Enzymatic Regulation of Protein-Protein Interactions in Artificial Cells.

Membraneless organelles are important for spatial organization of proteins and regulation of intracellular processes. Proteins can be recruited to these condensates by specific protein-protein or protein-nucleic acid interactions, which are often regulated by post-translational modifications. However, the mechanisms behind these dynamic, affinity-based protein recruitment events are not well understood. Here, a coacervate system that incorporates the 14-3-3 scaffold protein to study enzymatically regulated recruitment of 14-3-3-binding proteins is presented, which mostly bind in a phosphorylation-dependent manner. Synthetic coacervates are efficiently loaded with 14-3-3, and phosphorylated binding partners, such as the c-Raf pS233/pS259 peptide (c-Raf), show 14-3-3-dependent sequestration with up to 161-fold increase in local concentration. The c-Raf domain is fused to green fluorescent protein (GFP-c-Raf) to demonstrate recruitment of proteins. In situ phosphorylation of GFP-c-Raf by a kinase leads to enzymatically regulated uptake. The introduction of a phosphatase into coacervates preloaded with the phosphorylated 14-3-3-GFP-c-Raf complex results in a significant cargo efflux mediated by dephosphorylation. Finally, the general applicability of this platform to study protein-protein interactions is demonstrated by the phosphorylation-dependent and 14-3-3-mediated active reconstitution of a split-luciferase inside artificial cells. This work presents an approach to study dynamically regulated protein recruitment in condensates, using native interaction domains.

Switchable Control of Scaffold Protein Activity via Engineered Phosphoregulated Autoinhibition.

Scaffold proteins operate as organizing hubs to enable high-fidelity signaling, fulfilling crucial roles in the regulation of cellular processes. Bottom-up construction of controllable scaffolding platforms is attractive for the implementation of regulatory processes in synthetic biology. Here, we present a modular and switchable synthetic scaffolding system, integrating scaffold-mediated signaling with switchable kinase/phosphatase input control. Phosphorylation-responsive inhibitory peptide motifs were fused to 14-3-3 proteins to generate dimeric protein scaffolds with appended regulatory peptide motifs. The availability of the scaffold for intermolecular partner protein binding could be lowered up to 35-fold upon phosphorylation of the autoinhibition motifs, as demonstrated using three different kinases. In addition, a hetero-bivalent autoinhibitory platform design allowed for dual-kinase input regulation of scaffold activity. Reversibility of the regulatory platform was illustrated through phosphatase-controlled abrogation of autoinhibition, resulting in full recovery of 14-3-3 scaffold activity.

Modular bioengineered kinase sensors via scaffold protein-mediated split-luciferase complementation.

Phosphorylation is a key regulation event in cellular signaling. Sensing the underlying kinase activity is of crucial importance for its fundamental understanding and for drug development. For this, modular kinase activity sensing concepts are urgently needed. We engineered modular serine kinase sensors based on complementation of split NanoBiT luciferase on protein assembly platforms generated from the scaffold protein 14-3-3. The bioengineered platforms are modular and easy adaptable as exemplary shown using novel sensors for the kinases PKA, PKB, and CHK1. Two designs were conceptualized, both relying on binding of defined mono- or bivalent kinase recognition motifs to the 14-3-3 platform upon phosphorylation, resulting in reconstitution of active split-luciferase. Especially the design based on double phosphorylation and bivalent 14-3-3 binding exhibits high efficiency for signal amplification (>1000-fold) and sensitivity to specific kinases, including in cellular lysates.

Conjugated Protein Domains as Engineered Scaffold Proteins.

Assembly of proteins into higher-order complexes generates specificity and selectivity in cellular signaling. Signaling complex formation is facilitated by scaffold proteins that use modular scaffolding domains, which recruit specific pathway enzymes. Multimerization and recombination of these conjugated native domains allows the generation of libraries of engineered multidomain scaffold proteins. Analysis of these engineered proteins has provided molecular insight into the regulatory mechanism of the native scaffold proteins and the applicability of these synthetic variants. This topical review highlights the use of engineered, conjugated multidomain scaffold proteins on different length scales in the context of synthetic signaling pathways, metabolic engineering, liquid-liquid phase separation, and hydrogel formation.

Designed Asymmetric Protein Assembly on a Symmetric Scaffold.

Cellular signaling is regulated by the assembly of proteins into higher-order complexes. Bottom-up creation of synthetic protein assemblies, especially asymmetric complexes, is highly challenging. Presented here is the design and implementation of asymmetric assembly of a ternary protein complex facilitated by Rosetta modeling and thermodynamic analysis. The wild-type symmetric CT32-CT32 interface of the 14-3-3-CT32 complex was targeted, ultimately favoring asymmetric assembly on the 14-3-3 scaffold. Biochemical studies, supported by mass-balance models, allowed characterization of the parameters driving asymmetric assembly. Importantly, our work reveals that both the individual binding affinities and cooperativity between the assembling components are crucial when designing higher-order protein complexes. Enzyme complementation on the 14-3-3 scaffold highlighted that interface engineering of a symmetric ternary complex generates asymmetric protein complexes with new functions.

Protease-Activatable Scaffold Proteins as Versatile Molecular Hubs in Synthetic Signaling Networks.

