Polydopamine-immobilized yeast cells for portable electrochemical biosensors applied in environmental copper sensing.

The coupling of biological organisms with electrodes enables the development of sustainable, low cost, and potentially self-sustained biosensors. A critical aspect is to obtain portable bioelectrodes where the biological material is immobilized on the electrode surface to be utilized on demand. Herein, we developed an approach for the rapid entrapment and immobilization of metabolically active yeast cells in a biocompatible polydopamine layer, which does not require a separate and time-consuming synthesis. The reported approach allows obtaining the "electrical wire" of intact and active yeast cells with resulting current generation from glucose oxidation. Additionally, the electrochemical performance of the biohybrid yeast-based system has been characterized in the presence of CuSO4, a widely used pesticide, in the environmentally relevant concentration range of 20-100 µM. The system enabled the rapid preliminary monitoring of the contaminant based on variations in current generation, with a limit of detection of 12.5 µM CuSO4. The present approach for the facile preparation of portable yeast-based electrochemical biosensors paves the way for the future development of sustainable systems for environmental monitoring.

Unveiling the Influence of Hydrated Deep Eutectic Solvents on the Dynamics of Water-Soluble Proteins.

Deep eutectic solvents (DESs) are mixtures of two or more pure compounds (e.g., Lewis or Brønsted acids and bases, anionic and/or cationic species) in a well-defined stoichiometric proportion, with a melting point lower to that of an ideal liquid mixture. These neoteric solvents are highly tunable through varying the structure or relative ratio of parent components and have been evaluated as solvents able to improve biomolecules' performance, specifically their stability and biocatalytic properties. Inspired by a recent crystallographic study, we have explored through molecular dynamics (MD) simulations the dynamic properties of two different proteins (hen egg-white lysozyme and the human VH antibody fragment HEL4) in a (20% w/w) hydrated solution of choline chloride-glycerol (1:2). We have developed proper force fields to account for DES, protein, and DES-protein interactions, which have been calibrated using pair distribution function measurements of pure DES solutions. MD results show that the presence of DES quenches the protein motion, increasing the rigidity of the overall protein structure. Specific interactions among DES components and protein residues, such as those between choline ions and two Tryptophan residues of lysozyme, may amplify the protein-DES interactions and lead to protein crystallization in the presence of hydrated DES. These findings open new horizons to improve or achieve control on protein properties by a proper choice of hydrated DESs used as solvents.

Supramolecular Biohybrid Construct for Photoconversion Based on a Bacterial Reaction Center Covalently Bound to Cytochrome c by an Organic Light Harvesting Bridge.

A supramolecular construct for solar energy conversion is developed by covalently bridging the reaction center (RC) from the photosynthetic bacterium Rhodobacter sphaeroides and cytochrome c (Cyt c) proteins with a tailored organic light harvesting antenna (hCy2). The RC-hCy2-Cyt c biohybrid mimics the working mechanism of biological assemblies located in the bacterial cell membrane to convert sunlight into metabolic energy. hCy2 collects visible light and transfers energy to the RC, increasing the rate of photocycle between a RC and Cyt c that are linked in such a way that enhances proximity without preventing protein mobility. The biohybrid obtained with average 1 RC/10 hCy2/1.5 Cyt c molar ratio features an almost doubled photoactivity versus the pristine RC upon illumination at 660 nm, and ∼10 times higher photocurrent versus an equimolar mixture of the unbound proteins. Our results represent an interesting insight into photoenzyme chemical manipulation, opening the way to new eco-sustainable systems for biophotovoltaics.

Electroactivity of weak electricigen Bacillus subtilis biofilms in solution containing deep eutectic solvent components.

