Metabolomic and transcriptomic analysis of Lycium chinese and L. ruthenicum under salinity stress

Abstract Background High soil salinity often adversely affects plant physiology and agricultural productivity of almost all crops worldwide, such as the crude drug known as wolfberry. However, the mechanism of this action in wolfberry is not fully understood yet. Results Here in this study, we studied different mechanisms potentially in Chinese wolfberry (Lycium chinese, LC) and black wolfberry (L. ruthenicum, LR) under salinity stress, by analyzing their transcriptome, metabolome, and hormone changes. The hormone detection analysis revealed that the ABA content was significantly lower in LR than LC under normal condition, and increased sharply under salinity stress in LR but not in LC. The transcriptome analysis showed that the salinity-responsive genes in wolfberry were mainly enriched in MAPK signaling, amino sugar and nucleotide sugar metabolism, carbon metabolism, and plant hormone signal transduction pathways in LC, while mainly related to carbon metabolism and protein processing in endoplasmic reticulum in LR. Metabolome results indicated that LR harbored higher flavone and flavonoid contents than LC under normal condition. However, the flavone and flavonoid contents were hardly changed in LR, but increased substantially in LC when exposed to salinity stress. Conclusions Our results adds ABA and flavone to mechanism understanding of salinity tolerance in wolfberry. In addition, flavone plays a positive role in resistance to salinity stress in wolfberry.

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Metabolomic and Transcriptomic Analysis of Lycium chinese and L. ruthenicum Under Salinity Stress

10.21203/rs.3.rs-384516/v1 ◽

2021 ◽

Author(s):

Xiaoya Qin ◽

Yue Yin ◽

Jianhua Zhao ◽

Wei An ◽

Yunfang Fan ◽

...

Keyword(s):

Salinity Stress ◽

Carbon Metabolism ◽

Sugar Metabolism ◽

Amino Sugar ◽

Mapk Signaling ◽

Flavonoid Content ◽

Positive Role ◽

Detection Analysis ◽

Mechanistic Basis ◽

Almost All

Abstract Background: High soil salinity often adversely affects plant physiology and agricultural productivity of almost all crops worldwide, including the crude drug known as wolfberry. However, the mechanistic basis of this action in wolfberry is not fully understood yet.Results: Here in this study, we studied potentials different mechanisms in Chinese wolfberry (Lycium chinese, LC) and black wolfberry (L. ruthenicum, LR) under salinity stress, by analyzing their transcriptome and metabolome. The hormone detection analysis revealed that the ABA content was significantly lower in LR than LC under normal conditions, but increased sharply under salinity stress in LR but not in LC. The transcriptome analysis showed that the enriched salinity-responsive genes in wolfberry were mainly related to MAPK signaling, amino sugar and nucleotide sugar metabolism, carbon metabolism, and plant hormone signal transduction pathways in LC, while mainly related to carbon metabolism and protein processing in endoplasmic reticulum in LR. Metabolome results indicated that LR harbored higher flavone and flavonoid content than LC under normal conditions. However, when exposed to salinity stress, flavone and flavonoid content hardly changed in LR, whereas flavonoid and flavone biosynthesis was activated to resist to salinity stress in LC.Conclusions: Our results adds ABA and flavone metabolism to mechanistic understanding of salinity tolerance in wolfberry. In addition, flavone play a positive role in resistance to salinity stress in wolfberry.

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Transcriptome analysis of resistant and susceptible pepper (Capsicum annuum L.) in response to Xanthomonas campestris pv. Vesicatoria

10.1101/2020.09.24.311274 ◽

2020 ◽

Author(s):

Shenghua Gao ◽

Fei Wang ◽

Juntawong Niran ◽

Ning Li ◽

Yanxu Yin ◽

...

Keyword(s):

