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Highlights • Homotypic TMD interfaces identified by different techniques share strong similarities. • The GxxxG motif is the feature most strongly associated with interfaces. • Other features include conservation, polarity, coevolution, and depth in the membrane • The role of each of each feature strongly depends on the individual protein. • Machine-learning helps predict interfaces from evolutionary sequence data, Interactions between their transmembrane domains (TMDs) frequently support the assembly of single-pass membrane proteins to non-covalent complexes. Yet, the TMD-TMD interactome remains largely uncharted. With a view to predicting homotypic TMD-TMD interfaces from primary structure, we performed a systematic analysis of their physical and evolutionary properties. To this end, we generated a dataset of 50 self-interacting TMDs. This dataset contains interfaces of nine TMDs from bitopic human proteins (Ire1, Armcx6, Tie1, ATP1B1, PTPRO, PTPRU, PTPRG, DDR1, and Siglec7) that were experimentally identified here and combined with literature data. We show that interfacial residues of these homotypic TMD-TMD interfaces tend to be more conserved, coevolved and polar than non-interfacial residues. Further, we suggest for the first time that interface positions are deficient in β-branched residues, and likely to be located deep in the hydrophobic core of the membrane. Overrepresentation of the GxxxG motif at interfaces is strong, but that of (small)xxx(small) motifs is weak. The multiplicity of these features and the individual character of TMD-TMD interfaces, as uncovered here, prompted us to train a machine learning algorithm. The resulting prediction method, THOIPA (www.thoipa.org), excels in the prediction of key interface residues from evolutionary sequence data.

A large fraction of soluble and membrane-bound proteins exists as non-covalent dimers, trimers, and higher-order oligomers. The experimental determination of the oligomeric state or stoichiometry of proteins remains a nontrivial challenge. In one approach, the protein of interest is genetically fused to green fluorescent protein (GFP). If a fusion protein assembles into a non-covalent oligomeric complex, exciting their GFP moiety with polarized fluorescent light elicits homotypic Forster resonance energy transfer (homo-FRET), in which the emitted radiation is partially depolarized. Fluorescence depolarization is associated with a decrease in fluorescence anisotropy that can be exploited to calculate the oligomeric state. In a classical approach, several parameters obtained through time-resolved and steady-state anisotropy measurements are required for determining the stoichiometry of the oligomers. Here, we examined novel approaches in which time-resolved measurements of reference proteins provide the parameters that can be used to interpret the less expensive steady-state anisotropy data of candidates. In one approach, we find that using average homo-FRET rates (kFRET), average fluorescence lifetimes (τ), and average anisotropies of those fluorophores that are indirectly excited by homo-FRET (rET) do not compromise the accuracy of calculated stoichiometries. In the other approach, fractional photobleaching of reference oligomers provides a novel parameter a whose dependence on stoichiometry allows one to quantitatively interpret the increase of fluorescence anisotropy seen after photobleaching the candidates. These methods can at least reliably distinguish monomers from dimers and trimers.

The assembly of integral membrane protein complexes is frequently supported by transmembrane domain (TMD) interactions. Here, we present the BLaTM assay that measures homotypic as well as heterotypic TMD-TMD interactions in a bacterial membrane. The system is based on complementation of β-lactamase fragments genetically fused to interacting TMDs, which confers ampicillin resistance to expressing cells. We validated BLaTM by showing that the assay faithfully reports known sequence-specific interactions of both types. In a practical application, we used BLaTM to screen a focussed combinatorial library for heterotypic interactions driven by electrostatic forces. The results reveal novel patterns of ionizable amino acids within the isolated TMD pairs. Those patterns indicate that formation of heterotypic TMD pairs is most efficiently supported by closely spaced ionizable residues of opposite charge. In addition, TMD heteromerization can apparently be driven by hydrogen bonding between basic or between acidic residues.

