scholarly journals Arabidopsis thaliana computationally-generated next-state gene interaction models

2021 ◽  
pp. 17-26
Author(s):  
David J. John Bree ◽  
Ann LaPointe ◽  
James L. Norris ◽  
Alexandria F. Harkey ◽  
Joëlle K. Muhlemann ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Plant Hormone ◽  
Gene Interaction ◽  
Transcript Abundance ◽  
Measured Data ◽  
Interaction Models ◽  
Abundance Data ◽  
Statistical Framework ◽  
Algorithmic Techniques

The construction of gene interaction models must be a fully collaborative and intentional effort. All aspects of the research, such as growing the plants, extracting the mea-surements, refining the measured data, developing the statistical framework, and forming and applying the algorithmic techniques, must lend themselves to repeatable and  sound practices. This paper holistically focuses on the process of producing gene interaction models based on transcript abundance data from Arabidopsis thaliana after stimulation by a plant hormone.

scholarly journals Brassinosteroids repress the seed maturation program during the seed-to-seedling transition

2021 ◽  
Author(s):  
Jiuxiao Ruan ◽  
Huhui Chen ◽  
Tao Zhu ◽  
Yaoguang Yu ◽  
Yawen Lei ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Transcription Factor ◽  
Abscisic Acid ◽  
Plant Hormone ◽  
Flowering Plants ◽  
Seed Maturation ◽  
Domain Protein ◽  
Abscisic Acid Insensitive3 ◽  
Underlying Mechanisms ◽  
Embryonic Structure

Abstract In flowering plants, repression of the seed maturation program is essential for the transition from the seed to the vegetative phase, but the underlying mechanisms remain poorly understood. The B3-domain protein VIVIPAROUS1/ABSCISIC ACID-INSENSITIVE3-LIKE 1 (VAL1) is involved in repressing the seed maturation program. Here we uncovered a molecular network triggered by the plant hormone brassinosteroid (BR) that inhibits the seed maturation program during the seed-to-seedling transition in Arabidopsis (Arabidopsis thaliana). val1-2 mutant seedlings treated with a BR biosynthesis inhibitor form embryonic structures, whereas BR signaling gain-of-function mutations rescue the embryonic structure trait. Furthermore, the BR-activated transcription factors BRI1-EMS-SUPPRESSOR 1 and BRASSINAZOLE-RESISTANT 1 bind directly to the promoter of AGAMOUS-LIKE15 (AGL15), which encodes a transcription factor involved in activating the seed maturation program, and suppress its expression. Genetic analysis indicated that BR signaling is epistatic to AGL15 and represses the seed maturation program by downregulating AGL15. Finally, we showed that the BR-mediated pathway functions synergistically with the VAL1/2-mediated pathway to ensure the full repression of the seed maturation program. Together, our work uncovered a mechanism underlying the suppression of the seed maturation program, shedding light on how BR promotes seedling growth.

scholarly journals Extended JAZ degron sequence for plant hormone binding in jasmonate co-receptor of tomato SlCOI1-SlJAZ

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Rina Saito ◽  
Kengo Hayashi ◽  
Haruna Nomoto ◽  
Misuzu Nakayama ◽  
Yousuke Takaoka ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Plant Development ◽  
Genetic Modification ◽  
Tomato Plant ◽  
Plant Hormone ◽  
Herbivorous Insects ◽  
Hormone Binding ◽  
Plant Body

Abstract(+)-7-iso-Jasmonoyl-l-isoleucine (JA-Ile) is a lipid-derived phytohormone implicated in plant development, reproduction, and defense in response to pathogens and herbivorous insects. All these effects are instigated by the perception of JA-Ile by the COI1-JAZ co-receptor in the plant body, which in Arabidopsis thaliana is profoundly influenced by the short JAZ degron sequence (V/L)P(Q/I)AR(R/K) of the JAZ protein. Here, we report that SlJAZ-SlCOI1, the COI1-JAZ co-receptor found in the tomato plant, relies on the extended JAZ degron sequence (V/L)P(Q/I)AR(R/K)XSLX instead of the canonical JAZ degron. This finding illuminates our understanding of the mechanism of ligand perception by JA-Ile in this plant, and will inform both efforts to improve it by genetic modification of the SlCOI1-SlJAZ co-receptor, and the development of the synthetic agonists/antagonists.

