Sequence analysis of the Hsp70 family in moss and evaluation of their functions in abiotic stress responses

Genomics of ecological adaptation in Canary Island Descurainia (Brassicaceae) and comparisons with other Brassicaceae

Oceanic archipelagos provide striking examples of lineages that have radiated over pronounced ecological gradients. Accompanying this diversification, lineages have evolved adaptations allowing survival in extreme environments. Here, we investigate the genomic basis of ecological adaptation in Canary Island Descurainia (Brassicaceae), an island relative of Arabidopsis. The seven endemic species have diversified in situ along an elevational and ecological gradient, from low-elevation scrub to high-elevation sub-alpine desert. We first generated a reference genome for Descurainia millefolia, phylogenetic analysis of which placed it as sister to D. sophioides. Ninety-six gene families were found to be specific to D. millefolia and a further 1087 and 1469 gene families have expanded or contracted in size, respectively, along the D. millefolia branch. We then employed genome re-sequencing to sample 14 genomes across the seven species of Canary Island Descurainia and an outgroup. Phylogenomic analyses were consistent with previous reconstructions of Canary Island Descurainia in resolving low- and high-elevation clades. Using the branch-site dN/dS method, we detected positive selection for 275 genes on the branch separating the low- and high-elevation species and these positively selected genes (PSGs) were significantly enriched for functions related to reproduction and stress tolerance. Comparing PSGs to those in analyses of adaptation to elevation and/or latitude in other Brassicaceae, we found little evidence of widespread convergence and gene reuse, except for two examples, one of which was a significant overlap between Descurainia and Draba nivalis, a species restricted to high latitudes. The study of Canary Island Descurainia suggests that the transition to high-elevation environments such as that found in the high mountains of the Canary Islands involves selection on genes related to reproduction and stress tolerance but that repeated evolution across different lineages that have evolved into similar habitats is limited, indicating substantially different molecular trajectories to adaptation.

Unraveling the genetic and molecular basis of heat stress in cotton

Human activities and climate change have resulted in frequent and intense weather fluctuations, leading to diverse abiotic stresses on crops which hampers greatly their metabolic activities. Heat stress, a prevalent abiotic factor, significantly influences cotton plant biological activities resulting in reducing yield and production. We must deepen our understanding of how plants respond to heat stress across various dimensions, encompassing genes, RNAs, proteins, metabolites for effective cotton breeding. Multi-omics methods, primarily genomics, transcriptomics, proteomics, metabolomics, and phenomics, proves instrumental in studying cotton's responses to abiotic stresses. Integrating genomics, transcriptomics, proteomics, and metabolomic is imperative for our better understanding regarding genetics and molecular basis of heat tolerance in cotton. The current review explores fundamental omics techniques, covering genomics, transcriptomics, proteomics, and metabolomics, to highlight the progress made in cotton omics research.

Origin, evolution, and diversification of inositol 1,4,5-trisphosphate 3-kinases in plants and animals

BACKGROUND

In Eukaryotes, inositol polyphosphates (InsPs) represent a large family of secondary messengers and play crucial roes in various cellular processes. InsPs are synthesized through a series of pohophorylation reactions catalyzed by various InsP kinases in a sequential manner. Inositol 1,4,5-trisphosphate 3-kinase (IP3 3-kinase/IP3K), one member of InsP kinase, plays important regulation roles in InsPs metabolism by specifically phosphorylating inositol 1,4,5-trisphosphate (IP3) to inositol 1,3,4,5-tetrakisphosphate (IP4) in animal cells. IP3Ks were widespread in fungi, plants and animals. However, its evolutionary history and patterns have not been examined systematically.

RESULTS

A total of 104 and 31 IP3K orthologues were identified across 57 plant genomes and 13 animal genomes, respectively. Phylogenetic analyses indicate that IP3K originated in the common ancestor before the divergence of fungi, plants and animals. In most plants and animals, IP3K maintained low-copy numbers suggesting functional conservation during plant and animal evolution. In Brassicaceae and vertebrate, IP3K underwent one and two duplication events, respectively, resulting in multiple gene copies. Whole-genome duplication (WGD) was the main mechanism for IP3K duplications, and the IP3K duplicates have experienced functional divergence. Finally, a hypothetical evolutionary model for the IP3K proteins is proposed based on phylogenetic theory.

CONCLUSION

Our study reveals the evolutionary history of IP3K proteins and guides the future functions of animal, plant, and fungal IP3K proteins.

Systematic analysis of Heat Shock Protein 70 (HSP70) gene family in radish and potential roles in stress tolerance

The 70 kD heat shock proteins (HSP70s) represent a class of molecular chaperones that are widely distributed in all kingdoms of life, which play important biological roles in plant growth, development, and stress resistance. However, this family has not been systematically characterized in radish (Raphanus sativus L.). In this study, we identified 34 RsHSP70 genes unevenly distributed within nine chromosomes of R. sativus. Phylogenetic and multiple sequence alignment analyses classified the RsHSP70 proteins into six distinct groups (Group A-F). The characteristics of gene structures, motif distributions, and corresponding cellular compartments were more similar in closely linked groups. Duplication analysis revealed that segmental duplication was the major driving force for the expansion of RsHSP70s in radish, particularly in Group C. Synteny analysis identified eight paralogs (Rs-Rs) in the radish genome and 19 orthologs (Rs-At) between radish and Arabidopsis, and 23 orthologs (Rs-Br) between radish and Chinese cabbage. RNA-seq analysis showed that the expression change of some RsHSP70s were related to responses to heat, drought, cadmium, chilling, and salt stresses and Plasmodiophora brassicae infection, and the expression patterns of these RsHSP70s were significantly different among 14 tissues. Furthermore, we targeted a candidate gene, RsHSP70-23, the product of which is localized in the cytoplasm and involved in the responses to certain abiotic stresses and P. brassicae infection. These findings provide a reference for further molecular studies to improve yield and stress tolerance of radish.

