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Haplotype-based phylogenetic analysis and population genomics uncover the origin and domestication of sweetpotato

Molecular Plant 2024年第2期17卷 277-296页

作者： Mengxiao Yan Ming Li Yunze Wang Xinyi Wang M-Hossein Moeinzadeh Dora G.Quispe-Huamanquispe Weijuan Fan Yijie Fang Yuqin Wang Haozhen Nie Zhangying Wang Aiko Tanaka Bettina Heider Jan F.Kreuze Godelieve Gheysen Hongxia Wang Martin Vingron Ralph Bock Jun Yang Shanghai Key Laboratory of Plant Functional Genomics and Resources Shanghai Chenshan Botanical GardenShanghai 201602China College of Life Sciences Chongqing Normal UniversityChongqing 401331China Biotechnology and Nuclear Technology Research Institute Sichuan Academy of Agricultural SciencesChengdu 610061China College of Life Sciences Shanghai Normal UniversityShanghai 200234China Department of Computational Molecular Biology Max Planck Institute for Molecular GeneticsIhnestraBe 63-7314195 BerlinGermany Department of Biotechnology Ghent University9000 GhentBelgium Guangdong Provincial Key Laboratory of Crops Genetics and Improvement Crop Research InstituteGuangdong Academy of Agricultural SciencesGuangzhou 510640China Graduate School of Bioagricultural Sciences Nagoya UniversityChikusaNagoya 464-8601Japan international Potato Center(CIP) LimaPeru CAS Center for Excellence of Molecular Plant Sciences Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghai 200233China max-planck-Institut fur molekulare pflanzenphysiologie Am Muhlenberg 114476 Potsdam-GolmGermany

The hexaploid sweetpotato(lpomoea batatas)is one of the most important root crops worldwide.However,its genetic origin remains controversial,and its domestication history remains unknown.In this study,we used a range of genetic evidence and a newly developed haplotype-based phylogenetic analysis to identify two probable progenitors of sweetpotato.The diploid progenitor was likely closely related to lpomoea ae-quatoriensis and contributed the B,subgenome,IbT-DNA2,and the lineage 1 type of chloroplast genome to sweetpotato.The tetraploid progenitor of sweetpotato was most likely l.batatas 4x,which donated the B2 subgenome,IbT-DNA1,and the lineage 2 type of chloroplast genome.Sweetpotato most likely originated from reciprocal crosses between the diploid and tetraploid progenitors,followed by a subsequent whole-genome duplication.In addition,we detected biased gene exchanges between the subgenomes;the rate of B,to B2 subgenome conversions was nearly three times higher than that of B2 to B subgenome conver-sions.Our analyses revealed that genes involved in storage root formation,maintenance of genome stabil-ity,biotic resistance,sugar transport,and potassium uptake were selected during the speciation and domestication of sweetpotato.This study sheds light on the evolution of sweetpotato and paves the way forimprovementofthiscrop.

关键词： sweetpotato origin gene conversion domestication IbT-DNA HPA

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Control of a sap-sucking insect pest by plastidmediated RNA interference

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Molecular Plant 2022年第7期15卷 1176-1191页

作者： Yi Dong Mengting Wu Qi Zhang Jinqiu Fu F.Vanessa Loiacono Yong Yang Zican Wang Shengchun Li Ling Chang Ralph Bock Jiang Zhang State Key Laboratory of Biocatalysis and Enzyme Engineering Hubei Hongshan LaboratorySchool of Life SciencesHubei UniversityWuhan 430062China max-planck-Institut fur molekulare pflanzenphysiologie Am Mühlenberg 1D-14476 Potsdam-GolmGermany

