51
|
Super-resolution ribosome profiling reveals unannotated translation events in Arabidopsis. Proc Natl Acad Sci U S A 2016; 113:E7126-E7135. [PMID: 27791167 DOI: 10.1073/pnas.1614788113] [Citation(s) in RCA: 145] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Deep sequencing of ribosome footprints (ribosome profiling) maps and quantifies mRNA translation. Because ribosomes decode mRNA every 3 nt, the periodic property of ribosome footprints could be used to identify novel translated ORFs. However, due to the limited resolution of existing methods, the 3-nt periodicity is observed mostly in a global analysis, but not in individual transcripts. Here, we report a protocol applied to Arabidopsis that maps over 90% of the footprints to the main reading frame and thus offers super-resolution profiles for individual transcripts to precisely define translated regions. The resulting data not only support many annotated and predicted noncanonical translation events but also uncover small ORFs in annotated noncoding RNAs and pseudogenes. A substantial number of these unannotated ORFs are evolutionarily conserved, and some produce stable proteins. Thus, our study provides a valuable resource for plant genomics and an efficient optimization strategy for ribosome profiling in other organisms.
Collapse
|
52
|
Ghorbani S, Hoogewijs K, Pečenková T, Fernandez A, Inzé A, Eeckhout D, Kawa D, De Jaeger G, Beeckman T, Madder A, Van Breusegem F, Hilson P. The SBT6.1 subtilase processes the GOLVEN1 peptide controlling cell elongation. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:4877-87. [PMID: 27315833 PMCID: PMC4983112 DOI: 10.1093/jxb/erw241] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The GOLVEN (GLV) gene family encode small secreted peptides involved in important plant developmental programs. Little is known about the factors required for the production of the mature bioactive GLV peptides. Through a genetic suppressor screen in Arabidopsis thaliana, two related subtilase genes, AtSBT6.1 and AtSBT6.2, were identified that are necessary for GLV1 activity. Root and hypocotyl GLV1 overexpression phenotypes were suppressed by mutations in either of the subtilase genes. Synthetic GLV-derived peptides were cleaved in vitro by the affinity-purified SBT6.1 catalytic enzyme, confirming that the GLV1 precursor is a direct subtilase substrate, and the elimination of the in vitro subtilase recognition sites through alanine substitution suppressed the GLV1 gain-of-function phenotype in vivo Furthermore, the protease inhibitor Serpin1 bound to SBT6.1 and inhibited the cleavage of GLV1 precursors by the protease. GLV1 and its homolog GLV2 were expressed in the outer cell layers of the hypocotyl, preferentially in regions of rapid cell elongation. In agreement with the SBT6 role in GLV precursor processing, both null mutants for sbt6.1 and sbt6.2 and the Serpin1 overexpression plants had shorter hypocotyls. The biosynthesis of the GLV signaling peptides required subtilase activity and might be regulated by specific protease inhibitors. The data fit with a model in which the GLV1 signaling pathway participates in the regulation of hypocotyl cell elongation, is controlled by SBT6 subtilases, and is modulated locally by the Serpin1 protease inhibitor.
Collapse
Affiliation(s)
- Sarieh Ghorbani
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
| | - Kurt Hoogewijs
- Department of Organic Chemistry, Ghent University, B-9000 Ghent, Belgium
| | - Tamara Pečenková
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
| | - Ana Fernandez
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
| | - Annelies Inzé
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
| | - Dominique Eeckhout
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
| | - Dorota Kawa
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
| | - Geert De Jaeger
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
| | - Tom Beeckman
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
| | - Annemieke Madder
- Department of Organic Chemistry, Ghent University, B-9000 Ghent, Belgium
| | - Frank Van Breusegem
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
| | - Pierre Hilson
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, Saclay Plant Science, F-78026 Versailles, France
| |
Collapse
|
53
|
Hazak O, Hardtke CS. CLAVATA 1-type receptors in plant development. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:4827-33. [PMID: 27340234 DOI: 10.1093/jxb/erw247] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
A fundamental aspect of plant development is the coordination of growth through endogenous signals and its integration with environmental inputs. Similar to animals, plants frequently use cell surface-localized receptors to monitor such stimuli, for instance through plasma membrane-integral receptor-like kinases (RLKs). Compared to other organisms, plants possess a large number of RLKs (more than 600 in Arabidopsis thaliana), which implies that ligand-receptor-mediated molecular mechanisms regulate a wide range of processes during plant development. Here, we focus on A. thaliana RLKs of the CLAVATA 1 (CLV1) type, which orchestrate key steps during plant development, including the regulation of meristem maintenance, anther development, vascular tissue formation, and root system architecture. These receptors are regulated by small signalling peptides that belong to the family of CLE (CLV3 / EMBRYO SURROUNDING REGION) ligands. We discuss different aspects of plant development that are regulated by these receptors in light of their molecular mechanism of action. As so often, the intensive research on this group of plant RLKs has raised many intriguing questions, which remain to be answered.
