scholarly journals Integrated Metabolome and Transcriptome Analysis Uncovers the Role of Anthocyanin Metabolism in Michelia maudiae

2019 ◽  
Vol 2019 ◽  
pp. 1-14 ◽  
Author(s):  
Xiaoan Lang ◽  
Na Li ◽  
Lingfei Li ◽  
Shouzhou Zhang
Keyword(s):  
Expression Profiles ◽  
Ornamental Plants ◽  
Gene Expression Profiles ◽  
Syringic Acid ◽  
Biosynthesis Pathway ◽  
Early Angiosperm ◽  
R2r3 Myb ◽  
Flavonoid Biosynthesis Pathway ◽  
R2r3 Myb Transcription Factors

Michelia maudiae Dunn is one of the important ornamental plants in the Magnoliaceae family, and the color of its flowers usually appears naturally pure white. The discovery of a rubellis flower named M. maudiae Dunn var. rubicunda provides an opportunity to reveal the metabolism of the flavonoids and anthocyanins of this “early angiosperm” plant. Combined metabolome and transcriptome analyses were applied using white and rubellis mutant tepals. Seven stages have been divided for flower development, and forty-eight differentially altered metabolites were identified between white and rubellis tepals at a later stage. The major anthocyanins including peonidin O-hexoside, cyanidin O-syringic acid, cyanidin 3,5-O-diglucoside, cyanidin 3-O-glucoside, and pelargonidin 3-O-glucoside were upregulated over 157-fold in the mutant. Conversely, the highly significant accumulation of the colorless procyanidin or the slightly yellow epicatechin and catechin was found in white flowers. Putative homologues of color-related genes involved in the phenylpropanoid and flavonoid biosynthesis pathway were identified in the transcriptome. The increasing expression of dihydroflavonol 4-reductase (DFR) might play an important role in the occurrence of rubellis pigments, while the overexpression of anthocyanidin reductase (ANR) in white flowers may promote the biosynthesis of proanthocyanidins. Additionally, several coloration-related repressor R2R3-MYB transcription factors showed different expression levels in the tepals of the rubellis mutant. This study provides a comprehensive analysis relating color compounds to gene expression profiles of the Magnoliids plant M. maudiae. The newly generated information will provide a profound effect on horticultural applications of Magnoliaceae.

scholarly journals Fusarium verticillioides FvPex8 is a key component of peroxisomal docking/translocation module that serves important roles in fumonisin biosynthesis but not in virulence

2020 ◽  
Author(s):  
Wenying Yu ◽  
Mei Lin ◽  
Minghui Peng ◽  
Huijuan Yan ◽  
Jie Zhou ◽  
...  
Keyword(s):  
Expression Profiles ◽  
Fusarium Verticillioides ◽  
Fumonisin B1 ◽  
Gene Expression Profiles ◽  
Deletion Mutants ◽  
Altered Expression ◽  
The Core ◽  
Metabolic Functions ◽  
Peroxisome Membrane

AbstractPeroxisomes are ubiquitous organelles in eukaryotic cells that fulfill various important metabolic functions. In this study, we investigated the role of Docking/Translocation Module (DTM) peroxins, mainly FvPex8, FvPex13, FvPex14, and FvPex33, in Fusarium verticillioides virulence and fumonisin B1 (FB1) biosynthesis. Protein interaction experiments suggested that FvPex13 serves as the core subunit of F. verticillioides DTM. When we generated gene deletion mutants (ΔFvpex8, ΔFvpex13, ΔFvpex14, ΔFvpex33, ΔFvpex33/14) and examined whether the expression of other peroxin genes were affected in the DTM mutants, ΔFvpex8 strain showed most drastic changes to PEX gene expression profiles. Deletion mutants exhibited disparity in carbon source utilization and defect in cell wall integrity when stress agents were applied. Under nutrient starvation, mutants also showed higher levels of lipid droplet accumulation. Notably, ΔFvpex8 mutant showed significant FB1 reduction and altered expression of FUM1 and FUM19 genes. However, FvPex13 was primarily responsible for virulence, while ΔFvpex33/14 double mutant also showed virulence defect. In summary, our study suggests that FvPex13 is the core component of DTM, regulating peroxisome membrane biogenesis as well as PTS1- and PTS2-mediated transmembrane cargo transportation. Importantly, we predict FvPex8 as a key component in DTM that affects peroxisome function in FB1 biosynthesis in F. verticillioides.

scholarly journals Characterization of Genes Associated with TGA7 During the Floral Transition

2020 ◽  
Author(s):  
Xiaorui Xu ◽  
Jingya Xu ◽  
Chen Yuan ◽  
Yikai Hu ◽  
Qinggang Liu ◽  
...  
Keyword(s):  
Flowering Time ◽  
Expression Profiles ◽  
Plant Defence ◽  
Gene Expression Profiles ◽  
Floral Transition ◽  
Cdna Libraries ◽  
Genetic Pathways ◽  
Time Control ◽  
Pathways Analysis

