Transcript, protein and metabolite temporal dynamics in the CAM plant Agave

No abstract is available for this paper.

• Publication year

  2016

• Venue

  Nature Plants

• Publication date

  2016-11-21

• Fields of study

  Biology, Medicine, Environmental Science

• Identifiers
  DOI 10.1038/nplants.2016.178PMID 27869799
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• A molecular pathway for CO2 response in Arabidopsis guard cells

  2015cited by this paper
• Elevated CO2-Induced Responses in Stomata Require ABA and ABA Signaling

  2015cited by this paper
• Guard cell photosynthesis is critical for stomatal turgor production, yet does not directly mediate CO2 - and ABA-induced stomatal closing.

  2015cited by this paper
• Redox rhythm reinforces the circadian clock to gate immune response

  2015cited by this paper
• Trimmomatic: a flexible trimmer for Illumina sequence data

  2014cited by this paper
• A Diel Flux Balance Model Captures Interactions between Light and Dark Metabolism during Day-Night Cycles in C3 and Crassulacean Acid Metabolism Leaves1[C][W][OPEN]

  2014cited by this paper
• Fold change rank ordering statistics: a new method for detecting differentially expressed genes

  2014cited by this paper
• Facultative crassulacean acid metabolism (CAM) plants: powerful tools for unravelling the functional elements of CAM photosynthesis.

  2014cited by this paper
• Engineering crassulacean acid metabolism to improve water-use efficiency.

  2014cited by this paper
• voom: precision weights unlock linear model analysis tools for RNA-seq read counts

  2014cited by this paper
• Computational analysis of auxin responsive elements in the Arabidopsis thaliana L. genome

  2014cited by this paper
• Synthetic biology as it relates to CAM photosynthesis: challenges and opportunities.

  2014cited by this paper
• Light quality modulates metabolic synchronization over the diel phases of crassulacean acid metabolism

  2014cited by this paper
• PYR/PYL/RCAR Abscisic Acid Receptors Regulate K+ and Cl− Channels through Reactive Oxygen Species-Mediated Activation of Ca2+ Channels at the Plasma Membrane of Intact Arabidopsis Guard Cells1[W][OPEN]

  2013cited by this paper
• PATRIC, the bacterial bioinformatics database and analysis resource

  2013influential reference
• CYCLIN H;1 Regulates Drought Stress Responses and Blue Light-Induced Stomatal Opening by Inhibiting Reactive Oxygen Species Accumulation in Arabidopsis1[C][W][OA]

  2013cited by this paper
• Regulation of Circadian Clocks by Redox Homeostasis*

  2013cited by this paper
• Reconstruction of protein networks from an atlas of maize seed proteotypes

  2013cited by this paper
• Informing the improvement and biodesign of crassulacean acid metabolism via system dynamics modelling.

  2013cited by this paper
• Metabolic control and regulation of the tricarboxylic acid cycle in photosynthetic and heterotrophic plant tissues.

  2012cited by this paper
• CIRCADIAN CLOCK-ASSOCIATED 1 regulates ROS homeostasis and oxidative stress responses

  2012cited by this paper
• Combined inactivation of the Clostridium cellulolyticum lactate and malate dehydrogenase genes substantially increases ethanol yield from cellulose and switchgrass fermentations

  2012cited by this paper
• SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

  2012cited by this paper
• CpGAVAS, an integrated web server for the annotation, visualization, analysis, and GenBank submission of completely sequenced chloroplast genome sequences

  2012cited by this paper
• Defining the boundaries and characterizing the landscape of functional genome expression in vascular tissues of Populus using shotgun proteomics.

