Control of Cognate Sense mRNA Translation by cis-Natural Antisense RNAs.

Abstract:

:Cis-Natural Antisense Transcripts (cis-NATs), which overlap protein coding genes and are transcribed from the opposite DNA strand, constitute an important group of noncoding RNAs. Whereas several examples of cis-NATs regulating the expression of their cognate sense gene are known, most cis-NATs function by altering the steady-state level or structure of mRNA via changes in transcription, mRNA stability, or splicing, and very few cases involve the regulation of sense mRNA translation. This study was designed to systematically search for cis-NATs influencing cognate sense mRNA translation in Arabidopsis (Arabidopsis thaliana). Establishment of a pipeline relying on sequencing of total polyA+ and polysomal RNA from Arabidopsis grown under various conditions (i.e. nutrient deprivation and phytohormone treatments) allowed the identification of 14 cis-NATs whose expression correlated either positively or negatively with cognate sense mRNA translation. With use of a combination of cis-NAT stable over-expression in transgenic plants and transient expression in protoplasts, the impact of cis-NAT expression on mRNA translation was confirmed for 4 out of 5 tested cis-NAT:sense mRNA pairs. These results expand the number of cis-NATs known to regulate cognate sense mRNA translation and provide a foundation for future studies of their mode of action. Moreover, this study highlights the role of this class of noncoding RNAs in translation regulation.

journal_name

Plant Physiol

journal_title

Plant physiology

authors

Deforges J,Reis RS,Jacquet P,Sheppard S,Gadekar VP,Hart-Smith G,Tanzer A,Hofacker IL,Iseli C,Xenarios I,Poirier Y

doi

10.1104/pp.19.00043

subject

Has Abstract

pub_date

2019-05-01 00:00:00

pages

305-322

issue

1

eissn

0032-0889

issn

1532-2548

pii

pp.19.00043

journal_volume

180

pub_type

杂志文章
  • Subcellular localization of the inducible Chlorella HUP1 monosaccharide-H+ symporter and cloning of a Co-induced galactose-H+ symporter.

    abstract::The unicellular green alga Chlorella kessleri can induce monosaccharide-H+ symport catalyzing the energy-dependent transport of D-glucose (D-Glc) and several other pentoses and hexoses across the plasmalemma. The gene coding for the inducible HUP1 monosaccharide-H+ symporter has been cloned and the protein has been ch...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.107.1.33

    authors: Stadler R,Wolf K,Hilgarth C,Tanner W,Sauer N

    更新日期:1995-01-01 00:00:00

  • Effect of volatile methyl jasmonate on the oxylipin pathway in tobacco, cucumber, and arabidopsis.

    abstract::The effect of atmospheric methyl jasmonate on the oxylipin pathway was investigated in leaves of tobacco (Nicotiana tabacum L.), cucumber (Cucumis sativa L.), and Arabidopsis thaliana (L.). Differential sensitivities of test plants to methyl jasmonate were observed. Thus, different concentrations of methyl jasmonate w...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.109.4.1227

    authors: Avdiushko S,Croft KP,Brown GC,Jackson DM,Hamilton-Kemp TR,Hildebrand D

    更新日期:1995-12-01 00:00:00

  • Synergism between RPBF Dof and RISBZ1 bZIP activators in the regulation of rice seed expression genes.

    abstract::The Dof (DNA binding with one finger) transcriptional activator rice (Oryza sativa) prolamin box binding factor (RPBF), which is involved in gene regulation of rice seed storage proteins, has been isolated from rice cDNA expressed sequence tag clones containing the conserved Dof. RPBF is found as a single gene per hap...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.106.082826

    authors: Yamamoto MP,Onodera Y,Touno SM,Takaiwa F

    更新日期:2006-08-01 00:00:00

  • Actin-bundling protein isolated from pollen tubes of lily. Biochemical and immunocytochemical characterization

    abstract::A 135-kD actin-bundling protein was purified from pollen tubes of lily (Lilium longiflorum) using its affinity to F-actin. From a crude extract of the pollen tubes, this protein was coprecipitated with exogenously added F-actin and then dissociated from F-actin by treating it with high-ionic-strength solution. The pro...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.116.4.1421

    authors: Yokota E,Shimmen KiTT

    更新日期:1998-04-01 00:00:00

  • Sucrose phosphate synthase and sucrose accumulation at low temperature.

    abstract::The influence of growth temperature on the free sugar and sucrose phosphate synthase content and activity of spinach (Spinacia oleracea) leaf tissue was studied. When plants were grown at 25 degrees C for 3 weeks and then transferred to a constant 5 degrees C, sucrose, glucose, and fructose accumulated to high levels ...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.100.1.502

    authors: Guy CL,Huber JL,Huber SC

    更新日期:1992-09-01 00:00:00

  • The role of PENNYWISE and POUND-FOOLISH in the maintenance of the shoot apical meristem in Arabidopsis.

