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Phylogenetic analyses of the genes involved in carotenoid biosynthesis in algae

Acta Oceanologica Sinica 2018年第4期37卷 89-101页

作者： WANG Shanshan ZHANG Lei CHI Shan WANG Guoliang WANG Xumin LIU Tao TANG Xuexi College of Marine Life Sciences Ocean University of China CAS Key Laboratory of Genome Sciences and Information/Beijing Key Laboratory of Genome and Precision Medicine Technologies Beijing Institute of GenomicsChinese Academy of Sciences

carotenoids play a crucial role in absorbing light energy for photosynthesis,as well as in protecting chlorophyll from photodamage.In contrast to the Streptophyta,few studies have examined carotenoid biosynthetic pathways in algae,owing to a shortage of datasets.As part of the 1000 Plants Project,we sequenced and assembled the transcriptomes of 41 marine macroalgal species,including 22 rhodophytes and 19 phaeophytes,and then combined the datasets with publicly available data from Gen Bank（National Center for Biotechnology Information） and the U.S.Department of Energy Joint Genome Institute.As a result,we identified 68 and 79 fulllength homologs in the Rhodophyta and Phaeophyceae,respectively,of seven inferred carotenoid biosynthetic genes,including the genes for phytoene synthase（PSY）,phytoene desaturase（PDS）,ζ-carotene desaturase（ZDS）,ζ-carotene isomerase（Z-ISO）,prolycopene isomerase（crt ISO）,lycopene β-cyclase（LCYB）,and lycopene ε-cyclase（LCYE）.We found that the evolutionary history of the algal carotenoid biosynthetic pathway was more complex than that of the same pathway in the Streptophyta and,more specifically,that the evolutionary history involved endosymbiotic gene transfer,gene duplication,and gene loss.Almost all of the eukaryotic algae that we examined had inherited the seven carotenoid biosynthesis genes via endosymbiotic gene transfer.Moreover,PSY,crt ISO,and the ancestral lycopene cyclase gene（LCY） underwent duplication events that resulted in multiple gene copies,and the duplication and subsequent divergence of LCYB and LCYE specialized and complicated the cyclization of lycopene.Our findings also verify that the loss of LCYE in both the microphytic rhodophytes and phaeophytes explains the differences in their carotenoid patterns,when compared to the macrophytic rhodophytes.These analyses provide a molecular basis for further biochemical and physiological validation in additional algal species and should help elucidate the origin and evolution of carotenoid biosynthetic pathways.

关键词： carotenoid biosynthesis algae phylogenetic analysis

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The Arabidopsis Spontaneous Cell Death1 gene, encoding a ζ-carotene desaturase essential for carotenoid biosynthesis, is involved in chloroplast development, photoprotection and retrograde signalling

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Cell Research 2007年第6期17卷 458-470页

作者： Haili Dong1,2 Yan Deng1,2 Jinye Mu1 Qingtao Lu3 Yiqin Wang1 Yunyuan Xu3 Chengcai Chu1 Kang Chong3 Congming Lu3 Jianru Zuo11 State Key Laboratory of Plant Genomics and National Plant Gene Research Center (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beoing 100101, China2 Graduate School, Chinese Academy of Sciences, Beijing 100039, China3 Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China InstituteofGeneticsandDevelopmentalBiologyChineseAcademyofSciencesBeijing100101China GraduateSchoolChineseAcademyofSciences Beijing

carotenoids, a class of natural pigments found in all photosynthetic organisms, are involved in a variety of physiologi-cal processes, including coloration, photoprotection, biosynthesis of abscisic acid (ABA) and chloroplast biogenesis.Although carotenoid biosynthesis has been well studied biochemically, the genetic basis of the pathway is not wellunderstood. Here, we report the characterization of two allelic Arabidopsis mutants, spontaneous cell death 1-1 (spcl-1)and spcl-2. The weak allele spcl-1 mutant showed characteristics of bleached leaves, accumulation of superoxide andmosaic cell death. The strong mutant allele spcl-2 caused a complete arrest of plant growth and development shortlyafter germination, leading to a seedling-lethal phenotype. Genetic and molecular analyses indicated that SPC1 encodesa putative ζ-carotene desaturase (ZDS) in the carotenoid biosynthesis pathway. Analysis of carotenoids revealed thatseveral major carotenoid compounds downstream of SPC1/ZDS were substantially reduced in spcl-1, suggesting thatSPC1 is a functional ZDS. Consistent with the downregulated expression of CAO and PORB, the chlorophyll contentwas decreased in spcl-1 plants. In addition, expression of Lhcb1.1, Lhcb1.4 and RbcS was absent in spcl-2, suggestingthe possible involvement of carotenoids in the plastid-to-nucleus retrograde signaling. The spcl-1 mutant also displaysan ABA-deficient phenotype that can be partially rescued by the externally supplied phytohormone. These results suggestthat SPC1/ZDS is essential for biosynthesis of carotenoids and plays a crucial role in plant growth and development.