  2012cited by this paper
• Putting the Pieces Together: High-performance LC-MS/MS Provides Network-, Pathway-, and Protein-level Perspectives in Populus*

  2012influential reference
• This Provisional PDF corresponds to the article as it appeared upon acceptance. Fully formatted PDF and full text (HTML) versions will be made available soon. Down-regulation of the caffeic acid O-methyltransferase gene in switchgrass reveals a novel monolignol analog

  2012influential reference
• CD-HIT: accelerated for clustering the next-generation sequencing data

  2012influential reference
• FLASH: fast length adjustment of short reads to improve genome assemblies

  2011cited by this paper
• RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

  2011cited by this paper
• Ascorbate and Glutathione: The Heart of the Redox Hub1

  2011cited by this paper
• A Low-Cost Library Construction Protocol and Data Analysis Pipeline for Illumina-Based Strand-Specific Multiplex RNA-Seq

  2011cited by this paper
• Label-free quantitative proteomics for the extremely thermophilic bacterium Caldicellulosiruptor obsidiansis reveal distinct abundance patterns upon growth on cellobiose, crystalline cellulose, and switchgrass.

  2011cited by this paper
• Photosynthesis, Reorganized

  2011cited by this paper
• Molecular Mechanism for Inhibition of a Critical Component in the Arabidopsis thaliana Abscisic Acid Signal Transduction Pathways, SnRK2.6, by Protein Phosphatase ABI1*

  2011cited by this paper
• RNA-Seq analysis in MeV

  2011cited by this paper
• Evolution along the crassulacean acid metabolism continuum

  2010cited by this paper
• Comparison of the water-soluble carbohydrate composition and fructan structures of Agave tequilana plants of different ages.

  2010cited by this paper
• The Arabidopsis vacuolar anion transporter, AtCLCc, is involved in the regulation of stomatal movements and contributes to salt tolerance.

  2010cited by this paper
• The Arabidopsis rcn1-1 Mutation Impairs Dephosphorylation of Phot2, Resulting in Enhanced Blue Light Responses[C][W]

  2010cited by this paper
• Overexpression of SOS (Salt Overly Sensitive) genes increases salt tolerance in transgenic Arabidopsis.

  2009cited by this paper
• ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks

  2009cited by this paper
• Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

  2009cited by this paper
• Exploiting the potential of plants with crassulacean acid metabolism for bioenergy production on marginal lands.

  2009cited by this paper
• IDPicker 2.0: Improved protein assembly with high discrimination peptide identification filtering.

  2009influential reference
• Type 2C protein phosphatases directly regulate abscisic acid-activated protein kinases in Arabidopsis

  2009cited by this paper
• AtGRX4, an Arabidopsis chloroplastic monothiol glutaredoxin, is able to suppress yeast grx5 mutant phenotypes and respond to oxidative stress

  2008influential reference
• Monothiol glutaredoxins: a common domain for multiple functions

  2007cited by this paper
• Quantitative shotgun proteomics using a protease with broad specificity and normalized spectral abundance factors.

  2007influential reference
• The DIURNAL project: DIURNAL and circadian expression profiling, model-based pattern matching, and promoter analysis.

  2007cited by this paper
• MyriMatch: highly accurate tandem mass spectral peptide identification by multivariate hypergeometric analysis.

  2007cited by this paper
• Alteration of Organic Acid Metabolism in Arabidopsis Overexpressing the Maize C4 NADP-Malic Enzyme Causes Accelerated Senescence during Extended Darkness1[W]

  2007cited by this paper
• On the nature of facultative and constitutive CAM: environmental and developmental control of CAM expression during early growth of Clusia, Kalanchöe, and Opuntia.

  2007cited by this paper
• Deficiency of mitochondrial fumarase activity in tomato plants impairs photosynthesis via an effect on stomatal function.

  2007cited by this paper
• Normalization approaches for removing systematic biases associated with mass spectrometry and label-free proteomics.

  2006cited by this paper
• Water-soluble carbohydrates and fructan structure patterns from Agave and Dasylirion species.

  2006cited by this paper
• Arabidopsis HT1 kinase controls stomatal movements in response to CO2

  2006cited by this paper
• Inter-relationships between light and respiration in the control of ascorbic acid synthesis and accumulation in Arabidopsis thaliana leaves.

