Combined Analysis of the Metabolome and Transcriptome Identified Candidate Genes Involved in Phenolic Acid Biosynthesis in the Leaves of Cyclocarya paliurus

To assess changes of metabolite content and regulation mechanism of the phenolic acid biosynthesis pathway at different developmental stages of leaves, this study performed a combined metabolome and transcriptome analysis of Cyclocarya paliurus leaves at different developmental stages. Metabolite and transcript profiling were conducted by ultra-performance liquid chromatography quadrupole time-of-flight tandem mass spectrometer and high-throughput RNA sequencing, respectively. Transcriptome identification showed that 58 genes were involved in the biosynthesis of phenolic acid. Among them, 10 differentially expressed genes were detected between every two developmental stages. Identification and quantification of metabolites indicated that 14 metabolites were located in the phenolic acid biosynthetic pathway. Among them, eight differentially accumulated metabolites were detected between every two developmental stages. Association analysis between metabolome and transcriptome showed that six differentially expressed structural genes were significantly positively correlated with metabolite accumulation and showed similar expression trends. A total of 128 transcription factors were identified that may be involved in the regulation of phenolic acid biosynthesis; these include 12 MYBs and 10 basic helix–loop–helix (bHLH) transcription factors. A regulatory network of the phenolic acid biosynthesis was established to visualize differentially expressed candidate genes that are involved in the accumulation of metabolites with significant differences. The results of this study contribute to the further understanding of phenolic acid biosynthesis during the development of leaves of C. paliurus.

Download Full-text

Identification and fine mapping of a novel qGR6.2 locus controlling rice salt tolerance during seed germination

10.21203/rs.3.rs-24631/v1 ◽

2020 ◽

Author(s):

Peng Zeng ◽

Peiwen Zhu ◽

Luofeng Qian ◽

Xumei Qian ◽

Yuxin Mi ◽

...

Keyword(s):

Salt Tolerance ◽

Seed Germination ◽

Candidate Genes ◽

Fine Mapping ◽

Developmental Stages ◽

Indica Rice ◽

Germination Rate ◽

Differentially Expressed ◽

Germination Ability ◽

Germination Traits

Abstract Background Rice growth is frequently affected by salinity. When rice plants are exposed to high salinity, seed germination and seedling establishment are significantly inhibited. In particular, with the promotion of rice direct-seeding in Asia, improving rice salt tolerance during seed germination is of strong importance for rice breeding. Results In this study, we found that the indica rice landrace Wujiaozhan (WJZ) showed a high capability of seed germination under both water (H 2 O) and salt (NaCl) conditions, particularly under high salt stress. The BC 1 F 2 population produced by crossing WJZ with japonica Nipponbare (Nip) was used to evaluate the germination traits under water (H 2 O) and salt (300 mM NaCl) conditions using germination rate (GR) and germination index (GI). A total of 13 quantitative trait loci (QTLs) were identified, including eight QTLs of GR, two QTLs of GI under H 2 O conditions, six QTLs of GR, and three QTLs of GI under 300 mM NaCl conditions. Six QTLs ( qGR6.1 , qGR8.1 , qGR8.2 , qGR10.1 , qGR10.2 and qGI10.1 ) contributed to GR under both H 2 O and 300 mM NaCl conditions. Three QTLs ( qGR6.2 , qGR10.1 and qGR10.2 ) under 300 mM NaCl conditions were identified at different time points of seed germination and shared the same region with qGI6 , qGI10.1 and qGI10.2 for GI. These QTLs could be used to improve seed germination ability via marker-assisted selection (MAS). One major effective salt-tolerance-specific QTL, qGR6.2, on chromosome 6 was further confirmed via the BC 2 F 2 population, which explained more than 20% of the phenotypic variation. Fine mapping results showed that qGR6.2 was narrowed to a 65.9-kb region between the Z654 and Z619 molecular markers, with eleven candidate genes being predicted. Based on the microarray database, there were high transcript abundances of six genes ( LOC_Os06g10650 , LOC_Os06g10660 , LOC_Os06g10690 , LOC_Os06g10710 , LOC_Os06g10730 and LOC_Os06g10750 ) at all developmental stages, and only LOC_Os06g10750 was differentially expressed after salt incubation. RT-qPCR showed that two genes ( LOC_Os06g10650 and LOC_Os06g10750 ) were significantly differentially expressed at 300 mM NaCl during seed germination. This result suggested that LOC_Os06g10650 and LOC_Os06g10750 might be the causal candidate genes for the major effective salt-tolerance-specific QTL qGR6.2 identified in WJZ, which may facilitate map-based cloning and help to elucidate the molecular mechanism underlying salt tolerance during seed germination. Conclusions In our study, we identified 13 QTLs from indica landrace WJZ that confer seed germination traits under water and salt conditions. A major salt-tolerance-specific QTL qGR6.2 was confirmed and fine mapped to a 65.9-kb region flanked by the Z654 and Z619 markers. Our results provide information on the genetic basis of improving salt tolerance during seed germination by MAS.

