The emerging field of transport engineering of plant specialized metabolites

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Highlights► Transport engineering has the potential to increase nutritional value of crops. ► Transport engineering can increase yield of synthetic biology approaches. ► Neo-functionalization of primary metabolite transporters to specialized metabolism. ► Elimination of glucosinolate seed accumulation is achieved via transport engineering. ► Glucosinolates in Arabidopsis: a model for transport of specialized metabolites.     

The challenges of cellular compartmentalization in plant metabolic engineering

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Highlights► Targeting enzymes to organelles with highest precursor pool affects product yield. ► Targeting of nonendogenous enzymes to organelles is a useful tool for engineering. ► Identification of transporters is central for effective metabolic engineering. ► Advances in metabolomics of isolated organelles will impact engineering strategies. ► Future plant metabolic engineering will include introduction of entire pathways.     

Comparative genomics approaches to understanding and manipulating plant metabolism

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Highlights► Comparative genomics can help predict the function of unknown plant metabolic genes. ► Functional gene annotations are foundational to the construction of metabolic models. ► Models can simulate effects of genetic changes and thus guide metabolic engineering. ► Examples of comparative genomics facilitating gene discovery in plants are presented.     

Transcriptome data modeling for targeted plant metabolic engineering

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Highlights► Network analysis is essential for data mining of omics-based large-scale data sets. ► Gene coexpression analysis is useful for prediction of gene function. ► Comparative network analysis can reveal common and unique plant metabolic pathways. ► Novel genome editing tools facilitate rational metabolic engineering.     

Lipid metabolism in microalgae distinguishes itself

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Highlights► Triacylglycerol assembly in microalgae might occur at plastid envelopes. ► Starch-less mutants provide clues for the engineering of carbon partitioning in algae. ► New algal species emerge as models for lipid and biofuel research.     

Recent progress in the metabolic engineering of alkaloids in plant systems

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Highlights► Recent metabolic engineering efforts for plant alkaloids. ► Characterizing, reconfiguring and fine-tuning metabolic ‘parts’ improves titers. ► Additional strategies are necessary to produce ‘unnatural’ natural products.     

Enzyme and metabolic engineering for the production of novel biopolymers: crossover of biological and chemical processes

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Highlights► Poly(ω-hydroxy fatty acids) are polyethylene-like biobased polyester. ► Medium-chain-length polyhydroxyalkanoate homopolymers are processed to stretchy film. ► Microbial lactate-based polyesters exhibit transparent and flexible properties. ► Enzyme and metabolic engineering facilitates the expanding of bio-based polymers.     

Pathway and protein engineering approaches to produce novel and commodity small molecules

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Highlights► Production of novel pharmaceutical and commodity chemicals. ► Protein and pathway engineering pave the way for product diversifications. ► ‘Omics’ data have helped assembly of pathways from different species. ► Recombination of enzymatic domains and site-directed mutagenesis. ► Tunable control of pathways for better production.     

Engineering specialized metabolic pathways—is there a room for enzyme improvements?

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Highlights► Specialized metabolism offers challenging engineering opportunities. ► Unlike central metabolism, specialized metabolism is slow, sluggish and messy. ► Spontaneous reactions are relatively common in specialized metabolism. ► Enzymes can be engineered for higher rate and substrate specificity. ► Enzymes can be engineered for naturally spontaneous reactions.     

Metabolic network flux analysis for engineering plant systems

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Highlights► A powerful range of tools has been developed for metabolic network flux analysis. ► These tools yield insights that are used to aid microbial metabolic engineering. ► Plants present great opportunities and special challenges to applying these tools. ► Tool selection and knowledge of plant systems is key to practical success.     

Engineering plant metabolism into microbes: from systems biology to synthetic biology

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Highlights► Microbial production of pharmaceutical and fuel molecules. ► Systems biology tools advanced our understanding about synthetic pathway design. ► Synthetic biology led us to cell factories tailor-made for chemical production. ► Combinatorial gene assembly for synthetic pathway diversification. ► Engineering static, dynamic and spatial control for better production phenotype.     

The interface between plant metabolic engineering and human health

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Highlights► People should increase their consumption of fruit and vegetables to reduce their risk of chronic diseases. ► Despite many campaigns uptake of fruit and vegetable consumption has been limited. ► Metabolic engineering can improve understanding of the roles of dietary phytonutrients. ► Data from nutritional studies of model foods can set targets for crop improvements. ► Nutritionally enhanced fruit and vegetables, developed through breeding or metabolic engineering, could contribute to health.     

Expanded genetic code for the engineering of ribosomally synthetized and post-translationally modified peptide natural products (RiPPs)

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Highlights► RiPPs have high capabilities of target interaction far beyond the field of anti-infectives. ► RiPPs are especially suitable for design and engineering with the genetic code expansion. ► First published studies yielded RiPPs with unnatural/synthetic amino acids. ► Achievement: expanded scope of the in vivo (mainly bacterial) RiPPs synthesis. ► Perspective: design of RiPPS with novel chemistries and unique sequence combinations.     

Comparative genomics: a revolutionary tool for wine yeast strain development

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Highlights► Phylogeny of Saccharomyces cerevisiae reveals industry-relevant groupings. ► Comparative genomics reveals genomic variation across industrial yeast strains. ► Next-gen sequencing in next-gen wine yeast strain development. ► Precise mapping of QTLs for marker-assisted breeding of industrial yeast. ► Discovery of putative mobile gene cluster that uses novel type of transposition.     

Plant–bacteria interactions in the removal of pollutants

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Highlights► Rhizobacteria degrade a wide range of pollutants and efficiently colonize plant roots. ► Plants have an effect on the selection of their own rhizospheric microorganisms. ► Catabolic pathways can be induced by natural secondary plant products. ► Horizontal gene transfer has an important role in bioremediation. ► Manipulation of plant/microbe interactions could improve rhizoremediation outcomes.     

Magnetic nanoparticles-based diagnostics and theranostics

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Highlights► Magnetic nanoparticles (MNPs) can be in engineered and functionalized. ► MNPs can be used as magnetic resonance imaging contrast agents and targeted MNPs can be used in theranostic applications. ► MNPs are useful for in vivo drug and gene delivery. ► MNPs are useful for photodynamic, phototherapy and hyperthermia. ► MNPs can be used for controlled released and manipulation of cell in vivo.     

Alkylating enzymes

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Highlights► Alkylating enzymes allow regiospecific and chemospecific reactions where classical chemical syntheses fail or require an extensive protection strategy. ► Prenyltransferase and methyltransferase are increasingly applicable in biotechnology. ► Cofactor or cosubstrate availability can still be a limiting factor. ► Enzyme cascade reactions and/or whole-cell systems are applied to perform multiple step transformations. ► Alkyltransferases are crucial elements in pathway engineering and synthetic biology, especially toward plant derived (natural) products.     

From measurement to implementation of metabolic fluxes

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Highlights► In vivo flux distributions can be determined with increasing accuracy and breadth. ► Enzyme activity can partly be identified from codon usage and other DNA features. ► Stoichiometric constraints of metabolism set a frame that can be exploited to design efficient metabolic networks. ► Insights into DNA-sequence–function relationships lead to first examples of rational DNA writing. ► Increasing DNA synthesis speed moves metabolic engineering from tinkering to green field design.