  2006cited by this paper
• Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences

  2006influential reference
• Journal of Experimental Botany Advance Access published May 19, 2006 Journal of Experimental Botany, Page 1 of 11 Oxygen Metabolism ROS and Redox Signalling in Plants Special Issue

  2006cited by this paper
• Enhanced Photosynthetic Performance and Growth as a Consequence of Decreasing Mitochondrial Malate Dehydrogenase Activity in Transgenic Tomato Plants1

  2005cited by this paper
• Plant blue-light receptors

  2004cited by this paper
• RPT2 Is a Signal Transducer Involved in Phototropic Response and Stomatal Opening by Association with Phototropin 1 in Arabidopsis thaliana

  2004cited by this paper
• OrthoMCL: identification of ortholog groups for eukaryotic genomes.

  2003influential reference
• TM4: a free, open-source system for microarray data management and analysis.

  2003cited by this paper
• Leaf Mitochondria Modulate Whole Cell Redox Homeostasis, Set Antioxidant Capacity, and Determine Stress Resistance through Altered Signaling and Diurnal Regulation Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.009464.

  2003cited by this paper
• Cytoscape: a software environment for integrated models of biomolecular interaction networks.

  2003influential reference
• High light-induced switch from C(3)-photosynthesis to Crassulacean acid metabolism is mediated by UV-A/blue light.

  2002cited by this paper
• Diversity and regulation of plant Ca2+ pumps: insights from expression in yeast.

  2000cited by this paper
• Fumaric acid: an overlooked form of fixed carbon in Arabidopsis and other plant species

  2000cited by this paper
• Ascorbate function and associated transport systems in plants

  2000cited by this paper
• Plastidic metabolite transporters and their physiological functions in the inducible crassulacean acid metabolism plant Mesembryanthemum crystallinum.

  2000cited by this paper
• CAP3: A DNA sequence assembly program.

  1999influential reference
• Modulation of Rubisco Activity during the Diurnal Phases of the Crassulacean Acid Metabolism Plant Kalanchoë daigremontiana.

  1999cited by this paper
• Gas exchange and metabolite fluctuations in green and yellow bands of variegated leaves of the monocotyledonous CAM species Agave americana

  1998cited by this paper
• Phloem Transport of Fructans in the Crassulacean Acid Metabolism Species Agave deserti

  1998cited by this paper
• PHOSPHOENOLPYRUVATE CARBOXYLASE: A Ubiquitous, Highly Regulated Enzyme in Plants.

  1996cited by this paper
• Patterns of Carbon Partitioning in Leaves of Crassulacean Acid Metabolism Species during Deacidification

  1996cited by this paper
• Differential Involvement of the Circadian Clock in the Expression of Genes Required for Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase Synthesis, Assembly, and Activation in Arabidopsis thaliana

  1993cited by this paper
• Basic local alignment search tool.

  1990influential reference
• Regulation of malic-acid metabolism in Crassulacean-acid-metabolism plants in the dark and light: In-vivo evidence from 13C-labeling patterns after 13CO2 fixation

  1988cited by this paper
• Water-relation Parameters of Individual Mesophyll Cells of the Crassulacean Acid Metabolism Plant Kalanchoë daigremontiana.

  1980cited by this paper
• A Simple Sequentially Rejective Multiple Test Procedure

  1979cited by this paper
• BIOINFORMATICS APPLICATIONS NOTE

  year unknowncited by this paper

• Adaptive survival mechanisms of Lithops sp. in arid environments: Morphological and water regulation strategies

  2025cites this paper
• Regulation of Crassulacean acid metabolism at the protein level in Kalanchoë laxiflora

  2025cites this paper
• Unraveling the molecular choreography of C3 to CAM transition in Mesembryanthemum crystallinum using phosphoproteomics.

  2025cites this paper
• Mezcal: A Review of Chemistry, Processing, and Potential Health Benefits

  2025cites this paper
• Species‐Specific Epigenetic Signature Associates With Heat Stress Tolerance in the Perennial Tree Species Populus

  2025influential citation
• Blue light increases stomatal conductance and photosynthesis in Agave hybrid

  2025cites this paper
• Synthetic crassulacean acid metabolism (SynCAM) for improving water-use efficiency in plants.