Bacillus subtilis is a Gram-positive, spore-forming bacterium with a versatile and adaptable metabolism, which makes it a viable cell factory for microbial production. Electroactivity has recently been identified as a cellular characteristic linked with the metabolic activity of B. subtilis. The enhancement of B. subtilis electroactivity can positively enhance bioproduction of high-added value metabolites under electrofermentative conditions. Here, we explored the use of deep eutectic solvents (DESs) and DES components as biocompatible nutrient additives for enhancing electroactivity of B. subtilis. The strongest electroactivity was obtained in an aqueous choline chloride: glycerol (1:2 mol mol-1) eutectic mixture. At low concentration (50-500 mM), this mixture induced a pseudo-diauxic increase in planktonic growth and increased biofilm formation, likely due to a nutritional and osmoprotectant effect. Similarities in electroactivity enhancements of choline chloride-based eutectic mixtures and quinone redox metabolism in B. subtilis were detected using high performance liquid chromatography and differential pulse voltammetry. Results show that choline chloride-based aqueous eutectic mixtures can enhance biomass and productivity in biofilm-based electrofermentation. However, the specific mechanism needs to be fully elucidated.

Bio-Inspired Redox-Adhesive Polydopamine Matrix for Intact Bacteria Biohybrid Photoanodes.

Interfacing intact and metabolically active photosynthetic bacteria with abiotic electrodes requires both establishing extracellular electron transfer and immobilizing the biocatalyst on electrode surfaces. Artificial approaches for photoinduced electron harvesting through redox polymers reported in literature require the separate synthesis of artificial polymeric matrices and their subsequent combination with bacterial cells, making the development of biophotoanodes complex and less sustainable. Herein, we report a one-pot biocompatible and sustainable approach, inspired by the byssus of mussels, that provides bacterial cells adhesion on multiple surfaces under wet conditions to obtain biohybrid photoanodes with facilitated photoinduced electron harvesting. Purple bacteria were utilized as a model organism, as they are of great interest for the development of photobioelectrochemical systems for H2 and NH3 synthesis, biosensing, and bioremediation purposes. The polydopamine matrix preparation strategy allowed the entrapment of active purple bacteria cells by initial oxygenic polymerization followed by electrochemical polymerization. Our results unveil that the deposition of bacterial cells with simultaneous polymerization of polydopamine on the electrode surface enables a 5-fold enhancement in extracellular electron transfer at the biotic/abiotic interface while maintaining the viability of the cells. The presented approach paves the way for a more sustainable development of biohybrid photoelectrodes.

The periodic table of photosynthetic purple non-sulfur bacteria: intact cell-metal ions interactions.

Photosynthetic purple non-sulfur bacteria (PNB) have been widely utilized as model organisms to study bacterial photosynthesis. More recently, the remarkable resistance of these microorganisms to several metals ions called particular interest. As a result, several research efforts were directed toward clarifying the interactions of metal ions with PNB. The mechanisms of metal ions active uptake and bioabsorption have been studied in detail, unveiling that PNB enable harvesting and removing various toxic ions, thus fostering applications in environmental remediation. Herein, we present the most important achievements in the understanding of intact cell-metal ions interactions and the approaches utilized to study such processes. Following, the application of PNB-metal ions interactions toward metal removal from contaminated environments is presented. Finally, the possible coupling of PNB with abiotic electrodes to obtain biohybrid electrochemical systems is proposed as a sustainable pathway to tune and enhance metal removal and monitoring.

Chromatophores efficiently promote light-driven ATP synthesis and DNA transcription inside hybrid multicompartment artificial cells.

The construction of energetically autonomous artificial protocells is one of the most ambitious goals in bottom-up synthetic biology. Here, we show an efficient manner to build adenosine 5'-triphosphate (ATP) synthesizing hybrid multicompartment protocells. Bacterial chromatophores from Rhodobacter sphaeroides accomplish the photophosphorylation of adenosine 5'-diphosphate (ADP) to ATP, functioning as nanosized photosynthetic organellae when encapsulated inside artificial giant phospholipid vesicles (ATP production rate up to ∼100 ATP∙s-1 per ATP synthase). The chromatophore morphology and the orientation of the photophosphorylation proteins were characterized by cryo-electron microscopy (cryo-EM) and time-resolved spectroscopy. The freshly synthesized ATP has been employed for sustaining the transcription of a DNA gene, following the RNA biosynthesis inside individual vesicles by confocal microscopy. The hybrid multicompartment approach here proposed is very promising for the construction of full-fledged artificial protocells because it relies on easy-to-obtain and ready-to-use chromatophores, paving the way for artificial simplified-autotroph protocells (ASAPs).

