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ABP1-regulated gene expression in etiolated Arabidopsis seedlings

ABSTRACT: The AUXIN BINDING PROTEIN 1 (ABP1) is an essential plant protein involved in the control of growth and development all along the plant life. This protein was initially identified on its capacity to bind the phytohormone auxin. Binding of auxin to ABP1 was shown to enhance cell expansion of leaf cells. Conversely, the functional inactivation of ABP1 was demonstrated to severely impair cell expansion in shoot tissues. To date, the mechanism by which ABP1 controls cell expansion is still poorly understood. ABP1 was reported to affect expression of various auxin regulated genes but little is known on broader effects of ABP1 on gene expression. Here we have investigated the role of ABP1 in the control of cell expansion using dark grown hypocotyls by analyzing changes in gene expression resulting from ABP1 inactivation.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE46196 | GEO | 2015/04/07

SECONDARY ACCESSION(S): PRJNA198018

REPOSITORIES: GEO

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ABP1-regulated gene expression in etiolated Arabidopsis seedlings

Project description:The AUXIN BINDING PROTEIN 1 (ABP1) is an essential plant protein involved in the control of growth and development all along the plant life. This protein was initially identified on its capacity to bind the phytohormone auxin. Binding of auxin to ABP1 was shown to enhance cell expansion of leaf cells. Conversely, the functional inactivation of ABP1 was demonstrated to severely impair cell expansion in shoot tissues. To date, the mechanism by which ABP1 controls cell expansion is still poorly understood. ABP1 was reported to affect expression of various auxin regulated genes but little is known on broader effects of ABP1 on gene expression. Here we have investigated the role of ABP1 in the control of cell expansion using dark grown hypocotyls by analyzing changes in gene expression resulting from ABP1 inactivation. Experiments were performed using the control transgenic line Alc-GUS and the SS12K9, which express GUS and ABP1, respectively, in response to ethanol treatment. Three biological repeats were prepared. RNA samples were labelled with Cy5 and Cy3 as indicated below. Samples from the SS12K9 line were compared to the corresponding control line.

2015-04-07 | E-GEOD-46196 | biostudies-arrayexpress

ABP1-TMK auxin perception mediates rapid phosphorylation for regeneration and auxin canalization

Project description:The phytohormone auxin triggers transcriptional reprograming utilizing a well-characterized nuclear perception machinery. In contrast, mechanisms underlying other auxin effects, such as auxin feed-back on its transport, rapid regulation of ion fluxes or ultrafast global phospho-response, remain enigmatic. Auxin Binding Protein 1 (ABP1) has been contested as an auxin receptor candidate since decades. Here we show that a fraction of Arabidopsis thaliana ABP1 is secreted and binds auxin specifically at the acidic pH typical for the apoplast. ABP1 and its plasma membrane-localized partner, Transmembrane Kinase 1 (TMK1) are required for auxin-induced phosphorylation of about thousand proteins. Loss-of-function abp1 alleles but not complemented lines show defects in in vitro shoot regeneration and formation of auxin-transporting channels for vasculature formation and regeneration. These results support a role of ABP1-TMK1 in cell surface auxin perception mediating global auxin phospho-response and regenerative development.

2022-08-25 | PXD031063 | Pride

ABLs and TMKs are co-receptors for extracellular auxin

Project description:Extracellular perception of auxin, an essential phytohormone in plants, has been debated for decades. Auxin binding protein 1 (ABP1) physically interacts with quintessential transmembrane kinases (TMKs) and was proposed to act as an extracellular auxin receptor, but its role was disputed because abp1 knockout mutants lack obvious morphological phenotypes. Here we identified two new auxin-binding proteins, ABL1 and ABL2, that are localized to the apoplast and directly interact with the extracellular domain of TMKs in an auxin-dependent manner. Furthermore, functionally redundant ABL1 and ABL2 genetically interact with TMKs and exhibit functions that are overlapping with those of ABP1 as well as independent of ABP1. Importantly, the extracellular domain of TMK1 itself binds auxin and synergizes with either ABP1 or ABL1 in auxin binding. Thus, our findings discovered new auxin receptors ABL1 and ABL2 having functions overlapping with but distinct from ABP1 and acting together with TMKs as co-receptors for extracellular auxin.

