scholarly journals Transcriptome Analysis Identifies Key Genes Responsible for Red Coleoptiles in Triticum Monococcum

Molecules ◽  
2019 ◽  
Vol 24 (5) ◽  
pp. 932 ◽  
Author(s):  
Dong Cao ◽  
Jiequn Fan ◽  
Xingyuan Xi ◽  
Yuan Zong ◽  
Dongxia Wang ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Candidate Gene ◽  
Transcriptome Analysis ◽  
Anthocyanin Biosynthesis ◽  
Functional Domains ◽  
Transactivation Domain ◽  
Structural Genes ◽  
Transcript Levels ◽  
Key Genes

Red coleoptiles can help crops to cope with adversity and the key genes that are responsible for this trait have previously been isolated from Triticum aestivum, Triticum urartu, and Aegilops tauschii. This report describes the use of transcriptome analysis to determine the candidate gene that controls the trait for white coleoptiles in T. monococcum by screening three cultivars with white coleoptiles and two with red coleoptiles. Fifteen structural genes and two transcription factors that are involved in anthocyanin biosynthesis were identified from the assembled UniGene database through BLAST analysis and their transcript levels were then compared in white and red coleoptiles. The majority of the structural genes reflected lower transcript levels in the white than in the red coleoptiles, which implied that transcription factors related to anthocyanin biosynthesis could be candidate genes. The transcript levels of MYC transcription factor TmMYC-A1 were not significantly different between the white and red coleoptiles and all of the TmMYC-A1s contained complete functional domains. The deduced amino acid sequence of the MYB transcription factor TmMYB-A1 in red coleoptiles was homologous to TuMYB-A1, TaMYB-A1, TaMYB-B1, and TaMYB-D1, which control coleoptile color in corresponding species and contained the complete R2R3 MYB domain and the transactivation domain. TmMYB-a1 lost its two functional domains in white coleoptiles due to a single nucleotide deletion that caused premature termination at 13 bp after the initiation codon. Therefore, TmMYB-A1 is likely to be the candidate gene for the control of the red coleoptile trait, and its loss-of-function mutation leads to the white phenotype in T. monococcum.

scholarly journals Comparative transcriptome analysis reveals key genes associated with pigmentation in radish (Raphanus sativus L.) skin and flesh

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jifang Zhang ◽  
Jian Zhao ◽  
Qunyun Tan ◽  
Xiaojun Qiu ◽  
Shiyong Mei
Keyword(s):  
Transcription Factors ◽  
Raphanus Sativus ◽  
Regulatory Networks ◽  
Anthocyanin Biosynthesis ◽  
Comparative Transcriptome ◽  
Structural Genes ◽  
Key Genes ◽  
Transcript Profiles ◽  
Species Specific ◽  
Anthocyanin Biosynthetic Genes

AbstractRadish (Raphanus sativus) is an important vegetable worldwide that exhibits different flesh and skin colors. The anthocyanins responsible for the red and purple coloring in radishes possess nutritional value and pharmaceutical potential. To explore the structural and regulatory networks related to anthocyanin biosynthesis and identify key genes, we performed comparative transcriptome analyses of the skin and flesh of six colored radish accessions. The transcript profiles showed that each accession had a species-specific transcript profile. For radish pigmentation accumulation, the expression levels of anthocyanin biosynthetic genes (RsTT4, RsC4H, RsTT7, RsCCOAMT, RsDFR, and RsLDOX) were significantly upregulated in the red- and purple-colored accessions, but were downregulated or absent in the white and black accessions. The correlation test, combined with metabolome (PCC > 0.95), revealed five structural genes (RsTT4, RsDFR, RsCCOAMT, RsF3H, and RsBG8L) and three transcription factors (RsTT8-1, RsTT8-2, and RsPAR1) to be significantly correlated with flavonoids in the skin of the taproot. Four structural genes (RsBG8L, RsDFR, RsCCOAMT, and RsLDOX) and nine transcription factors (RsTT8-1, RsTT8-2, RsMYB24L, RsbHLH57, RsPAR2L, RsbHLH113L, RsOGR3L, RsMYB24, and RsMYB34L) were found to be significantly correlated with metabolites in the flesh of the taproot. This study provides a foundation for future studies on the gene functions and genetic diversity of radish pigmentation and should aid in the cultivation of new valuable radish varieties.

