Genome-Wide Analysis of Gene Expression Provides New Insights into Cold Responses in Thellungiella salsuginea

The genome of Haberlea rhodopensis provides insights into the mechanisms for tolerance to multiple extreme environments

Haberlea rhodopensis, a resurrection species, is the only plant known to be able to survive multiple extreme environments, including desiccation, freezing temperatures, and long-term darkness. However, the molecular mechanisms underlying tolerance to these stresses are poorly studied. Here, we present a high-quality genome of Haberlea and found that ~ 23.55% of the 44,306 genes are orphan. Comparative genomics analysis identified 89 significantly expanded gene families, of which 25 were specific to Haberlea. Moreover, we demonstrated that Haberlea preserves its resurrection potential even in prolonged complete darkness. Transcriptome profiling of plants subjected to desiccation, darkness, and low temperatures revealed both common and specific footprints of these stresses, and their combinations. For example, PROTEIN PHOSPHATASE 2C (PP2C) genes were substantially induced in all stress combinations, while PHYTOCHROME INTERACTING FACTOR 1 (PIF1) and GROWTH RESPONSE FACTOR 4 (GRF4) were induced only in darkness. Additionally, 733 genes with unknown functions and three genes encoding transcription factors specific to Haberlea were specifically induced/repressed upon combination of stresses, rendering them attractive targets for future functional studies. The study provides a comprehensive understanding of the genomic architecture and reports details of the mechanisms of multi-stress tolerance of this resurrection species that will aid in developing strategies that allow crops to survive extreme and multiple abiotic stresses.

Sex differences in colonic gene expression and fecal microbiota composition in a mouse model of obesity-associated colorectal cancer

This study investigated the sex-specific correlation between obesity and colorectal cancer emphasizing a more pronounced association in males. Estrogen, chromosomal genes, and gut bacteria were assessed in C57BL6/J male, female and ovariectomized (OVX) female mice, subjected to either a low-fat diet (LFD) or high-fat diet (HFD) for 14 weeks. Induction of colon tumor involved azoxymethane (10 mg/kg) administration, followed by three cycles of dextran sulfate sodium. Male mice on HFD exhibited higher final body weight and increased colon tumors compared to females. Colonic mucin 2 expression was significantly higher in females. HFD-modulated differentially expressed genes numbered 290 for males, 64 for females, and 137 for OVX females. Only one up-regulated gene (Gfra3) overlapped between females and OVX females, while two down-regulated genes (Thrsp and Gbp11) overlapped between males and OVX females. Genes up-regulated by HFD in males were linked to cytokine-cytokine interaction, HIF-1 signaling pathway, central carbon metabolism in cancer. Sex-specific changes in gut microbial composition in response to HFD were observed. These findings suggest a male-specific vulnerability to HFD-induced colon tumor formation, implicating key genes and colonic bacteria in colon tumorigenesis.

Isolation and characterization of wheat ice recrystallisation inhibition gene promoter involved in low temperature and methyl jasmonate responses

It is well known that plant growth, development, survival and geographical distribution are constrained by extreme climatic conditions, especially extreme low temperature. Under cold stress, cold-inducible promoters were identified as important molecular switches to transcriptionally regulate the initiation of genes associated with cold acclimation processes and enhance the adaptability of plants to cold stimulation. Wheat (Triticum aestivum L.) is one of the most dominating food crops in the world, and wheat crops are generally overwintering with strong cold resistance. Our previous study already proved that heterologous expression of wheat ice recrystallization inhibition (IRI) genes enhanced freezing tolerance in tobacco. However, the upstream regulatory mechanisms of TaIRI are ambiguous. In this study, the space-time specific expression of TaIRI genes in wheat was analyzed by quantitative real-time PCR (qRT-PCR), and results showed that the expression of TaIRI in all tissues was cold-induced and accelerate by exogenous methyl jasmonate (MeJA). Three promoters of TaIRI genes were isolated from wheat genome, and various 5'-deletion fragments of TaIRIp were integrated into β-glucuronidase (GUS) within vector pCAMBIA1301. The promoter activity of TaIRI genes was determined through transient expression system of tobacco and stable expression of Arabidopsis thaliana. Results revealed that the GUS activity were significantly strengthened by cold and MeJA treatments. This study will provide insights into elucidating the transcription-regulatory mechanism of IRI proteins responding to low temperature.

Multi-leveled insights into the response of the eelgrass Zostera marina L to Cu than Cd exposure

Seagrass beds are recognized as critical and among the most vulnerable habitats on the planet; seagrass colonize the coastal waters where heavy metal pollution is a serious problem. In this study, the toxic effects of copper and cadmium in the eelgrass Zostera marina L. were observed at the individual, subcellular, physiologically biochemical, and molecular levels. Both Cu and Cd stress significantly inhibited the growth and the maximal quantum yield of photosystem II (Fv/Fm); and high temperature increased the degree of heavy metal damage, while low temperatures inhibited damage. The half-effect concentration (EC₅₀) of eelgrass was 28.9 μM for Cu and 2246.8 μM for Cd, indicating Cu was much more toxic to eelgrass than Cd. The effect of Cu and Cd on photosynthesis was synergistic. After 14 days of enrichment, the concentration of Cu in leaves and roots of Z. marina was 48 and 37 times higher than that in leaf sheath, and 14 and 11 times higher than that in rhizome; and the order of Cd concentration in the organs was root > leaf > rhizome > sheath. Heavy metal uptake mainly occurred in the organelles, and Cd enrichment also occurred to a certain extent in the cytoplasm. Transcriptome results showed that a number of photosynthesis-related KEGG enrichment pathways and GO terms were significantly down-regulated under Cd stress, suggesting that the photosynthetic system of eelgrass was severely damaged at the transcriptome level, which was consistent with the significant inhibition of Fv/Fm and leaf yellowing. Under Cu stress, the genes related to glutathione metabolic pathway were significantly up-regulated, together with the increased autioxidant enzyme activity of GSH-PX. In addition, the results of recovery experiment indicated that the damage caused by short-term Cd and Cu stress under EC₅₀ was reversible. These results provide heavy metal toxic effects at multiple levels and information relating to the heavy metal resistance strategies evolved by Z. marina to absorb and isolate heavy metals, and highlight the phytoremediation potential of this species especially for Cd.

