A network perspective on nitrogen metabolism from model to crop plants using integrated 'omics' approaches.

Abstract:

:Nitrogen (N), as an essential element in amino acids, nucleotides, and proteins, is a key factor in plant growth and development. Omics approaches such as metabolomics and transcriptomics have become a promising way to inspect complex network interactions in N metabolism and can be used for monitoring the uptake and regulation, translocation, and remobilization of N. In this review, the authors highlight recent progress in omics approaches, including transcript profiling using microarrays and deep sequencing, and show recent technical developments in metabolite profiling for N studies. Further, network analysis studies including network inference methods with correlations, information-theoretic measures, and a network concept to examine gene expression clusters in relation to N regulatory systems in plants are introduced, and integrating network inference methods and integrated networks using multiple omics data are discussed. Finally, this review summarizes recent omics application examples using metabolite and/or transcript profiling analysis to elucidate the regulation of N metabolism and signalling and the coordination of N and carbon metabolism in model plants (Arabidopsis and rice), crops (tomato, maize, and legumes), and trees (Populus).

journal_name

J Exp Bot

authors

Fukushima A,Kusano M

doi

10.1093/jxb/eru322

subject

Has Abstract

pub_date

2014-10-01 00:00:00

pages

5619-30

issue

19

eissn

0022-0957

issn

1460-2431

pii

eru322

journal_volume

65

pub_type

杂志文章,评审
  • Transpiration efficiency: new insights into an old story.

    abstract::Producing more food per unit of water has never been as important as it is at present, and the demand for water by economic sectors other than agriculture will necessarily put a great deal of pressure on a dwindling resource, leading to a call for increases in the productivity of water in agriculture. This topic has b...

    journal_title:Journal of experimental botany

    pub_type: 杂志文章,评审

    doi:10.1093/jxb/eru040

    authors: Vadez V,Kholova J,Medina S,Kakkera A,Anderberg H

    更新日期:2014-11-01 00:00:00

  • Molecular analysis of plant sugar and amino acid transporters.

    abstract::Although plants are photoautotrophic organisms, they are composed of many heterotrophic tissue systems that must import sugars and amino acids in a process known as assimilate partitioning. While the general features of assimilate partitioning were well described by the early 1980s, little was known about the various ...

    journal_title:Journal of experimental botany

    pub_type: 杂志文章

    doi:10.1093/jxb/47.Special_Issue.1205

    authors: Bush DR,Chiou TJ,Chen L

    更新日期:1996-08-01 00:00:00

  • Transgenic expression of a functional fragment of harpin protein Hpa1 in wheat induces the phloem-based defence against English grain aphid.

    abstract::The harpin protein Hpa1 has multiple beneficial effects in plants, promoting plant growth and development, increasing crop yield, and inducing resistance to pathogens and insect pests. For these effects, the 10-40 residue fragment (Hpa1₁₀₋₄₂) isolated from the Hpa1 sequence is 1.3- to 7.5-fold more effective than the ...

    journal_title:Journal of experimental botany

    pub_type: 杂志文章

    doi:10.1093/jxb/ert488

    authors: Fu M,Xu M,Zhou T,Wang D,Tian S,Han L,Dong H,Zhang C

    更新日期:2014-04-01 00:00:00

  • Iron in Plant-pathogen Interactions.

    abstract::Iron is an essential element for most organisms. As an indispensable co-factor of many enzymes, iron is involved in various crucial metabolic processes, which are required for the survival of plants and pathogens. Conversely, excessive iron produces highly active reactive oxygen species (ROS) that is toxic to the cell...

    journal_title:Journal of experimental botany

    pub_type: 杂志文章

    doi:10.1093/jxb/eraa516

    authors: Liu Y,Kong D,Wu HL,Ling HQ

    更新日期:2020-11-08 00:00:00

  • Functional characterization of barley betaglucanless mutants demonstrates a unique role for CslF6 in (1,3;1,4)-β-D-glucan biosynthesis.

    abstract::(1,3;1,4)-β-D-glucans (mixed-linkage glucans) are found in tissues of members of the Poaceae (grasses), and are particularly high in barley (Hordeum vulgare) grains. The present study describes the isolation of three independent (1,3;1,4)-β-D-glucanless (betaglucanless; bgl) mutants of barley which completely lack (1,...