Combined transcriptomics and metabolomics analysis reveals the molecular mechanism of heat tolerance of Le023M, a mutant in Lentinulaedodes

Lentinula edodes, one of the most highly regarded edible mushrooms in China, is susceptible to damage from high temperatures. However, a mutant strain derived from L. edodes, known as Le023M, has shown exceptional thermotolerance. Compared to the original strain Le023, Le023M exhibited accelerated mycelial recovery following heat stress. Through RNA-seq analysis, the majority of differentially expressed genes (DEGs) were found to be associated with functions such as "protein refolding", "protein unfolding", "protein folding", and "response to heat", all of which are closely linked to heat shock proteins. Furthermore, qRT-PCR results revealed significant accumulation of heat shock-related genes in Le023M under heat stress. GC-MS analysis indicated elevated levels of trehalose, aspartate, and glutamate in Le023M when subjected to heat stress. The highly expressed genes involved in these metabolic pathways were predominantly found in Le023M. Collectively, these findings highlight the following: (i) the crucial role of heat shock proteins (HSPs) in the thermo-resistant mechanisms of Le023M; (ii) the potential of trehalose accumulation in Le023M to enhance mycelium resistance to heat stress; and (iii) the induction of aspartate and glutamate accumulation in response to heat stress. These results shed light on the molecular mechanisms underlying the thermotolerance of Le023M, providing valuable insights for further understanding and improving heat stress response in L. edodes. The findings also highlight the potential applications of Le023M in the cultivation and production of L. edodes under high-temperature conditions.

Membrane Fluidization Governs the Coordinated Heat-Inducible Expression of Nucleus- and Plastid Genome-Encoded Heat Shock Protein 70 Genes in the Marine Red Alga Neopyropia yezoensis

Heat shock protein 70 (HSP70) is an evolutionarily conserved protein chaperone in prokaryotic and eukaryotic organisms. This family is involved in the maintenance of physiological homeostasis by ensuring the proper folding and refolding of proteins. The HSP70 family in terrestrial plants can be divided into cytoplasm, endoplasmic reticulum (ER)-, mitochondrion (MT)-, and chloroplast (CP)-localized HSP70 subfamilies. In the marine red alga Neopyropia yezoensis, the heat-inducible expression of two cytoplasmic HSP70 genes has been characterized; however, little is known about the presence of other HSP70 subfamilies and their expression profiles under heat stress conditions. Here, we identified genes encoding one MT and two ER HSP70 proteins and confirmed their heat-inducible expression at 25 °C. In addition, we determined that membrane fluidization directs gene expression for the ER-, MT-, and CP-localized HSP70 proteins as with cytoplasmic HSP70s. The gene for the CP-localized HSP70 is carried by the chloroplast genome; thus, our results indicate that membrane fluidization is a trigger for the coordinated heat-driven induction of HSP70 genes harbored by the nuclear and plastid genomes in N. yezoensis. We propose this mechanism as a unique regulatory system common in the Bangiales, in which the CP-localized HSP70 is usually encoded in the chloroplast genome.

HY5-HDA9 orchestrates the transcription of HsfA2 to modulate salt stress response in Arabidopsis

Integration of light signaling and diverse abiotic stress responses contribute to plant survival in a changing environment. Some reports have indicated that light signals contribute a plant's ability to deal with heat, cold, and stress. However, the molecular link between light signaling and the salt-response pathways remains unclear. We demonstrate here that increasing light intensity elevates the salt stress tolerance of plants. Depletion of HY5, a key component of light signaling, causes Arabidopsis thaliana to become salinity sensitive. Interestingly, the small heat shock protein (sHsp) family genes are upregulated in hy5-215 mutant plants, and HsfA2 is commonly involved in the regulation of these sHsps. We found that HY5 directly binds to the G-box motifs in the HsfA2 promoter, with the cooperation of HISTONE DEACETYLASE 9 (HDA9), to repress its expression. Furthermore, the accumulation of HDA9 and the interaction between HY5 and HDA9 are significantly enhanced by salt stress. On the contrary, high temperature triggers HY5 and HDA9 degradation, which leads to dissociation of HY5-HDA9 from the HsfA2 promoter, thereby reducing salt tolerance. Under salt and heat stress conditions, fine tuning of protein accumulation and an interaction between HY5 and HDA9 regulate HsfA2 expression. This implies that HY5, HDA9, and HsfA2 play important roles in the integration of light signaling with salt stress and heat shock response.

Evolutionary analysis and expression profiling of the HSP70 gene family in response to abiotic stresses in tomato (Solanum lycopersicum)

Heat shock protein 70 (HSP70) genes play essential roles in guarding plants against abiotic stresses, including heat, drought, and salt. In this study, the SlHSP70 gene family in tomatoes has been characterized using bioinformatic tools. 25 putative SlHSP70 genes in the tomato genome were found and classified into five subfamilies, with multi-subcellular localizations. Twelve pairs of gene duplications were identified, and segmental events were determined as the main factor for the gene family expansion. Based on public RNA-seq data, gene expression analysis identified the majority of genes expressed in the examined organelles. Further RNA-seq analysis and then quantitative RT-PCR validation showed that many SlHSP70 members are responsible for cellular feedback to heat, drought, and salt treatments, in which, at least five genes might be potential key players in the stress response. Our results provided a thorough overview of the SlHSP70 gene family in the tomato, which may be useful for the evolutionary and functional analysis of SlHSP70 under abiotic stress conditions.

