Alternative polyadenylation is involved in auxin‐based plant growth and development

Hong, Liang; Ye, Congting; Lin, Juncheng; Fu, Haihui; Wu, Xiaohui; Li, Qingshun Quinn

doi:10.1111/tpj.13771

Cited by 42 publications

(43 citation statements)

References 69 publications

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“…S4, A and C). The trends of profiles were similar to those observed in Hong et al (2018). The slight difference in the frequencies of U in auxin-treated samples might be due to differences in durations of the auxin treatments in the two studies.…”

Section: Atcstf77 Affects Poly(a) Site Choicesupporting

confidence: 75%

Modulation of Auxin Signaling and Development by Polyadenylation Machinery

et al. 2018

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Polyadenylation influences gene expression by affecting mRNA stability, transport, and translatability. Here, we report that Cleavage stimulation Factor 77 (AtCstF77), a component of the pre-mRNA 3ʹ-end polyadenylation machinery, affects polyadenylation site (PAS) selection in transcripts of some auxin signaling genes in Arabidopsis (Arabidopsis thaliana). Disruption of AtCstF77 reduced auxin sensitivity and decreased the expression of the auxin reporter DR5-GFP. Null mutations of cstf77 caused severe developmental defects, but were not lethal as previously reported. cstf77-2 genetically interacted with transport inhibitor response 1 auxin signaling f-box 2 auxin receptor double mutants, further supporting that polyadenylation affects auxin signaling. AtCstF77 was ubiquitously expressed in embryos, seedlings, and adult plants. The AtCstF77 protein was localized in the nucleus, which is consistent with its function in pre-mRNA processing. We observed that PASs in transcripts from approximately 2,400 genes were shifted in the cstf77-2 mutant. Moreover, most of the PAS shifts were from proximal to distal sites. Auxin treatment also caused PAS shifts in transcripts from a small number of genes. Several auxin signaling or homeostasis genes had different PASs in their transcripts in the cstf77-2 mutant. The expression levels of AUXIN RESISTANT 2/INDOLE-3-ACETIC ACID 7 were significantly increased in the cstf77-2 mutant, which can partially account for the auxin resistance phenotype of this mutant. Our results demonstrate that AtCstF77 plays pleiotropic and critical roles in Arabidopsis development. Moreover, disruption of AtCstF64, another component of the polyadenylation machinery, led to developmental defects and reduced auxin response, similar to those of the cstf77-2 mutant. We conclude that AtCstF77 affects auxin responses, likely by controlling PAS selection of transcripts of some auxin signaling components. Auxin controls almost every aspect of plant growth and development, mainly by regulating gene expression at the transcriptional level (Salehin et al., 2015). Auxin is perceived by its receptor TRANSPORT INHIBITOR RESPONSE 1/AUXIN SIGNALING F-BOX (TIR1/AFB) and coreceptor AUXIN RESISTANT/INDOLE-3-ACETI C ACID (AUX/IAA). Auxin-regulated degradation of AUX/IAA proteins is a central step in auxin signaling. When auxin concentration is low, AUX/IAA repressors physically interact with auxin response factors (ARFs), preventing ARFs from binding to cis-elements of auxinresponsive genes. When auxin concentration is elevated, auxin binds to TIR1/AFBs, and enhances their interactions with AUX/IAA proteins. Subsequently, AUX/IAA proteins are ubiquitinated by the SCF TIR1/AFBs (SKP1-Cullin-F-box TIR1/AFBs) E3 ubiquitin ligases and are degraded by the 26S proteasome, freeing ARFs for transcription activation or repression (

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Section: Atcstf77 Affects Poly(a) Site Choicesupporting

confidence: 75%

Modulation of Auxin Signaling and Development by Polyadenylation Machinery

et al. 2018

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“…However, in oxt6, there was a significantly greater increase in the expression of ARF7 and ARF19 when exogenous IAA was applied than that of WT. This further validates the role of CPSF30 in auxin regulation of LRs growth and development to a greater extent through ARF19 [134].…”

Section: Fip1 and Cpsf30-l Regulatory Modulesupporting

confidence: 77%

Signalling Overlaps between Nitrate and Auxin in Regulation of The Root System Architecture: Insights from the Arabidopsis thaliana

