Genome-wide identification and characterization of small auxin-up RNA (SAUR) gene family in plants: evolution and expression profiles during normal growth and stress response

Zhang, Hao; Zhou, Yu; Yao, Xiaodie; Chen, Jingli; Chen, Xing; Zhou, Huiwen; Lou, Yuxia; Ming, Feng; Jin, Yue

doi:10.1186/s12870-020-02781-x

Cited by 45 publications

(39 citation statements)

References 60 publications

(40 reference statements)

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“…Two of these three calmodulin-binding proteins (Os02g0305950 and Os08g0534950) were also annotated as auxin-responsive proteins. Os02g0305950 ( OsSAUR7 ) belongs to the Small Auxin-Up RNA gene family, which is induced by exogenous auxin within minutes and has been shown to play important roles in diverse processes of plant development and stress responses [ 46 , 47 ]. The homeobox-leucine zipper transcriptional factor gene OsHOX22 (Os04g0541700) responded to sulfate resupply systemically in the split-root without sulfate resupply but not in the local split-root with sulfate resupply ( Table S5 , Gene set B).…”

Section: Discussionmentioning

confidence: 99%

Local and Systemic Response to Heterogeneous Sulfate Resupply after Sulfur Deficiency in Rice

Wang

Liu

Zhao

et al. 2022

IJMS

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Sulfur (S) is an essential mineral nutrient required for plant growth and development. Plants usually face temporal and spatial variation in sulfur availability, including the heterogeneous sulfate content in soils. As sessile organisms, plants have evolved sophisticated mechanisms to modify their gene expression and physiological processes in order to optimize S acquisition and usage. Such plasticity relies on a complicated network to locally sense S availability and systemically respond to S status, which remains poorly understood. Here, we took advantage of a split-root system and performed transcriptome-wide gene expression analysis on rice plants in S deficiency followed by sulfate resupply. S deficiency altered the expressions of 6749 and 1589 genes in roots and shoots, respectively, accounting for 18.07% and 4.28% of total transcripts detected. Homogeneous sulfate resupply in both split-root halves recovered the expression of 27.06% of S-deficiency-responsive genes in shoots, while 20.76% of S-deficiency-responsive genes were recovered by heterogeneous sulfate resupply with only one split-root half being resupplied with sulfate. The local sulfate resupply response genes with expressions only recovered in the split-root half resupplied with sulfate but not in the other half remained in S deficiency were identified in roots, which were mainly enriched in cellular amino acid metabolic process and root growth and development. Several systemic response genes were also identified in roots, whose expressions remained unchanged in the split-root half resupplied with sulfate but were recovered in the other split-root half without sulfate resupply. The systemic response genes were mainly related to calcium signaling and auxin and ABA signaling. In addition, a large number of S-deficiency-responsive genes exhibited simultaneous local and systemic responses to sulfate resupply, such as the sulfate transporter gene OsSULTR1;1 and the O-acetylserine (thiol) lyase gene, highlighting the existence of a systemic regulation of sulfate uptake and assimilation in S deficiency plants followed by sulfate resupply. Our studies provided a comprehensive transcriptome-wide picture of a local and systemic response to heterogeneous sulfate resupply, which will facilitate an understanding of the systemic regulation of S homeostasis in rice.

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Section: Discussionmentioning

confidence: 99%

Local and Systemic Response to Heterogeneous Sulfate Resupply after Sulfur Deficiency in Rice

Wang

Liu

Zhao

et al. 2022

IJMS

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“…To identify the conserved motifs in A. truncatum proteins, the motifs within the 54 A. truncatum WRKY protein sequences were detected using the Multiple EM for Motif Elicitation (MEME 5.3.2: , accessed on 20 July 2021) [ 36 ]. The maximum number of motifs was set to 10, and members of the same subfamily have similar conserved domain characteristics.…”

Section: Methodsmentioning

confidence: 99%

Genome-Wide Identification and Analysis of the WRKY Gene Family and Cold Stress Response in Acer truncatum

