Genome-Wide Transcriptomic and Proteomic Exploration of Molecular Regulations in Quinoa Responses to Ethylene and Salt Stress

Quinoa (Chenopodiumquinoa Willd.), originated from the Andean region of South America, shows more significant salt tolerance than other crops. To reveal how the plant hormone ethylene is involved in the quinoa responses to salt stress, 4-week-old quinoa seedlings of ‘NL-6′ treated with water, sodium chloride (NaCl), and NaCl with ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC) were collected and analyzed by transcriptional sequencing and tandem mass tag-based (TMT) quantitative proteomics. A total of 9672 proteins and 60,602 genes was identified. Among them, the genes encoding glutathione S-transferase (GST), peroxidase (POD), phosphate transporter (PT), glucan endonuclease (GLU), beta-galactosidase (BGAL), cellulose synthase (CES), trichome birefringence-like protein (TBL), glycine-rich cell wall structural protein (GRP), glucosyltransferase (GT), GDSL esterase/lipase (GELP), cytochrome P450 (CYP), and jasmonate-induced protein (JIP) were significantly differentially expressed. Further analysis suggested that the genes may mediate through osmotic adjustment, cell wall organization, reactive oxygen species (ROS) scavenging, and plant hormone signaling to take a part in the regulation of quinoa responses to ethylene and salt stress. Our results provide a strong foundation for exploration of the molecular mechanisms of quinoa responses to ethylene and salt stress.

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Transcriptomic profiling identifies candidate genes involved in salt tolerance of the xerophyte Pugionium cornutum

10.21203/rs.2.14265/v1 ◽

2019 ◽

Author(s):

Yan-Nong Cui ◽

Fang-Zhen Wang ◽

Cheng-Hang Yang ◽

Jian-Zhen Yuan ◽

Huan Guo ◽

...

Keyword(s):

Salt Stress ◽

Salt Tolerance ◽

Candidate Genes ◽

Molecular Mechanisms ◽

Carbon Fixation ◽

Assimilation Efficiency ◽

Carbon Assimilation ◽

Inorganic Ions ◽

Ros Scavenging ◽

Genes Encoding

Abstract Background: Pugionium cornutum is a xerophytic plant that primarily adapts to salt stress by accumulating inorganic ions (e.g., Cl-) for osmoregulation, improving its reactive oxygen species (ROS)-scavenging ability and maintaining high photosynthetic carbon assimilation efficiency, but the associated molecular mechanisms still remain unclear. Results: Here, we present an analysis of gene responses to salt stress based on the transcriptome of P. cornutum exposed to 50 mM NaCl treatment. The data revealed that, after NaCl treatment for 6 or 24 h, the transcript levels of multiple genes encoding proteins facilitating Cl- accumulation and NO3- homeostasis such as SLAH1, CLCg, CCC1, and NPF6.4, as well as the transport of other major inorganic osmoticums were significantly upregulated in roots and shoots, which should be favorable to enhancing osmotic adjustment capacity and maintaining the plant uptake and transport of nutrient elements; a large number of genes related to ROS-scavenging pathways were also significantly upregulated, which should be beneficial for mitigating salt-induced oxidative damage to the cell metabolism. Meanwhile, many genes encoding components of the photosynthetic electron transport and carbon fixation enzymes were significantly upregulated in shoots after salt treatment, possibly resulting in a high carbon assimilation efficiency in P. cornutum. Additionally, numerous salt-inducible transcription factor genes probably regulating the abovementioned processes were found. Conclusion: Candidate genes involved in salt tolerance of P. cornutum were identified, which lays a preliminary foundation for clarifying the molecular mechanism of the xerophytes adapting to harsh environments.

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Transcriptomic profiling identifies candidate genes involved in salt tolerance of the xerophyte Pugionium cornutum

10.21203/rs.2.14265/v2 ◽

2019 ◽

Author(s):

Yan-Nong Cui ◽

Fang-Zhen Wang ◽

Cheng-Hang Yang ◽

Jian-Zhen Yuan ◽

Huan Guo ◽

...

