@article{fernandez-moreno_yaschenko_neubauer_marchi_zhao_ascencio-ibanez_alonso_stepanova_2024, title={A rapid and scalable approach to build synthetic repetitive hormone-responsive promoters}, volume={2}, ISSN={["1467-7652"]}, url={https://doi.org/10.1111/pbi.14313}, DOI={10.1111/pbi.14313}, abstractNote={Advancement of DNA-synthesis technologies has greatly facilitated the development of synthetic biology tools. However, high-complexity DNA sequences containing tandems of short repeats are still notoriously difficult to produce synthetically, with commercial DNA synthesis companies usually rejecting orders that exceed specific sequence complexity thresholds. To overcome this limitation, we developed a simple, single-tube reaction method that enables the generation of DNA sequences containing multiple repetitive elements. Our strategy involves commercial synthesis and PCR amplification of padded sequences that contain the repeats of interest, along with random intervening sequence stuffers that include type IIS restriction enzyme sites. GoldenBraid molecular cloning technology is then employed to remove the stuffers, rejoin the repeats together in a predefined order, and subclone the tandem(s) in a vector using a single-tube digestion-ligation reaction. In our hands, this new approach is much simpler, more versatile and efficient than previously developed solutions to this problem. As a proof of concept, two different phytohormone-responsive, synthetic, repetitive proximal promoters were generated and tested in planta in the context of transcriptional reporters. Analysis of transgenic lines carrying the synthetic ethylene-responsive promoter 10x2EBS-S10 fused to the GUS reporter gene uncovered several developmentally regulated ethylene response maxima, indicating the utility of this reporter for monitoring the involvement of ethylene in a variety of physiologically relevant processes. These encouraging results suggest that this reporter system can be leveraged to investigate the ethylene response to biotic and abiotic factors with high spatial and temporal resolution.}, journal={PLANT BIOTECHNOLOGY JOURNAL}, author={Fernandez-Moreno, Josefina-Patricia and Yaschenko, Anna E. and Neubauer, Matthew and Marchi, Alex J. and Zhao, Chengsong and Ascencio-Ibanez, Jose T. and Alonso, Jose M. and Stepanova, Anna N.}, year={2024}, month={Feb} }
 @misc{vollen_zhao_alonso_stepanova_2024, title={Sourcing DNA parts for synthetic biology applications in plants}, volume={87}, ISSN={["1879-0429"]}, DOI={10.1016/j.copbio.2024.103140}, abstractNote={Transgenic approaches are now standard in plant biology research aiming to characterize gene function or improve crops. Recent advances in DNA synthesis and assembly make constructing transgenes a routine task. What remains nontrivial is the selection of the DNA parts and optimization of the transgene design. Early career researchers and seasoned molecular biologists alike often face difficult decisions on what promoter or terminator to use, what tag to include, and where to place it. This review aims to inform about the current approaches being employed to identify and characterize DNA parts with the desired functionalities and give general advice on basic construct design. Furthermore, we hope to share the excitement about new experimental and computational tools being developed in this field.}, journal={CURRENT OPINION IN BIOTECHNOLOGY}, author={Vollen, Katie and Zhao, Chengsong and Alonso, Jose M. and Stepanova, Anna N.}, year={2024}, month={Jun} }
 @article{mazzoni-putman_brumos_zhao_alonso_stepanova_2021, title={Auxin Interactions with Other Hormones in Plant Development}, volume={13}, ISSN={1943-0264}, url={http://dx.doi.org/10.1101/cshperspect.a039990}, DOI={10.1101/cshperspect.a039990}, abstractNote={Auxin is a crucial growth regulator that governs plant development and responses to environmental perturbations. It functions at the heart of many developmental processes, from embryogenesis to organ senescence, and is key to plant interactions with the environment, including responses to biotic and abiotic stimuli. As remarkable as auxin is, it does not act alone, but rather solicits the help of, or is solicited by, other endogenous signals, including the plant hormones abscisic acid, brassinosteroids, cytokinins, ethylene, gibberellic acid, jasmonates, salicylic acid, and strigolactones. The interactions between auxin and other hormones occur at multiple levels: hormones regulate one another's synthesis, transport, and/or response; hormone-specific transcriptional regulators for different pathways physically interact and/or converge on common target genes; etc. However, our understanding of this crosstalk is still fragmentary, with only a few pieces of the gigantic puzzle firmly established. In this review, we provide a glimpse into the complexity of hormone interactions that involve auxin, underscoring how patchy our current understanding is.}, number={10}, journal={Cold Spring Harbor Perspectives in Biology}, publisher={Cold Spring Harbor Laboratory}, author={Mazzoni-Putman, Serina M. and Brumos, Javier and Zhao, Chengsong and Alonso, Jose M. and Stepanova, Anna N.}, year={2021}, month={Apr}, pages={a039990} }
 @misc{zhao_yaschenko_alonso_stepanova_2021, title={Leveraging synthetic biology approaches in plant hormone research}, volume={60}, ISSN={["1879-0356"]}, DOI={10.1016/j.pbi.2020.10998}, journal={CURRENT OPINION IN PLANT BIOLOGY}, author={Zhao, Chengsong and Yaschenko, Anna and Alonso, Jose M. and Stepanova, Anna N.}, year={2021}, month={Apr} }
 @article{petzold_chanda_zhao_rigoulot_beers_brunner_2018, title={DIVARICATA AND RADIALIS INTERACTING FACTOR (DRIF) also interacts with WOX and KNOX proteins associated with wood formation in Populus trichocarpa}, volume={93}, ISSN={["1365-313X"]}, DOI={10.1111/tpj.13831}, abstractNote={Summary}, number={6}, journal={PLANT JOURNAL}, author={Petzold, H. Earl and Chanda, Bidisha and Zhao, Chengsong and Rigoulot, Stephen B. and Beers, Eric P. and Brunner, Amy M.}, year={2018}, month={Mar}, pages={1076–1087} }