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MapMan4: A Refined Protein Classification and Annotation Framework Applicable to Multi-Omics Data Analysis

molecular plant 2019年第6期12卷 879-892页

作者： Rainer Schwacke Gabriel Y.Ponce-Soto Kirsten Krause Anthony M.Bolger Borjana Arsova Asis Hallab Kristina Gruden Mark Stitt Marie E.Bolger Bjorn Usadel Institute for Bio- and Geosciences (IBG-2: plant Sciences) Forschungszentrum Julich Wilhelm Johnen StraBe Jiilich Germany Department of Arctic and Marine Biology The Arctic University of Norway Biology Building 9037 Tromso Norway Institute for Botany and molecular Genetics BioEconomy Science Center Worringer Weg RWTH Aachen University 52074 Aachen Germany National Institute of Biology Department of Biotechnology and Systems Biology Vedna Pot 111 1000 Ljubljana Slovenia Max Planck Institute for molecular plant physiology Department of Systems Regulation 14476 Potsdam-Golm Germany

Genome sequences from over 200 plant species have already been published, with this number expected to increase rapidly due to advances in sequencing technologies. Once a new genome has been assembled and the genes identified, the functional annotation of their putative translational products, proteins, using ontologies is of key importance as it places the sequencing data in a biological context. Furthermore, to keep pace with rapid production of genome sequences, this functional annotation process must be fully automated. Here we present a redesigned and significantly enhanced MapMan4 framework, together with a revised version of the associated online Mercator annotation tool. Compared with the original MapMan, the new ontology has been expanded almost threefold and enforces stricter assignment rules. This framework was then incorporated into Mercator4, which has been upgraded to reflect current knowledge across the land plant group, providing protein annotations for all embryophytes with a comparably high quality. The annotation process has been optimized to allow a plant genome to be annotated in a matter of minutes. The output results continue to be compatible with the established MapMan desktop application.

关键词： plant genomes Functional annotation MapMan Mercator Transcriptomes

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Cadmium Accumulation in Marsilea minutaLinn. and Its Antioxidative Responses

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American Journal of plant Sciences 2013年第2期4卷 365-371页

作者： Kingsuk Das Chiranjib Mandal Nirmalya Ghosh Narottam Dey Malay Kumar Adak Department of biotechnology Visva Bharati Visvavidyalaya Santiniketan India plant physiology and plant molecular Biology Research Unit Department of Botany University of Kalyani Kalyani India

The present study was carried out to investigate the extent of cadmium (Cd) accumulation with its possible impact on physiological and biochemical basis of heavy metal tolerance in Marsilea minuta Linn. Cd salt (0 μM, 50 μM and 100 μM) was allowed to absorb by the plants for prolong days in hydroponic culture and a significant deterioration of the plant biomass was recorded. However, roots absorbed more metals than the leaves. plants recorded a significant rise of superoxide (O-2) and hydrogen peroxide (H2O2). A noticeable amount of protein oxidation and lipid peroxidation were in proportionate to Cd accumulation. Anthocyanin and flavonoid content were decreased as compared to control condition. Superoxide dismutase (SOD), guaiacol peroxidase (GPX) and glutathione reductase (GR) contributed their antioxidative functions according to the Cd doses. The expression of GR was also evident from its activity staining in gel. So, it may suggest that antioxidative enzymes are up regulated and likely to be responsible for tolerance to Cd induced oxidative stress in Marsilea minuta Linn.

关键词： Oxidative Stress Heavy Metals Aquatic Fern

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The Phosphate Transporter PHT4;6 Is a Determinant of Salt Tolerance that Is Localized to the Golgi Apparatus of Arabidopsis

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molecular plant 2009年第3期2卷 535-552页

作者： Beatriz Cubero Yuko Nakagawa Xing-Yu Jiang Ken-Ji Miura Fang Li Kashchandra G. Raghothama Ray A. Bressan Paul M. Hasegawa Jose M. Pardo Instituto de Recursos Naturales y Agrobiologia Consejo Superior de Investigaciones Cientificas Avda Reina Mercedes 10 Sevilla-41012 Spain Center for Environmental Stress physiology Department of Horticulture and Landscape Architecture Purdue University West Lafayette IN 47907-2010 USA present address: Ichinoseki National College of Technology Department of Chemical Engineering Takanashi Hagisyo Ichinoseki 021-8511 Japan present address: Graduate School of Life and Environmental Sciences Gene Research Center 220 1-1-1 Ten-nou dai University of Tsukuba Tsukuba 305-8572 Japan

