scholarly journals Physiological and Transcriptomic Responses of Antioxidant System and Nitrogen Metabolism in Tomato Roots Treated With Nitrogen Starvation and Re-Supply

2021 ◽  
Author(s):  
Yanyan Dong ◽  
Manqi Wang ◽  
Fanzhang Wu ◽  
Jinping Yan ◽  
Kunzhi Li ◽  
...  
Keyword(s):  
Antioxidant System ◽  
Expression Patterns ◽  
Sugar Metabolism ◽  
Amino Sugar ◽  
Monodehydroascorbate Reductase ◽  
Kegg Pathways ◽  
Supply Condition ◽  
Tomato Roots ◽  
N Metabolism ◽  
N Starvation

Abstract Nitrogen (N) is one of the essential macronutrients that plays important roles in plant growth and development. To better understand the response of antioxidant system and N metabolism under N starvation and re-supply condition, physiological and transcriptomic analysis were performed in tomato roots. The malondialdehyde (MDA) and reactive oxygen species (ROS) contents increased significantly in tomato seedlings after N starvation for 24 h. The activities of superoxide dismutase (SOD), catalase (CAT), ascorbate peroxidase (APX) and monodehydroascorbate reductase (MDHAR), the ratio of ASA/DHA and GSH/GSSG, the NO3- contents, nitrate reductase (NR) activity were decreased after N starvation treatment and increased after N re-supply for 24 h. Compared with the control, 1766 genes were up-regulated and 2244 genes were down-regulated after N starvation in tomato. These differentially expressed genes (DEGs) are mainly enriched in functional items such as cellular process, metabolic process and catalytic activity. The KEGG pathways revealed that the DEGs were mainly involved in phenpropane biosynthesis, amino sugar and nucleotide sugar metabolism, and N metabolism. The expression patterns of tomato SlSOD, SlCAT, SlAPX, SlMDHAR, thioredoxin (SlTrxh), peroxiredoxin (SlPrx) and glutaredoxin (SlGrx) genes, and nitrate transporter SlNRT2.4, SlNR, glutamine synthetase (SlGS2), nitrite reductase (SlNiR) decreased after N starvation and increased after N re-supply, which were validated by qRT-PCR. Our results provide a basis for understanding the response of tomato to N deficiency and re-supply and a theoretical reference for cultivation regulation.

scholarly journals A Comparison Study of Age and Colorectal Cancer-Related Gut Bacteria

2021 ◽  
Vol 11 ◽  
Author(s):  
Yu-Kun Zhang ◽  
Qian Zhang ◽  
Yu-Liuming Wang ◽  
Wei-Yuan Zhang ◽  
Han-Qing Hu ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Sugar Metabolism ◽  
Operational Taxonomic Unit ◽  
Amino Sugar ◽  
Young Group ◽  
Gut Bacteria ◽  
Scaling Analysis ◽  
Protective Function ◽  
Kegg Pathways ◽  
Intestinal Bacterial Community

Intestinal microbiota is gaining increasing interest from researchers, and a series of studies proved that gut bacteria plays a significant role in various malignancies, especially in colorectal cancer (CRC). In this study, a cohort of 34 CRC patients (average age=65 years old), 26 young volunteers (below 30 years old), and 26 old volunteers (over 60 years old) was enrolled. 16S ribosomal RNA gene sequencing was used to explore fecal bacteria diversity. The operational taxonomic unit (OTU) clustering analysis and NMDS (non-metric multidimensional scaling) analysis were used to separate different groups. Cluster of ortholog genes (COG) functional annotation and Kyoto encyclopedia of genes and genomes (KEGG) were used to detect enriched pathways among three groups. Community separations were observed among the three groups of this cohort. Clostridia, Actinobacteria, Bifidobacterium, and Fusobacteria were the most enriched bacteria in the young group, old group, and CRC group respectively. Also, in the young, old, and CRC group, the ratio of Firmicutes/Bacteroidetes was increased sequentially despite no statistical differences. Further, COG showed that transcription, cell wall/membrane/envelope biogenesis, inorganic ion transport and metabolism, and signal transduction mechanisms were differentially expressed among three groups. KEGG pathways associated with ABC transporters, amino sugar and nucleotide sugar metabolism, arginine and proline metabolism, and aminoacyl-tRNA biosynthesis also showed statistical differences among the three groups. These results indicated that the intestinal bacterial community varied as age changed and was related to CRC, and we discussed that specific bacteria enriched in the young and old group may exert a protective function, while bacteria enriched in the CRC group may promote tumorigenesis.

