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Molecular Research in Arabidopsis thaliana

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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 (27 May 2022) | Viewed by 19787

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Special Issue Editors

Dr. Elke Barbez

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Guest Editor

1. Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
2. CIBSS- Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
Interests: Arabidopsis; auxin

Dr. Sascha Waidmann

E-Mail Website
Guest Editor

Faculty of Biology, Chair of Molecular Plant Physiology, University of Freiburg, 79104 Freiburg, Germany
Interests: molecular biology; cell biology; root architecture; auxin; cytokinin; plant development and genetics

Special Issue Information

Dear Colleagues,

Along the roadside, on meadows, parking lots, and railway embarkments, thale cress, also known as mouse-ear cress or Arabidopsis thaliana, is usually left unnoticed in our busy daily lives. This short-living annual plant with tiny white flowers is often considered a weed lacking any economic value. However, as quoted by the English author Alan Alexandre Milne: “Weeds are flowers too, once you get to know them”. This is also what Erna Reinholz must have thought when she published the first collection of A. thaliana mutants generated via X-ray mutagenesis in 1945. Over the following decades, A. thaliana became an indispensable model organism for molecular plant biology. Its small genome size, short lifecycle, and non-demanding growth conditions make this small plant easy to investigate. Decades of intensive research gave rise to high numbers of A. thaliana mutant lines, collections of natural variations, as well as molecular tools. Therefore, this small weed from the parking lot still remains popular today, due to its enormous value for molecular plant biology.

This Special Issue on “Molecular Research in Arabidopsis thaliana” welcomes high-quality research articles and reviews unveiling exciting and novel molecular insights into plant growth and development, with Arabidopsis thaliana in the main role.

Articles in this Special Issue will serve as highly relevant building blocks for the overall molecular knowledge in plant biology and beyond.

Dr. Elke Barbez
Dr. Sascha Waidmann
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

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Keywords

Arabidopsis growth and development
environmental adaptation
signaling processes
natural variation
hormone biology

Published Papers (7 papers)

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Research

18 pages, 2270 KiB

Open AccessArticle

The Hydrophilic Loop of Arabidopsis PIN1 Auxin Efflux Carrier Harbors Hallmarks of an Intrinsically Disordered Protein

by Veronika Bilanovičová, Nikola Rýdza, Lilla Koczka, Martin Hess, Elena Feraru, Jiří Friml and Tomasz Nodzyński

Int. J. Mol. Sci. 2022, 23(11), 6352; https://doi.org/10.3390/ijms23116352 - 6 Jun 2022

Cited by 3 | Viewed by 2972

Abstract

Much of plant development depends on cell-to-cell redistribution of the plant hormone auxin, which is facilitated by the plasma membrane (PM) localized PIN FORMED (PIN) proteins. Auxin export activity, developmental roles, subcellular trafficking, and polarity of PINs have been well studied, but their structure remains elusive besides a rough outline that they contain two groups of 5 alpha-helices connected by a large hydrophilic loop (HL). Here, we focus on the PIN1 HL as we could produce it in sufficient quantities for biochemical investigations to provide insights into its secondary structure. Circular dichroism (CD) studies revealed its nature as an intrinsically disordered protein (IDP), manifested by the increase of structure content upon thermal melting. Consistent with IDPs serving as interaction platforms, PIN1 loops homodimerize. PIN1 HL cytoplasmic overexpression in Arabidopsis disrupts early endocytic trafficking of PIN1 and PIN2 and causes defects in the cotyledon vasculature formation. In summary, we demonstrate that PIN1 HL has an intrinsically disordered nature, which must be considered to gain further structural insights. Some secondary structures may form transiently during pairing with known and yet-to-be-discovered interactors. Full article

(This article belongs to the Special Issue Molecular Research in Arabidopsis thaliana)