Transcriptome Analysis ◽

Xanthomonas Campestris ◽

Molecular Mechanisms ◽

Sugar Metabolism ◽

Amino Sugar ◽

Mapk Signaling ◽

Susceptible Variety ◽

Differentially Expressed ◽

Resistant Variety ◽

Sequencing Platform

AbstractBacterial spot (BS) disease of pepper, incited by Xanthomonas campestris pv. Vesicatoria (Xcv), is one of the most serious diseases. For a comparative analysis of defense response to Xcv infection, we performed a transcriptome analysis of BS -susceptible cultivar ECW and -resistant cultivar VI037601 using the HiSeq™ 2500 sequencing platform. Approximately 140.15 G clean data were generated from eighteen libraries. From the libraries generated, we identified 52,041 genes including 35,336 reference genes, 16,705 novel transcripts, and 4,794 differentially expressed genes (DEGs). There were 1,291, 2,956, 1,795 and 2,448 DEGs in ECW-24h-vs-ECW-0h, ECW-48h-vs-ECW-0h, VI037601-24h-vs-VI037601-0h and VI037601-48h-vs-VI037601-0h groups, respectively. Interestingly, DEGs involved in disease response in the resistant variety were induced at an earlier stage and at higher levels compared with the susceptible variety. Key enriched categories included amino sugar and nucleotide sugar metabolism, sesquiterpenoid and triterpenoid biosynthesis and MAPK signaling pathway. Moreover, 273 DEGs only differentially expressed in VI037601 and 436 overlapping DEGs in ECW and VI037601 post Xcv inoculation, including NBS-LRR genes, oxidoreductase gene, WRKY and NAC transcription factors were identified, which were mainly involved in metabolic process, response to stimulus and biological regulation pathways. Quantitative RT-PCR of sixteen selected DEGs further validated the RNA-seq differential gene expression analysis. Our results will provide a valuable resource for understanding the molecular mechanisms of pepper resistance to Xcv infection and improving pepper resistance cultivars against Xcv.

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Genome-Wide Transcriptional Changes of Rhodosporidium kratochvilovae at Low Temperature

Frontiers in Microbiology ◽

10.3389/fmicb.2021.727105 ◽

2021 ◽

Vol 12 ◽

Author(s):

Rui Guo ◽

Meixia He ◽

Xiaoqing Zhang ◽

Xiuling Ji ◽

Yunlin Wei ◽

...

Keyword(s):

Low Temperature ◽

Temperature Response ◽

Sugar Metabolism ◽

Enrichment Analysis ◽

Amino Sugar ◽

Mapk Signaling ◽

Pathway Enrichment Analysis ◽

Rna Seq ◽

Deep Sequencing Technology ◽

Rhodosporidium Kratochvilovae

Rhodosporidium kratochvilovae strain YM25235 is a cold-adapted oleaginous yeast strain that can grow at 15°C. It is capable of producing polyunsaturated fatty acids. Here, we used the Nanopore Platform to first assemble the R. kratochvilovae strain YM25235 genome into a 23.71 Mb size containing 46 scaffolds and 8,472 predicted genes. To explore the molecular mechanism behind the low temperature response of R. kratochvilovae strain YM25235, we analyzed the RNA transcriptomic data from low temperature (15°C) and normal temperature (30°C) groups using the next-generation deep sequencing technology (RNA-seq). We identified 1,300 differentially expressed genes (DEGs) by comparing the cultures grown at low temperature (15°C) and normal temperature (30°C) transcriptome libraries, including 553 significantly upregulated and 747 significantly downregulated DEGs. Gene ontology and pathway enrichment analysis revealed that DEGs were primarily related to metabolic processes, cellular processes, cellular organelles, and catalytic activity, whereas the overrepresented pathways included the MAPK signaling pathway, metabolic pathways, and amino sugar and nucleotide sugar metabolism. We validated the RNA-seq results by detecting the expression of 15 DEGs using qPCR. This study provides valuable information on the low temperature response of R. kratochvilovae strain YM25235 for further research and broadens our understanding for the response of R. kratochvilovae strain YM25235 to low temperature.

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Interplay among Antioxidant System, Hormone Profile and Carbohydrate Metabolism during Bud Dormancy Breaking in a High-Chill Peach Variety

Antioxidants ◽

10.3390/antiox10040560 ◽

2021 ◽

Vol 10 (4) ◽

pp. 560

Author(s):

José A. Hernández ◽

Pedro Díaz-Vivancos ◽

José Ramón Acosta-Motos ◽

Nuria Alburquerque ◽

Domingo Martínez ◽

...