  2025cites this paper
• The Agave genus in the genomics era: evolution, biodiversity, and sustainable innovation

  2025cites this paper
• Variation in flooding tolerance in Populus deltoides ‘D-124’ and P. trichocarpa × P. deltoides hybrid ‘52-225’

  2025cites this paper
• Leveraging hyperspectral phenotyping for accurate, non-destructive prediction of metabolite profiles in poplar under drought stress

  2025cites this paper
• Potential expansion of plants with crassulacean acid metabolism in the Anthropocene

  2024cites this paper
• Transcriptomic Analysis of the CAM Species Kalanchoë fedtschenkoi Under Low- and High-Temperature Regimes

  2024cites this paper
• Succulence and aquaporin expression during drought and recovery in the CAM epiphytic bromeliad Acanthostachys strobilacea (Schult. & Schult.f.) Klotzsch

  2024cites this paper
• Guard cell K+ channels of Kalanchoë follow the diel cycle of crassulacean acid metabolism

  2024cites this paper
• Metabolic modelling identifies mitochondrial Pi uptake and pyruvate efflux as key aspects of daytime metabolism and proton homeostasis in crassulacean acid metabolism leaves

  2024cites this paper
• Mechanisms Underlying the C3–CAM Photosynthetic Shift in Facultative CAM Plants

  2023cites this paper
• Petiole bending in Detached Leaves of Bryophyllum calycinum: Relevance to Polar Auxin Transport in Petioles

  2023influential citation
• Bringing CAM photosynthesis to the table: Paving the way for resilient and productive agricultural systems in a changing climate

  2023cites this paper
• High-quality Cymbidium mannii genome and multifaceted regulation of crassulacean acid metabolism in epiphytes

  2023influential citation
• Prospects and perspectives: inferring physiological and regulatory targets for CAM from molecular and modelling approaches

  2023influential citation
• Rescuing the Brazilian Agave breeding program: morphophysiological and molecular characterization of a new germplasm

  2023cites this paper
• The de novo transcriptome assembly of Agave angustifolia Haw, mining for carbohydrates and cellulose synthesis genes profiling, and molecular markers development

  2023cites this paper
• Elevated nocturnal respiratory rates in the mitochondria of CAM plants: current knowledge and unanswered questions

  2023cites this paper
• Defining Mechanisms of C3 to CAM Photosynthesis Transition toward Enhancing Crop Stress Resilience

  2023cites this paper
• The effect of exogenous dihydroxyacetone and methylglyoxal on growth, anthocyanin accumulation, and the glyoxalase system in Arabidopsis.

  2023cites this paper
• The Calvin-Benson-Bassham cycle in C4 and Crassulacean acid metabolism species.

  2023cites this paper
• Rethinking the potential productivity of crassulacean acid metabolism by integrating metabolic dynamics with shoot architecture, using the example of Agave tequilana.

  2023cites this paper
• Circadian regulation of metabolism across photosynthetic organisms

  2023cites this paper
• Variable lignin structure revealed in Populus leaves

  2023cites this paper
• Analysis of protein-protein interaction and weighted co-expression networks revealed key modules and genes in multiple organs of Agave sisalana

  2023influential citation
• Transcriptome Sequencing of Agave amaniensis Reveals Shoot-Related Expression Patterns of Expansin A Genes in Agave

  2023cites this paper
• The Agavoideae: an emergent model clade for CAM evolutionary biology.

  2023cites this paper
• Allantoin improves salinity tolerance in Arabidopsis and rice through synergid activation of abscisic acid and brassinosteroid biosynthesis

  2023cites this paper
• Diel dynamics of multi-omics in elkhorn fern provide new insights into weak CAM photosynthesis

  2023influential citation
• Expanding the Biological Role of Lipo-Chitooligosaccharides and Chitooligosaccharides in Laccaria bicolor Growth and Development

  2022cites this paper
• Agave REVEILLE1 regulates the onset and release of seasonal dormancy in Populus

  2022cites this paper
• Recent progression and future perspectives in Cotton genomic breeding.

  2022cites this paper
• A genome for Cissus illustrates features underlying its evolutionary success in dry savannas

  2022cites this paper
• The Biological Hierarchy, Time, and Temporal 'Omics in Evolutionary Biology: A Perspective.

