Publications
Exploring How Phasins Interact with PHA Granules
Binding Specificity and Granule Organization
Polyhydroxyalkanoates (PHAs) are biodegradable bacterial polyesters that accumulate inside cells as granules coated by specialized proteins, including phasins. These proteins help shape and stabilize PHA granules and can also be used to functionalize their surfaces for biotechnological applications. This study investigates how two phasins, PhaP1 and PhaI, interact with different types of PHAs in engineered Pseudomonas putida strains. The results show that phasin type and polymer composition influence both binding behaviour and granule morphology, with PhaP1 and PhaI displaying distinct preferences and effects on granule size and organization. These findings support the use of phasins as tunable bio-affinity tags for PHA-based materials and other biotechnological applications.
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Exploring phasin-polyhydroxyalkanoate interactions through in vivo and in vitro binding assays
Maria-Tsampika Manoli, Paula Llamas, Francisco G. Blanco, Ana Maria Hernandez-Arriaga, Maria Isabel Torices and M. Auxiliadora Prieto
February 2026
Governing the AI-biotech convergence
Publication for Science & Society
The convergence of AI and biotechnology is driving a revolution in biological engineering, but it is also creating a dangerous security gap. Because AI evolves at a lightning pace, it consistently outpaces the years-long process required to pass new government regulations. To close this gap, the authors advocate for adaptive and anticipatory governance: a flexible system designed to evolve alongside the science, ensuring that rapid progress never comes at the cost of safety, ethics, or global security.
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Benjamin D Trump, Christopher L Cummings, Beth Ellinport, Stephanie Galaitsi, Thomas Janisko, Elizaveta Pinigina, Hannah Herzig, Cindy S Groff-Vindman, Markus Schmidt, Gerald Epstein, Ruth Mampuys, Christian Haggenmiller, Tatyana Novossiolova, Travis Tubbs, James H Lambert, Alexander Titus & Igor Linkov
January 2026
How Enzyme Redundancy Supports Metabolic Robustness
Balancing Energy Production and Biosynthetic Needs
Metabolic robustness allows microorganisms to maintain stable function despite changing environmental conditions. In Pseudomonas putida KT2440, this study investigates two isocitrate dehydrogenase isoenzymes that control carbon flow through central metabolism. The results show that the two enzymes are not simply redundant: the monomeric IDH provides an essential, stable baseline of TCA cycle activity, while the dimeric ICD supports higher oxidative flux and responds more dynamically to nutrient conditions. Together, this conditional redundancy helps balance energy generation with the supply of biosynthetic precursors, offering a useful framework for engineering more robust microbial cell factories.
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Maria-Tsampika Manoli, Sandra Herrera Alarcon, Álvaro Gargantilla-Becerra, M. Auxiliadora Prieto and Juan Nogales
July 2026
Engineering E. coli W for Scalable Flavonoid Glycosylation
Combining Metabolic Engineering and Bioprocess Optimization
Flavonoids have valuable applications in the pharmaceutical, cosmetic, nutraceutical, and food sectors, but their poor solubility and bioavailability can limit their use. This study develops Escherichia coli W as a robust platform for flavonoid glycosylation, using sucrose as both a carbon source and a precursor for UDP-glucose production. By combining adaptive laboratory evolution, targeted metabolic engineering, and optimized fermentation strategies, the authors improved flavonoid tolerance, redirected carbon flux toward glycosylation, and demonstrated scalable production of chrysin-7-O-glucoside. The resulting process reached 1844 mg/L in a 3 L bioreactor, with an 82.1% recovery after extraction and purification, highlighting the potential of the platform for industrial bioproduction.
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Engineering a Robust Escherichia coli W Platform for Scalable Production of Flavonoid-O-Glucosides
Darwin Carranza-Saavedra, Jesús Torres-Bacete, Elodie Bouju, Sylvie Nuccio, Sandra Sordon, Ewa Huszcza, Jarosław Popłoński, René de Vaumas and Juan Nogales
October 2025
A Practical Protocol for Producing and Characterizing Bacterial Bioplastics
Protocol for Polyhydroxyalkanoate Production
Polyhydroxyalkanoates (PHAs) are biodegradable biopolymers naturally produced by bacteria and represent a promising alternative to conventional plastics. This article presents a practical protocol for PHA production using Pseudomonas putida and Cupriavidus necator, covering the complete workflow from small-scale cultivation and bioreactor production to polymer extraction, quantification, and characterization. By providing procedures for both short- and medium-chain-length PHAs, the protocol offers a reproducible framework for studying and optimizing microbial bioplastic production.
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Maria-Tsampika Manoli, Natalia Hernández-Herreros, Virginia Rivero-Buceta, Alberto Rodríguez and M. Auxiliadora Prieto
December 2025
Understanding the Complexity of Transcription Initiation in Prokaryotes
Review Article on Promoter Sequences
Promoter sequences are important genetic control elements. Through their interaction with RNA polymerase they determine transcription strength and specificity, thereby regulating the first step in gene expression. This article reviews the influence of promoter sequence on the mechanisms and kinetics of transcription initiation. This knowledge can be utilized in the development of a more rational approach to promoter engineering. It can help design more predictable, tuneable, and orthogonal promoter sequences, which is important in the context of regulation of gene expression and further, the development of robust microbial cell factories.
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Cara Deal, Lien De Wannemaeker and Marjan De Mey
March 2024
credit: Deal et al.
credit: Deal et al.