Keyword(s):

Starch Content ◽

Sugar Metabolism ◽

Bud Dormancy ◽

Dormancy Breaking ◽

Prunus Species ◽

Physiological Factors ◽

Antioxidant Metabolism ◽

Hormone Profile ◽

Aba Content ◽

Gas Ratio

(1) Background: Prunus species have the ability to suspend (induce dormancy) and restart growth, in an intricate process in which environmental and physiological factors interact. (2) Methods: In this work, we studied the evolution of sugars, antioxidant metabolism, and abscisic acid (ABA) and gibberellins (GAs) levels during bud dormancy evolution in a high-chill peach variety, grown for two seasons in two different geographical areas with different annual media temperature, a cold (CA) and a temperate area (TA). (3) Results: In both areas, starch content reached a peak at ecodormancy, and then decreased at dormancy release (DR). Sorbitol and sucrose declined at DR, mainly in the CA. In contrast, glucose and fructose levels progressively rose until DR. A decline in ascorbate peroxidase, dehydroascorbate reductase, superoxide dismutase and catalase activities occurred in both seasons at DR. Moreover, the H2O2-sensitive SOD isoenzymes, Fe-SOD and Cu,Zn-SOD, and two novel peroxidase isoenzymes, were detected. Overall, these results suggest the occurrence of a controlled oxidative stress during DR. GA7 was the major bioactive GA in both areas, the evolution of its levels being different between seasons and areas. In contrast, ABA content decreased during the dormancy period in both areas, resulting in a reduction in the ABA/total GAs ratio, being more evident in the CA. (4) Conclusion: A possible interaction sugars-hormones-ROS could take place in high-chill peach buds, favoring the DR process, suggesting that, in addition to sugar metabolism, redox interactions can govern bud DR, regardless of chilling requirements.

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Sugars promote graft union development in the heterograft of cucumber onto pumpkin

Horticulture Research ◽

10.1038/s41438-021-00580-5 ◽

2021 ◽

Vol 8 (1) ◽

Author(s):

Li Miao ◽

Qing Li ◽

Tian-shu Sun ◽

Sen Chai ◽

Changlin Wang ◽

...

Keyword(s):

Sugar Content ◽

Healing Process ◽

Energy Charge ◽

Sugar Metabolism ◽

Union Formation ◽

Graft Union ◽

Positive Role ◽

Exogenous Glucose ◽

Expression Of Genes ◽

Graft Interface

AbstractThe use of heterografts is widely applied for the production of several important commercial crops, but the molecular mechanism of graft union formation remains poorly understood. Here, cucumber grafted onto pumpkin was used to study graft union development, and genome-wide tempo-spatial gene expression at the graft interface was comprehensively investigated. Histological analysis suggested that resumption of the rootstock growth occurred after both phloem and xylem reconnection, and the scion showed evident callus production compared with the rootstock 3 days after grafting. Consistently, transcriptome data revealed specific responses between the scion and rootstock in the expression of genes related to cambium development, the cell cycle, and sugar metabolism during both vascular reconnection and healing, indicating distinct mechanisms. Additionally, lower levels of sugars and significantly changed sugar enzyme activities at the graft junction were observed during vascular reconnection. Next, we found that the healing process of grafted etiolated seedlings was significantly delayed, and graft success, xylem reconnection, and the growth of grafted plants were enhanced by exogenous glucose. This demonstrates that graft union formation requires the correct sugar content. Furthermore, we also found that graft union formation was delayed with a lower energy charge by the target of rapamycin (TOR) inhibitor AZD-8055, and xylem reconnection and the growth of grafted plants were enhanced under AZD-8055 with exogenous glucose treatment. Taken together, our results reveal that sugars play a positive role in graft union formation by promoting the growth of cucumber/pumpkin and provide useful information for understanding graft union healing and the application of heterografting in the future.

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BRAF mutation in hairy cell leukemia

Oncology Reviews ◽

10.4081/oncol.2014.253 ◽

2014 ◽

Cited By ~ 6

Author(s):

Ahmad Ahmadzadeh ◽

Saeid Shahrabi ◽

Kaveh Jaseb ◽

Fatemeh Norozi ◽

Mohammad Shahjahani ◽

...

Keyword(s):

B Cell ◽

Hairy Cell Leukemia ◽

Mapk Signaling ◽

Mitogen Activated Protein Kinase ◽

Braf V600e ◽

Common Mutation ◽

Hairy Cell ◽

Cell Leukemia ◽

Mitogen Activated Protein ◽

Almost All

BRAF is a serine/threonine kinase with a regulatory role in the mitogen-activated protein kinase (MAPK) signaling pathway. A mutation in the RAF gene, especially in BRAF protein, leads to an increased stimulation of this cascade, causing uncontrolled cell division and development of malignancy. Several mutations have been observed in the gene coding for this protein in a variety of human malignancies, including hairy cell leukemia (HCL). BRAF V600E is the most common mutation reported in exon15 of BRAF, which is observed in almost all cases of classic HCL, but it is negative in other B-cell malignancies, including the HCL variant. Therefore it can be used as a marker to differentiate between these B-cell disorders. We also discuss the interaction between miRNAs and signaling pathways, including MAPK, in HCL. When this mutation is present, the use of BRAF protein inhibitors may represent an effective treatment. In this review we have evaluated the role of the mutation of the BRAF gene in the pathogenesis and progression of HCL.