Download Full-text

Homologous BHLH transcription factors induce distinct deformations of torsionally-stressed DNA: a potential transcription regulation mechanism.

10.1101/2022.01.07.475332 ◽

2022 ◽

Author(s):

Johanna Hörberg ◽

Kevin Moreau ◽

Anna Reymer

Keyword(s):

Transcription Factors ◽

Specific Binding ◽

Torsional Rigidity ◽

Regulation Mechanism ◽

Regulation Of Transcription ◽

Torsional Stress ◽

Bioinformatics Analyses ◽

Helix Loop Helix ◽

Dynamics Simulations ◽

The Impact

Changing torsional restraints on DNA is essential for the regulation of transcription. Torsional stress, introduced by RNA polymerase, can propagate along chromatin facilitating topological transitions and modulating the specific binding of transcription factors (TFs) to DNA. Despite the importance, the mechanistic details on how torsional stress impacts the TFs-DNA complexation remain scarce. Herein we address the impact of torsional stress on DNA complexation with homologous human basic-helix-loop-helix (BHLH) hetero- and homodimers: MycMax, MadMax, and MaxMax. The three TF dimers exhibit specificity towards the same DNA consensus sequences, the E-box response element, while regulating different transcriptional pathways. Using microseconds-long atomistic molecular dynamics simulations together with the torsional restraint that controls DNA total helical twist, we gradually over- and underwind naked and complexed DNA to a maximum of ±5°/b.p. step. We observe that the binding of the BHLH dimers results in a similar increase in DNA torsional rigidity. However, under torsional stress the BHLH dimers induce distinct DNA deformations, characterised by changes in DNA grooves geometry and a significant asymmetric DNA bending. Supported by bioinformatics analyses, our data suggest that torsional stress may contribute to the execution of differential transcriptional programs of the homologous TFs by modulating their collaborative interactions.

Download Full-text

An Integrated Transcriptome and Proteome Analysis Reveals New Insights into Russeting of Bagging and Non-Bagging “Golden Delicious” Apple

International Journal of Molecular Sciences ◽

10.3390/ijms20184462 ◽

2019 ◽

Vol 20 (18) ◽

pp. 4462 ◽

Cited By ~ 1

Author(s):

Gaopeng Yuan ◽

Shuxun Bian ◽

Xiaolei Han ◽

Shanshan He ◽

Kai Liu ◽

...

Keyword(s):