scholarly journals Transcriptome Analysis Clarified Genes Involved in Betalain Biosynthesis in the Fruit of Red Pitayas (Hylocereus costaricensis)

Molecules ◽  
2019 ◽  
Vol 24 (3) ◽  
pp. 445 ◽  
Author(s):  
Xingyuan Xi ◽  
Yuan Zong ◽  
Shiming Li ◽  
Dong Cao ◽  
Xuemei Sun ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Transcriptome Analysis ◽  
Anthocyanin Biosynthesis ◽  
Average Length ◽  
Major Gene ◽  
Future Research ◽  
Structural Genes ◽  
Kegg Pathways ◽  
Lower Expression

The red flesh trait gives red pitayas more healthful components and a higher price, while the genetic mechanism behind this trait is unknown. In this manuscript, transcriptome analysis was employed to discover the genetic differences between white and red flesh in pitayas. A total of 27.99 Gb clean data were obtained for four samples. Unigenes, 79,049 in number, were generated with an average length of 1333 bp, and 52,618 Unigenes were annotated. Compared with white flesh, the expression of 10,215 Unigenes was up-regulated, and 4853 Unigenes were down-regulated in red flesh. The metabolic pathways accounted for 64.6% of all differentially expressed Unigenes in KEGG pathways. The group with high betalain content in red flesh and all structural genes, related to betalain biosynthesis, had a higher expression in red flesh than white flesh. The expression of the key gene, tyrosine hydroxylase CYP76AD1, was up-regulated 245.08 times, while 4,5-DOPA dioxygenase DODA was up-regulated 6.46 times. Moreover, the special isomers CYP76AD1α and DODAα were only expressed in red flesh. The competitive anthocyanin biosynthesis pathway had a lower expression in red flesh. Two MYB transcription factors were of the same branch as BvMYB1, regulating betalain biosynthesis in beet, and those transcription factors had expression differences in two kinds of pitayas, which indicated that they should be candidate genes controlling betalain accumulation in red pitayas. This research would benefit from identifying the major gene controlling red flesh trait and breed new cultivars with the red flesh trait. Future research should aim to prove the role of each candidate gene in betalain biosynthesis in red pitayas.

MdMYBL2 helps regulate cytokinin-induced anthocyanin biosynthesis in red-fleshed apple (Malus sieversii f. niedzwetzkyana) callus

2019 ◽  
Vol 46 (2) ◽  
pp. 187 ◽  
Author(s):  
Yicheng Wang ◽  
Jingjing Sun ◽  
Nan Wang ◽  
Haifeng Xu ◽  
Changzhi Qu ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Molecular Mechanisms ◽  
Anthocyanin Biosynthesis ◽  
Bimolecular Fluorescence Complementation ◽  
Structural Genes ◽  
Myb Transcription Factors ◽  
Malus Sieversii ◽  
Transcription Factor Genes ◽  
Transgenic Callus

Anthocyanin biosynthesis is induced by cytokinins, and is regulated by MYB transcription factors. However, the underlying molecular mechanisms have not been fully characterised. In the present study, red-fleshed apple callus were induced from the leaves of an R6/R6 homozygous line, which was the hybrid offspring of Malus sieversii f. niedzwetzkyana and ‘Fuji’. We analysed the callus anthocyanin contents in response to different cytokinin concentrations. We observed that cytokinin treatments upregulated the expression of anthocyanin structural genes MdDFR and MdUFGT and transcription factor genes MdMYB10 and MdbHLH3. Additionally, the expression of MdMYBL2, which encodes the bHLH and EAR motifs, was inhibited by cytokinin treatments. The MdMYBL2-overexpressing callus had lower anthocyanin contents than the wild-type controls. We noted that the expression levels of anthocyanin biosynthesis structural genes MdDFR and MdUFGT and transcription factor genes MdMYB10 and MdbHLH3 were strongly suppressed in the transgenic callus. Subsequent yeast two-hybrid, bimolecular fluorescence complementation, and pull-down assays indicated that MdMYBL2 interacts with MdbHLH3, which may influence the expression of anthocyanin biosynthesis-related genes. Our findings may provide new insights into how MYB transcription factors influence the cytokinin-regulated anthocyanin biosynthesis in red-fleshed apples.