Asim

Ullah

Oluwaseun

et al. 2020

IJMS

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Nitrate (NO 3 -) and auxin are key regulators of root growth and development, modulating the signalling cascades in auxin-induced lateral root formation. Auxin biosynthesis, transport, and transduction are significantly altered by nitrate. A decrease in nitrate (NO 3 -) supply tends to promote auxin translocation from shoots to roots and vice-versa. This nitrate mediated auxin biosynthesis regulating lateral roots growth is induced by the nitrate transporters and its downstream transcription factors. Most nitrate responsive genes (short-term and long-term) are involved in signalling overlap between nitrate and auxin, thereby inducing lateral roots initiation, emergence, and development. Moreover, in the auxin signalling pathway, the varying nitrate supply regulates lateral roots development by modulating the auxin accumulation in the roots. Here, we focus on the roles of nitrate responsive genes in mediating auxin biosynthesis in Arabidopsis root, and the mechanism involved in the transport of auxin at different nitrate levels. In addition, this review also provides an insight into the significance of nitrate responsive regulatory module and their downstream transcription factors in root system architecture in the model plant Arabidopsis thaliana.grow well when taking N only from NH 4 + [4]. This uptake system of N by the roots is under the synchronized control of nutrients availability and hormonal signalling [2,3]. Nitrate (NO 3 − ) plays a signal regulatory role in many physiological processes including root growth. The nutrient uptake efficiency depends on root system architecture in the soil [9], and these processes are controlled by several gene-transcript levels, which are regulated by NO 3 − [10].NO 3 regulates root branches under various signalling pathways, such as NRT1.1 (dual-affinity NO 3 − responsive gene), which is assumed to participate in the nitrate-sensing system [11,12], and also governed by auxin [13].Signalling communication is a general rule rather than an omission. For instance, it is cited that about 1545 genes were the nutrient-related signals of NO 3 − , NH 4 + , or both nitrogen forms. Also, 982 (64%) genes were controlled by hormonal signals [14]. Several studies reveal that hormone biosynthesis, transport, and transduction are significantly influenced by several mineral nutrients [11].Hormones play a key role in the root-growth adaptation to NO 3 − readiness [13]. Numerous studies have also shown that NO 3 − regulation of root system architecture (RSA) entails an overlap between NO 3 − and auxin signalling pathways [13,15]. IAA is the most researched and best naturally occurring active auxin [12], and it plays a specific role in the control of systemic inhibition of fresh lateral roots (LRs) developments in response to the sufficient supply of nitrate [16]. Both external NO 3 − and IAA supply significantly influence the auxin concentration in the tiller nodes [17]. As part of the root system, lateral root not only depends on the external NO 3 − supply, but also on the amount of inter...

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“…As mentioned above, Cd affects auxin signaling, which seems to involve changes in poly(A) site usage (Hong et al ., ). We found that a significant number of genes involved in auxin signaling were deregulated in fip1‐2 (Table S1e), and some of them displayed differential poly(A) usage (Table S1h).…”

Section: Resultsmentioning

confidence: 97%

“…In Arabidopsis, hypoxia leads to an increased usage of poly(A) sites within coding regions and the 5′‐UTR, affecting their stability and translation (De Lorenzo et al ., ). In addition, APA also seems to be important to maintain correct hormonal signaling, as in the case of auxin (Hong et al ., ). Recently, a T‐DNA insertional mutant in the FIP1 gene has been reported.…”

Section: Introductionmentioning

confidence: 97%

The polyadenylation factor FIP1 is important for plant development and root responses to abiotic stresses

et al. 2019

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Root development and its response to environmental changes is crucial for whole plant adaptation. These responses include changes in transcript levels. Here, we show that the alternative polyadenylation (APA) of mRNA is important for root development and responses. Mutations in FIP1, a component of polyadenylation machinery, affects plant development, cell division and elongation, and response to different abiotic stresses. Salt treatment increases the amount of poly(A) site usage within the coding region and 5 0 untranslated regions (5 0 -UTRs), and the lack of FIP1 activity reduces the poly(A) site usage within these non-canonical sites. Gene ontology analyses of transcripts displaying APA in response to salt show an enrichment in ABA signaling, and in the response to stresses such as salt or cadmium (Cd), among others. Root growth assays show that fip1-2 is more tolerant to salt but is hypersensitive to ABA or Cd. Our data indicate that FIP1-mediated alternative polyadenylation is important for plant development and stress responses.

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Alternative polyadenylation is involved in auxin‐based plant growth and development

Cited by 42 publications

References 69 publications

Modulation of Auxin Signaling and Development by Polyadenylation Machinery

Modulation of Auxin Signaling and Development by Polyadenylation Machinery

Signalling Overlaps between Nitrate and Auxin in Regulation of The Root System Architecture: Insights from the Arabidopsis thaliana

The polyadenylation factor FIP1 is important for plant development and root responses to abiotic stresses

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