Transcription Factors ◽

Molecular Mechanisms ◽

Developmental Stages ◽

Lignin Biosynthesis ◽

Proteome Analysis ◽

Differentially Expressed ◽

Proteomics Data ◽

Absolute Quantitation ◽

Physiological Disorder ◽

Golden Delicious

Apple skin russeting naturally occurs in many varieties, particularly in “Golden Delicious” and its pedigree, and is regarded as a non-invasive physiological disorder partly caused by excessive deposition of lignin. However, the understanding of its molecular mechanism is still limited. In this study, we used iTRAQ (isobaric tags for relative and absolute quantitation) and RNA-seq to detect the changes in the expression levels of genes and proteins in three developmental stages of russeting formation, in russeted (non-bagging) and non-russeted (bagging) skin of “Golden Delicious” apple. 2856 differentially expressed genes and 942 differentially expressed proteins in the comparison groups were detected at the transcript level and protein level, respectively. A correlation analysis of the transcriptomics and proteomics data revealed that four genes (MD03G1059200, MD08G1009200, MD17G1092400, and MD17G1225100) involved in lignin biosynthesis are significant changed during apple russeting formation. Additionally, 92 transcription factors, including 4 LIM transcription factors, may be involved in apple russeting formation. Among them, one LIM transcription factor (MD15G1068200) was capable of binding to the PAL-box like (CCACTTGAGTAC) element, which indicated it was potentially involved in lignin biosynthesis. This study will provide further views on the molecular mechanisms controlling apple russeting formation.

Download Full-text

ShcA Regulates Thymocyte Proliferation through Specific Transcription Factors and a c-Abl-Dependent Signaling Axis

Molecular and Cellular Biology ◽

10.1128/mcb.01084-14 ◽

2015 ◽

Vol 35 (8) ◽

pp. 1462-1476 ◽

Cited By ~ 4

Author(s):

Paul C. Trampont ◽

Li Zhang ◽

Amber J. Giles ◽

Scott F. Walk ◽

Jing J. Gu ◽

...

Keyword(s):

Transcription Factors ◽

Chemokine Receptors ◽

Developmental Stages ◽

Cell Receptor ◽

Cell Cycle Regulators ◽

Content Type ◽

Helix Loop Helix ◽

Thymocyte Proliferation ◽

Signaling Axis ◽

Immature Thymocytes

Signaling via the pre-T-cell receptor (pre-TCR), along with associated signals from Notch and chemokine receptors, regulates the β-selection checkpoint that operates on CD4−CD8−doubly negative (DN) thymocytes. Since many hematopoietic malignancies arise at the immature developmental stages of lymphocytes, understanding the signal integration and how specific signaling molecules and distal transcription factors regulate cellular outcomes is of importance. Here, a series of molecular and genetic approaches revealed that the ShcA adapter protein critically influences proliferation and differentiation during β-selection. We found that ShcA functions downstream of the pre-TCR and p56Lckand show that ShcA is important for extracellular signal-regulated kinase (ERK)-dependent upregulation of transcription factors early growth factor 1 (Egr1) and Egr3 in immature thymocytes and, in turn, of the expression and function of the Id3 and E2A helix-loop-helix (HLH) proteins. ShcA also contributes to pre-TCR-mediated induction of c-Myc and additional cell cycle regulators. Moreover, using an unbiasedSaccharomyces cerevisiae(yeast) screen, we identified c-Abl as a binding partner of phosphorylated ShcA and demonstrated the relevance of the ShcA–c-Abl interaction in immature thymocytes. Collectively, these data identify multiple modes by which ShcA can fine-tune the development of early thymocytes, including a previously unappreciated ShcA–c-Abl axis that regulates thymocyte proliferation.

Download Full-text

Screening and Identification of Transcription Factors Potentially Regulating Foxl2 Expression in Chlamys farreri Ovary

Biology ◽

10.3390/biology11010113 ◽

2022 ◽

Vol 11 (1) ◽

pp. 113

Author(s):

Shutong Fan ◽

Xixi Li ◽

Siyu Lin ◽

Yunpeng Li ◽

Huixin Ma ◽

...

