Rapid prototyping of microbial production strains for the biomanufacture of potential materials monomers

Bio-based production of industrial chemicals using synthetic biology can provide alternative green routes from renewable resources, allowing for cleaner production processes. To efficiently produce chemicals on-demand through microbial strain engineering, biomanufacturing foundries have developed automated pipelines that are largely compound agnostic in their time to delivery. Here we benchmark the capabilities of a biomanufacturing pipeline to enable rapid prototyping of microbial cell factories for the production of chemically diverse industrially relevant material building blocks. Over 85 days the pipeline was able to produce 17 potential material monomers and key intermediates by combining 160 genetic parts into 115 unique biosynthetic pathways. To explore the scale-up potential of our prototype production strains, we optimized the enantioselective production of mandelic acid and hydroxymandelic acid, achieving gram-scale production in fed-batch fermenters. The high success rate in the rapid design and prototyping of microbially-produced material building blocks reveals the potential role of biofoundries in leading the transition to sustainable materials production.

The role of conserved residues in Fdc decarboxylase in prenylated flavin mononucleotide oxidative maturation, cofactor isomerization, and catalysis

The UbiD family of reversible decarboxylases act on aromatic, heteroaromatic, and unsaturated aliphatic acids and utilize a prenylated flavin mononucleotide (prFMN) as cofactor, bound adjacent to a conserved Glu–Arg–Glu/Asp ionic network in the enzyme's active site. It is proposed that UbiD activation requires oxidative maturation of the cofactor, for which two distinct isomers, prFMN^ketimine and prFMN^iminium, have been observed. It also has been suggested that only the prFMN^iminium form is relevant to catalysis, which requires transient cycloaddition between substrate and cofactor. Using Aspergillus niger Fdc1 as a model system, we reveal that isomerization of prFMN^iminium to prFMN^ketimine is a light-dependent process that is largely independent of the Glu²⁷⁷–Arg¹⁷³–Glu²⁸² network and accompanied by irreversible loss of activity. On the other hand, efficient catalysis was highly dependent on an intact Glu–Arg–Glu network, as only Glu → Asp substitutions retain activity. Surprisingly, oxidative maturation to form the prFMN^iminium species is severely affected only for the R173A variant. In summary, the unusual irreversible isomerization of prFMN is light-dependent and probably proceeds via high-energy intermediates but is independent of the Glu–Arg–Glu network. Our results from mutagenesis, crystallographic, spectroscopic, and kinetic experiments indicate a clear role for the Glu–Arg–Glu network in both catalysis and oxidative maturation.

A unique CO-like micrometeorite hosting an exotic Al-Cu-Fe-bearing assemblage - close affinities with the Khatyrka meteorite

We report the discovery of a unique micrometeorite, containing an exotic Al-Cu-Fe alloy composed of two intermixed phases: khatyrkite (CuAl₂) and stolperite (CuAl) and both containing minor Fe (<1.4 wt%). These phases are dendritic and rapidly co-crystallized at the binary system's peritectic (~550 °C). The host micrometeorite is an otherwise typical S-type micro-porphyritic cosmic spherule containing relict olivine (Fo76-90, Cr₂O₃: 0.01-0.56 wt%, MnO: 0.03-0.32 wt% and CaO: 0.09-0.22 wt%) and a cumulate layered texture. These properties suggest the micrometeorite is derived from a carbonaceous chondrite (best matched to a CO chondrite) and entered the atmosphere a high speed (~16 kms^-1), implying an origin from a highly eccentric orbit. This particle represents the second independent discovery of naturally occurring intermetallic Al-Cu-Fe alloys and is thus similar to the previously reported Khatyrka meteorite - a CV chondrite containing near-identical alloys and the only known natural quasicrystals. We did not observe quasicrystalline phases in this micrometeorite, likely due to the low amounts of Fe in the alloy, insufficient to stabilize quasicrystals. Our discovery confirms the existence of Al-Cu-Fe intermetallic alloys on chondritic parent bodies. These unusual phases require a currently unexplained formation process, we tentatively suggest this could represent the delivery of exotic interstellar material to the inner solar system via impact.