Abstract BackgroundThe TGA family has ten members and plays vital roles in plant defence and development in Arabidopsis. However, involvement of TGAs in control of flowering time remains largely unknown and requires further investigation. ResultsTo study the role of TGA7 during the floral transition, we first tested phenotypes of tga7 mutant, which displayed delay-flowering phenotype under both long-day and short-day conditions. We then performed flowering genetic pathways analysis and found that both autonomous and thermosensory pathways may affect TGA7 expression. Furthermore, to reveal differential gene expression profiles between wild-type (WT) and tga7, cDNA libraries were generated for WT and tga7 mutant seedlings at 9 DAG (days after germination). For each library, deep-sequencing produced approximately 6.67 Gb of high-quality sequences with the majority (84.55%) of mRNAs between 500 and 3000 nucleotides in length. Three hundred and twenty-five differentially expressed genes (DEGs) were identified between WT and tga7 mutant seedlings. Among them, four genes are associated with flowering time control. Differential expression of the four flowering-related DEGs was further validated by qRT-PCR.ConclusionsTransciptomic sequencing coupled with flowering genetic pathways analysis provides a framework for further studying the role of TGA7 in promoting flowering.

scholarly journals Comparative Integrated Omics Analysis of the Hfq Regulon in Bordetella pertussis

2019 ◽  
Vol 20 (12) ◽  
pp. 3073 ◽  
Author(s):  
Ana Dienstbier ◽  
Fabian Amman ◽  
Daniel Štipl ◽  
Denisa Petráčková ◽  
Branislav Večerek
Keyword(s):  
Gene Expression ◽  
Bordetella Pertussis ◽  
Transcriptional Control ◽  
Whooping Cough ◽  
Expression Profiles ◽  
Bacterial Pathogen ◽  
Gene Expression Profiles ◽  
Control Of Gene Expression ◽  
Proteomic Data

Bordetella pertussis is a Gram-negative strictly human pathogen of the respiratory tract and the etiological agent of whooping cough (pertussis). Previously, we have shown that RNA chaperone Hfq is required for virulence of B. pertussis. Furthermore, microarray analysis revealed that a large number of genes are affected by the lack of Hfq. This study represents the first attempt to characterize the Hfq regulon in bacterial pathogen using an integrative omics approach. Gene expression profiles were analyzed by RNA-seq and protein amounts in cell-associated and cell-free fractions were determined by LC-MS/MS technique. Comparative analysis of transcriptomic and proteomic data revealed solid correlation (r2 = 0.4) considering the role of Hfq in post-transcriptional control of gene expression. Importantly, our study confirms and further enlightens the role of Hfq in pathogenicity of B. pertussis as it shows that Δhfq strain displays strongly impaired secretion of substrates of Type III secretion system (T3SS) and substantially reduced resistance to serum killing. On the other hand, significantly increased production of proteins implicated in transport of important metabolites and essential nutrients observed in the mutant seems to compensate for the physiological defect introduced by the deletion of the hfq gene.

scholarly journals THE ROLE OF TRANSCRIPTOMICS: PHYSIOLOGICAL EQUIVALENCE BASED ON GENE EXPRESSION PROFILES

2017 ◽  
Vol 5 (0) ◽  
pp. 21-35 ◽  
Author(s):  
Shiori Miura ◽  
Takehiro Himaki ◽  
Junko Takahashi ◽  
Hitoshi Iwahashi
Keyword(s):  
Gene Expression ◽  
Expression Profiles ◽  
Gene Expression Profiles

scholarly journals Divergence of chemosensing during the early stages of speciation

2020 ◽  
Vol 117 (28) ◽  
pp. 16438-16447 ◽  
Author(s):  
Bas van Schooten ◽  
Jesyka Meléndez-Rosa ◽  
Steven M. Van Belleghem ◽  
Chris D. Jiggins ◽  
John D. Tan ◽  
...  
Keyword(s):  
Host Plant ◽  
Expression Profiles ◽  
Life Stage ◽  
Gene Expression Profiles ◽  
Color Pattern ◽  
Mate Finding ◽  
Strong Candidate ◽  
Genomic Regions ◽  
Heliconius Cydno

