De novo transcriptome provides insights into the growth behaviour and resveratrol and trans-stilbenes biosynthesis in Dactylorhiza hatagirea - An endangered alpine terrestrial orchid of western Himalaya

Abstract This is the first report on de novo transcriptome of Dactylorhiza hatagirea, a critically-endangered, terrestrial orchid of alpine Himalayas. The plant is acclaimed for medicinal properties but little is known about its secondary-metabolites profile or cues regulating their biosynthesis. De novo transcriptome analysis was therefore, undertaken to gain basic understanding on these aspects, while circumventing the acute limitation of plant material availability. 65,384 transcripts and finally, 37,371 unigenes were assembled de novo from a total of 236 million reads obtained from shoot, tuber and leaves of the plant. Dominance of differentially-expressing-genes (DEGs) related to cold-stress-response and plant-hormone-signal-transduction; and those involved in photosynthesis, sugar-metabolism and secondary-metabolite-synthesis provided insights into carbohydrate-partitioning in the plant during its preparation for freezing winter at natural habitat. DEGs of glucomannan, ascorbic acid, carotenoids, phylloquinone/naphthoquinones, indole alkaloids, resveratrol and stilbene biosynthesis revealed the secondary-metabolite profile of D. hatagirea. UHPLC results confirmed appreciable amounts of resveratrol and trans-stilbene in D. hatagirea tubers, for the first time. Expression analysis of 15 selected genes including those of phenylpropanoid pathway confirmed the validity of RNA-seq data. Opportunistic growth, temperature- and tissue-specific-differential-expression of secondary metabolite biosynthesis and stress tolerant genes were confirmed using clonal plants growing at 8, 15 and 25 °C.

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Chitin Degradation Machinery and Secondary Metabolite Profiles in the Marine Bacterium Pseudoalteromonas rubra S4059

Marine Drugs ◽

10.3390/md19020108 ◽

2021 ◽

Vol 19 (2) ◽

pp. 108

Author(s):

Xiyan Wang ◽

Thomas Isbrandt ◽

Mikael Lenz Strube ◽

Sara Skøtt Paulsen ◽

Maike Wennekers Nielsen ◽

...

Keyword(s):

Secondary Metabolite ◽

Genetic Manipulation ◽

Genome Mining ◽

Hydrolytic Enzymes ◽

Metabolite Profile ◽

Chitinolytic Enzyme ◽

Chitin Degradation ◽

Metabolite Profiles ◽

Bioactive Potential ◽

Pseudoalteromonas Rubra

Genome mining of pigmented Pseudoalteromonas has revealed a large potential for the production of bioactive compounds and hydrolytic enzymes. The purpose of the present study was to explore this bioactivity potential in a potent antibiotic and enzyme producer, Pseudoalteromonas rubra strain S4059. Proteomic analyses (data are available via ProteomeXchange with identifier PXD023249) indicated that a highly efficient chitin degradation machinery was present in the red-pigmented P. rubra S4059 when grown on chitin. Four GH18 chitinases and two GH20 hexosaminidases were significantly upregulated under these conditions. GH19 chitinases, which are not common in bacteria, are consistently found in pigmented Pseudoalteromonas, and in S4059, GH19 was only detected when the bacterium was grown on chitin. To explore the possible role of GH19 in pigmented Pseudoalteromonas, we developed a protocol for genetic manipulation of S4059 and deleted the GH19 chitinase, and compared phenotypes of the mutant and wild type. However, none of the chitin degrading ability, secondary metabolite profile, or biofilm-forming capacity was affected by GH19 deletion. In conclusion, we developed a genetic manipulation protocol that can be used to unravel the bioactive potential of pigmented pseudoalteromonads. An efficient chitinolytic enzyme cocktail was identified in S4059, suggesting that this strain could be a candidate with industrial potential.

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De novo transcriptome and tissue specific expression analysis of genes associated with biosynthesis of secondary metabolites in Operculina turpethum (L.)

