scholarly journals Transcriptome Profiling of Ornithogalum dubium Leaves and Flowers to Identify Key Carotenoid Genes for CRISPR Gene Editing

Plants ◽  
2020 ◽  
Vol 9 (4) ◽  
pp. 540 ◽  
Author(s):  
Zunzheng Wei ◽  
Tzahi Arazi ◽  
Nofar Hod ◽  
Matat Zohar ◽  
Tal Isaacson ◽  
...  
Keyword(s):  
Gene Editing ◽  
Transcriptome Profiling ◽  
Carotenoid Biosynthesis ◽  
Cdna Libraries ◽  
Biosynthesis Pathway ◽  
Illumina Hiseq ◽  
Transcriptome Database ◽  
Suitable Target ◽  
Carotenoid Genes ◽  
Carotenoid Biosynthesis Pathway

Ornithogalum dubium is a popular ornamental monocot native to South Africa with flower colors ranging from pure white to deep orange. Gene editing based on the CRISPR/Cas9 system has recently been shown to hold potential for color improvement in ornamental flower crops. To apply this approach to Ornithogalum color manipulation, genomic or transcriptomic data must first be collected. Here, cDNA libraries of O. dubium leaves and flowers were constructed and sequenced using the Illumina HiSeq 2500. Over 155 million 100-bp paired-end reads were assembled into a transcriptome database of 360,689 contigs, of which 18,660 contigs were differentially expressed between leaves and flowers. Carotenoids are the main pigment imparting spectrum of orange hues to O. dubium flowers. By querying our database, we identified a total of 16 unique transcripts (unigenes) predicted to be involved in the carotenoid biosynthesis pathway of Ornithogalum. Combining carotenoid profiles, we further inferred several key unigenes responsible for floral coloration and accumulation in O. dubium, of which the gene LCYB/comp146645_c0 was found as a suitable target to generate potentially red flower varieties of O. dubium. Our research thus provides a framework for the application of CRISPR/Cas9 technology to improve this ornamental crop.

scholarly journals Genetic Characterization of the Carotenoid Biosynthetic Pathway in Methylobacterium extorquens AM1 and Isolation of a Colorless Mutant

2003 ◽  
Vol 69 (12) ◽  
pp. 7563-7566 ◽  
Author(s):  
Stephen J. Van Dien ◽  
Christopher J. Marx ◽  
Brooke N. O'Brien ◽  
Mary E. Lidstrom
Keyword(s):  
Biosynthetic Pathway ◽  
Genetic Characterization ◽  
Carotenoid Biosynthesis ◽  
Biosynthesis Pathway ◽  
Wild Type ◽  
Methylobacterium Extorquens ◽  
Growth Properties ◽  
Carotenoid Biosynthesis Pathway ◽  
Free Strain

ABSTRACT Genomic searches were used to reconstruct the putative carotenoid biosynthesis pathway in the pink-pigmented facultative methylotroph Methylobacterium extorquens AM1. Four genes for putative phytoene desaturases were identified. A colorless mutant was obtained by transposon mutagenesis, and the insertion was shown to be in one of the putative phytoene desaturase genes. Mutations in the other three did not affect color. The tetracycline marker was removed from the original transposon mutant, resulting in a pigment-free strain with wild-type growth properties useful as a tool for future experiments.

scholarly journals EPR study of thylakoid membrane dynamics in mutants of the carotenoid biosynthesis pathway of Synechocystis sp. PCC6803.

2012 ◽  
Vol 59 (1) ◽  
Author(s):  
Kinga Kłodawska ◽  
Przemysław Malec ◽  
Mihály Kis ◽  
Zoltán Gombos ◽  
Kazimierz Strzałka
Keyword(s):  
Optimal Growth ◽  
Carotenoid Biosynthesis ◽  
Growth Conditions ◽  
Thylakoid Membranes ◽  
Membrane Dynamics ◽  
Biosynthesis Pathway ◽  
Light Regimes ◽  
Genes Encoding ◽  
Splitting Parameter ◽  
Carotenoid Biosynthesis Pathway