Chemosensory communication is essential to insect biology, playing indispensable roles during mate-finding, foraging, and oviposition behaviors. These traits are particularly important during speciation, where chemical perception may serve to establish species barriers. However, identifying genes associated with such complex behavioral traits remains a significant challenge. Through a combination of transcriptomic and genomic approaches, we characterize the genetic architecture of chemoperception and the role of chemosensing during speciation for a young species pair ofHeliconiusbutterflies,Heliconius melpomeneandHeliconius cydno. We provide a detailed description of chemosensory gene-expression profiles as they relate to sensory tissue (antennae, legs, and mouthparts), sex (male and female), and life stage (unmated and mated female butterflies). Our results untangle the potential role of chemical communication in establishing barriers during speciation and identify strong candidate genes for mate and host plant choice behaviors. Of the 252 chemosensory genes,HmOBP20(involved in volatile detection) andHmGr56(a putative synephrine-related receptor) emerge as strong candidates for divergence in pheromone detection and host plant discrimination, respectively. These two genes are not physically linked to wing-color pattern loci or other genomic regions associated with visual mate preference. Altogether, our results provide evidence for chemosensory divergence betweenH. melpomeneandH. cydno, two rarely hybridizing butterflies with distinct mate and host plant preferences, a finding that supports a polygenic architecture of species boundaries.

Gene expression profiles predict the possible regulatory role of OPN-mediated signaling pathways in rat liver regeneration

Gene ◽  
2016 ◽  
Vol 576 (2) ◽  
pp. 782-790 ◽  
Author(s):  
Gaiping Wang ◽  
Shasha Chen ◽  
Congcong Zhao ◽  
Xiaofang Li ◽  
Ling Zhang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Liver Regeneration ◽  
Signaling Pathways ◽  
Rat Liver ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Regulatory Role ◽  
Rat Liver Regeneration

Overexpression of BRE in Pediatric MLL-Rearranged Acute Myeloid Leukemia Associated with t(9;11)(p22;q23).

Blood ◽  
2009 ◽  
Vol 114 (22) ◽  
pp. 3471-3471
Author(s):  
Brian Balgobind ◽  
C. Michel Zwaan ◽  
Susan T.C.J.M. Arentsen-Peters ◽  
Dirk Reinhardt ◽  
Ursula Creutzig ◽  
...  
Keyword(s):  
Gene Expression ◽  
Myeloid Leukemia ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Apoptotic Effect ◽  
The Mean ◽  
Pediatric Aml ◽  
Acute Myeloid

Abstract Abstract 3471 Poster Board III-359 One important cytogenetic subgroup of pediatric acute myeloid leukemia (AML) is characterized by translocations of chromosome 11q23, which accounts for 15 to 20% of all cases with an evaluable chromosome analysis. In most of these cases, the mixed lineage leukemia (MLL) gene is involved. More than 50 fusion translocation partners of the MLL gene have been identified and outcome differs by translocation partner, suggesting differences in the biological background. So far these biological differences have not been unravelled. Therefore, we investigated the gene expression profiles of MLL-rearranged subgroups in pediatric AML in order to discover and identify the role of differentially expressed genes. Affymetrix Human Genome U133 plus 2.0 microarrays were used to generate gene expression profiles of 257 pediatric AML cases, which included 21 pediatric AML cases with t(9;11)(p22;q23) and 33 with other MLL-rearrangements. With these profiles, we were able to identify a specific gene expression signature for t(9;11)(p22;q23) using an empirical Bayes linear regression model (Bioconductor package: Limma). This signature was mainly determined by overexpression of the BRE (brain and reproductive organ-expressed) gene. The mean average VSN normalized expression for BRE in the t(9;11)(p22;q23) subgroup was 3.7-fold higher compared with that in other MLL-rearranged cases (p<0.001). Validation by RQ-PCR confirmed this higher expression in t(9;11)(p22;q23) cases (p<0.001). In addition, we confirmed that overexpression of BRE was predominantly found in t(9;11)(p22;q23) in an independent gene expression profile cohort (Ross et al, Blood 2002). Remarkably, MLL-rearranged cases with a BRE expression higher than the mean expression showed a significant better 3 year disease free survival than MLL-rearranged cases with a lower expression (80±13% vs. 30±10%, p=0.02). Previously, overexpression of BRE has been described in hepatocellular carcinomas (HCC) (Chang et al., Oncogene 2008) and an anti-apoptotic effect was described. We transfected BRE in the monomac-1 cell line, which harbors a t(9;11)(p22;q23). We did not find a proliferative advantage for BRE overexpression using a BrDU-assay nor changes in drug sensitivity, indicating that the anti-apoptotic effect as described for HCC in vivo could not be confirmed in vitro in AML. In conclusion, overexpression of the BRE gene is predominantly involved in pediatric MLL-rearranged AML with t(9;11)(p22;q23). Moreover, high expression of BRE showed a favorable prognosis. We did not find any influence of BRE expression on cell proliferation or apoptosis in vitro. This indicates that further studies involving the role of the MLL-fusion protein on BRE transcription are necessary to unravel the leukemogenic role in pediatric AML. Disclosures No relevant conflicts of interest to declare.

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