2023-11-25 | PXD044623 | Pride

Arabidopsis SAURs Are Critical for Differential Light Regulation of the Development of Various Organs

Project description:During de-etiolation of Arabidopsis seedlings, light promotes the expansion of cotyledons but inhibits the elongation of hypocotyls. The mechanism of this differential regulation of cell enlargement is unclear. Our organ-specific transcriptomic analysis identified 32 Small Auxin Up RNA (SAUR) genes whose transcripts were light-induced in cotyledons and/or repressed in hypocotyls. We therefore named these SAURs as lirSAURs. Both overexpression and mutation analyses demonstrated that lirSAURs could promote cotyledon expansion and opening and enhance hypocotyl elongation, possibly by inhibiting phosphatase activity of PP2C-Ds. Light reduced auxin levels to down-regulate the expression of lirSAURs in hypocotyls. Further, phytochrome-interacting factors (PIFs) were shown

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TMK-based cell surface auxin signaling activates cell wall acidification in Arabidopsis

Project description:The phytohormone auxin controls a myriad of processes in plants, at least in part through its regulation of cell expansion. The "acid growth hypothesis" has been proposed to explain auxin-stimulated cell expansion for five decades, but the mechanism underlying auxin-induced cell wall acidification is poorly characterized. Auxin induces the phosphorylation and activation of the plasma membrane (PM) H+-ATPase that pumps protons into the apoplast, yet how auxin activates its phosphorylation remains elusive. Here, we show that the transmembrane kinase (TMK) auxin signaling proteins interact with PM H+-ATPases and activate their phosphorylation to promote cell wall acidification and hypocotyl cell elongation in Arabidopsis. Auxin induced TMK's interaction with H+-ATPase on the plasma membrane within 1-2 minutes as well as TMK-dependent phosphorylation of the penultimate Thr residue. Genetic, biochemical, and molecular evidence demonstrates that TMKs directly phosphorylate PM H+-ATPase and are required for auxin-induced PM H+-ATPase activation, apoplastic acidification, and cell expansion. Thus, our findings reveal a crucial connection between auxin and PM H+-ATPase activation in regulating apoplastic pH changes and cell expansion via TMK-based cell surface auxin signaling.

2021-07-14 | MSV000087822 | MassIVE

Bacillus subtilis strain:ABP1

Project description:Bacillus subtilis strain:ABP1 Genome sequencing and assembly

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The CENP-B fission yeast homolog, ABP1, is involved in the repression of cryptic transcription from the Tf2 and rRNA genes repeat [smallRNA-Seq]

Project description:In Schizosaccharomyces pombe, Abp1 is homologous to mammalian CENP-B. Abp1 has various seemingly independent functions in the yeast nucleus. It binds to pericentromeric repeats and contribute to heterochromatin formation (ref). Abp1 is involved in regulating the directionality of mating-type switching by regulating the transcription of a member of the recombination-promoting complex (refs). Abp1 also preserves genome integrity by silencing the Tf2 retrotransposons and protecting replication forks during pausing (ref). The profile of the RNA extracted from abp1Δ cells shows an accumulation of RNA in size ranging between 100 and 200 bp. Solexa sequencing of these “little RNA” (liRNA) and comparison of their levels with the WT showed an increase in liRNA coming from various classes of genomic features. The biggest fold changes are attributed to liRNA coming from LTR retrotransposons and the rDNA genes repeats. We show that these liRNAs are targeted for degradation by the exosome and are the products of pervasive RNA Polymerase II transcription. Finally, we describe the genetic interactions of various transcriptional gene silencing effectors with the abp1 deletion in the silencing of the liRNA.

2016-07-08 | GSE81280 | GEO

The CENP-B fission yeast homolog, ABP1, is involved in the repression of cryptic transcription from the Tf2 and rRNA genes repeat [ChIP-Seq_CNAG]

2016-07-08 | GSE81324 | GEO

The CENP-B fission yeast homolog, ABP1, is involved in the repression of cryptic transcription from the Tf2 and rRNA genes repeat [ChIP-Seq_BGI]

2016-07-08 | GSE81323 | GEO

Expression analysis of picloram responsive genes preceding cell elongation in Arabidopsis hypocotyls.

Project description:In this study we profile expression of target genes downstream of auxin signaling in Arabidopsis hypocotyls elongating in response to auxin. The synthetic auxin picloram is used in order to take advantage of the picloram-resistant auxin receptor mutant afb5-5, which fails to elongate in response to picloram. A 4-plex chip was used for analyzing the transcriptome in hypocotyls dissected from wild-type seedlings following a 30min and 2hr picloram or solvent control treatment. Three biological replicate samples were analyzed, each containing roughly 400 hypocotyls. A 12-plex chip was used for analyzing mRNA from hypocotyls dissected from wild-type and afb5-5 (SALK_110643) mutant seedlings following a 2hr picloram or solvent control treatment. Three biological replicates were analyzed, each containing roughly 700 hypocotyls.

2012-04-12 | E-GEOD-37217 | biostudies-arrayexpress

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