scholarly journals RNA sequencing on Amomum villosum Lour. induced by MeJA identifies the genes of WRKY and terpene synthases involved in terpene biosynthesis

Genome ◽  
2018 ◽  
Vol 61 (2) ◽  
pp. 91-102 ◽  
Author(s):  
Xueying He ◽  
Huan Wang ◽  
Jinfen Yang ◽  
Ke Deng ◽  
Teng Wang
Keyword(s):  
Rna Sequencing ◽  
Terpene Synthase ◽  
Wrky Transcription Factors ◽  
Terpene Biosynthesis ◽  
Terpene Synthases ◽  
New Information ◽  
Volatile Terpenes ◽  
Highly Correlated ◽  
Amomum Villosum ◽  
Chinese Medicinal Plant

Amomum villosum Lour. is an important Chinese medicinal plant that has diverse medicinal functions, and mainly contains volatile terpenes. This study aims to explore the WRKY transcription factors (TFs) and terpene synthase (TPS) unigenes that might be involved in terpene biosynthesis in A. villosum, and thus providing some new information on the regulation of terpenes in plants. RNA sequencing of A. villosum induced by methyl jasmonate (MeJA) revealed that the WRKY family was the second largest TF family in the transcriptome. Thirty-six complete WRKY domain sequences were expressed in response to MeJA. Further, six WRKY unigenes were highly correlated with eight deduced TPS unigenes. Ultimately, we combined the terpene abundance with the expression of candidate WRKY TFs and TPS unigenes to presume a possible model wherein AvWRKY61, AvWRKY28, and AvWRKY40 might coordinately trans-activate the AvNeoD promoter. We propose an approach to further investigate TF unigenes that might be involved in terpenoid biosynthesis, and identified four unigenes for further analyses.

scholarly journals Terpene synthase genes in eukaryotes beyond plants and fungi: Occurrence in social amoebae

2016 ◽  
Vol 113 (43) ◽  
pp. 12132-12137 ◽  
Author(s):  
Xinlu Chen ◽  
Tobias G. Köllner ◽  
Qidong Jia ◽  
Ayla Norris ◽  
Balaji Santhanam ◽  
...  
Keyword(s):  
Early Stage ◽  
Terpene Synthase ◽  
Functional Study ◽  
Terpene Biosynthesis ◽  
Terpene Synthases ◽  
Multicellular Development ◽  
Stage Of Development ◽  
The Social ◽  
Volatile Terpenes ◽  
Social Amoebae

Terpenes are structurally diverse natural products involved in many ecological interactions. The pivotal enzymes for terpene biosynthesis, terpene synthases (TPSs), had been described only in plants and fungi in the eukaryotic domain. In this report, we systematically analyzed the genome sequences of a broad range of nonplant/nonfungus eukaryotes and identified putative TPS genes in six species of amoebae, five of which are multicellular social amoebae from the order of Dictyosteliida. A phylogenetic analysis revealed that amoebal TPSs are evolutionarily more closely related to fungal TPSs than to bacterial TPSs. The social amoeba Dictyostelium discoideum was selected for functional study of the identified TPSs. D. discoideum grows as a unicellular organism when food is abundant and switches from vegetative growth to multicellular development upon starvation. We found that expression of most D. discoideum TPS genes was induced during development. Upon heterologous expression, all nine TPSs from D. discoideum showed sesquiterpene synthase activities. Some also exhibited monoterpene and/or diterpene synthase activities. Direct measurement of volatile terpenes in cultures of D. discoideum revealed essentially no emission at an early stage of development. In contrast, a bouquet of terpenes, dominated by sesquiterpenes including β-barbatene and (E,E)-α-farnesene, was detected at the middle and late stages of development, suggesting a development-specific function of volatile terpenes in D. discoideum. The patchy distribution of TPS genes in the eukaryotic domain and the evidence for TPS function in D. discoideum indicate that the TPS genes mediate lineage-specific adaptations.

scholarly journals Differential gene expression associated with a floral scent polymorphism in the evening primrose Oenothera harringtonii (Onagraceae)

2021 ◽  
Author(s):  
Lindsey L. Bechen ◽  
Matthew G. Johnson ◽  
Geoffrey T. Broadhead ◽  
Rachel A. Levin ◽  
Rick P. Overson ◽  
...  
Keyword(s):  
Gene Expression ◽  
Differential Gene Expression ◽  
Floral Scent ◽  
Terpene Synthase ◽  
Rna Seq ◽  
Loss Of Function ◽  
Terpene Biosynthesis ◽  
Terpene Synthases ◽  
Evening Primrose ◽  
Differential Gene

