scholarly journals Transcriptome Analysis Revealed Overlapping and Special Regulatory Roles of RpoN1 and RpoN2 in Motility, Virulence, and Growth of Xanthomonas oryzae pv. oryzae

2021 ◽  
Vol 12 ◽  
Author(s):  
Chao Yu ◽  
Doan-Phuong Nguyen ◽  
Fenghuan Yang ◽  
Jia Shi ◽  
Yiming Wei ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Regulatory Mechanism ◽  
Xanthomonas Oryzae ◽  
Bacterial Motility ◽  
Biological Functions ◽  
Functional Roles ◽  
Carbon And Nitrogen ◽  
Flagellar Assembly ◽  
Carbon And Nitrogen Metabolism ◽  
Independent Effects

σ54 factor (RpoN) plays a crucial role in bacterial motility, virulence, growth, and other biological functions. In our previous study, two homologous σ54 factors, RpoN1 and RpoN2, were identified in Xanthomonas oryzae pv. oryzae (Xoo), the causative agent of bacterial leaf blight in rice. However, their functional roles, i.e., whether they exert combined or independent effects, remain unknown. In the current study, rpoN1 or rpoN2 deletion in Xoo significantly disrupted bacterial swimming motility, flagellar assembly, and virulence. Transcriptome analysis led to the identification of 127 overlapping differentially expressed genes (DEGs) regulated by both RpoN1 and RpoN2. Furthermore, GO and KEGG classification demonstrated that these DEGs were highly enriched in flagellar assembly, chemotaxis, and c-di-GMP pathways. Interestingly, ropN1 deletion decreased ropN2 transcription, while rpoN2 deletion did not affect ropN1 transcription. No interaction between the rpoN2 promoter and RpoN1 was detected, suggesting that RpoN1 indirectly regulates rpoN2 transcription. In addition, RpoN1-regulated DEGs were specially enriched in ribosome, carbon, and nitrogen metabolism pathways. Besides, bacterial growth was remarkably repressed in ΔrpoN1 but not in ΔrpoN2. Taken together, this study demonstrates the overlapping and unique regulatory roles of RpoN1 and RpoN2 in motility, virulence, growth and provides new insights into the regulatory mechanism of σ54 factors in Xoo.

scholarly journals carbon and nitrogen metabolism of young plants of Ucuúba (Virola surinamensis) in the presence of cadmium

2020 ◽  
Author(s):  
Waldemar Viana ◽  
Cândido Oliveira Neto ◽  
Benedito Filho ◽  
Eniel Cruz ◽  
Cristine Amarante ◽  
...  
Keyword(s):  
Reducing Sugars ◽  
Regulatory Mechanism ◽  
Nitrate Concentration ◽  
Soluble Carbohydrates ◽  
Forest Species ◽  
Carbon And Nitrogen ◽  
Randomized Design ◽  
Carbon And Nitrogen Metabolism ◽  
Completely Randomized Design ◽  
Positive Effect

Abstract Virola surinamensis is a forest species widely distributed in the estuaries of the Amazon. These ecosystems are susceptible to contamination by Cadmium (Cd), indicating that the plant has strategies for tolerating this metal. The aim of this study was to assess the nitrogen and carbon metabolism of young plants of Ucuúba (Virola surinamensis) in the presence of cadmium with the perspective of the phytoremediation of contaminated environments. The used experimental design was a completely randomized design with five Cd concentrations (0, 15, 30, 45, and 60 mg L−1), for 60 days. In general, Cd did not affect nitrate concentration in the root but had a positive effect on leaves. The reduction of nitrate reductase (NR) in plants exposed to Cd was followed by a decrease in ammonia, total soluble amino acids (TSA), and total soluble proteins (TSP). Cd promoted an increase in the concentration of total soluble carbohydrates (TSC), proline, sucrose, and reducing sugars in the plants. The increase in TSC, sucrose and proline, suggests a metabolic regulatory mechanism of V. surinamensis against Cd stress.

scholarly journals Carbon And Nitrogen Metabolism of Young Plants of Ucuúba (Virola surinamensis) in the Presence Of Cadmium

