Profiling of the Receptor for Activated C Kinase 1a (RACK1a) interaction network in Arabidopsis thaliana

Guo, Jinggong; Hu, Yunhe; Zhou, Yaping; Zhu, Zhinan; Sun, Yijing; Li, Jiaoai; Wu, Rui; Miao, Yuchen; Sun, Xuwu

doi:10.1016/j.bbrc.2019.09.142

Cited by 15 publications

(18 citation statements)

References 41 publications

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“…PG0015970 was clustered with three AtRACK1 homologous genes in one cluster, namely RACK1A (AT1G18080), RACK1B (AT1G48630), and RACK1C (AT3G18130), respectively. Previous studies showed that RACK1 can interact with many signal molecules and affect different signal transduction pathways [72][73][74]. Liu, et al [72] found that overexpression of the MaRACK1 gene in Arabidopsis decreased tolerance to drought and salt stresses and MaRACK1 overexpression changed expression levels of genes in response to stress and stimuli.…”

Section: Expression Profile Analysis Of Stwd40 Genesmentioning

confidence: 99%

The WD40 Gene Family in Potato (Solanum Tuberosum L.): Genome-Wide Analysis and Identification of Anthocyanin and Drought-Related WD40s

Liu

Coulter

et al. 2020

Agronomy

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WD40 proteins, also known as WD40 domain proteins, constitute a large gene family in eukaryotes and play multiple roles in cellular processes. However, systematic identification and analysis of WD40 proteins have not yet been reported in potato (Solanum tuberosum L.). In the present study, 178 potato WD40 (StWD40) genes were identified and their distribution on chromosomes, gene structure, and conserved motifs were assessed. According to their structural and phylogenetic protein features, these 178 StWD40 genes were classified into 14 clusters and 10 subfamilies. Collinearity analysis showed that segmental duplication events played a major role in the expansion of the StWD40 gene family. Synteny analysis indicated that 45 and 23 pairs of StWD40 genes were orthologous to Arabidopsis and wheat (Triticum aestivum), respectively, and that these gene pairs evolved under strong purifying selection. RNA-seq data from different tissues and abiotic stresses revealed tissue-specific expression and abiotic stress-responsive StWD40 genes in doubled monoploid potato (DM). Furthermore, we further analyzed the WD40 genes might be involved in anthocyanin biosynthesis and drought stress in tetraploid potato cultivars based on RNA-seq data. In addition, a protein interaction network of two homologs of Arabidopsis TTG1, which is involved in anthocyanin biosynthesis, was constructed to identify proteins that might be related to anthocyanin biosynthesis. The result showed that there were 112 pairs of proteins interacting with TTG1, with 27 being differentially expressed in pigmented tissues. This study indicates that WD40 proteins in potato might be related to anthocyanin biosynthesis and abiotic stress responses.

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Section: Expression Profile Analysis Of Stwd40 Genesmentioning

confidence: 99%

The WD40 Gene Family in Potato (Solanum Tuberosum L.): Genome-Wide Analysis and Identification of Anthocyanin and Drought-Related WD40s

Liu

Coulter

et al. 2020

Agronomy

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“…Given the evidence of RACK1-lncCOBRA1 interaction (Figures 4-5) along with similarities in the phenotype of null mutants (Chen et al, 2006;Guo et al, 2019) and protein binding partners (Figures 4-5), we hypothesize that lncCOBRA1 functions with RACK1A as a scaffold to regulate plant germination and development.…”

Section: Lnccobra1-interacting Proteins May Mediate Germination Phenotype Observed In Mutantsmentioning

confidence: 86%

“…RACK1A is a major subunit of RACK1, which is a highly conserved scaffold protein present in all eukaryotic organisms studied, from Chlamydomonas to plants and humans (Adams et al, 2011). Several proteomics studies have identified a total of 293 proteins that interact with RACK1A (Stark et al, 2006;Cheng et al, 2015;Kundu et al, 2013;Guo et al, 2019;Olejnik et al, 2011;Speth et al, 2013), 40 of which (13.7%; p-value < 2.1 x 10 -28 ; hypergeometric test) were identified in at least 2 biological replicates of lncCOBRA1 pulldown in Col-0 (Figure 5E). This included RACK1B, another major subunit of RACK1 (Guo and Chen, 2008).…”

