Transcriptome analysis reveals novel enzymes for apo-carotenoid biosynthesis in saffron and allows construction of a pathway for crocetin synthesis in yeast

2019 ◽  
Vol 70 (18) ◽  
pp. 4819-4834 ◽  
Author(s):  
Hexin Tan ◽  
Xianghui Chen ◽  
Nan Liang ◽  
Ruibing Chen ◽  
Junfeng Chen ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Carotenoid Biosynthesis

Fifteen genes were predicted to be closely related to safranal and crocin production by multi-omic analysis in which CsALDH3 was validated and used to construct crocetin-producing yeast.

scholarly journals Physiological and transcriptome analysis of indica rice 'MH86' overexpressing OsSPL14

2018 ◽  
Author(s):  
Ling Lian ◽  
Wei He ◽  
Qiu hua Cai ◽  
Hui Zhang ◽  
Cheng rong Ren ◽  
...  
Keyword(s):  
Transgenic Plants ◽  
Transgenic Plant ◽  
Transcriptome Analysis ◽  
Indica Rice ◽  
Critical Role ◽  
Lignin Biosynthesis ◽  
Growth Period ◽  
Carotenoid Biosynthesis ◽  
Maturity Stage ◽  
Wild Type Plant

OsSPL14, identified as IDEAL PLANT ARCHITECTURE1 (IPA1) or WEALTHY FARMER'S PANICLE (WFP) gene, plays a critical role in regulating rice plant architecture. Here, the study showed that OsSPL14-overexpression transgenic rice plants had shorter growth period, short-narrow flag leaves, and thick-green leaves. Compared with wild type plant 'MH86', transgenic plants had higher chlorophyll a (Ca), chlorophyll b (Cb) and carotenoid (Cx) content at both seedling and maturity stage. Meanwhile, transcriptome analysis identified 473 up-regulated and 103 down-regulated genes in transgenic plant. The expression of differentially expressed genes (DEGs) involved in carotenoid biosynthesis, abscisic acid (ABA) metabolism and lignin biosynthesis increased significantly. Most of DEGs participated in 'plant hormone signal transduction' and 'starch and sucrose metabolism' are also up-regulated in transgenic plant. In addition, there were higher levels of ABA and gibberellin acid (GA3) in OsSPL14-overexpression transgenic plants. Moreover, the content of culm lignin, cellulose, silicon and potassium all increased dramatically. Thus, these results demonstrate that overexpression of OsSPL14 has influence on leaf development, hormone level and culm composition in rice, which provide more insight into understanding the function of OsSPL14.

scholarly journals Integrated metabolic profiling and transcriptome analysis of pigment accumulation in Lonicera japonica flower petals during colour-transition

2020 ◽  
Author(s):  
Yan Xia ◽  
Weiwei Chen ◽  
Weibo Xiang ◽  
Dan Wang ◽  
Baogui Xue ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Carotenoid Biosynthesis ◽  
Zeatin Riboside ◽  
Lonicera Japonica ◽  
Endogenous Hormones ◽  
Metabolome Analysis ◽  
Yellow Colour ◽  
Petal Colour ◽  
Gene Expression Dynamics ◽  
Pigment Accumulation

Abstract Background: Plants have remarkable diversity in petal colour through the biosynthesis and accumulation of various pigments. To better understand the mechanisms regulating petal pigmentation in Lonicera japonica, we used multiple approaches to investigate the changes in carotenoids, anthocyanins, endogenous hormones and gene expression dynamics during petal colour transitions, i.e., green bud petals (GB_Pe), white flower petals (WF_Pe) and yellow flower petals (YF_Pe). Results: Metabolome analysis showed that YF_Pe contained a much higher content of carotenoids than GB_Pe and WF_Pe, with α-carotene, zeaxanthin, violaxanthin and γ-carotene identified as the major carotenoid compounds in YF_Pe. Comparative transcriptome analysis revealed that the key differentially expressed genes (DEGs) involved in carotenoid biosynthesis, such as phytoene synthase, phytoene desaturase and ζ-carotene desaturase, were significantly upregulated in YF_Pe. The results indicated that upregulated carotenoid concentrations and carotenoid biosynthesis-related genes predominantly promote colour transition. Meanwhile, two anthocyanins (pelargonidin and cyanidin) were significantly increased in YF_Pe, and the expression level of an anthocyanidin synthase gene was significantly upregulated, suggesting that anthocyanins may contribute to vivid yellow colour in YF_Pe. Furthermore, analyses of changes in indoleacetic acid, zeatin riboside, gibberellin (GA), brassinosteroid (BR), methyl jasmonate and abscisic acid (ABA) levels indicated that colour transitions are regulated by endogenous hormones. The DEGs involved in the auxin, cytokinin, GA, BR, jasmonic acid and ABA signalling pathways were enriched and associated with petal colour transitions.Conclusion: Our results provide global insight into the pigment accumulation and the regulatory mechanisms underlying petal colour transitions during the flower development process in L. japonica.