An enzyme cascade enables production of therapeutic oligonucleotides in a single operation

Therapeutic oligonucleotides have emerged as a powerful drug modality with the potential to treat a wide range of diseases; however, the rising number of therapies poses a manufacturing challenge. Existing synthetic methods use stepwise extension of sequences immobilized on solid supports and are limited by their scalability and sustainability. We report a biocatalytic approach to efficiently produce oligonucleotides in a single operation where polymerases and endonucleases work in synergy to amplify complementary sequences embedded within catalytic self-priming templates. This approach uses unprotected building blocks and aqueous conditions. We demonstrate the versatility of this methodology through the synthesis of clinically relevant oligonucleotide sequences containing diverse modifications.

[On-scene times for helicopter services. Influence of central dispatch center strategy]

BACKGROUND

Previous studies have suggested that when using several emergency systems and air rescue prehospital and on-scene times are extended, depending on the dispatch strategy. Emergency medical services (EMS) in Germany are delivered by ambulances (AMB) staffed by paramedics alone or with physicians (EMD) and by helicopter emergency medical services (HEMS) always staffed by both. The advantages of HEMS in countries with short transport distances and high hospital density are controversial. The best dispatching strategy for HEMS has not been determined

OBJECTIVE

The BoLuS study in the German state of Hessen was designed to evaluate the influence of dispatch strategy on prehospital times for responses involving both HEMS and EMS.

METHODS

Rescue responses involving HEMS were prospectively evaluated in 12 regions of Hessen from July 2010 to September 2011. Although all regions had access to HEMS, only one had its own service. Data from both central dispatch centers and helicopter services were collected and combined to calculate the on-scene time (OST) and correlate it with dispatch strategy.

RESULTS

A total of 2111 emergency interventions were evaluated. Internal medicine emergencies accounted for 42.9 % of cases and trauma for 36.7 %. Just one patient was involved in 87.9 % of rescues. Two services were involved in 65.3 % of rescues and three or more in 31.5 %. The most common dispatch categories were initial dispatch of EMS and HEMS (50.6 %), initial dispatch of EMS with later request for HEMS (19.7 %) and initial dispatch of both EMS and EMD with later request for HEMS (17.4 %). The OST for these categories were 31.0 ± 13.7 min, 43.7 ± 16.2 min and 54.6 ± 21.3 min (p < 0.01), respectively.

CONCLUSION

OST varies significantly depending on the number of EMS involved and the dispatch strategy. Sequential dispatching of ground and later HEMS wastes time. Getting an emergency physician to the scene as quickly as possible, reducing transport time to an appropriate hospital and caring for more complex emergencies are the main indications for HEMS. If HEMS appears likely to be needed, it should be dispatched immediately.

Structure and Mechanism of Pseudomonas aeruginosa PA0254/HudA, a prFMN-Dependent Pyrrole-2-carboxylic Acid Decarboxylase Linked to Virulence

The UbiD family of reversible (de)carboxylases depends on the recently discovered prenylated-FMN (prFMN) cofactor for activity. The model enzyme ferulic acid decarboxylase (Fdc1) decarboxylates unsaturated aliphatic acids via a reversible 1,3-cycloaddition process. Protein engineering has extended the Fdc1 substrate range to include (hetero)aromatic acids, although catalytic rates remain poor. This raises the question how efficient decarboxylation of (hetero)aromatic acids is achieved by other UbiD family members. Here, we show that the Pseudomonas aeruginosa virulence attenuation factor PA0254/HudA is a pyrrole-2-carboxylic acid decarboxylase. The crystal structure of the enzyme in the presence of the reversible inhibitor imidazole reveals a covalent prFMN-imidazole adduct is formed. Substrate screening reveals HudA and selected active site variants can accept a modest range of heteroaromatic compounds, including thiophene-2-carboxylic acid. Together with computational studies, our data suggests prFMN covalent catalysis occurs via electrophilic aromatic substitution and links HudA activity with the inhibitory effects of pyrrole-2-carboxylic acid on P. aeruginosa quorum sensing.

