To New Beginnings: Riboproteogenomics Discovery of N-Terminal Proteoforms in Arabidopsis Thaliana
Alternative translation initiation is a widespread event in biology that can shape multiple protein forms or proteoforms from a single gene. However, the respective contribution of alternative translation to protein complexity remains largely enigmatic. By complementary ribosome profiling and N-term...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2022-01-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2021.778804/full |
| _version_ | 1798035223663869952 |
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| author | Patrick Willems Patrick Willems Elvis Ndah Veronique Jonckheere Frank Van Breusegem Frank Van Breusegem Petra Van Damme |
| author_facet | Patrick Willems Patrick Willems Elvis Ndah Veronique Jonckheere Frank Van Breusegem Frank Van Breusegem Petra Van Damme |
| author_sort | Patrick Willems |
| collection | DOAJ |
| description | Alternative translation initiation is a widespread event in biology that can shape multiple protein forms or proteoforms from a single gene. However, the respective contribution of alternative translation to protein complexity remains largely enigmatic. By complementary ribosome profiling and N-terminal proteomics (i.e., riboproteogenomics), we provide clear-cut evidence for ~90 N-terminal proteoform pairs shaped by (alternative) translation initiation in Arabidopsis thaliana. Next to several cases additionally confirmed by directed mutagenesis, identified alternative protein N-termini follow the enzymatic rules of co-translational N-terminal protein acetylation and initiator methionine removal. In contrast to other eukaryotic models, N-terminal acetylation in plants cannot generally be considered as a proxy of translation initiation because of its posttranslational occurrence on mature proteolytic neo-termini (N-termini) localized in the chloroplast stroma. Quantification of N-terminal acetylation revealed differing co- vs. posttranslational N-terminal acetylation patterns. Intriguingly, our data additionally hints to alternative translation initiation serving as a common mechanism to supply protein copies in multiple cellular compartments, as alternative translation sites are often in close proximity to cleavage sites of N-terminal transit sequences of nuclear-encoded chloroplastic and mitochondrial proteins. Overall, riboproteogenomics screening enables the identification of (differential localized) N-terminal proteoforms raised upon alternative translation. |
| first_indexed | 2024-04-11T20:55:14Z |
| format | Article |
| id | doaj.art-0694bd973b604539adb280eec7a6d256 |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-04-11T20:55:14Z |
| publishDate | 2022-01-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-0694bd973b604539adb280eec7a6d2562022-12-22T04:03:42ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2022-01-011210.3389/fpls.2021.778804778804To New Beginnings: Riboproteogenomics Discovery of N-Terminal Proteoforms in Arabidopsis ThalianaPatrick Willems0Patrick Willems1Elvis Ndah2Veronique Jonckheere3Frank Van Breusegem4Frank Van Breusegem5Petra Van Damme6Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, BelgiumVlaams Instituut voor Biotechnologie (VIB)-Center for Plant Systems Biology, Ghent, Belgiumintegrative Riboproteogenomics, Interactomics and Proteomics Unit, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgiumintegrative Riboproteogenomics, Interactomics and Proteomics Unit, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, BelgiumDepartment of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, BelgiumVlaams Instituut voor Biotechnologie (VIB)-Center for Plant Systems Biology, Ghent, Belgiumintegrative Riboproteogenomics, Interactomics and Proteomics Unit, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, BelgiumAlternative translation initiation is a widespread event in biology that can shape multiple protein forms or proteoforms from a single gene. However, the respective contribution of alternative translation to protein complexity remains largely enigmatic. By complementary ribosome profiling and N-terminal proteomics (i.e., riboproteogenomics), we provide clear-cut evidence for ~90 N-terminal proteoform pairs shaped by (alternative) translation initiation in Arabidopsis thaliana. Next to several cases additionally confirmed by directed mutagenesis, identified alternative protein N-termini follow the enzymatic rules of co-translational N-terminal protein acetylation and initiator methionine removal. In contrast to other eukaryotic models, N-terminal acetylation in plants cannot generally be considered as a proxy of translation initiation because of its posttranslational occurrence on mature proteolytic neo-termini (N-termini) localized in the chloroplast stroma. Quantification of N-terminal acetylation revealed differing co- vs. posttranslational N-terminal acetylation patterns. Intriguingly, our data additionally hints to alternative translation initiation serving as a common mechanism to supply protein copies in multiple cellular compartments, as alternative translation sites are often in close proximity to cleavage sites of N-terminal transit sequences of nuclear-encoded chloroplastic and mitochondrial proteins. Overall, riboproteogenomics screening enables the identification of (differential localized) N-terminal proteoforms raised upon alternative translation.https://www.frontiersin.org/articles/10.3389/fpls.2021.778804/fulltranslation initiation siteribosome profilingN-terminal proteomicsN-terminal acetylationArabidopsis thalianaalternative translation initiation |
| spellingShingle | Patrick Willems Patrick Willems Elvis Ndah Veronique Jonckheere Frank Van Breusegem Frank Van Breusegem Petra Van Damme To New Beginnings: Riboproteogenomics Discovery of N-Terminal Proteoforms in Arabidopsis Thaliana Frontiers in Plant Science translation initiation site ribosome profiling N-terminal proteomics N-terminal acetylation Arabidopsis thaliana alternative translation initiation |
| title | To New Beginnings: Riboproteogenomics Discovery of N-Terminal Proteoforms in Arabidopsis Thaliana |
| title_full | To New Beginnings: Riboproteogenomics Discovery of N-Terminal Proteoforms in Arabidopsis Thaliana |
| title_fullStr | To New Beginnings: Riboproteogenomics Discovery of N-Terminal Proteoforms in Arabidopsis Thaliana |
| title_full_unstemmed | To New Beginnings: Riboproteogenomics Discovery of N-Terminal Proteoforms in Arabidopsis Thaliana |
| title_short | To New Beginnings: Riboproteogenomics Discovery of N-Terminal Proteoforms in Arabidopsis Thaliana |
| title_sort | to new beginnings riboproteogenomics discovery of n terminal proteoforms in arabidopsis thaliana |
| topic | translation initiation site ribosome profiling N-terminal proteomics N-terminal acetylation Arabidopsis thaliana alternative translation initiation |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2021.778804/full |
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