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19 pages, 11420 KiB

Open AccessArticle

The Xyloglucan Endotransglucosylase/Hydrolase Gene XTH22/TCH4 Regulates Plant Growth by Disrupting the Cell Wall Homeostasis in Arabidopsis under Boron Deficiency

by Cheng Zhang, Mingliang He, Zhexuan Jiang, Lan Liu, Junbao Pu, Wenjun Zhang, Sheliang Wang and Fangsen Xu

Int. J. Mol. Sci. 2022, 23(3), 1250; https://doi.org/10.3390/ijms23031250 - 23 Jan 2022

Cited by 20 | Viewed by 3387

Abstract

TCH4 is a xyloglucan endotransglucosylase/hydrolase (XTH) family member. Extensive studies have shown that XTHs are very important in cell wall homeostasis for plant growth and development. Boron (B), as an essential micronutrient for plants, plays an essential role in the cross-linking of cell wall pectin. However, the effect of B on cell wall organization is unclear. This study aimed to explore the mechanism of plant adaption to B stress by investigating the role of TCH4 in cell wall homeostasis. We conducted both plate and hydroponic cultures of wild-type Col-0 and overexpression and gene knockout lines of XTH22/TCH4 to analyze the phenotype, components, and characteristics of the cell wall using immunofluorescence, atomic force microscopy (AFM), and transmission electron microscopy (TEM). B deficiency induces the expression of TCH4. The overexpression lines of TCH4 presented more sensitivity to B deficiency than the wild-type Col-0, while the knockout lines of TCH4 were more resistant to low B stress. Up-regulation of TCH4 influenced the ratio of chelator-soluble pectin to alkali-soluble pectin and decreased the degree of methylesterification of pectin under B-deficient conditions. Moreover, we found that B deficiency disturbed the arrangement of cellulose, enlarged the gap between cellulose microfibrils, and decreased the mechanical strength of the cell wall, leading to the formation of a thickened and deformed triangular region of the cell wall. These symptoms were more profound in the TCH4 overexpression lines. Consistently, compared with Col-0, the O₂⁻ and MDA contents in the TCH4 overexpression lines increased under B-deficient conditions. This study identified the B-deficiency-induced TCH4 gene, which regulates cell wall homeostasis to influence plant growth under B-deficient conditions. Full article

(This article belongs to the Special Issue Molecular Research in Arabidopsis thaliana)

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15 pages, 12908 KiB

Open AccessArticle

FLS2–RBOHD–PIF4 Module Regulates Plant Response to Drought and Salt Stress

by Zhixin Liu, Chenxi Guo, Rui Wu, Yunhe Hu, Yaping Zhou, Jiajing Wang, Xiaole Yu, Yixin Zhang, George Bawa and Xuwu Sun

Int. J. Mol. Sci. 2022, 23(3), 1080; https://doi.org/10.3390/ijms23031080 - 19 Jan 2022

Cited by 12 | Viewed by 2978

Abstract

As sessile organisms, plants are constantly challenged by several environmental stresses. Different kinds of stress often occur simultaneously, leading to the accumulation of reactive oxygen species (ROS) produced by respiratory burst oxidase homolog (RBOHD) and calcium fluctuation in cells. Extensive studies have revealed that flagellin sensitive 2 (FLS2) can sense the infection by pathogenic microorganisms and activate cellular immune response by regulating intracellular ROS and calcium signals, which can also be activated during plant response to abiotic stress. However, little is known about the roles of FLS2 and RBOHD in regulating abiotic stress. In this study, we found that although the fls2 mutant showed tolerance, the double mutant rbohd rbohf displayed hypersensitivity to abiotic stress, similar to its performance in response to immune stress. An analysis of the transcriptome of the fls2 mutant and rbohd rbohf double mutant revealed that phytochrome interacting factor 4 (PIF4) acted downstream of FLS2 and RBOHD to respond to the abiotic stress. Further analysis showed that both FLS2 and RBOHD regulated the response of plants to drought and salt stress by regulating the expression of PIF4. These findings revealed an FLS2–RBOHD–PIF4 module in regulating plant response to biotic and abiotic stresses. Full article

(This article belongs to the Special Issue Molecular Research in Arabidopsis thaliana)

