scholarly journals Transcriptome Dynamics of Double Recessive Mutant, o2o2o16o16, Reveals the Transcriptional Mechanisms in the Increase of Its Lysine and Tryptophan Content in Maize

Genes ◽  
2019 ◽  
Vol 10 (4) ◽  
pp. 316 ◽  
Author(s):  
Wei Wang ◽  
Yi Dai ◽  
Mingchun Wang ◽  
Wenpeng Yang ◽  
Degang Zhao
Keyword(s):  
Molecular Mechanisms ◽  
Degradation Pathway ◽  
Endosperm Development ◽  
Rna Seq ◽  
Wild Type ◽  
Genes Encoding ◽  
Recessive Mutant ◽  
Lysine Degradation ◽  
Tryptophan Content

In maize, pyramiding of o2 and o16 alleles can greatly improve the nutritional quality of grains. To dissect its molecular mechanism, we created a double recessive mutant line, o2o2o16o16, by introgression of the o2 and o16 alleles into the wild-type maize inbred line, by molecular marker-assisted backcross selection. The kernels (18 day after pollination (DAP), 28 DAP, and 38 DAP) of the o2o2o16o16 mutant and its parent lines were subject to RNA sequencing (RNA-Seq). The RNA-Seq analysis revealed that 59 differentially expressed genes (DEGs) were involved in lysine metabolism and 43 DEGs were involved in tryptophan metabolism. Among them, the genes encoding AK, ASADH, and Dap-F in the lysine synthesis pathway were upregulated at different stages of endosperm development, promoting the synthesis of lysine. Meanwhile, the genes encoding LKR/SDH and L-PO in the lysine degradation pathway were downregulated, inhibiting the degradation of lysine. Moreover, the genes encoding TAA and YUC in the tryptophan metabolic pathway were downregulated, restraining the degradation of tryptophan. Thus, pyramiding o2 and o16 alleles could increase the lysine and tryptophan content in maize. These above results would help to uncover the molecular mechanisms involved in the increase in lysine and the tryptophan content, through the introgression of o2 and o16 alleles into the wild-type maize.

scholarly journals Molecular Mechanisms Underlying Increase in Lysine Content of Waxy Maize through the Introgression of the opaque2 Allele

2019 ◽  
Vol 20 (3) ◽  
pp. 684 ◽  
Author(s):  
Wei Wang ◽  
Suzhen Niu ◽  
Yi Dai ◽  
Xinmi Zhai ◽  
Mingchun Wang ◽  
...  
Keyword(s):  
Nutritional Value ◽  
Molecular Mechanisms ◽  
Endosperm Development ◽  
Content Increase ◽  
Lysine Content ◽  
Biological Processes ◽  
Rna Seq ◽  
Waxy Maize ◽  
Marker Assisted Backcrossing

The opaque2 (o2) mutation in maize is associated with high lysine content in endosperm and good nutritional value. To improve the nutritional quality of waxy maize, the o2 allele was introgressed into the wxwx line using marker-assisted backcrossing selection technology. The lysine content of o2o2wxwx lines was higher than that of the wxwx line. To reveal the mechanism of increasing lysine content through introgression of the o2 in waxy maize, the transcriptome on kernels (18th day after pollination) of the o2o2wxwx and parent lines was analyzed using RNA-sequencing (RNA-Seq). The RNA-Seq analysis revealed 49 differentially expressed genes (DEGs). Functional analysis showed that these DEGs were mostly related to the catalytic activity and metabolic processes. The O2 gene regulated multiple metabolic pathways related to biological processes (BP) and molecular function (MP) during waxy maize endosperm development. In particular, in the o2o2wxwx lines, the two genes that encode the EF-1α and LHT1 were up-regulated, but the gene that encodes sulfur-rich proteins was down-regulated, raising the grain lysine content. These findings are of great importance for understanding the molecular mechanism underlying the lysine content increase due to o2 allele introgression into waxy maize.