A plastid-targeted heat shock cognate 70-kDa protein confers osmotic stress tolerance by enhancing ROS scavenging capability

Osmotic stress severely affects plant growth and development, resulting in massive loss of crop quality and quantity worldwide. The 70-kDa heat shock proteins (HSP70s) are highly conserved molecular chaperones that play essential roles in cellular processes including abiotic stress responses. However, whether and how plastid-targeted heat shock cognate 70 kDa protein (cpHSC70-1) participates in plant osmotic stress response remain elusive. Here, we report that the expression of cpHSC70-1 is significantly induced upon osmotic stress treatment. Phenotypic analyses reveal that the plants with cpHSC70-1 deficiency are sensitive to osmotic stress and the plants overexpressing cpHSC70-1 exhibit enhanced tolerance to osmotic stress. Consistently, the expression of the stress-responsive genes is lower in cphsc70-1 mutant but higher in 35S:: cpHSC70-1 lines than that in wild-type plants when challenged with osmotic stress. Further, the cphsc70-1 plants have less APX and SOD activity, and thus more ROS accumulation than the wild type when treated with mannitol, but the opposite is observed in the overexpression lines. Overall, our data reveal that cpHSC70-1 is induced and functions positively in plant response to osmotic stress by promoting the expression of the stress-responsive genes and reducing ROS accumulation.

Ethanol treatment enhances drought stress avoidance in cassava (Manihot esculenta Crantz)

External application of ethanol enhances tolerance to high salinity, drought, and heat stress in various plant species. However, the effects of ethanol application on increased drought tolerance in woody plants, such as the tropical crop "cassava," remain unknown. In the present study, we analyzed the morphological, physiological, and molecular responses of cassava plants subjected to ethanol pretreatment and subsequent drought stress treatment. Ethanol pretreatment induced a slight accumulation of abscisic acid (ABA) and stomatal closure, resulting in a reduced transpiration rate, higher water content in the leaves during drought stress treatment and the starch accumulation in leaves. Transcriptomic analysis revealed that ethanol pretreatment upregulated the expression of ABA signaling-related genes, such as PP2Cs and AITRs, and stress response and protein-folding-related genes, such as heat shock proteins (HSPs). In addition, the upregulation of drought-inducible genes during drought treatment was delayed in ethanol-pretreated plants compared with that in water-pretreated control plants. These results suggest that ethanol pretreatment induces stomatal closure through activation of the ABA signaling pathway, protein folding-related response by activating the HSP/chaperone network and the changes in sugar and starch metabolism, resulting in increased drought avoidance in plants.

Characterization of Inducible HSP70 Genes in an Antarctic Yeast, Glaciozyma antarctica PI12, in Response to Thermal Stress

The induction of highly conserved heat shock protein 70 (HSP70) is often related to a cellular response due to harmful stress or adverse life conditions. In this study, we determined the expression of Hsp70 genes in the Antarctic yeast, Glaciozyma antarctica, under different several thermal treatments for several exposure periods. The main aims of the present study were (1) to determine if stress-induced Hsp70 could be used to monitor the exposure of the yeast species G. antarctica to various types of thermal stress; (2) to analyze the structures of the G. antarctica HSP70 proteins using comparative modeling; and (3) to evaluate the relationship between the function and structure of HSP70 in G. antarctica. In this study, we managed to amplify and clone 2 Hsp70 genes from G. antarctica named GaHsp70-1 and GaHsp70-2. The cells of G. antarctica expressed significantly inducible Hsp70 genes after the heat and cold shock treatments. Interestingly, GaHsp70-1 showed 2–6-fold higher expression than GaHsp70-2 after the heat and cold exposure. ATP hydrolysis analysis on both G. antarctica HSP70s proved that these psychrophilic chaperones can perform activities in a wide range of temperatures, such as at 37, 25, 15, and 4 °C. The 3D structures of both HSP70s revealed several interesting findings, such as the substitution of a β-sheet to loop in the N-terminal ATPase binding domain and some modest residue substitutions, which gave the proteins the flexibility to function at low temperatures and retain their functional activity at ambient temperatures. In conclusion, both analyzed HSP70s played important roles in the physiological adaptation of G. antarctica.

Proteome analysis reveals a systematic response of cold-acclimated seedlings of an exotic mangrove plant Sonneratia apetala to chilling stress

Low temperature in winter was the most crucial abiotic stress that limits the mangrove afforestation northward. Previous study demonstrated that Sonneratia apetala initially transplanted to high latitude area exhibited a stronger plasticity of cold tolerance. To clarify the underlying mechanism, the physiological and proteomic responses to chilling stress were investigated in S. apetala leaves. Our results found that cold-acclimated seedlings had lower relative electrolyte leakage and MDA content than non-acclimated seedlings. On the contrary, higher chlorophyll content and photosynthetic capacity were observed in cold-acclimated seedlings. With proteomic analyses, the differentially accumulated proteins (DAPs) involved in ROS scavenging, photosynthesis and energy metabolism, carbohydrate metabolism, cofactor biosynthesis, and protein folding were suggested to play important roles in enhancing the cold tolerance of S. apetala. However, the down-regulation DAPs were suggested as a tradeoff between plant growth and chilling response. By the protein-protein interaction analyses, translation elongation factor G, chlorophyll A-B binding protein and ascorbate peroxidase 1 were suggested as the important regulators in cold-acclimated S. apetala seedlings under chilling stress. Based on the above results, a schematic diagram describing the mechanism of cold tolerance of exotic mangrove species S. apetala that was achieved by cold acclimation was presented in this study. SIGNIFICANCE: The major environmental factor limits the mangrove afforestation northward is the low temperature in winter. Previous study reported that Sonneratia apetala grew in high latitude exhibited a higher cold tolerance than that in low latitude, which was suggested as a result of cold acclimation. To further understand "how cold acclimation enhance the cold tolerance in S. apetala", the response of S. apetala subjected to chilling stress with or without cold acclimation was investigated in this study at the physiological and proteomic aspects. Our physiological results showed that S. apetala seedlings treated with cold acclimation exhibited a higher tolerance under chilling stress than that without cold acclimation. By using the comparative proteomic approaches and bioinformatic analyses, various biological processes were suggested to play an important role in enhancing the cold tolerance of S. apetala under chilling stress, such as ROS scavenging, photosynthesis and energy metabolism, carbohydrate metabolism, cofactor biosynthesis, and protein folding. Among these differentially accumulated proteins, translation elongation factor G (eEF-G), chlorophyll A-B binding protein (CAB) and ascorbate peroxidase 1 (APX1) were identified as the hub proteins function in coordinated regulating ROS scavenging, photosynthesis and protein biosynthesis in chloroplast and subsequently enhanced the cold tolerance of S. apetala under chilling stress. Our results provided a further understanding of cold acclimation in improving the cold tolerance in exotic mangrove species S. apetala.