Expression of double-stranded RNAs in plastids offers great potential for the efficient control of chewing insects.However,many insect pests do not consume plant tissue but rather feed on the host plant by sucking sap from the vascular system.Whether or not plastid-mediated RNA interference(RNAi)can be employed to control sap-sucking insects is unknown.Here,we show that five species of sap-sucking hemipteran insects acquire plastid RNA upon feeding on plants.We generated both nuclear transgenic and transplastomic tobacco plants expressing double-stranded RNAs targeting the MpDhc64C gene,a newly identified efficient target gene of RNAi whose silencing causes lethality to the green peach aphid Myzus persicae.In a whole-plant bioassay,transplastomic plants exhibited significant resistance to aphids,as evidenced by reduced insect survival,impaired fecundity,and decreased weight of survivors.The protective effect was comparable with that conferred by the best-performing nuclear transgenic plants.We found that the proportion of aphids on mature leaves of transplastomic plants was significantly lower compared with that of nuclear transgenic plants.When aphids were allowed to infest.only the mature leaves,transplastomic plants grew significantly faster and were overall better protected from the pest compared with nuclear transgenic plants.When monitored by electrical-penetration-graph analyses and aphid avoidance response experiments,the insects displayed remarkable alterations in feeding behavior,which was different in nuclear transgenic and transplastomic plants,likely reflecting specific avoidance strategies to toxic RNA molecules.Taken together,our study demonstrates that plastid-mediated RNAi provides an efficient strategy for controlling at least some sap-sucking insect pests,even though there is most likely no or only very little chloroplast RNA in the sap.

关键词： plastid transformation RNA interference pest control sap-sucking insect aphid hemiptera

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The Translational Apparatus of Plastids and Its Role in Plant Development

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Molecular Plant 2014年第7期7卷 1105-1120页

作者： Nadine Tiller Ralph Bock max-planck-Institut for molekulare pflanzenphysiologie Am Muhlenberg 1 D-14476 Potsdam-Golm Germany

Chloroplasts （plastids） possess a genome and their own machinery to express it. Translation in plastids occurs on bacterial-type 70S ribosomes utilizing a set of tRNAs that is entirely encoded in the plastid genome. In recent years, the components of the chloroplast translational apparatus have been intensely studied by proteomic approaches and by reverse genetics in the model systems tobacco （plastid-encoded components） and Arabidopsis （nucleus-encoded components）. This work has provided important new insights into the structure, function, and biogenesis of chloroplast ribosomes, and also has shed fresh light on the molecular mechanisms of the translation process in plastids. In addition, mutants affected in plastid translation have yielded strong genetic evidence for chloroplast genes and gene products influencing plant develop- ment at various levels, presumably via retrograde signaling pathway（s）. In this review, we describe recent progress with the functional analysis of components of the chloroplast translational machinery and discuss the currently available evidence that supports a significant impact of plastid translational activity on plant anatomy and morphology.

关键词： plastid translation ribosome ribosomal protein evolution plastid transformation retrograde signaling leaf development palisade cell.

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The Chlamydomonas Chloroplast HLP Protein Is Required for Nucleoid Organization and Genome Maintenance

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Molecular Plant 2009年第6期2卷 1223-1232页

作者： Daniel Karcher Dietrich Koster Anne Schadach Anja Klevesath Ralph Bock max-planck-lnstitut fur molekulare pflanzenphysiologie Am Muhlenberg 1 D-14476 Potsdam-Golm Germany

The chloroplasts genome （plastome） occurs at high copy numbers per cell. Several chloroplast genome copies are densely packed into nucleoprotein particles called nucleoids. How genome packaging occurs and which proteins organize chloroplast nucleoids are largely unknown. Here, we have analyzed the Chlamydornonas reinhardtii homolog of the bacterial architectural DNA-binding protein HU, the histone-like protein HLP. We show that the Chlarnydornonas HLP protein is targeted to chloroplasts and associates with nucleoids. Knockdown of HLP gene expression by RNA interference （RNAi） alters the structure of chloroplast nucleoids and appears to reduce the level of compaction of chloroplast DNA. Unexpectedly, also chloroplast genome copy numbers are significantly decreased in the RNAi strains, suggesting that, in addition to its architectural role in nucleoid formation, the HIP protein is also involved in chloroplast genome maintenance.