scholarly journals Physiological and Transcriptome Analysis Reveals the Differences in Nitrate Content Between Lamina and Midrib of Flue-Cured Tobacco

2021 ◽  
Author(s):  
Yuqing Feng ◽  
Yuanyuan Zhao ◽  
Yafei Li ◽  
Jun Zhou ◽  
Yujing Li ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Molecular Mechanisms ◽  
Carbon Fixation ◽  
High Capacity ◽  
Carotenoid Biosynthesis ◽  
Nitrate Content ◽  
Nitrate Accumulation ◽  
N Content ◽  
Chlorophyll Metabolism ◽  
Tobacco Specific Nitrosamines

Abstract Nitrate is an important precursor of tobacco-specific nitrosamines (TSNAs) and remarkable difference in nitrate accumulation between lamina and midrib of flue-cured tobacco has long been observed. However, the physiological and molecular mechanisms underpinning this difference remain poorly understood. In this study, physiological and genetic factors impacting nitrate accumulation were identified in pot experiments using flue-cured tobacco K326 with contrasting nitrate content between lamina and midrib. The results showed that three times higher of NO3-N content was observed in midrib than that in lamina, along with lower pigment, NH4-N content, NRA, SSA and GSA in midrib. Transcriptome analysis revealed that expression of genes involved in porphyrin and chlorophyll metabolism, carotenoid biosynthesis, photosynthesis-antenna proteins, photosynthesis, carbon fixation in photosynthetic organisms, starch and sucrose metabolism, nitrogen metabolism and biosynthesis of amino acids were significantly lower in midrib than in lamina. qRT-PCR results showed that the expression level of nitrate transporter genes LOC107782967, LOC107806749, LOC107775674, LOC107829632, LOC107799198, LOC107768465 decreased by 2.74, 1.81, 49.5, 3.5, 2.64 and 2.96 folds while LOC107789301 increased by 8.23 folds in midrib but not in lamina. Reduced chlorophyll content might result in low carbohydrate formation which is the source of energy and carbon skeleton supply, then the low capacity of nitrogen reduction, assimilation and transportation, and the poor ability of nitrate reallocation but high capacity of accumulation might lead to nitrate accumulation in midrib. The results laid the foundation for reducing nitrate content and TSNA formation in tobacco midribs and their products.

scholarly journals Transcriptome Analysis of the Rhodobacter sphaeroides PpsR Regulon: PpsR as a Master Regulator of Photosystem Development

2005 ◽  
Vol 187 (6) ◽  
pp. 2148-2156 ◽  
Author(s):  
Oleg V. Moskvin ◽  
Larissa Gomelsky ◽  
Mark Gomelsky
Keyword(s):  
Rhodobacter Sphaeroides ◽  
Transcriptome Analysis ◽  
Binding Sites ◽  
Transcriptome Profiling ◽  
Carotenoid Biosynthesis ◽  
Low Oxygen ◽  
Master Regulator ◽  
Core Proteins ◽  
Anoxygenic Phototrophic Bacterium

ABSTRACT PpsR from the anoxygenic phototrophic bacterium Rhodobacter sphaeroides has been known as an oxygen- and light-dependent repressor of bacteriochlorophyll and carotenoid biosynthesis genes and puc operons involved in photosystem development. However, the putative PpsR-binding sites, TGTN12ACA, are also located upstream of numerous nonphotosystem genes, thus raising the possibility that the role of PpsR is broader. To characterize the PpsR regulon, transcriptome profiling was performed on the wild-type strain grown at high and low oxygen tensions, on the strain overproducing PpsR, and on the ppsR mutant. Transcriptome analysis showed that PpsR primarily regulates photosystem genes; the consensus PpsR binding sequence is TGTcN10gACA (lowercase letters indicate lesser conservation); the presence of two binding sites is required for repression in vivo. These findings explain why numerous single TGTN12ACA sequences are nonfunctional. In addition to photosystem genes, the hemC and hemE genes involved in the early steps of tetrapyrrole biosynthesis were identified as new direct targets of PpsR repression. Unexpectedly, PpsR was found to indirectly repress the puf and puhA operons encoding photosystem core proteins. The upstream regions of these operons contain no PpsR binding sites. Involvement in regulation of these operons suggests that PpsR functions as a master regulator of photosystem development. Upregulation of the puf and puhA operons that resulted from ppsR inactivation was sufficient to restore the ability to grow phototrophically to the prrA mutant. PrrA, the global redox-dependent activator, was previously considered indispensable for phototrophic growth. It is revealed that the PrrBA and AppA-PpsR systems, believed to work independently, in fact interact and coordinately regulate photosystem development.