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Transcriptome analysis of bread wheat leaves in response to salt stress

PLoS ONE ◽

10.1371/journal.pone.0254189 ◽

2021 ◽

Vol 16 (7) ◽

pp. e0254189

Author(s):

Nazanin Amirbakhtiar ◽

Ahmad Ismaili ◽

Mohammad-Reza Ghaffari ◽

Raheleh Mirdar Mansuri ◽

Sepideh Sanjari ◽

...

Keyword(s):

Salt Tolerance ◽

Salinity Stress ◽

Expression Patterns ◽

Transcript Abundance ◽

Crop Productivity ◽

Mapk Signaling ◽

Salt Tolerant ◽

Illumina Hiseq ◽

Phenylpropanoid Biosynthesis ◽

Wheat Leaves

Salinity is one of the main abiotic stresses limiting crop productivity. In the current study, the transcriptome of wheat leaves in an Iranian salt-tolerant cultivar (Arg) was investigated in response to salinity stress to identify salinity stress-responsive genes and mechanisms. More than 114 million reads were generated from leaf tissues by the Illumina HiSeq 2500 platform. An amount of 81.9% to 85.7% of reads could be mapped to the wheat reference genome for different samples. The data analysis led to the identification of 98819 genes, including 26700 novel transcripts. A total of 4290 differentially expressed genes (DEGs) were recognized, comprising 2346 up-regulated genes and 1944 down-regulated genes. Clustering of the DEGs utilizing Kyoto Encyclopedia of Genes and Genomes (KEGG) indicated that transcripts associated with phenylpropanoid biosynthesis, transporters, transcription factors, hormone signal transduction, glycosyltransferases, exosome, and MAPK signaling might be involved in salt tolerance. The expression patterns of nine DEGs were investigated by quantitative real-time PCR in Arg and Moghan3 as the salt-tolerant and susceptible cultivars, respectively. The obtained results were consistent with changes in transcript abundance found by RNA-sequencing in the tolerant cultivar. The results presented here could be utilized for salt tolerance enhancement in wheat through genetic engineering or molecular breeding.

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Alterations of gut microbiota in gestational diabetes patients during the second trimester of pregnancy in the Shanghai Han population

Journal of Translational Medicine ◽

10.1186/s12967-021-03040-9 ◽

2021 ◽

Vol 19 (1) ◽

Author(s):

Yao Su ◽

Hong-Kun Wang ◽

Xu-Pei Gan ◽

Li Chen ◽

Yan-Nan Cao ◽

...

Keyword(s):

Gestational Diabetes ◽

Gut Microbiota ◽

Gut Microbiome ◽

Sugar Metabolism ◽

16S Rrna Gene Sequencing ◽

Amino Sugar ◽

Fecal Microbiota ◽

Rrna Gene ◽

Second Trimester ◽

Metabolic Hormone

Abstract Background The causes of gestational diabetes mellitus (GDM) are still unclear. Recent studies have found that the imbalance of the gut microbiome could lead to disorders of human metabolism and immune system, resulting in GDM. This study aims to reveal the different gut compositions between GDM and normoglycemic pregnant women and find the relationship between gut microbiota and GDM. Methods Fecal microbiota profiles from women with GDM (n = 21) and normoglycemic women (n = 32) were assessed by 16S rRNA gene sequencing. Fasting metabolic hormone concentrations were measured using multiplex ELISA. Results Metabolic hormone levels, microbiome profiles, and inferred functional characteristics differed between women with GDM and healthy women. Additionally, four phyla and seven genera levels have different correlations with plasma glucose and insulin levels. Corynebacteriales (order), Nocardiaceae (family), Desulfovibrionaceae (family), Rhodococcus (genus), and Bacteroidetes (phylum) may be the taxonomic biomarkers of GDM. Microbial gene functions related to amino sugar and nucleotide sugar metabolism were found to be enriched in patients with GDM. Conclusion Our study indicated that dysbiosis of the gut microbiome exists in patients with GDM in the second trimester of pregnancy, and gut microbiota might be a potential diagnostic biomarker for the diagnosis, prevention, and treatment of GDM.