关键词： carotenoid biosynthesis cell death chloroplast development photoprotection Arabidopsis SPC1/ZDS

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Installing the neurospora carotenoid pathway in plants enables cytosolic formation of provitamin A and its sequestration in lipid droplets

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Molecular Plant 2023年第6期16卷 1066-1081页

作者： Xiongjie Zheng Yasha Zhang Aparna Balakrishna Kit Xi Liew Hendrik N.J.Kuijer Ting Ting Xiao Ikram Blilou Salim Al-Babili The BioActives Lab Center for Desert Agriculture(CDA)Biological and Environmental Science and Engineering(BESE)King Abdullah University of Science and Technology(KAUST)Thuwal 23955-6900Saudi Arabia The Laboratory of Plant Cell and Developmental Biology(LPCDB) Center for Desert Agriculture(CDA)Biological and Environmental Science and Engineering(BESE)King Abdullah University of Science and Technology(KAUST)Thuwal 23955-6900Saudi Arabia Present address:College of Plant Science and Technology Bejing Key Laboratory for Agricultural Application and New TechniqueBeijing University of AgricultureBeijing 102206China

Vitamin A deficiency remains a severe global health issue,which creates a need to biofortify crops with provitamin A carotenoids(PACs).Expanding plant cell capacity for synthesis and storing of PACs outside the plastids is a promising biofortification strategy that has been little explored.Here,we engineered PAC formation and sequestration in the cytosol of Nicotiana benthamiana leaves,Arabidopsis seeds,and citrus callus cells,using a fungal(Neurospora crassa)carotenoid pathway that consists of only three enzymes converting C5 isopentenyl building blocks formed from mevalonic acid into PACs,including β-carotene.This strategy led to the accumulation of significant amounts of phytoene and γ-and β-carotene,in addition to fungal,health-promoting carotenes with 13 conjugated double bonds,such as the PAC torulene,in the cytosol.Increasing the isopentenyl diphosphate pool by adding a truncated Arabidopsis hydroxymethylglutaryl-coenzyme A reductase substantially increased cytosolic carotene production.Engineered carotenes accumulate in cytosolic lipid droplets(CLDs),which represent a novel sequestering sink for storing these pigments in plant cytosol.Importantly,β-carotene accumulated in the cytosol of citrus callus cells was more light stable compared to compared with plastidialβ-carotene.Moreover,engineering cytosolic carotene formation increased the number of large-sized CLDs and the levels of β-apocarotenoids,including retinal,the aldehyde corresponding to vitamin A.Collectively,our study opens up the possibility of exploiting the high-flux mevalonic acid pathway for PAC biosynthesis and enhancing carotenoid sink capacity in green and non-green plant tissues,especially in lipid-storing seeds,and thus paves the way for further optimization of carotenoid biofortification in crops.

关键词： Neurospora crassa carotenoid biosynthesis provitamin A metabolic engineering synthetic metabolism cytosolic lipid droplets carotenoid sequestration carotenoid stability

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Characterization of carotenoid biosynthetic pathway genes in the pea aphid(Acyrthosiphon pisum)revealed by heterologous complementation and RNA interference assays

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Insect Science 2022年第3期29卷 645-656页

作者： Bi-Yue Ding Xiu-Cheng Xie Feng Shang Guy Smagghe Jin-Zhi Niu Jin-Jun Wang Key Laboratory of Entomology and Pest Control Engineering College of Plant ProtectionSouthwest UniversityChongqingChina International Joint Laboratory of China-Belgium on Sustainable Crop Pest ControlAcademy of Agricultural SciencesSouthwest UniversityChongqingChina Department of Plants and Crops Faculty of Bioscience EngineeringGhent UniversityGhentBelgium