scholarly journals Comprehensive influences of overexpression of a MYB transcriptor regulating anthocyanin biosynthesis on transcriptome and metabolome of tobacco leaves

2019 ◽  
Author(s):  
Yuan Zong ◽  
Shiming Li ◽  
Xingyuan Xi ◽  
Dong Cao ◽  
Zhong Wang ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Anthocyanin Biosynthesis ◽  
Chemical Compounds ◽  
Myb Transcription Factor ◽  
Biosynthesis Pathway ◽  
Structural Genes ◽  
Leaf Phenotype ◽  
Transgenic Lines ◽  
Purple Leaf

Abstract Background Overexpression of MYB transcription factors can induce the expression of structural genes for anthocyanin biosynthesis and increase the anthocyanin content of plant tissues. However, it remains unclear whether MYB transcription factor overexpression effects the activation of other genes and the concomitant accumulation of chemical compounds. Results Overexpression of LrAN2 promoted anthocyanin accumulation in a variety of tissues in tobacco cultivar Samsun. Only 185 unigenes, from total of 160,965, were expressed differently in leaves and 241 chemical compounds exhibited differences in accumulation. Four anthocyanins, including apigeninidin chloride, cyanidin 3-O-malonylhexoside, pelargonidin 3-O-beta-D-glucoside, and cyanidin 3,5-O-diglucoside were detected only in transgenic lines, which could explain the purple leaf phenotype. Beside anthocyanins, the phenylpropanoids, polyphenols (catechins), flavonoids, flavones, and flavonols were also upregulated. Overexpression of LrAN2 activated the basic helix-loop-helix transcription factor AN1b, and the MYB transcription factor MYB3. Additionally, structural genes associated with the phenylpropanoid biosynthetic pathway were activated, which lead to the upregulated accumulation of phenylpropanoid, polyphenol (catechin), flavonoid, flavone, flavonol, and anthocyanin. The MYB transcription factor CPC, a negative regulator of anthocyanin biosynthesis, was also expressed at increased levels in transgenic lines, which implie that a negative regulation mechanism existed in the anthocyanin biosynthesis pathway. The relative contents of all 19 differently accumulated amino groups and derivatives were decreased in transgenic lines, which meant that the phenylalanine biosynthesis pathway used other amino acids as substrates. Interestingly, the expression of acetylalkylglycerol acetylhydrolase was suppressed in transgenic lines, which caused the accumulation of 19 lyso-phosphatidylcholine derivatives and a decrease in production of eight octodecane derivatives. Conclusions Overexpression of LrAN2 activates the pathway of anthocyanin synthesis and metabolism in tobacco. Four anthocyanins lead to the purple leaf phenotype The main pathways of flavonoid biosynthesis were up-regulated. This research provides more information about the function of MYB transcription factors in anthocyanin biosynthesis and the production of other chemical compounds. This work will help breeders to obtain new plant cultivars with high anthocyanin contents using biotechnology.

scholarly journals Analysis of structural genes and key transcription factors related to anthocyanin biosynthesis in potato tubers

2017 ◽  
Vol 225 ◽  
pp. 310-316 ◽  
Author(s):  
Huiling Zhang ◽  
Bo Yang ◽  
Jun Liu ◽  
Dalong Guo ◽  
Juan Hou ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Anthocyanin Biosynthesis ◽  
Potato Tubers ◽  
Structural Genes

scholarly journals Expression of Adhesive Pili and the Collagen-Binding Adhesin Ace Is Activated by ArgR Family Transcription Factors inEnterococcus faecalis

2018 ◽  
Vol 200 (18) ◽  
Author(s):  
Dawn A. Manias ◽  
Gary M. Dunny
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Enterococcus Faecalis ◽  
Opportunistic Infections ◽  
Structural Genes ◽  
Gene Encoding ◽  
Collagen Binding ◽  
Content Type ◽  
Surface Adhesins