  2022cites this paper
• As right as rain: deciphering drought-related metabolic flexibility in the C4–CAM Portulaca

  2022cites this paper
• Comparative genomics analysis of drought response between obligate CAM and C3 photosynthesis plants.

  2022cites this paper
• Transcriptome Sequencing of Agave angustifolia Reveals Conservation and Diversification in the Expression of Cinnamyl Alcohol Dehydrogenase Genes in Agave Species

  2022cites this paper
• Evolution of Crassulacean acid metabolism in response to the environment: past, present, and future

  2022cites this paper
• Proteomic and metabolic disturbances in lignin-modified Brachypodium distachyon

  2022cites this paper
• Transcriptome Mining Provides Insights into Cell Wall Metabolism and Fiber Lignification in Agave tequilana Weber

  2022cites this paper
• Fungal communities represent the majority of root-specific transcripts in the transcriptomes of Agave plants grown in semiarid regions

  2022cites this paper
• Proximate composition and spatio-temporal heterogeneity of phytochemicals in Agave sisalana Perrine (sisal) adapted in different agro-ecological zones of Punjab, Pakistan

  2022cites this paper
• Carbon fixation

  2022cites this paper
• The Contribution of Metabolomics to Systems Biology: Current Applications Bridging Genotype and Phenotype in Plant Science.

  2021cites this paper
• Differential timing of gene expression and recruitment in independent origins of CAM in the Agavoideae (Asparagaceae)

  2021influential citation
• Plant Morphological and Physiological Responses to Drought Stress

  2021cites this paper
• Transcriptome and Degradome Profiling Reveals a Role of miR530 in the Circadian Regulation of Gene Expression in Kalanchoë marnieriana

  2021cites this paper
• Extreme physiology: Biomass and transcriptional profiling of three abandoned Agave cultivars

  2021cites this paper
• CAM photosynthesis: the acid test

  2021cites this paper
• Proximate Composition and Spatio-temporal Heterogeneity of Phytochemicals in Agave sisalana (sisal) adapted in different agro-ecological zones of Punjab, Pakistan

  2021cites this paper
• Gene co-expression reveals the modularity and integration of C4 and CAM in Portulaca

  2021cites this paper
• Temporal dynamics of protein and post‐translational modification abundances in Populus leaf across a diurnal period

  2021influential citation
• Underwater CAM photosynthesis elucidated by Isoetes genome

  2021cites this paper
• 1H-NMR profile of mezcal and its distillation fractions using two sample preparation methods: direct analysis and solid-phase extraction

  2021cites this paper
• Mode of Action of 1-Naphthylphthalamic Acid in Conspicuous Local Stem Swelling of Succulent Plant, Bryophyllum calycinum: Relevance to the Aspects of Its Histological Observation and Comprehensive Analyses of Plant Hormones

  2021cites this paper
• Overexpression of an Agave Phosphoenolpyruvate Carboxylase Improves Plant Growth and Stress Tolerance

  2021influential citation
• Chapter 10 Climate Change Responses and Adaptations in Crassulacean Acid Metabolism (CAM) Plants

  2021cites this paper
• Transcriptome-based metabolic profiling of flavonoids in Agave lechuguilla waste biomass.

  2021cites this paper
• Evolutionary ecology of Agave: distribution patterns, phylogeny, and coevolution (an homage to Howard S. Gentry).

  2021cites this paper
• ALD1 accumulation in Arabidopsis epidermal plastids confers local and non-autonomous disease resistance

  2021cites this paper
• Improved method for isolation of high-quality total RNA from Agave tequilana Weber roots

  2021cites this paper
• Towards engineering ectomycorrhization into switchgrass bioenergy crops via a lectin receptor‐like kinase

  2021influential citation
• Keep Calm and Carry On: Climate-ready Crops and the Genetic Codification of Climate Myopia

  2020cites this paper
• The role of cis-elements in the evolution of crassulacean acid metabolism photosynthesis

  2020cites this paper
• Agave angustifolia albino plantlets lose stomatal physiology function by changing the development of the stomatal complex due to a molecular disruption

  2020cites this paper
• Model approaches to advance Crassulacean Acid Metabolism system integration.

