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Molecular Research in Arabidopsis

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: closed (31 December 2018) | Viewed by 34222

Special Issue Editor

Department of Life Science, Sogang University, Seoul 04107, Republic of Korea
Interests: plant abiotic stress tolerance; plant development; RNA processing and regulation
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Since Friedrich Laibach first described its potential as a model system in 1943 in Botanisches Archiv, Arabidopsis thaliana emerged as a popular plant model system. Arabidopsis is an ideal plant model system, as it has key characteristics such as a short life cycle and a small genome size. Additionally, it is small and easy to grow, easy to transform, and produces a high seed number.

The introduction of Arabidopsis as a plant model system led to the generation of a massive mutant collection which assisted in gene discovery. It also was the first plant genome sequenced and assembled, which was later complemented by vast genomic and epigenomic resources that enabled further gene discovery and additional molecular biology resources that are available to the scientific community at almost no cost. The study of induced mutants on phenotypes was later accompanied by a collection of more than 1000 natural accessions (or ecotypes) that were geographically distributed around the world, making it possible to study existing natural phenotypic variations.

Although Arabidopsis is not a crop, it is undeniable that studies using Arabidopsis have led to numerous pioneering discoveries in plant biology, which were/will be implemented for crop improvements. In addition, the tools and systems developed for Arabidopsis research are often utilized in the field of crop biology.

This year is the 75th year since Laibach’s paper in 1943 and the 53rd year since the first international Arabidopsis conference in 1965. Perhaps it is a time to re-emphasize the importance of Arabidopsis to the understanding of plant biology. This Special Issue “Molecular Research in Arabidopsis” will welcome research articles and reviews with novel and high-quality molecular biology of Arabidopsis. The topics to be considered include, but are not limited to:

  1. Arabidopsis physiology and development
  2. Genetics, genomics, and other “omics” of Arabidopsis
  3. Biochemistry and metabolism in Arabidopsis
  4. Interaction with environments and microbes
  5. Transcriptional, post-transcriptional, and epigenetic gene regulation
  6. Natural variation in Arabidopsis

I hope that the articles in this special issue will contribute to a better understanding of plant biology in general.

Dr. Byeong-ha Lee
Guest Editor

Manuscript Submission Information

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Keywords

  • Arabidopsis
  • Plant hormones
  • Physiology and Development
  • Genetics and Genomics
  • Biochemistry and Metabolism
  • Transcriptional and post-transcritional gene regulation
  • Epigenetics
  • Natural variation

Published Papers (7 papers)