ABSTRACTIt was shown previously that the disruption of theahrCgene encoding a predicted ArgR family transcription factor results in a severe defect in biofilm formationin vitro, as well as a significant attenuation of virulence ofEnterococcus faecalisstrain OG1RF in multiple experimental infection models. Using transcriptome sequencing (RNA-seq), we observedahrC-dependent changes in the expression of more than 20 genes. AhrC-repressed genes included predicted determinants of arginine catabolism and several other metabolic genes and predicted transporters, while AhrC-activated genes included determinants involved in the production of surface protein adhesins. Most notably, the structural and regulatory genes of theebplocus encoding adhesive pili were positively regulated, as well as theacegene, encoding a collagen-binding adhesin. UsinglacZtranscription reporter fusions, we determined thatahrCand a secondargRtranscription factor gene,argR2, both function to activate the expression ofebpR, which directly activates the transcription of the pilus structural genes. Our data suggest that in the wild-typeE. faecalis, the low levels of EbpR limit the expression of pili and that biofilm biomass is also limited by the amount of pili expressed by the bacteria. The expression ofaceis similarly enhanced by AhrC and ArgR2, butaceexpression is not dependent on EbpR. Our results demonstrate the existence of novel regulatory cascades controlled by a pair of ArgR family transcription factors that might function as a heteromeric protein complex.IMPORTANCECell surface adhesins play critical roles in the formation of biofilms, host colonization, and the pathogenesis of opportunistic infections byEnterococcus faecalis. Here, we present new results showing that the expression of two major enterococcal surface adhesins,ebppili, and the collagen-binding protein Ace is positively regulated at the transcription level by twoargRfamily transcription factors, AhrC and ArgR2. In the case of pili, the direct target of regulation is theebpRgene, previously shown to activate the transcription of the pilus structural genes, while the activation ofacetranscription appears to be directly impacted by the two ArgR proteins. These transcription factors may represent new targets for blocking enterococcal infections.

scholarly journals Mutational Analysis of AREA, a Transcriptional Activator Mediating Nitrogen Metabolite Repression in Aspergillus nidulans and a Member of the “Streetwise” GATA Family of Transcription Factors

1998 ◽  
Vol 62 (3) ◽  
pp. 586-596 ◽  
Author(s):  
Richard A. Wilson ◽  
Herbert N. Arst
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Dna Binding ◽  
Aspergillus Nidulans ◽  
Transcriptional Activator ◽  
Structural Genes ◽  
Gata Factor ◽  
Mutational Change ◽  
Nitrogen Metabolite Repression ◽  
Gata Family

SUMMARY The transcriptional activator AREA is a member of the GATA family of transcription factors and mediates nitrogen metabolite repression in the fungus Aspergillus nidulans. The nutritional versatility of A. nidulans and its amenability to classical and reverse genetic manipulations make the AREA DNA binding domain (DBD) a useful model for analyzing GATA family DBDs, particularly as structures of two AREA-DNA complexes have been determined. The 109 extant mutant forms of the AREA DBD surveyed here constitute one of the highest totals of eukaryotic transcription factor DBD mutants, are discussed in light of the roles of individual residues, and are compared to corresponding mutant sequence changes in other fungal GATA factor DBDs. Other topics include delineation of the DBD using both homology and mutational truncation, use of frameshift reversion to detect regions of tolerance to mutational change, the finding that duplication of the DBD can apparently enhance AREA function, and use of the AREA system to analyze a vertebrate GATA factor DBD. Some major points to emerge from work on the AREA DBD are (i) tolerance to sequence change (with retention of function) is surprisingly great, (ii) mutational changes in a transcription factor can have widely differing, even opposing, effects on expression of different structural genes so that monitoring expression of one or even several structural genes can be insufficient and possibly misleading, and (iii) a mutational change altering local hydrophobic packing and DNA binding target specificity can markedly influence the behavior of mutational changes elsewhere in the DBD.

scholarly journals CmMYB#7, an R3 MYB transcription factor, acts as a negative regulator of anthocyanin biosynthesis in chrysanthemum

