Identification of short open reading frames in plant genomes

Jiang, Mengyun; Yu, Weichang; Zhou, Jian

doi:10.3389/fpls.2023.1094715

Cited by 5 publications

(7 citation statements)

References 53 publications

(61 reference statements)

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“…SDS-PAGE or HPLC), are more likely to achieve high coverage with low FDR than DIA. Nonetheless, there are many efforts to improve the processing of DIA (Yu et al, 2023) and we are starting to develop a mechanism to integrate DIA data into the PeptideAtlas build process. Of the 99 PXDs that we evaluated, 74 PXDs passed our inspection criteria, their raw MS/MS data were searched, and results incorporated into the first maize PeptideAtlas build.…”

Section: Features Of Maize Proteomexchange Submissionsmentioning

confidence: 99%

“…Therefore, the impact of alternative splicing for the cellular proteome in eukaryotes is still under debate 13–15 . In addition, plant genomes may also contain an unknown number of various types of small Open Reading Frames (sORFs) encoding for small proteins or peptides, that could be detected by MS 16–18 . The use of proteomics data for plant genome annotation is summarized under the term ‘proteogenomics’ 19 , and has been applied for the genomes of Arabidopsis ( Arabidopsis thaliana ) 20, 21 , rice ( Oryza sativa ) 22, 23 , maize 24 , grape ( Vitis vinifera ) 25 , and sweet potato ( Ipomoea batatas ) 26 and the perennial fruit cherry 27 .…”

Section: Introductionmentioning

confidence: 99%

“…Therefore, the impact of alternative splicing for the cellular proteome in eukaryotes is still under debate (Blencowe, 2017; Chaudhary et al, 2019; Tress et al, 2017). In addition, plant genomes may also contain an unknown number of various types of small Open Reading Frames (sORFs) encoding for small proteins or peptides, that could be detected by MS (Feng et al, 2023; Hazarika et al, 2017; van Wijk et al, 2021). The use of proteomics data for plant genome annotation is summarized under the term ‘proteogenomics’ (Song et al, 2023), and has been applied for the genomes of Arabidopsis ( Arabidopsis thaliana ) (Zhang et al, 2019; Zhu et al, 2017), rice ( Oryza sativa ) (Chen et al, 2020; Ren et al, 2019), maize (Castellana et al, 2014), grape ( Vitis vinifera ) (Chapman and Bellgard, 2017), and sweet potato ( Ipomoea batatas ) (Al-Mohanna et al, 2019) and the perennial fruit cherry (Xanthopoulou et al, 2021).…”

Section: Introductionmentioning

confidence: 99%

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TheZea maysPeptideAtlas – a new maize community resource

van Wijk,

Leppert,

Sun

et al. 2023

Preprint

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We developed the Maize PeptideAtlas resource (www.peptideatlas.org/builds/maize) to help solve questions about the maize proteome. Publicly available raw tandem mass spectrometry (MS/MS) data for maize were collected from ProteomeXchange and reanalyzed through a uniform processing and metadata annotation pipeline. These data are from a wide range of genetic backgrounds, including the inbred lines B73 and W22, many hybrids and their respective parents. Samples were collected from field trials, controlled environmental conditions, a range of (a)biotic conditions and different tissues, cell types and subcellular fractions. The protein search space included different maize genome annotations for the B73 inbred line from MaizeGDB, UniProtKB, NCBI RefSeq and for the W22 inbred line. 445 million MS/MS spectra were searched, of which 120 million were matched to 0.37 million distinct peptides. Peptides were matched to 66.2% of the proteins (one isoform per protein coding gene) in the most recent B73 nuclear genome annotation (v5). Furthermore, most conserved plastid- and mitochondrial-encoded proteins (NCBI RefSeq annotations) were identified. Peptides and proteins identified in the other searched B73 genome annotations will aid to improve maize genome annotation. We also illustrate high confidence detection of unique SNPs in the W22 proteome as compared to the B73 proteome. N-terminal acetylation, phosphorylation, ubiquitination, and three lysine acylations (K-acetyl, K-malonyl, K-hydroxybutyryl) were identified and can be inspected through a PTM viewer in PeptideAtlas. All matched MS/MS-derived peptide data are linked to spectral, technical and biological metadata. This new PeptideAtlas will be integrated with community resources including MaizeGDB athttps://www.maizegdb.org/and its JBrowse tracks.