Keyword(s):

Salt Stress ◽

Salt Tolerance ◽

Candidate Genes ◽

Molecular Mechanisms ◽

Carbon Fixation ◽

Assimilation Efficiency ◽

Carbon Assimilation ◽

Inorganic Ions ◽

Ros Scavenging ◽

Genes Encoding

Abstract Background: Pugionium cornutum is a xerophytic plant that primarily adapts to salt stress by accumulating inorganic ions (e.g., Cl - ) for osmoregulation, improving its reactive oxygen species (ROS)-scavenging ability and maintaining high photosynthetic carbon assimilation efficiency, but the associated molecular mechanisms still remain unclear. Results : Here, we present an analysis of gene responses to salt stress based on the transcriptome of P. cornutum exposed to 50 mM NaCl treatment. The data revealed that, after NaCl treatment for 6 or 24 h, the transcript levels of multiple genes encoding proteins facilitating Cl - accumulation and NO 3 - homeostasis such as SLAH1, CLCg, CCC1, and NPF6.4, as well as the transport of other major inorganic osmoticums were significantly upregulated in roots and shoots, which should be favorable to enhancing osmotic adjustment capacity and maintaining the plant uptake and transport of nutrient elements; a large number of genes related to ROS-scavenging pathways were also significantly upregulated, which should be beneficial for mitigating salt-induced oxidative damage to the cell metabolism. Meanwhile, many genes encoding components of the photosynthetic electron transport and carbon fixation enzymes were significantly upregulated in shoots after salt treatment, possibly resulting in a high carbon assimilation efficiency in P. cornutum . Additionally, numerous salt-inducible transcription factor genes probably regulating the abovementioned processes were found. Conclusion : Candidate genes involved in salt tolerance of P. cornutum were identified, which lays a preliminary foundation for clarifying the molecular mechanism of the xerophytes adapting to harsh environments.

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Transcriptome Changes Reveal the Molecular Mechanisms of Humic Acid-Induced Salt Stress Tolerance in Arabidopsis

Molecules ◽

10.3390/molecules26040782 ◽

2021 ◽

Vol 26 (4) ◽

pp. 782

Author(s):

Joon-Yung Cha ◽

Sang-Ho Kang ◽

Myung Geun Ji ◽

Gyeong-Im Shin ◽

Song Yi Jeong ◽

...

Keyword(s):

Salt Stress ◽

Abiotic Stress ◽

Humic Acid ◽

Stress Tolerance ◽

Plant Development ◽

Molecular Mechanisms ◽

Abiotic Stress Tolerance ◽

Principal Component ◽

Salt Stress Tolerance ◽

Genes Encoding

Humic acid (HA) is a principal component of humic substances, which make up the complex organic matter that broadly exists in soil environments. HA promotes plant development as well as stress tolerance, however the precise molecular mechanism for these is little known. Here we conducted transcriptome analysis to elucidate the molecular mechanisms by which HA enhances salt stress tolerance. Gene Ontology Enrichment Analysis pointed to the involvement of diverse abiotic stress-related genes encoding HEAT-SHOCK PROTEINs and redox proteins, which were up-regulated by HA regardless of salt stress. Genes related to biotic stress and secondary metabolic process were mainly down-regulated by HA. In addition, HA up-regulated genes encoding transcription factors (TFs) involved in plant development as well as abiotic stress tolerance, and down-regulated TF genes involved in secondary metabolic processes. Our transcriptome information provided here provides molecular evidences and improves our understanding of how HA confers tolerance to salinity stress in plants.

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Transcriptomic Profiling Identifies Candidate Genes Involved in the Salt Tolerance of the Xerophyte Pugionium cornutum

Genes ◽

10.3390/genes10121039 ◽

2019 ◽

Vol 10 (12) ◽

pp. 1039 ◽

Cited By ~ 1

Author(s):

Yan-Nong Cui ◽

Fang-Zhen Wang ◽

Cheng-Hang Yang ◽

Jian-Zhen Yuan ◽

Huan Guo ◽

...

