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Gorjifard S, Jores T, Tonnies J, Mueth NA, Bubb K, Wrightsman T, Buckler ES, Fields S, Cuperus JT, Queitsch C. Arabidopsis and maize terminator strength is determined by GC content, polyadenylation motifs and cleavage probability. Nat Commun 2024; 15:5868. [PMID: 38997252 PMCID: PMC11245536 DOI: 10.1038/s41467-024-50174-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 07/03/2024] [Indexed: 07/14/2024] Open
Abstract
The 3' end of a gene, often called a terminator, modulates mRNA stability, localization, translation, and polyadenylation. Here, we adapted Plant STARR-seq, a massively parallel reporter assay, to measure the activity of over 50,000 terminators from the plants Arabidopsis thaliana and Zea mays. We characterize thousands of plant terminators, including many that outperform bacterial terminators commonly used in plants. Terminator activity is species-specific, differing in tobacco leaf and maize protoplast assays. While recapitulating known biology, our results reveal the relative contributions of polyadenylation motifs to terminator strength. We built a computational model to predict terminator strength and used it to conduct in silico evolution that generated optimized synthetic terminators. Additionally, we discover alternative polyadenylation sites across tens of thousands of terminators; however, the strongest terminators tend to have a dominant cleavage site. Our results establish features of plant terminator function and identify strong naturally occurring and synthetic terminators.
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Affiliation(s)
- Sayeh Gorjifard
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
| | - Tobias Jores
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
| | - Jackson Tonnies
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
- Graduate Program in Biology, University of Washington, Seattle, WA, 98195, USA
| | - Nicholas A Mueth
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
| | - Kerry Bubb
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
| | - Travis Wrightsman
- Section of Plant Breeding and Genetics, Cornell University, Ithaca, NY, 14853, USA
| | - Edward S Buckler
- Section of Plant Breeding and Genetics, Cornell University, Ithaca, NY, 14853, USA
- Agricultural Research Service, United States Department of Agriculture, Ithaca, NY, 14853, USA
- Institute for Genomic Diversity, Cornell University, Ithaca, NY, 14853, USA
| | - Stanley Fields
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
- Department of Medicine, University of Washington, Seattle, WA, 98195, USA
| | - Josh T Cuperus
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
| | - Christine Queitsch
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA.
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Gorjifard S, Jores T, Tonnies J, Mueth NA, Bubb K, Wrightsman T, Buckler ES, Fields S, Cuperus JT, Queitsch C. Arabidopsis and Maize Terminator Strength is Determined by GC Content, Polyadenylation Motifs and Cleavage Probability. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.16.545379. [PMID: 37398426 PMCID: PMC10312805 DOI: 10.1101/2023.06.16.545379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
The 3' end of a gene, often called a terminator, modulates mRNA stability, localization, translation, and polyadenylation. Here, we adapted Plant STARR-seq, a massively parallel reporter assay, to measure the activity of over 50,000 terminators from the plants Arabidopsis thaliana and Zea mays. We characterize thousands of plant terminators, including many that outperform bacterial terminators commonly used in plants. Terminator activity is species-specific, differing in tobacco leaf and maize protoplast assays. While recapitulating known biology, our results reveal the relative contributions of polyadenylation motifs to terminator strength. We built a computational model to predict terminator strength and used it to conduct in silico evolution that generated optimized synthetic terminators. Additionally, we discover alternative polyadenylation sites across tens of thousands of terminators; however, the strongest terminators tend to have a dominant cleavage site. Our results establish features of plant terminator function and identify strong naturally occurring and synthetic terminators.