Wei

et al. 2021

Genes

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WRKY transcription factors constitute one of the largest gene families in plants and are involved in many biological processes, including growth and development, physiological metabolism, and the stress response. In earlier studies, the WRKY gene family of proteins has been extensively studied and analyzed in many plant species. However, information on WRKY transcription factors in Acer truncatum has not been reported. In this study, we conducted genome-wide identification and analysis of the WRKY gene family in A. truncatum, 54 WRKY genes were unevenly located on all 13 chromosomes of A. truncatum, the highest number was found in chromosomes 5. Phylogenetic relationships, gene structure, and conserved motif identification were constructed, and the results affirmed 54 AtruWRKY genes were divided into nine subgroup groups. Tissue species analysis of AtruWRKY genes revealed which were differently exhibited upregulation in flower, leaf, root, seed and stem, and the upregulation number were 23, 14, 34, 18, and 8, respectively. In addition, the WRKY genes expression in leaf under cold stress showed that more genes were significantly expressed under 0, 6 and 12 h cold stress. The results of this study provide a new insight the regulatory function of WRKY genes under abiotic and biotic stresses.

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“…The transcription level of AUX1 , encoding a carrier protein involved in proton-driven auxin influx ( Swarup and Bhosale, 2019 ), and of three main components of the auxin signaling pathway—TRANSPORT INHIBITOR RESPONSE 1/AUXIN SIGNALING F-BOX (TIR1) and two AUXIN/IAA (auxin/indole-3-acetic acid) proteins—was higher in dormant buds ( Figure 8A ). Three genes encoding the small auxin up RNA (SAUR; Figure 8A ), corresponding to the largest family of early auxin-responsive genes in higher plants, are also upregulated in dormant buds ( Zhang et al, 2021 ). These findings indicate that auxin homeostasis and signaling within buds are under the combined effect of auxin and sugar availability.…”

Section: Resultsmentioning

confidence: 99%

Antagonistic Effect of Sucrose Availability and Auxin on Rosa Axillary Bud Metabolism and Signaling, Based on the Transcriptomics and Metabolomics Analysis

et al. 2022

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Shoot branching is crucial for successful plant development and plant response to environmental factors. Extensive investigations have revealed the involvement of an intricate regulatory network including hormones and sugars. Recent studies have demonstrated that two major systemic regulators—auxin and sugar—antagonistically regulate plant branching. However, little is known regarding the molecular mechanisms involved in this crosstalk. We carried out two complementary untargeted approaches—RNA-seq and metabolomics—on explant stem buds fed with different concentrations of auxin and sucrose resulting in dormant and non-dormant buds. Buds responded to the combined effect of auxin and sugar by massive reprogramming of the transcriptome and metabolome. The antagonistic effect of sucrose and auxin targeted several important physiological processes, including sink strength, the amino acid metabolism, the sulfate metabolism, ribosome biogenesis, the nucleic acid metabolism, and phytohormone signaling. Further experiments revealed a role of the TOR-kinase signaling pathway in bud outgrowth through at least downregulation of Rosa hybrida BRANCHED1 (RhBRC1). These new findings represent a cornerstone to further investigate the diverse molecular mechanisms that drive the integration of endogenous factors during shoot branching.

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Genome-wide identification and characterization of small auxin-up RNA (SAUR) gene family in plants: evolution and expression profiles during normal growth and stress response

Cited by 45 publications

References 60 publications

Local and Systemic Response to Heterogeneous Sulfate Resupply after Sulfur Deficiency in Rice

Local and Systemic Response to Heterogeneous Sulfate Resupply after Sulfur Deficiency in Rice

Genome-Wide Identification and Analysis of the WRKY Gene Family and Cold Stress Response in Acer truncatum

Antagonistic Effect of Sucrose Availability and Auxin on Rosa Axillary Bud Metabolism and Signaling, Based on the Transcriptomics and Metabolomics Analysis

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