The femur–tibia control system in a proscopiid (Caelifera, Orthoptera): a test for assumptions on the functional basis and evolution of twig mimesis in stick insects

The extremely slow return movements observed in stick insects (phasmids) after imposed changes in posture are termed catalepsy. In the literature, catalepsy is treated as a behavioural component of the twig mimesis observed in walking stick insects. It is produced by the high gain of the velocity-sensitive component of the relevant joint control systems and by the non-linear dependency of its time constant on movement velocity. The high gain, in turn, causes the system to work close to instability, and this may have driven the evolution of gain control mechanisms. Although these statements represent plausible assumptions, based on correlated occurrence, they remain largely hypothetical like many ideas concerning evolutionary tendencies. To test these hypotheses, we studied catalepsy and the relevant properties of the femur–tibia control system in the middle and hind legs of Prosarthria teretrirostris.cf. Prosarthria teretrirostris is a proscopiid closely related to grasshoppers and locusts. With its slender, green-to-brown body and legs, it shows clear morphological twig mimesis, which has evolved independently of the well-known twig mimesis in stick insects. The animals show clear catalepsy. The main properties of femur–tibia joint control are remarkably similar between proscopiids and stick insects (e.g. the marked sensitivity to movement velocity rather than to joint position and the non-linear dependency of the time constants of response decay on movement velocity), but there are also important differences (habituation and activity-related mechanisms of gain control are absent). Together, these results validate the main concepts that have been developed concerning the neural basis and evolution of catalepsy in stick insects and its relationship to twig mimesis, while demonstrating that ideas on the role of habituation and gain control should be refined.

Ferulic Acid Decarboxylase Controls Oxidative Maturation of the Prenylated Flavin Mononucleotide Cofactor

Prenylated flavin mononucleotide (prFMN) is a recently discovered modified flavin cofactor containing an additional nonaromatic ring, connected to the N5 and C6 atoms. This cofactor underpins reversible decarboxylation catalyzed by members of the widespread UbiD enzyme family and is produced by the flavin prenyltransferase UbiX. Oxidative maturation of the UbiX product prFMNH₂ to the corresponding oxidized prFMN^iminium is required for ferulic acid decarboxylase (Fdc1; a UbiD-type enzyme) activity. However, it is unclear what role the Fdc1 enzyme plays in this process. Here, we demonstrate that, in the absence of Fdc1, prFMNH₂ oxidation by O₂ proceeds via a transient semiquinone prFMN^radical species and culminates in a remarkably stable prFMN-hydroperoxide species. Neither forms of prFMN are able to support Fdc1 activity. Instead, enzyme activation using O₂-mediated oxidation requires prFMNH₂ binding prior to oxygen exposure, confirming that UbiD enzymes play a role in O₂-mediated oxidative maturation. In marked contrast, alternative oxidants such as potassium ferricyanide support prFMN^iminium formation both in solution and in Fdc1.

Directed evolution of prenylated FMN-dependent Fdc supports efficient in vivo isobutene production

Isobutene is a high value gaseous alkene used as fuel additive and a chemical building block. As an alternative to fossil fuel derived isobutene, we here develop a modified mevalonate pathway for the production of isobutene from glucose in vivo. The final step in the pathway consists of the decarboxylation of 3-methylcrotonic acid, catalysed by an evolved ferulic acid decarboxylase (Fdc) enzyme. Fdc belongs to the prFMN-dependent UbiD enzyme family that catalyses reversible decarboxylation of (hetero)aromatic acids or acrylic acids with extended conjugation. Following a screen of an Fdc library for inherent 3-methylcrotonic acid decarboxylase activity, directed evolution yields variants with up to an 80-fold increase in activity. Crystal structures of the evolved variants reveal that changes in the substrate binding pocket are responsible for increased selectivity. Solution and computational studies suggest that isobutene cycloelimination is rate limiting and strictly dependent on presence of the 3-methyl group.

Isobutene is a high value gaseous alkene that is widely used as fuel additive and a chemical building block. Here, the authors report an alternative pathway for isobutene bioproduction by directed evolution of prenylated FMN-dependent ferulic acid decarboxylase.

[Doctor-patient interaction in the context of migration]

Doctors are often challenged by their interaction with migrants. The difficulties they describe are essentially the same as the ones they experience with Swiss patients. However, these encounters are frequently encumbered by factors relating to the migrant's situation. This article will delineate the various problem areas of doctor-patient interactions in the context of migration: difficulties understanding one another lack of mutual reference points between doctors and patients and structural frameworks. These problem areas will be discussed and concrete solutions and practical recommendations will be outlined.

