Ned Budisa

Editorial: Harnessing synthetic biology for ecosystem sustainability and biodiversity conservation

David B. Levin

Computational design of orthogonal operators and synthetic repressors for transcriptional logic gates

Nathaniel Howitz, Stephen N. Rondthaler, Lauren B. Andrews

Orthogonal repressor-based logic gates have enabled the predictive design of genetic circuits using automated design algorithms. However, engineering complex genetic circuits has been limited by the availability of transcriptional logic gates that are orthogonal, exhibit low cytotoxicity, and have a large dynamic range. Here, we present an algorithmic approach to design orthogonal synthetic repressors and logic gates de novo. To demonstrate the approach, we used programmable DNA-binding proteins called “transcription activator-like effectors” (TALEs) to build orthogonal transcriptional logic gates. We automated the design of synthetic repressors by developing a Python script that implements a search algorithm and genetic design rules to generate a set of operator sequences that are orthogonal from one another, the specified host genome, and an optional set of other heterologous sequences. We demonstrate this approach by creating a library of 20 characterized synthetic repressors for Escherichia coli that complements natural TetR-family repressors used to build genetic circuits. TALE repressors were built from monomer DNA modules to enable prototyping of any 19 bp DNA-binding sequence and then recoded to remove repetitive sequences for final use in logic gates. A library of 20 orthogonal NOT logic gates was tuned and characterized. Synthetic logic gates were used to construct genetic circuits for sequential logic in combination with existing natural repressor gates and genetic circuit design algorithms. This study demonstrates a computational approach to designing orthogonal operator and repressor sequences for creating logic gates and scalable genetic circuit construction.

A comparative review of microplastic remediation strategies: constraints of physical and chemical approaches and opportunities for synthetic biology

Hening Guo, Tsz Yam Liu, Tianlin Wen, Mingce Yang, Yihong Zhang, Boxuan Tu

Microplastic pollution has emerged as a critical environmental challenge, yet existing remediation strategies remain limited in their ability to achieve more complete mineralization under environmentally relevant conditions. In this review, we examine different physical, chemical, and synthetic biology-based methods of microplastic remediation in terms of degradation efficiency, environmental safety, and applicability. The physical techniques can be used to obtain efficient particle removal, but they often lead to shifting contaminants from one environmental matrix to another rather than eliminating them. Chemical approaches enable partial polymer degradation, but they often require energy-intensive processes and generate secondary products. In contrast, synthetic biology-based strategies offer opportunities for a more selective, programmable, and even sustainable breakdown of polymers under less harsh conditions. More precisely, genetically engineered microbes and biological systems can increase the selectivity of such processes while minimizing the impact of traditional techniques on the environment. This review examines the possibilities as well as the constraints of using synthetic biology for microplastic remediation, along with its complementation by physical and chemical treatment strategies.

Exploring the potential of Rhodosporidium toruloides in biomanufacturing: a comprehensive review

Shubhasish Goswami, Blake A. Simmons, Taek Soon Lee

Rhodosporidium toruloides is an emerging non-conventional yeast host gaining significant attention in synthetic biology and metabolic engineering due to its innate ability to accumulate lipids, produce carotenoids, and utilize diverse carbon sources including lignocellulosic hydrolysates. Its robust metabolism, natural tolerance to environmental stress, and efficient routing of the carbon flux through the mevalonate pathway position R. toruloides as a promising platform for the biomanufacturing of isoprenoids-based biofuels, nutraceuticals, and other acetyl-CoA-derived compounds. Despite its metabolic advantages, however, the genetic engineering of R. toruloides remains challenging due to a limited transformation efficiency, a scarcity of genetic parts, a poor homologous recombination efficiency, and the absence of stable plasmid systems. This review provides a comprehensive summary of the current progress in genetic tool development for R. toruloides, with a particular focus on Agrobacterium tumefaciens -mediated transformation (ATMT), CRISPR/Cas-based genome editing, and counter-selection strategies. We discuss the advantages and limitations of existing tools, benchmark their genetic tractability against conventional hosts, and highlight emerging solutions aimed at accelerating the design-build-test-learn (DBTL) cycle. Special emphasis is placed on engineering R. toruloides for isoprenoid biosynthesis as a case study exemplifying both the organism’s industrial promise and its engineering bottlenecks. By identifying key challenges and recent innovations, this review aims to inform and guide future efforts to establish R. toruloide s as a versatile chassis for next-generation biomanufacturing.

Advancing synthetic biology in African academia: institutional barriers, capacity gaps, and the impact of a pilot online training program

Erikan Baluku, Sebunya Emmanuel Kato, Steven Malemia, Rosemond Nyatefe Tawiah, Charity Serwaa, Shakira Namuli, Simon Anguzu, Hazvinei Mang’anda, Perez Mweine, Brendah Namugamba

Synthetic biology has emerged as a promising field with the potential to address challenges in agriculture, healthcare, and environmental sustainability. However, limited studies have focused on Africa’s perspective and potential applications. Public understanding and teaching of synthetic biology, especially within African academic institutions, could play a central role in driving its application in Africa. This study assessed the awareness, perceptions and barriers of synthetic biology among 140 students, lecturers and researchers from 17 countries. The study employed a stratified purposive survey to collect both qualitative and quantitative data from the respondents. Most participants reported their first encounter with synthetic biology as conducting internet searches and participating in online synthetic biology training. Health innovation was reported as the sector most likely to benefit from its advancements, followed by agriculture, industrial applications and environmental sustainability. Key themes on the concerns included access to trained staff, ethical and biosecurity considerations, biosafety and environmental risks and governance. Themes describing barriers to the application of synthetic biology were dominated by inadequate laboratory infrastructure, followed by less institutional support, limited funding and insufficient training opportunities. In addition, an online synthetic biology course was piloted, and participants reported improved awareness and understanding of synthetic biology following course completion. Generally, our findings highlight the need to strengthen academic curricula, expand access to affordable training platforms, invest in laboratory infrastructure, and promote a biosecurity and biosafety regulatory framework to support the growth of synthetic biology research in Africa.