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The keystone species of Precambrian deep bedrock biosphere belong to <i>Burkholderiales</i> and <i>Clostridiales</i>

Biogeosciences Discussions ◽

10.5194/bgd-12-18103-2015 ◽

2015 ◽

Vol 12 (21) ◽

pp. 18103-18150 ◽

Cited By ~ 3

Author(s):

L. Purkamo ◽

M. Bomberg ◽

R. Kietäväinen ◽

H. Salavirta ◽

M. Nyyssönen ◽

...

Keyword(s):

Microbial Communities ◽

Carbon Fixation ◽

Keystone Species ◽

Carbon Assimilation ◽

Sugar Metabolism ◽

Archaeal Community ◽

Amino Sugar ◽

Amplicon Sequencing ◽

Fracture Zones ◽

Crystalline Bedrock

Abstract. The bacterial and archaeal community composition and the possible carbon assimilation processes and energy sources of microbial communities in oligotrophic, deep, crystalline bedrock fractures is yet to be resolved. In this study, intrinsic microbial communities from six fracture zones from 180–2300 m depths in Outokumpu bedrock were characterized using high-throughput amplicon sequencing and metagenomic prediction. Comamonadaceae-, Anaerobrancaceae- and Pseudomonadaceae-related OTUs form the core community in deep crystalline bedrock fractures in Outokumpu. Archaeal communities were mainly composed of Methanobacteraceae-affiliating OTUs. The predicted bacterial metagenomes showed that pathways involved in fatty acid and amino sugar metabolism were common. In addition, relative abundance of genes coding the enzymes of autotrophic carbon fixation pathways in predicted metagenomes was low. This indicates that heterotrophic carbon assimilation is more important for microbial communities of the fracture zones. Network analysis based on co-occurrence of OTUs revealed the keystone genera of the microbial communities belonging to Burkholderiales and Clostridiales. Bacterial communities in fractures resemble those found from oligotrophic, hydrogen-enriched environments. Serpentinization reactions of ophiolitic rocks in Outokumpu assemblage may provide a source of energy and organic carbon compounds for the microbial communities in the fractures. Sulfate reducers and methanogens form a minority of the total microbial communities, but OTUs forming these minor groups are similar to those found from other deep Precambrian terrestrial bedrock environments.

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STRUCTURE AND FUNCTION OF THE FRUIT MICROBIOME IN HEALTHY AND DISEASED KIWIFRUIT

The Pakistan Journal of Agricultural Sciences ◽

10.21162/pakjas/19.8820 ◽

2019 ◽

Vol 56 (03) ◽

pp. 577-585

Author(s):

Wenneng Wu

Keyword(s):

Microbial Diversity ◽

Relative Abundance ◽

Foodborne Pathogens ◽

Fungal Pathogens ◽

Sugar Metabolism ◽

Amino Sugar ◽

Disease Diagnosis ◽

Postharvest Disease ◽

Pathogen Infection ◽

Microbiome Composition

The fruit surface is an infection court where foodborne pathogens compete with indigenous microbiota for microsites to invade the fruits for nutrients acquisition. However, our current understanding of the structure and functions of fruit microbiome visa-vis postharvest pathogen infection is still nascent. Here, we sequenced the metagenomic DNA to understand the structural and functional attributes of healthy and diseased kiwifruit microbiome. The healthy fruits exhibited higher microbial diversity and distinct microbiome composition compared with diseased fruits. The microbiome of diseased fruit was dominated by fungal pathogens Neofusicoccum parvum and Diplodiaseriata, while the microbiome of healthy fruits were enriched by bacteria from Methylobacteriaceae, Sphingomonadaceae, Nocardioidaceae and fungi in Pleosporaceae. Importantly, the healthy fruit microbiome had a higher relative abundance of genes related to ABC transporter, two-component system, bacterial chemotaxis, bacterial secretion system, but had a lower relative abundance of genes associated with polycyclic aromatic hydrocarbon degradation, amino sugar and nucleotide sugar metabolism, glycine, serine and threonine metabolism compared with diseased fruits. Our results indicate that pathogen infection disrupts the fruit microbiome. The changes in microbiome composition and functions could also increase the possibility of secondary pathogen infection as the reduced microbial diversity may demonstrate less resistance to pathogens infection. Therefore, monitoring the microbiome dynamics and their functions using metagenomic approaches could be useful to build a predictive understanding of accurate postharvest disease diagnosis and management in the future

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