AbstractBackgroundPlant volatiles play an important role in both plant-pollinator and plant-herbivore interactions. Intraspecific polymorphisms in volatile production are ubiquitous, but studies that explore underlying differential gene expression are rare. Oenothera harringtonii populations are polymorphic in floral emission of the monoterpene (R)-(-)-linalool; some plants emit (R)-(-)-linalool (linalool+ plants) while others do not (linalool-plants). However, the genes associated with differential production of this floral volatile in Oenothera are unknown. We used RNA-Seq to broadly characterize differential gene expression involved in (R)-(-)-linalool biosynthesis. To identify genes that may be associated with the polymorphism for this trait, we used RNA-Seq to compare gene expression in six different Oenothera harringtonii tissues from each of three linalool+ and linalool-plants.ResultsThree clusters of differentially expressed genes were enriched for terpene synthase activity: two were characterized by tissue-specific upregulation and one by upregulation only in plants with flowers that produce (R)-(-)-linalool. A molecular phylogeny of all terpene synthases identified two putative (R)-(-)-linalool synthase transcripts in Oenothera harringtonii, a single allele of which is found exclusively in linalool+ plants.ConclusionsBy using a naturally occurring polymorphism and comparing different tissues, we were able to identify genes putatively involved in the biosynthesis of (R)-(-)-linalool. Expression of these genes in linalool-plants suggests a regulatory polymorphism, rather than a population-specific loss-of-function allele. Additional terpene biosynthesis-related genes that are up-regulated in plants that emit (R)-(-)-linalool may be associated with herbivore defense, suggesting a potential economy of scale between plant reproduction and defense.

scholarly journals Diversity and function of terpene synthases in the production of carrot aroma and flavor compounds

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Andrew Muchlinski ◽  
Mwafaq Ibdah ◽  
Shelby Ellison ◽  
Mossab Yahyaa ◽  
Bhagwat Nawade ◽  
...  
Keyword(s):  
Expression Profiles ◽  
Terpene Synthase ◽  
Terpene Synthases ◽  
Specific Expression ◽  
Metabolite Profiles ◽  
Germacrene D ◽  
Volatile Terpenes ◽  
And Function ◽  
Volatile Terpene

Abstract Carrot (Daucus carota L.) is an important root vegetable crop with high nutritional value, characteristic flavor, and benefits to human health. D. carota tissues produce an essential oil that is rich in volatile terpenes and plays a major role in carrot aroma and flavor. Although terpene composition represents a critical quality attribute of carrots, little is known about the biosynthesis of terpenes in this crop. Here, we functionally characterized 19 terpene synthase (TPS) genes in an orange carrot (genotype DH1) and compared tissue-specific expression profiles and in vitro products of their recombinant proteins with volatile terpene profiles from DH1 and four other colored carrot genotypes. In addition to the previously reported (E)-β-caryophyllene synthase (DcTPS01), we biochemically characterized several TPS proteins with direct correlations to major compounds of carrot flavor and aroma including germacrene D (DcTPS7/11), γ-terpinene (DcTPS30) and α-terpinolene (DcTPS03). Random forest analysis of volatiles from colored carrot cultivars identified nine terpenes that were clearly distinct among the cultivars and likely contribute to differences in sensory quality. Correlation of TPS gene expression and terpene metabolite profiles supported the function of DcTPS01 and DcTPS03 in these cultivars. Our findings provide a roadmap for future breeding efforts to enhance carrot flavor and aroma.

scholarly journals Terpene Biosynthesis in Red Algae Is Catalyzed by Microbial Type But Not Typical Plant Terpene Synthases

2018 ◽  
Vol 179 (2) ◽  
pp. 382-390 ◽  
Author(s):  
Guo Wei ◽  
Qidong Jia ◽  
Xinlu Chen ◽  
Tobias G. Köllner ◽  
Debashish Bhattacharya ◽  
...  
Keyword(s):  
Red Algae ◽  
Terpene Biosynthesis ◽  
Terpene Synthases

scholarly journals Transcriptome and proteome of the corm, leaf and flower of Hypoxis hemerocallidea (African potato)

PLoS ONE ◽  
2021 ◽  
Vol 16 (7) ◽  
pp. e0253741
Author(s):  
Mihai-Silviu Tomescu ◽  
Selisha Ann Sooklal ◽  
Thuto Ntsowe ◽  
Previn Naicker ◽  
Barbara Darnhofer ◽  
...  
Keyword(s):  
De Novo ◽  
Differential Expression Analysis ◽  
Terpene Synthase ◽  
Future Research ◽  
Terpene Synthases ◽  
Illumina Hiseq ◽  
Prostate Hyperplasia ◽  
Inflammatory Conditions ◽  
Urinary Infections ◽  
Hypoxis Hemerocallidea