carotenoids are involved in many essential physiological functions and are produced from geranylgeranyl pyrophosphate through synthase,desaturase,and cyclase activities.In the pea aphid(Acyrthosiphon pisum),the duplication of carotenoid biosynthetic genes,including carotenoid synthases/cyclases(ApCscA-C)and desaturases(ApCdeA-D),through horizontal gene transfer from fungi has been detected,and ApCdeB has known dehydrogenation functions.However,whether other genes contribute to aphid carotenoid biosynthesis,and its specific regulatory pathway,remains unclear.In the current study,functional analyses of seven genes were performed using heterologous complementation and RNA interference assays.The bifunctional enzymes ApCscA-C were responsible for the synthase of phytoene,and ApCscC may also have a cyclase activity.ApCdeA,ApCdeC,and ApCdeD had diverse dehydrogenation functions.ApCdeA catalyzed the enzymatic conversion of phytoene to neurosporene(three-step product),ApCdeC catalyzed the enzymatic conversion of phytoene to ζ-carotene(two-step product),and ApCdeD catalyzed the enzymatic conversion of phytoene to lycopene(four-step product).Silencing of ApCscs reduced the expression levels of ApCdes,and silencing these carotenoid biosynthetic genes reduced the α-,β-,and γ-carotene levels,as well as the total carotenoid level.The results suggest that these genes were activated and led to carotenoid biosynthesis in the pea aphid.

关键词： carotenoid biosynthesis heterologous complementary pea aphid RNA interference

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Mutation of the PHYTOENE DESATURASE 3 gene causes yellowish-white petals in Brassica napus

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The Crop Journal 2021年第5期9卷 1124-1134页

作者： Chuanji Zhao Luqman Bin Safdar Meili Xie Meijuan Shi Zhixue Dong Li Yang Xiaohui Cheng Yueying Liu Zetao Bai Yang Xiang Chaobo Tong Junyan Huang Lijiang Liu Shengyi Liu Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/The Key Laboratory of Biology and Genetic Improvement of Oil Crops The Ministry of Agriculture and Rural AffairsWuhan 430062HubeiChina National Key Laboratory of Crop Genetic Improvement National Center of Rapeseed ImprovementHuazhong Agricultural UniversityWuhan 430070HubeiChina Biosystematics Group Experimental Plant SciencesWageningen University and ResearchWageningenNetherlands Guizhou Rapeseed Institute Guizhou Academy of Agricultural SciencesGuiyang 550008GuizhouChina

Oilseed rape (Brassica napus) with yellow flowers is an attractive ornamental landscape plant during the flowering period,and the development of different petal colors has become a breeding objective.Although yellowish flower color is a common variant observed in field-grown oilseed rape,the genetics behind this variation remains unclear.We obtained a yellowish-white flower (ywf) mutant from Zhongshuang 9 (ZS9) by ethyl methanesulfonate mutagenesis (EMS) treatment.Compared with ZS9,ywf exhibited a lower carotenoid content with a reduced and defective chromoplast ultrastructure in the petals.Genetic analysis revealed that the yellowish-white trait was controlled by a single recessive gene.Using bulked-segregant analysis sequencing (BSA-seq) and kompetitive allele-specific PCR(KASP),we performed map-based cloning of the ywf locus on chromosome A08 and found that ywf harbored a C-to-T substitution in the coding region,resulting in a premature translation termination.YWF,encoding phytoene desaturase 3 (PDS3),was highly expressed in oilseed rape petals and involved in carotenoid biosynthesis.Pathway enrichment analysis of the transcriptome profiles from ZS9 and ywf indicated the carotenoid biosynthesis pathway to be highly enriched.Further analyses of differentially expressed genes and carotenoid components revealed that the truncated Bna A08.PDS3 resulted in decreased carotenoid biosynthesis in the mutant.These results contribute to an understanding of the carotenoid biosynthesis pathway and manipulation of flower-color variation in B.napus.

关键词： Yellowish-white flower BSA-seq RNA-seq BnaA08.PDS3 carotenoid biosynthesis

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Chloroplast Proteomics and the Compartmentation of Plastidial Isoprenoid Biosynthetic Pathways

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Molecular Plant 2009年第6期2卷 1154-1180页

作者： Jacques Joyard Myriam Ferro Christophe Masselon Daphne Seigneurin-Berny Daniel Salvi Jerome Garin Norbert Rolland Laboratoire de Physiologie Cellulaire Vegetale UMR 5168 CEA CNRS INRA Universite Joseph Fourier iRTSV CEA-Grenoble 38054 Grenoble-cedex 9 France Laboratoirre Etude de la Dynamique des Proteomes U880 CEA INSERM Universite Joseph Fourrier iRTSV CEA-Grenoble 38054 Grenoble-cedex 9 France