Single-span membrane proteins take part in biological processes. In many cases their function has been shown to require dimerization via their transmembrane domains (TMDs). Research into the dimerization of TMDs has revealed sequence dependence, driven by a combination of amino acids. The helix interactions of multi-pass membrane proteins are well understood, as analysis of crystal structures shows that helix interfaces tend to contain small, polar and highly conserved residues. Unfortunately, for single-pass proteins structural data is scarce.The aim of this study is to characterize interfaces of TMDs that show strong self-interaction. In one study of this kind, we examine amino acid composition and conservation in order to identify patterns characteristic of interface residues. Our aim is to develop a method to predict the TMD interfaces from sequences alone.We used the ToxR assay in Escherichia coli to measure TMD homodimerization. In this assay, dimerization driven by TMDs results in the transcriptional activation of ctx promoter, inducing the expression of a reporter enzyme. The amount of reporter enzyme activity is a measure of the strength of the dimerization.Here, we present the scanning mutagenesis followed by ToxR analysis of 10 TMDs with strong self-interaction. Mutations were made to all amino acids within the TM helix. Some TMD interfaces were found to contain sequence patterns previously associated with parallel helix interactions, such as the GxxxG motif. However, in other cases motif searching would not have identified the interface, and the key residues in the interactions were diverse. The conservation of each amino acid in each TMD was calculated based on amino acid alignments against homologs. Preliminary analysis shows that amino acid conservation is a good indicator for the interface of some, but not all interacting TMDs.

Cytochrome P450 enzymes catalyse a wide variety of reactions, including the hydroxylation and epoxidation of C C bonds, and dealkylation reactions. There is high interest in these reactions for biotechnology and pharmaceutical processes. Many P450s require membrane surroundings and have substrates that do not cross biological membranes. To circumvent these obstacles, CYP106A2 from Bacillus megaterium was expressed on the outer membrane of Escherichia coli cells by Autodisplay. Exposure on the surface was confirmed by a protease accessibility test and flow cytometry after immunolabelling. HPLC assays showed that 0.5 ml of cells displaying the enzyme (OD 578 = 6) converted 9.13 μmol of deoxycorticosterone to 15β-OH-deoxycorticosterone within 1 h. Imipramine and abietic acid were also accepted as substrates. The number of active enzyme molecules per cell was calculated to be 20,000. Surprisingly, surface-exposed CYP106A2 was active in E. coli BL21 without the external addition of the heme group. However, when CYP106A2 was expressed on the surface of an E. coli strain lacking the TolC channel protein (JW5503), enzymatic activity was almost completely abolished. The activity of CYP106A2 on the surface of E. coli JW5503 could be restored by the external addition of the heme group. This suggests, as has been reported before, that E. coli uses a TolC-dependent mechanism to export heme into the growth media, where it can be scavenged by a surface-displayed apoenzyme. Our results indicate that Autodisplay enables the functional surface display of P450 enzymes and provides a new platform to access their synthetic potential.

Protein-protein interactions are the fundamental driving force of numerous cellular processes and cell signaling pathways. Characterizing whether proteins interact as dimers, trimers, or higher oligomers is essential to understanding these interactions. Several microscopy and advanced imaging techniques relying on Forster resonance energy transfer (FRET) between identical fluorophores (homo-FRET) have been developed to estimate protein stoichiometry. The increased FRET in oligomers is detected by measuring depolarization or emission time. Homo-FRET methods have a strong advantage in requiring only a single fluorophore, greatly simplifying sample preparation in comparison to conventional hetero-FRET methods. However, most homo-FRET methods require sophisticated imaging equipment, and both theoretical models and applications have been restricted to the study of membrane-bound proteins. Using a simple bulk homo-FRET and laser photobleaching approach, we demonstrate the feasibility of characterizing the oligomerization state of an interacting protein in-vitro. To simulate oligomers in a proof of concept, we constructed an extensive repertoire of fusion proteins with 1-6 consecutive green fluorescent protein (GFP) domains. We show how the resulting homo-FRET (measurable via steady-state anisotropy or fluorescence polarization) is proportional to the oligomerization state of proximal GFP domains. For the first time, this is demonstrated with soluble proteins. In both membrane and soluble proteins, oligomerization increases FRET and therefore anisotropy. However for soluble proteins oligomerization also slows fluorophore rotation, leading to a size-dependent decrease in anisotropy. Through gradual photobleaching of fluorophores these two effects can be distinguished, and the oligomerization state of a labeled protein of interest can be estimated. We therefore show how the theoretical framework developed for membrane proteins needs to be adjusted to account for this additional degree of freedom in soluble proteins. Overall, bulk homo-FRET and laser photobleaching is a promising method to determine the oligomerization state of a protein of interest, which can have a low concentration (0.1-0.5 µM) and needs only a single fluorescent label. The method requires only a photometer or microplate reader capable of measuring steady-state anisotropy.

