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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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Sadre R. Plant synthetic biology for human health: advances in producing medicines in heterologous expression systems. Curr Opin Biotechnol 2024; 87:103142. [PMID: 38735192 DOI: 10.1016/j.copbio.2024.103142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 04/23/2024] [Indexed: 05/14/2024]
Abstract
Plant synthetic biology has the capability to provide solutions to global challenges in the production and supply of medicines. Recent advances in 'omics' technologies have accelerated gene discoveries in medicinal plant research so that even multistep biosynthetic pathways for bioactive plant natural products with high structural complexity can be reconstituted in heterologous plant expression systems more rapidly. This review provides an overview of concept and strategies used to produce high-value plant natural products in heterologous plant systems and highlights recent successes in engineering the biosynthesis of conventional and new medicines in alternative plant hosts.
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Affiliation(s)
- Radin Sadre
- Pelotonia Research Center, Department of Horticulture and Crop Science, the Ohio State University, 2255 Kenny Rd, Columbus, OH 43210, USA.
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3
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Islam T, Kalkar S, Tinker-Kulberg R, Ignatova T, Josephs EA. The "Duckweed Dip": Aquatic Spirodela polyrhiza Plants Can Efficiently Uptake Dissolved, DNA-Wrapped Carbon Nanotubes from Their Environment for Transient Gene Expression. ACS Synth Biol 2024; 13:687-691. [PMID: 38127817 PMCID: PMC10877602 DOI: 10.1021/acssynbio.3c00620] [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: 10/06/2023] [Revised: 11/22/2023] [Accepted: 11/27/2023] [Indexed: 12/23/2023]
Abstract
Duckweeds (Lemnaceae) are aquatic nongrass monocots that are the smallest and fastest-growing flowering plants in the world. While having simplified morphologies, relatively small genomes, and many other ideal traits for emerging applications in plant biotechnology, duckweeds have been largely overlooked in this era of synthetic biology. Here, we report that Greater Duckweed (Spirodela polyrhiza), when simply incubated in a solution containing plasmid-wrapped carbon nanotubes (DNA-CNTs), can directly uptake the DNA-CNTs from their growth media with high efficiency and that transgenes encoded within the plasmids are expressed by the plants─without the usual need for large doses of nanomaterials or agrobacterium to be directly infiltrated into plant tissue. This process, called the "duckweed dip", represents a streamlined, "hands-off" tool for transgene delivery to a higher plant that we expect will enhance the throughput of duckweed engineering and help to realize duckweed's potential as a powerhouse for plant synthetic biology.
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Affiliation(s)
- Tasmia Islam
- Department of Nanoscience, University of North Carolina at Greensboro, 2907 E. Gate City Blvd., Greensboro, North Carolina 27401, United States
| | - Swapna Kalkar
- Department of Nanoscience, University of North Carolina at Greensboro, 2907 E. Gate City Blvd., Greensboro, North Carolina 27401, United States
| | - Rachel Tinker-Kulberg
- Department of Nanoscience, University of North Carolina at Greensboro, 2907 E. Gate City Blvd., Greensboro, North Carolina 27401, United States
| | - Tetyana Ignatova
- Department of Nanoscience, University of North Carolina at Greensboro, 2907 E. Gate City Blvd., Greensboro, North Carolina 27401, United States
| | - Eric A. Josephs
- Department of Nanoscience, University of North Carolina at Greensboro, 2907 E. Gate City Blvd., Greensboro, North Carolina 27401, United States
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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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Yang EJY, Maranas CJ, Nemhauser JL. A comparative analysis of stably expressed genes across diverse angiosperms exposes flexibility in underlying promoter architecture. G3 (BETHESDA, MD.) 2023; 13:jkad206. [PMID: 37697043 PMCID: PMC10627262 DOI: 10.1093/g3journal/jkad206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 08/25/2023] [Accepted: 09/01/2023] [Indexed: 09/13/2023]
Abstract
Promoters regulate both the amplitude and pattern of gene expression-key factors needed for optimization of many synthetic biology applications. Previous work in Arabidopsis found that promoters that contain a TATA-box element tend to be expressed only under specific conditions or in particular tissues, while promoters that lack any known promoter elements, thus designated as Coreless, tend to be expressed more uniformly. To test whether this trend represents a conserved promoter design rule, we identified stably expressed genes across multiple angiosperm species using publicly available RNA-seq data. Comparisons between core promoter architectures and gene expression stability revealed differences in core promoter usage in monocots and eudicots. Furthermore, when tracing the evolution of a given promoter across species, we found that core promoter type was not a strong predictor of expression pattern. Our analysis suggests that core promoter types are correlative rather than causative in promoter expression patterns and highlights the challenges in finding or building constitutive promoters that will work across diverse plant species.
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Affiliation(s)
- Eric J Y Yang
- Department of Biology, University of Washington, Seattle, WA 98105-1800, USA
| | - Cassandra J Maranas
- Department of Biology, University of Washington, Seattle, WA 98105-1800, USA
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Yang EJ, Maranas CJ, Nemhauser JL. A comparative analysis of stably expressed genes across diverse angiosperms exposes flexibility in underlying promoter architecture. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.12.544596. [PMID: 37398445 PMCID: PMC10312641 DOI: 10.1101/2023.06.12.544596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Promoters regulate both the amplitude and pattern of gene expression-key factors needed for optimization of many synthetic biology applications. Previous work in Arabidopsis found that promoters that contain a TATA-box element tend to be expressed only under specific conditions or in particular tissues, while promoters which lack any known promoter elements, thus designated as Coreless, tend to be expressed more ubiquitously. To test whether this trend represents a conserved promoter design rule, we identified stably expressed genes across multiple angiosperm species using publicly available RNA-seq data. Comparisons between core promoter architectures and gene expression stability revealed differences in core promoter usage in monocots and eudicots. Furthermore, when tracing the evolution of a given promoter across species, we found that core promoter type was not a strong predictor of expression stability. Our analysis suggests that core promoter types are correlative rather than causative in promoter expression patterns and highlights the challenges in finding or building constitutive promoters that will work across diverse plant species.
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Affiliation(s)
- Eric J.Y. Yang
- University of Washington, Department of Biology, Seattle, WA 98105-1800, USA
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