Small open reading frames in plant research: from prediction to functional characterization

Ong, Sheue Ni; Tan, Boon Chin; Al-Idrus, Aisyafaznim; Teo, Chee How

doi:10.1007/s13205-022-03147-w

Cited by 13 publications

(27 citation statements)

References 153 publications

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“…For the enriched KEGG pathways, the transcribed sORFs in both varieties were enriched in KEGG Ontology (KO) terms of plant hormone signal transduction. Plant sORFs have been demonstrated to play important roles in cell signalling, abiotic stress response, morphogenesis, and growth regulation (Hanada et al, 2013; Bashir et al, 2014; Ong et al, 2022). Apart from that, some of the transcribed sORFs identified in C. sativus var.…”

Section: Resultsmentioning

confidence: 99%

“…To date, there is still no standard classification for sORFs but researchers have made attempts to classify them into different categories (Ong et al, 2022). Ong et al (2022) have summarized classifications from several studies, namely, sORF (Orr et al, 2020), upstream ORF (uORF; Couso and Patraquim, 2017; Fesenko et al, 2019; Khitun et al, 2019; Orr et al, 2020; Takahashi et al, 2019), intergenic sORF (Couso and Patraquim, 2017; Khitun et al, 2019), sORF with translational potential (Khitun et al, 2019), long noncoding ORF (lncORF; Couso and Patraquim, 2017), short CDS (Couso and Patraquim, 2017), short isoform (Couso and Patraquim, 2017), downstream ORF (dORF; Fesenko et al, 2019), CDS-sORF (Fesenko et al, 2019), interlaced-sORF (Fesenko et al, 2019), miPEP (Takahashi et al, 2019), microprotein (Takahashi et al, 2019), hormone-like peptides (Takahashi et al, 2019), and defensin (Takahashi et al, 2019). Other than coding regions, sORFs can also be found in mitochondrial RNAs, circular RNAs, and long noncoding RNAs (lncRNAs) (Orr et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

“…sORFs have been reported to get translated into small peptides and have functional roles in plants (Castellana et al, 2008; Hanada et al, 2013; Cabrera-Quio et al, 2016). Ong et al (2022) reviewed the roles of sORF-encoded proteins (SEPs) in several biological processes, including cell signaling, abiotic stress responses, morphogenesis, and growth regulations. In addition, studies also reported that short proteins also function as secreted peptides and hormones.…”

Section: Introductionmentioning

confidence: 99%

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In silicocomparative RNA-seq analysis reveals varietal-specific intergenic small open reading frames inCucumis sativusL.

Chieng

Tan

Teo

2022

Preprint

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Small open reading frames (sORFs) have been reported to play important roles in growth, regulation of morphogenesis, and abiotic stress responses in various plant species. However, their sequences and functions remain poorly understood in many plant species including Cucumis sativus. Cucumis sativus (commonly known as cucumber) is Asia's fourth most important vegetable and the second most important crop in Western Europe. The breeding of climate-resilient cucumbers is of great importance to ensure their sustainability under extreme climate conditions. In this study, we aim to isolate the intergenic sORFs from C. sativus var. hardwickii genome and determine their sequence diversity and expression profiles in C. sativus var. hardwickii and different cultivars of C. sativus var. sativus using bioinformatics tools. We identified a total of 50,191 coding sORFs with coding potential (coding sORFs) from C. sativus var. hardwickii genome. In addition, 1,311 transcribed sORFs were detected in RNA-seq datasets of C. sativus var. hardwickii and shared homology to sequences deposited in the cucumber EST database, and among these, 91 transcribed sORFs with translation potential were detected. A total of 629 high-confident C. sativus-specific sORFs were identified in both varieties. Varietal-specific transcribed sORFs were also identified in C. sativus var. hardwickii (87) and C. sativus var. sativus (2,906). Furthermore, cultivar- and tissue-specific transcribed sORFs were identified in different cultivars and tissue samples. The findings of this study provide insight into sequence diversity and expression patterns of sORFs in C. sativus, which could help in developing climate-resilient cucumbers.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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In silicocomparative RNA-seq analysis reveals varietal-specific intergenic small open reading frames inCucumis sativusL.

Chieng

Tan

Teo

2022

Preprint

Self Cite

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“…Short/small open reading frames (sORFs) with the capacity of encoding micropeptides shorter than 100 amino acids (aa) are widely distributed in plants, ranging from green algae ( Xu et al., 2017a ) to rice ( Yang et al., 2021 ) and Arabidopsis ( Hanada et al., 2007 ), and are engaged in various biological and molecular processes, such as plant growth, nitrogen response, symbiosis nitrogen fixation, stomatal closure, plant circadian clock, anther development, pollen tube growth, abiotic responses, plant disease resistance, morphogenesis, and growth regulation ( Ong et al., 2022 ; Wu et al., 2022 ). sORFs are pervasive in plant genomes and have been detected beyond the known coding regions.…”

Section: Introductionmentioning

confidence: 99%

“…Overexpressing miPEP171b in M. truncatula roots specifically improves the accumulation of endogenous mature miRNAs, resulting in a reduction in lateral root density to a similar extent as overexpression of the corresponding pri-miR171b . Furthermore, the peptides encoded by the sORFs, per se , can also be functional, involving various biological processes (reviewed in Ong et al., 2022 ). Given that sORFs can substantially regulate the translation of downstream ORFs and encode proteins with crucial functions, the mutation of many sORFs, particularly uORFs, would lead to dramatic phenotype changes in plants and crops.…”

Section: Introductionmentioning

confidence: 99%

Identification of short open reading frames in plant genomes

Jiang¹,

Yu²,

Zhou³

2023

Front. Plant Sci.

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The roles of short/small open reading frames (sORFs) have been increasingly recognized in recent years due to the rapidly growing number of sORFs identified in various organisms due to the development and application of the Ribo-Seq technique, which sequences the ribosome-protected footprints (RPFs) of the translating mRNAs. However, special attention should be paid to RPFs used to identify sORFs in plants due to their small size (~30 nt) and the high complexity and repetitiveness of the plant genome, particularly for polyploidy species. In this work, we compare different approaches to the identification of plant sORFs, discuss the advantages and disadvantages of each method, and provide a guide for choosing different methods in plant sORF studies.

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Shining in the dark: the big world of small peptides in plants

et al. 2023

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Small peptides represent a subset of dark matter in plant proteomes. Through differential expression patterns and modes of action, small peptides act as important regulators of plant growth and development. Over the past 20 years, many small peptides have been identified due to technical advances in genome sequencing, bioinformatics, and chemical biology. In this article, we summarize the classification of plant small peptides and experimental strategies used to identify them as well as their potential use in agronomic breeding. We review the biological functions and molecular mechanisms of small peptides in plants, discuss current problems in small peptide research and highlight future research directions in this field. Our review provides crucial insight into small peptides in plants and will contribute to a better understanding of their potential roles in biotechnology and agriculture.

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Small open reading frames in plant research: from prediction to functional characterization

Cited by 13 publications

References 153 publications

In silicocomparative RNA-seq analysis reveals varietal-specific intergenic small open reading frames inCucumis sativusL.

In silicocomparative RNA-seq analysis reveals varietal-specific intergenic small open reading frames inCucumis sativusL.

Identification of short open reading frames in plant genomes

Shining in the dark: the big world of small peptides in plants

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