The corm of Hypoxis hemerocallidea, commonly known as the African potato, is used in traditional medicine to treat several medical conditions such as urinary infections, benign prostate hyperplasia, inflammatory conditions and testicular tumours. The metabolites contributing to the medicinal properties of H. hemerocallidea have been identified in several studies and, more recently, the active terpenoids of the plant were profiled. However, the biosynthetic pathways and the enzymes involved in the production of the terpene metabolites in H. hemerocallidea have not been characterised at a transcriptomic or proteomic level. In this study, total RNA extracted from the corm, leaf and flower tissues of H. hemerocallidea was sequenced on the Illumina HiSeq 2500 platform. A total of 143,549 transcripts were assembled de novo using Trinity and 107,131 transcripts were functionally annotated using the nr, GO, COG, KEGG and SWISS-PROT databases. Additionally, the proteome of the three tissues were sequenced using LC-MS/MS, revealing aspects of secondary metabolism and serving as data validation for the transcriptome. Functional annotation led to the identification of numerous terpene synthases such as nerolidol synthase, germacrene D synthase, and cycloartenol synthase amongst others. Annotations also revealed a transcript encoding the terpene synthase phytoalexin momilactone A synthase. Differential expression analysis using edgeR identified 946 transcripts differentially expressed between the three tissues and revealed that the leaf upregulates linalool synthase compared to the corm and the flower tissues. The transcriptome as well as the proteome of Hypoxis hemerocallidea presented here provide a foundation for future research.

scholarly journals Identification of Sesquiterpene Synthases from Nostoc punctiforme PCC 73102 and Nostoc sp. Strain PCC 7120

2008 ◽  
Vol 190 (18) ◽  
pp. 6084-6096 ◽  
Author(s):  
Sean A. Agger ◽  
Fernando Lopez-Gallego ◽  
Thomas R. Hoye ◽  
Claudia Schmidt-Dannert
Keyword(s):  
Functional Expression ◽  
Terpene Synthase ◽  
Putative Hybrid ◽  
Nostoc Punctiforme ◽  
Terpene Synthases ◽  
E Coli ◽  
Reductase Gene ◽  
Pcc 7120 ◽  
Defense Compound

ABSTRACT Cyanobacteria are a rich source of natural products and are known to produce terpenoids. These bacteria are the major source of the musty-smelling terpenes geosmin and 2-methylisoborneol, which are found in many natural water supplies; however, no terpene synthases have been characterized from these organisms to date. Here, we describe the characterization of three sesquiterpene synthases identified in Nostoc sp. strain PCC 7120 (terpene synthase NS1) and Nostoc punctiforme PCC 73102 (terpene synthases NP1 and NP2). The second terpene synthase in N. punctiforme (NP2) is homologous to fusion-type sesquiterpene synthases from Streptomyces spp. shown to produce geosmin via an intermediate germacradienol. The enzymes were functionally expressed in Escherichia coli, and their terpene products were structurally identified as germacrene A (from NS1), the eudesmadiene 8a-epi-α-selinene (from NP1), and germacradienol (from NP2). The product of NP1, 8a-epi-α-selinene, so far has been isolated only from termites, in which it functions as a defense compound. Terpene synthases NP1 and NS1 are part of an apparent minicluster that includes a P450 and a putative hybrid two-component protein located downstream of the terpene synthases. Coexpression of P450 genes with their adjacent located terpene synthase genes in E. coli demonstrates that the P450 from Nostoc sp. can be functionally expressed in E. coli when coexpressed with a ferredoxin gene and a ferredoxin reductase gene from Nostoc and that the enzyme oxygenates the NS1 terpene product germacrene A. This represents to the best of our knowledge the first example of functional expression of a cyanobacterial P450 in E. coli.

scholarly journals A Comprehensive Survey on the Terpene Synthase Gene Family Provides New Insight into Its Evolutionary Patterns

2019 ◽  
Vol 11 (8) ◽  
pp. 2078-2098 ◽  
Author(s):  
Shu-Ye Jiang ◽  
Jingjing Jin ◽  
Rajani Sarojam ◽  
Srinivasan Ramachandran
Keyword(s):  
Gene Family ◽  
Large Scale ◽  
Family Members ◽  
Terpene Synthase ◽  
Limited Information ◽  
Terpene Synthases ◽  
Genome Wide ◽  
A Genome ◽  
Family Expansion ◽  
Insight Into