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Section: Features Of Maize Proteomexchange Submissionsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

TheZea maysPeptideAtlas – a new maize community resource

van Wijk,

Leppert,

Sun

et al. 2023

Preprint

View full text Add to dashboard Cite

show abstract

“…Bioinformatic approaches based on evolutionary conservation or sequence homology to known sORFs have been attempted ( Olsen et al 2002 ; Lease and Walker 2006 ; Hanada et al 2007 , 2009 ; Zhou et al 2013 ; de Bang et al 2017 ; Feng et al 2023 ; Li et al 2023 ). However, accumulating evidence suggests that many sORFs have evolved recently during evolution ( Ruiz-Orera et al 2014 ; Sandmann et al 2023 ), and some sORFs are only conserved in specific families or small groups of plants.…”

Section: Introductionmentioning

confidence: 99%

Improved super-resolution ribosome profiling reveals prevalent translation of upstream ORFs and small ORFs in Arabidopsis

Wu,

Ai,

Teixeira

et al. 2023

The Plant Cell

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A crucial step in functional genomics is identifying actively translated ORFs and linking them to biological functions. The challenge lies in identifying short ORFs, as their identification is greatly influenced by data quality and depth. Here, we improved the coverage of super-resolution Ribo-seq in Arabidopsis (Arabidopsis thaliana), revealing uncharacterized translation events for nuclear, chloroplastic, and mitochondrial genes. Assisted by a transcriptome assembly, we identified 7,751 unconventional translation events, comprising 6,996 upstream ORFs (uORFs) and 209 downstream ORFs on annotated protein-coding genes, as well as 546 ORFs in presumed noncoding RNAs. Proteomic data confirmed the production of stable proteins from some of these unannotated translation events. We present evidence of active translation from primary transcripts of trans-acting small interfering RNAs (TAS1–4) and microRNAs (pri-MIR163 and pri-MIR169) and periodic ribosome stalling supporting cotranslational decay. Additionally, we developed a method for identifying extremely short uORFs, including 370 minimum uORFs (AUG-stop), and 2,921 tiny uORFs (2 to 10 amino acids) and 681 uORFs that overlap with each other. Remarkably, these short uORFs exhibit strong translational repression as do longer uORFs. We also systematically discovered 594 uORFs regulated by alternative splicing, suggesting widespread isoform-specific translational control. Finally, these prevalent uORFs are associated with numerous important pathways. In summary, our improved Arabidopsis translational landscape provides valuable resources to study gene expression regulation.

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“…Bioinformatic approaches based on evolutionary conservation or sequence homology to known sORFs have been attempted (Olsen et al, 2002;Lease and Walker, 2006;Hanada et al, 2007Hanada et al, , 2009Zhou et al, 2013;de Bang et al, 2017;Feng et al, 2023;Li et al, 2023). However, accumulating evidence suggests that many sORFs have evolved recently during evolution (Ruiz-Orera et al, 2014;Sandmann et al, 2023), and some sORFs are only conserved in specific families or small groups of plants.…”

Section: Introductionmentioning

confidence: 99%

Improved Super-Resolution Ribosome Profiling Revealed Prevalent Translation of Upstream ORFs and Small ORFs in Arabidopsis

Wu,

Ai,

Teixeira

et al. 2023

Preprint

View full text Add to dashboard Cite

A crucial step in functional genomics is identifying actively translated open reading frames (ORFs) that link biological functions. The challenge lies in identifying short ORFs, as they are greatly impacted by data quality and depth. Here, we improved the coverage of super-resolution Ribo-seq in Arabidopsis, revealing uncharacterized translation events in nucleus-, chloroplast-, and mitochondria-encoded genes. We identified 7,751 unconventional translation events, including 6,996 upstream ORFs (uORFs) and 209 downstream ORFs on annotated protein-coding genes, as well as 546 ncORFs on presumed non-coding RNAs. Proteomics data confirmed the production of stable proteins from some of the unannotated translation events. We present evidence of active translation on primary transcripts of tasiRNAs (TAS1-4) and microRNAs (pri-miR163, pri-miR169), and periodic ribosome stalling supporting co-translational decay. Additionally, we developed a method for identifying extremely short uORFs, including 370 minimum uORF (AUG-stop), and 2,984 tiny uORFs (2-10 aa), as well as 681 uORFs that overlap with each other. Remarkably, these short uORFs exhibit strong translational repression as longer uORFs. We also systematically discovered 594 uORFs regulated by alternative splicing, suggesting widespread isoform-specific translational control. Finally, these prevalent uORFs are associated with numerous important pathways. In summary, our improved Arabidopsis translational landscape provides valuable resources to study gene expression regulation.

show abstract

Identification of short open reading frames in plant genomes

Cited by 5 publications

References 53 publications

TheZea maysPeptideAtlas – a new maize community resource

TheZea maysPeptideAtlas – a new maize community resource

Improved super-resolution ribosome profiling reveals prevalent translation of upstream ORFs and small ORFs in Arabidopsis

Improved Super-Resolution Ribosome Profiling Revealed Prevalent Translation of Upstream ORFs and Small ORFs in Arabidopsis

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