EPR spectroscopy using 5-doxylstearic acid (5-SASL) and 16-doxylstearic acid (16-SASL) spin probes was used to study the fluidity of thylakoid membranes. These were isolated from wild type Synechocystis and from several mutants in genes encoding selected enzymes of the carotenoid biosynthesis pathway and/or acyl-lipid desaturases. Cyanobacteria were cultivated at 25°C and 35°C under different light regimes: photoautotrophically (PAG) and/or in light-activated heterotrophic conditions (LAHG). The relative fluidity of membranes was estimated from EPR spectra based on the empirical outermost splitting parameter in a temperature range from 15°C to 40°C. Our findings demonstrate that in native thylakoid membranes the elimination of xanthophylls decreased fluidity in the inner membrane region under optimal growth conditions (25°C) and increased it under sublethal heat stress (35°C). This indicated that the overall fluidity of native photosynthetic membranes in cyanobacteria may be influenced by the ratio of polar to non-polar carotenoid pools under different environmental conditions.

scholarly journals Combining transcriptomics and metabolomics to reveal the underlying molecular mechanism of ergosterol biosynthesis during the fruiting process of Flammulina velutipes

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Ruihong Wang ◽  
Pengda Ma ◽  
Chen Li ◽  
Lingang Xiao ◽  
Zongsuo Liang ◽  
...  
Keyword(s):  
Molecular Mechanism ◽  
Differentially Expressed ◽  
Flammulina Velutipes ◽  
Cdna Libraries ◽  
Ergosterol Biosynthesis ◽  
Biosynthesis Pathway ◽  
Fruiting Bodies ◽  
Regulatory Relationship ◽  
Illumina Hiseq ◽  
Hiv Drugs

Abstract Background Flammulina velutipes has been recognized as a useful basidiomycete with nutritional and medicinal values. Ergosterol, one of the main sterols of F. velutipes is an important precursor of novel anticancer and anti-HIV drugs. Therefore, many studies have focused on the biosynthesis of ergosterol and have attempted to upregulate its content in multiple organisms. Great progress has been made in understanding the regulation of ergosterol biosynthesis in Saccharomyces cerevisiae. However, this molecular mechanism in F. velutipes remains largely uncharacterized. Results In this study, nine cDNA libraries, prepared from mycelia, young fruiting bodies and mature fruiting bodies of F. velutipes (three replicate sets for each stage), were sequenced using the Illumina HiSeq™ 4000 platform, resulting in at least 6.63 Gb of clean reads from each library. We studied the changes in genes and metabolites in the ergosterol biosynthesis pathway of F. velutipes during the development of fruiting bodies. A total of 13 genes (6 upregulated and 7 downregulated) were differentially expressed during the development from mycelia to young fruiting bodies (T1), while only 1 gene (1 downregulated) was differentially expressed during the development from young fruiting bodies to mature fruiting bodies (T2). A total of 7 metabolites (3 increased and 4 reduced) were found to have changed in content during T1, and 4 metabolites (4 increased) were found to be different during T2. A conjoint analysis of the genome-wide connection network revealed that the metabolites that were more likely to be regulated were primarily in the post-squalene pathway. Conclusions This study provides useful information for understanding the regulation of ergosterol biosynthesis and the regulatory relationship between metabolites and genes in the ergosterol biosynthesis pathway during the development of fruiting bodies in F. velutipes.

Molecular genetics of the carotenoid biosynthesis pathway in plants and algae

1997 ◽  
Vol 69 (10) ◽  
pp. 2151-2158 ◽  
Author(s):  
Joseph Hirschberg ◽  
M. Cohen ◽  
Mark Harker ◽  
Tamar Lotan ◽  
Varda Mann ◽  
...  
Keyword(s):  
Molecular Genetics ◽  
Carotenoid Biosynthesis ◽  
Biosynthesis Pathway ◽  
Carotenoid Biosynthesis Pathway

Metabolic engineering of Lilium × formolongi using multiple genes of the carotenoid biosynthesis pathway

2010 ◽  
Vol 4 (4) ◽  
pp. 269-280 ◽  
Author(s):  
Pejman Azadi ◽  
Ntui Valentaine Otang ◽  
Dong Poh Chin ◽  
Ikuo Nakamura ◽  
Masaki Fujisawa ◽  
...  
Keyword(s):  
Metabolic Engineering ◽  
Carotenoid Biosynthesis ◽  
Biosynthesis Pathway ◽  
Multiple Genes ◽  
Carotenoid Biosynthesis Pathway