Scientific Reports ◽

10.1038/s41598-021-01906-y ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Bhagyashree Biswal ◽

Biswajit Jena ◽

Alok Kumar Giri ◽

Laxmikanta Acharya

Keyword(s):

Secondary Metabolite ◽

De Novo ◽

Differentially Expressed Gene ◽

Homology Search ◽

Biosynthesis Pathway ◽

Terpenoid Biosynthesis ◽

De Novo Transcriptome ◽

Illumina Hiseq ◽

Secondary Metabolite Biosynthesis ◽

Root Tissues

AbstractThis study reported the first-ever de novo transcriptome analysis of Operculina turpethum, a high valued endangered medicinal plant, using the Illumina HiSeq 2500 platform. The de novo assembly generated a total of 64,259 unigenes and 20,870 CDS (coding sequence) with a mean length of 449 bp and 571 bp respectively. Further, 20,218 and 16,458 unigenes showed significant similarity with identified proteins of NR (non-redundant) and UniProt database respectively. The homology search carried out against publicly available database found the best match with Ipomoea nil sequences (82.6%). The KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis identified 6538 unigenes functionally assigned to 378 modules with phenylpropanoid biosynthesis pathway as the most enriched among the secondary metabolite biosynthesis pathway followed by terpenoid biosynthesis. A total of 17,444 DEGs were identified among which majority of the DEGs (Differentially Expressed Gene) involved in secondary metabolite biosynthesis were found to be significantly upregulated in stem as compared to root tissues. The qRT-PCR validation of 9 unigenes involved in phenylpropanoid and terpenoid biosynthesis also showed a similar expression pattern. This finding suggests that stem tissues, rather than root tissues, could be used to prevent uprooting of O. turpethum in the wild, paving the way for the plant's effective conservation. Moreover, the study formed a valuable repository of genetic information which will provide a baseline for further molecular research.

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Heterochromatin influences the secondary metabolite profile in the plant pathogen Fusarium graminearum

Fungal Genetics and Biology ◽

10.1016/j.fgb.2011.11.002 ◽

2012 ◽

Vol 49 (1) ◽

pp. 39-47 ◽

Cited By ~ 44

Author(s):

Yazmid Reyes-Dominguez ◽

Stefan Boedi ◽

Michael Sulyok ◽

Gerlinde Wiesenberger ◽

Norbert Stoppacher ◽

...

Keyword(s):

Secondary Metabolite ◽

Fusarium Graminearum ◽

Plant Pathogen ◽

Metabolite Profile

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Reproductive success in a reintroduced population of a critically endangered shrub, Symonanthus bancroftii (Solanaceae)

Australian Journal of Botany ◽

10.1071/bt06136 ◽

2007 ◽

Vol 55 (4) ◽

pp. 425 ◽

Cited By ~ 4

Author(s):

Qigang Ye ◽

Eric Bunn ◽

Siegfried L. Krauss ◽

Kingsley W. Dixon

Keyword(s):

Reproductive Success ◽

Pollen Viability ◽

Natural Habitat ◽

Female Parent ◽

Clonal Plants ◽

Critically Endangered ◽

Positive Sign ◽

Male And Female ◽

Sterile Culture

Symonanthus bancroftii is a critically endangered dioecious shrub, with only one male and one female plant known in the wild. Micropropagated, clonal plants of the male and female parents were hand-pollinated. Seed was germinated in sterile culture and a subsequent daughter (F1) seedling was multiplied in vitro. Micropropagated plants of the original parents and daughter were reintroduced to a natural habitat site. We detail the first study of pollination biology and reproductive success in this extremely rare species. Floral morphology, flowering phenology, pollen viability, female receptivity and fruit set of reintroduced plants of S. bancroftii were investigated. Flower viability of S. bancroftii shows a 25-day maximum for male flowers, whereas non-pollinated female flowers remain viable for a maximum of 38 days (female parent) and 41 days (daughter), respectively. Flowering of reintroduced male and female plants overlaps from mid-June to early November. Pollen remained viable for at least 8 days after anther dehiscence. Maximum stigma longevity recorded was 28 days (female parent) and 39 days (daughter) and maximum ovule longevity varied from 13 days (female parent) to 28 days (daughter). The mean percentage of flowers setting fruit was 39 ± 13% for female parent plants and 48 ± 4% for daughter plants. Empirical reproductive success measures for male–daughter crosses generally exceeded those of the original parent crosses. The reproductive success of S. bancroftii so soon after reintroduction of plants is a positive sign indicating that rapid accumulation of a soil seedbank is feasible and is thus an important first step towards successful establishment of self-sustaining populations of this critically endangered species.