De novo full length transcriptome analysis and gene expression profiling to identify genes involved in phenylethanol glycosides biosynthesis in Cistanche tubulosa

Background

The dried stem of Cistanche, is a famous Chinese traditional medicine. The main active pharmacodynamic components are phenylethanol glycosides (PhGs). Cistanche tubulosa produces higher level of PhGs in its stems than that of Cistanche deserticola. However, the key genes in the PhGs biosynthesis pathway is not clear in C. tubulosa.

Results

In this study, we performed the full-length transcriptome sequencing and gene expression profiling of C. tubulosa using PacBio combined with BGISEQ-500 RNA-seq technology. Totally, 237,772 unique transcripts were obtained, ranging from 199 bp to 31,857 bp. Among the unique transcripts, 188,135 (79.12%) transcripts were annotated. Interestingly, 1080 transcripts were annotated as 22 enzymes related to PhGs biosynthesis. We measured the content of echinacoside, acteoside and total PhGs at two development stages, and found that the content of PhGs was 46.74% of dry matter in young fleshy stem (YS1) and then decreased to 31.22% at the harvest stage (HS2). To compare with YS1, 13,631 genes were up-regulated, and 15,521 genes were down regulated in HS2. Many differentially expressed genes (DEGs) were identified to be involved in phenylpropanoid biosynthesis pathway, phenylalanine metabolism pathway, and tyrosine metabolism pathway.

Conclusions

This is the first report of transcriptome study of C. tubulosa which provided the foundation for understanding of PhGs biosynthesis. Based on these results, we proposed a potential model for PhGs biosynthesis in C. tubulosa.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08921-x.

Cytokinin and abiotic stress tolerance -What has been accomplished and the way forward?

More than a half-century has passed since it was discovered that phytohormone cytokinin (CK) is essential to drive cytokinesis and proliferation in plant tissue culture. Thereafter, cytokinin has emerged as the primary regulator of the plant cell cycle and numerous developmental processes. Lately, a growing body of evidence suggests that cytokinin has a role in mitigating both abiotic and biotic stress. Cytokinin is essential to defend plants against excessive light exposure and a unique kind of abiotic stress generated by an altered photoperiod. Secondly, cytokinin also exhibits multi-stress resilience under changing environments. Furthermore, cytokinin homeostasis is also affected by several forms of stress. Therefore, the diverse roles of cytokinin in reaction to stress, as well as its interactions with other hormones, are discussed in detail. When it comes to agriculture, understanding the functioning processes of cytokinins under changing environmental conditions can assist in utilizing the phytohormone, to increase productivity. Through this review, we briefly describe the biological role of cytokinin in enhancing the performance of plants growth under abiotic challenges as well as the probable mechanisms underpinning cytokinin-induced stress tolerance. In addition, the article lays forth a strategy for using biotechnological tools to modify genes in the cytokinin pathway to engineer abiotic stress tolerance in plants. The information presented here will assist in better understanding the function of cytokinin in plants and their effective investigation in the cropping system.

Cold stress regulates accumulation of flavonoids and terpenoids in plants by phytohormone, transcription process, functional enzyme, and epigenetics

Plants make different defense mechanisms in response to different environmental stresses. One common way is to produce secondary metabolites. Temperature is the main environmental factor that regulates plant secondary metabolites, especially flavonoids and terpenoids. Stress caused by temperature decreasing to 4-10 °C is conducive to the accumulation of flavonoids and terpenoids. However, the accumulation mechanism under cold stress still lacks a systematic explanation. In this review, we summarize three aspects of cold stress promoting the accumulation of flavonoids and terpenoids in plants, that is, by affecting (1) the content of endogenous plant hormones, especially jasmonic acid and abscisic acid; (2) the expression level and activity of important transcription factors, such as bHLH and MYB families. This aspect also includes post-translational modification of transcription factors caused by cold stress; (3) key enzyme genes expression and activity in the biosynthesis pathway, in addition, the rate-limiting enzyme and glycosyltransferases genes are responsive to cold stress. The systematic understanding of cold stress regulates flavonoids, and terpenoids will contribute to the future research of genetic engineering breeding, metabolism regulation, glycosyltransferases mining, and plant synthetic biology.

AhNPR3 regulates the expression of WRKY and PR genes, and mediates the immune response of the peanut (Arachis hypogaea L.)

Systemic acquired resistance is an essential immune response that triggers a broad-spectrum disease resistance throughout the plant. In the present study, we identified a peanut lesion mimic mutant m14 derived from an ethyl methane sulfonate-mutagenized mutant pool of peanut cultivar "Yuanza9102." Brown lesions were observed in the leaves of an m14 mutant from seedling stage to maturity. Using MutMap together with bulked segregation RNA analysis approaches, a G-to-A point mutation was identified in the exon region of candidate gene Arahy.R60CUW, which is the homolog of AtNPR3 (Nonexpresser of PR genes) in Arabidopsis. This point mutation caused a transition from Gly to Arg within the C-terminal transactivation domain of AhNPR3A. The mutation of AhNPR3A showed no effect in the induction of PR genes when treated with salicylic acid. Instead, the mutation resulted in upregulation of WRKY genes and several PR genes, including pathogenesis-related thaumatin- and chitinase-encoding genes, which is consistent with the resistant phenotype of m14 to leaf spot disease. Further study on the AhNPR3A gene will provide valuable insights into understanding the molecular mechanism of systemic acquired resistance in peanut. Moreover, our results indicated that a combination of MutMap and bulked segregation RNA analysis is an effective method for identifying genes from peanut mutants.

BSA‑seq and genetic mapping reveals AhRt2 as a candidate gene responsible for red testa of peanut

The candidate recessive gene AhRt2 responsible for red testa of peanut was identified through combined BSA-seq and linkage mapping approaches. The testa color of peanuts (Arachis hypogaea L.) is an important trait, and those with red testa are particularly popular owing to the high-anthocyanin content. However, the identification of genes underlying the regulation of the red testa trait in peanut are rarely reported. In order to fine map red testa gene, two F_2:4 populations were constructed through the cross of YZ9102 (pink testa) with ZH12 (red testa) and ZH2 (red testa). Genetic analysis indicated that red testa was controlled by a single recessive gene named as AhRt2 (Red testa gene 2). Using BSA-seq approach, AhRt2 was preliminary identified on chromosome 12, which was further mapped to a 530-kb interval using 220 recombinant lines through linkage mapping. Furthermore, functional annotation, expression profiling, and the analyses of sequence variation confirmed that the anthocyanin reductase namely (Arahy.IK60LM) was the most likely candidate gene for AhRt2. It was found that a SNP in the third exon of AhRt2 altered the encoding amino acids, and was associated with red testa in peanut. In addition, a closely linked molecular marker linked with red testa trait in peanut was also developed for future studies. Our results provide valuable insight into the molecular mechanism underlying peanut testa color and present significant diagnostic marker resources for marker-assisted selected breeding in peanut.