scholarly journals Control of auxin-regulated root development by the Arabidopsis thaliana SHY2/IAA3 gene

Development ◽  
1999 ◽  
Vol 126 (4) ◽  
pp. 711-721 ◽  
Author(s):  
Q. Tian ◽  
J.W. Reed
Keyword(s):  
Arabidopsis Thaliana ◽  
Lateral Root ◽  
Tissue Specificity ◽  
Plant Hormone ◽  
Root Formation ◽  
Auxin Transport ◽  
Feedback Regulation ◽  
Loss Of Function ◽  
Leaf Formation ◽  
Induced Genes

The plant hormone auxin controls many aspects of development and acts in part by inducing expression of various genes. Arabidopsis thaliana semidominant shy2 (short hypocotyl) mutations cause leaf formation in dark-grown plants, suggesting that SHY2 has an important role in regulating development. Here we show that the SHY2 gene encodes IAA3, a previously known member of the Aux/IAA family of auxin-induced genes. Dominant shy2 mutations cause amino acid changes in domain II, conserved among all members of this family. We isolated loss-of-function shy2 alleles including a putative null mutation. Gain-of-function and loss-of-function shy2 mutations affect auxin-dependent root growth, lateral root formation, and timing of gravitropism, indicating that SHY2/IAA3 regulates multiple auxin responses in roots. The phenotypes suggest that SHY2/IAA3 may activate some auxin responses and repress others. Models invoking tissue-specificity, feedback regulation, or control of auxin transport may explain these results.

Identification of IAA-regulated genes in Pseudomonas syringae pv. tomato strain DC3000

2021 ◽  
Author(s):  
Arnaud-Thierry Djami-Tchatchou ◽  
Zipeng Alex Li ◽  
Paul Stodghill ◽  
Melanie J. Filiatrault ◽  
Barbara N. Kunkel
Keyword(s):  
Gene Expression ◽  
Arabidopsis Thaliana ◽  
Acetic Acid ◽  
Stress Response ◽  
Pseudomonas Syringae ◽  
Plant Pathogen ◽  
Type Iii Secretion ◽  
Plant Hormone ◽  
Indole 3 Acetic Acid ◽  
Exogenous Iaa

The auxin indole-3-acetic acid (IAA) is a plant hormone that not only regulates plant growth and development but also plays important roles in plant-microbe interactions. We previously reported that IAA alters expression of several virulence-related genes in the plant pathogen Pseudomonas syringae pv. tomato strain DC3000 ( Pto DC3000). To learn more about the impact of IAA on regulation of Pto DC3000 gene expression we performed a global transcriptomic analysis of bacteria grown in culture, in the presence or absence of exogenous IAA. We observed that IAA repressed expression of genes involved in the Type III secretion (T3S) system and motility and promoted expression of several known and putative transcriptional regulators. Several of these regulators are orthologs of factors known to regulate stress responses and accordingly expression of several stress response-related genes was also upregulated by IAA. Similar trends in expression for several genes were also observed by RT-qPCR. Using an Arabidopsis thaliana auxin receptor mutant that accumulates elevated auxin, we found that many of the P. syringae genes regulated by IAA in vitro were also regulated by auxin in planta . Collectively the data indicate that IAA modulates many aspects of Pto DC3000 biology, presumably to promote both virulence and survival under stressful conditions, including those encountered in or on plant leaves. IMPORTANCE Indole-3-acetic acid (IAA), a form of the plant hormone auxin, is used by many plant-associated bacteria as a cue to sense the plant environment. Previously, we showed that IAA can promote disease in interactions between the plant pathogen Pseudomonas syringae strain Pto DC000 and one of its hosts, Arabidopsis thaliana . However, the mechanisms by which IAA impacts the biology of Pto DC3000 and promotes disease are not well understood. Here we demonstrate that IAA is a signal molecule that regulates gene expression in Pto DC3000. The presence of exogenous IAA affects expression of over 700 genes in the bacteria, including genes involved in Type III secretion and genes involved in stress response. This work offers insight into the roles of auxin promoting pathogenesis.

