Plant Promoters and Terminators for High-Precision Bioengineering

Liu, Wusheng; Brooks, Edward G.; Elorriaga, Estefania; Liu, Yang; Duduit, James R; Yuan, Guoliang; Tsai, C. Jillian; Tuskan, Gerald A.; Ranney, Thomas G.; Yang, Xiaohan

doi:10.34133/bdr.0013

Cited by 22 publications

(5 citation statements)

References 194 publications

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“…The properties of synthetic promoters and their applications have been described in several review articles [256][257][258][259][260][261]. However, research in this field is progressing rapidly, fueled by climate change, decreasing arable land area, and a fast-growing global population [1].…”

Section: Discussionmentioning

confidence: 99%

Plant Synthetic Promoters

Szymczyk,

Majewska

2024

Applied Sciences

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This article examines the structure and functions of the plant synthetic promoters frequently used to precisely regulate complex regulatory routes. It details the composition of native promoters and their interacting proteins to provide a better understanding of the tasks associated with synthetic promoter development. The production of synthetic promoters is performed by relatively small libraries produced generally by basic molecular or genetic engineering methods such as cis-element shuffling or domain swapping. The article also describes the preparation of large-scale libraries supported by synthetic DNA fragments, directed evolution, and machine or deep-learning methodologies. The broader application of novel, synthetic promoters reduces the prevalence of homology-based gene silencing or improves the stability of transgenes. A particularly interesting group of synthetic promoters are bidirectional forms, which can enable the expression of up to eight genes by one regulatory element. The introduction and controlled expression of several genes after one transgenic event strongly decreases the frequency of such problems as complex segregation patterns and the random integration of multiple transgenes. These complications are commonly observed during the transgenic crop development enabled by traditional, multistep transformation using genetic constructs containing a single gene. As previously tested DNA promoter fragments demonstrate low complexity and homology, their abundance can be increased by using orthogonal expression systems composed of synthetic promoters and trans-factors that do not occur in nature or arise from different species. Their structure, functions, and applications are rendered in the article. Among them are presented orthogonal systems based on transcription activator-like effectors (dTALEs), synthetic dTALE activated promoters (STAPs) and dCas9-dependent artificial trans-factors (ATFs). Synthetic plant promoters are valuable tools for providing precise spatiotemporal regulation and introducing logic gates into the complex genetic traits that are important for basic research studies and their application in crop plant development. Precisely regulated metabolic routes are less prone to undesirable feedback regulation and energy waste, thus improving the efficiency of transgenic crops.

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Section: Discussionmentioning

confidence: 99%

Plant Synthetic Promoters

Szymczyk,

Majewska

2024

Applied Sciences

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“…The properties of synthetic promoters and their applications were described in several review articles [252][253][254][255][256][257]. However, research in this field is progressing rapidly, fueled by progressing climate changes, decreasing arable land area, and a fast-growing global population [1].…”

Section: Discussionmentioning

confidence: 99%

Plant Synthetic Promoters

Szymczyk,

Majewska

2024

Preprint

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The article features the structure and functions of plant synthetic promoters frequently exercised to precisely regulate complex regulatory routes. The composition of plant native promoters together with interacting proteins is presented to provide a better understanding of tasks associated with synthetic promoter development. The production of synthetic promoters is conferred on relatively small libraries produced generally by basic molecular or genetic engineering methods such as cis-element shuffling or domain swapping. Moreover, the preparation of large-scale libraries supported by synthetic DNA fragments, directed evolution, and machine or deep learning methodologies is presented. A particularly interesting group of synthetic promoters are bidirectional forms that enable the putative expression of up to 6–8 genes by one regulatory element. The introduction and controlled expression of several genes after one transgenic event strongly decreases the frequency of such problems as complex segregation patterns and random integration of multiple transgenes. These complications are commonly observed during transgenic crop development through traditional, multistep transformation by genetic constructs containing a single gene. Another path to solving problems associated with the low complexity and homology of already tested DNA fragments is through orthogonal expression systems composed of synthetic promoters and trans-factors that do not occur in nature or arise from different species. Their structure, functions, and applications are rendered in the article.

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“…This may be because variations in the TATA box can affect binding of RNA Polymerase II to the core promoter region that drives not only basal gene expression but also environmentdependent gene expression (Grace et al, 2004). The TATA box, identified by its consensus sequence of eight base pairs, "TATA(A/T)A(A/T)(A/G)," typically resides between 30 and 70 base pairs upstream from the transcription start site in plant promoters (Brooks et al, 2023) but some studies identified the 13 bp TCACTATATATAG as the consensus sequence in promoters of highly expressed plant genes (Kiran et al, 2006). These GC-rich TATA extension sequences that flank the TATA motif are thought to govern the formation of alternative transcriptional complexes needed in different physiological settings and alter the rate and stability of TATA binding protein and TFIIB transcription factor binding to the TATA box to recruit RNA Polymerase II (Wolner and Gralla, 2001;Kiran et al, 2006;Shi and Zhou, 2006).…”

Section: Known Nodulation Genes Included (Associated Traits)mentioning

confidence: 99%

A Multitrait Genome-Wide Association Study Reveals a Requirement for the Strigolactone Receptor MtDWARF14 in Optimal GOLVEN Signaling

Roy,

Kang,

Zhang

et al. 2024

Preprint

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GOLVEN/ROOT MERISTEM GROWTH FACTOR family of signaling peptides have been shown to control root lateral organ number, density and positioning in plants, although the signaling pathways involved remain obscure. A diverse set of 171Medicago truncatulaHapMap accessions with variation in responses to the GOLVEN 10 peptide, GLV10, were used to identify 74 significant loci controlling seven traits related to nodule formation and root architecture. Importantly, a single nucleotide polymorphism (SNP) in the upstream region of the MtGLV10 peptide-inducible strigolactone receptor gene,MtDWARF14was significantly associated with insensitivity of nodule density to GLV10, suggesting a link between strigolactone signaling and GLV10 responsiveness. Three independentd14mutants of the DWARF14gene were found to hypernodulate, while overexpression of the gene led to reduction in nodule number, phenocopying GLV10. A null mutant,mtd14-1, remained sensitive to GLV10’s effect on nodule density. However, at the transcriptional level, the mutant failed to effectively induce the expression of the GOLVEN marker genes,MtPLETHORA3andMtPINLIKES2. Our study uncovers a hitherto unknown link between the strigolactone and GLV peptide signaling pathways using genotype x environment analysis of Medicago HapMap lines and provides a putative molecular mechanism for recovery from frost damage to fine roots.

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Plant Promoters and Terminators for High-Precision Bioengineering

Cited by 22 publications

References 194 publications

Plant Synthetic Promoters

Plant Synthetic Promoters

Plant Synthetic Promoters

A Multitrait Genome-Wide Association Study Reveals a Requirement for the Strigolactone Receptor MtDWARF14 in Optimal GOLVEN Signaling

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