2020 ◽  
Author(s):  
Waldemar Viana ◽  
Cândido Oliveira Neto ◽  
Benedito Filho ◽  
Eniel Cruz ◽  
Cristine Amarante ◽  
...  
Keyword(s):  
Carbon Metabolism ◽  
Reducing Sugars ◽  
Regulatory Mechanism ◽  
Nitrate Concentration ◽  
Soluble Carbohydrates ◽  
Cd Stress ◽  
Forest Species ◽  
Carbon And Nitrogen ◽  
Carbon And Nitrogen Metabolism ◽  
Positive Effect

Abstract Virola surinamensis is a forest species widely distributed in the estuaries of the Amazon. These ecosystems are susceptible to contamination by Cadmium (Cd), indicating that the plant has strategies for tolerating this metal. This study aimed to assess the nitrogen and carbon metabolism of young plants of Ucuúba (Virola surinamensis) in the presence of cadmium with the perspective of the phytoremediation of contaminated environments. The experimental design was completely randomized with five Cd concentrations (0, 15, 30, 45, and 60 mg L−1) for 60 days. In general, Cd did not affect nitrate concentration in the root but had a positive effect on leaves. The reduction of nitrate reductase (NR) in plants exposed to Cd was followed by a decrease in ammonia, total soluble amino acids (TSA), and total soluble proteins (TSP). Cd promoted an increase in total soluble carbohydrates (TSC), proline, sucrose, and reducing sugars in the plants. The increase in TSC, sucrose and proline suggests a metabolic regulatory mechanism of V. surinamensis against Cd stress.

scholarly journals Plant Hormone Metabolome and Transcriptome Analysis of Dwarf and Wild-type Banana

2021 ◽  
Author(s):  
Biao Deng ◽  
Xuan Wang ◽  
Xing Long ◽  
Ren Fang ◽  
Shuangyun Zhou ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Transcriptome Analysis ◽  
Regulatory Mechanism ◽  
Feedback Regulation ◽  
Wild Type ◽  
Hormone Levels ◽  
Transporter Protein ◽  
Repressor Proteins ◽  
Differential Gene ◽  
The Relationship

AbstractGibberellin (GA), auxin (IAA) and brassinosteroid (BR) are indispensable in the process of plant growth and development. Currently, research on the regulatory mechanism of phytohormones in banana dwarfism is mainly focused on GA, and few studies are focused on IAA and BR. In this study, we measured the contents of endogenous GA, IAA and BR and compared the transcriptomes of wild-type Williams banana and its dwarf mutant across five successive growth periods. We investigated the relationship between hormones and banana dwarfism and explored differential gene expression through transcriptome analysis, thus revealing the possible metabolic regulatory mechanism. We inferred a complex regulatory network of banana dwarfing. In terms of endogenous hormone levels, GA and IAA had significant effects on banana dwarfing, while BR had little effect. The key gene in GA biosynthesis of is GA2ox, and the key genes in IAA biosynthesis are TDC and YUCCA. The differential expression of these genes might be the main factor affecting hormone levels and plant height. In terms of hormone signal transduction, DELLA and AUX/IAA repressor proteins were the core regulators of GA and IAA, respectively. They inhibited the process of signal transduction and had feedback regulation on hormone levels. Finally, the transporter protein PIN, AUX1/LAX protein family and ABCB subfamily played supplementary roles in the transport of IAA. These results provide new insights into GA and IAA regulation of banana growth and a reliable foundation for the improvement of dwarf varieties.

scholarly journals Activities of carbon and nitrogen metabolism enzymes during germinating sorghum seeds and early seedlings growth

2017 ◽  
Vol 45 (4) ◽  
pp. 587-597
Author(s):  
R. Ben Mrid ◽  
R. El Omari ◽  
Y. Bouargalne ◽  
N. El Mourabit ◽  
M. Nhiri
Keyword(s):  
Nitrogen Metabolism ◽  
Carbon And Nitrogen ◽  
Metabolism Enzymes ◽  
Carbon And Nitrogen Metabolism

scholarly journals Assessing Genetic Diversity among Brettanomyces Yeasts by DNA Fingerprinting and Whole-Genome Sequencing