2019 ◽  
Vol 70 (12) ◽  
pp. 3111-3123 ◽  
Author(s):  
Lili Xiang ◽  
Xiaofen Liu ◽  
Heng Li ◽  
Xueren Yin ◽  
Donald Grierson ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Binding Site ◽  
Transient Expression ◽  
Regulatory Mechanism ◽  
Anthocyanin Biosynthesis ◽  
Expression Patterns ◽  
Negative Regulator ◽  
Myb Transcription Factor ◽  
Anthocyanin Content

Abstract ‘Jimba’, a well-known white flowered chrysanthemum cultivar, occasionally and spontaneously produces red colored petals under natural cultivation, but there is little information about the molecular regulatory mechanism underlying this process. We analysed the expression patterns of 91 MYB transcription factors in ‘Jimba’ and ‘Turning red Jimba’ and identified an R3 MYB, CmMYB#7, whose expression was significantly decreased in ‘Turning red Jimba’ compared with ‘Jimba’, and confirmed it is a passive repressor of anthocyanin biosynthesis. CmMYB#7 competed with CmMYB6, which together with CmbHLH2 is an essential component of the anthocyanin activation complex, for interaction with CmbHLH2 through the bHLH binding site in the R3 MYB domain. This reduced binding of the CmMYB6–CmbHLH2 complex and inhibited its ability to activate CmDFR and CmUFGT promoters. Moreover, using transient expression assays we demonstrated that changes in the expression of CmMYB#7 accounted for alterations in anthocyanin content. Taken together, our findings illustrate that CmMYB#7 is a negative regulator of anthocyanin biosynthesis in chrysanthemum.

scholarly journals The Wheat GENIE3 Network Provides Biologically-Relevant Information in Polyploid Wheat

2020 ◽  
Vol 10 (10) ◽  
pp. 3675-3686 ◽  
Author(s):  
Sophie A. Harrington ◽  
Anna E. Backhaus ◽  
Ajit Singh ◽  
Keywan Hassani-Pak ◽  
Cristobal Uauy
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Candidate Gene ◽  
Web Application ◽  
Regulatory Networks ◽  
Target Genes ◽  
Gene Prediction ◽  
Relevant Information ◽  
Rna Seq ◽  
Biologically Relevant

Gene regulatory networks are powerful tools which facilitate hypothesis generation and candidate gene discovery. However, the extent to which the network predictions are biologically relevant is often unclear. Recently a GENIE3 network which predicted targets of wheat transcription factors was produced. Here we used an independent RNA-Seq dataset to test the predictions of the wheat GENIE3 network for the senescence-regulating transcription factor NAM-A1 (TraesCS6A02G108300). We re-analyzed the RNA-Seq data against the RefSeqv1.0 genome and identified a set of differentially expressed genes (DEGs) between the wild-type and nam-a1 mutant which recapitulated the known role of NAM-A1 in senescence and nutrient remobilisation. We found that the GENIE3-predicted target genes of NAM-A1 overlap significantly with the DEGs, more than would be expected by chance. Based on high levels of overlap between GENIE3-predicted target genes and the DEGs, we identified candidate senescence regulators. We then explored genome-wide trends in the network related to polyploidy and found that only homeologous transcription factors are likely to share predicted targets in common. However, homeologs which vary in expression levels across tissues are less likely to share predicted targets than those that do not, suggesting that they may be more likely to act in distinct pathways. This work demonstrates that the wheat GENIE3 network can provide biologically-relevant predictions of transcription factor targets, which can be used for candidate gene prediction and for global analyses of transcription factor function. The GENIE3 network has now been integrated into the KnetMiner web application, facilitating its use in future studies.

Identification of key genes and transcription factors in ageing Arabidopsis papilla cells by transcriptome analysis

2020 ◽  
Vol 147 ◽  
pp. 1-9 ◽  
Author(s):  
Hong Ye ◽  
Fei Ren ◽  
Haoyu Guo ◽  
Liping Guo ◽  
Jianfang Bai ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Transcriptome Analysis ◽  
Key Genes
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