关键词： Chloroplast nucleoid Chlamydomonas reinhardtii HLP DNA-binding protein genome maintenance

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Synthetic biology identifies the minimal gene set required for paclitaxel biosynthesis in a plant chassis

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Molecular Plant 2023年第12期16卷 1951-1961页

作者： Youjun Zhang Lorenz Wiese Hao Fang Saleh Alseekh Leonardo Perez de Souza Federico Scossa John Molloy Mathias Christmann Alisdair R.Fernie max-planck-Institut fur molekulare pflanzenphysiologie Am Muhlenberg 114476 Potsdam-GolmGermany Center of Plant Systems Biology and Biotechnology 4000 PlovdivBulgaria Institute of Chemistry and Biochemistry Freie Universitat BerlinTakustraBe 314195 BerlinGermany Department of Biomolecular Systems Max Planck Institute of Colloids and Interfaces14476 PotsdamGermany Research Center for Genomics and Bioinformatics(CREA-GB) Via Ardeatina 54600178 RomeItaly

The diterpenoid paclitaxel(Taxol)is a chemotherapy medication widely used as a first-line treatment against several types of solid cancers.The supply of paclitaxel from natural sources is limited.However,missing knowledge about the genes involved in several specific metabolic steps of paclitaxel biosynthesis has rendered it difficult to engineer the full pathway.In this study,we used a combination of transcriptomics,cell biology,metabolomics,and pathway reconstitution to identify the complete gene set required for the heterologous production of paclitaxel.We identified the missing steps from the current model of paclitaxel biosynthesis and confirmed the activity of most of the missing enzymes via heterologous expression in Nicotiana benthamiana.Notably,we identified a new C4β-C20 epoxidase that could overcome the first bottleneck of metabolic engineering.We used both previously characterized and newly identified oxomutases/epoxidases,taxane 1β-hydroxylase,taxane 9aα-hydroxylase,taxane 9α-dioxygenase,and phenylalanine-CoA ligase,to successfully biosynthesize the key intermediate baccatin Ill and to convert baccatin Ill into paclitaxel in N.benthamiana.In combination,these approaches establisha metabolic route to taxoidbiosynthesis and provide insights into the unique chemistry that plants use to generate complex bioactive metabolites.

关键词： paclitaxel biosynthesis synthetic biology baccatin Ill biosynthesis Taxus

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The conditional mitochondrial protein complexome in the Arabidopsis thaliana root and shoot

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Plant Communications 2023年第5期4卷 172-190页

作者： Youjun Zhang Silvia Martinez Jaime Mustafa Bulut Alexander Graf Alisdair R.Fernie Center of Plant Systems Biology and Biotechnology 4000 PlovdivBulgaria max-planck-Institut f€ur molekulare pflanzenphysiologie Am Muhlenberg 114476 Potsdam-GolmGermany

Protein complexes are important for almost all biological processes.Hence,to fully understand how cells work,it is also necessary to characterize protein complexes and their dynamics in response to various cellular cues.Moreover,the dynamics of protein interaction play crucial roles in regulating the(dis)association of protein complexes and,in turn,regulating biological processes such as metabolism.Here,mitochondrial protein complexes were investigated by blue native PAGE and size-exclusion chromatography under conditions of oxidative stress in order to monitor their dynamic(dis)associations.Rearrangements of enzyme interactions and changes in protein complex abundance were observed in response to oxidative stress induced by menadione treatment.These included changes in enzymatic protein complexes involving g-amino butyric acid transaminase(GABA-T),D-ornithine aminotransferase(D-OAT),or proline dehydrogenase 1(POX1)that are expected to affect proline metabolism.Menadione treatment also affected interactions between several enzymes of the tricarboxylic acid(TCA)cycle and the abundance of complexes of the oxidative phosphorylation pathway.In addition,we compared the mitochondrial complexes of roots and shoots.Considerable differences between the two tissues were observed in the mitochondrial import/export apparatus,the formation of super-complexes in the oxidative phosphorylation pathway,and specific interactions between enzymes of the TCA cycle that we postulate may be related to the metabolic/energetic requirements of roots and shoots.