Transcriptome Profiling of the Salt Stress Response in the Leaves and Roots of Halophytic Eutrema salsugineum

Eutrema salsugineum can grow in natural harsh environments; however, the underlying mechanisms for salt tolerance of Eutrema need to be further understood. Herein, the transcriptome profiling of Eutrema leaves and roots exposed to 300 mM NaCl is investigated, and the result emphasized the role of genes involved in lignin biosynthesis, autophagy, peroxisome, and sugar metabolism upon salt stress. Furthermore, the expression of the lignin biosynthesis and autophagy-related genes, as well as 16 random selected genes, was validated by qRT-PCR. Notably, the transcript abundance of a large number of lignin biosynthesis genes such as CCoAOMT, C4H, CCR, CAD, POD, and C3′H in leaves was markedly elevated by salt shock. And the examined lignin content in leaves and roots demonstrated salt stress led to lignin accumulation, which indicated the enhanced lignin level could be an important mechanism for Eutrema responding to salt stress. Additionally, the differentially expressed genes (DEGs) assigned in the autophagy pathway including Vac8, Atg8, and Atg4, as well as DEGs enriched in the peroxisome pathway such as EsPEX7, EsCAT, and EsSOD2, were markedly induced in leaves and/or roots. In sugar metabolism pathways, the transcript levels of most DEGs associated with the synthesis of sucrose, trehalose, raffinose, and xylose were significantly enhanced. Furthermore, the expression of various stress-related transcription factor genes including WRKY, AP2/ERF-ERF, NAC, bZIP, MYB, C2H2, and HSF was strikingly improved. Collectively, the increased expression of biosynthesis genes of lignin and soluble sugars, as well as the genes in the autophagy and peroxisome pathways, suggested that Eutrema encountering salt shock possibly possess a higher capacity to adjust osmotically and facilitate water transport and scavenge reactive oxidative species and oxidative proteins to cope with the salt environment. Thus, this study provides a new insight for exploring the salt tolerance mechanism of halophytic Eutrema and discovering new gene targets for the genetic improvement of crops.

De novo full length transcriptome analysis of Arachis glabrata provides insights into gene expression dynamics in response to biotic and abiotic stresses

The perennial ornamental peanut Arachis glabrata represents one of the most adaptable wild Arachis species. This study used PacBio combined with BGISEQ-500 RNA-seq technology to study the transcriptome and gene expression dynamics of A. glabrata. Of the total 109,747 unique transcripts obtained, >90,566 transcripts showed significant homology to known proteins and contained the complete coding sequence (CDS). RNA-seq revealed that 1229, 1039, 1671, 3923, 1521 and 1799 transcripts expressed specifically in the root, stem, leaf, flower, peg and pod, respectively. We also identified thousands of differentially expressed transcripts in response to drought, salt, cold and leaf spot disease. Furthermore, we identified 30 polyphenol oxidase encoding genes associated with the quality of forage, making A. glabrata suitable as a forage crop. Our findings presented the first transcriptome study of A. glabrata which will facilitate genetic and genomics studies and lays the groundwork for a deeper understanding of the A. glabrata genome.

Acceleration of Carbon Fixation in Chilling-Sensitive Banana under Mild and Moderate Chilling Stresses

Banana is one of the most important food and fruit crops in the world and its growth is ceasing at 10–17 °C. However, the mechanisms determining the tolerance of banana to mild (>15 °C) and moderate chilling (10–15 °C) are elusive. Furthermore, the biochemical controls over the photosynthesis in tropical plant species at low temperatures above 10 °C is not well understood. The purpose of this research was to reveal the response of chilling-sensitive banana to mild (16 °C) and moderate chilling stress (10 °C) at the molecular (transcripts, proteins) and physiological levels. The results showed different transcriptome responses between mild and moderate chilling stresses, especially in pathways of plant hormone signal transduction, ABC transporters, ubiquinone, and other terpenoid-quinone biosynthesis. Interestingly, functions related to carbon fixation were assigned preferentially to upregulated genes/proteins, while photosynthesis and photosynthesis-antenna proteins were downregulated at 10 °C, as revealed by both digital gene expression and proteomic analysis. These results were confirmed by qPCR and immunofluorescence labeling methods. Conclusion: Banana responded to the mild chilling stress dramatically at the molecular level. To compensate for the decreased photosynthesis efficiency caused by mild and moderate chilling stresses, banana accelerated its carbon fixation, mainly through upregulation of phosphoenolpyruvate carboxylases.

Abiotic stress signalling in extremophile land plants

Plant life relies on complex arrays of environmental stress sensing and signalling mechanisms. Extremophile plants develop and grow in harsh environments with extremes of cold, heat, drought, desiccation, or salinity, which have resulted in original adaptations. In accordance with their polyphyletic origins, extremophile plants likely possess core mechanisms of plant abiotic stress signalling. However, novel properties or regulations may have emerged in the context of extremophile adaptations. Comparative omics of extremophile genetic models, such as Arabidopsis lyrata, Craterostigma plantagineum, Eutrema salsugineum, and Physcomitrella patens, reveal diverse strategies of sensing and signalling that lead to a general improvement in abiotic stress responses. Current research points to putative differences of sensing and emphasizes significant modifications of regulatory mechanisms, at the level of secondary messengers (Ca2+, phospholipids, reactive oxygen species), signal transduction (intracellular sensors, protein kinases, transcription factors, ubiquitin-mediated proteolysis) or signalling crosstalk. Involvement of hormone signalling, especially ABA signalling, cell homeostasis surveillance, and epigenetic mechanisms, also shows that large-scale gene regulation, whole-plant integration, and probably stress memory are important features of adaptation to extreme conditions. This evolutionary and functional plasticity of signalling systems in extremophile plants may have important implications for plant biotechnology, crop improvement, and ecological risk assessment under conditions of climate change.