scholarly journals ITRAQ-based quantitative proteomic analysis of Fusarium moniliforme (Fusarium verticillioides) in response to Phloridzin inducers

2020 ◽  
Author(s):  
Rong Zhang ◽  
Weitao Jiang ◽  
Xin Liu ◽  
Yanan Duan ◽  
Li Xiang ◽  
...  
Keyword(s):  
Fusarium Moniliforme ◽  
Abiotic Factors ◽  
Fusarium Verticillioides ◽  
Sugar Metabolism ◽  
Amino Sugar ◽  
Apple Replant Disease ◽  
Kegg Pathways ◽  
Itraq Analysis ◽  
Before And After ◽  
Functional Pathway

Abstract Apple replant disease (ARD) has been reported from all major fruit-growing regions of the world, and is often caused by biotic factors (pathogen fungi) and abiotic factors (phenolic compounds). In order to clarify the proteomic differences of Fusarium moniliforme under the action of phloridzin, and to explore the potential mechanism of F. moniliforme as the pathogen of ARD, the role of Fusarium spp in ARD was further clarified. In this paper, the quantitative proteomics method iTRAQ analysis technology was used to analyze the proteomic differences of F. moniliforme before and after phloridzin treatment. A total of 4535 proteins were detected, and 293 proteins were found with more than 1.2 times (P<0.05) differences. In-depth data analysis revealed that differentially expressed proteins were influenced a variety of cellular processes, particularly metabolic processes. Among these metabolic pathways, a total of 8 significantly enriched KEGG pathways were identified with at least 2 affiliated proteins with different abundance in conidia and mycelium. Functional pathway analysis indicated that 46 up-regulated proteins were mainly distributed in amino sugar, nucleotide sugar metabolism, glycolysis/ gluconeogenesis and phagosome pathways. The results deepened our understanding of the proteome in F. moniliforme in response to phloridzin inducers and provide a basis for further exploration for improving the efficiency of the fungi as biocontrol agents to control ARD.

Distinct physiological and transcriptional responses of leaves of paper mulberry (Broussonetia kazinoki × B. papyrifera) under different nitrogen supply levels

2020 ◽  
Vol 40 (5) ◽  
pp. 667-682
Author(s):  
Jianwei Ni ◽  
Shang Su ◽  
Hui Li ◽  
Yonghang Geng ◽  
Houjun Zhou ◽  
...  
Keyword(s):  
Nitrogen Metabolism ◽  
Expression Patterns ◽  
Sugar Metabolism ◽  
Glutamate Synthase ◽  
Amino Sugar ◽  
Nitrogen Supply ◽  
Inorganic Pyrophosphatase ◽  
Transcriptional Responses ◽  
Nitrogenous Compounds ◽  
Nitrogen Concentrations

Abstract Paper mulberry, a vigorous pioneer species used for ecological reclamation and a high-protein forage plant for economic development, has been widely planted in China. To further develop its potential value, it is necessary to explore the regulatory mechanism of nitrogen metabolism for rational nitrogen utilization. In this study, we investigated the morphology, physiology and transcriptome of a paper mulberry hybrid (Broussonetia kazinoki × B. papyrifera) in response to different nitrogen concentrations. Moderate nitrogen promoted plant growth and biomass accumulation. Photosynthetic characteristics, concentration of nitrogenous compounds and activities of enzymes were stimulated under nitrogen treatment. However, these enhancements were slightly or severely inhibited under excessive nitrogen supply. Nitrite reductase and glutamate synthase were more sensitive than nitrate reductase and glutamine synthetase and more likely to be inhibited under high nitrogen concentrations. Transcriptome analysis of the leaf transcriptome identified 161,961 unigenes. The differentially expressed genes associated with metabolism of nitrogen, alanine, aspartate, glutamate and glycerophospholipid showed high transcript abundances after nitrogen application, whereas those associated with glycerophospholipid, glycerolipid, amino sugar and nucleotide sugar metabolism were down-regulated. Combined with weighted gene coexpression network analysis, we uncovered 16 modules according to similarity in expression patterns. Asparagine synthetase and inorganic pyrophosphatase were considered two hub genes in two modules, which were associated with nitrogen metabolism and phosphorus metabolism, respectively. The expression characteristics of these genes may explain the regulation of morphological, physiological and other related metabolic strategies harmoniously. This multifaceted study provides valuable insights to further understand the mechanism of nitrogen metabolism and to guide utilization of paper mulberry.