scholarly journals Analysis of saponins detoxification genes in Ilyonectria mors-panacis G3B inducing root rot of Panax notoginseng by RNA-Seq

2021 ◽  
Author(s):  
Guohong Zeng ◽  
Jin Li ◽  
Yuxiu Ma ◽  
Qian Pu ◽  
Tian Xiao ◽  
...  
Keyword(s):  
Root Rot ◽  
Molecular Mechanisms ◽  
Management Strategies ◽  
Panax Notoginseng ◽  
Glycoside Hydrolases ◽  
Rna Seq ◽  
Host Interaction ◽  
Excellent Starting Point ◽  
Starting Point ◽  
Genes Encoding

AbstractSaponins are kinds of antifungal compounds produced by Panax notoginseng to resist invasion by pathogens. Ilyonectria mors-panacis G3B was the dominant pathogen inducing root rot of P. notoginseng, and the abilities to detoxify saponins were the key to infect P. notoginseng successfully. To research the molecular mechanisms of detoxifying saponins in I. mors-panacis G3B, we used high-throughput RNA-Seq to identify 557 and 1519 differential expression genes (DEGs) in I. mors-panacis G3B with saponins treatments for 4H (Hours) and 12H (Hours) compared with no saponins treatments, respectively. Among these DEGs, we found 93 genes which were simultaneously highly expressed in I. mors-panacis G3B with saponins treatments for 4H and 12H, they mainly belong to genes encoding transporters, glycoside hydrolases, oxidation–reduction enzymes, transcription factors and so on. In addition, there were 21 putative PHI (Pathogen–Host Interaction) genes out of those 93 up-regulated genes. In this report, we analyzed virulence-associated genes in I. mors-panacis G3B which may be related to detoxifying saponins to infect P. notoginseng successfully. They provided an excellent starting point for in-depth study on pathogenicity of I. mors-panacis G3B and developed appropriate root rot disease management strategies in the future.

scholarly journals Dual RNA-Seq Analysis of Trichophyton rubrum and HaCat Keratinocyte Co-Culture Highlights Important Genes for Fungal-Host Interaction

Genes ◽  
2018 ◽  
Vol 9 (7) ◽  
pp. 362 ◽  
Author(s):  
Monise Petrucelli ◽  
Kamila Peronni ◽  
Pablo Sanches ◽  
Tatiana Komoto ◽  
Josie Matsuda ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Trichophyton Rubrum ◽  
Glyoxylate Cycle ◽  
Human Keratinocytes ◽  
Rna Seq ◽  
Fungal Host ◽  
Host Interaction ◽  
Genes Encoding ◽  
Hacat Keratinocyte

The dermatophyte Trichophyton rubrum is the major fungal pathogen of skin, hair, and nails that uses keratinized substrates as the primary nutrients during infection. Few strategies are available that permit a better understanding of the molecular mechanisms involved in the interaction of T. rubrum with the host because of the limitations of models mimicking this interaction. Dual RNA-seq is a powerful tool to unravel this complex interaction since it enables simultaneous evaluation of the transcriptome of two organisms. Using this technology in an in vitro model of co-culture, this study evaluated the transcriptional profile of genes involved in fungus-host interactions in 24 h. Our data demonstrated the induction of glyoxylate cycle genes, ERG6 and TERG_00916, which encodes a carboxylic acid transporter that may improve the assimilation of nutrients and fungal survival in the host. Furthermore, genes encoding keratinolytic proteases were also induced. In human keratinocytes (HaCat) cells, the SLC11A1, RNASE7, and CSF2 genes were induced and the products of these genes are known to have antimicrobial activity. In addition, the FLG and KRT1 genes involved in the epithelial barrier integrity were inhibited. This analysis showed the modulation of important genes involved in T. rubrum–host interaction, which could represent potential antifungal targets for the treatment of dermatophytoses.

scholarly journals Identification of Point Mutations in Clinical Staphylococcus aureus Strains That Produce Small-Colony Variants Auxotrophic for Menadione