2014 ◽  
Vol 80 (14) ◽  
pp. 4398-4413 ◽  
Author(s):  
Sam Crauwels ◽  
Bo Zhu ◽  
Jan Steensels ◽  
Pieter Busschaert ◽  
Gorik De Samblanx ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Dna Fingerprinting ◽  
Wine Industry ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Content Type ◽  
Carbon And Nitrogen ◽  
Spoilage Yeasts ◽  
Off Flavors ◽  
Carbon And Nitrogen Metabolism

ABSTRACTBrettanomycesyeasts, with the speciesBrettanomyces(Dekkera)bruxellensisbeing the most important one, are generally reported to be spoilage yeasts in the beer and wine industry due to the production of phenolic off flavors. However,B. bruxellensisis also known to be a beneficial contributor in certain fermentation processes, such as the production of certain specialty beers. Nevertheless, despite its economic importance,Brettanomycesyeasts remain poorly understood at the genetic and genomic levels. In this study, the genetic relationship between more than 50Brettanomycesstrains from all presently known species and from several sources was studied using a combination of DNA fingerprinting techniques. This revealed an intriguing correlation between theB. bruxellensisfingerprints and the respective isolation source. To further explore this relationship, we sequenced a (beneficial) beer isolate ofB. bruxellensis(VIB X9085; ST05.12/22) and compared its genome sequence with the genome sequences of two wine spoilage strains (AWRI 1499 and CBS 2499). ST05.12/22 was found to be substantially different from both wine strains, especially at the level of single nucleotide polymorphisms (SNPs). In addition, there were major differences in the genome structures between the strains investigated, including the presence of large duplications and deletions. Gene content analysis revealed the presence of 20 genes which were present in both wine strains but absent in the beer strain, including many genes involved in carbon and nitrogen metabolism, and vice versa, no genes that were missing in both AWRI 1499 and CBS 2499 were found in ST05.12/22. Together, this study provides tools to discriminateBrettanomycesstrains and provides a first glimpse at the genetic diversity and genome plasticity ofB. bruxellensis.

scholarly journals De novo Transcriptome Assembly and Comparative Analysis Highlight the Primary Mechanism Regulating the Response to Selenium Stimuli in Oats (Avena sativa L.)

2021 ◽  
Vol 12 ◽  
Author(s):  
Tao Liu ◽  
Xiaoting Liu ◽  
Rangrang Zhou ◽  
Hong Chen ◽  
Huaigang Zhang ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Regulatory Mechanism ◽  
De Novo ◽  
Average Length ◽  
Transcriptome Assembly ◽  
Processing Technique ◽  
Sodium Selenate ◽  
Control Group ◽  
Primary Mechanism ◽  
High Selenium

Selenium is an essential microelement for humans and animals. The specific processing technique of oats can maximize the preservation of its nutrients. In this study, to understand the genetic response of oats in a high-selenium environment, oats were treated with sodium selenate for 24 h, and transcriptome analysis was performed. A total of 211,485,930 clean reads composing 31.30 Gb of clean data were retained for four samples. After assembly, 186,035 unigenes with an average length of 727 bp were generated, and the N50 length was 1,149 bp. Compared with that in the control group, the expression of 7,226 unigenes in the treatment group was upregulated, and 2,618 unigenes were downregulated. Based on the sulfur assimilation pathway and selenocompound metabolic pathway, a total of 27 unigenes related to selenate metabolism were identified. Among them, the expression of both key genes APS (ATP sulfurylase) and APR (adenosine 5′-phosphosulfate reductase) was upregulated more than 1,000-fold under selenate treatment, while that of CBL (cystathionine-β-synthase) was upregulated 3.12-fold. Based on the transcriptome analysis, we suspect that the high-affinity sulfur transporter Sultr1;2 plays a key role in selenate uptake in oats. A preliminary regulatory mechanism explains the oat response to selenate treatment was ultimately proposed based on the transcriptome analysis and previous research.

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