Keyword(s):

Transcription Factors ◽

Ovarian Function ◽

Developmental Stages ◽

Promoter Sequence ◽

Luciferase Reporter ◽

Ovary Development ◽

Regulation Mechanism ◽

Specific Expression ◽

Screening And Identification ◽

Specific Regulation

Foxl2 is an evolutionarily conserved female sex gene, which is specifically expressed in the ovary and mainly involved in oogenesis and ovarian function maintenance. However, little is known about the mechanism that regulates Foxl2 specific expression during the ovary development. In the present study, we constructed the gonadal yeast one-hybrid (Y1H) library of Chlamysfarreri with ovaries and testes at different developmental stages using the Gateway technology. The library capacity was more than 1.36 × 107 CFU, and the length of the inserted fragment was 0.75 Kb~2 Kb, which fully met the demand of yeast library screening. The highly transcriptional activity promoter sequence of C. farreri Foxl2 (Cf-Foxl2) was determined at −1000~−616 bp by dual-luciferase reporter (DLR) assay and was used as bait to screen possible transcription factors from the Y1H library. Eleven candidate factors, including five unannotated factors, were selected based on Y1H as well as their expressional differences between ovaries and testes and were verified for the first time to be involved in the transcriptional regulation of Cf-Foxl2 by RT-qPCR and DLR. Our findings provided valuable data for further studying the specific regulation mechanism of Foxl2 in the ovary.

Download Full-text

Transcriptome regulation of carotenoids in five flesh-colored watermelon (Citrullus lanatus)

10.21203/rs.3.rs-42816/v2 ◽

2021 ◽

Author(s):

Pingli Yuan ◽

Muhammad Jawad Umer ◽

Nan He ◽

Shengjie Zhao ◽

Xuqiang Lu ◽

...

Keyword(s):

Transcription Factors ◽

Candidate Genes ◽

Differentially Expressed Genes ◽

Fruit Development ◽

Citrullus Lanatus ◽

Carotenoid Biosynthesis ◽

Differentially Expressed ◽

Flesh Color ◽

Hub Genes ◽

Data Resource

Abstract Background: Fruit flesh color in watermelon (Citrullus lanatus) is a great index for evaluation of the appearance quality and a key contributor influencing consumers' preferences, but the molecular mechanism of this intricate trait remain largely unknown. Here, the carotenoids and transcriptome dynamics during the fruit development of cultivated watermelon with five different flesh colors were analyzed.Results: A total of 13 carotenoids and 16781 differentially expressed genes (DEGs) including 1295 transcription factors (TFs) were detected in five watermelon genotypes during the fruit development. The comprehensive accumulation patterns of carotenoids were closely related to flesh color. A number of potential structural genes and transcription factors were found to be associated with the carotenoid biosynthesis pathway using comparative transcriptome analysis. The differentially expressed genes were divided into six subclusters and distributed in different GO terms and metabolic pathways. Furthermore, we performed weighted gene co-expression network analysis and predicted hub genes in six main modules determining carotenoid contents. Cla018406 (a chaperone protein dnaJ-like protein) may be a candidate gene for β-carotene accumulation and highly expressed in orange flesh-colored fruit. Cla007686 (a zinc finger CCCH domain-containing protein) was highly expressed in the red flesh-colored watermelon, maybe a key regulator of lycopene accumulation. Cla003760 (membrane protein) and Cla021635 (photosystem I reaction center subunit II) were predicted to be hub genes and may play an essential role in yellow flesh formation.Conclusions: The composition and contents of carotenoid in five watermelon genotypes vary greatly. A series of candidate genes were revealed through combined analysis of metabolites and transcriptome. These results provide an important data resource for dissecting the candidate genes and molecular basis governing flesh color formation in watermelon fruit.

Download Full-text

Transcriptional Regulatory Network of GA Floral Induction Pathway in LA Hybrid Lily

International Journal of Molecular Sciences ◽

10.3390/ijms20112694 ◽

2019 ◽

Vol 20 (11) ◽

pp. 2694 ◽

Cited By ~ 1

Author(s):

Wenqi Li ◽

Yubing Yong ◽

Yue Zhang ◽

Yingmin Lyu

Keyword(s):

