Integration of full-length transcriptomics and targeted metabolomics to identify benzylisoquinoline alkaloid biosynthetic genes in Corydalis yanhusuo

AbstractCorydalis yanhusuo W.T. Wang is a classic herb that is frequently used in traditional Chinese medicine and is efficacious in promoting blood circulation, enhancing energy, and relieving pain. Benzylisoquinoline alkaloids (BIAs) are the main bioactive ingredients in Corydalis yanhusuo. However, few studies have investigated the BIA biosynthetic pathway in C. yanhusuo, and the biosynthetic pathway of species-specific chemicals such as tetrahydropalmatine remains unclear. We performed full-length transcriptomic and metabolomic analyses to identify candidate genes that might be involved in BIA biosynthesis and identified a total of 101 full-length transcripts and 19 metabolites involved in the BIA biosynthetic pathway. Moreover, the contents of 19 representative BIAs in C. yanhusuo were quantified by classical targeted metabolomic approaches. Their accumulation in the tuber was consistent with the expression patterns of identified BIA biosynthetic genes in tubers and leaves, which reinforces the validity and reliability of the analyses. Full-length genes with similar expression or enrichment patterns were identified, and a complete BIA biosynthesis pathway in C. yanhusuo was constructed according to these findings. Phylogenetic analysis revealed a total of ten enzymes that may possess columbamine-O-methyltransferase activity, which is the final step for tetrahydropalmatine synthesis. Our results span the whole BIA biosynthetic pathway in C. yanhusuo. Our full-length transcriptomic data will enable further molecular cloning of enzymes and activity validation studies.

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The biosynthetic pathway of the nonsugar, high-intensity sweetener mogroside V from Siraitia grosvenorii

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1604828113 ◽

2016 ◽

Vol 113 (47) ◽

pp. E7619-E7628 ◽

Cited By ~ 58

Author(s):

Maxim Itkin ◽

Rachel Davidovich-Rikanati ◽

Shahar Cohen ◽

Vitaly Portnoy ◽

Adi Doron-Faigenboim ◽

...

Keyword(s):

Metabolic Pathway ◽

Biosynthetic Pathway ◽

Genomic Organization ◽

Expression Patterns ◽

Functional Expression ◽

Docking Studies ◽

Gene Clustering ◽

Siraitia Grosvenorii ◽

Coordinated Expression ◽

Species Specific

The consumption of sweeteners, natural as well as synthetic sugars, is implicated in an array of modern-day health problems. Therefore, natural nonsugar sweeteners are of increasing interest. We identify here the biosynthetic pathway of the sweet triterpenoid glycoside mogroside V, which has a sweetening strength of 250 times that of sucrose and is derived from mature fruit of luo-han-guo (Siraitia grosvenorii, monk fruit). A whole-genome sequencing of Siraitia, leading to a preliminary draft of the genome, was combined with an extensive transcriptomic analysis of developing fruit. A functional expression survey of nearly 200 candidate genes identified the members of the five enzyme families responsible for the synthesis of mogroside V: squalene epoxidases, triterpenoid synthases, epoxide hydrolases, cytochrome P450s, and UDP-glucosyltransferases. Protein modeling and docking studies corroborated the experimentally proven functional enzyme activities and indicated the order of the metabolic steps in the pathway. A comparison of the genomic organization and expression patterns of these Siraitia genes with the orthologs of other Cucurbitaceae implicates a strikingly coordinated expression of the pathway in the evolution of this species-specific and valuable metabolic pathway. The genomic organization of the pathway genes, syntenously preserved among the Cucurbitaceae, indicates, on the other hand, that gene clustering cannot account for this novel secondary metabolic pathway.

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Key genes in the phenylpropanoids biosynthesis pathway have different expression patterns under various abiotic stresses in the Iranian red and green cultivars of sweet basil (Ocimum basilicum L.)

