Cross-feeding promotes heterogeneity within yeast cell populations.

Cellular heterogeneity in cell populations of isogenic origin is driven by intrinsic factors such as stochastic gene expression, as well as external factors like nutrient availability and interactions with neighbouring cells. Heterogeneity promotes population fitness and thus has important implications in antimicrobial and anticancer treatments, where stress tolerance plays a significant role. Here, we study plasmid retention dynamics within a population of plasmid-complemented ura3∆0 yeast cells, and show that the exchange of complementary metabolites between plasmid-carrying prototrophs and plasmid-free auxotrophs allows the latter to survive and proliferate in selective environments. This process also affects plasmid copy number in plasmid-carrying prototrophs, further promoting cellular functional heterogeneity. Finally, we show that targeted genetic engineering can be used to suppress cross-feeding and reduce the frequency of plasmid-free auxotrophs, or to exploit it for intentional population diversification and division of labour in co-culture systems.

An Ultrastable Self-Assembled Antibacterial Nanospears Made of Protein.

Protein-based nanomaterials have broad applications in the biomedical and bionanotechnological sectors owing to their outstanding properties such as high biocompatibility and biodegradability, structural stability, sophisticated functional versatility, and being environmentally benign. They have gained considerable attention in drug delivery, cancer therapeutics, vaccines, immunotherapies, biosensing, and biocatalysis. However, so far, in the battle against the increasing reports of antibiotic resistance and emerging drug-resistant bacteria, unique nanostructures of this kind are lacking, hindering their potential next-generation antibacterial agents. Here, the discovery of a class of supramolecular nanostructures with well-defined shapes, geometries, or architectures (termed "protein nanospears") based on engineered proteins, exhibiting exceptional broad-spectrum antibacterial activities, is reported. The protein nanospears are engineered via spontaneous cleavage-dependent or precisely tunable self-assembly routes using mild metal salt-ions (Mg2+ , Ca2+ , Na+ ) as a molecular trigger. The nanospears' dimensions collectively range from entire nano- to micrometer scale. The protein nanospears display exceptional thermal and chemical stability yet rapidly disassemble upon exposure to high concentrations of chaotropes (>1 mm sodium dodecyl sulfate (SDS)). Using a combination of biological assays and electron microscopy imaging, it is revealed that the nanospears spontaneously induce rapid and irreparable damage to bacterial morphology via a unique action mechanism provided by their nanostructure and enzymatic action, a feat inaccessible to traditional antibiotics. These protein-based nanospears show promise as a potent tool to combat the growing threats of resistant bacteria, inspiring a new way to engineer other antibacterial protein nanomaterials with diverse structural and dimensional architectures and functional properties.

Engineering Self-Assembled Endolysin Nanoparticles against Antibiotic-Resistant Bacteria.

Antibiotic resistance represents a serious global health concern and has stimulated the development of antimicrobial nanomaterials to combat resistant bacteria. Protein-based nanoparticles combining characteristics of both proteins and nanoparticles offer advantages including high biocompatibility, attractive biodegradability, enhanced bioavailability and functional versatility. They have played an increasing role as promising candidates for broad applications ranging from biocatalysts and drug delivery to vaccine development to cancer therapeutics. However, their application as antibacterial biomaterials to address challenging antibiotic-resistance problems has not been explicitly pursued. Herein, we describe engineering protein-only nanoparticles against resistant Gram-positive bacteria. A self-assembling peptide (P114) enables the assembly of a phage lytic enzyme (P128) into nanoparticles in response to pH reduction. Compared to native P128 and monomeric P114-P128, P128 nanoparticles (P128NANO) demonstrated a stronger bactericidal ability with high potency at lower concentrations (2-3-fold lower), particularly for methicillin-resistant Staphylococcus aureus strains. In addition, P128NANO showed an enhanced thermal (up to 65 °C) and storage stability and elicited extensive damages to bacterial cell walls. These remarkable antibacterial abilities are likely due to the P128NANO nanostructure, mediating multivalent interactions with bacterial cell walls at increased local concentrations of endolysin. The engineered endolysin nanoparticles offer a promising antimicrobial alternative to conventional antibiotics.

Understanding the Interplay between Self-Assembling Peptides and Solution Ions for Tunable Protein Nanoparticle Formation.

