Proteogenomics-based functional genome research: approaches, applications, and perspectives in plants

Song, Yuanlin; Das, Debatosh; Zhang, Youjun; Chen, Moxian; Fernie, Alisdair R.; Zhu, Fu Yuan; Han, Jun

doi:10.1016/j.tibtech.2023.05.010

Cited by 10 publications

(7 citation statements)

References 118 publications

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“…Advanced computational tools and bioinformatics approaches are employed to cross-reference and align data across these layers. This involves mapping proteomic data back to the genome and transcriptome, identifying correlations, and interpreting the functional implications of these associations [5,17].…”

Section: Methodological Framework Of Proteogenomicsmentioning

confidence: 99%

“…For instance, the study "Proteogenomics of clear cell renal cell carcinoma response to tyrosine kinase inhibitor" offers a deep dive into the intricate dynamics of ccRCC and its response to the tyrosine kinase inhibitor, sunitinib [17]. This comprehensive analysis, integrating proteogenomic data, provides a clearer understanding of the molecular differences between patients who respond to sunitinib treatment and those who do not.…”

Section: Proteogenomic Breakthroughs In Nephrology: Case Study Insightsmentioning

confidence: 99%

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Proteogenomics in Nephrology: A New Frontier in Nephrological Research

Chavali,

Coker,

Youngblood

et al. 2024

CIMB

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Proteogenomics represents a transformative intersection in nephrology, uniting genomics, transcriptomics, and proteomics to unravel the molecular intricacies of kidney diseases. This review encapsulates the methodological essence of proteogenomics and its profound implications in chronic kidney disease (CKD) research. We explore the proteogenomic pipeline, highlighting the integrated analysis of genomic, transcriptomic, and proteomic data and its pivotal role in enhancing our understanding of kidney pathologies. Through case studies, we showcase the application of proteogenomics in clear cell renal cell carcinoma (ccRCC) and Autosomal Recessive Polycystic Kidney Disease (ARPKD), emphasizing its potential in personalized treatment strategies and biomarker discovery. The review also addresses the challenges in proteogenomic analysis, including data integration complexities and bioinformatics limitations, and proposes solutions for advancing the field. Ultimately, this review underscores the prospective future of proteogenomics in nephrology, particularly in advancing personalized medicine and providing novel therapeutic insights.

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Section: Methodological Framework Of Proteogenomicsmentioning

confidence: 99%

Section: Proteogenomic Breakthroughs In Nephrology: Case Study Insightsmentioning

confidence: 99%

Proteogenomics in Nephrology: A New Frontier in Nephrological Research

Chavali,

Coker,

Youngblood

et al. 2024

CIMB

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“…An omics area that has a growing significance that can improve draft plant genomes, correct gene annotation, discover new translation initial sites, ORFs, and alternative splicing, and verify novel genes of the peptide/protein level is called proteogenomics (Nesvizhskii 2014 ; Song et al 2023 ). The usefulness of proteogenomics has been illustrated for instance for the model organism Arabidopsis (e.g., Castellana et al 2008 ; Zhu et al 2017 ; Willems et al 2017 , 2022 ).…”

Section: How Plant Genomes Facilitate Plant Functional Genomicsmentioning

confidence: 99%

Plant genome information facilitates plant functional genomics

Bernal-Gallardo,

de Folter

2024

Planta

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Main conclusion In this review, we give an overview of plant sequencing efforts and how this impacts plant functional genomics research. Abstract Plant genome sequence information greatly facilitates the studies of plant biology, functional genomics, evolution of genomes and genes, domestication processes, phylogenetic relationships, among many others. More than two decades of sequencing efforts have boosted the number of available sequenced plant genomes. The first plant genome, of Arabidopsis, was published in the year 2000 and currently, 4604 plant genomes from 1482 plant species have been published. Various large sequence initiatives are running, which are planning to produce tens of thousands of sequenced plant genomes in the near future. In this review, we give an overview on the status of sequenced plant genomes and on the use of genome information in different research areas.

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“…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%

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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Proteogenomics-based functional genome research: approaches, applications, and perspectives in plants

Cited by 10 publications

References 118 publications

Proteogenomics in Nephrology: A New Frontier in Nephrological Research

Proteogenomics in Nephrology: A New Frontier in Nephrological Research

Plant genome information facilitates plant functional genomics

TheZea maysPeptideAtlas – a new maize community resource

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