39,899 results match your criteria arabidopsis genes

A family of pathogen-induced cysteine-rich transmembrane proteins is involved in plant disease resistance.

Planta 2021 Apr 15;253(5):102. Epub 2021 Apr 15.

Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, 800.56, 3508 TB, Utrecht, The Netherlands.

Main Conclusion: Overexpression of pathogen-induced cysteine-rich transmembrane proteins (PCMs) in Arabidopsis thaliana enhances resistance against biotrophic pathogens and stimulates hypocotyl growth, suggesting a potential role for PCMs in connecting both biological processes. Plants possess a sophisticated immune system to protect themselves against pathogen attack. The defense hormone salicylic acid (SA) is an important player in the plant immune gene regulatory network. Read More

View Article and Full-Text PDF

Metatranscriptomic comparison of endophytic and pathogenic Fusarium-Arabidopsis interactions reveals plant transcriptional plasticity.

Mol Plant Microbe Interact 2021 Apr 15. Epub 2021 Apr 15.

University of Massachusetts Amherst, Biochemistry and Molecular Biology, 240 Thatcher Road, Amherst, Amherst, Massachusetts, United States, 01003;

Plants are continuously exposed to beneficial and pathogenic microbes, but how plants recognize and respond to friends versus foes remains poorly understood. Here, we compared the molecular response of independently challenged with a endophyte Fo47 versus a pathogen Fo5176. These two strains share a core genome of about 46 Mb, in addition to unique 1,229 and 5,415 accessory genes. Read More

View Article and Full-Text PDF

Evaluation and application of tools for the identification of known microRNAs in plants.

Appl Plant Sci 2021 Mar 7;9(3):e11414. Epub 2021 Apr 7.

Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Co-Innovation Center for Modern Production Technology of Grain Crops College of Agriculture Yangzhou University Yangzhou 225009 China.

MicroRNAs (miRNAs), endogenous non-coding RNA regulators, post-transcriptionally inhibit the expression of their target genes. Several tools have been developed for predicting annotated known miRNAs, but there is no consensus about how to select the most suitable method for any given species. In this study, eight miRNA prediction tools (mirnovo, miRPlant, miRDeep-P2, miRExpress, miRkwood, miRDeep2, miR-PREFeR, and sRNAbench) were selected for evaluation. Read More

View Article and Full-Text PDF

Effect of thermospermine on expression profiling of different gene using massive analysis of cDNA ends (MACE) and vascular maintenance in Arabidopsis.

Physiol Mol Biol Plants 2021 Mar 14;27(3):577-586. Epub 2021 Mar 14.

Senckenberg Biodiversity and Climate Research Center, Georg-Voigt-Str. 14-16, 60325 Frankfurt am Main, Germany.

polyamine oxidase 5 gene () functions as a thermospermine (T-Spm) oxidase. Aerial growth of its knock-out mutant () was significantly repressed by low dose(s) of T-Spm but not by other polyamines. To figure out the underlying mechanism, massive analysis of 3'-cDNA ends was performed. Read More

View Article and Full-Text PDF

The molecular signatures of compatible and incompatible pollination in Arabidopsis.

BMC Genomics 2021 Apr 14;22(1):268. Epub 2021 Apr 14.

Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Inria, F-69342, Lyon, France.

Background: Fertilization in flowering plants depends on the early contact and acceptance of pollen grains by the receptive papilla cells of the stigma. Deciphering the specific transcriptomic response of both pollen and stigmatic cells during their interaction constitutes an important challenge to better our understanding of this cell recognition event.

Results: Here we describe a transcriptomic analysis based on single nucleotide polymorphisms (SNPs) present in two Arabidopsis thaliana accessions, one used as female and the other as male. Read More

View Article and Full-Text PDF

MYB30 and ETHYLENE INSENEITIVE3 antagonistically regulate root hair growth and phosphorus uptake under phosphate deficiency in Arabidopsis.

Plant Signal Behav 2021 Apr 15:1913310. Epub 2021 Apr 15.

Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China.

Phosphate (Pi) deficiency is one of the major adverse factors limiting plant growth and production. Enhanced RH development is thought to be the typical root morphological response under Pi deficiency, which will enhance the utilization of Pi resources from soil. Here, we report that MYB30-EIN3 module is functionally implicated in Pi deficiency-induced RH development in Arabidopsis. Read More

View Article and Full-Text PDF

Systematic analysis of JmjC gene family and stress--response expression of KDM5 subfamily genes in .