Genome-wide analysis of HSP70 gene superfamily in Pyropia yezoensis (Bangiales, Rhodophyta): identification, characterization and expression profiles in response to dehydration stress

BACKGROUND

Heat shock proteins (HSPs) perform a fundamental role in protecting plants against abiotic stresses. Individual family members have been analyzed in previous studies, but there has not yet been a comprehensive analysis of the HSP70 gene family in Pyropia yezoensis.

RESULTS

We investigated 15 putative HSP70 genes in Py. yezoensis. These genes were classified into two sub-families, denoted as DnaK and Hsp110. In each sub-family, there was relative conservation of the gene structure and motif. Synteny-based analysis indicated that seven and three PyyHSP70 genes were orthologous to HSP70 genes in Pyropia haitanensis and Porphyra umbilicalis, respectively. Most PyyHSP70s showed up-regulated expression under different degrees of dehydration stress. PyyHSP70-1 and PyyHSP70-3 were expressed in higher degrees compared with other PyyHSP70s in dehydration treatments, and then expression degrees somewhat decreased in rehydration treatment. Subcellular localization showed PyyHSP70-1-GFP and PyyHSP70-3-GFP were in the cytoplasm and nucleus/cytoplasm, respectively. Similar expression patterns of paired orthologs in Py. yezoensis and Py. haitanensis suggest important roles for HSP70s in intertidal environmental adaptation during evolution.

CONCLUSIONS

These findings provide insight into the evolution and modification of the PyyHSP70 gene family and will help to determine the functions of the HSP70 genes in Py. yezoensis growth and development.

Heat stress in Marchantia polymorpha: Sensing and mechanisms underlying a dynamic response

Sensing and response to high temperatures are crucial to prevent heat-related damage and to preserve cellular and metabolic functions. The response to heat stress is a complex and coordinated process that involves several subcellular compartments and multi-level regulatory networks that are synchronized to avoid cell damage while maintaining cellular homeostasis. In this review, we provide an insight into the most recent advances in elucidating the molecular mechanisms involved in heat stress sensing and response in Marchantia polymorpha. Based on the signaling pathways and genes that were identified in Marchantia, our analyses indicate that although with specific particularities, the core components of the heat stress response seem conserved in bryophytes and angiosperms. Liverworts not only constitute a powerful tool to study heat stress response and signaling pathways during plant evolution, but also provide key and simple mechanisms to cope with extreme temperatures. Given the increasing prevalence of high temperatures around the world as a result of global warming, this knowledge provides a new set of molecular tools with potential agronomical applications.

Genome-wide identification of heat shock factors and heat shock proteins in response to UV and high intensity light stress in lettuce

BACKGROUND

Heat shock factors (Hsfs) and Heat shock proteins (Hsps) belong to an essential group of molecular regulators involved in controlling cellular processes under normal and stress conditions. The role of Hsfs and Hsps is well known in model plant species under diverse stress conditions. While plants Hsfs are vital components of the signal transduction response to maintain cellular homeostasis, Hsps function as chaperones helping to maintain folding of damaged and newly formed proteins during stress conditions. In lettuce (Lactuca sativa), a highly consumed vegetable crop grown in the field and in hydroponic systems, the role of these gene families in response to artificial light is not well characterized.

RESULTS

Using a genome-wide analysis approach, we identified 32 Hsfs and 22 small heat shock proteins (LsHsps) in lettuce, some of which do not have orthologs in Arabidopsis, poplar, and rice. LsHsp60s, LsHsp90s, and LsHsp100s are highly conserved among dicot and monocot species. Surprisingly, LsHsp70s have three times more members than Arabidopsis and two times more than rice. Interestingly, the lettuce genome triplication did not contribute to the increased number of LsHsp70s genes. The large number of LsHsp70s was the result of genome tandem duplication. Chromosomal distribution analysis shows larger tandem repeats of LsHsp70s genes in Chr1, Chr7, Chr8, and Chr9. At the transcriptional level, some genes of the LsHsfs, LsHsps, LsHsp60s, and LsHsp70s families were highly responsive to UV and high intensity light stress, in contrast to LsHsp90s and LsHsp100s which did not respond to a light stimulus.

CONCLUSIONS

Our genome-wide analysis provides a detailed identification of Hsfs and Hsps in lettuce. Chromosomal location and syntenic region analysis together with our transcriptional analysis under different light conditions provide candidate genes for breeding programs aiming to produce lettuce varieties able to grow healthy under hydroponic systems that use artificial light.