scholarly journals Conserved and Opposite Transcriptome Patterns during Germination in Hordeum vulgare and Arabidopsis thaliana

2020 ◽  
Vol 21 (19) ◽  
pp. 7404
Author(s):  
Yanqiao Zhu ◽  
Oliver Berkowitz ◽  
Jennifer Selinski ◽  
Andreas Hartmann ◽  
Reena Narsai ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Hordeum Vulgare ◽  
Mitochondrial Biogenesis ◽  
Expression Patterns ◽  
Tca Cycle ◽  
Transcript Abundance ◽  
Pentatricopeptide Repeat ◽  
Orthologous Genes ◽  
Regulatory Processes ◽  
High Level

Seed germination is a critical process for completion of the plant life cycle and for global food production. Comparing the germination transcriptomes of barley (Hordeum vulgare) to Arabidopsis thaliana revealed the overall pattern was conserved in terms of functional gene ontology; however, many oppositely responsive orthologous genes were identified. Conserved processes included a set of approximately 6000 genes that peaked early in germination and were enriched in processes associated with RNA metabolism, e.g., pentatricopeptide repeat (PPR)-containing proteins. Comparison of orthologous genes revealed more than 3000 orthogroups containing almost 4000 genes that displayed similar expression patterns including functions associated with mitochondrial tricarboxylic acid (TCA) cycle, carbohydrate and RNA/DNA metabolism, autophagy, protein modifications, and organellar function. Biochemical and proteomic analyses indicated mitochondrial biogenesis occurred early in germination, but detailed analyses revealed the timing involved in mitochondrial biogenesis may vary between species. More than 1800 orthogroups representing 2000 genes displayed opposite patterns in transcript abundance, representing functions of energy (carbohydrate) metabolism, photosynthesis, protein synthesis and degradation, and gene regulation. Differences in expression of basic-leucine zippers (bZIPs) and Apetala 2 (AP2)/ethylene-responsive element binding proteins (EREBPs) point to differences in regulatory processes at a high level, which provide opportunities to modify processes in order to enhance grain quality, germination, and storage as needed for different uses.

scholarly journals EoRNA, a barley gene and transcript abundance database

2020 ◽  
Author(s):  
Linda Milne ◽  
Micha Bayer ◽  
Paulo Rapazote-Flores ◽  
Claus-Dieter Mayer ◽  
Robbie Waugh ◽  
...  
Keyword(s):  
Statistical Significance ◽  
Transcript Abundance ◽  
Specific Gene ◽  
Rna Seq ◽  
Scottish Gaelic ◽  
On Demand ◽  
Abundance Data ◽  
Reference Transcript ◽  
Abundance Variation ◽  
Meta Analyses

AbstractA high-quality, barley gene reference transcript dataset (BaRTv1.0), was used to quantify gene and transcript abundances from 22 RNA-seq experiments, covering 843 separate samples. Using the abundance data we developed a Barley Expression Database (EoRNA* – Expression of RNA) to underpin a visualisation tool that displays comparative gene and transcript abundance data on demand as transcripts per million (TPM) across all samples and all the genes. EoRNA provides gene and transcript models for all of the transcripts contained in BaRTV1.0, and these can be conveniently identified through either BaRT or HORVU gene names, or by direct BLAST of query sequences. Browsing the quantification data reveals cultivar, tissue and condition specific gene expression and shows changes in the proportions of individual transcripts that have arisen via alternative splicing. TPM values can be easily extracted to allow users to determine the statistical significance of observed transcript abundance variation among samples or perform meta analyses on multiple RNA-seq experiments. * Eòrna is the Scottish Gaelic word for Barley

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