Non-additive phenotypic and transcriptomic inheritance in a citrus allotetraploid somatic hybrid between C. reticulata and C. limon: the case of pulp carotenoid biosynthesis pathway

2009 ◽  
Vol 28 (11) ◽  
pp. 1689-1697 ◽  
Author(s):  
Jean Baptiste Bassene ◽  
Yann Froelicher ◽  
Claudie Dhuique-Mayer ◽  
Waffa Mouhaya ◽  
Rosa Mar Ferrer ◽  
...  
Keyword(s):  
Somatic Hybrid ◽  
Carotenoid Biosynthesis ◽  
Biosynthesis Pathway ◽  
Carotenoid Biosynthesis Pathway

scholarly journals Metabolic and transcriptional elucidation of the carotenoid biosynthesis pathway in peel and flesh tissue of loquat fruit during on-tree development

2017 ◽  
Vol 17 (1) ◽  
Author(s):  
Margarita Hadjipieri ◽  
Egli C. Georgiadou ◽  
Alicia Marin ◽  
Huertas M. Diaz-Mula ◽  
Vlasios Goulas ◽  
...  
Keyword(s):  
Carotenoid Biosynthesis ◽  
Biosynthesis Pathway ◽  
Carotenoid Biosynthesis Pathway ◽  
Tree Development

Overexpression of Thalassiosira pseudonana violaxanthin de-epoxidase-like 2 (VDL2) increases fucoxanthin while stoichiometrically reducing diadinoxanthin cycle pigment abundance

2020 ◽  
Author(s):  
Olga Gaidarenko ◽  
Dylan W. Mills ◽  
Maria Vernet ◽  
Mark Hildebrand
Keyword(s):  
Light Harvesting ◽  
Photosynthetic Pigment ◽  
Carotenoid Biosynthesis ◽  
Thalassiosira Pseudonana ◽  
Physiological Data ◽  
Biosynthesis Pathway ◽  
Chloroplast Targeting ◽  
Light Harvesting Complexes ◽  
Carotenoid Biosynthesis Pathway ◽  
Transcriptomic Responses

ABSTRACTDespite the ubiquity and ecological importance of diatoms, much remains to be understood about their physiology and metabolism, including their carotenoid biosynthesis pathway. Early carotenoid biosynthesis steps are well-conserved, while the identity of the enzymes that catalyze the later steps and their order remain unclear. Those steps lead to the biosynthesis of the final pathway products: the main accessory light-harvesting pigment fucoxanthin (Fx) and the main photoprotective pigment pool comprised of diadinoxanthin (Ddx) and its reversibly de-epoxidized form diatoxanthin (Dtx). We used sequence comparison to known carotenoid biosynthesis enzymes to identify novel candidates in the diatom Thalassiosira pseudonana. Microarray and RNA-seq data was used to select candidates with transcriptomic responses similar to known carotenoid biosynthesis genes and to create full-length gene models, and we focused on those that encode proteins predicted to be chloroplast-localized. We identified a violaxanthin de-epoxidase-like gene (Thaps3_11707, VDL2) that when overexpressed results in increased Fx abundance while stoichiometrically reducing Ddx+Dtx. Based on transcriptomics, we hypothesize that Thaps3_10233 may also contribute to Fx biosynthesis, in addition to VDL2. Separately using antisense RNA to target VDL2, VDL1, and both LUT1-like copies (hypothesized to catalyze an earlier step in the pathway) simultaneously, reduced the overall cellular photosynthetic pigment content, including chlorophylls, suggesting destabilization of light-harvesting complexes by Fx deficiency. Based on transcriptomic and physiological data, we hypothesize that the two predicted T. pseudonana zeaxanthin epoxidases have distinct functions and that different copies of phytoene synthase and phytoene desaturase may serve to initiate carotenoid biosynthesis in response to different cellular needs. Finally, nine carotene cis/trans isomerase (CRTISO) candidates identified based on sequence identity to known CRTISO proteins were narrowed to two most likely to be part of the T. pseudonana carotenoid biosynthesis pathway based on transcriptomic responses and predicted chloroplast targeting.

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