10.21203/rs.3.rs-205855/v1 ◽

2021 ◽

Author(s):

Mojgan Shahivand ◽

Reza Mir Drikvand ◽

Masoud Gomarian ◽

Kamran Samiei

Keyword(s):

Abiotic Stresses ◽

Biosynthetic Pathway ◽

Expression Patterns ◽

Plant Secondary Metabolites ◽

Environmental Stresses ◽

Sequence Length ◽

Biosynthetic Genes ◽

Breeding Programs ◽

Sweet Basil ◽

First Time

Abstract Phenylpropanoids are a large and important family of plant secondary metabolites. The biosynthetic pathway of phenylpropanoids is induced in plants under environmental stresses to cope with these harmful conditions. In the present study, for the first time, we identified and characterized one reference gene (ACTIN) and three key biosynthetic genes (4CL, C4H and CVOMT) in the Iranian red and green cultivars of sweet basil. Also, the expression patterns of 4CL, C4H and CVOMT biosynthetic genes were determined for the first time in the Iranian red and green cultivars of sweet basil under cold, drought, heat, light and salt stresses. The results showed that the ACTIN, 4CL, C4H and CVOMT genes identified in the Iranian cultivars are identical to other cultivars in terms of all characteristics such as ORF length, protein sequence length, molecular weight, functional domains, lack of signal peptide, subcellular localization site, and secondary structures. Our results also revealed that the 4CL, C4H and CVOMT biosynthetic genes have different expression in the Iranian red and green cultivars of sweet basil under abiotic stresses and their expression patterns are cultivar-dependent. The findings of this study can advance our knowledge of phenylpropanoids biosynthesis in plants under environmental stresses. These findings also can be used in plant breeding programs for stress tolerance in sweet basil and other plants.

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Systematic analysis of the Capsicum ERF transcription factor family uncovers new insights into the regulation of species-specific metabolites

10.21203/rs.3.rs-17593/v1 ◽

2020 ◽

Author(s):

Jiali Song ◽

Changming Chen ◽

Shuanglin Zhang ◽

Juntao Wang ◽

Zhubin Huang ◽

...

Keyword(s):

Regulatory Networks ◽

Biosynthetic Pathway ◽

Expression Patterns ◽

Vital Role ◽

Systematic Analysis ◽

Development Processes ◽

Ethylene Responsive Factor ◽

Responsive Element ◽

Species Specific ◽

Β Carotene

Abstract Background: ERF transcription factors (TFs) belong to the Apetala2/Ethylene responsive Factor (AP2/ERF) TF family and play a vital role in plant growth and development processes. Capsorubin and capsaicinoids have relatively high economic and nutritional value, and they are specifically found in Capsicum. However, there is little understanding of how ERFs participate in the regulatory networks of capsorubin and capsaicinoids biosynthesis. Results: In this study, a total of 142 ERFs were identified in the Capsicum annuum genome. Subsequent phylogenetic analysis allowed us to divide ERFs into DREB (dehydration responsive element binding proteins) and ERF subfamilies, and further classify them into 11 groups with several subgroups. Expression analysis of biosynthetic pathway genes and CaERFs facilitated the identification of candidate genes related to the regulation of capsorubin and capsaicinoids biosynthesis; the candidates were focused in cluster C9 and cluster C10, as well as cluster L3 and cluster L4, respectively. The expression patterns of CaERF82, CaERF97, CaERF66, CaERF107 and CaERF101, which were found in cluster C9 and cluster C10, were consistent with those of accumulating of carotenoids (β-carotene, zeaxanthin and capsorubin) in the pericarp. In cluster L3 and cluster L4, the expression patterns of CaERF102, CaERF53, CaERF111 and CaERF92 were similar to those of the accumulating capsaicinoids. Furthermore, CaERF92, CaERF102 and CaERF111 were found to be potentially involved in temperature-mediated capsaicinoids biosynthesis. Conclusion: This study will provide an extremely useful foundation for the study of candidate ERFs in the regulation of carotenoids and capsaicinoids biosynthesis in peppers.