scholarly journals Transcriptomic Analysis for Indica and Japonica Rice Varieties under Aluminum Toxicity

2019 ◽  
Vol 20 (4) ◽  
pp. 997 ◽  
Author(s):  
Peng Zhang ◽  
Zhuoran Ding ◽  
Zhengzheng Zhong ◽  
Hanhua Tong
Keyword(s):  
Gene Expression ◽  
Sulfur Metabolism ◽  
Expression Patterns ◽  
Sugar Metabolism ◽  
Amino Sugar ◽  
Transcriptomic Analysis ◽  
Gene Expression Patterns ◽  
Japonica Rice ◽  
Al Tolerance ◽  
Nucleotide Sugar

Aluminum (Al) at high concentrations inhibits root growth, damage root systems, and causes significant reductions in rice yields. Indica and Japonica rice have been cultivated in distinctly different ecological environments with different soil acidity levels; thus, they might have different mechanisms of Al-tolerance. In the present study, transcriptomic analysis in the root apex for Al-tolerance in the seedling stage was carried out within Al-tolerant and -sensitive varieties belonging to different subpopulations (i.e., Indica, Japonica, and mixed). We found that there were significant differences between the gene expression patterns of Indica Al-tolerant and Japonica Al-tolerant varieties, while the gene expression patterns of the Al-tolerant varieties in the mixed subgroup, which was inclined to Japonica, were similar to the Al-tolerant varieties in Japonica. Moreover, after further GO (gene ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) analyses of the transcriptomic data, we found that eight pathways, i.e., “Terpenoid backbone biosynthesis”, “Ribosome”, “Amino sugar and nucleotide sugar metabolism”, “Plant hormone signal transduction”, “TCA cycle”, “Synthesis and degradation of ketone bodies”, and “Butanoate metabolism” were found uniquely for Indica Al-tolerant varieties, while only one pathway (i.e., “Sulfur metabolism”) was found uniquely for Japonica Al-tolerant varieties. For Al-sensitive varieties, one identical pathway was found, both in Indica and Japonica. Three pathways were found uniquely in “Starch and sucrose metabolism”, “Metabolic pathway”, and “Amino sugar and nucleotide sugar metabolism”.

scholarly journals Identification of Differentially Expressed Genes in Porcine Ovaries at Proestrus and Estrus Stages Using RNA-Seq Technique

2018 ◽  
Vol 2018 ◽  
pp. 1-8 ◽  
Author(s):  
Songbai Yang ◽  
Xiaolong Zhou ◽  
Yue Pei ◽  
Han Wang ◽  
Ke He ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Hormone Secretion ◽  
Differentially Expressed ◽  
Receptor Interaction ◽  
The Novel ◽  
Kegg Pathways ◽  
Go Enrichment ◽  
Single Organism

Estrus is an important factor for the fecundity of sows, and it is involved in ovulation and hormone secretion in ovaries. To better understand the molecular mechanisms of porcine estrus, the expression patterns of ovarian mRNA at proestrus and estrus stages were analyzed using RNA sequencing technology. A total of 2,167 differentially expressed genes (DEGs) were identified (P≤0.05, log2  Ratio≥1), of which 784 were upregulated and 1,383 were downregulated in the estrus compared with the proestrus group. Gene Ontology (GO) enrichment indicated that these DEGs were mainly involved in the cellular process, single-organism process, cell and cell part, and binding and metabolic process. In addition, a pathway analysis showed that these DEGs were significantly enriched in 33 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, including cell adhesion molecules, ECM-receptor interaction, and cytokine-cytokine receptor interaction. Quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR) confirmed the differential expression of 10 selected DEGs. Many of the novel candidate genes identified in this study will be valuable for understanding the molecular mechanisms of the sow estrous cycle.

scholarly journals Transcriptomic Analysis Reveals Candidate Genes Responsive to Sclerotinia scleroterum and Cloning of the Ss-Inducible Chitinase Genes in Morus laevigata