Enhanced detoxification is the major mechanism responsible for pyrethroid resistance in Chinese populations of Helicoverpa armigera. Previous work has shown that enhanced oxidation contributes to resistance in the fenvalerate-selected Chinese strain, YGF. The current study provides evidence that enhanced hydrolysis by esterase isozymes also contributes to the resistance in this strain. The average esterase activity of third instar YGF larvae was 1.9-fold compared with that of a susceptible SCD strain. Much of this difference was attributed to isozymes at two zones which hydrolysed the model carboxylester substrate 1-naphthyl acetate and also a 1-naphthyl analogue of fenvalerate. A preparation enriched for enzymes migrating to one of these zones from YGF was shown to hydrolyse fenvalerate with a specific activity of about 2.9 nmol/min/mg. This material was also matched by mass spectrometry with four putative carboxylesterase genes, all of which clustered within a phylogenetic clade of secreted midgut esterases. Quantitative PCR on these four genes showed several-fold greater expression in tissues of YGF compared to SCD but no differences was found in the number of copies of the genes between the strains.

Elevated esterase activities and increased band intensities of multiple esterase isozymes after electrophoresis are commonly associated with resistance to organophosphate, pyrethroid and carbamate insecticides in various heliothine and spodopteran pests. One possible explanation for this involves a ‘master regulator’ mutation in a more general chemical stress response. An association between elevated esterase activities and isozyme intensities has also been reported for resistance to the Cry1Ac toxin of Helicoverpa armigera. The basis for this is unclear albeit some involvement of esterases could be mediated by the toxin’s affinity for N-acetyl galactosamine glycans on certain gut-expressed esterases in this species. © Pesticide Science Society of Japan

Tailoring surface properties of degradable polymer scaffolds is key to progress in various tissue engineering strategies. Poly(3-hydroxybutyrate) and poly(3-hydroxybutyrate- co -4-hydroxybutyrate) thin films were modified by low pressure ammonia plasma, low pressure water vapour plasma, or immersion in a sodium hydroxide solution to elaborate means to control the cell–matrix adhesion of human umbilical cord vein endothelial cells grown on these materials. Fibronectin (FN) heteroexchange and cell adhesion were correlated to the physicochemical characteristics of the modified polymer surfaces which were investigated by X-ray photoelectron spectroscopy (XPS), scanning force microscopy (SFM), electrokinetic measurements, and contact angle measurements. All treatments increased the hydrophilicity of the polymer samples, which could be accounted to newly created amine or carboxyl functionalities for ammonia plasma or water vapour plasma treatments, respectively, and ester hydrolysis for treatments with alkaline aqueous solutions. Main features of cell adhesion and FN reorganisation—evaluated after 1 h and after 5 days—could be attributed to the anchorage strength of pre-coated FN layers at the polymer surface, which was, in turn found to be triggered by the type of modification applied. In line with earlier studies referring to different materials cell adhesion and matrix reorganisation were shown to be sensitively controlled through the physicochemical profile of poly(hydroxybutyrate) surfaces.