PeerJ 2021 31;9:e11137. Epub 2021 Mar 31.

Key Laboratory of Crop Epigenetic Regulation and Development, Hunan Province, Changsha, China.

Background: Jumonji C (JmjC) proteins exert critical roles in plant development and stress response through the removal of lysine methylation from histones. which originated from spontaneous hybridization by and , is the most important oilseed crop after soybean. In JmjC proteins of species, the structure and function and its relationship with the parents and model plant remain uncharacterized. Read More

View Article and Full-Text PDF

Analysis of Populus glycosyl hydrolase family I members and their potential role in the ABA treatment and drought stress response.

Plant Physiol Biochem 2021 Apr 5;163:178-188. Epub 2021 Apr 5.

State Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, Guangdong, 510520, China. Electronic address:

Glycoside hydrolase family 1 (GH1) β-glucosidases (BGLUs) are encoded by a large number of genes and are involved in many developmental processes and stress responses in plants. Due to their importance in plant growth and development, genome-wide analyses have been conducted in the model plant species Arabidopsis thaliana, rice and maize but not in woody plant species, which have important economic and ecological value. In this study, we systematically analyzed Populus BGLUs (PtBGLUs) and demonstrated the involvement of several genes under stress conditions. Read More

View Article and Full-Text PDF

Calmodulin-Binding Protein 60b is a central transcriptional activator of immunity.

Plant Physiol 2021 Apr 12. Epub 2021 Apr 12.

State Key laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China.

Plants use a dual defense system to cope with microbial pathogens. The first involves pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) which is conferred by membrane receptors, and the second involves effector-triggered immunity (ETI), which is conferred by disease-resistance proteins (nucleotide-binding leucine-rich repeat containing proteins; NLRs). Calmodulin-Binding Protein 60 (CBP60) family transcription factors are crucial for pathogen defense: CBP60g and Systemic Acquired Resistance Deficient 1 (SARD1) positively regulate immunity, whereas CBP60a negatively regulates immunity. Read More

View Article and Full-Text PDF

Integrative inference of transcriptional networks in Arabidopsis yields novel ROS signalling regulators.

Nat Plants 2021 Apr 12. Epub 2021 Apr 12.

Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.

Gene regulation is a dynamic process in which transcription factors (TFs) play an important role in controlling spatiotemporal gene expression. To enhance our global understanding of regulatory interactions in Arabidopsis thaliana, different regulatory input networks capturing complementary information about DNA motifs, open chromatin, TF-binding and expression-based regulatory interactions were combined using a supervised learning approach, resulting in an integrated gene regulatory network (iGRN) covering 1,491 TFs and 31,393 target genes (1.7 million interactions). Read More

View Article and Full-Text PDF

Identification and functional characterization of two bamboo FD gene homologs having contrasting effects on shoot growth and flowering.

Sci Rep 2021 Apr 12;11(1):7849. Epub 2021 Apr 12.

Department of Life Sciences, Presidency University, Kolkata, India.

Bamboos, member of the family Poaceae, represent many interesting features with respect to their fast and extended vegetative growth, unusual, yet divergent flowering time across species, and impact of sudden, large scale flowering on forest ecology. However, not many studies have been conducted at the molecular level to characterize important genes that regulate vegetative and flowering habit in bamboo. In this study, two bamboo FD genes, BtFD1 and BtFD2, which are members of the florigen activation complex (FAC) have been identified by sequence and phylogenetic analyses. Read More

View Article and Full-Text PDF

Evolutionary diversification of cytokinin-specific glucosyltransferases in angiosperms and enigma of missing cis-zeatin O-glucosyltransferase gene in Brassicaceae.

Sci Rep 2021 Apr 12;11(1):7885. Epub 2021 Apr 12.

Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02, Prague 6, Czech Republic.

In the complex process of homeostasis of phytohormones cytokinins (CKs), O-glucosylation catalyzed by specific O-glucosyltransferases represents one of important mechanisms of their reversible inactivation. The CK O-glucosyltransferases belong to a highly divergent and polyphyletic multigene superfamily of glycosyltransferases, of which subfamily 1 containing UDP-glycosyltransferases (UGTs) is the largest in the plant kingdom. It contains recently discovered O and P subfamilies present in higher plant species but not in Arabidopsis thaliana. Read More

View Article and Full-Text PDF

Genome-wide discovery of G-quadruplexes in barley.