Insertion mutations that disrupt the function of PHT4;6 （At5g44370） cause NaCI hypersensitivity of Arabidopsis seedlings that is characterized by reduced growth of the primary root, enhanced lateral branching, and swelling of root tips. Mutant phenotypes were exacerbated by sucrose, but not by equiosmolar concentrations of mannitol, and attenuated by low inorganic phosphate in the medium. Protein PHT4;6 belongs to the Major Facilitator Superfamily of permeases that shares significant sequence similarity to mammalian type-I Pi transporters and vesicular glutamate transporters, and is a member of the PHT4 family of putative intracellular phosphate transporters of plants. PHT4;6 localizes to the Golgi membrane and transport studies indicate that PHT4;6 facilitates the selective transport of Pi but not of chloride or inorganic anions. Phenotypic similarities with other mutants displaying root swelling suggest that PHT4;6 likely functions in protein N-glycosylation and cell wall biosynthesis, which are essential for salt tolerance. Together, our results indicate that PHT4;6 transports Pi out of the Golgi lumenal space for the re-cycling of the Pi released from glycosylation processes.

关键词： Phosphate transport Golgi glycosylation salt stress.

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Systematic optimization of the yeast cell factory for sustainable and high efficiency production of bioactive ginsenoside compound K

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Synthetic and Systems biotechnology 2021年第2期6卷 69-76页

作者： Pingping Wang Jiali Wang Guoping Zhao Xing Yan Zhihua Zhou CAS-Key Laboratory of Synthetic Biology CAS Center for Excellence in Molecular Plant SciencesInstitute of Plant Physiology and EcologyChinese Academy of Sciences300 Fenglin RdShanghai200032China School of Life Sciences Henan UniversityKaifeng475001China

Ginsenoside Compound K(CK)has been recognized as a major functional component that is absorbed into the systemic circulation after oral administration of *** demonstrates diverse bioactivities.A phase I clinical study indicated that CK was a potential candidate for arthritis ***,a phase II clinical study was suspended because of the high cost associated with the present CK manufacturing approach,which is based on the traditional planting-extracting-biotransforming *** previously elucidated the complete CK biosynthetic pathway and realized for the first time de novo biosynthesis of CK from glucose by engineered ***,CK production was not sufficient for industrial ***,we systematically engineered Saccharomyces cerevisiae to achieve high titer production of CK from glucose using a previously constructed protopanaxadiol(PPD)-producing chassis,optimizing UGTPg1 expression,improving UDP-glucose biosynthesis,and tuning down UDP-glucose *** final engineered yeast strain produced CK with a titer of 5.74 g/L in fed-batch fermentation,which represents the highest CK production in microbes reported to *** scaled-up,this high titer de novo microbial biosynthesis platform will enable a robust and stable supply of CK,thus facilitating study and medical application of CK.

关键词： Compound K UDP-Glucose Glycosylation efficiency Cell factory Synthetic biology

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Disruptions in AUXl-Dependent Auxin Influx Alter Hypocotyl Phototropism in Arabidopsis

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molecular plant 2008年第1期1卷 129-144页

作者： Bethany B. Stonea Emily L. Stowe-Evans Reneé M. Harper R. Brandon Celaya Karin Ljung Goran Sandbergc Emmanuel Liscum Division of Biological Sciences University of Missouri Columbia Missouri 65211 USA Christopher S. Bond Life Sciences Center University of Missouri Columbia Missouri 65211 USA Department of Forest Genetics and plant physiology Umea Plant Science Center SE-90183 Umea Sweden Current address: Biology Department Bucknell University Lewisburg Pennsylvania 17837 USA.