Transmembrane (TM) helices of integral membrane proteins can facilitate strong and specific noncovalent protein-protein interactions. Mutagenesis and structural analyses have revealed numerous examples in which the interaction between TM helices of single-pass membrane proteins is dependent on a GxxxG or (small)xxx(small) motif. It is therefore tempting to use the presence of these simple motifs as an indicator of TM helix interactions. In this Current Topic review, we point out that these motifs are quite common, with more than 50% of single-pass TM domains containing a (small)xxx(small) motif. However, the actual interaction strength of motif-containing helices depends strongly on sequence context and membrane properties. In addition, recent studies have revealed several GxxxG-containing TM domains that interact via alternative interfaces involving hydrophobic, polar, aromatic, or even ionizable residues that do not form recognizable motifs. In multipass membrane proteins, GxxxG motifs can be important for protein folding, and not just oligomerization. Our current knowledge thus suggests that the presence of a GxxxG motif alone is a weak predictor of protein dimerization in the membrane.

A new optimized system for the surface display and secretion of recombinant proteins is described, termed MATE (maximized autotransporter-mediated expression). It is based on an artificial gene consisting of the coding region for the signal peptide of CtxB, a multiple cloning site for passenger gene insertion, flanked by coding sequences for linear epitopes for monoclonal antibodies and OmpT, and factor Xa protease cleavage sites followed by a codon-optimized DNA sequence of the linker and the β-barrel of the type V autotransporter EhaA from Escherichia coli under control of an IPTG-inducible T5 promoter. The MATE system enabled the continuous secretion of recombinant passenger mCherry via OmpT-mediated cleavage, using native OmpT protease activity in E. coli when grown at 37 °C. It is the first example to show that native OmpT activity is sufficient to facilitate the secretion of a correctly folded target protein in preparative amounts obtaining 240 µg of purified mCherry from 800 mL of crude culture supernatant. Because the release of mCherry was achieved by a simple transfer of the encoding plasmid from an OmpT-negative to an OmpT-positive strain, it bears the option to use surface display for screening purposes and secretion for production of the selected variant. A single plasmid could therefore be used for continuous secretion in OmpT-positive strains or surface display in OmpT-negative strains. In conclusion, the MATE system appears to be a versatile tool for the surface display and for the secretion of target proteins in E. coli.

Using genetic reporter assays, significant self-interaction has been discovered in over 50 transmembrane (TM) helices from single-pass membrane proteins. To understand the biological functions of these TM interactions, which include signal transfer across the membrane in cancer-related pathways, it is necessary to construct accurate structural models of the TM oligomer. However in most cases this is not possible because the oligomerization state (stoichiometry) is unknown. It is often assumed that the helices form a dimer, though biologically relevant TM oligomers include dimers, trimers, and pentamers, as exemplified by GpA, HLA II Ii, and phospholamban, respectively.To characterize the stoichiometry of interacting single-pass membrane proteins, we are establishing a novel method based on Forster resonance energy transfer between identical fluorophores (homo-FRET). In order to allow the rapid bacterial expression and the purification of a wide range of fluorophore-coupled TM helices, we have developed TM fusion proteins with green fluorescent protein (GFP) and affinity tags. The measured homoFRET (via steady-state anisotropy) is proportional to both the affinity of the helices and the oligomerization state. Using only a fluorescence microplate reader, we demonstrate significant homo-FRET-coupling for GFP fusion proteins. Theoretical studies have shown that gradual photobleaching should yield a pattern of polarization that depends on the oligomerization state. High-profile experimental studies have confirmed this in-vivo using advanced microscopy. We show for the first time that the “fingerprint”-like curves after laser photobleaching can be achieved in-vitro with relatively simple equipment, allowing us to differentiate between oligomerization states. This demonstrates the feasibility of a rapid homo-FRET assay to determine the stoichiometry of transmembrane proteins in liposomes.