Protease signaling and scaffold-induced control of protein-protein interactions represent two important mechanisms for intracellular signaling. Here we report a generic and modular approach to control the activity of scaffolding proteins by protease activity, creating versatile molecular platforms to construct synthetic signaling networks. Using 14-3-3 proteins as a structurally well-characterized and important class of scaffold proteins, three different architectures were explored to achieve optimal protease-mediated control of scaffold activity, fusing either one or two monovalent inhibitory ExoS peptides or a single bivalent ExoS peptide to T14-3-3 using protease-cleavable linkers. Analysis of scaffolding activity before and after protease-induced cleavage revealed optimal control of 14-3-3 activity for the system that contained monovalent ExoS peptides fused to both the N-and C-terminus, each blocking a single T14-3-3 binding site. The protease-activatable 14-3-3 scaffolds were successfully applied to construct a three-step signaling cascade in which dimerization and activation of FGG-caspase-9 on an orthogonal supramolecular platform resulted in activation of a 14-3-3 scaffold, which in turn allowed 14-3-3-templated complementation of a split-luciferase. In addition, by combining 14-3-3-templated activation of caspase-9 with a caspase-9-activatable 14-3-3 scaffold, the first example of a synthetic self-activating protease signaling network was created. Protease-activatable 14-3-3 proteins thus represent a modular platform whose properties can be rationally engineered to fit different applications, both to create artificial in vitro synthetic molecular networks and as a novel signaling hub to re-engineer intracellular signaling pathways.

Small-Molecule-Induced and Cooperative Enzyme Assembly on a 14-3-3 Scaffold.

Scaffold proteins regulate cell signalling by promoting the proximity of putative interaction partners. Although they are frequently applied in cellular settings, fundamental understanding of them in terms of, amongst other factors, quantitative parameters has been lagging behind. Here we present a scaffold protein platform that is based on the native 14-3-3 dimeric protein and is controllable through the action of a small-molecule compound, thus permitting study in an in vitro setting and mathematical description. Robust small-molecule regulation of caspase-9 activity through induced dimerisation on the 14-3-3 scaffold was demonstrated. The individual parameters of this system were precisely determined and used to develop a mathematical model of the scaffolding concept. This model was used to elucidate the strong cooperativity of the enzyme activation mediated by the 14-3-3 scaffold. This work provides an entry point for the long-needed quantitative insights into scaffold protein functioning and paves the way for the optimal use of reengineered 14-3-3 proteins as chemically inducible scaffolds in synthetic systems.

Helicobacter pylori eradication with doxycycline-metronidazole-bismuth subcitrate triple therapy.

Triple therapy containing tetracycline HCl is currently among the most efficient combination therapies for eradication of Helicobacter pylori. Substitution of doxycycline for tetracycline HCl offers advantages of less frequent dosing and extrarenal excretion. In this study patients with duodenal ulcer or non-ulcer dyspepsia positive for H. pylori were randomized to either doxycycline or tetracycline HCl triple therapy in conjunction with bismuth subcitrate and metronidazole. Of the 34 patients taking doxycycline, only 22 (65%) achieved H. pylori eradication at the 4-week rebiopsy, compared with 36 of 39 (92%) taking tetracycline HCl (p = 0.004). We conclude that doxycycline-containing triple therapy is less effective for H. pylori eradication and offers no clinical advantage over tetracycline HCl-containing triple therapy.

Xiphinema llanosum and Trophurus vultus, Two New Plant Nematode Species from Pasture Soils in Colombia.

Xiphinema llanosum n. sp. and Trophurus vultus n. sp. are described and illustrated from grass soils in Llanos Orientales, Colombia. Xiphinema llanosum is a bisexual species. The female body length is 2.3-2.7 mm, odontostyle 86-96 mum, and odontophore 58-65 mum long; vulva at 42-47%; anterior ovary is absent; the anterior uterus and oviduct are similar to the posterior branch but slightly reduced; and the tail is dorsally convex-conoid with a blunt hemispherical terminus. Male body length is 2.06-2.96 mm; spicules are 40-44 mum long; and four (rarely three or five) anterior ventromedian supplementary papillae are present. Trophurus vultus females are 0.52-0.67 mm long; vulva at 56-60%; stylet is 10.5-13.5 mum long; isthmus is as long as the basal esophageal bulb; the tail is subclavate, 1.6-2.2 times anal body width long; and the terminal cuticle thickness is about one-sixth of the tail length.

Recurrence of duodenal ulcer and Campylobacter pylori infection after eradication.

The role of Campylobacter pylori gastritis in dyspepsia could be clarified more readily if reliable eradication therapy were available. Antibiotic monotherapy and combined therapy with an antibiotic agent plus a bismuth compound have yielded poor long-term results. In this study, bismuth-tetracycline-metronidazole triple therapy has been used to eradicate C. pylori infection in 100 consecutive patients who were suffering from either a duodenal ulcer or non-ulcer dyspepsia. Examination of a follow-up endoscopic biopsy at eight weeks after treatment showed an eradication rate of C. pylori of 94%. Of 64 patients whose biopsy samples were free of C. pylori infection at eight weeks and who were available for reassessment, 60 (94%) patients had samples that remained free of C. pylori infection on examination of a repeat endoscopic biopsy at 12-37 months (mean, 19.3 months). It is concluded that "triple chemotherapy" can achieve long-term eradication of C. pylori infection effectively in the majority of treated patients and that the recurrence of duodenal ulcers thus may be diminished.

Pterotylenchus cecidogenus n. gen., n. sp., a New Stem-gall Nematode Parasitizing Desmodium ovalifolium in Colombia.

Pterotylenchus cecidogenus n. gen., n. sp. from stem-galls of Desmodium ovalifolium Wall. in Colombia is described and illustrated. The new genus belongs to Anguinidae and is related to Orrina Brzeski, 1980 but is unique in having large vulval flaps. P. cecidogenus has females with body 0.59-0.8 mm long, stylet 9-11 mum long, no median oesophageal bulb, a crustaformeria of 32-36 cells, a short post-vulval uterine sac, and a conical pointed tail.