Research Progress on the Roles of Cytokinin in Plant Response to Stress

Cytokinins promote plant growth and development under normal plant growth conditions and also play an important role in plant resistance to stress. Understanding the working mechanisms of cytokinins under adverse conditions will help to make full use of cytokinins in agriculture to increase production and efficiency of land use. In this article, we review the progress that has been made in cytokinin research in plant response to stress and propose its future application prospects.

Automatic Identification of Players in the Flavonoid Biosynthesis with Application on the Biomedicinal Plant Croton tiglium

The flavonoid biosynthesis is a well-characterised model system for specialised metabolism and transcriptional regulation in plants. Flavonoids have numerous biological functions such as UV protection and pollinator attraction, but also biotechnological potential. Here, we present Knowledge-based Identification of Pathway Enzymes (KIPEs) as an automatic approach for the identification of players in the flavonoid biosynthesis. KIPEs combines comprehensive sequence similarity analyses with the inspection of functionally relevant amino acid residues and domains in subjected peptide sequences. Comprehensive sequence sets of flavonoid biosynthesis enzymes and knowledge about functionally relevant amino acids were collected. As a proof of concept, KIPEs was applied to investigate the flavonoid biosynthesis of the medicinal plant Croton tiglium on the basis of a transcriptome assembly. Enzyme candidates for all steps in the biosynthesis network were identified and matched to previous reports of corresponding metabolites in Croton species.

Integrative analyses of transcriptomics and metabolomics upon seed germination of foxtail millet in response to salinity

Salinity stress has become an expanding threat to food security worldwide. Revealing the mechanisms of salinity tolerance in plants has immense significance. Foxtail millet (Setaria italica L.) has been regarded as a model crop for exploring mechanisms under stress, considering its extreme adaptation abilities to adverse ecologies. In present study, two foxtail millet cultivars of Yugu2 and An04 with contrasting salt tolerance properties were investigated through integrative analyses of transcriptomics and metabolomics. In the transcriptomics results, 8887 and 12,249 DEGs were identified in Yugu2 and An04 in response to salinity, respectively, and 3149 of which were overlapped between two varieties. These salinity-responsive genes indicated that ion transport, redox homeostasis, phytohormone metabolism, signaling and secondary metabolism were enriched in Yugu2 by GO and KEGG analyses. The integrative omics analysis implied that phenylpropanoid, flavonoid and lignin biosynthesis pathways, and lysophospholipids were vital in determining the foxtail millet salinity tolerance. Importantly, the tolerance of Yugu2 attributed to higher efficiencies of ion channel and antioxidant system. All these provide a comprehensive regulatory network of foxtail millet to cope with salinity, and shed some lights on salt tolerance which is relevant for other cereal crops.

Integrated small RNA and mRNA expression profiles reveal miRNAs and their target genes in response to Aspergillus flavus growth in peanut seeds

BACKGROUND

MicroRNAs are important gene expression regulators in plants immune system. Aspergillus flavus is the most common causal agents of aflatoxin contamination in peanuts, but information on the function of miRNA in peanut-A. flavus interaction is lacking. In this study, the resistant cultivar (GT-C20) and susceptible cultivar (Tifrunner) were used to investigate regulatory roles of miRNAs in response to A. flavus growth.

RESULTS

A total of 30 miRNAs, 447 genes and 21 potential miRNA/mRNA pairs were differentially expressed significantly when treated with A. flavus. A total of 62 miRNAs, 451 genes and 44 potential miRNA/mRNA pairs exhibited differential expression profiles between two peanut varieties. Gene Ontology (GO) analysis showed that metabolic-process related GO terms were enriched. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses further supported the GO results, in which many enriched pathways were related with biosynthesis and metabolism, such as biosynthesis of secondary metabolites and metabolic pathways. Correlation analysis of small RNA, transcriptome and degradome indicated that miR156/SPL pairs might regulate the accumulation of flavonoids in resistant and susceptible genotypes. The miR482/2118 family might regulate NBS-LRR gene which had the higher expression level in resistant genotype. These results provided useful information for further understanding the roles of miR156/157/SPL and miR482/2118/NBS-LRR pairs.

CONCLUSIONS

Integration analysis of the transcriptome, miRNAome and degradome of resistant and susceptible peanut varieties were performed in this study. The knowledge gained will help to understand the roles of miRNAs of peanut in response to A. flavus.

Identification of the Eutrema salsugineum EsMYB90 gene important for anthocyanin biosynthesis

BACKGROUND

Anthocyanins contribute to coloration and antioxidation effects in different plant tissues. MYB transcription factors have been demonstrated to be a key regulator for anthocyanin synthesis in many plants. However, little information was available about the MYB genes in the halophyte species Eutrema salsugineum.

RESULT

Here we report the identification of an important anthocyanin biosynthesis regulator EsMYB90 from Eutrema salsugineum, which is a halophyte tolerant to multiple abiotic stresses. Our phylogenetic and localization analyses supported that EsMYB90 is an R2R3 type of MYB transcription factor. Ectopic expression of EsMYB90 in tobacco and Arabidopsis enhanced pigmentation and anthocyanin accumulation in various organs. The transcriptome analysis revealed that 42 genes upregulated by EsMYB90 in 35S:EsMYB90 tobacco transgenic plants are required for anthocyanin biosynthesis. Moreover, our qRT-PCR results showed that EsMYB90 promoted expression of early (PAL, CHS, and CHI) and late (DFR, ANS, and UFGT) anthocyanin biosynthesis genes in stems, leaves, and flowers of 35S:EsMYB90 tobacco transgenic plants.

CONCLUSIONS

Our results indicated that EsMYB90 is a MYB transcription factor, which regulates anthocyanin biosynthesis genes to control anthocyanin biosynthesis. Our work provides a new tool to enhance anthocyanin production in various plants.

Identification of the Eutrema salsugineum EsMYB90 gene important for anthocyanin biosynthesis

BACKGROUND

Anthocyanins contribute to coloration and antioxidation effects in different plant tissues. MYB transcription factors have been demonstrated to be a key regulator for anthocyanin synthesis in many plants. However, little information was available about the MYB genes in the halophyte species Eutrema salsugineum.