Sci Rep 2021 Apr 12;11(1):7876. Epub 2021 Apr 12.

Crop Improvement and Genetics Research Unit, Western Regional Research Center, U.S. Department of Agriculture - Agricultural Research Service, 800 Buchanan St, Albany, CA, 94710, USA.

G-quadruplexes (G4s) are four-stranded nucleic acid structures with closely spaced guanine bases forming square planar G-quartets. Aberrant formation of G4 structures has been associated with genomic instability. However, most plant species are lacking comprehensive studies of G4 motifs. Read More

View Article and Full-Text PDF

Biological pathway expression complementation contributes to biomass heterosis in .

Proc Natl Acad Sci U S A 2021 Apr;118(16)

School of Advanced Agricultural Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China;

The mechanisms underlying heterosis have long remained a matter of debate, despite its agricultural importance. How changes in transcriptional networks during plant development are relevant to the continuous manifestation of growth vigor in hybrids is intriguing and unexplored. Here, we present an integrated high-resolution analysis of the daily dynamic growth phenotypes and transcriptome atlases of young seedlings (parental ecotypes [Col-0 and Per-1] and their F hybrid). Read More

View Article and Full-Text PDF

A multilayered cross-species analysis of GRAS transcription factors uncovered their functional networks in plant adaptation to the environment.

J Adv Res 2021 Mar 29;29:191-205. Epub 2020 Oct 29.

Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China.

Introduction: Environmental stress is both a major force of natural selection and a prime factor affecting crop qualities and yields. The impact of the GRAS [gibberellic acid-insensitive (GAI), repressor of GA1-3 mutant (RGA), and scarecrow (SCR)] family on plant development and the potential to resist environmental stress needs much emphasis.

Objectives: This study aims to investigate the evolution, expansion, and adaptive mechanisms of of important representative plants during polyploidization. Read More

View Article and Full-Text PDF

The Candidate Photoperiod Gene Promotes Growth and Flowering in .

Front Plant Sci 2021 26;12:634091. Epub 2021 Mar 26.

The Flowering Lab, School of Biological Sciences, University of Auckland, Auckland, New Zealand.

Flowering time influences the yield and productivity of legume crops. is a reference temperate legume that, like the winter annual , shows accelerated flowering in response to vernalization (extended cold) and long-day (LD) photoperiods (VLD). However, unlike , appears to lack functional homologs of core flowering time regulators () and () which act upstream of the mobile florigen FLOWERING LOCUS T (FT). Read More

View Article and Full-Text PDF

Is Induced by Short Days in Soybean and May Accelerate Flowering When Overexpressed in via Inhibiting .

Front Plant Sci 2021 26;12:629069. Epub 2021 Feb 26.

Key Laboratory of Soybean Biology of Ministry of Education, China (Key Laboratory of Biology and Genetics and Breeding for Soybean in Northeast China), Northeast Agricultural University, Harbin, China.

Photoperiod is one of the main climatic factors that determine flowering time and yield. Some members of the INDETERMINATE DOMAIN (IDD) transcription factor family have been reported to be involved in regulation of flowering time in Arabidopsis, maize, and rice. In this study, the domain analysis showed that GmIDD had a typical ID domain and was a member of the soybean IDD transcription factor family. Read More

View Article and Full-Text PDF
February 2021

Flavonols modulate lateral root emergence by scavenging reactive oxygen species in Arabidopsis thaliana.

J Biol Chem 2020 Dec 25;296:100222. Epub 2020 Dec 25.

Biology Department, Wake Forest University, Winston Salem, North Carolina, USA. Electronic address:

Flavonoids are a class of specialized metabolites with subclasses including flavonols and anthocyanins, which have unique properties as antioxidants. Flavonoids modulate plant development, but whether and how they impact lateral root development is unclear. We examined potential roles for flavonols in this process using Arabidopsis thaliana mutants with defects in genes encoding key enzymes in flavonoid biosynthesis. Read More

View Article and Full-Text PDF
December 2020

NLM-Gene, a richly annotated gold standard dataset for gene entities that addresses ambiguity and multi-species gene recognition.

J Biomed Inform 2021 Apr 8:103779. Epub 2021 Apr 8.

National Library of Medicine, National Institutes of Health, Bethesda MD, USA.