Mapping the Initial Stages of a Protective Pathway that Enhances Catalytic Turnover by a Lytic Polysaccharide Monooxygenase

Oxygenase and peroxygenase enzymes generate intermediates at their active sites which bring about the controlled functionalization of inert C-H bonds in substrates, such as in the enzymatic conversion of methane to methanol. To be viable catalysts, however, these enzymes must also prevent oxidative damage to essential active site residues, which can occur during both coupled and uncoupled turnover. Herein, we use a combination of stopped-flow spectroscopy, targeted mutagenesis, TD-DFT calculations, high-energy resolution fluorescence detection X-ray absorption spectroscopy, and electron paramagnetic resonance spectroscopy to study two transient intermediates that together form a protective pathway built into the active sites of copper-dependent lytic polysaccharide monooxygenases (LPMOs). First, a transient high-valent species is generated at the copper histidine brace active site following treatment of the LPMO with either hydrogen peroxide or peroxyacids in the absence of substrate. This intermediate, which we propose to be a CuII-(histidyl radical), then reacts with a nearby tyrosine residue in an intersystem-crossing reaction to give a ferromagnetically coupled (S = 1) CuII-tyrosyl radical pair, thereby restoring the histidine brace active site to its resting state and allowing it to re-enter the catalytic cycle through reduction. This process gives the enzyme the capacity to minimize damage to the active site histidine residues "on the fly" to increase the total turnover number prior to enzyme deactivation, highlighting how oxidative enzymes are evolved to protect themselves from deleterious side reactions during uncoupled turnover.

Dilution and microfiltration of particulate corticosteroids for spinal epidural injections: impact on drug concentration and agglomerate formation

Particulate corticosteroids have been described to lead to greater pain improvement compared with their non-particulate counterparts when used in epidural injections. It is hypothesised that filtering may significantly impact their concentration and long-term efficacy. We investigated if passing particulate suspensions through different commonly-used filters affects drug dosage. Two particulate corticosteroid formulations, triamcinolone acetonide and methylprednisolone acetate, were mixed at different concentrations with either bupivacaine hydrochloride or 0.9% sodium chloride. Solutions were passed through a 5-μm and a 0.2-μm filter. Mass spectroscopy results indicated a complete loss of corticosteroid from the solutions using both filters, and light microscopy imaging demonstrated agglomerate formation, suggesting that filtering interferes with drug dosage. The choice of diluents must also be considered to reduce large agglomerate formation. Clinicians should be aware of the consequences of filtering particulate suspensions and carefully consider the selection of diluent when considering treatment plans.

Galactose Oxidase Enables Modular Assembly of Conjugates from Native Antibodies with High Drug-to-Antibody Ratios

The potential of antibody conjugates with high drug loading in anticancer therapy has recently been highlighted by the approval of Trastuzumab deruxtecan and Sacituzumab govitecan. These biopharmaceutical approaches have spurred interest in bioconjugation strategies with high and defined degrees of drug-to-antibody ratio (DAR), in particular on native antibodies. Here, a glycoengineering methodology was developed to generate antibody drug conjugates with DAR of up to eight, by combining highly selective enzymatic galactosylation and oxidation with biorthogonal tandem Knoevenagel-Michael addition chemistry. This four-step approach offers a selective route to conjugates from native antibodies with high drug loading, and thus illustrates how biocatalysis can be used for the generation of biopharmaceuticals using mild reaction conditions.

Enzymatic elaboration of oxime-linked glycoconjugates in solution and on liposomes

Oxime formation is a convenient one-step method for ligating reducing sugars to surfaces, producing a mixture of closed ring α- and β-anomers along with open-chain (E)- and (Z)-isomers. Here we show that despite existing as a mixture of isomers, N-acetylglucosamine (GlcNAc) oximes can still be substrates for β(1,4)-galactosyltransferase (β4GalT1). β4GalT1 catalysed the galactosylation of GlcNAc oximes by a galactose donor (UDP-Gal) both in solution and in situ on the surface of liposomes, with conversions up to 60% in solution and ca. 15-20% at the liposome surface. It is proposed that the β-anomer is consumed preferentially but long reaction times allow this isomer to be replenished by equilibration from the remaining isomers. Adding further enzymes gave more complex oligosaccharides, with a combination of α-1,3-fucosyltransferase, β4GalT1 and the corresponding sugar donors providing Lewis X coated liposomes. However, sialylation using T. cruzi trans-sialidase and sialyllactose provided only very small amounts of sialyl Lewis X (sLex) capped lipid. These observations show that combining oxime formation with enzymatic elaboration will be a useful method for the high-throughput surface modification of drug delivery vehicles, such as liposomes, with cell-targeting oligosaccharides.