Recent advances in the proteomic field have allowed high-throughput experiments to be conducted on chloroplast samples. Many proteomic investigations have focused on either whole chloroplast or sub-plastidial fractions. To date, the Plant Protein Database （PPDB, Sun et al., 2009） presents the most exhaustive chloroplast proteome available online. However, the accurate localization of many proteins that were identified in different sub-plastidial compartments remains hypothetical. Ferro et al. （2009） went a step further into the knowledge of Arabidopsis thaliana chloroplast proteins with regards to their accurate localization within the chloroplast by using a semi-quantitative proteomic approach known as spectral counting. Their proteomic strategy was based on the accurate mass and time tags （AMT） database approach and they built up AT_CHLORO, a comprehensive chloroplast proteome database with sub-plastidial localization and curated information on envelope proteins. Comparing these two extensive databases, we focus here on about 100 enzymes involved in the synthesis of chloroplast-specific isoprenoids. Well known pathways （i.e. compartmentation of the methyl erythritol phosphate biosynthetic pathway, of tetrapyrroles and chlorophyll biosynthesis and breakdown within chloroplasts） validate the spectral counting-based strategy. The same strategy was then used to identify the precise localization of the biosynthesis of carotenoids and prenylquinones within chloroplasts （i.e. in envelope membranes, stroma, and/or thylakoids） that remains unclear until now.

关键词： Non-mevalonate pathway chlorophyll biosynthesis chlorophyll degradation carotenoid biosynthesis prenylquinone biosynthesis envelope stroma thylakoids.

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Dissecting genetic control of yellowish-white flower in Brassica napus mutant

Dissecting genetic control of yellowish-white flower in Bras...

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中国作物学会油料作物专业委员会第八次会员代表大会暨学术...

作者： ZHAO Chuan-ji SHI Mei-juan HUANG Jun-yan LIU Yue-ying CHENG Xiao-hui LIU Sheng-yi Key Laboratory of Biology and Genetic Improvement of Oil Crops Ministry of AgricultureOil Crops Research InstituteChinese Academy of Agricultural Sciences

Flower color is an important ornamental trait and considered a major visual signal to pollinate plants for insect.Brassica napus L.,allotetraploid rapeseed(2 n = 38),which has yellow flowers,is a widely cultivated oil crop.In our study,a B.napus mutant,exhibited yellowish-white flower(ywf),was isolated and derived from Zhongshuang 9(ZS9) by ethyl methanesulfonate(EMS) mutagenesis.Transmission electron microscopy showed that the density of chromoplasts and the pigmentation accumulation were decreased significantly with the abnormal shaped chromoplast in the petals of ywf mutant.Genetic analysis confirmed that the phenotype of ywf mutant was controlled by a single recessive gene.The ywf locus was mapped to chromosome A08 by the approach of whole genome re-sequencing(WGS) and bulk segregation analysis(BSA).Sequence analysis suggested that YWF contains a C’to T’substitution in coding region generated a premature stop codon,and involved in the carotenoid biosynthesis pathway.RNA-seq and qRT-PCR analysis revealed that expression level of BnaA08.ywf was significantly repressed in ywf mutant.Taken together,our results show that BnaA08.ywf,the most likely candidate gene responsible for the ywf phenotype,functioned in chromoplast and played an essential role in carotenoid biosynthesis pathway.

关键词： yellowish-white flower BSA BnaA08.ywf gene carotenoid biosynthesis

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Dissecting the genetic control of yellowish-white flower in Brassica napus L.mutant

Dissecting the genetic control of yellowish-white flower in ...

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2018全国植物生物学大会

作者： Chuanji Zhao Meijuan Shi Junyan Huang Yueying Liu Xiaohui Cheng Shengyi Liu The Key Laboratory of Biology and Genetic Improvement of Oil Crops The Ministry of Agriculture of PRCOil Crops Research InstituteChinese Academy of Agriculture Sciences

Flower color is an important ornamental trait and considered a major visual signal to pollinate plants for insect.Brassica napus.L,allotetraploid rapeseed(2 n=38),which has yellow flowers,is a widely cultivated oil crop.In our study,a Brassica napus L.mutant,exhibited yellowish-white flower(ywf),was isolated and derived from Zhongshuang 9(ZS9) by ethyl methanesulfonate mutagenesis.Transmission electron microscopy showed that the density of chromoplasts and the pigmentation accumulation were decreased significantly with the abnormal shaped chromoplast in the petals of ywf mutant.Genetic analysis confirmed that the phenotypeof ywf mutant was controlled by a single recessive gene.The ywf locus was mapped to chromosome A08 by the approach of whole genome re-sequencing(WGS) and Bulk Segregation Analysis(BSA).Sequence analysis suggested that YWF contains a ’C’ to ’T’substitution in coding region generated a premature stop codon,and involved in the carotenoid biosynthesis pathway.RNA-seq and qRT-PCR analysis revealed that expression level of BnaA08.ywf was significantly repressed in ywf mutant.Taken together,our results show that BnaA08.ywf,the most likely candidate gene responsible for the ywf phenotype,functioned in chromoplast and played an essential role in carotenoid biosynthesis pathway.

关键词： yellowish-white flower BSA BnaA08.ywf gene carotenoid biosynthesis

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