Plant PUF RNA-binding proteins: A wealth of diversity for post-transcriptional gene regulation

Joshna, Chris R.; Saha, Pritha; Atugala, Dilini; Chua, Gordon; Muench, Douglas G.

doi:10.1016/j.plantsci.2020.110505

Cited by 12 publications

(9 citation statements)

References 93 publications

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“…The transcription factor (TF) gene MYB75 (AT1G56650) regulates various biosynthetic pathways and is involved in the responses to light [63] and to fungus [64], for instance, and we confirmed its mRNA as a target of a novel miRNA by 5 RACE (Figure 9); this means that MYB75 could be regulated by ABA via the novel miRNA (ath-miRn-6) in Arabidopsis. Another novel miRNA target gene highlighted in our study is PUM3 (AT2G29140), whose cognate protein was previously reported to be a mRNA-binding protein [65,66]. Thus, we propose that these novel miRNAs could be involved in many functions controlled by various mechanisms in Arabidopsis.…”

Section: Discussionmentioning

confidence: 61%

Identification of Novel miRNAs and Their Target Genes in the Response to Abscisic Acid in Arabidopsis

Mehdi

Krishnamoorthy

Szcześniak

et al. 2021

IJMS

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miRNAs are involved in various biological processes, including adaptive responses to abiotic stress. To understand the role of miRNAs in the response to ABA, ABA-responsive miRNAs were identified by small RNA sequencing in wild-type Arabidopsis, as well as in abi1td, mkkk17, and mkkk18 mutants. We identified 10 novel miRNAs in WT after ABA treatment, while in abi1td, mkkk17, and mkkk18 mutants, three, seven, and nine known miRNAs, respectively, were differentially expressed after ABA treatment. One novel miRNA (miRn-8) was differentially expressed in the mkkk17 mutant. Potential target genes of the miRNA panel were identified using psRNATarget. Sequencing results were validated by quantitative RT-PCR of several known and novel miRNAs in all genotypes. Of the predicted targets of novel miRNAs, seven target genes of six novel miRNAs were further validated by 5′ RLM-RACE. Gene ontology analyses showed the potential target genes of ABA-responsive known and novel miRNAs to be involved in diverse cellular processes in plants, including development and stomatal movement. These outcomes suggest that a number of the identified miRNAs have crucial roles in plant responses to environmental stress, as well as in plant development, and might have common regulatory roles in the core ABA signaling pathway.

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Section: Discussionmentioning

confidence: 61%

Identification of Novel miRNAs and Their Target Genes in the Response to Abscisic Acid in Arabidopsis

Mehdi

Krishnamoorthy

Szcześniak

et al. 2021

IJMS

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“…Few sequence-specific RNA binding proteins have been identified in plants that regulate the translation of specific mRNAs. However, members of the PUF (Pumilio/FBF) family are attractive candidates because they are known to regulate translation and RNA stability by binding specific UTRs in animals and fungi (Goldstrohm et al, 2018; Wang et al, 2018), and the PUF family is unusually large in plants (Dedow and Bailey-Serres, 2019; Joshna et al, 2020). Furthermore, the UGUGCCG motif that is enriched in 3’ UTRs of the BS set (Fig.…”

Section: Resultsmentioning

confidence: 99%

Ribosome profiling elucidates differential gene expression in bundle sheath and mesophyll cells in maize

Chotewutmontri

Barkan

2020

Preprint

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The efficiencies offered by C4 photosynthesis have motivated efforts to understand its biochemical, genetic and developmental basis. Reactions underlying C4 traits in most C4 plants are partitioned between two cell types, bundle sheath (BS) and mesophyll (M) cells. RNA-seq has been used to catalog differential gene expression in BS and M cells in maize and several other C4 species. However, the contribution of translational control to maintaining the distinct proteomes of BS and M cells has not been addressed. In this study, we used ribosome profiling (ribo-seq) and RNA-seq to describe translatomes, translational efficiencies, and microRNA abundance in BS and M-enriched fractions of maize seedling leaves. A conservative interpretation of our data revealed 39 genes exhibiting cell-type dependent differences in translational efficiency, fourteen of which encode proteins with core roles in C4 photosynthesis. Use of more relaxed criteria that are widely used in ribo-seq studies increased the set of differentially translated genes to several hundred. In addition, our data expand the set of genes known to be differentially expressed in BS and M cells, including genes encoding transcription factors and microRNAs. These data add to the resources for understanding the evolutionary and developmental basis of C4 photosynthesis and for its engineering into C3 crops.

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“…Pumilio (Pum)/Puf family RNA binding proteins are highly conserved in various organisms [ 10 , 11 ]. Interestingly, plant Pum genes have more highly diverse members than mammalian Pum genes.…”

Section: Evolutionally Conserved Pumilio Rna Binding Proteinsmentioning

confidence: 99%

“…APUM5 has a putative transmembrane domain in the N-terminal region and localizes to cytoplasmic-punctuated structures and vacuolar structures in tobacco epidermal cells [ 40 ]. Recently, regarding APUM6 subcellular localization, it has been clearly observed that APUM6 localizes on the surface of the endoplasmic reticulum (ER) but still shows dynamic localization patterns [ 10 ]. APUM6 might have diverse functions in different organelles.…”

Section: Dynamic Subcellular Localization Of Plant Pummentioning

confidence: 99%

The Role of Pumilio RNA Binding Protein in Plants

Huh

2021

Biomolecules

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Eukaryotic organisms have a posttranscriptional/translational regulation system for the control of translational efficiency. RNA binding proteins (RBPs) have been known to control target genes. One type of protein, Pumilio (Pum)/Puf family RNA binding proteins, show a specific binding of 3′ untranslational region (3′ UTR) of target mRNA and function as a post-transcriptional/translational regulator in eukaryotic cells. Plant Pum protein is involved in development and biotic/abiotic stresses. Interestingly, Arabidopsis Pum can control target genes in a sequence-specific manner and rRNA processing in a sequence-nonspecific manner. As shown in in silico Pum gene expression analysis, Arabidopsis and rice Pum genes are responsive to biotic/abiotic stresses. Plant Pum can commonly contribute to host gene regulation at the post-transcriptional/translational step, as can mammalian Pum. However, the function of plant Pum proteins is not yet fully known. In this review, we briefly summarize the function of plant Pum in defense, development, and environmental responses via recent research and bioinformatics data.

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Plant PUF RNA-binding proteins: A wealth of diversity for post-transcriptional gene regulation

Cited by 12 publications

References 93 publications

Identification of Novel miRNAs and Their Target Genes in the Response to Abscisic Acid in Arabidopsis

Identification of Novel miRNAs and Their Target Genes in the Response to Abscisic Acid in Arabidopsis

Ribosome profiling elucidates differential gene expression in bundle sheath and mesophyll cells in maize

The Role of Pumilio RNA Binding Protein in Plants

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