Autodisplay, i.e. surface expression of recombinant proteins by virtue of the autotransporter secretion pathway, has been used predominantly with Escherichia coli as host organism, which often limits the applicability of this technique to laboratory purposes and scales. The aim of this study was to investigate if the fermentative bacteria Zymomonas mobilis and Zymobacter palmae, representing attractive candidates for industrial applications, can serve as host organisms for autodisplay. We therefore used the carboxylesterase EstA from Burkholderia gladioli as an autotransporter passenger to display it on the surfaces of Z. palmae and Z. mobilis. Expression and outer membrane localization of the EstA-autotransporter fusion protein were verified by SDS-PAGE, and surface display of the enzyme was demonstrated by ELISA and flow cytometer analysis. Whole-cell activity assays revealed that EstA retained its activity on the cell surface. Recombinant Z. palmae cells exhibited significant higher esterase activity (294 mU/mL/OD 1) in comparison to Z. mobilis (88 mU/mL/OD 1) and the control E. coli (113 mU/mL/OD 1). This appears even more noteworthy, as about 30% of EstA was released from the cell surface of Z. palmae. Nevertheless, our results indicate that both species are suitable autodisplay hosts, in particular Z. palmae for displaying esterase, opening up new horizons for biocatalytic applications.

A previously unidentified oxidoreductase from Escherichia coli catalyzes the regioselective reduction of eukaryotic steroid hormone 11-deoxycorticosterone (11-DOC) to the valuable bioactive product 4-pregnen-20,21-diol-3-one. In nature, a reduction of C-20 carbonyl of C21 steroids is catalyzed by diverse NAD(P)H-dependent oxidoreductases. Enzymes that possess 20-ketosteroid reductase activity, however, have never before been described in E. coli. Our present study aimed to identify and characterize the E. coli enzyme which possesses 20-ketosteroid reductase activity against eukaryotic steroid hormone 11-DOC. We partially purified the enzyme from E. coli DH5α using protein chromatography techniques. Mass spectrometry revealed the presence of three NADH-specific oxidoreductases in the sample. The genes encoding these oxidoreductases were cloned and overexpressed in E. coli UT5600 (DE3). Only the overexpression of 2-dehydro-3-deoxy-d-gluconate 5-dehydrogenase (KduD) encoded by kduD gene enabled the whole-cell biotransformation of 11-DOC. A 6xHis-tagged version of KduD was purified to homogeneity and found to reduce several eukaryotic steroid hormones and catalyze the conversion of novel sugar substrates. KduD from E. coli is therefore a promiscuous enzyme that has a predicted role in sugar conversion in vivo but can be used for the production of valuable bioactive 20-hydroxysteroids.

Inhibitors of the UDP-3-O-[(R)-3-hydroxymyristoyl]-N-acetylglucosamine deacetylase (LpxC) represent promising candidates for the development of antibiotics possessing a so far unexploited mechanism of action. In a chiral pool synthesis, starting from the D-mannose derived mannonolactone 4, conformationally constrained C-glycosidic as well as open chained hydroxamic acids with a defined stereochemistry were prepared. Diversity was introduced by performing C–C coupling reactions like the Sonogashira and Suzuki cross-coupling reactions. The biological evaluation of the synthesized compounds revealed that in the case of the C-glycosides a long, linear and rigid hydrophobic side chain is required for antibiotic activity against E. coli. The open chain derivatives show higher biological activity than the conformationally constrained C-glycosides. The morpholinomethyl substituted open chain derivative 43, being the most potent compound presented in this paper, inhibits LpxC with a Ki value of 0.35 μM and represents a promising lead structure.

Two mutations have been found in five closely related insect esterases (from four higher Diptera and a hymenopteran) which each confer organophosphate (OP) hydrolase activity on the enzyme and OP resistance on the insect. One mutation converts a Glycine to an Aspartate, and the other converts a Tryptophan to a Leucine in the enzymes’ active site. One of the dipteran enzymes with the Leucine mutation also shows enhanced activity against pyrethroids. Introduction of the two mutations in vitro into eight esterases from six other widely separated insect groups has also been reported to increase substantially the OP hydrolase activity of most of them. These data suggest that the two mutations could contribute to OP, and possibly pyrethroid, resistance in a variety of insects. We therefore introduced them in vitro into eight Helicoverpa armigera esterases from a clade that has already been implicated in OP and pyrethroid resistance. We found that they do not generally enhance either OP or pyrethroid hydrolysis in these esterases but the Aspartate mutation did increase OP hydrolysis in one enzyme by about 14 fold and the Leucine mutation caused a 4–6 fold increase in activity (more in one case) of another three against some of the most insecticidal isomers of fenvalerate and cypermethrin. The Aspartate enzyme and one of the Leucine enzymes occur in regions of the H. armigera esterase isozyme profile that have been previously implicated in OP and pyrethroid resistance, respectively.

