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1.  Setting the PAS, the role of circadian PAS domain proteins during environmental adaptation in plants 
The per-ARNT-sim (PAS) domain represents an ancient protein module that can be found across all kingdoms of life. The domain functions as a sensing unit for a diverse array of signals, including molecular oxygen, small metabolites, and light. In plants, several PAS domain-containing proteins form an integral part of the circadian clock and regulate responses to environmental change. Moreover, these proteins function in pathways that control development and plant stress adaptation responses. Here, we discuss the role of PAS domain-containing proteins in anticipation, and adaptation to environmental changes in plants.
PMCID: PMC4496561  PMID: 26217364
PAS domain; circadian clock; signal transduction; environmental stress response; growth adaptation
2.  Promotion of growth by elevated carbon dioxide is coordinated through a flexible transcriptional network in Arabidopsis 
Plant Signaling & Behavior  2013;8(3):e23356.
Although gibberellins (GAs) promote many developmental responses in plants, little is known about how the hormone interacts with environmental signals at the molecular level for regulating plant growth. Recently, we have demonstrated that inhibition of growth by the GA biosynthesis inhibitor paclobutrazol (PAC) at ambient [CO2] (350 µmol CO2 mol-1) is reverted by elevated [CO2] (750 μmol CO2 mol-1). Our finding points to an important role of elevated [CO2] as a signal allowing higher growth rates of low-GA plants. GA promotes plant growth via a complex transcriptional network that integrates multiple signaling pathways. Herein, we discuss how elevated [CO2] stimulates biomass accumulation in a GA-independent manner by regulating the expression of growth-related genes.
PMCID: PMC3676502  PMID: 23333969
elevated carbon dioxide concentration; transcription factor; gibberellin; growth; paclobutrazol
3.  NFXL2 modifies cuticle properties in Arabidopsis 
Plant Signaling & Behavior  2012;7(5):551-555.
Loss of the Arabidopsis NFX1-LIKE2 (NFXL2) gene (At5g05660) results in elevated ABA levels, elevated hydrogen peroxide levels, reduced stomatal aperture, and enhanced drought stress tolerance. Introduction of the NFXL2–78 isoform into the nfxl2–1 mutant is largely sufficient for complementation of the phenotype. We show here that cuticular properties are altered in the nfxl2–1 mutant. The NFXL2–78 protein binds to the SHINE1 (SHN1), SHN2, SHN3, and BODYGUARD1 (BDG1) promoters and mediates weaker expression of these genes. The SHN AP2 domain transcription factors influence cuticle properties. Stronger SHN1, SHN2, and SHN3 expression in the nfxl2–1 mutant may cause altered cuticle properties including reduced stomatal density, and partly explain the enhanced drought stress tolerance. The BDG1 protein also controls cuticle development and is essential for osmotic stress regulation of ABA biosynthesis. Stronger BDG1 expression in nfxl2–1 plants may allow elevated ABA accumulation under drought stress. We conclude that the NFXL2–78 protein is part of a regulatory network that integrates the biosynthesis and action of ABA, ROS, and cuticle components.
PMCID: PMC3419017  PMID: 22516817
cuticle; drought stress; epidermis; NFXL2; SHINE
4.  Translatome and metabolome effects triggered by gibberellins during rosette growth in Arabidopsis 
Journal of Experimental Botany  2012;63(7):2769-2786.
Although gibberellins (GAs) are well known for their growth control function, little is known about their effects on primary metabolism. Here the modulation of gene expression and metabolic adjustment in response to changes in plant (Arabidopsis thaliana) growth imposed on varying the gibberellin regime were evaluated. Polysomal mRNA populations were profiled following treatment of plants with paclobutrazol (PAC), an inhibitor of GA biosynthesis, and gibberellic acid (GA3) to monitor translational regulation of mRNAs globally. Gibberellin levels did not affect levels of carbohydrates in plants treated with PAC and/or GA3. However, the tricarboxylic acid cycle intermediates malate and fumarate, two alternative carbon storage molecules, accumulated upon PAC treatment. Moreover, an increase in nitrate and in the levels of the amino acids was observed in plants grown under a low GA regime. Only minor changes in amino acid levels were detected in plants treated with GA3 alone, or PAC plus GA3. Comparison of the molecular changes at the transcript and metabolite levels demonstrated that a low GA level mainly affects growth by uncoupling growth from carbon availability. These observations, together with the translatome changes, reveal an interaction between energy metabolism and GA-mediated control of growth to coordinate cell wall extension, secondary metabolism, and lipid metabolism.
PMCID: PMC3346235  PMID: 22291129
Gibberellin; growth; paclobutrazol; primary metabolism; translatome
5.  Transcription factor OsHsfC1b regulates salt tolerance and development in Oryza sativa ssp. japonica 
AoB Plants  2012;2012:pls011.
The paper describes the functional analysis of a class C heat shock transcription factor from rice (Oryza sativa). OsHsfC1b is shown to play a role in ABA-mediated salt stress tolerance and is required for plant growth under non-stress conditions.
