment with ascorbic acid outperformed the other treatments in adjusting frost stress damages.

CONCLUSION

The use of compounds, such as ascorbic ac id, salicylic acid, and putrescine, modulates the effects of frost stress, thereby increasing the antioxidant defense system of cells, reducing its damage, and stabilizing stable cell conditions, so it can be used to reduce frost damage to different grape cultivars.

LHC-like Proteins: The Guardians of Photosynthesis

The emergence of chlorophyll-containing light-harvesting complexes (LHCs) was a crucial milestone in the evolution of photosynthetic eukaryotic organisms. Light-harvesting chlorophyll-binding proteins form complexes in proximity to the reaction centres of photosystems I and II and serve as an antenna, funnelling the harvested light energy towards the reaction centres, facilitating photochemical quenching, thereby optimizing photosynthesis. It is now generally accepted that the LHC proteins evolved from LHC-like proteins, a diverse family of proteins containing up to four transmembrane helices. Interestingly, LHC-like proteins do not participate in light harvesting to elevate photosynthesis activity under low light. Instead, they protect the photosystems by dissipating excess energy and taking part in non-photochemical quenching processes. Although there is evidence that LHC-like proteins are crucial factors of photoprotection, the roles of only a few of them, mainly the stress-related psbS and lhcSR, are well described. Here, we summarize the knowledge gained regarding the evolution and function of the various LHC-like proteins, with emphasis on those strongly related to photoprotection. We further suggest LHC-like proteins as candidates for improving photosynthesis in significant food crops and discuss future directions in their research.

Reactivation of the Photosynthetic Apparatus of Resurrection Plant Haberlea rhodopensis during the Early Phase of Recovery from Drought- and Freezing-Induced Desiccation

Haberlea rhodopensis is a unique desiccation-tolerant angiosperm that also survives winter frost. As, upon freezing temperatures, H. rhodopensis desiccates, the taxon is proposed to survive low temperature stress using its desiccation tolerance mechanisms. To reveal the validity of this hypothesis, we analyzed the structural alterations and organization of photosynthetic apparatus during the first hours of recovery after drought- and freezing-induced desiccation. The dynamics of the ultrastructure remodeling in the mesophyll cells and the restoration of the thylakoid membranes shared similarities independent of the reason for desiccation. Among the most obvious changes in thylakoid complexes, the proportion of the PSI-LHCII complex strongly increased around 70% relative water content (RWC), whereas the proportion of Lhc monomers decreased from the beginning of rehydration. We identified enhanced levels of cyt b₆f complex proteins that contributed to the enhanced electron flow. The high abundance of proteins related to excitation energy dissipation, PsbS, Lhcb5, Lhcb6 and ELIPs, together with the increased content of dehydrins contributed to the preservation of cellular integrity. ELIP expression was maintained at high levels up to 9 h into recovery. Although the recovery processes from drought- and freezing-induced desiccation were found to be similar in progress and time scale, slight variations indicate that they are not identical.

Physiological and transcription level responses of microalgae Auxenochlorella protothecoides to cold and heat induced oxidative stress

Temperature is a crucial factor affecting microalgae CO₂ capture and utilization. However, an in-depth understanding of how microalgae respond to temperature stress is still unclear. In particular, the regulation mechanism under opposite temperature (heat and cold) stress had not yet been reported. In this study, the physicochemical properties and transcription level of related genes of microalgae Auxenochlorella protothecoides UTEX 2341 under heat and cold stress were investigated. Heat stress (Hs) caused a drastic increase of reactive oxygen species (ROS) in UTEX 2341. As key elements responded to Hs, superoxide dismutase (SOD) enzyme increased by 150%, 70%, and 30% in activity, and nitric oxide (NO) grew by 409.6%, 212.5%, and 990.4% in content compared with the control at 48 h, 96 h, 168 h. Under cold stress (Cs), ROS increased in the early stage and decreased in the later stage. As key factors responded to Cs, proline (Pro) increased respectively by 285%, 383%, and 81% in content, and heat shock transcriptional factor HSFA1d increased respectively by 161%, 71%, and 204% in transcript level compared with the control at 48 h, 96 h, 168 h. Furthermore, the transcript level of antioxidant enzymes or antioxidant coding genes was consistent with the changing trend of enzymes activity or antioxidant content. Notably, both glutathione (GSH) and heat shock protein 97 (hsp 97) were up-regulated in response to Hs and Cs. In conclusion, GSH and hsp 97 were the core elements of UTEX 2341 in response to both Hs and Cs. SOD and NO were the key elements that responded to Hs, while proline and HSFA1d were the key elements that responded to Cs. This study provided a basis for the understanding of the response mechanism of microalgae under temperature stress and the improvement of the microalgae tolerance to temperature stress.