    journal_title:Journal of experimental botany

    pub_type: 杂志文章

    doi:10.1093/jxb/err285

    authors: Taketa S,Yuo T,Tonooka T,Tsumuraya Y,Inagaki Y,Haruyama N,Larroque O,Jobling SA

    更新日期:2012-01-01 00:00:00

  • PGL, encoding chlorophyllide a oxygenase 1, impacts leaf senescence and indirectly affects grain yield and quality in rice.

    abstract::Chlorophyll (Chl) b is a ubiquitous accessory pigment in land plants, green algae, and prochlorophytes. This pigment is synthesized from Chl a by chlorophyllide a oxygenase and plays a key role in adaptation to various environments. This study characterizes a rice mutant, pale green leaf (pgl), and isolates the gene P...

    journal_title:Journal of experimental botany

    pub_type: 杂志文章

    doi:10.1093/jxb/erv529

    authors: Yang Y,Xu J,Huang L,Leng Y,Dai L,Rao Y,Chen L,Wang Y,Tu Z,Hu J,Ren D,Zhang G,Zhu L,Guo L,Qian Q,Zeng D

    更新日期:2016-03-01 00:00:00

  • Mutational analysis of functional domains within plant K+ uptake channels.

    abstract::Site-directed mutations have been generated in the pore and voltage sensor regions of the inwardly rectifying potassium channels KAT1 and KST1. The properties of mutant channels have been analysed in Xenopus oocytes, and give insights into the structure-function relations of these channels. ...

    journal_title:Journal of experimental botany

    pub_type: 杂志文章

    doi:10.1093/jxb/48.Special_Issue.415

    authors: Hoth S,Dreyer I,Hedrich R

    更新日期:1997-03-01 00:00:00

  • The role of VuMATE1 expression in aluminium-inducible citrate secretion in rice bean (Vigna umbellata) roots.

    abstract::Aluminium (Al)-activated citrate secretion plays an important role in Al resistance in a number of plant species, such as rice bean (Vigna umbellata). This study further characterized the regulation of VuMATE1, an aluminium-activated citrate transporter. Al stress induced VuMATE1 expression, followed by the secretion ...

    journal_title:Journal of experimental botany

    pub_type: 杂志文章

    doi:10.1093/jxb/ert039

    authors: Liu MY,Chen WW,Xu JM,Fan W,Yang JL,Zheng SJ

    更新日期:2013-04-01 00:00:00

  • The metal transporter PgIREG1 from the hyperaccumulator Psychotria gabriellae is a candidate gene for nickel tolerance and accumulation.

    abstract::Nickel is an economically important metal and phytotechnologies are being developed to limit the impact of nickel mining on the environment. More than 300 plant species are known to hyperaccumulate nickel. However, our knowledge of the mechanisms involved in nickel accumulation in plants is very limited because it has...

    journal_title:Journal of experimental botany

    pub_type: 杂志文章

    doi:10.1093/jxb/eru025

    authors: Merlot S,Hannibal L,Martins S,Martinelli L,Amir H,Lebrun M,Thomine S

    更新日期:2014-04-01 00:00:00

  • Brefeldin A affects adhesion of zoospores of the green alga Enteromorpha.

    abstract::Primary adhesion of zoospores of the green macroalga Enteromorpha to substrata involves a massive release of adhesive glycoproteins from Golgi-derived, membrane-bounded vesicles in the anterior region of the spore, followed by rapid curing. This process is sensitive to low concentrations (5-10 microg x ml(-1)) of the ...

    journal_title:Journal of experimental botany

    pub_type: 杂志文章

    doi:10.1093/jexbot/52.360.1409

    authors: Callow ME,Crawford S,Wetherbee R,Taylor K,Finlay JA,Callow JA

    更新日期:2001-07-01 00:00:00

  • Aethionema arabicum: a novel model plant to study the light control of seed germination.

    abstract::The timing of seed germination is crucial for seed plants and is coordinated by internal and external cues, reflecting adaptations to different habitats. Physiological and molecular studies with lettuce and Arabidopsis thaliana have documented a strict requirement for light to initiate germination and identified many ...