2014 ◽  
Vol 82 (4) ◽  
pp. 1600-1605 ◽  
Author(s):  
Melissa A. Dean ◽  
Randall J. Olsen ◽  
S. Wesley Long ◽  
Adriana E. Rosato ◽  
James M. Musser
Keyword(s):  
Staphylococcus Aureus ◽  
Pathway Analysis ◽  
Molecular Mechanisms ◽  
Point Mutations ◽  
Biosynthesis Pathway ◽  
Wild Type ◽  
Small Colony Variants ◽  
Content Type ◽  
Genes Encoding ◽  
Small Colony

ABSTRACTStaphylococcus aureussmall-colony variants (SCVs) are implicated in chronic and relapsing infections that are difficult to diagnose and treat. Despite many years of study, the underlying molecular mechanisms and virulence effect of the small-colony phenotype remain incompletely understood. We sequenced the genomes of fiveS. aureusSCV strains recovered from human patients and discovered previously unidentified nonsynonymous point mutations in three genes encoding proteins in the menadione biosynthesis pathway. Analysis of genetic revertants and complementation with wild-type alleles confirmed that these mutations caused the SCV phenotype and decreased virulence for mice.

scholarly journals Chromatin conformation capture (Hi-C) sequencing of patient-derived xenografts: analysis guidelines

2020 ◽  
Author(s):  
Mikhail G. Dozmorov ◽  
Katarzyna M. Tyc ◽  
Nathan C. Sheffield ◽  
David C. Boyd ◽  
Amy L. Olex ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Genetic Material ◽  
Human Tumor ◽  
Chromatin Conformation ◽  
Library Preparation ◽  
Rna Seq ◽  
Chromatin Conformation Capture ◽  
Alignment Strategy ◽  
Preparation Strategy

AbstractSequencing of patient-derived xenograft (PDX) mouse models allows investigation of the molecular mechanisms of human tumor samples engrafted in a mouse host. Thus, both human and mouse genetic material is sequenced. Several methods have been developed to remove mouse sequencing reads from RNA-seq or exome sequencing PDX data and improve the downstream signal. However, for more recent chromatin conformation capture technologies (Hi-C), the effect of mouse reads remains undefined.We evaluated the effect of mouse read removal on the quality of Hi-C data using in silico created PDX Hi-C data with 10% and 30% mouse reads. Additionally, we generated two experimental PDX Hi-C datasets using different library preparation strategies. We evaluated three alignment strategies (Direct, Xenome, Combined) and three processing pipelines (Juicer, HiC-Pro, HiCExplorer) on the quality of Hi-C data.Removal of mouse reads had little-to-no effect on data quality than the results obtained with Direct alignment strategy. Juicer pipeline extracted the most useful information from PDX Hi-C data. However, library preparation strategy had the largest effect on all quality metrics. Together, our study presents comprehensive guidelines on PDX Hi-C data processing.

scholarly journals Clostridium difficile exploits a host metabolite produced during toxin-mediated infection

2021 ◽  
Author(s):  
Kali M. Pruss ◽  
Justin L. Sonnenburg
Keyword(s):  
Clostridium Difficile ◽  
Immune Cells ◽  
Molecular Mechanisms ◽  
Mouse Genetics ◽  
Enteric Pathogens ◽  
Rna Seq ◽  
Wild Type ◽  
Isogenic Mutant ◽  
Model Combining ◽  
The U.S