Phototropism represents a differential growth response by which plant organs can respond adaptively to changes in the direction of incident light to optimize leaf/stem positioning for photosynthetic light capture and root growth orientation for water/nutrient acquisition. Studies over the past few years have identified a number of compo- nents in the signaling pathway（s） leading to development of phototropic curvatures in hypocotyls. These include the pho- totropin photoreceptors （photl and phot2） that perceive directional blue-light （BL） cues and then stimulate signaling, leading to relocalization of the plant hormone auxin, as well as the auxin response factor NPH4/ARF7 that responds to changes in local auxin concentrations to directly mediate expression of genes likely encoding proteins necessary for development of phototropic curvatures, While null mutations in NPH4/ARF7 condition an aphototropic response to unidirectional BL, seedlings carrying the same mutations recover BL-dependent phototropic responsiveness if coirradiated with red light （RL） or pre-treated with either ethylene. In the present study, we identify second-site enhancer mutations in the nph4 background that abrogate these recovery responses. One of these mutations-mapl （modifier of arf7 phenotypes 1）-was found to represent a missense allele of AUX1-a gene encoding a high-affinity auxin influx carrier previously associated with a number of root responses. Pharmocological studies and analyses of additional auxl mutants confirmed that AUX1 functions as a modulator of hypocotyl phototropism. Moreover, we have found that the strength of dependence of hypocotyl phototropism on AUX1-mediated auxin influx is directly related to the auxin responsiveness of the seedling in question.

关键词： AUX1-Dependent Auxin NPH4/ARF7

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Tomato Ovary-to-Fruit Transition is Characterized by a Spatial Shift of mRNAs for Cell Wall Invertase and its Inhibitor with the Encoded Proteins Localized to Sieve Elements

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molecular plant 2015年第2期8卷 315-328页

作者： William M. Palmer School of Environmental and Life Sciences The University of Newcastle NSW 2308 Callaghan Australia Australia-China Research Centre for Crop Improvement The University of Newcastle NSW 2308 Callaghan Australia Institute of plant physiology and Ecology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences 300 Fenglin Road Shanghai 200032 China These authors contributed equally to the article. present address: College of Life Sciences. Central China Normal University Wuhan 430079 China

Central to understanding fruit development is to elucidate the processes mediating a successful transition from pre-pollination ovaries to newly set fruit, a key step in establishing fruit yield potential. In tomato, cell wall invertase （CWIN） LIN5 and its inhibitor INH1 are essential for fruit growth. However, the molecular and cellular basis by which they exert their roles in ovary-to-fruit transition remains unknown. To address this issue, we conducted a study focusing on ovaries and fruitlets at 2 days before and 2 days after anthesis, respectively. In situ hybridization analyses revealed that LIN5 and INH1 exhibited a dispersed expression in ovaries compared with their phloem-specific expression in fruitlets. Remarkably, LIN5 and INH1 proteins were immunologically co-localized to cell walls of sieve elements （SEs） in ovaries immediately prior to anthesis and in young fruitlets, but were undetectable in provascular bundles of younger ovaries. A burst in CWlN activity occurred during ovary-to-fruit transition. Interestingly, the ovaries, but not the fruit- lets, exhibited high expression of a defective invertase, SldeCWIN1, an ortholog of which is known to enhance inhibition of INH on CWlN activity in tobacco. Imaging of a fluorescent symplasmic tracer indicated an apoplasmic phloem unloading pathway operated in ovaries, contrary to the previously observed symplasmic unloading pathway in fruit pericarp. These new data indicate that （1） a phloem-specific patterning of the CWIN and INH mRNAs is induced during ovary-to-fruit transition, and （2） LIN5 protein functions specifically in walls of SEs and increases its activity during ovary-to-fruit transition, probably to facilitate phloem unloading and to generate a glucose signal positively regulating cell division, hence fruit set.

关键词： fruit set invertase invertase inhibitor phloem unloading sugar signaling

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Physio-Biochemical and Genetic Exploration for Submergence Tolerance in Rice (Oryza sativaL.) Landraces with Special References to Sub1 Loci

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American Journal of plant Sciences 2015年第12期6卷 1893-1904页

作者： Sayani Goswami Reha Labar Anupam Paul Malay Kumar Adak Narottam Dey Department of biotechnology Visva-Bharati Santiniketan India Agricultural Training Centre Fulia India Department of Botany Plant Physiology and Plant Molecular Biology Research Unit University of Kalyani Kalyani India