Genome-wide analysis of Hsp70 and Hsp100 gene families in Ziziphus jujuba

The Ziziphus species are naturally tolerant to a range of abiotic stresses. Therefore, it is expected that they are an enriched source of genes conferring stress tolerance. Heat shock proteins (Hsps) play a significant role in plants in imparting tolerance against abiotic stress conditions. To get an insight into potential Hsp function in Ziziphus, we performed a genome-wide analysis and expression study of Hsp70 and Hsp100 gene families in Ziziphus jujuba. We identified 21 and 6 genes of the ZjHsp70 and ZjHsp100 families, respectively. Physiochemical properties, chromosomal location, gene structure, motifs, and protein domain organization were analysed for structural and functional characterization. We identified the contribution of tandem and segmental gene duplications in expansions of ZjHsp70s and ZjHsp100s in Z. jujuba. Promoter analysis suggested that ZjHsp70s and ZjHsp100s perform diverse functions related to abiotic stress. Furthermore, expression analyses revealed that most of the Z. jujuba Hsp genes are differentially expressed in response to heat, drought, and salinity stress. Our analyses suggested ZjHsp70-3, ZjHsp70-5, ZjHsp70-6, ZjHsp70-16, ZjHsp70-17, ZjHsp70-20, ZjHsp100-1, ZjHsp100-2, and ZjHsp100-3 are potential candidates for further functional analysis and with regard to breeding new more resilient strains. The present analysis laid the foundation for understanding the molecular mechanism of Hsps70 and Hsp100 gene families regulating abiotic stress tolerance in Z. jujuba.

Comparative proteomic analysis reveals that the Heterosis of two maize hybrids is related to enhancement of stress response and photosynthesis respectively

BACKGROUND

Heterosis refers to superior traits exhibiting in a hybrid when compared with both parents. Generally, the hybridization between parents can change the expression pattern of some proteins such as non-additive proteins (NAPs) which might lead to heterosis. 'Zhongdan808' (ZD808) and 'Zhongdan909' (ZD909) are excellent maize hybrids in China, however, the heterosis mechanism of them are not clear. Proteomics has been wildly used in many filed, and comparative proteomic analysis of hybrid and its parents is helpful for understanding the mechanism of heterosis in the two maize hybrids.

RESULTS

Over 2000 protein groups were quantitatively identified from second seedling leaves of two hybrids and their parents by label-free quantification. Statistical analysis of total identified proteins, differentially accumulated proteins (DAPs) and NAPs of the two hybrids revealed that both of them were more similar to their female parents. In addition, most of DAPs were up-regulated and most of NAPs were high parent abundance or above-high parent abundance in ZD808, while in ZD909, most of DAPs were down-regulated and most of NAPs were low parent abundance or below-low parent abundance. Pathway enrichment analysis showed that more of stress response-related NAPs in ZD808 were high parent abundance or above-high parent abundance, and most of PS related NAPs in ZD909 were high parent abundance or above-high parent abundance. Finally, four stress response-related proteins and eight proteins related to PS were verified by PRM, ten of them had significant differences between hybrid and midparent value.

CONCLUSIONS

Even though every one of the two hybrids were more similar to its female parent at proteome level, the biological basis of heterosis is different in the two maize hybrids. In comparison with their parents, the excellent agronomic traits of hybrid ZD808 is mainly correlated with the high expression levels of some proteins related to stress responses and metabolic functions, while traits of ZD909 is mainly correlated with high expressed proteins related to photosynthesis. Our proteomics results support previous physiological and morphological research and have provided useful information in understanding the reason of valuable agronomic traits.

FLOURY ENDOSPERM11-2 encodes plastid HSP70-2 involved with the temperature-dependent chalkiness of rice (Oryza sativa L.) grains

The frequent occurrence of chalky rice (Oryza sativa L.) grains becomes a serious problem as a result of climate change. The molecular mechanism underlying chalkiness is largely unknown, however. In this study, the temperature-sensitive floury endosperm11-2 (flo11-2) mutant was isolated from ion beam-irradiated rice of 1116 lines. The flo11-2 mutant showed significantly higher chalkiness than the wild type grown under a mean temperature of 28°C, but similar levels of chalkiness to the wild type grown under a mean temperature of 24°C. Whole-exome sequencing of the flo11-2 mutant showed three causal gene candidates, including Os12g0244100, which encodes the plastid-localized 70-kDa heat shock protein 2 (cpHSP70-2). The cpHSP70-2 of the flo11-2 mutant has an amino acid substitution on the 259th aspartic acid with valine (D259V) in the conserved Motif 5 of the ATPase domain. Transgenic flo11-2 mutants that express the wild-type cpHSP70-2 showed significantly lower chalkiness than the flo11-2 mutant. Moreover, the accumulation level of cpHSP70-2 was negatively correlated with the chalky ratio, indicating that cpHSP70-2 is a causal gene for the chalkiness of the flo11-2 mutant. The intrinsic ATPase activity of recombinant cpHSP70-2 was lower by 23% at V_max for the flo11-2 mutant than for the wild type. The growth of DnaK-defective Escherichia coli cells complemented with DnaK with the D201V mutation (equivalent to the D259V mutation) was severely reduced at 37°C, but not in the wild-type DnaK. The results indicate that the lowered cpHSP70-2 function is involved with the chalkiness of the flo11-2 mutant.