Rapeseed (Brassica napus) Mitogen-Activated Protein Kinase 1 Enhances Shading Tolerance by Regulating the Photosynthesis Capability of Photosystem II

Rapeseed (Brassica napus) is the third-largest source of vegetable oil in the world with an edible, medicinal, and ornamental value. However, insufficient light or high planting density directly affects its growth, development, yield, and quality. Mitogen-activated protein kinases (MAPKs) are serine/threonine protein kinases that play key roles in regulating the responses to biotic and abiotic stresses in plants. In this study, we found that the promoter of BnaMAPK1 contained several light-responsive elements (including the AT1-motif, G-Box, and TCT-motif), consistent with its shading stress-induced upregulation. Compared with the wild type under shading stress, BnaMAPK1-overexpressing plants showed higher light capture efficiency and carbon assimilation capacity, enhancing their shading tolerance. Using RNA sequencing, we systematically investigated the function of BnaMAPK1 in shading stress on photosynthetic structure, Calvin cycle, and light-driven electron transport. Notably, numerous genes encoding light-harvesting chlorophyll a/b-binding proteins (BnaLHCBs) in photosystem II-light-harvesting complex (LHC) II supercomplex were significantly downregulated in the BnaMAPK1-overexpressing lines relative to the wild type under shading stress. Combining RNA sequencing and yeast library screening, a candidate interaction partner of BnaMAPK1 regulating in shading stress, BnaLHCB3, was obtained. Moreover, yeast two-hybrid and split-luciferase complementation assays confirmed the physical interaction relationship between BnaLHCB3 and BnaMAPK1, suggesting that BnaMAPK1 may involve in stabilizing the photosystem II-LHC II supercomplex. Taken together, our results demonstrate that BnaMAPK1 positively regulates photosynthesis capability to respond to shading stress in rapeseed, possibly by controlling antenna proteins complex in photosystem II, and could provide valuable information for further breeding for rapeseed stress tolerance.

Systems biology of resurrection plants

Plant species that exhibit vegetative desiccation tolerance can survive extreme desiccation for months and resume normal physiological activities upon re-watering. Here we survey the recent knowledge gathered from the sequenced genomes of angiosperm and non-angiosperm desiccation-tolerant plants (resurrection plants) and highlight some distinct genes and gene families that are central to the desiccation response. Furthermore, we review the vast amount of data accumulated from analyses of transcriptomes and metabolomes of resurrection species exposed to desiccation and subsequent rehydration, which allows us to build a systems biology view on the molecular and genetic mechanisms of desiccation tolerance in plants.

Study of Triticum aestivum Resistome in Response to Wheat dwarf India Virus Infection

Susceptible and resistant germplasm respond differently to pathogenic attack, including virus infections. We compared the transcriptome changes between a resistant wheat cultivar, Sonalika, and a susceptible cultivar, WL711, to understand this process in wheat against wheat dwarf India virus (WDIV) infection. A total of 2760 and 1853 genes were differentially expressed in virus-infected and mock-inoculated Sonalika, respectively, compared to WL711. The overrepresentation of genes involved in signaling, hormone metabolism, enzymes, secondary metabolites, proteolysis, and transcription factors was documented, including the overexpression of multiple PR proteins. We hypothesize that the virus resistance in Sonalika is likely due to strong intracellular surveillance via the action of multiple PR proteins (PR1, RAR1, and RPM1) and ChiB. Other genes such as PIP1, LIP1, DnaJ, defensins, oxalate oxidase, ankyrin repeat protein, serine-threonine kinase, SR proteins, beta-1,3-glucanases, and O-methyltransferases had a significant differential expression and play roles in stress tolerance, may also be contributing towards the virus resistance in Sonalika. In addition, we identified putative genes with unknown functions, which are only expressed in response to WDIV infection in Sonalika. The role of these genes could be further validated and utilized in engineering resistance in wheat and other crops.