Signal Transduction ◽

Transcription Factors ◽

Protein Kinase ◽

Low Temperature ◽

Candidate Genes ◽

Floral Induction ◽

Differentially Expressed ◽

Transcriptional Analysis ◽

Rna Seq ◽

Exogenous Gibberellin

Background: The LA hybrid lily ‘Aladdin’ has both excellent traits of Longiflorum hybrids and Asiatic hybrids—such as big and vivid flower, strong stem, high self-propagation coefficient, and shorter low temperature time required to release bulb dormancy in contrast to Oriental hybrids. A genome-wide transcriptional analysis using transcriptome RNA-Seq was performed in order to explore whether there is a gibberellin floral induction pathway in the LA hybrid lily. Subsequently, gene co-expression network analysis was used to analyze the possible interactions of key candidate genes screened from transcriptome data. At the same time, a series of physiological, biochemical, and cultivation tests were carried out. Results: The content of five endogenous hormones changed sharply in the shoot apex during the treatment of 200 mg/L exogenous gibberellin and the ratio of ABA/GA3 dropped and stayed at a lower level after 4 hours’ treatment from the higher levels initially, reaching a dynamic balance. In addition, the metabolism of carbohydrates in the bulbs increase during exogenous gibberellin treatment. A total of 124,041 unigenes were obtained by RNA-seq. With the transcriptome analysis, 48,927 unigenes and 48,725 unigenes respectively aligned to the NR database and the Uniprot database. 114,138 unigenes, 25,369 unigenes, and 19,704 unigenes respectively aligned to the COG, GO, and KEGG databases. 2148 differentially expression genes (DEGs) were selected with the indicators RPKM ≥ 0, FDR ≤ 0.05 and |log2(ratio)| ≥ 2. The number of the upregulated unigenes was significantly more than the number of the downregulated unigenes. Some MADS-box genes related to flowering transformation—such as AGL20, SOC1, and CO—were found to be upregulated. A large number of gibberellin biosynthesis related genes such as GA2ox, GA3ox, GA20ox, Cytochrome P450, CYP81, and gibberellin signal transduction genes such as DELLA, GASA, and GID1 were significantly differentially expressed. The plant hormones related genes such as NCED3 and sugar metabolism related genes such as α-amylase, sucrose synthase hexokinase, and so on were also found expressing differentially. In addition, stress resistance related genes such as LEA1, LEA2, LEA4, serine/threonine protein kinase, LRR receptor-like serine/threonine protein kinase, P34 kinase, histidine kinase 3 and epigenetic related genes in DNA methylation, histone methylation, acetylation, ubiquitination of ribose were also found. Particularly, a large number of transcription factors responsive to the exogenous gibberellin signal including WRKY40, WRKY33, WRKY27, WRKY21, WRKY7, MYB, AP2/EREBP, bHLH, NAC1, NAC2, and NAC11 were found to be specially expressing. 30 gene sequences were selected from a large number of differentially expressed candidate genes for qRT-PCR expression verification (0, 2, 4, 8, and 16 h) and compared with the transcriptome expression levels. Conclusions: 200mg/L exogenous GA3 can successfully break the bulb’s dormancy of the LA hybrid lily and significantly accelerated the flowering process, indicating that gibberellin floral induction pathway is present in the LA lily ‘Aladdin’. With the GCNs analysis, two second messenger G protein-coupled receptor related genes that respond to gibberellin signals in the cell were discovered. The downstream transport proteins such as AMT, calcium transport ATPase, and plasma membrane ATPase were also discovered participating in GA signal transduction. Transcription factors including WRKY7, NAC2, NAC11, and CBF specially regulated phosphorylation and glycosylation during the ubiquitination degradation process of DELLA proteins. These transcription factors also activated in abscisic acid metabolism. A large number of transcription factors such as WRKY21, WRKY22, NAC1, AP2, EREB1, P450, and CYP81 that both regulate gibberellin signaling and low-temperature signals have also been found. Finally, the molecular mechanism of GA floral induction pathway in the LA hybrid lily ‘Aladdin’ was constructed.

Download Full-text

Transcriptional Analysis of the Early Ripening of ‘Kyoho’ Grape in Response to the Treatment of Riboflavin

Genes ◽

10.3390/genes10070514 ◽

2019 ◽

Vol 10 (7) ◽

pp. 514 ◽

Cited By ~ 3

Author(s):

Zhen-Guang Wang ◽

Li-Li Guo ◽

Xiao-Ru Ji ◽

Yi-He Yu ◽

Guo-Hai Zhang ◽

...

