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Newfound Coding Potential of Transcripts Unveils Missing Members of Human Protein Communities.

التفاصيل البيبلوغرافية
العنوان: Newfound Coding Potential of Transcripts Unveils Missing Members of Human Protein Communities.
المؤلفون: Leblanc S; Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada; PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Quebec City, QC G1V 0A6, Canada., Brunet MA; Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada; PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Quebec City, QC G1V 0A6, Canada., Jacques JF; Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada; PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Quebec City, QC G1V 0A6, Canada., Lekehal AM; Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada; PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Quebec City, QC G1V 0A6, Canada., Duclos A; Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada., Tremblay A; Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada., Bruggeman-Gascon A; Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada., Samandi S; Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada; PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Quebec City, QC G1V 0A6, Canada., Brunelle M; Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada; PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Quebec City, QC G1V 0A6, Canada., Cohen AA; Department of Family Medicine, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada., Scott MS; Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada., Roucou X; Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada; PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Quebec City, QC G1V 0A6, Canada. Electronic address: xavier.roucou@usherbrooke.ca.
المصدر: Genomics, proteomics & bioinformatics [Genomics Proteomics Bioinformatics] 2023 Jun; Vol. 21 (3), pp. 515-534. Date of Electronic Publication: 2022 Sep 30.
نوع المنشور: Journal Article; Research Support, Non-U.S. Gov't
اللغة: English
بيانات الدورية: Publisher: Science Press and Elsevier Country of Publication: England NLM ID: 101197608 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 2210-3244 (Electronic) Linking ISSN: 16720229 NLM ISO Abbreviation: Genomics Proteomics Bioinformatics Subsets: MEDLINE
أسماء مطبوعة: Original Publication: Beijing, China : Science Press and Elsevier
مواضيع طبية MeSH: Proteomics* , Proteins*/genetics, Humans ; Peptides ; Databases, Protein ; Open Reading Frames
مستخلص: Recent proteogenomic approaches have led to the discovery that regions of the transcriptome previously annotated as non-coding regions [i.e., untranslated regions (UTRs), open reading frames overlapping annotated coding sequences in a different reading frame, and non-coding RNAs] frequently encode proteins, termed alternative proteins (altProts). This suggests that previously identified protein-protein interaction (PPI) networks are partially incomplete because altProts are not present in conventional protein databases. Here, we used the proteogenomic resource OpenProt and a combined spectrum- and peptide-centric analysis for the re-analysis of a high-throughput human network proteomics dataset, thereby revealing the presence of 261 altProts in the network. We found 19 genes encoding both an annotated (reference) and an alternative protein interacting with each other. Of the 117 altProts encoded by pseudogenes, 38 are direct interactors of reference proteins encoded by their respective parental genes. Finally, we experimentally validate several interactions involving altProts. These data improve the blueprints of the human PPI network and suggest functional roles for hundreds of altProts.
(Copyright © 2023 The Authors. Published by Elsevier B.V. All rights reserved.)
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فهرسة مساهمة: Keywords: Affinity purification mass spectrometry; Alternative protein; Protein network; Protein–protein interaction; Pseudogene
المشرفين على المادة: 0 (Proteins)
0 (Peptides)
تواريخ الأحداث: Date Created: 20221002 Date Completed: 20240101 Latest Revision: 20240710
رمز التحديث: 20240711
مُعرف محوري في PubMed: PMC10787177
DOI: 10.1016/j.gpb.2022.09.008
PMID: 36183975
قاعدة البيانات: MEDLINE
الوصف
تدمد:2210-3244
DOI:10.1016/j.gpb.2022.09.008