In the present study a group of four indigenous and less popular rice genotypes (Meghi, Panibhasha, Jabra and Sholey) reported by growers as submergence tolerant lines from flood prone areas of south Bengal were explored through study of nodal anatomy, physio-biochemical screening under submergence and genotyping with submergence tolerance linked rice microsatellite loci (RM loci). To identify the different allelic forms of different Sub1 compnents (Sub1A, Sub1B and Sub1C) among the studied lines, the genomic DNA of individual genotypes was amplified with three ethylene response factor like genes from Sub1 loci, located on rice chromosome 9. From the different physio-biochemical experiments performed in this investigation, it has been shown that Meghi and Jabra are the two probable potent genotypes which share common properties of both submergence tolerant and deep water nature whereas rest two genotypes (Sholey and Panibhasha) behave like typical deep water rice. The submergence tolerance property of Meghi was also confirmed from submergence tolerance linked SSR based genotyping by sharing with FR13A for some common alleles as reflected in fingerprint derived dendrogram. The rest of the genotypes shared a number of alleles and were included in a separate cluster. The common behaviour of Meghi and FR13A under submergence was also confirmed from genetic study of Sub1 loci through sharing of some common alleles for three Sub1 components (Sub1A, Sub1B and Sub1C loci). One SSR loci (RM 285) was identified as a potent molecular marker for submergence tolerance breeding programme involving these two selected rice lines (Meghi and Jabra) as donor plant through marker assisted selection.

关键词： Rice Submergence Tolerance Rice Microsatellite Sub1 Loci Marker Assisted Breeding

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Complex Regulation of Prolyl-4-Hydroxylases Impacts Root Hair Expansion

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molecular plant 2015年第5期8卷 734-746页

作者： Silvia M. Velasauez Martiniano M. Ricardi Christian Peter Poulsen Ai Oikawa Adiphol Dilokpimol Adnan Halim Silvina Mangano Silvina Paola Denita Juarez Eliana Marzol Juan D. Salgado Salter Javier Gloazzo Dorosz Cecilia Borassi Svenning Rune Moller Rafael Buono Yukiko Ohsawa Ken Matsuoka Marisa S. Otegui Henrik V. Scheller Naomi Geshi Bent Larsen Petersen Norberto D. lusem Jose M. Estevez Instituto de Fisiologfa Biologia Molecular y Neurociencias (IFIBYNE-CONICET) Facultad de Ciencias Exactas y Naturales Universidad de Buenos AiresBuenos Aires C1428EGA Argentina VKR Research Centre Department of Plant and Environmental Sciences University of Copenhagen DK-1871 Frededksberg C Denmark Joint BioEnergy Institute Feedstocks Division Lawrence Berkeley National Laboratory 5885 Hollis Street Emeryville CA 94608 USA Copenhagen Center for Glycomios Department of Cellular and Molecular Faculty of Health and Medical Sciences University of CopenhagenDK-2200 Copenhagen N Denmark Department of Botany University of Wisconsin Madison WI 53706 USA RIKEN plant Science Center Tsurumi-ku Yokohama 230-0045 Japan Laboratory of plant Nutrition Faculty of Agriculture Kyushu University Hakozaki 6-10-1 Higashi-ku Fukuoka 812-8581 Japan Departamento de Fisiologia Biologia Molecular y Celular Facultad de Ciencias Exactas y Naturales Universidad de Buenos Aires Buenos Aires C1428EGAArgentina These authors contributed equally to the article. present address: Fungal physiology CBS-KNAW Fungal Biodiversity Center Uppsalalaan 8 Utrecht 3584 CT The Netherlands present address: The Danish Stem Cell Center The Panum Institute Blegdamsvej 3B DK-2200 Copenhagen Denmark

Root hairs are single cells that develop by tip growth, a process shared with pollen tubes, axons, and fungal hyphae. However, structural plant cell walls impose constraints to accomplish tip growth. In addition to polysaccharides, plant cell walls are composed of hydroxyproline-rich glycoproteins （HRGPs）, which include several groups of O-glycoproteins, including extensins （EXTs）. Proline hydroxylation, an early post-translational modification （PTM） of HRGPs catalyzed by prolyl 4-hydroxylases （P4Hs）, defines their subsequent O-glycosylation sites. In this work, our genetic analyses prove that P4H5, and to a lesser extent P4H2 and P4H13, are pivotal for root hair tip growth. Second, we demonstrate that P4H5 has in vitro preferred specificity for EXT substrates rather than for other HRGPs. Third, by P4H promoter and protein swapping approaches, we show that P4H2 and P4H13 have interchangeable functions but cannot replace P4H5. These three P4Hs are shown to be targeted to the secretory pathway, where P4H5 forms dimers with P4H2 and P4H13. Finally, we explore the impact of deficient proline hydroxylation on the cell wall architec- ture. Taken together, our results support a model in which correct peptidyl-proline hydroxylation on EXTs, and possibly in other HRGPs, is required for proper cell wall self-assembly and hence root hair elongation in Arabidopsis thaliana.