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Systematic analysis of the Capsicum ERF transcription factor family: identification of regulatory factors involved in the regulation of species-specific metabolites

10.21203/rs.3.rs-17593/v2 ◽

2020 ◽

Author(s):

Jiali Song ◽

Changming Chen ◽

Shuanglin Zhang ◽

Juntao Wang ◽

Zhubin Huang ◽

...

Keyword(s):

Regulatory Networks ◽

Biosynthetic Pathway ◽

Expression Patterns ◽

Vital Role ◽

Systematic Analysis ◽

Development Processes ◽

Ethylene Responsive Factor ◽

Responsive Element ◽

Species Specific ◽

Β Carotene

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Haplotype-resolved genome of diploid ginger (Zingiber officinale) and its unique gingerol biosynthetic pathway

Horticulture Research ◽

10.1038/s41438-021-00627-7 ◽

2021 ◽

Vol 8 (1) ◽

Author(s):

Hong-Lei Li ◽

Lin Wu ◽

Zhaoming Dong ◽

Yusong Jiang ◽

Sanjie Jiang ◽

...

Keyword(s):

Biosynthetic Pathway ◽

Southwest China ◽

Reference Genome ◽

Zingiber Officinale ◽

Gene Families ◽

Chromosome Conformation ◽

Long Reads ◽

Transcription Factor Networks ◽

Species Specific ◽

Haplotype 1

AbstractGinger (Zingiber officinale), the type species of Zingiberaceae, is one of the most widespread medicinal plants and spices. Here, we report a high-quality, chromosome-scale reference genome of ginger ‘Zhugen’, a traditionally cultivated ginger in Southwest China used as a fresh vegetable, assembled from PacBio long reads, Illumina short reads, and high-throughput chromosome conformation capture (Hi-C) reads. The ginger genome was phased into two haplotypes, haplotype 1 (1.53 Gb with a contig N50 of 4.68 M) and haplotype 0 (1.51 Gb with a contig N50 of 5.28 M). Homologous ginger chromosomes maintained excellent gene pair collinearity. In 17,226 pairs of allelic genes, 11.9% exhibited differential expression between alleles. Based on the results of ginger genome sequencing, transcriptome analysis, and metabolomic analysis, we proposed a backbone biosynthetic pathway of gingerol analogs, which consists of 12 enzymatic gene families, PAL, C4H, 4CL, CST, C3’H, C3OMT, CCOMT, CSE, PKS, AOR, DHN, and DHT. These analyses also identified the likely transcription factor networks that regulate the synthesis of gingerol analogs. Overall, this study serves as an excellent resource for further research on ginger biology and breeding, lays a foundation for a better understanding of ginger evolution, and presents an intact biosynthetic pathway for species-specific gingerol biosynthesis.

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Transcriptome and Metabolome Dynamics Explain Aroma Differences between Green and Red Prickly Ash Fruit

Foods ◽

10.3390/foods10020391 ◽

2021 ◽

Vol 10 (2) ◽

pp. 391

Author(s):

Xitong Fei ◽

Yichen Qi ◽

Yu Lei ◽

Shujie Wang ◽

Haichao Hu ◽

...

Keyword(s):