2020 ◽  
Vol 21 (21) ◽  
pp. 8358
Author(s):  
Huanhuan Jiang ◽  
Xiaoyun Jin ◽  
Xiaofeng Shi ◽  
Yufei Xue ◽  
Jiayi Jiang ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Molecular Basis ◽  
Expression Patterns ◽  
Interaction Network ◽  
Sclerotinia Stem Rot ◽  
Response Characteristics ◽  
Kegg Pathways ◽  
Cdna Sequences ◽  
Chitinase Genes ◽  
Morus Laevigata

Sclerotinia sclerotiorum (Ss) is a devastating fungal pathogen that causes Sclerotinia stem rot in rapeseed (Brassica napus), and is also detrimental to mulberry and many other crops. A wild mulberry germplasm, Morus laevigata, showed high resistance to Ss, but the molecular basis for the resistance is largely unknown. Here, the transcriptome response characteristics of M. laevigata to Ss infection were revealed by RNA-seq. A total of 833 differentially expressed genes (DEGs) were detected after the Ss inoculation in the leaf of M. laevigata. After the GO terms and KEGG pathways enrichment analyses, 42 resistance-related genes were selected as core candidates from the upregulated DEGs. Their expression patterns were detected in the roots, stems, leaves, flowers, and fruits of M. laevigata. Most of them (30/42) were specifically or mainly expressed in flowers, which was consistent with the fact that Ss mainly infects plants through floral organs, and indicated that Ss-resistance genes could be induced by pathogen inoculation on ectopic organs. After the Ss inoculation, these candidate genes were also induced in the two susceptible varieties of mulberry, but the responses of most of them were much slower with lower extents. Based on the expression patterns and functional annotation of the 42 candidate genes, we cloned the full-length gDNA and cDNA sequences of the Ss-inducible chitinase gene set (MlChi family). Phylogenetic tree construction, protein interaction network prediction, and gene expression analysis revealed their special roles in response to Ss infection. In prokaryotic expression, their protein products were all in the form of an inclusion body. Our results will help in the understanding of the molecular basis of Ss-resistance in M. laevigata, and the isolated MlChi genes are candidates for the improvement in plant Ss-resistance via biotechnology.

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

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.

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

2015 ◽  
Vol 12 (21) ◽  
pp. 18103-18150 ◽  
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.

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

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

scholarly journals Genome-Wide Gene Expression Profiles Analysis Reveal Novel Insights into Drought Stress in Foxtail Millet (Setaria italica L.)

2020 ◽  
Vol 21 (22) ◽  
pp. 8520
Author(s):  
Ling Qin ◽  
Erying Chen ◽  
Feifei Li ◽  
Xiao Yu ◽  
Zhenyu Liu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Signal Transduction ◽  
Drought Stress ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Foxtail Millet ◽  
Gene Expression Profiles ◽  
Sugar Metabolism ◽  
Setaria Italica ◽  
Phenylpropanoid Biosynthesis

Foxtail millet (Setaria italica (L.) P. Beauv) is an important food and forage crop because of its health benefits and adaptation to drought stress; however, reports of transcriptomic analysis of genes responding to re-watering after drought stress in foxtail millet are rare. The present study evaluated physiological parameters, such as proline content, p5cs enzyme activity, anti-oxidation enzyme activities, and investigated gene expression patterns using RNA sequencing of the drought-tolerant foxtail millet variety (Jigu 16) treated with drought stress and rehydration. The results indicated that drought stress-responsive genes were related to many multiple metabolic processes, such as photosynthesis, signal transduction, phenylpropanoid biosynthesis, starch and sucrose metabolism, and osmotic adjustment. Furthermore, the Δ1-pyrroline-5-carboxylate synthetase genes, SiP5CS1 and SiP5CS2, were remarkably upregulated in foxtail millet under drought stress conditions. Foxtail millet can also recover well on rehydration after drought stress through gene regulation. Our data demonstrate that recovery on rehydration primarily involves proline metabolism, sugar metabolism, hormone signal transduction, water transport, and detoxification, plus reversal of the expression direction of most drought-responsive genes. Our results provided a detailed description of the comparative transcriptome response of foxtail millet variety Jigu 16 under drought and rehydration environments. Furthermore, we identify SiP5CS2 as an important gene likely involved in the drought tolerance of foxtail millet.

Sign in / Sign up

Export Citation Format

Share Document