PsORF: a database of small ORFs in plants

Chen, Yanjun; Li, Danyang; Fan, Weiliang; Zheng, Xiaoming; Zhou, Yifan; Ye, Hanzhe; Liang, Xiaodong; Du, Wei; Zhou, Yu; Wang, Kun

doi:10.1111/pbi.13389

Cited by 41 publications

(30 citation statements)

References 10 publications

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“…MicroProteins are small proteins that interact with and modulate the activity of large proteins [ 45 ]. Recently, an improved algorithm capable of processing poorly annotated genomes and advanced translatomics was employed to predict small proteins and their interacting partners [ 46 , 47 ]. This strategy can be used to identify the function of the small protein itself or the effects of small proteins on their interacting partners.…”

Section: Discussionmentioning

confidence: 99%

Overexpression of Rice OsS1Fa1 Gene Confers Drought Tolerance in Arabidopsis

Kim

Lee

Kwak

et al. 2021

Plants

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Small peptides and proteins play critical regulatory roles in plant development and environmental stress responses; however, only a few of these molecules have been identified and characterized to date because of their poor annotation and other experimental challenges. Here, we present that rice (Oryza sativa L.) OsS1Fa1, a small 76-amino acid protein, confers drought stress tolerance in Arabidopsis thaliana. OsS1Fa1 was highly expressed in leaf, culm, and root tissues of rice seedlings during vegetative growth and was significantly induced under drought stress. OsS1Fa1 overexpression in Arabidopsis induced the expression of selected drought-responsive genes and enhanced the survival rate of transgenic lines under drought. The proteasome inhibitor MG132 protected the OsS1Fa1 protein from degradation. Together, our data indicate that the small protein OsS1Fa1 is induced by drought and is post-translationally regulated, and the ectopic expression of OsS1Fa1 protects plants from drought stress.

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Section: Discussionmentioning

confidence: 99%

Overexpression of Rice OsS1Fa1 Gene Confers Drought Tolerance in Arabidopsis

Kim

Lee

Kwak

et al. 2021

Plants

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“…Most of the intergenic smORFs are probably not translated and non-functional [ 173 ]. Nevertheless, smORFs have been shown to be a source of functional peptides, regulating key processes in cells [ 117 , 174 ]. Well-studied examples of functional peptides or microproteins encoded by short CDSs are some classes of antimicrobial peptides (AMP), which have been found in a range of organisms from bacteria to plants and animals [ 175 ].…”

Section: Biological Function Of Different Peptide Groupsmentioning

confidence: 99%

“…Plants also have homologs of mammalian defensins that are encoded by short CDS [ 179 ]. Peptides encoded by lncRNAs are the least studied component of peptide pools, but this group may potentially include thousands of peptides [ 174 ]. The functional analysis of peptides encoded by lncRNA transcripts was mainly performed on animals [ 117 ].…”

Section: Biological Function Of Different Peptide Groupsmentioning

confidence: 99%

Peptidome: Chaos or Inevitability

Lyapina

Иванов

Fesenko

2021

IJMS

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Thousands of naturally occurring peptides differing in their origin, abundance and possible functions have been identified in the tissue and biological fluids of vertebrates, insects, fungi, plants and bacteria. These peptide pools are referred to as intracellular or extracellular peptidomes, and besides a small proportion of well-characterized peptide hormones and defense peptides, are poorly characterized. However, a growing body of evidence suggests that unknown bioactive peptides are hidden in the peptidomes of different organisms. In this review, we present a comprehensive overview of the mechanisms of generation and properties of peptidomes across different organisms. Based on their origin, we propose three large peptide groups—functional protein “degradome”, small open reading frame (smORF)-encoded peptides (smORFome) and specific precursor-derived peptides. The composition of peptide pools identified by mass-spectrometry analysis in human cells, plants, yeast and bacteria is compared and discussed. The functions of different peptide groups, for example the role of the “degradome” in promoting defense signaling, are also considered.

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“…Currently, there are a few databases for small proteins such as ARA-PEPs [69], PsORF [70], and sORFs.org [71]. ARA-PEPs and PsORF only harbors small proteins in plants.…”

Section: Database Content and Usagementioning

confidence: 99%

SmProt: A Reliable Repository with Comprehensive Annotation of Small Proteins Identified from Ribosome Profiling

Zhou

Chen

et al. 2021

Preprint

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Small proteins specifically refer to proteins consisting of less than 100 amino acids translated from small open reading frames (sORFs), which were usually missed in previous genome annotation. The significance of small proteins has been revealed in current years, along with the discovery of their diverse functions. However, systematic annotation of small proteins is still insufficient. SmProt was specially developed to provide valuable information on small proteins for scientific community. Here we present the update of SmProt, which emphasizes reliability of translated sORFs, genetic variants in translated sORFs, disease-specific sORFs translation events or sequences, and significantly increased data volume. More components such as non-AUG translation initiation, function, and new sources are also included. SmProt incorporated 638,958 unique small proteins curated from 3,165,229 primary records, which were computationally predicted from 419 ribosome profiling (Ribo-seq) datasets and collected from the literature and other sources originating from 370 cell lines or tissues in 8 species (Homo sapiens, Mus musculus, Rattus norvegicus, Drosophila melanogaster, Danio rerio, Saccharomyces cerevisiae, Caenorhabditis elegans, and Escherichia coli). In addition, small protein families identified from human microbiomes were collected. All datasets in SmProt are free to access, and available for browse, search, and bulk downloads at http://bigdata.ibp.ac.cn/SmProt/.

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PsORF: a database of small ORFs in plants

Cited by 41 publications

References 10 publications

Overexpression of Rice OsS1Fa1 Gene Confers Drought Tolerance in Arabidopsis

Overexpression of Rice OsS1Fa1 Gene Confers Drought Tolerance in Arabidopsis

Peptidome: Chaos or Inevitability

SmProt: A Reliable Repository with Comprehensive Annotation of Small Proteins Identified from Ribosome Profiling

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