RESULT

Here we report the identification of an important anthocyanin biosynthesis regulator EsMYB90 from Eutrema salsugineum, which is a halophyte tolerant to multiple abiotic stresses. Our phylogenetic and localization analyses supported that EsMYB90 is an R2R3 type of MYB transcription factor. Ectopic expression of EsMYB90 in tobacco and Arabidopsis enhanced pigmentation and anthocyanin accumulation in various organs. The transcriptome analysis revealed that 42 genes upregulated by EsMYB90 in 35S:EsMYB90 tobacco transgenic plants are required for anthocyanin biosynthesis. Moreover, our qRT-PCR results showed that EsMYB90 promoted expression of early (PAL, CHS, and CHI) and late (DFR, ANS, and UFGT) anthocyanin biosynthesis genes in stems, leaves, and flowers of 35S:EsMYB90 tobacco transgenic plants.

CONCLUSIONS

Our results indicated that EsMYB90 is a MYB transcription factor, which regulates anthocyanin biosynthesis genes to control anthocyanin biosynthesis. Our work provides a new tool to enhance anthocyanin production in various plants.

Advances in salt tolerance molecular mechanism in tobacco plants

Tobacco, an economic crop and important model plant, has received more progress in salt tolerance with the aid of transgenic technique. Salt stress has become a key research field in abiotic stress. The study of tobacco promotes the understanding about the important adjustment for survival in high salinity environments, including cellular ion transport, osmotic regulation, antioxidation, signal transduction and expression regulation, and protection of cells from stress damage. Genes, which response to salt, have been studied using targeted transgenic technologies in tobacco plants to investigate the molecular mechanisms. The transgenic tobacco plants exhibited higher seed germination and survival rates, better root and shoot growth under salt stress treatments. Transgenic approach could be the promising option for enhancing tobacco production under saline condition. This review highlighted the salt tolerance molecular mechanisms of tobacco.

C2H2 Zinc Finger Proteins: Master Regulators of Abiotic Stress Responses in Plants

Abiotic stresses such as drought and salinity are major environmental factors that limit crop yields. Unraveling the molecular mechanisms underlying abiotic stress resistance is crucial for improving crop performance and increasing productivity under adverse environmental conditions. Zinc finger proteins, comprising one of the largest transcription factor families, are known for their finger-like structure and their ability to bind Zn2+. Zinc finger proteins are categorized into nine subfamilies based on their conserved Cys and His motifs, including the Cys2/His2-type (C2H2), C3H, C3HC4, C2HC5, C4HC3, C2HC, C4, C6, and C8 subfamilies. Over the past two decades, much progress has been made in understanding the roles of C2H2 zinc finger proteins in plant growth, development, and stress signal transduction. In this review, we focus on recent progress in elucidating the structures, functions, and classifications of plant C2H2 zinc finger proteins and their roles in abiotic stress responses.

Cell Cycle Regulation in the Plant Response to Stress

As sessile organisms, plants face a variety of environmental challenges. Their reproduction and survival depend on their ability to adapt to these stressors, which include water, heat stress, high salinity, and pathogen infection. Failure to adapt to these stressors results in programmed cell death and decreased viability, as well as reduced productivity in the case of crop plants. The growth and development of plants are maintained by meiosis and mitosis as well as endoreduplication, during which DNA replicates without cytokinesis, leading to polyploidy. As in other eukaryotes, the cell cycle in plants consists of four stages (G1, S, G2, and M) with two major check points, namely, the G1/S check point and G2/M check point, that ensure normal cell division. Progression through these checkpoints involves the activity of cyclin-dependent kinases and their regulatory subunits known as cyclins. In order for plants to survive, cell cycle control must be balanced with adaption to dynamic environmental conditions. In this review, we summarize recent advances in our understanding of cell cycle regulation in plants, with a focus on the molecular interactions of cell cycle machinery in the context of stress tolerance.

Genetic mechanisms of salt stress responses in halophytes

Abiotic stress is a major threat to plant growth and development, resulting in extensive crop loss worldwide. Plants react to abiotic stresses through physiological, biochemical, molecular, and genetic adaptations that promote survival. Exploring the molecular mechanisms involved in abiotic stress responses across various plant species is essential for improving crop yields in unfavorable environments. Halophytes are characterized as plants that survive to reproduce in soils containing high salt concentrations, and thus act as an ideal model to comprehend complicated genetic and physiological mechanisms of salinity stress tolerance. Plant ecologists classify halophytes into three main groups: euhalophytes, recretohalophytes, and pseudo-halophytes. Recent genetic and molecular research has showed complicated regulatory networks by which halophytes coordinate stress adaptation and tolerance. Furthermore, investigation of natural variations in these stress responses has supplied new perspectives on the evolution of mechanisms that regulate tolerance and adaptation. This review discusses the current understanding of the genetic mechanisms that contribute to salt-stress tolerance among different classes of halophytes.

New Insights Into the Role of Seed Oil Body Proteins in Metabolism and Plant Development

Oil bodies (OBs) are ubiquitous dynamic organelles found in plant seeds. They have attracted increasing attention recently because of their important roles in plant physiology. First, the neutral lipids stored within these organelles serve as an initial, essential source of energy and carbon for seed germination and post-germinative growth of the seedlings. Secondly, they are involved in many other cellular processes such as stress responses, lipid metabolism, organ development, and hormone signaling. The biological functions of seed OBs are dependent on structural proteins, principally oleosins, caleosins, and steroleosins, which are embedded in the OB phospholipid monolayer. Oleosin and caleosin proteins are specific to plants and mainly act as OB structural proteins and are important for the biogenesis, stability, and dynamics of the organelle; whereas steroleosin proteins are also present in mammals and play an important role in steroid hormone metabolism and signaling. Significant progress using new genetic, biochemical, and imaging technologies has uncovered the roles of these proteins. Here, we review recent work on the structural or metabolic roles of these proteins in OB biogenesis, stabilization and degradation, lipid homeostasis and mobilization, hormone signal transduction, stress defenses, and various aspects of plant growth and development.