The automatic recognition of gene names and their corresponding database identifiers in biomedical text is an important first step for many downstream text-mining applications. While current methods for tagging gene entities have been developed for biomedical literature, their performance on species other than human is substantially lower due to the lack of annotation data. We therefore present the NLM-Gene corpus, a high-quality manually annotated corpus for genes developed at the US National Library of Medicine (NLM), covering ambiguous gene names, with an average of 29 gene mentions (10 unique identifiers) per document, and a broader representation of different species (including Homo sapiens, Mus musculus, Rattus norvegicus, Drosophila melanogaster, Arabidopsis thaliana, Danio rerio, etc. Read More

View Article and Full-Text PDF

Identification and evolution analysis of the JAZ gene family in maize.

Yang Han Dawn Luthe

BMC Genomics 2021 Apr 10;22(1):256. Epub 2021 Apr 10.

The Pennsylvania State University, Plant Science, University Park, PA, USA.

Background: Jasmonates (JAs) are important for plants to coordinate growth, reproduction, and defense responses. In JA signaling, jasmonate ZIM-domain (JAZ) proteins serve as master regulators at the initial stage of herbivores attacks. Although discovered in many plant species, little in-depth characterization of JAZ gene expression has been reported in the agronomically important crop, maize (Zea mays L. Read More

View Article and Full-Text PDF

SLI1 confers broad-spectrum resistance to phloem-feeding insects.

Plant Cell Environ 2021 Apr 10. Epub 2021 Apr 10.

Laboratory of Entomology, Wageningen University & Research, AA, Wageningen, The Netherlands.

Resistance (R) genes usually compete in a coevolutionary arms race with reciprocal effectors to confer strain-specific resistance to pathogens or herbivorous insects. Here, we investigate the specificity of SLI1, a recently identified R gene in Arabidopsis that encodes a small heat shock-like protein involved in resistance to Myzus persicae aphids. In a panel with several aphid and whitefly species, SLI1 compromised reproductive rates of three species: the tobacco aphid M. Read More

View Article and Full-Text PDF

Alleles disrupting LBD37-like gene by an 136 bp insertion show different distributions between green and purple cabbages (Brassica oleracea var. capitata).

Genes Genomics 2021 Apr 10. Epub 2021 Apr 10.

Department of Biological Sciences, College of Biological Science and Biotechnology, Chungnam National University, Daejeon, 34134, Republic of Korea.

Background: In Arabidopsis thaliana (Arabidopsis), clade IIb lateral organ boundary domain (LBD) 37, 38, and 39 proteins negatively regulate anthocyanin biosynthesis and affect nitrogen responses.

Objective: To investigate the possible role of LBD genes in anthocyanin accumulations among green and purple cabbages (Brassica oleracea var. capitata), we determined sequence variations and expression levels of cabbage homologs of Arabidopsis LBD37, 38, and 39. Read More

View Article and Full-Text PDF

A C-terminal fragment of Arabidopsis OXIDATIVE STRESS 2 can play a positive role in salt tolerance.

Biochem Biophys Res Commun 2021 Apr 6;556:23-30. Epub 2021 Apr 6.

Plant Gene Engineering Center, Chinese Academy of Sciences Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China. Electronic address:

The zinc finger transcription factor OXIDATIVE STRESS 2 (OXS2) was previously reported to be involved in oxidative stress tolerance and stress escape. Here we report that an Arabidopsis oxs2-1 mutant is also more sensitive to salt stress. Conversely, the overproduction of a C-terminal fragment of OXS2, the 'AT3' fragment, can enhance salt tolerance in Arabidopsis by upregulating the transcription of at least six salt-induced genes: COR15A, COR47, RD29B, KIN1, ACS2 and ACS6. Read More

View Article and Full-Text PDF

Understanding the regulatory relationship of abscisic acid and bZIP transcription factors towards amylose biosynthesis in wheat.

Mol Biol Rep 2021 Apr 8. Epub 2021 Apr 8.

National Agri-Food Biotechnology Institute, Knowledge City Sector-81, Mohali, Punjab, 140306, India.

Starch is biosynthesized during seed development and this process is regulated by many bZIP proteins in bread wheat. Abscisic acid (ABA), an important phyto-hormone involved in various physiological processes mediated by bZIPs in plants including seed development. The 'Group A' TabZIP transcription factors play important roles in the ABA signaling pathway in Arabidopsis, rice and other cereal crops but their role in regulation of amylose biosynthesis in wheat is limited. Read More

View Article and Full-Text PDF

The chromatin remodeler DDM1 prevents transposon mobility through deposition of histone variant H2A.W.