    abstract::Growth of the aerial part of the plant is dependent upon the maintenance of the shoot apical meristem (SAM). A balance between the self-renewing stem cells in the central zone (CZ) and organogenesis in the peripheral zone (PZ) is essential for the integrity, function, and maintenance of the SAM. Understanding how the ...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.110.171462

    authors: Ung N,Lal S,Smith HM

    更新日期:2011-06-01 00:00:00

  • A Model of the Regulation of Nitrogenase Electron Allocation in Legume Nodules (I. The Diffusion Barrier and H2 Inhibition of N2 Fixation).

    abstract::A mathematical model is presented to explain the regulation of nitrogenase electron allocation to N2 fixation (EAC) in legume nodules. The model is based on two assumptions: (a) that H2 inhibits N2 fixation in a competitive manner; and (b) that O2, H2, and N2 move into and out of nodules by diffusion and their movemen...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.103.2.421

    authors: Moloney AH,Layzell DB

    更新日期:1993-10-01 00:00:00

  • Photosynthesis and inorganic carbon transport in isolated asparagus mesophyll cells.

    abstract::The possibility of HCO(3) (-) transport into isolated leaf mesophyll cells of Asparagus sprengeri Regel has been investigated. Measurement of the inorganic carbon pool in these cells over an external pH range 6.2 to 8.0, using the silicone-fluid filtration technique, indicated that the pool was larger than predicted b...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.70.3.649

    authors: Espie GS,Colman B

    更新日期:1982-09-01 00:00:00

  • Identification of microRNAs involved in pathogen-associated molecular pattern-triggered plant innate immunity.

    abstract::Pathogen-associated molecular patterns (PAMPs) trigger plant defenses when perceived by surface-localized immune receptors. PAMP-triggered immunity (PTI) plays a vital role in the resistance of plants to numerous potential pathogens. MicroRNA (miRNA) biogenesis is known to be important for PTI, but miRNA species invol...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.109.151803

    authors: Li Y,Zhang Q,Zhang J,Wu L,Qi Y,Zhou JM

    更新日期:2010-04-01 00:00:00

  • Subcellular Distribution of Enzymes of Glycolate Metabolism in the Alga Cyanidium caldarium.

    abstract::The intracellular distribution of enzymes capable of catalyzing the reactions from phosphoglycolate to glycerate in the bluegreen colored eucaryotic alga Cyanidium caldarium has been studied. After separating the organelles from a crude homogenate on a linear flotation gradient, the enzymes glycolate oxidase and gluta...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.90.3.799

    authors: Gross W,Beevers H

    更新日期:1989-07-01 00:00:00

  • Novel roles for the polyphenol oxidase enzyme in secondary metabolism and the regulation of cell death in walnut.

    abstract::The enzyme polyphenol oxidase (PPO) catalyzes the oxidation of phenolic compounds into highly reactive quinones. Polymerization of PPO-derived quinones causes the postharvest browning of cut or bruised fruit, but the native physiological functions of PPOs in undamaged, intact plant cells are not well understood. Walnu...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.113.228593

    authors: Araji S,Grammer TA,Gertzen R,Anderson SD,Mikulic-Petkovsek M,Veberic R,Phu ML,Solar A,Leslie CA,Dandekar AM,Escobar MA

    更新日期:2014-03-01 00:00:00

  • Protein and RNA Synthesizing Activities during Sexual Process of Heterothallic Closterium.

    abstract::Protein and RNA synthesizing activities increased markedly during the mating process and decreased during the maturation stage of zygotes in heterothallic strains of Closterium peracerosum-strigosum-littoale, KAS-4-29 (mating-type minus) and KAS -4-30 (mating-type plus) and a homothallic Closterium acerosum. Different...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.78.4.696

    authors: Kato A,Sasaki K

    更新日期:1985-08-01 00:00:00

  • An Improved Brome mosaic virus Silencing Vector: Greater Insert Stability and More Extensive VIGS.

    abstract::Virus-induced gene silencing (VIGS) is used extensively for gene function studies in plants. VIGS is inexpensive and rapid compared with silencing conducted through stable transformation, but many virus-silencing vectors, especially in grasses, induce only transient silencing phenotypes. A major reason for transient p...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.17.00905

    authors: Ding XS,Mannas SW,Bishop BA,Rao X,Lecoultre M,Kwon S,Nelson RS

    更新日期:2018-01-01 00:00:00

  • Glyphosate-resistant goosegrass. Identification of a mutation in the target enzyme 5-enolpyruvylshikimate-3-phosphate synthase.

