Newfound Coding Potential of Transcripts Unveils Missing Members of Human Protein Communities
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 p...
| Main Authors: | , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2023-06-01
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| Series: | Genomics, Proteomics & Bioinformatics |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S1672022922001243 |
| _version_ | 1797372046110359552 |
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| author | Sébastien Leblanc Marie A. Brunet Jean-François Jacques Amina M. Lekehal Andréa Duclos Alexia Tremblay Alexis Bruggeman-Gascon Sondos Samandi Mylène Brunelle Alan A. Cohen Michelle S. Scott Xavier Roucou |
| author_facet | Sébastien Leblanc Marie A. Brunet Jean-François Jacques Amina M. Lekehal Andréa Duclos Alexia Tremblay Alexis Bruggeman-Gascon Sondos Samandi Mylène Brunelle Alan A. Cohen Michelle S. Scott Xavier Roucou |
| author_sort | Sébastien Leblanc |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-08T18:29:45Z |
| format | Article |
| id | doaj.art-7063003343fe4f088a982f401b17848e |
| institution | Directory Open Access Journal |
| issn | 1672-0229 |
| language | English |
| last_indexed | 2024-03-08T18:29:45Z |
| publishDate | 2023-06-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Genomics, Proteomics & Bioinformatics |
| spelling | doaj.art-7063003343fe4f088a982f401b17848e2023-12-30T04:42:50ZengElsevierGenomics, Proteomics & Bioinformatics1672-02292023-06-01213515534Newfound Coding Potential of Transcripts Unveils Missing Members of Human Protein CommunitiesSébastien Leblanc0Marie A. Brunet1Jean-François Jacques2Amina M. Lekehal3Andréa Duclos4Alexia Tremblay5Alexis Bruggeman-Gascon6Sondos Samandi7Mylène Brunelle8Alan A. Cohen9Michelle S. Scott10Xavier Roucou11Department 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, CanadaDepartment 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, CanadaDepartment 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, CanadaDepartment 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, CanadaDepartment of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, CanadaDepartment of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, CanadaDepartment of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, CanadaDepartment 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, CanadaDepartment 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, CanadaDepartment of Family Medicine, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, CanadaDepartment of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, CanadaDepartment 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; Corresponding author.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.http://www.sciencedirect.com/science/article/pii/S1672022922001243Alternative proteinProtein networkProtein–protein interactionPseudogeneAffinity purification mass spectrometry |
| spellingShingle | Sébastien Leblanc Marie A. Brunet Jean-François Jacques Amina M. Lekehal Andréa Duclos Alexia Tremblay Alexis Bruggeman-Gascon Sondos Samandi Mylène Brunelle Alan A. Cohen Michelle S. Scott Xavier Roucou Newfound Coding Potential of Transcripts Unveils Missing Members of Human Protein Communities Genomics, Proteomics & Bioinformatics Alternative protein Protein network Protein–protein interaction Pseudogene Affinity purification mass spectrometry |
| title | Newfound Coding Potential of Transcripts Unveils Missing Members of Human Protein Communities |
| title_full | Newfound Coding Potential of Transcripts Unveils Missing Members of Human Protein Communities |
| title_fullStr | Newfound Coding Potential of Transcripts Unveils Missing Members of Human Protein Communities |
| title_full_unstemmed | Newfound Coding Potential of Transcripts Unveils Missing Members of Human Protein Communities |
| title_short | Newfound Coding Potential of Transcripts Unveils Missing Members of Human Protein Communities |
| title_sort | newfound coding potential of transcripts unveils missing members of human protein communities |
| topic | Alternative protein Protein network Protein–protein interaction Pseudogene Affinity purification mass spectrometry |
| url | http://www.sciencedirect.com/science/article/pii/S1672022922001243 |
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