Protein-based nanomaterials are gaining importance in biomedical and biosensor applications where tunability of the protein particle size is highly desirable. Rationally designed proteins and peptides offer control over molecular interactions between monomeric protein units to modulate their self-assembly and thus particle formation. Here, using an example enzyme-peptide system produced as a single construct by bacterial expression, we explore how solution conditions affect the formation and size of protein nanoparticles. We found two independent routes to particle formation, one facilitated by charge interactions between protein-peptide and peptide-peptide exemplified by pH change or the presence of NO3- or NH4+ and the second route via metal-ion coordination ( e.g., Mg2+) within peptides. We further demonstrate that the two independent factors of pH and Mg2+ ions can be combined to regulate nanoparticle size. Charge interactions between protein-peptide monomers play a key role in either promoting or suppressing protein assembly; the intermolecular contact points within protein-peptide monomers involved in nanoparticle formation were identified by chemical cross-linking mass spectrometry. Importantly, the protein nanoparticles retain their catalytic activities, suggesting that their native structures are unaffected. Once formed, protein nanoparticles remain stable over long periods of storage or with changed solution conditions. Nevertheless, formation of nanoparticles is also reversible-they can be disassembled by desalting the buffer to remove complexing agents ( e.g., Mg2+). This study defines the factors controlling formation of protein nanoparticles driven by self-assembly peptides and an understanding of complex ion-peptide interactions involved within, offering a convenient approach to tailor protein nanoparticles without changing amino acid sequence.

Functional assessment of plant and microalgal lipid pathway genes in yeast to enhance microbial industrial oil production.

As promising alternatives to fossil-derived oils, microbial lipids are important as industrial feedstocks for biofuels and oleochemicals. Our broad aim is to increase lipid content in oleaginous yeast through expression of lipid accumulation genes and use Saccharomyces cerevisiae to functionally assess genes obtained from oil-producing plants and microalgae. Lipid accumulation genes DGAT (diacylglycerol acyltransferase), PDAT (phospholipid: diacylglycerol acyltransferase), and ROD1 (phosphatidylcholine: diacylglycerol choline-phosphotransferase) were separately expressed in yeast and lipid production measured by fluorescence, solvent extraction, thin layer chromatography, and gas chromatography (GC) of fatty acid methyl esters. Expression of DGAT1 from Arabidopsis thaliana effectively increased total fatty acids by 1.81-fold above control, and ROD1 led to increased unsaturated fatty acid content of yeast lipid. The functional assessment approach enabled the fast selection of candidate genes for metabolic engineering of yeast for production of lipid feedstocks.

Diversity of Δ12 fatty acid desaturases in santalaceae and their role in production of seed oil acetylenic fatty acids.

Plants in the Santalaceae family, including the native cherry Exocarpos cupressiformis and sweet quandong Santalum acuminatum, accumulate ximenynic acid (trans-11-octadecen-9-ynoic acid) in their seed oil and conjugated polyacetylenic fatty acids in root tissue. Twelve full-length genes coding for microsomal Δ12 fatty acid desaturases (FADs) from the two Santalaceae species were identified by degenerate PCR. Phylogenetic analysis of the predicted amino acid sequences placed five Santalaceae FADs with Δ12 FADs, which include Arabidopsis thaliana FAD2. When expressed in yeast, the major activity of these genes was Δ12 desaturation of oleic acid, but unusual activities were also observed: i.e. Δ15 desaturation of linoleic acid as well as trans-Δ12 and trans-Δ11 desaturations of stearolic acid (9-octadecynoic acid). The trans-12-octadecen-9-ynoic acid product was also detected in quandong seed oil. The two other FAD groups (FADX and FADY) were present in both species; in a phylogenetic tree of microsomal FAD enzymes, FADX and FADY formed a unique clade, suggesting that are highly divergent. The FADX group enzymes had no detectable Δ12 FAD activity but instead catalyzed cis-Δ13 desaturation of stearolic acid when expressed in yeast. No products were detected for the FADY group when expressed recombinantly. Quantitative PCR analysis showed that the FADY genes were expressed in leaf rather than developing seed of the native cherry. FADs with promiscuous and unique activities have been identified in Santalaceae and explain the origin of some of the unusual lipids found in this plant family.

Fifty years later: the sequence, structure and function of lacewing cross-beta silk.

Classic studies of protein structure in the 1950s and 1960s demonstrated that green lacewing egg stalk silk possesses a rare native cross-beta sheet conformation. We have identified and sequenced the silk genes expressed by adult females of a green lacewing species. The two encoded silk proteins are 109 and 67 kDa in size and rich in serine, glycine and alanine. Over 70% of each protein sequence consists of highly repetitive regions with 16-residue periodicity. The repetitive sequences can be fitted to an elegant cross-beta sheet structural model with protein chains folded into regular 8-residue long beta strands. This model is supported by wide-angle X-ray scattering data and tensile testing from both our work and the original papers. We suggest that the silk proteins assemble into stacked beta sheet crystallites bound together by a network of cystine cross-links. This hierarchical structure gives the lacewing silk high lateral stiffness nearly threefold that of silkworm silk, enabling the egg stalks to effectively suspend eggs and protect them from predators.