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Research

15 pages, 2649 KiB  
Article
The Effect of AtHKT1;1 or AtSOS1 Mutation on the Expressions of Na+ or K+ Transporter Genes and Ion Homeostasis in Arabidopsis thaliana under Salt Stress
by Qian Wang, Chao Guan, Pei Wang, Qing Ma, Ai-Ke Bao, Jin-Lin Zhang and Suo-Min Wang
Int. J. Mol. Sci. 2019, 20(5), 1085; https://doi.org/10.3390/ijms20051085 - 02 Mar 2019
Cited by 32 | Viewed by 4240
Abstract
HKT1 and SOS1 are two key Na+ transporters that modulate salt tolerance in plants. Although much is known about the respective functions of HKT1 and SOS1 under salt conditions, few studies have examined the effects of HKT1 and SOS1 mutations on the [...] Read more.
HKT1 and SOS1 are two key Na+ transporters that modulate salt tolerance in plants. Although much is known about the respective functions of HKT1 and SOS1 under salt conditions, few studies have examined the effects of HKT1 and SOS1 mutations on the expression of other important Na+ and K+ transporter genes. This study investigated the physiological parameters and expression profiles of AtHKT1;1, AtSOS1, AtHAK5, AtAKT1, AtSKOR, AtNHX1, and AtAVP1 in wild-type (WT) and athkt1;1 and atsos1 mutants of Arabidopsis thaliana under 25 mM NaCl. We found that AtSOS1 mutation induced a significant decrease in transcripts of AtHKT1;1 (by 56–62% at 6–24 h), AtSKOR (by 36–78% at 6–24 h), and AtAKT1 (by 31–53% at 6–24 h) in the roots compared with WT. This led to an increase in Na+ accumulation in the roots, a decrease in K+ uptake and transportation, and finally resulted in suppression of plant growth. AtHKT1;1 loss induced a 39–76% (6–24 h) decrease and a 27–32% (6–24 h) increase in transcripts of AtSKOR and AtHAK5, respectively, in the roots compared with WT. At the same time, 25 mM NaCl decreased the net selective transport capacity for K+ over Na+ by 92% in the athkt1;1 roots compared with the WT roots. Consequently, Na+ was loaded into the xylem and delivered to the shoots, whereas K+ transport was restricted. The results indicate that AtHKT1;1 and AtSOS1 not only mediate Na+ transport but also control ion uptake and the spatial distribution of Na+ and K+ by cooperatively regulating the expression levels of relevant Na+ and K+ transporter genes, ultimately regulating plant growth under salt stress. Full article
(This article belongs to the Special Issue Molecular Research in Arabidopsis)
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15 pages, 2118 KiB  
Article
PACLOBUTRAZOL-RESISTANCE Gene Family Regulates Floral Organ Growth with Unequal Genetic Redundancy in Arabidopsis thaliana
by Kihye Shin, Inhye Lee, Eunsun Kim, Soon Ki Park, Moon-Soo Soh and Sumin Lee
Int. J. Mol. Sci. 2019, 20(4), 869; https://doi.org/10.3390/ijms20040869 - 17 Feb 2019
Cited by 12 | Viewed by 4101
Abstract
A PACLOBUTRAZOL-RESISTANCE (PRE) gene family, consisting of six genes in Arabidopsis thaliana, encodes a group of helix-loop-helix proteins that act in the growth-promoting transcriptional network. To delineate the specific role of each of the PRE genes in organ growth, we [...] Read more.
A PACLOBUTRAZOL-RESISTANCE (PRE) gene family, consisting of six genes in Arabidopsis thaliana, encodes a group of helix-loop-helix proteins that act in the growth-promoting transcriptional network. To delineate the specific role of each of the PRE genes in organ growth, we took a reverse genetic approach by constructing high order pre loss-of-function mutants of Arabidopsis thaliana. In addition to dwarf vegetative growth, some double or high order pre mutants exhibited defective floral development, resulting in reduced fertility. While pre2pre5 is normally fertile, both pre2pre6 and pre5pre6 showed reduced fertility. Further, the reduced fertility was exacerbated in the pre2pre5pre6 mutant, indicative of the redundant and critical roles of these PREs. Self-pollination assay and scanning electron microscopy analysis showed that the sterility of pre2pre5pre6 was mainly ascribed to the reduced cell elongation of anther filament, limiting access of pollens to stigma. We found that the expression of a subset of flower-development related genes including ARGOS, IAA19, ACS8, and MYB24 was downregulated in the pre2pre5pre6 flowers. Given these results, we propose that PREs, with unequal functional redundancy, take part in the coordinated growth of floral organs, contributing to successful autogamous reproduction in Arabidopsis thaliana. Full article
(This article belongs to the Special Issue Molecular Research in Arabidopsis)
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15 pages, 3188 KiB  
Article
Expression Pattern and Function Analysis of AtPPRT1, a Novel Negative Regulator in ABA and Drought Stress Responses in Arabidopsis
by Linsen Pei, Lu Peng, Xia Wan, Jie Xiong, Zhibin Liu, Xufeng Li, Yi Yang and Jianmei Wang
Int. J. Mol. Sci. 2019, 20(2), 394; https://doi.org/10.3390/ijms20020394 - 17 Jan 2019
Cited by 14 | Viewed by 4843
Abstract
Abscisic acid (ABA) plays a fundamental role in plant growth and development, as well as in the responses to abiotic stresses. Previous studies have revealed that many components in ABA and drought stress signaling pathways are ubiquitinated by E3 ligases. In this study, [...] Read more.