Redundancy Analysis ◽

Biosynthetic Pathway ◽

Expression Patterns ◽

Gas Chromatography Mass Spectrometry ◽

Zanthoxylum Armatum ◽

Aroma Characteristics ◽

Main Factors ◽

Key Genes ◽

Zanthoxylum Bungeanum ◽

Aroma Components

Green prickly ash (Zanthoxylum armatum) and red prickly ash (Zanthoxylum bungeanum) fruit have unique flavor and aroma characteristics that affect consumers’ purchasing preferences. However, differences in aroma components and relevant biosynthesis genes have not been systematically investigated in green and red prickly ash. Here, through the analysis of differentially expressed genes (DEGs), differentially abundant metabolites, and terpenoid biosynthetic pathways, we characterize the different aroma components of green and red prickly ash fruits and identify key genes in the terpenoid biosynthetic pathway. Gas chromatography-mass spectrometry (GC-MS) was used to identify 41 terpenoids from green prickly ash and 61 terpenoids from red prickly ash. Piperitone was the most abundant terpenoid in green prickly ash fruit, whereas limonene was most abundant in red prickly ash. Intergroup correlation analysis and redundancy analysis showed that HDS2, MVK2, and MVD are key genes for terpenoid synthesis in green prickly ash, whereas FDPS2 and FDPS3 play an important role in the terpenoid synthesis of red prickly ash. In summary, differences in the composition and content of terpenoids are the main factors that cause differences in the aromas of green and red prickly ash, and these differences reflect contrasting expression patterns of terpenoid synthesis genes.

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Rhythmic Serotonin N-Acetyltransferase mRNA Degradation Is Essential for the Maintenance of Its Circadian Oscillation

Molecular and Cellular Biology ◽

10.1128/mcb.25.8.3232-3246.2005 ◽

2005 ◽

Vol 25 (8) ◽

pp. 3232-3246 ◽

Cited By ~ 58

Author(s):

Tae-Don Kim ◽

Jong-So Kim ◽

Jong Heon Kim ◽

Jihwan Myung ◽

Hee-Don Chae ◽

...

Keyword(s):

Circadian Rhythm ◽

Expression Patterns ◽

Mrna Level ◽

Mrna Degradation ◽

Circadian Oscillation ◽

Oscillatory Mechanism ◽

Key Enzyme ◽

Mrna Profile ◽

Species Specific ◽

Nuclear Ribonucleoprotein

ABSTRACT Serotonin N-acetyltransferase (arylalkylamine N-acetyltransferase [AANAT]) is the key enzyme in melatonin synthesis regulated by circadian rhythm. To date, our understanding of the oscillatory mechanism of melatonin has been limited to autoregulatory transcriptional and posttranslational regulations of AANAT mRNA. In this study, we identify three proteins from pineal glands that associate with cis-acting elements within species-specific AANAT 3′ untranslated regions to mediate mRNA degradation. These proteins include heterogeneous nuclear ribonucleoprotein R (hnRNP R), hnRNP Q, and hnRNP L. Their RNA-destabilizing function was determined by RNA interference and overexpression approaches. Expression patterns of these factors in pineal glands display robust circadian rhythm. The enhanced levels detected after midnight correlate with an abrupt decline in AANAT mRNA level. A mathematical model for the AANAT mRNA profile and its experimental evidence with rat pinealocytes indicates that rhythmic AANAT mRNA degradation mediated by hnRNP R, hnRNP Q, and hnRNP L is a key process in the regulation of its circadian oscillation.

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Systematic silencing of benzylisoquinoline alkaloid biosynthetic genes reveals the major route to papaverine in opium poppy

The Plant Journal ◽

10.1111/j.1365-313x.2012.05084.x ◽

2012 ◽

Vol 72 (2) ◽

pp. 331-344 ◽

Cited By ~ 51

Author(s):

Isabel Desgagné-Penix ◽

Peter J. Facchini

Keyword(s):

Opium Poppy ◽

Biosynthetic Genes ◽

Benzylisoquinoline Alkaloid ◽

Major Route

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Rhythmic Clock Gene Expression in Atlantic Salmon Parr Brain

Frontiers in Physiology ◽

10.3389/fphys.2021.761109 ◽

2021 ◽

Vol 12 ◽

Author(s):

Charlotte M. Bolton ◽

Michaël Bekaert ◽

Mariann Eilertsen ◽

Jon Vidar Helvik ◽

Herve Migaud

Keyword(s):