Keyword(s):

Salt Stress ◽

Salt Tolerance ◽

Candidate Genes ◽

Osmotic Adjustment ◽

Assimilation Efficiency ◽

Carbon Assimilation ◽

Ros Scavenging ◽

Transport Pathway ◽

Genes Encoding ◽

Assimilation Capacity

The xerophyte Pugionium cornutum adapts to salt stress by accumulating inorganic ions (e.g., Cl−) for osmotic adjustment and enhancing the activity of antioxidant enzymes, but the associated molecular basis remains unclear. In this study, we first found that P. cornutum could also maintain cell membrane stability due to its prominent ROS-scavenging ability and exhibits efficient carbon assimilation capacity under salt stress. Then, the candidate genes associated with the important physiological traits of the salt tolerance of P. cornutum were identified through transcriptomic analysis. The results showed that after 50 mM NaCl treatment for 6 or 24 h, multiple genes encoding proteins facilitating Cl− accumulation and NO3− homeostasis, as well as the transport of other major inorganic osmoticums, were significantly upregulated in roots and shoots, which should be favorable for enhancing osmotic adjustment capacity and maintaining the uptake and transport of nutrient elements; a large number of genes related to ROS-scavenging pathways were also significantly upregulated, which might be beneficial for mitigating salt-induced oxidative damage to the cells. Meanwhile, many genes encoding components of the photosynthetic electron transport pathway and carbon fixation enzymes were significantly upregulated in shoots, possibly resulting in high carbon assimilation efficiency in P. cornutum. Additionally, numerous salt-inducible transcription factor genes that probably regulate the abovementioned processes were found. This work lays a preliminary foundation for clarifying the molecular mechanism underlying the adaptation of xerophytes to harsh environments.

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Transcriptome and Proteome Profiling Revealed Molecular Mechanism of Selenium Responses in Bread Wheat (Triticum Aestivum L.)

10.21203/rs.3.rs-795746/v1 ◽

2021 ◽

Author(s):

Qian Ma ◽

Xiaoqing Feng

Keyword(s):

Molecular Mechanism ◽

Bread Wheat ◽

Triticum Aestivum L ◽

Ros Scavenging ◽

Glutathione S Transferase ◽

Cysteine Synthase ◽

Wheat Seedlings ◽

Oxidative Stresses ◽

Tandem Mass Tag ◽

Shock Proteins

Abstract Background: Although selenium (Se) plays important roles in scavenging free radicals, alleviating oxidative stresses, and strengthening immune system, the knowledge about Se response in bread wheat is still limited. In order to clarify the molecular mechanism of Se response in bread wheat, 2-week-old wheat seedlings of cultivar ‘Jimai22’ treated with 10 μM disodium selenate (Na2SeO4) for 0 h, 3 h, and 24 h were collected and analyzed by transcriptional sequencing and tandem mass tag-based (TMT) quantitative proteomics. Results: At least 11656 proteins and 133911 genes were identified, and proteins including ATP sulfurylase (APS), cysteine synthase (CS), SeCys lyase, sulfate transporters, glutathione S-transferase (GSTs), glutathione peroxidase (GSH-Px), glutaredoxins (GRXs), superoxide dismutases (SODs), catalases (CATs), heat shock proteins (HSPs), UDP-glycose flavonoid glycosyltransferases (UFGTs), sucrose-6-phosphate hydrolases (Suc-6-PHs), archaeal phosphoglucose isomerases (APGIs), malate synthases (MSs), and endo-1,4-beta-xylanase (Xyn) in Se accumulation, ROS scavenging, secondary metabolism, and carbohydrate metabolism were significantly differently expressed.Conclusions: This is the first complementary analyses of the transcriptome and proteome related with selenium responses in bread wheat. Our work enhances the understanding about the molecular mechanism of selenium responses in bread wheat.

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Developmental Transcript Profiling of Cyst Nematode Feeding Cells in Soybean Roots

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi-20-5-0510 ◽

2007 ◽

Vol 20 (5) ◽

pp. 510-525 ◽

Cited By ~ 167

Author(s):

Nagabhushana Ithal ◽

Justin Recknor ◽

Dan Nettleton ◽

Tom Maier ◽

Thomas J. Baum ◽

...