Abscisic acid (ABA) plays a fundamental role in plant growth and development, as well as in the responses to abiotic stresses. Previous studies have revealed that many components in ABA and drought stress signaling pathways are ubiquitinated by E3 ligases. In this study, AtPPRT1, a putative C3HC4 zinc-finger ubiquitin E3 ligase, was explored for its role in abiotic stress response in Arabidopsis thaliana. The expression of AtPPRT1 was induced by ABA. In addition, the β-glucuronidase (GUS) gene driven by the AtPPRT1 promoter was more active in the root hair zone and root tips of primary and major lateral roots of young seedlings in the presence of ABA. The assays for seed germination, stomatal aperture, root length, and water deficit demonstrated that the AtPPRT1-overexpressing Arabidopsis was insensitive to ABA and sensitive to drought stress compared with wild-type (WT) plants. The analysis by quantitative real-time PCR (qRT-PCR) revealed that the expression of three stress-inducible genes (AtRAB18, AtERD10, and AtKIN1) were upregulated in the atpprt1 mutant and downregulated in AtPPRT1-overexpressing plants, while two ABA hydrolysis genes (AtCYP707A1 and AtCYP707A3) were downregulated in the atpprt1 mutant and upregulated in AtPPRT1-overexpressing plants in the presence of ABA. AtPPRT1 was localized in the mitochondria. Our findings indicate that AtPPRT1 plays a negative role in ABA and drought stress responses. Full article
(This article belongs to the Special Issue Molecular Research in Arabidopsis)
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13 pages, 4892 KiB  
Article
Overexpression of the Jojoba Aquaporin Gene, ScPIP1, Enhances Drought and Salt Tolerance in Transgenic Arabidopsis
by Xing Wang, Fei Gao, Jie Bing, Weimin Sun, Xiuxiu Feng, Xiaofeng Ma, Yijun Zhou and Genfa Zhang
Int. J. Mol. Sci. 2019, 20(1), 153; https://doi.org/10.3390/ijms20010153 - 03 Jan 2019
Cited by 51 | Viewed by 5138
Abstract
Plasma membrane intrinsic proteins (PIPs) are a subfamily of aquaporin proteins located on plasma membranes where they facilitate the transport of water and small uncharged solutes. PIPs play an important role throughout plant development, and in response to abiotic stresses. Jojoba (Simmondsia [...] Read more.
Plasma membrane intrinsic proteins (PIPs) are a subfamily of aquaporin proteins located on plasma membranes where they facilitate the transport of water and small uncharged solutes. PIPs play an important role throughout plant development, and in response to abiotic stresses. Jojoba (Simmondsia chinensis (Link) Schneider), as a typical desert plant, tolerates drought, salinity and nutrient-poor soils. In this study, a PIP1 gene (ScPIP1) was cloned from jojoba and overexpressed in Arabidopsis thaliana. The expression of ScPIP1 at the transcriptional level was induced by polyethylene glycol (PEG) treatment. ScPIP1 overexpressed Arabidopsis plants exhibited higher germination rates, longer roots and higher survival rates compared to the wild-type plants under drought and salt stresses. The results of malonaldehyde (MDA), ion leakage (IL) and proline content measurements indicated that the improved drought and salt tolerance conferred by ScPIP1 was correlated with decreased membrane damage and improved osmotic adjustment. We assume that ScPIP1 may be applied to genetic engineering to improve plant tolerance based on the resistance effect in transgenic Arabidopsis overexpressing ScPIP1. Full article
(This article belongs to the Special Issue Molecular Research in Arabidopsis)
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18 pages, 13285 KiB  
Article
TCO, a Putative Transcriptional Regulator in Arabidopsis, Is a Target of the Protein Kinase CK2
by Laina M. Weinman, Katherine L. D. Running, Nicholas S. Carey, Erica J. Stevenson, Danielle L. Swaney, Brenda Y. Chow, Nevan J. Krogan and Naden T. Krogan
Int. J. Mol. Sci. 2019, 20(1), 99; https://doi.org/10.3390/ijms20010099 - 28 Dec 2018
Viewed by 4905
Abstract
As multicellular organisms grow, spatial and temporal patterns of gene expression are strictly regulated to ensure that developmental programs are invoked at appropriate stages. In this work, we describe a putative transcriptional regulator in Arabidopsis, TACO LEAF (TCO), whose overexpression results in [...] Read more.
As multicellular organisms grow, spatial and temporal patterns of gene expression are strictly regulated to ensure that developmental programs are invoked at appropriate stages. In this work, we describe a putative transcriptional regulator in Arabidopsis, TACO LEAF (TCO), whose overexpression results in the ectopic activation of reproductive genes during vegetative growth. Isolated as an activation-tagged allele, tco-1D displays gene misexpression and phenotypic abnormalities, such as curled leaves and early flowering, characteristic of chromatin regulatory mutants. A role for TCO in this mode of transcriptional regulation is further supported by the subnuclear accumulation patterns of TCO protein and genetic interactions between tco-1D and chromatin modifier mutants. The endogenous expression pattern of TCO and gene misregulation in tco loss-of-function mutants indicate that this factor is involved in seed development. We also demonstrate that specific serine residues of TCO protein are targeted by the ubiquitous kinase CK2. Collectively, these results identify TCO as a novel regulator of gene expression whose activity is likely influenced by phosphorylation, as is the case with many chromatin regulators. Full article
