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1. Time‐resolved Interaction Proteomics of the GIGANTEA Protein Under Diurnal Cycles in Arabidopsis

   https://doi.org/10.1002/1873-3468.13311  

   Krahmer, Johanna; Goralogia, Greg S.; Kubota, Akane; Zardilis, Argyris; Johnson, Richard S.; Song, Young Hun; MacCoss, Michael J.; LeBihan, Thierry; Halliday, Karen J.; Imaizumi, Takato; et al (December 2018, FEBS Letters)
2. Surface plasmon resonance aptasensing and computational analysis of Staphylococcus aureus IsdA surface protein

   https://doi.org/10.1002/btpr.3475  

   Bruce‐Tagoe, Tracy_Ann; Harnish, Michael_T; Soleimani, Shokoufeh; Ullah, Najeeb; Shen, Tongye; Danquah, Michael_K (April 2024, Biotechnology Progress)

   Abstract Staphylococcus aureus(S. aureus), a common foodborne pathogen, poses significant public health challenges due to its association with various infectious diseases. A key player in its pathogenicity, which is the IsdA protein, is an essential virulence factor inS. aureusinfections. In this work, we present an integrated in‐silico and experimental approach using MD simulations and surface plasmon resonance (SPR)‐based aptasensing measurements to investigateS. aureusbiorecognition via IsdA surface protein binding. SPR, a powerful real‐time and label‐free technique, was utilized to characterize interaction dynamics between the aptamer and IsdA protein, and MD simulations was used to characterize the stable and dynamic binding regions. By characterizing and optimizing pivotal parameters such as aptamer concentration and buffer conditions, we determined the aptamer's binding performance. Under optimal conditions of pH 7.4 and 150 mM NaCl concentration, the kinetic parameters were determined;k_a = 3.789 × 10⁴/Ms,k_d = 1.798 × 10³/s, andK_D = 4.745 × 10⁻⁸ M. The simulations revealed regions of interest in the IsdA‐aptamer complex. Region I, which includes interactions between amino acid residues H106 and R107 and nucleotide residues 9G, 10U, 11G and 12U of the aptamer, had the strongest interaction, based on ΔG and B‐factor values, and hence contributed the most to the stability of the interaction. Region II, which covers residue 37A reflects the dynamic nature of the interaction due to frequent contacts. The approach presents a rigorous characterization of aptamer‐IsdA binding behavior, supporting the potential application of the IsdA‐binding aptamer system forS. aureusbiosensing. 

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3. Plasmid‐encoded protein attenuates Escherichia coli swimming velocity and cell growth, not reprogrammed regulatory functions

   https://doi.org/10.1002/btpr.2778  

   Virgile, Chelsea; Hauk, Pricila; Wu, Hsuan‐Chen; Bentley, William_E (February 2019, Biotechnology Progress)

   In addition to engineering new pathways for synthesis, synthetic biologists rewire cells to carry out “programmable” functions, an example being the creation of wound‐healing probiotics. Engineering regulatory circuits and synthetic machinery, however, can be deleterious to cell function, particularly if the “metabolic burden” is significant. Here, a synthetic regulatory circuit previously constructed to directEscherichiacolito swim toward hydrogen peroxide, a signal of wound generation, was shown to work even with coexpression of antibiotic resistance genes and genes associated with lactose utilization. We found, however, that cotransformation with a second vector constitutively expressing GFP (as a marker) and additionally conferring resistance to kanamycin and tetracycline resulted in slower velocity (Δ~6 μm/s) and dramatically reduced growth rate (Δ > 50%). The additional vector did not, however, alter the run‐and‐tumble ratio or directional characteristics of H₂O₂–dependent motility. The main impact of this additional burden was limited to slowing cell velocity and growth, suggesting that reprogrammed cell motility by minimally altering native regulatory circuits can be maintained even when extraneous burden is placed on the host cell. © 2019 American Institute of Chemical EngineersBiotechnol. Prog., 35: e2778, 2019. 

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4. CRISPR /Cas9‐based editing of NF‐YC4 promoters yields high‐protein rice and soybean

   https://doi.org/10.1111/nph.20141  

   Wang, Lei; O'Conner, Seth; Tanvir, Rezwan; Zheng, Wenguang; Cothron, Samuel; Towery, Katherine; Bi, Honghao; Ellison, Evan_E; Yang, Bing; Voytas, Daniel_F; et al (September 2024, New Phytologist)

   Summary Genome editing is a revolution in biotechnology for crop improvement with the final product lacking transgenes. However, most derived traits have been generated through edits that create gene knockouts.Our study pioneers a novel approach, utilizing gene editing to enhance gene expression by eliminating transcriptional repressor binding motifs.Building upon our prior research demonstrating the protein‐boosting effects of the transcription factor NF‐YC4, we identified conserved motifs targeted by RAV and WRKY repressors in theNF‐YC4promoters from rice (Oryza sativa) and soybean (Glycine max). Leveraging CRISPR/Cas9 technology, we deleted these motifs, resulting in reduced repressor binding and increasedNF‐YC4expression. This strategy led to increased protein content and reduced carbohydrate levels in the edited rice and soybean plants, with rice exhibiting up to a 68% increase in leaf protein and a 17% increase in seed protein, and soybean showing up to a 25% increase in leaf protein and an 11% increase in seed protein.Our findings provide a blueprint for enhancing gene expression through precise genomic deletions in noncoding sequences, promising improved agricultural productivity and nutritional quality. 

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5. Yersinia ruckeri YRB periplasmic binding protein YiuA selectively recognizes a Fe( iii )-mono-catecholate siderophore

   https://doi.org/10.1039/D5CC05103G  

   Thomsen, Emil; Thompson, Seán; Stow, Parker R; Cukor, Maren; Grogan, Gideon; Duhme-Klair, Anne-K; Butler, Alison (October 2025, Chemical Communications)

   Yersinia ruckeriproduces the tri-catechol siderophore ruckerbactin, Rb, yet its periplasmic binding protein YiuA has unprecedented selectivity for the 1 : 2 Fe(iii) complex of the mono-catechol siderophore, Fe(iii)–(Rb_MC)₂. 

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