Identification of modules and hub genes associated with platinum-based chemotherapy resistance and treatment response in ovarian cancer by weighted gene co-expression network analysis

High-grade serous ovarian carcinoma (HGSOC) is the most prevalent and malignant ovarian tumor.To identify co-expression modules and hub genes correlated with platinum-based chemotherapy resistant and sensitive HGSOC, we performed weighted gene co-expression network analysis (WGCNA) on microarray data of HGSOC with 12 resistant samples and 16 sensitive samples of GSE51373 dataset.A total of 5122 genes were included in WGCNA, and 16 modules were identified. Module-trait analysis identified that the module salmon (cor = 0.50), magenta (cor = 0.49), and black (cor = 0.45) were discovered associated with chemotherapy resistant, and the significance for these platinum-resistant modules were validated in the GSE63885 dataset. Given that the black module was validated to be the most related one, hub genes of this module, alcohol dehydrogenase 1B, cadherin 11, and vestigial like family member 3were revealed to be expressional related with platinum resistance, and could serve as prognostic markers for ovarian cancer.Our analysis might provide insight for molecular mechanisms of platinum-based chemotherapy resistance and treatment response in ovarian cancer.

Global transcriptome analysis provides new insights in Thellungiella salsuginea stress response

Thellungiella salsuginea is highly tolerant to abiotic stress, while its a close relative Arabidopsis thaliana is sensitive to stress. This characteristic makes T. salsuginea an excellent model for uncovering the mechanisms of abiotic stress tolerance. Abscisic acid (ABA) plays essential roles in plant abiotic and biotic stress tolerance. To test the changes in gene expression of T. salsuginea under ABA treatment, in this study, the transcriptomes of T. salsuginea roots and leaves were compared in response to exogenously application of ABA. The results showed that ABA treatment caused different expression of 2,200 and 3,305 genes in leaves and roots, respectively, compared with the untreated control. In particular, genes encoding transcription factors such as WRKY, MYB, NAC, GATA, ethylene-responsive factors (ERFs), heat stress transcription factors, basic helix-loop-helix, PLATZ and B3 domain-containing family members were enriched. In addition, 49 and 114 differentially expressed genes were identified as ABA-regulated genes, separately in leaves and roots, respectively, which were related to biotic and abiotic stresses. The expression levels of some genes were validated by qRT-PCR. Different responses of genes to ABA treatment were discovered in T. salsuginea and A. thaliana. This transcriptome analysis expands our understanding of the role of ABA in stress tolerance in T. salsuginea. Our study provides a wealth of information for improving stress tolerance in crop plants.

Roles of malic enzymes in plant development and stress responses

Malic enzyme (ME) comprises a family of proteins with multiple isoforms located in different compartments of eukaryotic cells. It is a key enzyme regulating malic acid metabolism and can catalyze the reversible reaction of oxidative decarboxylation of malic acid. And it is also one of the important enzymes in plant metabolism and is involved in multiple metabolic processes. ME is widely present in plants and mainly discovered in cytoplasmic stroma, mitochondria, chloroplasts. It is involved in plant growth, development, and stress response. Plants are stressed by various environmental factors such as drought, high salt, and high temperature during plant growth, and the mechanisms of plant response to various environmental stresses are synergistic. Numerous studies have shown that ME participates in the process of coping with the above environmental factors by increasing water use efficiency, improving photosynthesis of plants, providing reducing power, and so on. In this review, we discuss the important role of ME in plant development and plant stress response, and prospects for its application. It provides a theoretical basis for the future use of ME gene for molecular resistance breeding.

Characterization of the complete plastome of Atriplex centralasiatica (Chenopodiaceae), an annual halophytic herb

Atriplex centralasiatica, an annual halophytic herb, is one of the most important Chinese herbal medicines, forages and indicator plants for saline-alkali soil. In this study, we report the complete plastome of A. centralasiatica. The plastome was 152,237 bp in length and comprises a large single-copy region (83,721 bp), a small single-copy region (18,096 bp), and a pair of inverted repeats (25,210 bp). It encodes 113 unique genes, including 79 protein-coding genes (PCGs), 30 tRNAs and 4 rRNAs. The overall GC content of this plastome was 37.3%. Phylogenomic analysis based on 21 plastomes revealed that A. centralasiatica was closely related to the genus Chenopodium.

The microtubule cytoskeleton acts as a sensor for stress response signaling in plants

Stress tolerance pathways are protective mechanisms that have evolved to protect plant growth and increase production under various environmental stress conditions. Enhancing stress tolerance in crop plants has become an area of intense study with aims of increasing crop production and enhancing economic benefits. A growing number of studies suggest that in addition to playing vital roles in mechanical architecture and cell division, microtubules are also involved the adaptation to severe environmental conditions in plants. However, the mechanisms that integrate microtubule regulation, cellular metabolism and cell signaling in plant stress responses remain unclear. Recent studies suggest that microtubules act as sensors for different abiotic stresses and maintain mechanical stability by forming bundles. Characterizing the diverse roles of plant microtubules is vital to furthering our understanding of stress tolerance in plants.

ZmMYB31, a R2R3-MYB transcription factor in maize, positively regulates the expression of CBF genes and enhances resistance to chilling and oxidative stress

Maize (Zea mays L.) is an important model plant with an important role in agriculture and national economies all over the world. The optimum growth temperature of maize is between 25 and 28 °C. At temperatures below 12 °C, maize is vulnerable to damage by chilling stress. MYB transcription factors play important roles in plants' response to low temperature stress. Maize ZmMYB31 encodes a R2R3-MYB transcription factor, ZmMYB31, which localized in the nucleus. ZmMYB31 expression was induced by chilling stress and the highest expression level was detected with the 24 h chilling treatment. ZmMYB31 expression also increased in overexpressing Arabidopsis lines. The minimal fluorescence (Fo) with all photosystem II reaction centers open increased in wild type (WT) and transgenic plants under chilling stress, with the highest increase in WT. The maximal photochemical efficiency of photosystem II (Fv/Fm) decreased more in WT than in transgenic plants during chilling stress. Furthermore, the ZmMYB31-overexpressing lines showed higher superoxide dismutase and ascorbate peroxidase activity and lower reactive oxygen species (ROS) content than the WT. The expression of genes related to chilling stress was higher in transgenic plants than in WT. These results suggest that ZmMYB31 plays a positive regulatory role in chilling and peroxide stress by regulating the expression of chilling stress-related genes to reduce ion extravasation, ROS content, and low-temperature photoinhibition, thereby improving low temperature resistance.

