Transcriptional regulation: efficient genetic engineering tools for non-conventional yeasts

A decoupled transcription platform enables tunable and predictable gene expression in yeast

CRISPR-Activated Promoter-based Orthogonal expression (CAPO) is developed, a CRISPR-guided system that tunes gene activity in yeast and enables multiplex colour generation and faster optimization of metabolic pathways.

Spatiotemporal Metabolic Regulation for Programmable Microbial Cell Factories.

Advances in Key Genetic Elements and Strategies for High-Yield Heterologous Protein Expression in Komagataella phaffii

This review summarizes recent advances in engineering key expression elements underlying heterologous protein production in K. phaffii, with particular emphasis on promoter architecture redesign, signal peptide replacement and sequence engineering, molecular chaperone co-expression, and quantitative regulation of the unfolded protein response.

Design principles for stable and balanced multigene expression in plant synthetic biology

Plant synthetic biology is increasingly moving from single-gene transformation toward multigene systems that reconstruct metabolic pathways, produce valuable proteins, implement synthetic circuits, and respond to environmental inputs. However, stable multigene expression in plants is limited by failures that arise across multiple biological layers, including DNA delivery and integration, chromatin context, transcription and RNA processing, translation, protein targeting, and physiological burden. In this review, we discuss multigene expression as a context-aware and burden-aware design problem rather than a simple DNA assembly problem. We first summarize major mechanisms that destabilize transgene expression, including structural rearrangement, transcriptional and post-transcriptional gene silencing, inefficient 3’-end processing, transcriptional interference, combinatorial part effects, and metabolic burden. We then describe part-level and architecture-level strategies for improving expression stability. Finally, we highlight the need for context-aware and burden-aware validation of every introduced gene across stable events, generations, tissues, and environmental conditions.

Gene Editing-Driven Engineering of Microbial Systems and Metabolites for Precision Medicine and Sustainable Environmental Remediation.

The engineering of microorganisms is undergoing a fundamental paradigm shift, transitioning from the construction of static cell factories to the programming of dynamically responsive living materials. However, translating molecular interventions into robust macroscopic functions requires overcoming distinct microbial-specific barriers, including delivery bottlenecks and genetic stability. In this review, we establish a unified Edit-Reprogram-Functionalize conceptual framework that systematically delineates transient genetic regulation from permanent genomic engineering. We critically examine the evolutionary trajectories of five foundational technologies: plasmid engineering, CRISPR-Cas systems, base editors, prime editors, and enzyme engineering. Rather than analyzing these toolsets in isolation, we map their convergence into an integrated engineering continuum that drives the precise synthesis of two distinct output classes: engineered living microbial materials and robust microbial metabolite-derived materials. By evaluating representative breakthroughs-from ultrasound-actuated bacterial therapeutics to ultra-tough, biosynthesized protein composites-through the strict lens of host-dependent constraints, we reveal the mechanistic principles governing successful preclinical translation. Finally, we propose an actionable roadmap centered on systemic miniaturization, closed-loop control, and multi-scale integration, providing a definitive blueprint for the next generation of precision medicine, advanced biomanufacturing, and ecological remediation.

Synthetic Orthogonal Promoters and Transcription Factor Platforms in Algae: Rational Design Principles and Applications in Synthetic Biology

Algae biomass and cellular exudated compounds have several biotechnological applications in various areas, such as agriculture, pharmaceutical, human and animal feed, and bioenergy, among others. However, many of these applications have not been developed to their full capability, in part due to the need to better understand the underlying principles of their cellular regulation of growth and metabolism. Recently, synthetic biology has been implemented as a new option to not only build new biological devices and systems but also comprehend the natural biochemical pathways present in living organisms. The use of this technology is still underdeveloped in algae research when compared to yeast and bacterial applications. Part of this effect is due to restraints on building multi-gene circuits, which are associated with the lack of controllable promoters and transcription factors in algae. This scenario could be improved by the development of orthogonal gene promoters, supported by the understanding of global biological responses related to their function in the host metabolism. With the integrative analysis of genomics, transcriptomics and proteomics, we may be able to find patterns of optimal orthogonality and address the rational design of optimal gene promoters that enhance algae biotechnological applications. In this paper, we will review the existing approaches and discuss future perspectives on the creation of orthogonal gene promoters in algae.