Atlantic Salmon ◽

Clock Genes ◽

Expression Patterns ◽

Circadian Expression ◽

Clock Gene Expression ◽

Sister Clade ◽

Before And After ◽

Salmon Parr ◽

Species Specific ◽

Atlantic Salmon Parr

To better understand the complexity of clock genes in salmonids, a taxon with an additional whole genome duplication, an analysis was performed to identify and classify gene family members (clock, arntl, period, cryptochrome, nr1d, ror, and csnk1). The majority of clock genes, in zebrafish and Northern pike, appeared to be duplicated. In comparison to the 29 clock genes described in zebrafish, 48 clock genes were discovered in salmonid species. There was also evidence of species-specific reciprocal gene losses conserved to the Oncorhynchus sister clade. From the six period genes identified three were highly significantly rhythmic, and circadian in their expression patterns (per1a.1, per1a.2, per1b) and two was significantly rhythmically expressed (per2a, per2b). The transcriptomic study of juvenile Atlantic salmon (parr) brain tissues confirmed gene identification and revealed that there were 2,864 rhythmically expressed genes (p < 0.001), including 1,215 genes with a circadian expression pattern, of which 11 were clock genes. The majority of circadian expressed genes peaked 2 h before and after daylight. These findings provide a foundation for further research into the function of clock genes circadian rhythmicity and the role of an enriched number of clock genes relating to seasonal driven life history in salmonids.

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Full-length transcriptome analysis of shade-induced promotion of tuber production in Pinellia ternata

BMC Plant Biology ◽

10.1186/s12870-019-2197-9 ◽

2019 ◽

Vol 19 (1) ◽

Author(s):

Tao Xue ◽

Han Zhang ◽

Yuanyuan Zhang ◽

Shuqin Wei ◽

Qiujie Chao ◽

...

Keyword(s):

Single Molecule ◽

Gene Annotation ◽

Expression Patterns ◽

Full Length ◽

Tuber Growth ◽

Strong Light ◽

Chlorophyll Fluorescence Parameters ◽

Pinellia Ternata ◽

Tuber Production ◽

Sun Light

Abstract Background Pinellia ternata is native to China and has been used as a traditional herb due to its antiemetic, antitussive, analgesic, and anxiolytic effects. When exposed to strong light intensity and high temperature during the reproductive growth process, P. ternata withers in a phenomenon known as “sprout tumble”, which largely limits tuber production. Shade was previously found to delay sprout tumble formation (STF); however, no information exists regarding this process at the molecular level. Hence, we determined the genes involved in tuber development and STF in P. ternata. Results Compared to that with natural sun-light (control), shade significantly induced chlorophyll accumulation, increased chlorophyll fluorescence parameters including initial fluorescence, maximal fluorescence, and qP, and dramatically repressed chlorophyll a:b and NPQ. Catalase (CAT) activity was largely induced by shade, and tuber products were largely increased in this environment. Transcriptome profiles of P. ternata grown in natural sun-light and shaded environments were analyzed by a combination of next generation sequencing (NGS) and third generation single-molecule real-time (SMRT) sequencing. Corrections of SMRT long reads based on NGS short reads yielded 136,163 non-redundant transcripts, with an average N50 length of 2578 bp. In total, 6738 deferentially-expressed genes (DEGs) were obtained from the comparisons, specifically D5S vs D5CK, D20S vs D20CK, D20S vs D5S, and D20CK vs D5CK, of which, 6384 DEGs (94.8%) were generated from the D20S vs D20CK comparison. Gene annotation and functional analyses revealed that these genes were related to auxin signal transduction, polysaccharide and sugar metabolism, phenylpropanoid biosynthesis, and photosynthesis. Moreover, the expression of genes enriched in photosynthesis appeared to be significantly altered by shade. The expression patterns of 16 candidate genes were consistent with changes in their transcript abundance as identified by RNA-Seq, and these might contribute to STF and tuber production. Conclusion The full-length transcripts identified in this study have provided a more accurate depiction of P. ternata gene transcription. Further, we identified potential genes involved in STF and tuber growth. Such data could serve as a genetic resource and a foundation for further research on this important traditional herb.

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