Keyword(s):

Cell Wall ◽

Soybean Cyst Nematode ◽

Molecular Mechanisms ◽

Cyst Nematode ◽

Transcript Profiling ◽

Cyst Nematodes ◽

Root Cells ◽

Genes Encoding ◽

Soybean Roots ◽

And Function

Cyst nematodes of the genus Heterodera are obligate, sedentary endoparasites that have developed highly evolved relationships with specific host plant species. Successful parasitism involves significant physiological and morphological changes to plant root cells for the formation of specialized feeding cells called syncytia. To better understand the molecular mechanisms that lead to the development of nematode feeding cells, transcript profiling was conducted on developing syncytia induced by the soybean cyst nematode Heterodera glycines in soybean roots by coupling laser capture microdissection with high-density oligonucleotide microarray analysis. This approach has identified pathways that may play intrinsic roles in syncytium induction, formation, and function. Our data suggest interplay among phytohormones that likely regulates synchronized changes in the expression of genes encoding cell-wall-modifying proteins. This process appears to be tightly controlled and coordinately regulated with cell wall rigidification processes that may involve lignification of feeding cell walls. Our data also show local downregulation of jasmonic acid biosynthesis and responses in developing syncytia, which suggest a local suppression of plant defense mechanisms. Moreover, we identified genes encoding putative transcription factors and components of signal transduction pathways that may be important in the regulatory processes governing syncytium formation and function. Our analysis provides a broad mechanistic picture that forms the basis for future hypothesis-driven research to understand cyst nematode parasitism and to develop effective management tools against these pathogens.

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Comparative Transcriptome Analysis of Halophyte Zoysia macrostachya in Response to Salinity Stress

Plants ◽

10.3390/plants9040458 ◽

2020 ◽

Vol 9 (4) ◽

pp. 458 ◽

Cited By ~ 2

Author(s):

Rong Wang ◽

Xi Wang ◽

Kuan Liu ◽

Xue-Jie Zhang ◽

Luo-Yan Zhang ◽

...

Keyword(s):

Salt Stress ◽

Salt Tolerance ◽

Molecular Mechanisms ◽

Plant Hormone ◽

Ion Homeostasis ◽

Oxygen Species ◽

Molecular Processes ◽

Salt Tolerant ◽

Salt Glands ◽

Differently Expressed Genes

As one of the most severe environmental stresses, salt stress can cause a series of changes in plants. In salt tolerant plant Zoysia macrostachya, germination, physiology, and genetic variation under salinity have been studied previously, and the morphology and distribution of salt glands have been clarified. However, no study has investigated the transcriptome of such species under salt stress. In the present study, we compared transcriptome of Z. macrostachya under normal conditions and salt stress (300 mmol/L NaCl, 24 h) aimed to identify transcriptome responses and molecular mechanisms under salt stress in Z. macrostachya. A total of 8703 differently expressed genes (DEGs) were identified, including 4903 up-regulated and 3800 down-regulated ones. Moreover, a series of molecular processes were identified by Gene Ontology (GO) analysis, and these processes were suggested to be closely related to salt tolerance in Z. macrostachya. The identified DEGs concentrated on regulating plant growth via plant hormone signal transduction, maintaining ion homeostasis via salt secretion and osmoregulatory substance accumulation and preventing oxidative damage via increasing the activity of ROS (reactive oxygen species) scavenging system. These changes may be the most important responses of Z. macrostachya under salt stress. Some key genes related to salt stress were identified meanwhile. Collectively, our findings provided valuable insights into the molecular mechanisms and genetic underpinnings of salt tolerance in Z. macrostachya.