Abstract Terpenes are organic compounds and play important roles in plant growth and development as well as in mediating interactions of plants with the environment. Terpene synthases (TPSs) are the key enzymes responsible for the biosynthesis of terpenes. Although some species were employed for the genome-wide identification and characterization of the TPS family, limited information is available regarding the evolution, expansion, and retention mechanisms occurring in this gene family. We performed a genome-wide identification of the TPS family members in 50 sequenced genomes. Additionally, we also characterized the TPS family from aromatic spearmint and basil plants using RNA-Seq data. No TPSs were identified in algae genomes but the remaining plant species encoded various numbers of the family members ranging from 2 to 79 full-length TPSs. Some species showed lineage-specific expansion of certain subfamilies, which might have contributed toward species or ecotype divergence or environmental adaptation. A large-scale family expansion was observed mainly in dicot and monocot plants, which was accompanied by frequent domain loss. Both tandem and segmental duplication significantly contributed toward family expansion and expression divergence and played important roles in the survival of these expanded genes. Our data provide new insight into the TPS family expansion and evolution and suggest that TPSs might have originated from isoprenyl diphosphate synthase genes.

scholarly journals Estimating Conditional Transfer Entropy in Time Series Using Mutual Information and Nonlinear Prediction

Entropy ◽  
2020 ◽  
Vol 22 (10) ◽  
pp. 1124
Author(s):  
Payam Shahsavari Baboukani ◽  
Carina Graversen ◽  
Emina Alickovic ◽  
Jan Østergaard
Keyword(s):  
Time Series ◽  
State Of The Art ◽  
Difficult Case ◽  
Nonlinear Prediction ◽  
False Detection ◽  
Uniform Embedding ◽  
Embedding Technique ◽  
New Information ◽  
Highly Correlated ◽  
Intracranial Electroencephalography

We propose a new estimator to measure directed dependencies in time series. The dimensionality of data is first reduced using a new non-uniform embedding technique, where the variables are ranked according to a weighted sum of the amount of new information and improvement of the prediction accuracy provided by the variables. Then, using a greedy approach, the most informative subsets are selected in an iterative way. The algorithm terminates, when the highest ranked variable is not able to significantly improve the accuracy of the prediction as compared to that obtained using the existing selected subsets. In a simulation study, we compare our estimator to existing state-of-the-art methods at different data lengths and directed dependencies strengths. It is demonstrated that the proposed estimator has a significantly higher accuracy than that of existing methods, especially for the difficult case, where the data are highly correlated and coupled. Moreover, we show its false detection of directed dependencies due to instantaneous couplings effect is lower than that of existing measures. We also show applicability of the proposed estimator on real intracranial electroencephalography data.

The murine transcriptome reveals global aging nodes with organ-specific phase and amplitude

2019 ◽  
Author(s):  
Nicholas Schaum ◽  
Benoit Lehallier ◽  
Oliver Hahn ◽  
Shayan Hosseinzadeh ◽  
Song E. Lee ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Mitochondrial Function ◽  
Cell Activation ◽  
Plasma Cells ◽  
Immune Cell ◽  
Age Of Onset ◽  
Systemic Circulation ◽  
Protein Levels ◽  
Organ Specific ◽  
Highly Correlated

Aging is the single greatest cause of disease and death worldwide, and so understanding the associated processes could vastly improve quality of life. While the field has identified major categories of aging damage such as altered intercellular communication, loss of proteostasis, and eroded mitochondrial function1, these deleterious processes interact with extraordinary complexity within and between organs. Yet, a comprehensive analysis of aging dynamics organism-wide is lacking. Here we performed RNA-sequencing of 17 organs and plasma proteomics at 10 ages across the mouse lifespan. We uncover previously unknown linear and non-linear expression shifts during aging, which cluster in strikingly consistent trajectory groups with coherent biological functions, including extracellular matrix regulation, unfolded protein binding, mitochondrial function, and inflammatory and immune response. Remarkably, these gene sets are expressed similarly across tissues, differing merely in age of onset and amplitude. Especially pronounced is widespread immune cell activation, detectable first in white adipose depots in middle age. Single-cell RNA-sequencing confirms the accumulation of adipose T and B cells, including immunoglobulin J-expressing plasma cells, which also accrue concurrently across diverse organs. Finally, we show how expression shifts in distinct tissues are highly correlated with corresponding protein levels in plasma, thus potentially contributing to aging of the systemic circulation. Together, these data demonstrate a similar yet asynchronous inter- and intra-organ progression of aging, thereby providing a foundation to track systemic sources of declining health at old age.

scholarly journals Promiscuous terpene synthases from Prunella vulgaris highlight the importance of substrate and compartment switching in terpene synthase evolution

2019 ◽  
Vol 223 (1) ◽  
pp. 323-335 ◽  
Author(s):  
Sean R. Johnson ◽  
Wajid Waheed Bhat ◽  
Radin Sadre ◽  
Garret P. Miller ◽  
Alekzander Sky Garcia ◽  
...  
Keyword(s):  
Terpene Synthase ◽  
Prunella Vulgaris ◽  
Terpene Synthases
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