    journal_title:Journal of experimental botany

    pub_type: 杂志文章

    doi:10.1093/jxb/erz146

    authors: Mérai Z,Graeber K,Wilhelmsson P,Ullrich KK,Arshad W,Grosche C,Tarkowská D,Turečková V,Strnad M,Rensing SA,Leubner-Metzger G,Mittelsten Scheid O

    更新日期:2019-06-28 00:00:00

  • Root exudation from Hordeum vulgare in response to localized nitrate supply.

    abstract::Root proliferation as a response to exploit zones of nutrient enrichment in soil has been demonstrated for a wide range of plant species. However, the effectiveness of this as a strategy to acquire nutrients is also dependent on interactions with the soil microbial community. Specifically, C-flow from roots modifies m...

    journal_title:Journal of experimental botany

    pub_type: 杂志文章

    doi:10.1093/jxb/erj214

    authors: Paterson E,Sim A,Standing D,Dorward M,McDonald AJ

    更新日期:2006-01-01 00:00:00

  • Ascorbic acid accumulates as a defense response to Turnip mosaic virus in resistant Brassica rapa cultivars.

    abstract::We initially observed that Brassica rapa cultivars containing the Turnip mosaic virus (TuMV) resistance gene, Rnt1-1, accumulated a high level of endogenous ascorbic acid (AS) and dehydroascobic acid (DHA) when infected with TuMV. We here hypothesized a possible contribution of an elevated level of AS+DHA (TAA) to the...

    journal_title:Journal of experimental botany

    pub_type: 杂志文章

    doi:10.1093/jxb/erw223

    authors: Fujiwara A,Togawa S,Hikawa T,Matsuura H,Masuta C,Inukai T

    更新日期:2016-07-01 00:00:00

  • Plants grow with a little help from their organelle friends.

    abstract::Chloroplasts and mitochondria are indispensable for plant development. They not only provide energy and carbon sources to cells, but also have evolved to become major players in a variety of processes such as amino acid metabolism, hormone biosynthesis and cellular signalling. As semi-autonomous organelles, they conta...

    journal_title:Journal of experimental botany

    pub_type: 杂志文章,评审

    doi:10.1093/jxb/erw399

    authors: Van Dingenen J,Blomme J,Gonzalez N,Inzé D

    更新日期:2016-12-01 00:00:00

  • The role of abscisic acid and low temperature in chickpea (Cicer arietinum) cold tolerance. II. Effects on plasma membrane structure and function.

    abstract::The frost hardiness of many plants such as chickpea can be increased by exposure to low non-freezing temperatures and/or the application of abscisic acid (ABA), a process known as frost acclimation. Experiments were conducted to study the response over a 14 d period of enriched plasma membrane fractions isolated from ...

    journal_title:Journal of experimental botany

    pub_type: 杂志文章

    doi:10.1093/jxb/erl120

    authors: Bakht J,Bano A,Dominy P

    更新日期:2006-01-01 00:00:00

  • Identification of predominant genes involved in regulation and execution of senescence-associated nitrogen remobilization in flag leaves of field grown barley.

    abstract::The transcriptomes of senescing flag leaves collected from barley field plots with standard or high nitrogen supply were compared to identify genes specifically associated with nitrogen remobilization during leaf senescence under agronomically relevant conditions. In flag leaves collected in field plots with high nitr...

    journal_title:Journal of experimental botany

    pub_type: 杂志文章

    doi:10.1093/jxb/eru094

    authors: Hollmann J,Gregersen PL,Krupinska K

    更新日期:2014-07-01 00:00:00

  • The mitochondrial pentatricopeptide repeat protein EMP12 is involved in the splicing of three nad2 introns and seed development in maize.

    abstract::Plant mitochondrial genes contain cis- and trans-group II introns that must be spliced before translation. The mechanism by which these introns are spliced is not well understood. Several families of proteins have been implicated in the intron splicing, of which the pentatricopeptide repeat (PPR) proteins are proposed...

    journal_title:Journal of experimental botany

    pub_type: 杂志文章

    doi:10.1093/jxb/ery432

    authors: Sun F,Xiu Z,Jiang R,Liu Y,Zhang X,Yang YZ,Li X,Zhang X,Wang Y,Tan BC

    更新日期:2019-02-05 00:00:00

  • Genetic association mapping identifies single nucleotide polymorphisms in genes that affect abscisic acid levels in maize floral tissues during drought.