Neural regulation of discontinuous gas exchange in Periplaneta americana.

Patterns of gas exchange among terrestrial arthropods are highly variable from continuous to discontinuous with discretely partitioned phases. The underlying initiation and co-ordination of these patterns is relatively poorly understood. Here we present a novel method for the simultaneous measurement of central nervous system (CNS) activity of the metathoracic ganglion and VCO(2) in medium to large sized live terrestrial arthropods. Using Periplaneta americana at four oxygen levels (40%, 21%, 10% and 2% at 25 degrees C; n=6 per treatment), we present minimally invasive visualization of nervous output relative to typical resting discontinuous gas exchange (DGE) data for the first time. DGE was maintained when cockroaches were exposed to hyperoxia or moderate hypoxia, but was lost in severe hypoxia. CNS activity was manifested in three signal types: large CNS output coinciding with peak CO(2) production during a burst, moderate CNS output coinciding with CO(2) sawtoothing and fluttering, and minimal CNS activity during the closed phase of DGE in normoxia. Large and moderate CNS outputs were associated with observed abdominal pumping and congruent CO(2) peaks. At 10% oxygen, VCO(2) was significantly elevated during the inter-burst period in association with almost constant moderate CNS output between the periodic large CNS output. At 2% oxygen, DGE and large CNS output are lost to continuous CO(2) release and largely continuous moderate CNS output. As previously reported for this species, a central pattern generator for ventilation in the metathoracic ganglion is supported and we infer the presence of localized oxygen chemoreceptors based on clear CNS response to a change in oxygen tension.

Effects of phosphine on the neural regulation of gas exchange in Periplaneta americana.

Phosphine is used for fumigating stored commodities, however an understanding of the physiological response to phosphine in insects is limited. Here we show how the central pattern generator for ventilation in the central nervous system (CNS) responds to phosphine and influences normal resting gas exchange. Using the American cockroach, Periplaneta americana, that perform discontinuous gas exchange (DGE) at rest, we simultaneously measure ventilatory nervous output from the intact CNS, VCO(2) and water loss from live specimens. Exposure to 800 ppm phosphine at 25 degrees C for 2 h (n=13) during recording did not cause any mortality or obvious sub-lethal effects. Within 60 s of introducing phosphine into the air flow, all animals showed a distinct CNS response accompanied by a burst release of CO(2). The initial ventilatory response to phosphine displaced DGE and was typically followed by low, stable and continuous CO(2) output. CNS output was highest and most orderly under normoxic conditions during DGE. Phosphine caused a series of ventilatory CNS spikes preceding almost complete cessation of CNS output. Minimal CNS output was maintained during the 2 h normoxic recovery period and DGE was not reinstated. VCO(2) was slightly reduced and water loss significantly lower during the recovery period compared with those rates prior to phosphine exposure. A phosphine narcosis effect is rejected based on animals remaining alert at all times during exposure.

Cyclic gas exchange in the giant burrowing cockroach, Macropanesthia rhinoceros: effect of oxygen tension and temperature.

The giant burrowing cockroach, Macropanesthia rhinoceros, is endemic to north-eastern Australia and excavates a permanent burrow up to 1m deep into soil. Using flow-through respirometry, we investigated gas exchange and water loss at three different oxygen tensions (21%, 10% and 2% at 20 degrees C) and temperatures (10, 20 and 30 degrees C at 21% oxygen). M. rhinoceros employ cyclic gas exchange (CGE) making the species by far the largest insect known to engage in discontinuous ventilation. CGE featured rhythmic bursts of CO(2) dispersed among inter-burst periods of reduced output. CGE was most commonly observed at 20 degrees C and degraded at <10% oxygen. Mild hypoxia (10% oxygen) resulted in a lengthening of the burst period by approximately two-fold; this result is complementary to oxygen consumption data that suggests that the burst period is important in oxygen uptake. When exposed to severe hypoxia (2% oxygen), CGE was degraded to a more erratic continuous pattern. Also, during severe hypoxia, total water loss increased significantly, although CO(2) release was maintained at the same level as in 21% oxygen. During CGE, an increase in temperature from 10 to 20 degrees C caused both water loss and CO(2) output to double; from 20 to 30 degrees C, CO(2) output again doubled but water loss increased by only 31%.