Nat Cell Biol 2021 Apr 8;23(4):391-400. Epub 2021 Apr 8.

Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria.

Mobile transposable elements (TEs) not only participate in genome evolution but also threaten genome integrity. In healthy cells, TEs that encode all of the components that are necessary for their mobility are specifically silenced, yet the precise mechanism remains unknown. Here, we characterize the mechanism used by a conserved class of chromatin remodelers that prevent TE mobility. Read More

View Article and Full-Text PDF

Involvement of the R2R3-MYB transcription factors MYB21 and its homologs in regulating the stamen flavonols accumulation in Arabidopsis.

J Exp Bot 2021 Apr 8. Epub 2021 Apr 8.

State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China.

Flavonols are a subclass of flavonoids that exhibit a wide array of physiological functions in plants. Commonly found flavonols are synthesized from dihydroflavonols by flavonol synthase (FLS). The genome of Arabidopsis thaliana contains six FLS genes, among which, FLS1, encodes a functional enzyme. Read More

View Article and Full-Text PDF

Differential Activation of Partially Redundant Δ9 Stearoyl-ACP Desaturase Genes Is Critical for Omega-9 Monounsaturated Fatty Acid Biosynthesis During Seed Development in Arabidopsis.

Plant Cell 2020 Nov;32(11):3613-3637

Institut Jean-Pierre Bourgin, INRAE, CNRS, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France.

The spatiotemporal pattern of deposition, final amount, and relative abundance of oleic acid (cis-ω-9 C18:1) and its derivatives in the different lipid fractions of the seed of Arabidopsis (Arabidopsis thaliana) indicates that omega-9 monoenes are synthesized at high rates in this organ. Accordingly, we observed that four Δ9 stearoyl-ACP desaturase (SAD)-coding genes (FATTY ACID BIOSYNTHESIS2 [FAB2], ACYL-ACYL CARRIER PROTEIN5 [AAD5], AAD1, and AAD6) are transcriptionally induced in seeds. We established that the three most highly expressed ones are directly activated by the WRINKLED1 transcription factor. Read More

View Article and Full-Text PDF
November 2020

Mutations in the Pectin Methyltransferase QUASIMODO2 Influence Cellulose Biosynthesis and Wall Integrity in Arabidopsis.

Plant Cell 2020 Nov;32(11):3576-3597

Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, People's Republic of China.

Pectins are abundant in the cell walls of dicotyledonous plants, but how they interact with other wall polymers and influence wall integrity and cell growth has remained mysterious. Here, we verified that QUASIMODO2 (QUA2) is a pectin methyltransferase and determined that QUA2 is required for normal pectin biosynthesis. To gain further insight into how pectin affects wall assembly and integrity maintenance, we investigated cellulose biosynthesis, cellulose organization, cortical microtubules, and wall integrity signaling in two mutant alleles of Arabidopsis (Arabidopsis thaliana) QUA2, qua2 and tsd2. Read More

View Article and Full-Text PDF
November 2020

The Transcription Factor NIGT1.2 Modulates Both Phosphate Uptake and Nitrate Influx during Phosphate Starvation in Arabidopsis and Maize.

Plant Cell 2020 Nov;32(11):3519-3534

State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Center for Crop Functional Genomics and Molecular Breeding, Beijing 100193, China.

Phosphorus and nitrogen are essential macronutrients for plant growth and crop production. During phosphate (Pi) starvation, plants enhanced Pi but reduced nitrate (NO3-) uptake capacity, and the mechanism is unclear. Here, we show that a GARP-type transcription factor NITRATE-INDUCIBLE, GARP-TYPE TRANSCRIPTIOANL REPRESSOR1. Read More

View Article and Full-Text PDF
November 2020

The bacterial biocontrol agent Paenibacillus alvei K165 confers inherited resistance against Verticillium dahliae.

J Exp Bot 2021 Apr 8. Epub 2021 Apr 8.

Laboratory of Plant Pathology, Agricultural University of Athens, Athens, Greece.

The biocontrol agent Paenibacillus alvei K165 was previously shown to protect Arabidopsis thaliana plants against Verticillium dahliae. Here we show that K165 also confers inherited immune resistance against V. dahliae. Read More

View Article and Full-Text PDF