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Affiliation(s)
- Sayeh Gorjifard
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Tobias Jores
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Jackson Tonnies
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
- Graduate Program in Biology, University of Washington, Seattle, WA 98195
| | - Nicholas A Mueth
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Kerry Bubb
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Travis Wrightsman
- Section of Plant Breeding and Genetics, Cornell University, Ithaca, NY 14853
| | - Edward S Buckler
- Section of Plant Breeding and Genetics, Cornell University, Ithaca, NY 14853
- Agricultural Research Service, United States Department of Agriculture, Ithaca, NY 14853
- Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853
| | - Stanley Fields
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
- Department of Medicine, University of Washington, Seattle, WA 98195
| | - Josh T Cuperus
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Christine Queitsch
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
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Abstract
Robust plant immune systems are fine-tuned by both protein-coding genes and non-coding RNAs. Long non-coding RNAs (lncRNAs) refer to RNAs with a length of more than 200 nt and usually do not have protein-coding function and do not belong to any other well-known non-coding RNA types. The non-protein-coding, low expression, and non-conservative characteristics of lncRNAs restrict their recognition. Although studies of lncRNAs in plants are in the early stage, emerging studies have shown that plants employ lncRNAs to regulate plant immunity. Moreover, in response to stresses, numerous lncRNAs are differentially expressed, which manifests the actions of low-expressed lncRNAs and makes plant-microbe/insect interactions a convenient system to study the functions of lncRNAs. Here, we summarize the current advances in plant lncRNAs, discuss their regulatory effects in different stages of plant immunity, and highlight their roles in diverse plant-microbe/insect interactions. These insights will not only strengthen our understanding of the roles and actions of lncRNAs in plant-microbe/insect interactions but also provide novel insight into plant immune responses and a basis for further research in this field.
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Affiliation(s)
- Juan Huang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Wenling Zhou
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoming Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
- HainanYazhou Bay Seed Lab, Sanya, China
| | - Yi Li
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
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Fang L, Guo L, Zhang M, Li X, Deng Z. Analysis of Polyadenylation Signal Usage with Full-Length Transcriptome in Spodoptera frugiperda (Lepidoptera: Noctuidae). INSECTS 2022; 13:803. [PMID: 36135504 PMCID: PMC9505298 DOI: 10.3390/insects13090803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 08/29/2022] [Accepted: 08/30/2022] [Indexed: 06/16/2023]
Abstract
During the messenger RNA (mRNA) maturation process, RNA polyadenylation is a key step, and is coupled to the termination of transcription. Various cis-acting elements near the cleavage site and their binding factors would affect the process of polyadenylation, and AAUAAA, a highly conserved hexamer, was the most important polyadenylation signal (PAS). PAS usage is one of the critical modification determinants targeted at mRNA post-transcription. The full-length transcriptome has recently generated a massive amount of sequencing data, revealing poly(A) variation and alternative polyadenylation (APA) in Spodoptera frugiperda. We identified 50,616 polyadenylation signals in Spodoptera frugiperda via analysis of full-length transcriptome combined with expression Sequence Tags Technology (EST). The polyadenylation signal usage in Spodoptera frugiperda is conserved, and it is similar to that of flies and other animals. AAUAAA and AUUAAA are the most highly conserved polyadenylation signals of all polyadenylation signals we identified. Additionally, we found the U/GU-rich downstream sequence element (DSE) in the cleavage site. These results demonstrate that APA in Spodoptera frugiperda plays a significant role in root growth and development. This is the first polyadenylation signal usage analysis in agricultural pests, which can deepen our understanding of Spodoptera frugiperda and provide a theoretical basis for pest control.