    abstract::The spontaneous occurrence of resistance to the herbicide glyphosate in weed species has been an extremely infrequent event, despite over 20 years of extensive use. Recently, a glyphosate-resistant biotype of goosegrass (Eleusine indica) was identified in Malaysia exhibiting an LD(50) value approximately 2- to 4-fold ...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.001560

    authors: Baerson SR,Rodriguez DJ,Tran M,Feng Y,Biest NA,Dill GM

    更新日期:2002-07-01 00:00:00

  • Substitution of redox chemicals for radiation in phytochrome-mediated photomorphogenesis.

    abstract::The reducing agents, potassium ferrocyanide, beta-mercaptoethylamine, cysteine, reduced DPN, ferrous sulfate, methyl viologen and ascorbic acid caused the expansion in darkness of disks of primary leaf tissue cut from dark-grown bean plants. The reducing agents interacted synergistically with low irradiances of red ra...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.41.6.949

    authors: Klein RM,Edsall PC

    更新日期:1966-06-01 00:00:00

  • Isolation of chloroplastic phosphoglycerate kinase : kinetics of the two-enzyme phosphoglycerate kinase/glyceraldehyde-3-phosphate dehydrogenase couple.

    abstract::We report here a method for the isolation of high specific activity phosphoglycerate kinase (EC 2.7.2.3) from chloroplasts. The enzyme has been purified over 200-fold from pea (Pisum sativum L.) stromal extracts to apparent homogeneity with 23% recovery. Negative cooperativity is observed with the two enzyme phosphogl...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.94.1.291

    authors: Macioszek J,Anderson JB,Anderson LE

    更新日期:1990-09-01 00:00:00

  • Replication of cauliflower mosaic virus DNA in leaves and suspension culture protoplasts of cotton.

    abstract::Cauliflower mosaic virus (CaMV) replicated in protoplasts and in inoculated leaves of the non-host, cotton (Gossypium hirsutum, L.). Protoplasts prepared from suspension-cultured cotton cells were infected by incubation with liposome-encapsulated CaMV virions. During a 1-week culture period the amount of CaMV nucleic ...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.83.3.633

    authors: Hussain MM,Melcher U,Whittle T,Williams A,Brannan CM,Mitchell ED

    更新日期:1987-03-01 00:00:00

  • A fast and easy technique for the isolation of aleurone layers.

    abstract::Although the aleurone layer of ceral grain seeds has many advantages for the study of gibberellin action, it has the disadvantage that the hand-isolation of the aleurone layers is time-consuming. To overcome this disadvantage, a commercially available pasta machine was modified and used to remove aleurone layers from ...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.90.2.388

    authors: Murthy PP

    更新日期:1989-06-01 00:00:00

  • Subcellular distribution of gluconeogenetic enzymes in germinating castor bean endosperm.

    abstract::The intracellular distribution of enzymes capable of catalyzing the reactions from oxaloacetate to sucrose in germinating castor bean endosperm has been studied by sucrose density gradient centrifugation. One set of glycolytic enzyme activities was detected in the plastids and another in the cytosol. The percentages o...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.64.1.31

    authors: Nishimura M,Beevers H

    更新日期:1979-07-01 00:00:00

  • Chill-Induced Changes in the Activity and Abundance of the Vacuolar Proton-Pumping Pyrophosphatase from Mung Bean Hypocotyls.

    abstract::Changes in the properties of extractable vacuolar H+-pumping pyrophosphatase (V-PPase) and vacuolar ATPase activities in chilling-sensitive seedlings of mung bean (Vigna radiata) were investigated. Following chilling at 4[deg]C for 48 h, both hydrolytic and proton-pumping activities of the V-PPase increased 1.5- to 2-...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.109.2.659

    authors: Darley CP,Davies JM,Sanders D

    更新日期:1995-10-01 00:00:00

  • The wheat mitogen-activated protein kinases TaMPK3 and TaMPK6 are differentially regulated at multiple levels during compatible disease interactions with Mycosphaerella graminicola.

    abstract::Many race- or isolate-specific disease resistance responses of plants toward pathogens (incompatible interactions) invoke hypersensitive response (HR)-like programmed cell death (PCD) and the coordinated activation of mitogen-activated protein kinases homologous with Arabidopsis (Arabidopsis thaliana) AtMPK6 and AtMPK...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.108.119511

    authors: Rudd JJ,Keon J,Hammond-Kosack KE

    更新日期:2008-06-01 00:00:00

  • Apyrase functions in plant phosphate nutrition and mobilizes phosphate from extracellular ATP.

    abstract::ATP, which is present in the extracellular matrix of multicellular organisms and in the extracellular fluid of unicellular organisms, has been shown to function as a signaling molecule in animals. The concentration of extracellular ATP (xATP) is known to be functionally modulated in part by ectoapyrases, membrane-asso...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.119.2.543

    authors: Thomas C,Sun Y,Naus K,Lloyd A,Roux S

    更新日期:1999-02-01 00:00:00

  • Effect of water stress on the reduction of nitrate and nitrite by soybean nodules.

