Identification of transcription factors that bind to the 5′-UTR of the barley PHO2 gene

Sega, Pawel; Kruszka, Katarzyna; Szewc, Lukasz; Szweykowska-Kulińska, Zofia; Pacak, Andrzej

doi:10.1007/s11103-019-00932-9

Cited by 18 publications

(26 citation statements)

References 86 publications

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“…Furthermore, our data may be used as a reference tool for parallel studies in other crop plants. [131]) growing under Pi-deficient (8 mg P/kg soil) and Pi-sufficient conditions (after addition of 60 mg P/kg soil), as described before [43]. On the 23rd day after sowing plant shoots (Zadoks decimal code 22-23 [132]), they were cut off and fresh tissue weight was measured.…”

Section: Discussionmentioning

confidence: 99%

“…In general, genes that are affected by Pi status possess characteristic cis-regulatory elements within either promoter or 5'-UTR regions [100]. Previously, we have shown the importance of the P1BS motif (PHR1 binding sequence, consensus GnATATnC, [101]) and P-responsive PHO elements (consensus ATGCCAT, [102]) in the expression efficiency of the barley PHO2 gene [43]. Both motifs may bind PHR-like (PHOSPHATE STARVATION RESPONSE) transcription factors (TFs) and act as activators or repressors of downstream gene expression in a Pi-dependent manner [103].…”

Section: Pi-responsive Motifs Found In the Promoters Of Degsmentioning

confidence: 99%

“…(ii) PARE library construction PARE library construction was performed as described previously [43,133]. Ligation was performed using a Rapid DNA Ligation Kit (Roche), according to the manufacturer instructions.…”

Section: Preparation Of Ngs Librariesmentioning

confidence: 99%

“…Transcriptome libraries were carried out using a mRNA-seq library prep kit v2 (Lexogen), according to the manufacturer's protocol and as previously described [43]. A 420 pg of Spike-In RNA Variants SIRV-set3 (Lexogen) was added to 1500 ng of total RNA.…”

Section: (Iii) Transcriptome Librariesmentioning

confidence: 99%

“…MiRNA399 targets the 5'-UTR of the barley PHO2 (PHOSPHATE 2) transcripts [43], encoding an ubiquitin-conjugating E2 enzyme (UBC24), a negative regulator of Pi uptake and root-to-shoot translocation. PHO2 is involved in ubiquitination of Pi transporters [44].…”

Section: Introductionmentioning

confidence: 99%

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Pi-starvation induced transcriptional changes in barley revealed by a comprehensive RNA-Seq and degradome analyses

Sega

Kruszka

Bielewicz

et al. 2020

Preprint

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Background: Small RNAs (sRNAs) are 18–24 nt regulatory elements which are responsible for plant development regulation and participate in many plant stress responses. Insufficient inorganic phosphate (Pi) concentration triggers plant responses to balance the internal Pi level. Results: In this study, we describe Pi-starvation-responsive small RNAs and transcriptome changes in barley (Hordeum vulgare L.) using Next-Generation Sequencing (NGS) data derived from three different types of NGS libraries: (i) small RNAs, (ii) degraded RNAs, and (iii) functional mRNAs. We find that differentially and significantly expressed miRNAs (DEMs, p-value < 0.05) are represented by 162 (44.88 % of total differentially expressed small RNAs) molecules in shoot and 138 (7.14 %) in root; mainly various miR399 and miR827 isomiRs. The remaining small RNAs (i.e., those without perfect match to reference sequences deposited in miRBase) are considered as differentially expressed other sRNAs (DESs, Bonferroni correction). In roots, a more abundant and diverse set of other sRNAs (1796 unique sequences, 0.13 % from total unique reads obtained under low-Pi) contributes more to the compensation of low-Pi stress than that in shoots (199 unique sequences, 0.01 %). More than 80 % of differentially expressed other sRNAs are upregulated in both organs. Additionally, in barley shoots, upregulation of small RNAs is accompanied by strong induction of two nucleases (S1/P1 endonuclease and 3’-5’ exonuclease). This suggests that most small RNAs may be generated upon endonucleolytic cleavage to increase the internal Pi pool. Transcriptomic profiling of Pi-starved barley shoots identify 98 differentially expressed genes (DEGs). A majority of the DEGs possess characteristic Pi-responsive cis-regulatory elements (P1BS and/or PHO element), located mostly in the proximal promoter regions. GO analysis shows that the discovered DEGs primarily alter plant defense, plant stress response, nutrient mobilization, or pathways involved in the gathering and recycling of phosphorus from organic pools.Conclusions: Our results provide comprehensive data to demonstrate complex responses at the RNA level in barley to maintain Pi homeostasis and indicate that barley adapts to Pi scarcity through elicitation of RNA degradation. Novel P-responsive genes were selected as putative candidates to overcome low-Pi stress in barley plants.

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Section: Discussionmentioning

confidence: 99%

Section: Pi-responsive Motifs Found In the Promoters Of Degsmentioning

confidence: 99%

Section: Preparation Of Ngs Librariesmentioning

confidence: 99%

Section: (Iii) Transcriptome Librariesmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Pi-starvation induced transcriptional changes in barley revealed by a comprehensive RNA-Seq and degradome analyses

Sega

Kruszka

Bielewicz

et al. 2020

Preprint

Self Cite

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MicroRNAs as potent regulators in nitrogen and phosphorus signaling transduction and their applications

Yang,

Liang,

Wang

et al. 2024

Stress Biology

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Nitrogen (N) and phosphorus (Pi) are essential macronutrients that affect plant growth and development by influencing the molecular, metabolic, biochemical, and physiological responses at the local and whole levels in plants. N and Pi stresses suppress the physiological activities of plants, resulting in agricultural productivity losses and severely threatening food security. Accordingly, plants have elaborated diverse strategies to cope with N and Pi stresses through maintaining N and Pi homeostasis. MicroRNAs (miRNAs) as potent regulators fine-tune N and Pi signaling transduction that are distinct and indivisible from each other. Specific signals, such as noncoding RNAs (ncRNAs), interact with miRNAs and add to the complexity of regulation. Elucidation of the mechanisms by which miRNAs regulate N and Pi signaling transduction aids in the breeding of plants with strong tolerance to N and Pi stresses and high N and Pi use efficiency by fine-tuning MIR genes or miRNAs. However, to date, there has been no detailed and systematic introduction and comparison of the functions of miRNAs in N and Pi signaling transduction from the perspective of miRNAs and their applications. Here, we summarized and discussed current advances in the involvement of miRNAs in N and Pi signaling transduction and highlighted that fine-tuning the MIR genes or miRNAs involved in maintaining N and Pi homeostasis might provide valuable sights for sustainable agriculture.

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Mysteries of gene regulation: Promoters are not the sole triggers of gene expression

Chow

Tseng

Hou

et al. 2022

Computational and Structural Biotechnology Journal

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Identification of transcription factors that bind to the 5′-UTR of the barley PHO2 gene

Cited by 18 publications

References 86 publications

Pi-starvation induced transcriptional changes in barley revealed by a comprehensive RNA-Seq and degradome analyses

Pi-starvation induced transcriptional changes in barley revealed by a comprehensive RNA-Seq and degradome analyses

MicroRNAs as potent regulators in nitrogen and phosphorus signaling transduction and their applications

Mysteries of gene regulation: Promoters are not the sole triggers of gene expression

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