  2020cites this paper
• Kalanchoë PPC1 Is Essential for Crassulacean Acid Metabolism and the Regulation of Core Circadian Clock and Guard Cell Signaling Genes[CC-BY]

  2020cites this paper
• Physiological Changes in Mesembryanthemum crystallinum During the C3 to CAM Transition Induced by Salt Stress

  2020cites this paper
• Editorial: Systems Biology and Synthetic Biology in Relation to Drought Tolerance or Avoidance in Plants

  2020cites this paper
• Peeling back the layers of Crassulacean acid metabolism: functional differentiation between Kalanchoë fedtschenkoi epidermis and mesophyll proteomes.

  2020influential citation
• CAM guard cell anion channel activity follows transcript abundance and is suppressed by apoplastic malate.

  2020cites this paper
• Transcriptome analysis of three Agave fiber-producing cultivars suitable for biochemicals and biofuels production in semiarid regions

  2020cites this paper
• Hybridization History and Repetitive Element Content in the Genome of a Homoploid Hybrid, Yucca gloriosa (Asparagaceae)

  2020cites this paper
• Exploring C4–CAM plasticity within the Portulaca oleracea complex

  2020cites this paper
• Diurnal dynamics of the Arabidopsis rosette proteome and phosphoproteome

  2020cites this paper
• Developing Portulaca oleracea as a model system for functional genomics analysis of C4/CAM photosynthesis.

  2020cites this paper
• Rapid screening of secondary aromatic metabolites in Populus trichocarpa leaves

  2020cites this paper
• Identification and expression of PAL genes in sisal

  2020influential citation
• Transcriptome Dataset of Leaf Tissue in Agave H11648

  2019cites this paper
• Transcriptomic Analysis of Differentially Expressed Genes and Alternative Splicing Events Associated with Crassulacean Acid Metabolism in Orchids

  2019cites this paper
• An energy restriction‐based weight loss intervention is able to reverse the effects of obesity on the expression of liver tumor‐promoting genes

  2019cites this paper
• CRISPR/Cas9-mediated targeted mutagenesis for functional genomics research of crassulacean acid metabolism plants

  2019cites this paper
• Comparative genomics can provide new insights into the evolutionary mechanisms and gene function in CAM plants

  2019influential citation
• Inference of Gene Regulatory Network Uncovers the Linkage between Circadian Clock and Crassulacean Acid Metabolism in Kalanchoë fedtschenkoi

  2019cites this paper
• Integrative omics of Lonicera japonica Thunb. Flower development unravels molecular changes regulating secondary metabolites

  2019cites this paper
• Identification and Expression of SAUR Genes in the CAM Plant Agave

  2019cites this paper
• Silencing PHOSPHOENOLPYRUVATE CARBOXYLASE1 in the Obligate Crassulacean Acid Metabolism Species Kalanchoë laxiflora causes Reversion to C3-like Metabolism and Amplifies Rhythmicity in a Subset of Core Circadian Clock Genes

  2019cites this paper
• Transcriptomic and proteomic responses to very low CO2 suggest multiple carbon concentrating mechanisms in Nannochloropsis oceanica

  2019cites this paper
• Understanding trait diversity associated with crassulacean acid metabolism (CAM).

  2019cites this paper
• Integration of proteome and transcriptome refines key molecular processes underlying oil production in Nannochloropsis oceanica

  2019cites this paper
• Updates on molecular mechanisms in the development of branched trichome in Arabidopsis and nonbranched in cotton

  2019cites this paper
• Transcript and metabolite changes during the early phase of abscisic acid-mediated induction of crassulacean acid metabolism in Talinum triangulare

  2019cites this paper
• Undervalued potential of crassulacean acid metabolism for current and future agricultural production

  2019influential citation
• Molecular changes in Mesembryanthemum crystallinum guard cells underlying the C3 to CAM transition

  2019cites this paper
• C4/CAM Facultative Photosynthesis as a Means to Improve Plant Sustainable Productivity Under Abiotic-Stressed Conditions

  2019cites this paper