关键词： mitochondrial complexes BN-PAGE size-exclusion chromatography TCA cycle

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The metabolic changes that effect fruit quality during tomato fruit ripening

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Molecular Horticulture 2022年第1期2卷 11-29页

作者： Feng Zhu Weiwei Wen Yunjiang Cheng Alisdair R.Fernie National R&D Center for Citrus Preservation Key Laboratory of Horticultural Plant BiologyMinistry of EducationHuazhong Agricultural UniversityWuhan 430070China max-planck-Institut für molekulare pflanzenphysiologie Am Mühlenberg 114476 PotsdamGolmGermany

As the most valuable organ of tomato plants,fruit has attracted considerable attention which most focus on its quality formation during the ripening process.A considerable amount of research has reported that fruit quality is affected by metabolic shifts which are under the coordinated regulation of both structural genes and transcriptional regulators.In recent years,with the development of the next generation sequencing,molecular and genetic analysis methods,lots of genes which are involved in the chlorophyll,carotenoid,cell wall,central and secondary metabolism have been identified and confirmed to regulate pigment contents,fruit softening and other aspects of fruit flavor quality.Here,both research concerning the dissection of fruit quality related metabolic changes,the transcriptional and post-translational regulation of these metabolic pathways are reviewed.Furthermore,a weighted gene correlation network analysis of representative genes of fruit quality has been carried out and the potential of the combined application of the gene correlation network analysis,fine-mapping strategies and next generation sequencing to identify novel candidate genes determinants of fruit quality is discussed.

关键词： Tomato Ripening Metabolites regulation Fruit quality

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Two mitochondrial phosphatases,PP2c63 and Sal2,are required for posttranslational regulation of the TCA cycle in Arabidopsis

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Molecular Plant 2021年第7期14卷 1104-1118页

作者： Youjun Zhang Jonas Giese Sandra M.Kerbler Beata Siemiatkowska Leonardo Perez de Souza Jessica Alpers David Barbosa Medeiros Dirk K.Hincha Danilo M.Daloso Mark Stitt Iris Finkemeier Alisdair R.Fernie max-planck-lnstitut fur molekulare pflanzenphysiologie Am Muhlenberg 114476 Potsdam-GolmGermany Center of Plant Systems Biology and Biotechnology 4000 PlovdivBulgaria lnstitute of Plant Biology and Biotechnology University of MuensterSchlossplatz 748149 MuensterGermany Departamento de Bioquimica e Biologia Molecular Universidade Federal do CearaFortalezaCearaBrasil

Protein phosphorylation is a well-established post-translational mechanism that regulates protein functions and metabolic pathways.It is known that several plant mitochondrial proteins are phosphorylated in a reversible manner.However,the identities of the protein kinases/phosphatases involved in this mech-anism and their roles in the regulation of the tricarboxylic acid(TCA)cycle remain unclear.In this study,we isolated and characterized plants lacking two mitochondrially targeted phosphatases(Sal2 and PP2c63)along with pyruvate dehydrogenase kinase(PDK),Protein-protein interaction analysis,quantitative phos-phoproteomics,and enzymatic analyses revealed that PDK specifically regulates pyruvate dehydrogenase complex(PDC),while PP2c63 nonspecifically regulates PDC.When recombinant PP2c63 and Sal2 proteins were added to mitochondria isolated from mutant plants,protein-protein interaction and enzymatic analyses showed that PP2c63 directly phosphorylates and modulates the activity of PDC,while Sal2 only indirectly affects TCA cycle enzymes.Characterization of steady-state metabolite levels and fluxes in the mutant lines further revealed that these phosphatases regulate flux through the TCA cycle,and that altered metabolism in the sa/2 pp2c63 double mutant compromises plant growth.These results are discussed in the context of current models of the control of respiration in plants.