    abstract::In maize, water stress at flowering causes loss of kernel set and productivity. While changes in the levels of sugars and abscisic acid (ABA) are thought to play a role in this stress response, the mechanistic basis and genes involved are not known. A candidate gene approach was used with association mapping to identi...

    journal_title:Journal of experimental botany

    pub_type: 杂志文章

    doi:10.1093/jxb/erq308

    authors: Setter TL,Yan J,Warburton M,Ribaut JM,Xu Y,Sawkins M,Buckler ES,Zhang Z,Gore MA

    更新日期:2011-01-01 00:00:00

  • Salicylic acid improves salinity tolerance in Arabidopsis by restoring membrane potential and preventing salt-induced K+ loss via a GORK channel.

    abstract::Despite numerous reports implicating salicylic acid (SA) in plant salinity responses, the specific ionic mechanisms of SA-mediated adaptation to salt stress remain elusive. To address this issue, a non-invasive microelectrode ion flux estimation technique was used to study kinetics of NaCl-induced net ion fluxes in Ar...

    journal_title:Journal of experimental botany

    pub_type: 杂志文章

    doi:10.1093/jxb/ert085

    authors: Jayakannan M,Bose J,Babourina O,Rengel Z,Shabala S

    更新日期:2013-05-01 00:00:00

  • Resurrection plants optimize photosynthesis despite very thick cell walls by means of chloroplast distribution.

    abstract::Resurrection plants are vascular species able to sustain extreme desiccation in their vegetative tissues. Despite its potential interest, the role of leaf anatomy in CO2 diffusion and photosynthesis under non-stressed conditions has not been explored in these species. Net CO2 assimilation (An) and its underlying diffu...

    journal_title:Journal of experimental botany

    pub_type: 杂志文章

    doi:10.1093/jxb/erab022

    authors: Nadal M,Perera-Castro AV,Gulías J,Farrant JM,Flexas J

    更新日期:2021-01-23 00:00:00

  • The peripheral xylem of grapevine (Vitis vinifera) berries. 2. Anatomy and development.

    abstract::It has been hypothesized that the substantial reductions in xylemic water flow occurring at veraison are due to physical disruption (breaking) of the xylem as a result of renewed berry growth. In a companion paper, evidence was presented that the vast majority of xylem tracheary elements remained intact despite the gr...

    journal_title:Journal of experimental botany

    pub_type: 杂志文章

    doi:10.1093/jxb/ern061

    authors: Chatelet DS,Rost TL,Matthews MA,Shackel KA

    更新日期:2008-01-01 00:00:00

  • Interaction of bZIP transcription factor TGA6 with salicylic acid signaling modulates artemisinin biosynthesis in Artemisia annua.

    abstract::Artemisinin is a sesquiterpene lactone produced by the Chinese traditional herb Artemisia annua and is used for the treatment of malaria. It is known that salicylic acid (SA) can enhance artemisinin content but the mechanism by which it does so is not known. In this study, we systematically investigated a basic leucin...

    journal_title:Journal of experimental botany

    pub_type: 杂志文章

    doi:10.1093/jxb/erz166

    authors: Lv Z,Guo Z,Zhang L,Zhang F,Jiang W,Shen Q,Fu X,Yan T,Shi P,Hao X,Ma Y,Chen M,Li L,Zhang L,Chen W,Tang K

    更新日期:2019-08-07 00:00:00

  • Is C4 photosynthesis less phenotypically plastic than C3 photosynthesis?

    abstract::C4 photosynthesis is a complex specialization that enhances carbon gain in hot, often arid habitats where photorespiration rates can be high. Certain features unique to C4 photosynthesis may reduce the potential for phenotypic plasticity and photosynthetic acclimation to environmental change relative to what is possib...

    journal_title:Journal of experimental botany

    pub_type: 杂志文章,评审

    doi:10.1093/jxb/erj040

    authors: Sage RF,McKown AD

    更新日期:2006-01-01 00:00:00

  • ZMPP2, a novel type-2C protein phosphatase from maize.

    abstract::A cDNA clone was selected as a candidate for the catalytic subunit of phospho-pyruvate dehydrogenase phosphatase (PDP) by screening a Zea mays expressed sequence tag database with the bovine PDP deduced amino acid sequence. Both strands of the cDNA were completely sequenced. The maize clone contains an open reading fr...