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Transcriptome Analysis of Salt Stress Response in Roots of Halophyte Zoysia macrostachya

International Journal of Agriculture and Biology ◽

10.17957/ijab/15.1705 ◽

2021 ◽

Vol 25 (03) ◽

pp. 591-600

Author(s):

Huaguang Hu

Keyword(s):

Salt Stress ◽

Salt Tolerance ◽

Transcriptome Analysis ◽

Molecular Mechanisms ◽

Expression Profiles ◽

Transcript Abundance ◽

Nacl Stress ◽

Ros Scavenging ◽

Salt Stress Response ◽

Sequencing Platform

Zoysia macrostachya Franch. et Sav. is a halophyte with very strong tolerance to salinity, which can serve as an alternative turfgrass for landscaping in saline-alkali land and provide the salt-tolerance genes for turfgrass breeding. To further illustrate the salt-tolerance mechanisms in this species at molecular level, the roots transcriptome of Z. macrostachya was investigated under salt stress using the Illumina sequencing platform. Altogether 47,325 unigenes were assembled, among which, 32,542 (68.76%) were annotated, and 87.61% clean reads were mapped to the unigenes. Specifically, 14,558 unigenes were shown to be the differentially expressed genes (DEGs) following exposure to 710 mM NaCl stress compared with control, including 7972 up-regulated and 6586 down-regulated DEGs. Among these DEGs, 24 were associated with the reactive oxygen species (ROS) scavenging system, 61 were found to be related to K+ and Na+ transportation, and 16 were related to the metabolism of osmotic adjustment substances. Additionally, 2327 DEGs that encoded the transcription factors (TFs) were also identified. The expression profiles for 10 DEGs examined through quantitative real-time PCR conformed to the individual alterations of transcript abundance verified through RNA-Seq. Taken together, results of transcriptome analysis in this study provided useful insights for salt-tolerance molecular mechanisms of Z. macrostachya. Furthermore, these DEGs under salt stress provided important clues for future salt-tolerance genes cloning of Z. macrostachya. © 2021 Friends Science Publishers

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Salinity stress-induced modification of pectin activates stress signaling pathways and requires HERK/THE and FER to attenuate the response

10.1101/2020.12.18.423458 ◽

2020 ◽

Author(s):

Nora Gigli-Bisceglia ◽

Eva Van Zelm ◽

Wenying Huo ◽

Jasper Lamers ◽

Christa Testerink

Keyword(s):

Cell Wall ◽

Salt Stress ◽

Signaling Pathways ◽

Stress Responses ◽

Molecular Mechanisms ◽

Structural Integrity ◽

Marker Gene ◽

Mitogen Activated Protein Kinase ◽

Growth And Yield ◽

Receptor Like Kinase

AbstractSoil salinity is an increasing worldwide problem for agriculture, affecting plant growth and yield. In our attempt to understand the molecular mechanisms activated in response to salt in plants, we investigated the Catharanthus roseus Receptor like Kinase 1 Like (CrRLK1L) family, which contains well described sensors previously shown to be involved in maintaining and sensing the structural integrity of the cell walls. We have observed that herk1the1-4 double mutants, lacking the function of the Arabidopsis thaliana Receptor like Kinase HERKULES1 combined with a gain of function allele of THESEUS1, phenocopied the phenotypes previously reported in plants lacking FERONIA (FER) function. We report that both fer-4 and herk1the1-4 mutants respond strongly to salt application, resulting in a more intense activation of early and late stress responses. We also show that salt triggers de-methyl esterification of loosely bound pectins. These cell wall modifications might be partly responsible for the activation of the signaling pathways required to activate salt stress responses. In fact, by adding calcium chloride or by chemically inhibiting pectin methyl esterase (PME) activity we observed reduced activation of the early signaling protein Mitogen Activated Protein Kinase 6 (MPK6) as well as a reduced amplitude in salt-induced marker gene induction. We show that MPK6 is required for the full induction of the salt-induced gene expression markers we tested. However, the sodium specific root halotropism response is likely regulated by a different branch of the pathway being independent of MPK6 or calcium application but influenced by the cell wall sensors FER/HERK1/THE1-4 and PME activity. We hypothesize a model where salt-triggered modification of pectin requires the functionality of FER alone or the HERK1/THE1 combination to attenuate salt responses. Collectively, our results show the complexity of salt stress responses and salt sensing mechanisms and their connection to cell wall modifications, likely being in part responsible for the response phenotypes observed in salt treated plants.

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