Several enteric pathogens can gain specific metabolic advantages over other members of the microbiota by inducing host pathology and inflammation. The pathogen Clostridium difficile (Cd) is responsible for a toxin-mediated colitis that causes 15,000 deaths in the U.S. yearly1, yet the molecular mechanisms by which Cd benefits from toxin-induced colitis remain understudied. Up to 21% of healthy adults are asymptomatic carriers of toxigenic Cd2, indicating that Cd can persist as part of a healthy microbiota; antibiotic-induced perturbation of the gut ecosystem is associated with transition to toxin-mediated disease. To understand how Cd metabolism adapts from a healthy gut to the inflamed conditions its toxins induce, we used RNA-seq to define the metabolic state of wild-type Cd versus an isogenic mutant lacking toxins in a mouse model. Combining bacterial and mouse genetics, we demonstrate that Cd utilizes sorbitol derived from both diet and host. Host-derived sorbitol is produced by the enzyme aldose reductase, which is expressed by diverse immune cells and is upregulated during inflammation, including during Cd toxin-mediated disease. This work highlights a mechanism by which Cd can utilize a host-derived nutrient generated during toxin-induced disease by an enzyme not previously associated with infection.

scholarly journals Changes in splicing and neuromodulatory gene expression programs in sensory neurons with pheromone signaling and social experience

2021 ◽  
Author(s):  
Pelin C Volkan ◽  
Bryson Deanhardt ◽  
Qichen Duan ◽  
Chengcheng Du ◽  
Charles Soeder ◽  
...  
Keyword(s):  
Sensory Neurons ◽  
Molecular Mechanisms ◽  
Social Experience ◽  
Rna Seq ◽  
Male Courtship ◽  
Wild Type ◽  
Pheromone Signaling ◽  
Courtship Behaviors ◽  
Necessary And Sufficient ◽  
Splicing Patterns

Social experience and pheromone signaling in ORNs affect pheromone responses and male courtship behaviors in Drosophila, however, the molecular mechanisms underlying this circuit-level neuromodulation remain less clear. Previous studies identified social experience and pheromone signaling-dependent modulation of chromatin around behavioral switch gene fruitless, which encodes a transcription factor necessary and sufficient for male behaviors. To identify the molecular mechanisms driving social experience-dependent neuromodulation, we performed RNA-seq from antennal samples of mutant fruit flies in pheromone receptors and fruitless, as well as grouped or isolated wild-type males. We found that loss of pheromone detection differentially alters the levels of fruitless exons suggesting changes in splicing patterns. In addition, many Fruitless target neuromodulatory genes, such as neurotransmitter receptors, ion channels, and ion transporters, are differentially regulated by social context and pheromone signaling. Our results suggest that modulation of circuit activity and behaviors in response to social experience and pheromone signaling arise due to changes in transcriptional programs for neuromodulators downstream of behavioral switch gene function.

scholarly journals Continuous inflorescence removal changes parameters, lignin and saponin a content and alters the transcriptome of root of Bupleurum chinense DC

2020 ◽  
Author(s):  
Hui Wang ◽  
Gaixia Zhang ◽  
Zhihui Gao ◽  
Chun Sui ◽  
Jianhe Wei
Keyword(s):  
Molecular Mechanisms ◽  
Signal Transduction Pathway ◽  
Fold Increase ◽  
Transcriptome Profile ◽  
Root Numbers ◽  
Yield And Quality ◽  
Genes Encoding ◽  
Radix Bupleuri ◽  
Yield Quality

Abstract BackgroundBupleurum chinense DC. is an important traditional medicinal plant, and its root as the only medicinal part named Radix Bupleuri is used widely for the treatments of influenza, fever, inflammation, etc. in China, Japan and Korea. As a bulk herb, this herbal medicine occupies a comparatively big market share and is widely cultivated. However, because of the vigorous flowering and fruiting, the root growth is influenced seriously. ResultsWe assessed the effect of the continuous inflorescence removal (CIR) on improving the yield and quality of Radix Bupleuri. The results showed that the taproot length, root head diameter, and lateral root numbers were significantly elevated by CIR. We also found an average 1.71-fold increase in root biomass, and the lower lignin and higher saponin a content were detected in roots of CIR-treated plants. Based on a comparative transcriptome analysis, 172, 243, 1974 and 3024 differentially expressed genes (DEGs) were respectively identified in the CIR-treated roots. Gene Ontology and KEGG pathway functional annotation analysis of the DEGs showed that multiple genes were involved sugars metabolism pathway, lignin and terpenoids biosynthesis pathway, and the plant hormones signal transduction pathway. In addition, 295 genes encoding transcription factors (TFs), including members of the ERF, MYB-related, bHLH, NAC, MYB, AUX/IAA and bZIP families etc, were identified as CIR responsive. ConclusionThe CIR treatment could improve the yield, quality and market value of B. chinense DC. medicine, and the first transcriptome profile of CIR-treated roots of B. chinense DC. provides a series of clues of the molecular mechanisms of these phenotype changes induced by CIR.