    journal_title:Journal of experimental botany

    pub_type: 杂志文章

    doi:

    authors: Broz AK,Thelen JJ,Muszynski MG,Miernyk JA,Randall DD

    更新日期:2001-08-01 00:00:00

  • Phosphorylation of SPICK2, an AKT2 channel homologue from Samanea motor cells.

    abstract::SPICK2, a homologue of the weakly-inward-rectifying Shaker-like Arabidopsis K channel, AKT2, is a candidate K+-influx channel participating in light- and clock-regulated leaf movements of the legume, Samanea saman. Light and the biological clock regulate the in situ K+-influx channel activity differentially in extenso...

    journal_title:Journal of experimental botany

    pub_type: 杂志文章

    doi:10.1093/jxb/erl104

    authors: Yu L,Becker D,Levi H,Moshelion M,Hedrich R,Lotan I,Moran A,Pick U,Naveh L,Libal Y,Moran N

    更新日期:2006-01-01 00:00:00

  • Effect of activase level and isoform on the thermotolerance of photosynthesis in Arabidopsis.

    abstract::Ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) activation decreases under moderate heat stress. This decrease is caused by an impairment of activase function, which is exacerbated by faster rates of Rubisco deactivation at elevated temperatures. To determine if stromal oxidation causes inhibition of activas...

    journal_title:Journal of experimental botany

    pub_type: 杂志文章

    doi:10.1093/jxb/erl140

    authors: Salvucci ME,DeRidder BP,Portis AR Jr

    更新日期:2006-01-01 00:00:00

  • Boron deficiency inhibits root cell elongation via an ethylene/auxin/ROS-dependent pathway in Arabidopsis seedlings.

    abstract::One of the earliest symptoms of boron (B) deficiency is the inhibition of root elongation which can reasonably be attributed to the damaging effects of B deprivation on cell wall integrity. It is shown here that exposure of wild-type Arabidopsis thaliana seedlings to B deficiency for 4h led to a drastic inhibition of ...

    journal_title:Journal of experimental botany

    pub_type: 杂志文章

    doi:10.1093/jxb/erv186

    authors: Camacho-Cristóbal JJ,Martín-Rejano EM,Herrera-Rodríguez MB,Navarro-Gochicoa MT,Rexach J,González-Fontes A

    更新日期:2015-07-01 00:00:00

  • Jasmonic acid deficiency leads to scattered floret opening time in cytoplasmic male sterile rice Zhenshan 97A.

    abstract::Cytoplasmic male sterile (CMS) rice has been widely used for hybrid rice seed production in China. However, CMS rice suffers from undesirable flowering habits including scattered floret opening time (FOT), which causes different FOTs among parental rice plants and greatly reduces hybrid rice seed production. Little is...

    journal_title:Journal of experimental botany

    pub_type: 杂志文章

    doi:10.1093/jxb/erx251

    authors: Liu L,Zou Z,Qian K,Xia C,He Y,Zeng H,Zhou X,Riemann M,Yin C

    更新日期:2017-07-20 00:00:00

  • The evolution, function, structure, and expression of the plant sHSPs.

    abstract::Small heat shock proteins are a diverse, ancient, and important family of proteins. All organisms possess small heat shock proteins (sHSPs), indicating that these proteins evolved very early in the history of life prior to the divergence of the three domains of life (Archaea, Bacteria, and Eukarya). Comparing the stru...

    journal_title:Journal of experimental botany

    pub_type: 杂志文章,评审

    doi:10.1093/jxb/ers355

    authors: Waters ER

    更新日期:2013-01-01 00:00:00

  • Chilling root temperature causes rapid ultrastructural changes in cortical cells of cucumber (Cucumis sativus L.) root tips.

    abstract::Examination of root tips from cucumber (Cucumis sativus L.) seedlings grown at 8 degrees C for varying periods ranging from 15 min to 96 h, showed marked changes in the ultrastructure of cortical cells within only 15 min of exposure. Greater parts of the cortex were affected with longer periods of exposure, but the se...

    journal_title:Journal of experimental botany

    pub_type: 杂志文章

    doi:10.1093/jxb/erf071

    authors: Lee SH,Singh AP,Chung GC,Kim YS,Kong IB

    更新日期:2002-11-01 00:00:00