Translocation of Drought-Responsive Proteins from the Chloroplasts

Some chloroplast proteins are known to serve as messengers to transmit retrograde signals from chloroplasts to the nuclei in response to environmental stresses. However, whether particular chloroplast proteins respond to drought stress and serve as messengers for retrograde signal transduction are unclear. Here, we used isobaric tags for relative and absolute quantitation (iTRAQ) to monitor the proteomic changes in tobacco (Nicotiana benthamiana) treated with drought stress/re-watering. We identified 3936 and 1087 differentially accumulated total leaf and chloroplast proteins, respectively, which were grouped into 16 categories. Among these, one particular category of proteins, that includes carbonic anhydrase 1 (CA1), exhibited a great decline in chloroplasts, but a remarkable increase in leaves under drought stress. The subcellular localizations of CA1 proteins from moss (Physcomitrella patens), Arabidopsis thaliana and rice (Oryza sativa) in P. patens protoplasts consistently showed that CA1 proteins gradually diminished within chloroplasts but increasingly accumulated in the cytosol under osmotic stress treatment, suggesting that they could be translocated from chloroplasts to the cytosol and act as a signal messenger from the chloroplast. Our results thus highlight the potential importance of chloroplast proteins in retrograde signaling pathways and provide a set of candidate proteins for further research.

Cold Acclimation Improves the Desiccation Stress Resilience of Polar Strains of Klebsormidium (Streptophyta)

Biological soil crusts (BSCs) are complex communities of autotrophic, heterotrophic, and saprotrophic (micro)organisms. In the polar regions, these biocrust communities have essential ecological functions such as primary production, nitrogen fixation, and ecosystem engineering while coping with extreme environmental conditions (temperature, desiccation, and irradiation). The microalga Klebsormidium is commonly found in BSCs all across the globe. The ecophysiological resilience of various Klebsormidium species to desiccation and other stresses has been studied intensively. Here we present the results of transcriptomic analyses of two different Klebsormidium species, K. dissectum and K. flaccidum, isolated from Antarctic and Arctic BSCs. We performed desiccation stress experiments at two different temperatures mimicking fluctuations associated with global change. Cultures grown on agar plates were desiccated on membrane filters at 10% relative air humidity until the photosynthetic activity as reflected in the effective quantum yield of photosystem II [Y(II)] ceased. For both species, the response to dehydration was much faster at the higher temperature. At the transcriptome level both species responded more strongly to the desiccation stress at the higher temperature suggesting that adaptation to cold conditions enhanced the resilience of both algae to desiccation stress. Interestingly, the two different species responded differently to the applied desiccation stress with respect to the number as well as function of genes showing differential gene expression. The portion of differentially expressed genes shared between both taxa was surprisingly low indicating that both Klebsormidium species adapted independently to the harsh conditions of Antarctica and the Arctic, respectively. Overall, our results indicate that environmental acclimation has a great impact on gene expression and the response to desiccation stress in Klebsormidium.

Different Roles of Heat Shock Proteins (70 kDa) During Abiotic Stresses in Barley (Hordeum vulgare) Genotypes

In this work, the involvement of heat shock proteins (HSP70) in barley (Hordeum vulgare) has been studied in response to drought and salinity. Thus, 3 barley genotypes usually cultivated and/or selected in Italy, 3 Middle East/North Africa landraces and genotypes and 1 improved genotype from ICARDA have been studied to identify those varieties showing the best stress response. Preliminarily, a bioinformatic characterization of the HSP70s protein family in barley has been made by using annotated Arabidopsis protein sequences. This study identified 20 putative HSP70s orthologs in the barley genome. The construction of un-rooted phylogenetic trees showed the partition into four main branches, and multiple subcellular localizations. The enhanced HSP70s presence upon salt and drought stress was investigated by both immunoblotting and expression analyses. It is worth noting the Northern Africa landraces showed peculiar tolerance behavior versus drought and salt stresses. The drought and salinity conditions indicated the involvement of specific HSP70s to counteract abiotic stress. Particularly, the expression of cytosolic MLOC_67581, mitochondrial MLOC_50972, and encoding for HSP70 isoforms showed different expressions and occurrence upon stress. Therefore, genotypes originated in the semi-arid area of the Mediterranean area can represent an important genetic source for the improvement of commonly cultivated high-yielding varieties.

Genome-wide identification and expression analysis of Hsp70, Hsp90, and Hsp100 heat shock protein genes in barley under stress conditions and reproductive development

Abiotic stress including extreme temperature disturbs the plant cellular homeostasis consequently limiting the yield potential of crop plants. Heat shock proteins (Hsps) are part of major rescue machinery of plants which aid to combat these stressed conditions by re-establishing protein homeostasis. Hsps with their chaperone and co-chaperone mechanisms regulate the activity of their substrate proteins in an ATP-dependent manner. In the present investigation, a genome-wide identification, evolutionary relationship, and comprehensive expression analysis of Hsp70, Hsp90, and Hsp100 gene families have been done in barley. The barley genome possesses 13 members of the Hsp70 gene family, along with 4 members of the Hsp110 subfamily, and 6 members of Hsp90 and 8 members of the Hsp100 gene family. Hsp genes are distributed on all 7 chromosomes of barley, and their encoded protein members are predicted to be localized to cell organelles such as cytosol, mitochondria, chloroplast, and ER. Despite a larger genome size, there are lesser members of these Hsp genes in barley, owing to less duplication events. The variable expression pattern obtained for genes encoding proteins localized to the same subcellular compartment suggests their diverse roles and involvement in different cellular responses. Expression profiling of these genes was performed by qRT-PCR in an array of 32 tissues, which showed a differential and tissue-specific expression of various members of Hsp gene families. We found the upregulation of HvHspc70-4, HvHsp70Mt70-2, HvHspc70-5a, HvHspc70-5b, HvHspc70-N1, HvHspc70-N2, HvHsp110-3, HvHsp90-1, HvHsp100-1, and HvHsp100-2 upon exposure to heat stress during reproductive development. Furthermore, their higher expression during heat stress, heavy metal stress, drought, and salinity stress was also observed in a tissue-specific manner.