scholarly journals Crosstalk between Flavonoids and the Plant Circadian Clock

2021 ◽  
Author(s):  
Sherry B. Hildreth ◽  
Evan S. Littleton ◽  
Leor C. Clark ◽  
Gabrielle C. Puller ◽  
Shihoko Kojima ◽  
...  
Keyword(s):  
Circadian Clock ◽  
Null Allele ◽  
Clock Genes ◽  
Rna Seq ◽  
Wild Type ◽  
Specialized Metabolites ◽  
Genes Encoding ◽  
Circadian Clock Genes ◽  
Central Clock ◽  
Line Analysis

Flavonoids are a well-known class of specialized metabolites that play key roles in plant development, reproduction, and survival. Flavonoids are also of considerable interest from the perspective of human health, both as phytonutrients and pharmaceuticals. RNA-Seq analysis of an Arabidopsis null allele for chalcone synthase (CHS), which catalyzes the first step in flavonoid biosynthesis, has uncovered evidence that these compounds influence the expression of circadian clock genes in plants. Analysis of promoter-luciferase constructs showed that the transcriptional activity of genes encoding two components of the central clock, CCA1 and TOC1, across the day/night cycle is altered in CHS-deficient seedlings. The effect of flavonoids on circadian function was furthermore reflected in photosynthetic activity, with chlorophyll cycling abolished in the mutant line. Analysis of a mutant lacking flavonoid 3'-hydroxylase (F3'H) activity, and thus able to synthesize mono- but not di-hydroxylated B-ring flavonoids, suggests that the latter are at least partially responsible, as further supported by the effects of quercetin on CCA1 promoter activity in wild-type seedlings. Collectively, these experiments point to a previously-unknown connection between flavonoids and circadian cycling in plants and open the way to better understanding of the molecular basis of flavonoid action.

scholarly journals ClusterMap: Comparing analyses across multiple Single Cell RNA-Seq profiles

2018 ◽  
Author(s):  
Xin Gao ◽  
Deqing Hu ◽  
Madelaine Gogol ◽  
Hua Li
Keyword(s):  
Single Cell ◽  
Molecular Mechanisms ◽  
Population Level ◽  
Marker Genes ◽  
Rna Seq ◽  
Matching Problem ◽  
Cut Method ◽  
Underlying Mechanisms

AbstractSingle cell RNA-Seq facilitates the characterization of cell type heterogeneity and developmental processes. Further study of single cell profiles across different conditions enables the understanding of biological processes and underlying mechanisms at the sub-population level. However, developing proper methodology to compare multiple scRNA-Seq datasets remains challenging. We have developed ClusterMap, a systematic method and workflow to facilitate the comparison of scRNA profiles across distinct biological contexts. Using hierarchical clustering of the marker genes of each sub-group, ClusterMap matches the sub-types of cells across different samples and provides “similarity” as a metric to quantify the quality of the match. We introduce a purity tree cut method designed specifically for this matching problem. We use Circos plot and regrouping method to visualize the results concisely. Furthermore, we propose a new metric “separability” to summarize sub-population changes among all sample pairs. In three case studies, we demonstrate that ClusterMap has the ability to offer us further insight into the different molecular mechanisms of cellular sub-populations across different conditions. ClusterMap is implemented in R and available at https://github.com/xgaoo/ClusterMap.

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