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 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 role of membrane transport in metabolic engineering of plant primary metabolism

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Highlights► The plastidial pyruvate transporter in plants is driven by sodium symport. ► The mitochondrial pyruvate transporter MPC has been identified. ► All transporters needed for a synthetic PEP-CK/C₄ photosynthetic cycle are now known. ► The SWEET proteins define a new class of sugar efflux carriers in plants.     

Building robust functionality in synthetic circuits using engineered feedback regulation

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Highlights► Engineered feedback loops implement elaborate functionality in synthetic circuits. ► The homeostatic potential of feedback loops is under-utilized in synthetic biology. ► Feedback control of engineered or natural cellular functions can be achieved using biological components or in silico regulation. ► Optogenetics and microfluidic technologies are important for implementing in silico control.     

New opportunities by synthetic biology for biopharmaceutical production in Pichia pastoris

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Highlights► The application of Pichia pastoris for biopharmaceutical production is described. ► Synthetic biology approaches and perspectives to improve production are reviewed. ► Glycoengineering efforts to produce humanized, uniform glycoproteins are covered. ► The design and application of synthetic promoter variants are highlighted. ► The molecular toolbox available for synthetic biology in P. pastoris is discussed.     

Nanotechnology meets electrophysiology

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Highlights► We focus on the latest developments in nanotechnology-based electrophysiology. ► Methods for extracellular recording via nanoFET-based devices are described. ► Metal nanoelectrodes for the recording of electrogenic cells are reviewed. ► The latest developments of intracellular FET-based probes are shortly covered. ► Pioneering electrical scaffold devices for the interfacing with tissues are described.     

Aerobic degradation of aromatic compounds

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Highlights► Metabolic and regulatory networks are finely tuned for biodegradation of aromatics. ► New pathways and widespread bacterial biodegradation capabilities revealed by omics. ► Full characterization of hybrid pathways expands the scope of aromatic biodegradation. ► The metabolism of aromatics plays a pivotal role in cell to cell communication. ► Computational and synthetic biology approaches design novel biodegradation pathways.     

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.     

Progress toward single cell metabolomics

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Highlights► Single cell metabolomics provides information on the heterogeneity of populations of cells. ► Current technologies allow hundreds of metabolites to be measured from a single cell. ► Quantitative metabolome information at the single cell level aids systems biology modeling. ► Sample preparation remains a significant challenge in single cell metabolomics.     

Tissue engineering on the nanoscale: lessons from the heart

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Highlights► Nanotechnologies are used to mimic natural components of the cell microenvironment. ► Inorganic nanomaterials interact with cells to promote physiological processes. ► Nanoelectronic devices are integrated with engineered tissues to monitor function.     

Priming ammonia lyases and aminomutases for industrial and therapeutic applications

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Highlights► Ammonia lyases and aminomutases are emerging in green synthetic routes to chiral amines. ► An ammonia lyase is being explored as an enzyme therapeutic for treating phenylketonuria and cancer. ► The restricted substrate range of the wild-type enzymes limits their widespread application. ► The non-reliance on external cofactors and direct functionalization of an olefinic bond make ammonia lyases attractive biocatalysts for use in the synthesis of natural and non-natural amino acids. ► The approach of combining structure-guided enzyme engineering with efficient mutant library screening has broadened the synthetic scope of these biocatalysts.     

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.     

Environmental factors influencing the efficacy of probiotic bacteria

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Highlights► Probiotics are living cells and not typical food ingredients. ► Probiotics rapidly adapt to changing conditions in consumer products and the gut. ► Processing, consumer product, and host differences might influence probiotic efficacy. ► Clinical studies should include measurements of probiotic effector expression levels.     

Metagenomics of microbial life in extreme temperature environments

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Highlights► Metagenomic microbial community characterization. ► Extreme environment microbiology. ► High and low temperature adaptation.     

Signaling networks in human pluripotent stem cells

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Highlights► Signaling in pluripotent stem cells is a complex, dynamic process. ► Multiple signaling pathways are required for maintenance of the stem cell state: Fgf/MAPK, TGFβ/SMAD2,3 and insulin/PI3K. ► These pathways are highly interactive and form a finely-balanced signaling network. ► Thresholds, temporal changes and combinatorial effects make important contributions to cell fate outcomes.     

Clawing back: broadening the notion of metal chelators in medicine

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Highlights► Not all chelators are the same: more than metal sequestration and elimination. ► Metal chelates can redistribute metals across biological membranes. ► Metal-chelating fragments provide leads for metalloenzyme inhibition. ► Metal chelation can enhance metal reactivity and thus cytotoxicity. ► Prochelators provide site-activated metal chelation and passivation.     

Progress in understanding and engineering primary plant metabolism

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Highlights► Crop yield depends on efficiency of conversion of light energy into biomass. ► Models have estimated energy conversion efficiency in photosynthesis and metabolism. ► Research is exploring strategies to modify or suppress photorespiration. ► Energy loss during conversion of photosynthate to biomass is also large ► Research is addressing uncertainties over where these losses occur.     

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.     

Pangenomics – an avenue to improved industrial starter cultures and probiotics

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Highlights► Genome sequencing is an efficient, cost-effective way of characterizing microbes. ► Pangenome analysis gives new insight into texture formation in yoghurt. ► Pangenome analysis of probiotic strains has identified new effect or molecules. ► Pangenome analysis gives insight into probiotic–host specificity. ► Future perspectives include improved strains for food fermentations and probiotics.