Acetic Acid Treatment Enhances Drought Avoidance in Cassava (Manihot esculenta Crantz)

The external application of acetic acid has recently been reported to enhance survival of drought in plants such as Arabidopsis, rapeseed, maize, rice, and wheat, but the effects of acetic acid application on increased drought tolerance in woody plants such as a tropical crop "cassava" remain elusive. A molecular understanding of acetic acid-induced drought avoidance in cassava will contribute to the development of technology that can be used to enhance drought tolerance, without resorting to transgenic technology or advancements in cassava cultivation. In the present study, morphological, physiological, and molecular responses to drought were analyzed in cassava after treatment with acetic acid. Results indicated that the acetic acid-treated cassava plants had a higher level of drought avoidance than water-treated, control plants. Specifically, higher leaf relative water content, and chlorophyll and carotenoid levels were observed as soils dried out during the drought treatment. Leaf temperatures in acetic acid-treated cassava plants were higher relative to leaves on plants pretreated with water and an increase of ABA content was observed in leaves of acetic acid-treated plants, suggesting that stomatal conductance and the transpiration rate in leaves of acetic acid-treated plants decreased to maintain relative water contents and to avoid drought. Transcriptome analysis revealed that acetic acid treatment increased the expression of ABA signaling-related genes, such as OPEN STOMATA 1 (OST1) and protein phosphatase 2C; as well as the drought response and tolerance-related genes, such as the outer membrane tryptophan-rich sensory protein (TSPO), and the heat shock proteins. Collectively, the external application of acetic acid enhances drought avoidance in cassava through the upregulation of ABA signaling pathway genes and several stress responses- and tolerance-related genes. These data support the idea that adjustments of the acetic acid application to plants is useful to enhance drought tolerance, to minimize the growth inhibition in the agricultural field.

Identification of Early Salinity Stress-Responsive Proteins in Dunaliella salina by isobaric tags for relative and absolute quantitation (iTRAQ)-Based Quantitative Proteomic Analysis

Salt stress is one of the most serious abiotic factors that inhibit plant growth. Dunaliella salina has been recognized as a model organism for stress response research due to its high capacity to tolerate extreme salt stress. A proteomic approach based on isobaric tags for relative and absolute quantitation (iTRAQ) was used to analyze the proteome of D. salina during early response to salt stress and identify the differentially abundant proteins (DAPs). A total of 141 DAPs were identified in salt-treated samples, including 75 upregulated and 66 downregulated DAPs after 3 and 24 h of salt stress. DAPs were annotated and classified into gene ontology functional groups. The Kyoto Encyclopedia of Genes and Genomes pathway analysis linked DAPs to tricarboxylic acid cycle, photosynthesis and oxidative phosphorylation. Using search tool for the retrieval of interacting genes (STRING) software, regulatory protein⁻protein interaction (PPI) networks of the DAPs containing 33 and 52 nodes were built at each time point, which showed that photosynthesis and ATP synthesis were crucial for the modulation of early salinity-responsive pathways. The corresponding transcript levels of five DAPs were quantified by quantitative real-time polymerase chain reaction (qRT-PCR). These results presented an overview of the systematic molecular response to salt stress. This study revealed a complex regulatory mechanism of early salt tolerance in D. salina and potentially contributes to developing strategies to improve stress resilience.

Thermopriming reprograms metabolic homeostasis to confer heat tolerance

Heat stress threatens agriculture worldwide. Plants acquire heat stress tolerance through priming, which establishes stress memory during mild or severe transient heat stress. Such induced thermotolerance restructures metabolic networks and helps maintain metabolic homeostasis under heat stress. Here, we used an electrospray ionization mass spectrometry-based platform to explore the composition and dynamics of the metabolome of Arabidopsis thaliana under heat stress and identify metabolites involved in thermopriming. Primed plants performed better than non-primed plants under severe heat stress due to altered energy pathways and increased production of branched-chain amino acids, raffinose family oligosaccharides (RFOs), lipolysis products, and tocopherols. These metabolites serve as osmolytes, antioxidants and growth precursors to help plants recover from heat stress, while lipid metabolites help protect membranes against heat stress. The carbohydrate (e.g., sucrose and RFOs) and lipid superpathway metabolites showed the most significant increases. Under heat stress, there appears to be crosstalk between carbohydrate metabolism (i.e., the thermomemory metabolites stachyose, galactinol, and raffinose) and tyrosine metabolism towards the production of the thermomemory metabolite salidroside, a phenylethanoid glycoside. Crosstalk occurs between two glycerophospholipid pathways (the biosynthetic pathways of the thermomemory metabolite S-adenosyl-L-homocysteine and the terpenoid backbone) and the δ-tocopherol (chloroplast lipid) pathway, which favors the production of glycine betaine and other essential tocopherols, respectively, compounds which are essential for abiotic stress tolerance in plants. Therefore, metabolomic analysis can provide comprehensive insights into the metabolites involved in stress responses, which could facilitate plant breeding to maximize crop yields under adverse conditions.

Thermopriming triggers splicing memory in Arabidopsis

Abiotic and biotic stresses limit crop productivity. Exposure to a non-lethal stress, referred to as priming, can allow plants to survive subsequent and otherwise lethal conditions; the priming effect persists even after a prolonged stress-free period. However, the molecular mechanisms underlying priming are not fully understood. Here, we investigated the molecular basis of heat-shock memory and the role of priming in Arabidopsis thaliana. Comprehensive analysis of transcriptome-wide changes in gene expression and alternative splicing in primed and non-primed plants revealed that alternative splicing functions as a novel component of heat-shock memory. We show that priming of plants with a non-lethal heat stress results in de-repression of splicing after a second exposure to heat stress. By contrast, non-primed plants showed significant repression of splicing. These observations link 'splicing memory' to the ability of plants to survive subsequent and otherwise lethal heat stress. This newly discovered priming-induced splicing memory may represent a general feature of heat-stress responses in plants and other organisms as many of the key components are conserved among eukaryotes. Furthermore, this finding could facilitate the development of novel approaches to improve plant survival under extreme heat stress.