关键词： enzymology cell expansion cell walls protein targeting proline hydroxylation root hairs

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Antioxidant lignans sesamin and sesamolin in sesame(Sesamum indicum L.):a comprehensive review and future prospects

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Journal of Integrative Agriculture 2023年第1期22卷 14-30页

作者： Senouwa Segla Koffi DOSSOU XU Fang-tao Komivi DOSSA ZHOU Rong ZHAO Ying-zhong WANG Lin-hai Oil Crops Research Institute Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of Agriculture and Rural AffairsWuhan 430062P.R.China Laboratory of plant biotechnology and physiology University of LoméLome 01 BP 1515Togo French Agricultural Research Center for International Development(CIRAD) Genetic Improvement and Adaptation of Mediterranean and Tropical Plants-UMR AGAP InstituteMontpellier F-34398France UMR AGAP Institute University of MontpellierCIRADFrench National Research Institute for AgricultureFood and Environment(INRAE)Montpellier F-34398France

Sesame(Sesamum indicum L.)is a significantly lucrative cash crop for millions of small-holder *** seeds are an important source of a highly appreciated vegetable oil globally and two clinically essential antioxidant lignans,sesamin and ***,many countries import millions of tons of sesame seed every *** demand for lignan-rich sesame seeds has been increasing in recent years due to the continuous discovery of several pharmacological attributes of sesamin and *** meet this demand,the sesame breeder’s primary objective is to release sesame cultivars that are enriched in oil and ***,it is necessary to summarize the information related to the sesamin and sesamolin contents in sesame in order to promote the joint efforts of specialized research teams on this important oilseed *** this article,we present the current knowledge on the sesamin and sesamolin contents in *** *** respect to the updated biosynthesis pathway,associated markers,governing loci,available variability in sesame germplasm,the in planta potential roles of these compounds in sesame,and the newly discovered pharmacological *** addition,we propose and discuss some required studies that might facilitate genomics-assisted breeding of high lignan content sesame varieties.

关键词： Sesamum indicum lignan biosynthesis antioxidants molecular breeding sesamin and sesamolin

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Regulation of Root-Knot Nematode Behavior by Seed-Coat Mucilage-Derived Attractants

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molecular plant 2019年第1期12卷 99-112页

作者： Allen Yi-Lun Tsai Takumi Higaki Chinh-Nghia Nguyen Laetitia Perfus-Barbeoch Bruno Favery Shinichiro Sawa Graduate School of Science &Technology Kumamoto University2-39-1 KurokamiChuo-kuKumamoto 860-8555Japan Graduate School of Frontier Sciences The University of Tokyo5-1-5 KashiwanohaKashtwa-shiChiba 277-8562Japan INRA Universite Cote d'AzurCNRSUMR 1355-7254 Institut Sophia Agrobiotech06900 Sophia AntipolJsFrance present address:Internattonal Research Organization for Advanced Science &Technology Kumamoto University2-39-1 KurokamiChuo-kuKumamoto 860-8555Japan present address:School of biotechnology and Food Technology Hanoi University of Science and Technology10 000 HanoiVietnam

Seed exudates influence the behavior of soil organisms,but howthis occurs remains unclear,particularly for multicellular *** we show that compounds associated with Arabidopsis seed-coat mucilage regulate the behavior of soil-borne animals,specifically root-knot nematodes (RKNs).Infective RKN J2 larvae actively travel toward Arabidopsis seeds through *** of Arabidopsis mucilage mutants demonstrated that the attraction of RKNs toArabidopsis seeds requires the synthesis and extrusion ***-coat *** mucilage alone is not sufficient to attract RKNs,but seed-surface carbohydrates and proteins are required for this *** findings suggest that the RKN chemoattractant is synthesized de novo upon mucilage extrusion but may be highly *** attracted by thismucilage-dependent mechanism can infect the emerging ***,the attraction signal from seedling roots likely acts independently of the seed-coat signal and may mask the attraction to seed-coat mucilage after *** RKN species are attracted byArabidopsis seeds,suggesting that this mechanism is conserved in *** findings indicate that seed exudate can regulate the behavior of multicellular animals and highlight the potential roles of seed-coat mucilage in biotic interactions with soil microorganisms.

关键词： chemotaxis seed-coat mucilage root-knot nematode plant-pathogen interaction

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