Protein-protein interactions (PPIs) contribute to regulate many aspects of cell physiology and metabolism. Protein domains involved in PPIs are important building blocks for engineering genetic circuits through synthetic biology. These domains can be obtained from known proteins and rationally engineered to produce orthogonal scaffolds, or computationally designed de novo thanks to recent advances in structural biology and molecular dynamics prediction. Such circuits based on PPIs (or protein circuits) appear of particular interest, as they can directly affect transcriptional outputs, as well as induce behavioral/adaptational changes in cell metabolism, without the need for further protein synthesis. This last example was highlighted in recent works to enable the production of fast-responding circuits which can be exploited for biosensing and diagnostics. Notably, PPIs can also be engineered to develop new drugs able to bind specific intra- and extra-cellular targets. In this review, we summarize recent findings in the field of protein circuit design, with particular focus on the use of peptides as scaffolds to engineer these circuits.

The NAC transcription factor family is a large class of DNA-binding proteins found in several plant species. In the model plant Arabidopsis thaliana, NAC transcription factors are expressed in different organs, and they are known to modulate many diverse developmental processes, such as meristem formation, flower and fruit development, leaf and fruit senescence. From a previous time-lapse transcriptomic analysis of developing siliques performed by our group, we found a NAC transcription factor, NAC100, that is upregulated during silique development. In this work, we characterized the role of the NAC100 transcription factor and demonstrated that NAC100 contributes to regulating silique growth during the initial phase of their development. nac100 mutant siliques are smaller but such defects can be rescued through the application of exogenous bioactive gibberellin. Gene expression analysis, transactivation assay and endogenous gibberellin quantification indicate that NAC100 modulates gibberellin metabolism, by both directly and indirectly regulating GA-metabolic genes expression, ultimately affecting silique elongation.

Precise control of gene expression is critical to allow the design of tunable synthetic gene circuits. To date, our ability to precisely predict orthogonal expression in plants lags well behind that of animals and bacteria. This is largely because traditional attempts to characterize plant promoters have found few reliable sequence patterns. Even the TATA box is found in a minority of plant promoters ( 1). As a result, plant biologists are still relying on a set of promoters that are not completely orthogonal and that often cannot ensure homogenous expression between different tissues; moreover, the length of these promoters, the local DNA environment of the insertion and other unknown factors often do not allow for tunable and specific expression.

Phytophthora infestans , the causal agent of late blight in potato and tomato, is a historically devastating pathogen that continues to pose a major threat to global food security. Although conventional fungicides remain a cornerstone of crop protection, growing concerns over their environmental impact and long‐term sustainability have driven the search for safer and more selective alternatives. In this context, next‐generation fungicides with high specificity and minimal ecological footprint are urgently needed. This study introduces CP32, a small cyclic peptide, identified via yeast two‐hybrid screening of a genetically encoded combinatorial peptide library, based on its specific interaction with the catalytic domain of the P. infestans enzyme Cellulose Synthase 2. CP32 exhibits anti‐oomycete activity, effectively inhibits sporangial growth at low micromolar concentrations, and significantly reduces late blight symptoms on tomato leaves and entire plants. In silico docking analyses, supported by molecular and biochemical evidence, confirm that CP32 compromises cell‐wall integrity by interfering with cellulose deposition and altering glucan composition. Furthermore, CP32 readily permeates the Phytophthora membrane and displays oomycete‐static properties, while showing no detectable toxicity toward non‐target organisms, such as bacteria, yeast, or plants. Collectively, these findings identify CP32 as a promising, targeted anti‐oomycete agent with a unique mode of action, targeting the P. infestans cell wall, representing a valuable contribution to the development of sustainable strategies for the control of late blight.