Collapse
Affiliation(s)
- Ora Hazak
- Department of Plant Molecular Biology, University of Lausanne, Biophore Building, CH-1015 Lausanne, Switzerland
| | - Christian S Hardtke
- Department of Plant Molecular Biology, University of Lausanne, Biophore Building, CH-1015 Lausanne, Switzerland
| |
Collapse
|
54
|
Liu Z, Yang N, Lv Y, Pan L, Lv S, Han H, Wang G. The CLE gene family in Populus trichocarpa. PLANT SIGNALING & BEHAVIOR 2016; 11:e1191734. [PMID: 27232947 PMCID: PMC4973754 DOI: 10.1080/15592324.2016.1191734] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The CLE (CLAVATA3/Embryo Surrounding Region-related) peptides are small secreted signaling peptides that are primarily involved in the regulation of stem cell homeostasis in different plant meristems. Particularly, the characterization of the CLE41-PXY/TDR signaling pathway has greatly advanced our understanding on the potential roles of CLE peptides in vascular development and wood formation. Nevertheless, our knowledge on this gene family in a tree species is limited. In a recent study, we reported on a systematically investigation of the CLE gene family in Populus trichocarpa. The potential roles of PtCLE genes were studied by comparative analysis and transcriptional profiling. Among fifty PtCLE members, many PtCLE proteins share identical CLE motifs or contain the same CLE motif as that of AtCLEs, while PtCLE genes exhibited either comparable or distinct expression patterns comparing to their Arabidopsis counterparts. These findings indicate the existence of both functional conservation and functional divergence between PtCLEs and their AtCLE orthologues. Our results provide valuable resources for future functional investigations of these critical signaling molecules in woody plants.
Collapse
Affiliation(s)
- Zhijun Liu
- Key Laboratory of Ministry of Education for Medicinal Plant Resource and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Developing of Endangered Chinese Crude Drugs in Northwest of China, College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Nan Yang
- Key Laboratory of Ministry of Education for Medicinal Plant Resource and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Developing of Endangered Chinese Crude Drugs in Northwest of China, College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Yanting Lv
- Key Laboratory of Ministry of Education for Medicinal Plant Resource and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Developing of Endangered Chinese Crude Drugs in Northwest of China, College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Lixia Pan
- Key Laboratory of Ministry of Education for Medicinal Plant Resource and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Developing of Endangered Chinese Crude Drugs in Northwest of China, College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Shuo Lv
- Key Laboratory of Ministry of Education for Medicinal Plant Resource and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Developing of Endangered Chinese Crude Drugs in Northwest of China, College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Huibin Han
- Institute of Science and Technology Austria (IST Austria), Klosterneuburg, Austria
| | - Guodong Wang
- Key Laboratory of Ministry of Education for Medicinal Plant Resource and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Developing of Endangered Chinese Crude Drugs in Northwest of China, College of Life Sciences, Shaanxi Normal University, Xi'an, China
- CONTACT Dr. Guodong Wang Key Laboratory of Ministry of Education for Medicinal Plant Resource and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Developing of Endangered Chinese Crude Drugs in Northwest of China, College of Life Sciences, Shaanxi Normal University, Xi'an, China
| |
Collapse
|