Strangers in a foreign land: 'Yeastizing' plant enzymes.

Expressing plant metabolic pathways in microbial platforms is an efficient, cost-effective solution for producing many desired plant compounds. As eukaryotic organisms, yeasts are often the preferred platform. However, expression of plant enzymes in a yeast frequently leads to failure because the enzymes are poorly adapted to the foreign yeast cellular environment.

Comparative Genomic and Genetic Evidence on a Role for the OarX Protein in Thiamin Salvage.

Salvage pathways for thiamin and its thiazole and pyrimidine moieties are poorly characterized compared to synthesis pathways. A candidate salvage gene is , which encodes a short-chain dehydrogenase/reductase. In diverse bacteria, clusters on the chromosome with genes of thiamin synthesis, salvage, or transport and is preceded by a thiamin pyrophosphate riboswitch.

A pilot oral history of plant synthetic biology.

The whole field of synthetic biology (SynBio) is only about 20 years old, and plant SynBio is younger still. Nevertheless, within that short time, SynBio in general has drawn more scientific, philosophical, government, and private-sector interest than anything in biology since the recombinant DNA revolution. Plant SynBio, in particular, is now drawing more and more interest in relation to plants' potential to help solve planetary problems such as carbon capture and storage and replacing fossil fuels and feedstocks.

Adapting enzymes to improve their functionality in plants: why and how.

Synthetic biology creates new metabolic processes and improves existing ones using engineered or natural enzymes. These enzymes are often sourced from cells that differ from those in the target plant organ with respect to, e.g.

Running the numbers on plant synthetic biology solutions to global problems.

Synthetic biology and metabolic engineering promise to deliver sustainable solutions to global problems such as phasing out fossil fuels and replacing industrial nitrogen fixation. While this promise is real, scale matters, and so do knock-on effects of implementing solutions. Both scale and knock-on effects can be estimated by 'Fermi calculations' (aka 'back-of-envelope calculations') that use uncontroversial input data plus simple arithmetic to reach rough but reliable conclusions.

Synthetic Biology─High Time to Deliver?

Synthetic biology (SynBio) has attracted like no other recent development the attention not only of Life Science researchers and engineers but also of intellectuals, technology think-tanks, and private and public investors. This is largely due to its promise to propel biotechnology beyond its traditional realms in medicine, agriculture, and environment toward new territories historically dominated by the chemical and manufacturing industries─but now claimed to be amenable to complete . For this to happen, it is crucial for the field to remain true to its foundational engineering drive, which relies on mathematics and quantitative tools to construct practical solutions to real-world problems.

Continuous Directed Evolution of a Feedback-Resistant Arogenate Dehydratase in Plantized .

Continuous directed evolution (CDE) is a powerful tool for enzyme engineering due to the depth and scale of evolutionary search that it enables. If suitably controlled and calibrated, CDE could be widely applied in plant breeding and biotechnology to improve plant enzymes . We tested this concept by evolving arogenate dehydratase (AtADT2) for resistance to feedback inhibition.

Respiratory energy demands and scope for demand expansion and destruction.

Nonphotosynthetic plant metabolic processes are powered by respiratory energy, a limited resource that metabolic engineers—like plants themselves—must manage prudently.

Fluoroacetate distribution, response to fluoridation, and synthesis in juvenile Gastrolobium bilobum plants.

Like angiosperms from several other families, the leguminous shrub Gastrolobium bilobum R.Br. produces and accumulates fluoroacetate, indicating that it performs the difficult chemistry needed to make a C-F bond.

Metabolite Damage and Damage Control in a Minimal Genome.

Analysis of the genes retained in the minimized JCVI-Syn3A genome established that systems that repair or preempt metabolite damage are essential to life. Several genes known to have such functions were identified and experimentally validated, including 5-formyltetrahydrofolate cycloligase, coenzyme A (CoA) disulfide reductase, and certain hydrolases. Furthermore, we discovered that an enigmatic YqeK hydrolase domain fused to NadD has a novel proofreading function in NAD synthesis and could double as a MutT-like sanitizing enzyme for the nucleotide pool.

Chemical-damage MINE: A database of curated and predicted spontaneous metabolic reactions.

Spontaneous reactions between metabolites are often neglected in favor of emphasizing enzyme-catalyzed chemistry because spontaneous reaction rates are assumed to be insignificant under physiological conditions. However, synthetic biology and engineering efforts can raise natural metabolites' levels or introduce unnatural ones, so that previously innocuous or nonexistent spontaneous reactions become an issue. Problems arise when spontaneous reaction rates exceed the capacity of a platform organism to dispose of toxic or chemically active reaction products.

A Core Metabolome Response of Maize Leaves Subjected to Long-Duration Abiotic Stresses.

Abiotic stresses reduce crop growth and yield in part by disrupting metabolic homeostasis and triggering responses that change the metabolome. Experiments designed to understand the mechanisms underlying these metabolomic responses have usually not used agriculturally relevant stress regimes. We therefore subjected maize plants to drought, salt, or heat stresses that mimic field conditions and analyzed leaf responses at metabolome and transcriptome levels.

The Moderately (D)efficient Enzyme: Catalysis-Related Damage and Its Repair.

Enzymes have life spans. Analysis of life spans, i.e.

Using continuous directed evolution to improve enzymes for plant applications.

Continuous directed evolution of enzymes and other proteins in microbial hosts is capable of outperforming classical directed evolution by executing hypermutation and selection concurrently in vivo, at scale, with minimal manual input. Provided that a target enzyme's activity can be coupled to growth of the host cells, the activity can be improved simply by selecting for growth. Like all directed evolution, the continuous version requires no prior mechanistic knowledge of the target.

The Mutation of Arabidopsis Highlights How the Thiamin Economy Impacts the Methylerythritol 4-Phosphate Pathway.

The thiamin-requiring mutants of Arabidopsis have a storied history as a foundational model for biochemical genetics in plants and have illuminated the central role of thiamin in metabolism. Recent integrative genetic and biochemical analyses of thiamin biosynthesis and utilization imply that leaf metabolism normally operates close to thiamin-limiting conditions. Thus, the mechanisms that allocate thiamin-diphosphate (ThDP) cofactor among the diverse thiamin-dependent enzymes localized in plastids, mitochondria, peroxisomes, and the cytosol comprise an intricate thiamin economy.