Genome-Wide Characterization of Heat-Shock Protein 70s from Chenopodium quinoa and Expression Analyses of Cqhsp70s in Response to Drought Stress

Heat-shock proteins (HSPs) are ubiquitous proteins with important roles in response to biotic and abiotic stress. The 70-kDa heat-shock genes (Hsp70s) encode a group of conserved chaperone proteins that play central roles in cellular networks of molecular chaperones and folding catalysts across all the studied organisms including bacteria, plants and animals. Several Hsp70s involved in drought tolerance have been well characterized in various plants, whereas no research on Chenopodium quinoa HSPs has been completed. Here, we analyzed the genome of C. quinoa and identified sixteen Hsp70 members in quinoa genome. Phylogenetic analysis revealed the independent origination of those Hsp70 members, with eight paralogous pairs comprising the Hsp70 family in quinoa. While the gene structure and motif analysis showed high conservation of those paralogous pairs, the synteny analysis of those paralogous pairs provided evidence for expansion coming from the polyploidy event. With several subcellular localization signals detected in CqHSP70 protein paralogous pairs, some of the paralogous proteins lost the localization information, indicating the diversity of both subcellular localizations and potential functionalities of those HSP70s. Further gene expression analyses revealed by quantitative polymerase chain reaction (qPCR) analysis illustrated the significant variations of Cqhsp70s in response to drought stress. In conclusion, the sixteen Cqhsp70s undergo lineage-specific expansions and might play important and varied roles in response to drought stress.

Not changes in membrane fluidity but proteotoxic stress triggers heat shock protein expression in Chlamydomonas reinhardtii

A conserved reaction of all organisms exposed to heat stress is an increased expression of heat shock proteins (HSPs). Several studies have proposed that HSP expression in heat-stressed plant cells is triggered by an increased fluidity of the plasma membrane. Among the main lines of evidence in support of this model are as follows: (a) the degree of membrane lipid saturation was higher in cells grown at elevated temperatures and correlated with a lower amplitude of HSP expression upon a temperature upshift, (b) membrane fluidizers induce HSP expression at physiological temperatures, and (c) membrane rigidifier dimethylsulfoxide dampens heat-induced HSP expression. Here, we tested whether this holds also for Chlamydomonas reinhardtii. We show that heat-induced HSP expression in cells grown at elevated temperatures was reduced because they already contained elevated levels of cytosolic HSP70A/90A that apparently act as negative regulators of heat shock factor 1. We find that membrane rigidifier dimethylsulfoxide impaired translation under heat stress conditions and that membrane fluidizer benzyl alcohol not only induced HSP expression but also caused protein aggregation. These findings support the classical model for the cytosolic unfolded protein response, according to which HSP expression is induced by the accumulation of unfolded proteins. Hence, the membrane fluidity model should be reconsidered.

The heat-shock protein/chaperone network and multiple stress resistance

Crop yield has been greatly enhanced during the last century. However, most elite cultivars are adapted to temperate climates and are not well suited to more stressful conditions. In the context of climate change, stress resistance is a major concern. To overcome these difficulties, scientists may help breeders by providing genetic markers associated with stress resistance. However, multistress resistance cannot be obtained from the simple addition of single stress resistance traits. In the field, stresses are unpredictable and several may occur at once. Consequently, the use of single stress resistance traits is often inadequate. Although it has been historically linked with the heat stress response, the heat-shock protein (HSP)/chaperone network is a major component of multiple stress responses. Among the HSP/chaperone 'client proteins', many are primary metabolism enzymes and signal transduction components with essential roles for the proper functioning of a cell. HSPs/chaperones are controlled by the action of diverse heat-shock factors, which are recruited under stress conditions. In this review, we give an overview of the regulation of the HSP/chaperone network with a focus on Arabidopsis thaliana. We illustrate the role of HSPs/chaperones in regulating diverse signalling pathways and discuss several basic principles that should be considered for engineering multiple stress resistance in crops through the HSP/chaperone network.

A subclass of HSP70s regulate development and abiotic stress responses in Arabidopsis thaliana

Members of the HSP70 family function as molecular chaperones to maintain cellular homeostasis and help plants cope with environmental stimuli. However, due to functional redundancy and lack of effective chemical inhibitors, our knowledge of functions of individual HSP70s has remained limited. Here, we confirmed a subclass of HSP70s, including HSP70-1, -2, -3, -4, and -5, localized to the cytosol and nucleus in Arabidopsis thaliana. Histochemical analyses of promoter:GUS reporter lines showed that HSP70-1, -2, -3, and -4 genes were widely expressed, but HSP70-5 was not. In addition, individual HSP70 showed not only similar but also distinct transcriptions when treated by different abiotic stresses and phytohormones. No apparent phenotype was observed when individual HSP70 genes were overexpressed or knocked-out/down, but the double mutant hsp70-1 hsp70-4 and triple mutant hsp70-2 hsp70-4 hsp70-5 plants exhibited developmental phenotypes with shortened specific growth periods, curly and round leaves, twisted petioles, thin stems, and short siliques. Moreover, both mutants were hypersensitive to heat, cold, high glucose, salt and osmotic stress, but hyposensitive to abscisic acid. Genes related to flowering, and the cytokinin, brassinosteroid, and abscisic acid signaling pathways were differentially expressed in both mutants. Our studies suggest that, the individual HSP70 possibly performs both redundant and specific functions with the other members in the cytosolic/nuclear HSP70 subclass, and apart from enabling plants to cope with abiotic stresses, this subclass of cytosolic/nuclear HSP70 proteins also participates in diverse developmental processes and signaling pathways.