(This article belongs to the Special Issue Molecular Research in Arabidopsis)
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16 pages, 3563 KiB  
Article
The Maize WRKY Transcription Factor ZmWRKY40 Confers Drought Resistance in Transgenic Arabidopsis
by Chang-Tao Wang, Jing-Na Ru, Yong-Wei Liu, Jun-Feng Yang, Meng Li, Zhao-Shi Xu and Jin-Dong Fu
Int. J. Mol. Sci. 2018, 19(9), 2580; https://doi.org/10.3390/ijms19092580 - 30 Aug 2018
Cited by 84 | Viewed by 6642
Abstract
Abiotic stresses restrict the growth and yield of crops. Plants have developed a number of regulatory mechanisms to respond to these stresses. WRKY transcription factors (TFs) are plant-specific transcription factors that play essential roles in multiple plant processes, including abiotic stress response. At [...] Read more.
Abiotic stresses restrict the growth and yield of crops. Plants have developed a number of regulatory mechanisms to respond to these stresses. WRKY transcription factors (TFs) are plant-specific transcription factors that play essential roles in multiple plant processes, including abiotic stress response. At present, little information regarding drought-related WRKY genes in maize is available. In this study, we identified a WRKY transcription factor gene from maize, named ZmWRKY40. ZmWRKY40 is a member of WRKY group II, localized in the nucleus of mesophyll protoplasts. Several stress-related transcriptional regulatory elements existed in the promoter region of ZmWRKY40. ZmWRKY40 was induced by drought, high salinity, high temperature, and abscisic acid (ABA). ZmWRKY40 could rapidly respond to drought with peak levels (more than 10-fold) at 1 h after treatment. Overexpression of ZmWRKY40 improved drought tolerance in transgenic Arabidopsis by regulating stress-related genes, and the reactive oxygen species (ROS) content in transgenic lines was reduced by enhancing the activities of peroxide dismutase (POD) and catalase (CAT) under drought stress. According to the results, the present study may provide a candidate gene involved in the drought stress response and a theoretical basis to understand the mechanisms of ZmWRKY40 in response to abiotic stresses in maize. Full article
(This article belongs to the Special Issue Molecular Research in Arabidopsis)
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22 pages, 3623 KiB  
Article
Comparative Proteomic Analysis of Coregulation of CIPK14 and WHIRLY1/3 Mediated Pale Yellowing of Leaves in Arabidopsis
by Zhe Guan, Wanzhen Wang, Xingle Yu, Wenfang Lin and Ying Miao
Int. J. Mol. Sci. 2018, 19(8), 2231; https://doi.org/10.3390/ijms19082231 - 31 Jul 2018
Cited by 14 | Viewed by 3390
Abstract
Pale yellowing of leaf variegation is observed in the mutant Arabidopsis lines Calcineurin B-Like-Interacting Protein Kinase14 (CIPK14) overexpression (oeCIPK14) and double-knockout WHIRLY1/WHIRLY3 (why1/3). Further, the relative distribution of WHIRLY1 (WHY1) protein between plastids and the nucleus is affected by [...] Read more.
Pale yellowing of leaf variegation is observed in the mutant Arabidopsis lines Calcineurin B-Like-Interacting Protein Kinase14 (CIPK14) overexpression (oeCIPK14) and double-knockout WHIRLY1/WHIRLY3 (why1/3). Further, the relative distribution of WHIRLY1 (WHY1) protein between plastids and the nucleus is affected by the phosphorylation of WHY1 by CIPK14. To elucidate the coregulation of CIPK14 and WHIRLY1/WHIRLY3-mediated pale yellowing of leaves, a differential proteomic analysis was conducted between the oeCIPK14 variegated (oeCIPK14-var) line, why1/3 variegated (why1/3-var) line, and wild type (WT). More than 800 protein spots were resolved on each gel, and 67 differentially abundant proteins (DAPs) were identified by matrix-assisted laser desorption ionization-time of flight/time of flight mass spectrometry (MALDI-TOF/TOF-MS). Of these 67 proteins, 34 DAPs were in the oeCIPK14-var line and 33 DAPs were in the why1/3-var line compared to the WT. Five overlapping proteins were differentially expressed in both the oeCIPK14-var and why1/3-var lines: ATP-dependent Clp protease proteolytic subunit-related protein 3 (ClpR3), Ribulose bisphosphate carboxylase large chain (RBCL), Beta-amylase 3 (BAM3), Ribosome-recycling factor (RRF), and Ribulose bisphosphate carboxylase small chain (RBCS). Bioinformatics analysis showed that most of the DAPs are involved in photosynthesis, defense and antioxidation pathways, protein metabolism, amino acid metabolism, energy metabolism, malate biosynthesis, lipid metabolism, and transcription. Thus, in the why1/3-var and oeCIPK14-var lines, there was a decrease in the photosystem parameters, including the content of chlorophyll, the photochemical efficiency of photosystem (PS II) (Fv/Fm), and electron transport rates (ETRs), but there was an increase in non-photochemical quenching (NPQ). Both mutants showed high sensitivity to intense light. Based on the annotation of the DAPs from both why1/3-var and oeCIPK14-var lines, we conclude that the CIPK14 phosphorylation-mediated WHY1 deficiency in plastids is related to the impairment of protein metabolism, leading to chloroplast dysfunction. Full article
(This article belongs to the Special Issue Molecular Research in Arabidopsis)
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