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16 pages, 5178 KiB

Open AccessArticle

Mitogen-Activated Protein Kinase 4-Regulated Metabolic Networks

by Chuwei Lin, Aneirin Alan Lott, Wei Zhu, Craig P. Dufresne and Sixue Chen

Int. J. Mol. Sci. 2022, 23(2), 880; https://doi.org/10.3390/ijms23020880 - 14 Jan 2022

Cited by 5 | Viewed by 2470

Abstract

Mitogen-activated protein kinase 4 (MPK4) was first identified as a negative regulator of systemic acquired resistance. It is also an important kinase involved in many other biological processes in plants, including cytokinesis, reproduction, and photosynthesis. Arabidopsis thaliana mpk4 mutant is dwarf and sterile. Previous omics studies including genomics, transcriptomics, and proteomics have revealed new functions of MPK4 in different biological processes. However, due to challenges in metabolomics, no study has touched upon the metabolomic profiles of the mpk4 mutant. What metabolites and metabolic pathways are potentially regulated by MPK4 are not known. Metabolites are crucial components of plants, and they play important roles in plant growth and development, signaling, and defense. Here we used targeted and untargeted metabolomics to profile metabolites in the wild type and the mpk4 mutant. We found that in addition to the jasmonic acid and salicylic acid pathways, MPK4 is involved in polyamine synthesis and photosynthesis. In addition, we also conducted label-free proteomics of the two genotypes. The integration of metabolomics and proteomics data allows for an insight into the metabolomic networks that are potentially regulated by MPK4. Full article

(This article belongs to the Special Issue Molecular Research in Arabidopsis thaliana)

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19 pages, 42705 KiB

Open AccessArticle

COE2 Is Required for the Root Foraging Response to Nitrogen Limitation

by Rui Wu, Zhixin Liu, Jiajing Wang, Chenxi Guo, Yaping Zhou, George Bawa, Jean-David Rochaix and Xuwu Sun

Int. J. Mol. Sci. 2022, 23(2), 861; https://doi.org/10.3390/ijms23020861 - 13 Jan 2022

Cited by 6 | Viewed by 1608

Abstract

There are numerous exchanges of signals and materials between leaves and roots, including nitrogen, which is one of the essential nutrients for plant growth and development. In this study we identified and characterized the Chlorophyll A/B-Binding Protein (CAB) (named coe2 for CAB overexpression 2) mutant, which is defective in the development of chloroplasts and roots under normal growth conditions. The phenotype of coe2 is caused by a mutation in the Nitric Oxide Associated (NOA1) gene that is implicated in a wide range of chloroplast functions including the regulation of metabolism and signaling of nitric oxide (NO). A transcriptome analysis reveals that expression of genes involved in metabolism and lateral root development are strongly altered in coe2 seedlings compared with WT. COE2 is expressed in hypocotyls, roots, root hairs, and root caps. Both the accumulation of NO and the growth of lateral roots are enhanced in WT but not in coe2 under nitrogen limitation. These new findings suggest that COE2-dependent signaling not only coordinates gene expression but also promotes chloroplast development and function by modulating root development and absorption of nitrogen compounds. Full article

(This article belongs to the Special Issue Molecular Research in Arabidopsis thaliana)

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22 pages, 4373 KiB

Open AccessArticle

Frequency and Spectrum of Mutations Induced by Gamma Rays Revealed by Phenotype Screening and Whole-Genome Re-Sequencing in Arabidopsis thaliana

by Yan Du, Zhuo Feng, Jie Wang, Wenjie Jin, Zhuanzi Wang, Tao Guo, Yuze Chen, Hui Feng, Lixia Yu, Wenjian Li and Libin Zhou

Int. J. Mol. Sci. 2022, 23(2), 654; https://doi.org/10.3390/ijms23020654 - 7 Jan 2022