Background and aims
Salt stress leads to attenuated growth and productivity in rice. Transcription factors like heat shock factors (HSFs) represent central regulators of stress adaptation. Heat shock factors of the classes A and B are well established as regulators of thermal and non-thermal stress responses in plants; however, the role of class C HSFs is unknown. Here we characterized the function of the OsHsfC1b (Os01g53220) transcription factor from rice.
We analysed the expression of OsHsfC1b in the rice japonica cultivars Dongjin and Nipponbare exposed to salt stress as well as after mannitol, abscisic acid (ABA) and H2O2 treatment. For functional characterization of OsHsfC1b, we analysed the physiological response of a T-DNA insertion line (hsfc1b) and two artificial micro-RNA (amiRNA) knock-down lines to salt, mannitol and ABA treatment. In addition, we quantified the expression of small Heat Shock Protein (sHSP) genes and those related to signalling and ion homeostasis by quantitative real-time polymerase chain reaction in roots exposed to salt. The subcellular localization of OsHsfC1b protein fused to green fluorescent protein (GFP) was determined in Arabidopsis mesophyll cell protoplasts.
Principal results
Expression of OsHsfC1b was induced by salt, mannitol and ABA, but not by H2O2. Impaired function of OsHsfC1b in the hsfc1b mutant and the amiRNA lines led to decreased salt and osmotic stress tolerance, increased sensitivity to ABA, and temporal misregulation of salt-responsive genes involved in signalling and ion homeostasis. Furthermore, sHSP genes showed enhanced expression in knock-down plants under salt stress. We observed retarded growth of hsfc1b and knock-down lines in comparison with control plants under non-stress conditions. Transient expression of OsHsfC1b fused to GFP in protoplasts revealed nuclear localization of the transcription factor.
OsHsfC1b plays a role in ABA-mediated salt stress tolerance in rice. Furthermore, OsHsfC1b is involved in the response to osmotic stress and is required for plant growth under non-stress conditions.
PMCID: PMC3357053  PMID: 22616023
6.  Positional Information Resolves Structural Variations and Uncovers an Evolutionarily Divergent Genetic Locus in Accessions of Arabidopsis thaliana 
Genome sequencing of closely related individuals has yielded valuable insights that link genome evolution to phenotypic variations. However, advancement in sequencing technology has also led to an escalation in the number of poor quality–drafted genomes assembled based on reference genomes that can have highly divergent or haplotypic regions. The self-fertilizing nature of Arabidopsis thaliana poses an advantage to sequencing projects because its genome is mostly homozygous. To determine the accuracy of an Arabidopsis drafted genome in less conserved regions, we performed a resequencing experiment on a ∼371-kb genomic interval in the Landsberg erecta (Ler-0) accession. We identified novel structural variations (SVs) between Ler-0 and the reference accession Col-0 using a long-range polymerase chain reaction approach to generate an Illumina data set that has positional information, that is, a data set with reads that map to a known location. Positional information is important for accurate genome assembly and the resolution of SVs particularly in highly duplicated or repetitive regions. Sixty-one regions with misassembly signatures were identified from the Ler-0 draft, suggesting the presence of novel SVs that are not represented in the draft sequence. Sixty of those were resolved by iterative mapping using our data set. Fifteen large indels (>100 bp) identified from this study were found to be located either within protein-coding regions or upstream regulatory regions, suggesting the formation of novel alleles or altered regulation of existing genes in Ler-0. We propose future genome-sequencing experiments to follow a clone-based approach that incorporates positional information to ultimately reveal haplotype-specific differences between accessions.
PMCID: PMC3157834  PMID: 21622917
haplotype; allelic variants; drafted genomes; genome partitioning; comparative genomics
7.  Transcriptional control of ROS homeostasis by KUODA1 regulates cell expansion during leaf development 
Nature Communications  2014;5:3767.
The final size of an organism, or of single organs within an organism, depends on an intricate coordination of cell proliferation and cell expansion. Although organism size is of fundamental importance, the molecular and genetic mechanisms that control it remain far from understood. Here we identify a transcription factor, KUODA1 (KUA1), which specifically controls cell expansion during leaf development in Arabidopsis thaliana. We show that KUA1 expression is circadian regulated and depends on an intact clock. Furthermore, KUA1 directly represses the expression of a set of genes encoding for peroxidases that control reactive oxygen species (ROS) homeostasis in the apoplast. Disruption of KUA1 results in increased peroxidase activity and smaller leaf cells. Chemical or genetic interference with the ROS balance or peroxidase activity affects cell size in a manner consistent with the identified KUA1 function. Thus, KUA1 modulates leaf cell expansion and final organ size by controlling ROS homeostasis.
During plant development, organ size is controlled by cell proliferation and expansion, but the molecular mechanisms involved are unclear. Here, Lu et al. show that leaf cell expansion is controlled by the KUA1 transcription factor that acts in a circadian manner and modulates the expression of genes encoding cell wall-localized peroxidases.
PMCID: PMC4024751  PMID: 24806884

Results 1-7 (7)