scholarly journals Integrated metabolic profiling and transcriptome analysis of pigment accumulation in Lonicera japonica flower petals during colour-transition

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Yan Xia ◽  
Weiwei Chen ◽  
Weibo Xiang ◽  
Dan Wang ◽  
Baogui Xue ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Carotenoid Biosynthesis ◽  
Zeatin Riboside ◽  
Lonicera Japonica ◽  
Endogenous Hormones ◽  
Metabolome Analysis ◽  
Yellow Colour ◽  
Petal Colour ◽  
Gene Expression Dynamics ◽  
Pigment Accumulation

Abstract Background Plants have remarkable diversity in petal colour through the biosynthesis and accumulation of various pigments. To better understand the mechanisms regulating petal pigmentation in Lonicera japonica, we used multiple approaches to investigate the changes in carotenoids, anthocyanins, endogenous hormones and gene expression dynamics during petal colour transitions, i.e., green bud petals (GB_Pe), white flower petals (WF_Pe) and yellow flower petals (YF_Pe). Results Metabolome analysis showed that YF_Pe contained a much higher content of carotenoids than GB_Pe and WF_Pe, with α-carotene, zeaxanthin, violaxanthin and γ-carotene identified as the major carotenoid compounds in YF_Pe. Comparative transcriptome analysis revealed that the key differentially expressed genes (DEGs) involved in carotenoid biosynthesis, such as phytoene synthase, phytoene desaturase and ζ-carotene desaturase, were significantly upregulated in YF_Pe. The results indicated that upregulated carotenoid concentrations and carotenoid biosynthesis-related genes predominantly promote colour transition. Meanwhile, two anthocyanins (pelargonidin and cyanidin) were significantly increased in YF_Pe, and the expression level of an anthocyanidin synthase gene was significantly upregulated, suggesting that anthocyanins may contribute to vivid yellow colour in YF_Pe. Furthermore, analyses of changes in indoleacetic acid, zeatin riboside, gibberellic acid, brassinosteroid (BR), methyl jasmonate and abscisic acid (ABA) levels indicated that colour transitions are regulated by endogenous hormones. The DEGs involved in the auxin, cytokinin, gibberellin, BR, jasmonic acid and ABA signalling pathways were enriched and associated with petal colour transitions. Conclusion Our results provide global insight into the pigment accumulation and the regulatory mechanisms underlying petal colour transitions during the flower development process in L. japonica.

scholarly journals Transcriptome analysis identifies key genes involved in carotenoid biosynthesis in the flesh of red pummelo (Citrus maxima)

2020 ◽  
Vol 34 (1) ◽  
pp. 614-622
Author(s):  
Dongxia Wang ◽  
Shiming Li ◽  
Le Wei ◽  
Zongren Li ◽  
Baolong Liu ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Carotenoid Biosynthesis ◽  
Citrus Maxima ◽  
Key Genes

scholarly journals Comparative transcriptome analysis implied a ZEP paralog was a key gene involved in carotenoid accumulation in yellow-fleshed sweetpotato

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Keisuke Suematsu ◽  
Masaru Tanaka ◽  
Rie Kurata ◽  
Yumi Kai
Keyword(s):  
Rna Sequencing ◽  
Transcriptome Analysis ◽  
Carotenoid Biosynthesis ◽  
Comparative Transcriptome ◽  
Storage Roots ◽  
Zeaxanthin Epoxidase ◽  
Carotenoid Accumulation ◽  
Carotenoid Composition ◽  
Yellow Flesh ◽  
Β Carotene

AbstractThe mechanisms of carotenoid accumulation in yellow-fleshed sweetpotato cultivars are unclear. In this study, we compared the transcriptome profiles of a yellow-fleshed cultivar, Beniharuka (BH) and two of its spontaneous white-fleshed mutants (WH2 and WH3) to reveal the genes involved in yellow flesh. As a result of RNA sequencing, a total of 185 differentially expressed genes (DEGs) were commonly detected in WH2 and WH3 compared to BH. Of these genes, 85 DEGs and 100 DEGs were commonly upregulated and downregulated in WH2 and WH3 compared to BH, respectively. g1103.t1, a paralog of zeaxanthin epoxidase (ZEP), was only DEG common to WH2 and WH3 among 38 genes considered to be involved in carotenoid biosynthesis in storage roots. The expression level of g1103.t1 was also considerably lower in five white-fleshed cultivars than in five yellow-fleshed cultivars. Analysis of carotenoid composition in the storage roots showed that the epoxidised carotenoids were drastically reduced in both WH2 and WH3. Therefore, we propose that the ZEP paralog, g1103.t1, may be involved in carotenoid accumulation through the epoxidation of β-carotene and β-cryptoxanthin in sweetpotato.

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