To display an enzyme on the surface of a living cell is an important step forward towards a broader use of biocatalysts. Enzymes immobilized on surfaces appeared to be more stable compared to free molecules. It is possible by standard techniques to let the bacterial cell (e.g. Escherichia coli) decorate its surface with the enzyme and produce it on high amounts with a minimum of costs and equipment. Moreover, these cells can be recovered and reused in several subsequent process cycles. Among other systems, autodisplay has some extra features that could overcome limitations in the industrial applications of enzymes. One major advantage of autodisplay is the motility of the anchoring domain. Enzyme subunits exposed at the cell surface having affinity to each other will spontaneously form dimers or multimers. Using autodisplay enzymes with prosthetic groups can be displayed, expanding the application of surface display to the industrial important P450 enzymes. Finally, up to 105–106 enzyme molecules can be displayed on a single cell. In the present review, we summarize recent achievements in the autodisplay of enzymes with particular attention to industrial needs and process development. Applications that will provide sustainable solutions towards a bio-based industry are discussed.

Some of the resistance of Helicoverpa armigera to conventional insecticides such as organophosphates and synthetic pyrethroids appears to be due to metabolic detoxification by carboxylesterases. To investigate the H. armigera carboxyl/cholinesterases, we created a data set of 39 putative paralogous H. armigera carboxyl/cholinesterase sequences from cDNA libraries and other sources. Phylogenetic analysis revealed a close relationship between these sequences and 70 carboxyl/cholinesterases from the recently sequenced genome of the silkworm, Bombyx mori, including several conserved clades of non-catalytic proteins. A juvenile hormone esterase candidate from H. armigera was identified, and B. mori orthologues were proposed for 31% of the sequences examined, however low similarity was found between lepidopteran sequences and esterases previously associated with insecticide resistance from other insect orders. A proteomic analysis of larval esterases then enabled us to match seven of the H. armigera carboxyl/cholinesterase sequences to specific esterase isozymes. All identified sequences were predicted to encode catalytically active carboxylesterases, including six proteins with N-terminal signal peptides and N-glycans, with two also containing C-terminal signals for glycosylphosphatidylinositol anchor attachment. Five of these sequences were matched to zones of activity on native PAGE at relative mobility values previously associated with insecticide resistance in this species.

Enzymes are central to the biology of many pesticides, influencing their modes of action, environmental fates and mechanisms of target species resistance. Since the introduction of synthetic xenobiotic pesticides, enzymes responsible for pesticide turnover have evolved rapidly, in both the target organisms and incidentally exposed biota. Such enzymes are a source of significant biotechnological potential and form the basis of several bioremediation strategies intended to reduce the environmental impacts of pesticide residues. This review describes examples of enzymes possessing the major activities employed in the bioremediation of pesticide residues, and some of the strategies by which they are employed. In addition, several examples of specific achievements in enzyme engineering are considered, highlighting the growing trend in tailoring enzymatic activity to a specific biotechnologically relevant function.

Corrigendum to “Gene identification and proteomic analysis of the esterases of the cotton bollworm, Helicoverpa armigera” [Insect Biochem. Mol. Biol. 40 (2010) 1e16] Mark G. Teese , Peter M. Campbell , Colin Scott , Karl H.J. Gordon , Adam Southon , Daniel Hovan , Charles Robin , Robyn J. Russell , John G. Oakeshott a,* CSIRO Entomology, GPO Box 1700, Canberra ACT 2601, Australia Research School of Chemistry, Australian National University, Canberra ACT 0200, Australia Department of Genetics, The University of Melbourne, Vic. 3010, Australia