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Kinetic model of cell growth and secondary metabolite synthesis in plant cell culture ofThalictrum rugosum

Biotechnology and Bioprocess Engineering ◽

10.1007/bf02932383 ◽

1999 ◽

Vol 4 (2) ◽

pp. 129-137 ◽

Cited By ~ 7

Author(s):

Jeong-Woo Choi ◽

Young-Kee Kim ◽

Won Hong Lee ◽

Henrik Pedersen ◽

Chee-Kok Chin

Keyword(s):

Cell Culture ◽

Cell Growth ◽

Kinetic Model ◽

Secondary Metabolite ◽

Plant Cell ◽

Plant Cell Culture ◽

Metabolite Synthesis

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Bioprospecting potential and secondary metabolite profile of a novel sediment-derived fungus Penicillium sp. ArCSPf from continental slope of Eastern Arabian Sea

Mycology&#58 An International Journal on Fungal Biology ◽

10.1080/21501203.2019.1572034 ◽

2019 ◽

Vol 10 (2) ◽

pp. 109-117 ◽

Cited By ~ 3

Author(s):

Arakkaveettil Kabeer Farha ◽

Abdulla Mohamed Hatha

Keyword(s):

Secondary Metabolite ◽

Continental Slope ◽

Arabian Sea ◽

Metabolite Profile ◽

Penicillium Sp ◽

Eastern Arabian Sea

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Proteasome Inhibition in Brassica napus Roots Increases Amino Acid Synthesis to Offset Reduced Proteolysis

Plant and Cell Physiology ◽

10.1093/pcp/pcaa047 ◽

2020 ◽

Vol 61 (6) ◽

pp. 1028-1040

Author(s):

Dan Pereksta ◽

Dillon King ◽

Fahmida Saki ◽

Amith Maroli ◽

Elizabeth Leonard ◽

...

Keyword(s):

Amino Acid ◽

Brassica Napus ◽

De Novo ◽

Metabolic Response ◽

Sugar Metabolism ◽

Proteasome Inhibition ◽

Acid Synthesis ◽

Amino Acid Synthesis ◽

Amino Acid Depletion ◽

Metabolic Activities

Abstract Cellular homeostasis is maintained by the proteasomal degradation of regulatory and misfolded proteins, which sustains the amino acid pool. Although proteasomes alleviate stress by removing damaged proteins, mounting evidence indicates that severe stress caused by salt, metal(oids), and some pathogens can impair the proteasome. However, the consequences of proteasome inhibition in plants are not well understood and even less is known about how its malfunctioning alters metabolic activities. Lethality causes by proteasome inhibition in non-photosynthetic organisms stem from amino acid depletion, and we hypothesized that plants respond to proteasome inhibition by increasing amino acid biosynthesis. To address these questions, the short-term effects of proteasome inhibition were monitored for 3, 8 and 48 h in the roots of Brassica napus treated with the proteasome inhibitor MG132. Proteasome inhibition did not affect the pool of free amino acids after 48 h, which was attributed to elevated de novo amino acid synthesis; these observations coincided with increased levels of sulfite reductase and nitrate reductase activities at earlier time points. However, elevated amino acid synthesis failed to fully restore protein synthesis. In addition, transcriptome analysis points to perturbed abscisic acid signaling and decreased sugar metabolism after 8 h of proteasome inhibition. Proteasome inhibition increased the levels of alternative oxidase but decreased aconitase activity, most sugars and tricarboxylic acid metabolites in root tissue after 48 h. These metabolic responses occurred before we observed an accumulation of reactive oxygen species. We discuss how the metabolic response to proteasome inhibition and abiotic stress partially overlap in plants.

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