Phylostratigraphic analysis of gene co-expression network reveals the evolution of functional modules for ovarian cancer

Ovarian cancer (OV) is an extremely lethal disease. However, the evolutionary machineries of OV are still largely unknown. Here, we used a method that combines phylostratigraphy information with gene co-expression networks to extensively study the evolutionary compositions of OV. The present co-expression network construction yielded 18,549 nodes and 114,985 edges based on 307 OV expression samples obtained from the Genome Data Analysis Centers database. A total of 20 modules were identified as OV related clusters. The human genome sequences were divided into 19 phylostrata (PS), the majority (67.45%) of OV genes was already present in the eukaryotic ancestor. There were two strong peaks of the emergence of OV genes screened by hypergeometric test: the evolution of the multicellular metazoan organisms (PS5 and PS6, P value = 0.002) and the emergence of bony fish (PS11 and PS12, P value = 0.009). Hence, the origin of OV is far earlier than its emergence. The integrated analysis of the topology of OV modules and the phylogenetic data revealed an evolutionary pattern of OV in human, namely, OV modules have arisen step by step during the evolution of the respective lineages. New genes have evolved and become locked into a pathway, where more and more biological pathways are fixed into OV modules by recruiting new genes during human evolution.

Abiotic Stresses: General Defenses of Land Plants and Chances for Engineering Multistress Tolerance

Abiotic stresses, such as low or high temperature, deficient or excessive water, high salinity, heavy metals, and ultraviolet radiation, are hostile to plant growth and development, leading to great crop yield penalty worldwide. It is getting imperative to equip crops with multistress tolerance to relieve the pressure of environmental changes and to meet the demand of population growth, as different abiotic stresses usually arise together in the field. The feasibility is raised as land plants actually have established more generalized defenses against abiotic stresses, including the cuticle outside plants, together with unsaturated fatty acids, reactive species scavengers, molecular chaperones, and compatible solutes inside cells. In stress response, they are orchestrated by a complex regulatory network involving upstream signaling molecules including stress hormones, reactive oxygen species, gasotransmitters, polyamines, phytochromes, and calcium, as well as downstream gene regulation factors, particularly transcription factors. In this review, we aimed at presenting an overview of these defensive systems and the regulatory network, with an eye to their practical potential via genetic engineering and/or exogenous application.

Therapeutic targeting of cellular stress responses in cancer

Similar to bacteria, yeast, and other organisms that have evolved pathways to respond to environmental stresses, cancer cells develop mechanisms that increase genetic diversity to facilitate adaptation to a variety of stressful conditions, including hypoxia, nutrient deprivation, exposure to DNA-damaging agents, and immune responses. To survive, cancer cells trigger mechanisms that drive genomic instability and mutation, alter gene expression programs, and reprogram the metabolic pathways to evade growth inhibition signaling and immune surveillance. A deeper understanding of the molecular mechanisms that underlie the pathways used by cancer cells to overcome stresses will allow us to develop more efficacious strategies for cancer therapy. Herein, we overview several key stresses imposed on cancer cells, including oxidative, metabolic, mechanical, and genotoxic, and discuss the mechanisms that drive cancer cell responses. The therapeutic implications of these responses are also considered, as these factors pave the way for the targeting of stress adaption pathways in order to slow cancer progression and block resistance to therapy.

Integrative transcriptional and metabolic analyses provide insights into cold spell response mechanisms in young shoots of the tea plant

Green tea has attracted an increasing number of consumers worldwide due to its multiple health benefits. With the increase in global warming, more frequent cold spells in the spring often cause more serious damage to green tea production because of the young leaves used. We recorded the changes in climatic conditions during a typical cold spell and the damage symptoms caused by the cold spell in different tea cultivars and breeding lines. By simulating the low temperature of a cold spell under controlled conditions, comparative transcriptome and metabolic analyses were performed with sprouting shoots. Many pathways and genes were regulated differentially by the cold spell conditions. Taking into account the metabolic analysis, the results suggested that the mitogen-activated protein kinase (MAPK)-dependent ethylene and calcium signalling pathways were two major early cold-responsive mechanisms involved in sprouting shoots and were followed by the induction of the Inducer of CBF Expressions (ICE)-C-repeat binding factors (CBF)-cold-responsive (COR) signalling pathway to augment cold tolerance. During the cold shock, growth, photosynthesis and secondary metabolism-mainly involving flavonoid biosynthesis-were remarkably affected. Notably, the increased starch metabolism, which might be dependent on the high expression of β-amylase3 (BAM3) induced by CBF, played crucial roles in protecting young shoots against freezing cold. A schematic diagram of cold spell response mechanisms specifically involved in the sprouting shoots of the tea plant is ultimately proposed. Some essential transcriptional and metabolic changes were further confirmed in the plant materials under natural cold spell conditions. Our results provide a global view of the reprograming of transcription and metabolism in sprouting tea shoots during a cold spell and meaningful information for future practices.

Survival Mechanisms to Selective Pressures and Implications

Organisms have evolved a spectrum of strategies that facilitate survival in the face of adverse environmental conditions. In order to make full use of the unfavorable resources of nature, human beings usually impose selective pressures to breed phenotypic traits that can survive in adverse environments. Animals are frequently under attack by biotic stress, such as bacterial and viral infections, while plants are more often subjected to abiotic stress, including high salinity, drought, and cold. In response to these diverse stresses, animals and plants initiate wide-ranging changes in gene expression by altering regulation of transcriptional and post-transcriptional activities. Recent studies have identified a number of key responsive components that promote survival of animals and plants in response to biotic and abiotic stresses. Importantly, with recent developments in genome-editing technology based on the CRISPR/Cas9 system, manipulation of genetic elements to generate stress-resistant animals and plants has become both feasible and cost-effective. Herein, we review important mechanisms that govern the response of organisms to biotic and abiotic stresses with the aim of applying our understanding to the agriculture and animal husbandry industries.

Identification of Salt Stress Responding Genes Using Transcriptome Analysis in Green Alga Chlamydomonas reinhardtii

Salinity is one of the most important abiotic stresses threatening plant growth and agricultural productivity worldwide. In green alga Chlamydomonas reinhardtii, physiological evidence indicates that saline stress increases intracellular peroxide levels and inhibits photosynthetic-electron flow. However, understanding the genetic underpinnings of salt-responding traits in plantae remains a daunting challenge. In this study, the transcriptome analysis of short-term acclimation to salt stress (200 mM NaCl for 24 h) was performed in C. reinhardtii. A total of 10,635 unigenes were identified as being differently expressed by RNA-seq, including 5920 up- and 4715 down-regulated unigenes. A series of molecular cues were screened for salt stress response, including maintaining the lipid homeostasis by regulating phosphatidic acid, acetate being used as an alternative source of energy for solving impairment of photosynthesis, and enhancement of glycolysis metabolism to decrease the carbohydrate accumulation in cells. Our results may help understand the molecular and genetic underpinnings of salt stress responses in green alga C. reinhardtii.