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Affiliation(s)
- Liying Fang
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Lina Guo
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Min Zhang
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Xianchun Li
- Department of Entomology, BIO5 Institute, University of Arizona, Tucson, AZ 85721, USA
| | - Zhongyuan Deng
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
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To JPC, Davis IW, Marengo MS, Shariff A, Baublite C, Decker K, Galvão RM, Gao Z, Haragutchi O, Jung JW, Li H, O'Brien B, Sant A, Elich TD. Expression Elements Derived From Plant Sequences Provide Effective Gene Expression Regulation and New Opportunities for Plant Biotechnology Traits. FRONTIERS IN PLANT SCIENCE 2021; 12:712179. [PMID: 34745155 PMCID: PMC8569612 DOI: 10.3389/fpls.2021.712179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 09/15/2021] [Indexed: 06/13/2023]
Abstract
Plant biotechnology traits provide a means to increase crop yields, manage weeds and pests, and sustainably contribute to addressing the needs of a growing population. One of the key challenges in developing new traits for plant biotechnology is the availability of expression elements for efficacious and predictable transgene regulation. Recent advances in genomics, transcriptomics, and computational tools have enabled the generation of new expression elements in a variety of model organisms. In this study, new expression element sequences were computationally generated for use in crops, starting from native Arabidopsis and maize sequences. These elements include promoters, 5' untranslated regions (5' UTRs), introns, and 3' UTRs. The expression elements were demonstrated to drive effective transgene expression in stably transformed soybean plants across multiple tissues types and developmental stages. The expressed transcripts were characterized to demonstrate the molecular function of these expression elements. The data show that the promoters precisely initiate transcripts, the introns are effectively spliced, and the 3' UTRs enable predictable processing of transcript 3' ends. Overall, our results indicate that these new expression elements can recapitulate key functional properties of natural sequences and provide opportunities for optimizing the expression of genes in future plant biotechnology traits.
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Affiliation(s)
- Jennifer P. C. To
- Bayer Crop Science, Chesterfield, MO, United States
- GrassRoots Biotechnology, Durham, NC, United States
- Monsanto Company, Research Triangle Park, Durham, NC, United States
| | - Ian W. Davis
- Bayer Crop Science, Chesterfield, MO, United States
- GrassRoots Biotechnology, Durham, NC, United States
- Monsanto Company, Research Triangle Park, Durham, NC, United States
| | - Matthew S. Marengo
- Bayer Crop Science, Chesterfield, MO, United States
- GrassRoots Biotechnology, Durham, NC, United States
- Monsanto Company, Research Triangle Park, Durham, NC, United States
| | - Aabid Shariff
- GrassRoots Biotechnology, Durham, NC, United States
- Monsanto Company, Research Triangle Park, Durham, NC, United States
- Pairwise Plants, Durham, NC, United States
| | | | - Keith Decker
- Bayer Crop Science, Chesterfield, MO, United States
| | - Rafaelo M. Galvão
- Bayer Crop Science, Chesterfield, MO, United States
- GrassRoots Biotechnology, Durham, NC, United States
- Monsanto Company, Research Triangle Park, Durham, NC, United States
| | - Zhihuan Gao
- Bayer Crop Science, Chesterfield, MO, United States
- GrassRoots Biotechnology, Durham, NC, United States
- Monsanto Company, Research Triangle Park, Durham, NC, United States
| | - Olivia Haragutchi
- Bayer Crop Science, Chesterfield, MO, United States
- GrassRoots Biotechnology, Durham, NC, United States
- Monsanto Company, Research Triangle Park, Durham, NC, United States
| | - Jee W. Jung
- Bayer Crop Science, Chesterfield, MO, United States
- GrassRoots Biotechnology, Durham, NC, United States
- Monsanto Company, Research Triangle Park, Durham, NC, United States
- Duke University, Office for Translation and Commercialization, Durham, NC, United States
| | - Hong Li
- Bayer Crop Science, Chesterfield, MO, United States
| | - Brent O'Brien
- Bayer Crop Science, Chesterfield, MO, United States
- GrassRoots Biotechnology, Durham, NC, United States
- Monsanto Company, Research Triangle Park, Durham, NC, United States
| | - Anagha Sant
- Bayer Crop Science, Chesterfield, MO, United States
| | - Tedd D. Elich
- GrassRoots Biotechnology, Durham, NC, United States
- Monsanto Company, Research Triangle Park, Durham, NC, United States
- LifeEDIT Therapeutics, Durham, NC, United States
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