Cited by 11 | Viewed by 2818

Abstract

Genetic variations are an important source of germplasm diversity, as it provides an allele resource that contributes to the development of new traits for plant breeding. Gamma rays have been widely used as a physical agent for mutation creation in plants, and their mutagenic effect has attracted extensive attention. However, few studies are available on the comprehensive mutation profile at both the large-scale phenotype mutation screening and whole-genome mutation scanning. In this study, biological effects on M₁ generation, large-scale phenotype screening in M₂ generation, as well as whole-genome re-sequencing of seven M₃ phenotype-visible lines were carried out to comprehensively evaluate the mutagenic effects of gamma rays on Arabidopsis thaliana. A total of 417 plants with visible mutated phenotypes were isolated from 20,502 M₂ plants, and the phenotypic mutation frequency of gamma rays was 2.03% in Arabidopsis thaliana. On average, there were 21.57 single-base substitutions (SBSs) and 11.57 small insertions and deletions (InDels) in each line. Single-base InDels accounts for 66.7% of the small InDels. The genomic mutation frequency was 2.78 × 10⁻¹⁰/bp/Gy. The ratio of transition/transversion was 1.60, and 64.28% of the C > T events exhibited the pyrimidine dinucleotide sequence; 69.14% of the small InDels were located in the sequence with 1 to 4 bp terminal microhomology that was used for DNA end rejoining, while SBSs were less dependent on terminal microhomology. Nine genes, on average, were predicted to suffer from functional alteration in each re-sequenced line. This indicated that a suitable mutation gene density was an advantage of gamma rays when trying to improve elite materials for one certain or a few traits. These results will aid the full understanding of the mutagenic effects and mechanisms of gamma rays and provide a basis for suitable mutagen selection and parameter design, which can further facilitate the development of more controlled mutagenesis methods for plant mutation breeding. Full article

(This article belongs to the Special Issue Molecular Research in Arabidopsis thaliana)

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11 pages, 2847 KiB

Open AccessArticle

Overlapping Functions of the Paralogous Proteins AtPAP2 and AtPAP9 in Arabidopsis thaliana

by Renshan Zhang, Xiaoqian Guan, Meijing Yang, Yee-Song Law, Chia Pao Voon, Junran Yan, Feng Sun and Boon Leong Lim

Int. J. Mol. Sci. 2021, 22(14), 7243; https://doi.org/10.3390/ijms22147243 - 6 Jul 2021

Cited by 1 | Viewed by 2417

Abstract

Arabidopsis thaliana purple acid phosphatase 2 (AtPAP2), which is anchored to the outer membranes of chloroplasts and mitochondria, affects carbon metabolism by modulating the import of some preproteins into chloroplasts and mitochondria. AtPAP9 bears a 72% amino acid sequence identity with AtPAP2, and both proteins carry a hydrophobic motif at their C-termini. Here, we show that AtPAP9 is a tail-anchored protein targeted to the outer membrane of chloroplasts. Yeast two-hybrid and bimolecular fluorescence complementation experiments demonstrated that both AtPAP9 and AtPAP2 bind to a small subunit of rubisco 1B (AtSSU1B) and a number of chloroplast proteins. Chloroplast import assays using [³⁵S]-labeled AtSSU1B showed that like AtPAP2, AtPAP9 also plays a role in AtSSU1B import into chloroplasts. Based on these data, we propose that AtPAP9 and AtPAP2 perform overlapping roles in modulating the import of specific proteins into chloroplasts. Most plant genomes contain only one PAP-like sequence encoding a protein with a hydrophobic motif at the C-terminus. The presence of both AtPAP2 and AtPAP9 in the Arabidopsis genome may have arisen from genome duplication in Brassicaceae. Unlike AtPAP2 overexpression lines, the AtPAP9 overexpression lines did not exhibit early-bolting or high-seed-yield phenotypes. Their differential growth phenotypes could be due to the inability of AtPAP9 to be targeted to mitochondria, as the overexpression of AtPAP2 on mitochondria enhances the capacity of mitochondria to consume reducing equivalents. Full article

(This article belongs to the Special Issue Molecular Research in Arabidopsis thaliana)

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