关键词： TCA cycle pyruvate dehydrogenase phosphorylation mitochondrial protein phosphatase TCA cycle enzymes phosphorylation

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Predicting Arabidopsis Freezing Tolerance and Heterosis in Freezing Tolerance from Metabolite Composition

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Molecular Plant 2010年第1期3卷 224-235页

作者： Marina Korn Tanja Gaetner Alexander Erban Joachim Kopka Joachim Selbig Dirk K. Hincha max-planck-lnstitut fur molekulare pflanzenphysiologie Am Muhlenberg 1 D-14476 Potsdam Germany Abteilung Bioinformatik Institut for Biochemie und Biologie Universit~t Potsdam Karl-Liebknecht-Str. 24-25 D-14476 Potsdam Germany

Heterosis, or hybrid vigor, is one of the most important tools in plant breeding and has previously been dem- onstrated for plant freezing tolerance. Freezing tolerance is an important trait because it can limit the geographical dis- tribution of plants and their agricultural yield. Plants from temperate climates increase in freezing tolerance during exposure to low, non-freezing temperatures in a process termed ＇cold acclimation＇. Metabolite profiling has indicated a major reprogramming of plant metabolism in the cold, but it has remained unclear in previous studies which of these changes are related to freezing tolerance. In the present study, we have used metabolic profiling to discover combinations of metabolites that predict freezing tolerance and its heterosis in Arabidopsis thaliana. We identified compatible solutes and, in particular, the pathway leading to raffinose as crucial statistical predictors for freezing tolerance and its heterosis, while some TCA cycle intermediates contribute only to predicting the heterotic phenotype. This indicates coordinate links between heterosis and metabolic pathways, suggesting that a limited number of regulatory genes may determine the extent of heterosis in this complex trait. In addition, several unidentified metabolites strongly contributed to the prediction of both freezing tolerance and its heterosis and we present an exemplary analysis of one of these, identifying it as a hexose conjugate.

关键词： Abiotic/environmental stress cold acclimation metabolomics bioinformatics biostatistics Arabidopsis.

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Complex Assembly and Metabolic Profiling of Arabidopsis thaliana PlantsOverexpressing Vitamin B6 Biosynthesis Proteins

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Molecular Plant 2010年第5期3卷 890-903页

作者： Jan Erik Leuendorf Sonia Osorio Agnieszka Szewczyk Alisdair R. Fernie Hanjo Hellmann Angewandte Genetik Freie Universitat Berlin 14195 Berlin Germany max-planck-lnstitut for molekulare pflanzenphysiologie Potsdam-Golm 14476 Germany Pharmaceutical Faculty of the Collegium Medicum Jagiellonian University Krakow Poland School of Biological Sciences Washington State University Pullman USA

In plants, vitamin B6 biosynthesis requires the activity of PDX1 and PDX2 proteins. Arabidopsis thaliana encodes for three PDX1 proteins, named PDXI.1, 1.2, and 1.3, but only one PDX2. Here, we show in planta complex assembly of PDX proteins, based on split-YFP and FPLC assays, and can demonstrate their presence in higher complexes of around 750 kDa. Metabolic profiling of plants ectopically expressing the different PDX proteins indicates a negative influence of PDX1.2 on vitamin Be biosynthesis and a correlation between aberrant vitamin B6 content, PDX1 gene expression, and light sensitivity specifically for PDX1.3. These findings provide first insights into in planta vitamin B6 synthase complex assembly and new information on how the different PDX proteins affect plant metabolism.

关键词： Abiotic/environmental stress metabolomics metabolic regulation molecular physiology.

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