    abstract::The effects of water stress on nitrate reductase and nitrite reductase activities in symbiotic nodules were examined in field-grown soybean plants (Glycine max L Merr. cv Clark). The in vitro assays of enzyme activity indicated that the nodule cytosol and bacteroids contained both nitrate reductase and nitrite reducta...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.73.4.1065

    authors: Chen CL,Sung JM

    更新日期:1983-12-01 00:00:00

  • Effect of temperature on photosynthesis and growth in marine Synechococcus spp.

    abstract::In this study, we develop a mechanistic understanding of how temperature affects growth and photosynthesis in 10 geographically and physiologically diverse strains of Synechococcus spp. We found that Synechococcus spp. are able to regulate photochemistry over a range of temperatures by using state transitions and alte...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.113.221937

    authors: Mackey KR,Paytan A,Caldeira K,Grossman AR,Moran D,McIlvin M,Saito MA

    更新日期:2013-10-01 00:00:00

  • FLAVODIIRON2 and FLAVODIIRON4 proteins mediate an oxygen-dependent alternative electron flow in Synechocystis sp. PCC 6803 under CO2-limited conditions.

    abstract::This study aims to elucidate the molecular mechanism of an alternative electron flow (AEF) functioning under suppressed (CO2-limited) photosynthesis in the cyanobacterium Synechocystis sp. PCC 6803. Photosynthetic linear electron flow, evaluated as the quantum yield of photosystem II [Y(II)], reaches a maximum shortly...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.114.249987

    authors: Shimakawa G,Shaku K,Nishi A,Hayashi R,Yamamoto H,Sakamoto K,Makino A,Miyake C

    更新日期:2015-02-01 00:00:00

  • Fructosyl Transfer between 1-Kestose and Sucrose in Wheat Leaves.

    abstract::The labeling pattern of the sugar moieties of 1-kestose after in vivo pulse labeling with (14)CO(2) was not the same as that after in vitro labeling with (14)C-sucrose. The two fructosyl residues of 1-kestose had similar specific radioactivities after in vitro synthesis, but after in vivo radiolabeling the specific ra...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.96.1.251

    authors: Kanabus J,Gibeaut DM,Carpita NC,Housley TL

    更新日期:1991-05-01 00:00:00

  • Characterization and subcellular compartmentation of recombinant 4-hydroxyphenylpyruvate dioxygenase from Arabidopsis in transgenic tobacco.

    abstract::4-Hydroxyphenylpyruvate dioxygenase (4HPPD) catalyzes the formation of homogentisate (2,5-dihydroxyphenylacetate) from p-hydroxyphenylpyruvate and molecular oxygen. In plants this enzyme activity is involved in two distinct metabolic processes, the biosynthesis of prenylquinones and the catabolism of tyrosine. We repo...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.119.4.1507

    authors: Garcia I,Rodgers M,Pepin R,Hsieh TF,Matringe M

    更新日期:1999-04-01 00:00:00

  • Tomato Atypical Receptor Kinase1 Is Involved in the Regulation of Preinvasion Defense.

    abstract::Tomato Atypical Receptor Kinase 1 (TARK1) is a pseudokinase required for postinvasion immunity. TARK1 was originally identified as a target of the Xanthomonas euvesicatoria effector protein Xanthomonas outer protein N (XopN), a suppressor of early defense signaling. How TARK1 participates in immune signal transduction...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.19.01400

    authors: Guzman AR,Kim JG,Taylor KW,Lanver D,Mudgett MB

    更新日期:2020-07-01 00:00:00

  • Directed mutation of the Rubisco large subunit of tobacco influences photorespiration and growth.

    abstract::The gene for the large subunit of Rubisco was specifically mutated by transforming the chloroplast genome of tobacco (Nicotiana tabacum). Codon 335 was altered to encode valine instead of leucine. The resulting mutant plants could not grow without atmospheric CO2 enrichment. In 0.3% (v/v) CO2, the mutant and wild-type...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.121.2.579

    authors: Whitney SM,von Caemmerer S,Hudson GS,Andrews TJ

    更新日期:1999-10-01 00:00:00

  • Fructose 2,6-bisphosphate inhibition of phosphoglucomutase.

    abstract::Fructose 2,6-bisphosphate inhibits phosphoglucomutase noncompetitively with respect to the cofactor glucose 1,6-bisphosphate. Previous studies from our laboratory had shown that phosphoglucomutase was activated by fructose 2,6-bisphosphate in the absence of added glucose 1,6-bisphosphate. The fructose 2,6-bisphosphate...

    journal_title:Plant physiology

    pub_type: 杂志文章

    doi:10.1104/pp.88.4.980

    authors: Galloway CM,Dugger WM,Black CC

    更新日期:1988-12-01 00:00:00