Keyword(s):

Differentially Expressed Genes ◽

Developmental Stages ◽

Expression Patterns ◽

Enrichment Analysis ◽

Grape Berry ◽

Differentially Expressed ◽

Transcriptional Analysis ◽

Regulation Mechanism ◽

Chlorophyll Metabolism ◽

Early Ripening

Previous study has demonstrated that the riboflavin treatment promoted the early ripening of the ‘Kyoho’ grape berry. However, the molecular mechanism causing this was unclear. In order to reveal the regulation mechanism of riboflavin treatment on grape berry development and ripening, the different berry developmental stages of the ‘Kyoho’ berry treated with 0.5 mmol/L of riboflavin was sampled for transcriptome profiling. RNA-seq revealed that 1526 and 430 genes were up-regulated and down-regulated, respectively, for the comparisons of the treatment to the control. TCseq analysis showed that the expression patterns of most of the genes were similar between the treatment and the control, except for some genes that were related to the chlorophyll metabolism, photosynthesis–antenna proteins, and photosynthesis, which were revealed by the enrichment analysis of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). The differentially expressed genes and weighted gene co-expression network analysis (WGCNA) analysis identified some significantly differentially expressed genes and some hub genes, including up-regulation of the photosynthesis-related ELIP1 and growth and development-related GDSL; and down-regulation of the oxidative stress-related ATHSP22 and berry softening-related XTH32 and GH9B15. The results suggested that the riboflavin treatment resulted in the variations of the expression levels of these genes, and then led to the early ripening of the ‘Kyoho’ berry.

Download Full-text

Differentially Expressed Genes Related to Flowering Transition between Once- and Continuous-Flowering Roses

Biomolecules ◽

10.3390/biom12010058 ◽

2021 ◽

Vol 12 (1) ◽

pp. 58

Author(s):

Xingwan Yi ◽

Huabei Gao ◽

Yi Yang ◽

Shumin Yang ◽

Le Luo ◽

...

Keyword(s):

Candidate Genes ◽

Developmental Stages ◽

Expression Patterns ◽

Ornamental Plants ◽

Promoter Sequence ◽

Regulation Mechanism ◽

Relationship Of ◽

Molecular Regulatory Mechanisms ◽

The Relationship ◽

Apetala 2

Roses are the most important cut flower crops and widely used woody ornamental plants in gardens throughout the world, and they are model plants for studying the continuous-flowering trait of woody plants. To analyze the molecular regulation mechanism of continuous flowering, comparative transcriptome data of once- and continuous-flowering roses in our previous study were used to conduct weighted gene co-expression network analysis (WGCNA) to obtain the candidate genes related to flowering transitions. The expression patterns of candidate genes at different developmental stages between Rosa chinensis “Old Blush” (continuous-flowering cultivar) and R. “Huan Die” (once-flowering cultivar) were investigated, and the relationship of the key gene with the endogenous hormone was analyzed. The results showed that the expression trends of VIN3-LIKE 1 (VIL1), FRIGIDA- LIKE 3 (FRI3), APETALA 2- LIKE (AP2-like) and CONSTANS-LIKE 2 (CO-like 2) genes were significantly different between “Old Blush” and “Huan Die”, and the expression trends of SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1) and CO-like 2 were consistent in the flowering transition of “Old Blush” under different environments. The changes in cytokinin and gibberellic acid (GA3) content were different in the two rose cultivars. The overall change trend of the abscisic acid and GA3 in the flowering transition of “Old Blush” under different environments was consistent. The promoter sequence of CO-like 2 contained a P-box element associated with gibberellin response, as well as binding sites for transcription factors. In a word, we found CO-like 2 associated with continuous flowering and some factors that may synergistically regulate continuous flowering. The results provided a reference for elucidating the molecular regulatory mechanisms of continuous-flowering traits in roses.

Download Full-text