Section: Lnccobra1-interacting Proteins Are Highly Interconnectedmentioning

confidence: 99%

A conserved long intergenic non-coding RNA containing snoRNA sequences, lncCOBRA1, affects Arabidopsis germination and development

Kramer¹,

Kim

Palos

et al. 2021

Preprint

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Long non-coding RNAs (lncRNAs) are an increasingly studied group of non-protein-coding transcripts with a wide variety of molecular functions gaining attention for their roles in numerous biological processes. Nearly 6,000 lncRNAs have been identified in Arabidopsis thaliana but many have yet to be studied. Here, we examine a class of previously uncharacterized lncRNAs termed CONSERVED INBRASSICA RAPA (lncCOBRA) transcripts that were previously identified for their high level of sequence conservation in the related crop species Brassica rapa, their nuclear-localization and protein-bound nature. In particular, we focus on lncCOBRA1 and demonstrate that its abundance is highly tissue and developmental specific, with particularly high levels early in germination. lncCOBRA1 contains two snoRNAs domains within it, making it the first sno-lincRNA example in a non-mammalian system, though we find that it is processed differently than its mammalian counterparts. We further show that plants lacking lncCOBRA1 display patterns of delayed gemination and are overall smaller than wild-type plants. Lastly, we identify the proteins that interact with lncCOBRA1 and examine the protein-protein interaction network of lncCOBRA1-interacting proteins.

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“…In addition, we registered the significant downregulation of the S-adenosyl-L-homocysteine hydrolase HOG1. HOG1 is known to interact with the likewise repressed RECEPTOR FOR ACTIVATED C KINASE 1A product RACK1 [71], and hog1 knockout mutants are described to have an embryo growth arrest at the globular stage [72]. The downregulation of the HOG1 hub may contribute to the curtailed embryo development of the ami1/rty mutant.…”

Section: The Ami1/rty Mutant Shows Major Impairments In Gene Transcrimentioning

confidence: 99%

Accumulation of the Auxin Precursor Indole-3-Acetamide Curtails Growth through the Repression of Cell Proliferation and Development-Related Transcriptional Networks

Sánchez-Parra¹,

Pérez‐Alonso²,

Ortiz‐García³

et al. 2021

Preprint

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The major auxin, indole-3-acetic acid (IAA), is associated with a plethora of growth and developmental processes including embryo development, expansion growth, cambial activity, and the induction of lateral root growth. Accumulation of the auxin precursor indole-3-acetamide (IAM) induces stress related processes by stimulating abscisic acid (ABA) biosynthesis. How IAM signaling is controlled is, at present, unclear. Here, we characterize an ami1/rooty double mutant, that we initially generated to study the metabolic and phenotypic consequences of a genetic blockade of the indole glucosinolate and IAM pathways in Arabidopsis thaliana. Our mass spectrometric analyses of the mutant revealed that the combination of the two mutations is not sufficient to fully prevent the conversion of IAM to IAA. The detected strong accumulation of IAM was, however, recognized to substantially impair seed development. We further show by genome-wide expression studies that the double mutant is broadly affected in its translational capacity, and that a small number of cell proliferation and plant growth regulating transcriptional circuits are repressed by the high IAM content in the seed. In accordance with the previously described growth reduction in response to elevated IAM levels, our data support the hypothesis that IAM is a growth repressing counterpart to IAA.

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Profiling of the Receptor for Activated C Kinase 1a (RACK1a) interaction network in Arabidopsis thaliana

Cited by 15 publications

References 41 publications

The WD40 Gene Family in Potato (Solanum Tuberosum L.): Genome-Wide Analysis and Identification of Anthocyanin and Drought-Related WD40s

The WD40 Gene Family in Potato (Solanum Tuberosum L.): Genome-Wide Analysis and Identification of Anthocyanin and Drought-Related WD40s

A conserved long intergenic non-coding RNA containing snoRNA sequences, lncCOBRA1, affects Arabidopsis germination and development

Accumulation of the Auxin Precursor Indole-3-Acetamide Curtails Growth through the Repression of Cell Proliferation and Development-Related Transcriptional Networks

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