Interspecies Evolution and Networks Investigation of the Auxin Response Protein (AUX/IAA) Family Reveals the Adaptation Mechanisms of Halophytes Crops in Nitrogen Starvation Agroecological Environments

The maintenance of adaptability to the exposure to agroecological extreme environments is generally a feature after the long-term domestication of crops. Auxin influences plant growth in all environments. At present, the research on the auxin response factors (ARFs) has been very in-depth. However, there is still a large gap in the research on the origin, evolution, and regulatory networks of the Auxin-responsive protein (AUX/IAA) family. Here, we identified 495 AUX/IAAs from 19 representative species covering aquatic algae to angiosperms and found that they originated from early bryophytes and mainly expanded by polyploidy in angiosperms. In the domesticated crop quinoa, the evolutionary model of the IAA family is relatively independent and forms a robust regulatory network with auxin signals and energy metabolism pathways. In the nitrogen-deficient environment, CqIAAs (Chenopodium quinoa AUX/IAAs), auxin signals, and TCA pathway genes induced expression in young roots to promote root elongation and could regulate the balance of carbon and nitrogen metabolism to maintain the adaptation of early seedlings in poor environments. Furthermore, a rapidly evolving CqIAA (AUR62011942) not only has different expression levels in two quinoa seeds but also has a significant stress response when seedlings face nitrogen deficiency stress, which may be a key factor in the adaptive regulation of the barren environment. Our research provides valuable clues for understanding the origin, evolution, and functional innovation of auxin signaling and also provides a reference for future agricultural breeding in the context of global environmental changes.

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Noncoding RNAs, Emerging Regulators in Root Endosymbioses

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi-10-15-0240-fi ◽

2016 ◽

Vol 29 (3) ◽

pp. 170-180 ◽

Cited By ~ 27

Author(s):

Christine Lelandais-Brière ◽

Jérémy Moreau ◽

Caroline Hartmann ◽

Martin Crespi

Keyword(s):

Gene Expression ◽

Regulatory Networks ◽

Plant Root ◽

Arbuscular Mycorrhizal ◽

Auxin Response ◽

Response Factors ◽

Auxin Response Factors ◽

Control Gene Expression ◽

Small Ncrnas ◽

Am Symbiosis

Endosymbiosis interactions allow plants to grow in nutrient-deficient soil environments. The arbuscular mycorrhizal (AM) symbiosis is an ancestral interaction between land plants and fungi, whereas nitrogen-fixing symbioses are highly specific for certain plants, notably major crop legumes. The signaling pathways triggered by specific lipochitooligosaccharide molecules involved in these interactions have common components that also overlap with plant root development. These pathways include receptor-like kinases, transcription factors (TFs), and various intermediate signaling effectors, including noncoding (nc)RNAs. These latter molecules have emerged as major regulators of gene expression and small ncRNAs, composed of micro (mi)RNAs and small interfering (si)RNAs, are known to control gene expression at transcriptional (chromatin) or posttranscriptional levels. In this review, we describe exciting recent data connecting variants of conserved si/miRNAs with the regulation of TFs, such as NSP2, NFY-A1, auxin-response factors, and AP2-like proteins, known to be involved in symbiosis. The link between hormonal regulations and these si- and miRNA-TF nodes is proposed in a model in which different feedback loops or regulations controlling endosymbiosis signaling are integrated. The diversity and emerging regulatory networks of young legume miRNAs are also highlighted.

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Auxin Response Factors — output control in auxin biology

10.1101/129122 ◽

2017 ◽

Cited By ~ 1

Author(s):

Mark Roosjen ◽

Sébastien Paque ◽

Dolf Weijers

Keyword(s):

Gene Expression ◽

Transcription Factors ◽

Structural Biology ◽

Auxin Signaling ◽

Auxin Response ◽

Response Factors ◽

Output Control ◽

Auxin Response Factors ◽

Almost All ◽

Near Future

AbstractThe phytohormone auxin is involved in almost all developmental processes in land plants. Most, if not all, of these processes are mediated by changes in gene expression. Auxin acts on gene expression through a short nuclear pathway that converges upon the activation of a family of DNA-binding transcription factors. These AUXIN RESPONSE FACTORS (ARFs) are thus the effector of auxin response and translate the chemical signal to the regulation of a defined set of genes. Given the limited number of dedicated components in auxin signaling, distinct properties among the ARF family likely contributes to the establishment of multiple unique auxin responses in plant development. In the two decades following the identification of the first ARF in Arabidopsis much has been learnt about how these transcription factors act, and how they generate unique auxin responses. Progress in genetics, biochemistry, genomics and structural biology have helped to develop mechanistic models for ARF action. However, despite intensive efforts, many central questions are yet to be addressed. In this review we highlight what has been learnt about ARF transcription factors, and identify outstanding questions and challenges for the near future.

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ARF5/MONOPTEROS directly regulates miR390 expression in the Arabidopsis thaliana primary root meristem

10.1101/463943 ◽

2018 ◽

Cited By ~ 1

Author(s):

Mouli Ghosh Dastidar ◽

Andrea Scarpa ◽

Ira Mägele ◽

Paola Ruiz-Duarte ◽

Patrick von Born ◽

...

Keyword(s):

Stem Cells ◽

Root Meristem ◽

Primary Root ◽

Cell Types ◽

Auxin Signaling ◽

Auxin Response ◽

Response Factors ◽

Auxin Response Factors ◽

Regulatory Module ◽

Developmental Contexts

SUMMARYThe root meristem is organized around a quiescent centre surrounded by stem cells that generate all cell types of the root. In the transit amplifying compartment progeny of stem cells further divide prior to differentiation. Auxin controls the size of this transit-amplifying compartment via Auxin Response Factors (ARF) that interact with Auxin Response Elements (AuxRE) in the promoter of their targets. The microRNA miR390 regulates abundance of ARF2, ARF3 and ARF4 by triggering the production of trans-acting (ta)-siRNA from TAS3. This miR390/TAS3/ARF regulatory module confers sensitivity and robustness to auxin responses in diverse developmental contexts. Here, we show that miR390 is expressed in the transit-amplifying compartment of the root meristem where it modulates response to auxin. A single AuxRE bound by ARF5/MONOPTEROS (MP) in miR390 promoter is necessary for miR390 expression in this compartment. We show that interfering with ARF5/MP dependent auxin signaling attenuates miR390 expression in the transit-amplifying compartment. Our results show that ARF5/MP regulates directly the expression of miR390 in the basal root meristem. We propose that ARF5, miR390 and the ta-siRNAs-regulated ARFs are necessary to maintain the size of the transit-amplifying region of the meristem.One sentence summaryThe expression of miR390 in the Arabidopsis basal root meristem is controlled by ARF5/MONOPTEROS.

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