Novel Transcriptome Study and Detection of Metabolic Variations in UV-B-Treated Date Palm (Phoenix dactylifera cv. Khalas)

Date palm (Phoenix dactylifera) is one of the most widespread fruit crop species and can tolerate drastic environmental conditions that may not be suitable for other fruit species. Excess UV-B stress is one of the greatest concerns for date palm trees and can cause genotoxic effects. Date palm responds to UV-B irradiation through increased DEG expression levels and elaborates upon regulatory metabolic mechanisms that assist the plants in adjusting to this exertion. Sixty-day-old Khalas date palm seedlings (first true-leaf stage) were treated with UV-B (wavelength, 253.7 nm; intensity, 75 μW cm-2 for 72 h (16 h of UV light and 8 h of darkness). Transcriptome analysis revealed 10,249 and 12,426 genes whose expressions were upregulated and downregulated, respectively, compared to the genes in the control. Furthermore, the differentially expressed genes included transcription factor-encoding genes and chloroplast- and photosystem-related genes. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) was used to detect metabolite variations. Fifty metabolites, including amino acids and flavonoids, showed changes in levels after UV-B excess. Amino acid metabolism was changed by UV-B irradiation, and some amino acids interacted with precursors of different pathways that were used to synthesize secondary metabolites, i.e., flavonoids and phenylpropanoids. The metabolite content response to UV-B irradiation according to hierarchical clustering analysis showed changes in amino acids and flavonoids compared with those of the control. Amino acids might increase the function of scavengers of reactive oxygen species by synthesizing flavonoids that increase in response to UV-B treatment. This study enriches the annotated date palm unigene sequences and enhances the understanding of the mechanisms underlying UV-B stress through genetic manipulation. Moreover, this study provides a sequence resource for genetic, genomic and metabolic studies of date palm.

Effect of cold stress on polyamine metabolism and antioxidant responses in chickpea

Metabolic and genomic characteristics of polyamines (PAs) may be associated with the induction of cold tolerance (CT) responses in plants. Characteristics of PAs encoding genes in chickpea (Cicer arietinum L.) and their function under cold stress (CS) are currently unknown. In this study, the potential role of PAs along with the antioxidative defense systems were assessed in two chickpea genotypes (Sel96th11439, cold-tolerant and ILC533, cold-sensitive) under CS conditions. Six days after exposure to CS, the leaf H₂O₂ content and electrolyte leakage index increased in the sensitive genotype by 47.7 and 59 %, respectively, while these values decreased or remained unchanged, respectively, in the tolerant genotype. In tolerant genotype, the enhanced activity of superoxide dismutase (SOD) (by 50 %) was accompanied by unchanged activities of ascorbate peroxidase (APX), guaiacol peroxidase (GPX) and catalase (CAT) as well as the accumulation of glutathione (GSH) (by 43 %) on the sixth day of CS. Higher levels of putrescine (Put) (322 %), spermidine (Spd) (45 %), spermine (Spm) (69 %) and the highest ratio of Put/(Spd + Spm) were observed in tolerant genotype compared to the sensitive one on the sixth day of CS. Gamma-aminobutyric acid (GABA) accumulation was 74 % higher in tolerant genotype compared to the sensitive one on the sixth day of CS. During CS, the activity of diamine oxidase (DAO) and polyamine oxidase (PAO) increased in tolerant (by 3.02- and 2.46-fold) and sensitive (by 2.51- and 2.8-fold) genotypes, respectively, in comparison with the respective non-stressed plants (normal conditions). The highest activity of DAO and PAO in the tolerant genotype was accompanied by PAs decomposition and a peak in GABA content on the sixth day of CS. The analysis of chickpea genome revealed the presence of five PAs biosynthetic genes, their chromosomal locations, and cis-regulatory elements. A significant increase in transcript levels of arginine decarboxylase (ADC) (24.26- and 7.96-fold), spermidine synthase 1 (SPDS1) (3.03- and 1.53-fold), SPDS2 (5.5- and 1.62-fold) and spermine synthase (SPMS) (3.92- and 1.65-fold) genes was detected in tolerant and sensitive genotypes, respectively, whereas the expression of ornithine decarboxylase (ODC) genes decreased significantly under CS conditions in both genotypes. Leaf chlorophyll and carotenoid contents exhibited declining trends in the sensitive genotype, while these photosynthetic pigments were stable in the tolerant genotype due to the superior performance of defensive processes under CS conditions. Overall, these results suggested the specific roles of putative PAs genes and PAs metabolism in development of effective CT responses in chickpea.