Applications of SERS in the Detection of Stress-Related Substances

A wide variety of biotic and abiotic stresses continually attack plants and animals, which adversely affect their growth, development, reproduction, and yield realization. To survive under stress conditions, highly sophisticated and efficient tolerance mechanisms have been evolved to adapt to stresses, which consist of the variation of effector molecules playing vital roles in physiological regulation. The development of a sensitive, facile, and rapid analytical methods for stress factors and effector molecules detection is significant for gaining deeper insight into the tolerance mechanisms. As a nondestructive analysis technique, surface-enhanced Raman spectroscopy (SERS) has unique advantages regarding its biosensing applications. It not only provides specific fingerprint spectra of the target molecules, conformation, and structure, but also has universal capacity for simultaneous detection and imaging of targets owing to the narrow width of the Raman vibrational bands. Herein, recent progress on biotic and abiotic stresses, tolerance mechanisms and effector molecules is summarized. Moreover, the development and promising future trends of SERS detection for stress-related substances combined with nanomaterials as substrates and SERS tags are discussed. This comprehensive and critical review might shed light on a new perspective for SERS applications.

Analysis of Biomolecules Based on the Surface Enhanced Raman Spectroscopy

Analyzing biomolecules is essential for disease diagnostics, food safety inspection, environmental monitoring and pharmaceutical development. Surface-enhanced Raman spectroscopy (SERS) is a powerful tool for detecting biomolecules due to its high sensitivity, rapidness and specificity in identifying molecular structures. This review focuses on the SERS analysis of biomolecules originated from humans, animals, plants and microorganisms, combined with nanomaterials as SERS substrates and nanotags. Recent advances in SERS detection of target molecules were summarized with different detection strategies including label-free and label-mediated types. This comprehensive and critical summary of SERS analysis of biomolecules might help researchers from different scientific backgrounds spark new ideas and proposals.

Mechanisms of Salt Tolerance in Halophytes: Current Understanding and Recent Advances

Halophytes are plants that exhibit high salt tolerance, allowing them to survive and thrive under extremely saline conditions. The study of halophytes advances our understanding about the important adaptations that are required for survival in high salinity conditions, including secretion of salt through the salt glands, regulation of cellular ion homeostasis and osmotic pressure, detoxification of reactive oxygen species, and alterations in membrane composition. To explore the mechanisms that contribute to tolerance to salt stress, salt-responsive genes have been isolated from halophytes and expressed in non-salt tolerant plants using targeted transgenic technologies. In this review, we discuss the mechanisms that underpin salt tolerance in different halophytes.

Histone deacetylase 6 modulates macrophage infiltration during inflammation

Mice with histone deacetylase 6 (HDAC6) deficiency grow and develop normally but exhibit impaired immune response. The molecular mechanisms for this phenotype remain largely elusive.

Methods: A mouse acute peritonitis model was used to study the infiltration of neutrophils and monocyte-derived macrophages. In vitro cell motility assays were performed to analyze monocyte/macrophage recruitment. Fluorescence microscopy and flow cytometry were performed to examine the phagocytic ability of macrophages. Immunofluorescence microscopy was used to investigate protein localization, protrusion formation, and microtubule acetylation.

Results: HDAC6 deficiency does not affect neutrophil infiltration, but instead attenuates the infiltration of monocyte-derived macrophages into the peritoneal cavity. HDAC6 plays a specific role in monocyte/macrophage recruitment. Loss of HDAC6 suppresses the phagocytic capacity of macrophages challenged with E. coli. Lipopolysaccharide stimulation results in the translocation of HDAC6 and cortactin from the cytosol to the cell periphery, promotes the formation of filopodial protrusions, and enhances microtubule acetylation around the microtubule-organizing center, all of which are abrogated by HDAC6 deficiency.

Conclusion: These findings implicate HDAC6 in the innate immune response and suggest that it may serve as a promising target for the treatment of macrophage-associated immune diseases.

Exopolysaccharides from a Codonopsis pilosula endophyte activate macrophages and inhibit cancer cell proliferation and migration

BACKGROUND

Exopolysaccharides with structural diversity have shown wide applications in biomaterial, food, and pharmaceutical industries. Herein, we isolated an endophytic strain, 14-DS-1, from the traditional medicinal plant Codonopsis pilosula to elucidate the characteristics and anti-cancer activities of purified exopolysaccharides.

METHODS

HPLC and GC-MS were conducted to purify and characterize the exopolysaccharides isolated from 14-DS-1. Quantitative RT-PCR, cell migration assays, immunofluorescence staining, and flow cytometry analysis were conducted to investighate the biological activity of DSPS.

RESULTS

We demonstrated that exopolysaccharides isolated from 14-DS-1 (DSPS), which were predominately composed of six monosaccharides, showed anti-cancer activities. Biological activity analysis revealed that exposure to DSPS induced macrophage activation and polarization by promoting the production of TNF-α and nitric oxide. Further analysis revealed that DSPS treatment promoted macrophage infiltration, whereas cancer cell migration was suppressed. In addition, DSPS exposure led to S-phase arrest and apoptosis in cancer cells. Immunofluorescence staining revealed that treatment with DSPS resulted in defects in spindle orientation and positioning.

CONCLUSION

These findings thus suggest that DSPS may have promising potential in cancer therapy.

Molecular mechanisms underlying stress response and adaptation

Environmental stresses are ubiquitous and unavoidable to all living things. Organisms respond and adapt to stresses through defined regulatory mechanisms that drive changes in gene expression, organismal morphology, or physiology. Immune responses illustrate adaptation to bacterial and viral biotic stresses in animals. Dysregulation of the genotoxic stress response system is frequently associated with various types of human cancer. With respect to plants, especially halophytes, complicated systems have been developed to allow for plant growth in high salt environments. In addition, drought, waterlogging, and low temperatures represent other common plant stresses. In this review, we summarize representative examples of organismal response and adaptation to various stresses. We also discuss the molecular mechanisms underlying the above phenomena with a focus on the improvement of organismal tolerance to unfavorable environments.