About the origin of the large Stokes shift in aminoalkyl substituted heptamethine cyanine dyes.

Aminoalkyl-substituted heptamethine cyanine dyes are characterized by a large Stokes shift, an uncommon feature for cyanine molecules yet very promising for their application as fluorescent probes in bioimaging and as light harvesting antennas in biohybrid systems for solar energy conversion. The origin of this photophysical feature has not been adequately explored so far, and a combined experimental and theoretical work is herein provided to shed light on the role played by the central aminoalkyl substituent bound to the heptamethine cyanine backbone in defining the unusual properties of the dye. The spectra recorded in solvents of different polarities point to a marginal role of the medium in the definition of the Stokes shift, which conversely can be ascribed to the relaxation of the molecular geometry upon photoexcitation. This hypothesis is supported by an extensive theoretical investigation of the ground and excited states of the dye. TD-DFT results on the aminoalkyl-substituted dye and its unsubstituted precursor demonstrate a very similar cyanine-like structure for both molecules in the relaxed excited state. Conversely, in the ground state the amino substitution disrupts the conjugation in the polymethine chain, leading to a broken-symmetry, non-planar structure.

A highly efficient heptamethine cyanine antenna for photosynthetic Reaction Center: From chemical design to ultrafast energy transfer investigation of the hybrid system.

The photosynthetic Reaction Center (RC) from the purple bacterium Rhodobacter sphaeroides has unique photoconversion capabilities, that can be exploited in assembly biohybrid devices for applications in solar energy conversion. Extending the absorption cross section of isolated RC through covalent functionalization with ad-hoc synthesized artificial antennas is a successful strategy to outperform the efficiency of the pristine photoenzyme under visible light excitation. Here we report a new heptamethine cyanine antenna that, upon covalent binding to RC, forms a biohybrid (hCyN7-RC) which, under white light excitation, has doubled photoconversion efficiency versus the bare photoenzyme. The artificial antenna hCyN7 successfully meets appropriate optical properties, i.e. peak position of absorption and emission maximum in the visible and NIR region respectively, large Stokes shift, and high fluorescence quantum yield, required for improving the efficiency of the biohybrid in the production of the charge-separated state in the RC. The kinetics of energy transfer and charge separation of hCyN7-RC studied via ultrafast visible and IR spectroscopies are here presented. The antenna transfers energy to RC chromophores within <10 ps and the rate of QA reduction is doubled compared to the native RC. These experiments further demonstrate hCyN7-RC, besides being an extremely efficient white light photoconverter, fully retains the charge separation mechanism and integrity of the native RC photoenzyme, thus allowing to envisage its suitability as biohybrid material in bioinspired systems for solar energy conversion.

Draft Genome Sequences of Three Novel Staphylococcus arlettae Strains Isolated from a Disused Biological Safety Cabinet.

The genome sequences of three new strains of Staphylococcus arlettae named Bari1, Bari2, and Bari3 are presented. The strains exhibited tolerance to hexavalent chromium ions. An sprC gene encoding a putative chromium transporter was present in each of the three draft genome sequences.

Interaction between the photosynthetic anoxygenic microorganism Rhodobacter sphaeroides and soluble gold compounds. From toxicity to gold nanoparticle synthesis.

Biological processes using microorganisms for nanoparticle synthesis are appealing as eco-friendly nanofactories. The response of the photosynthetic bacterium Rhodobacter sphaeroides to gold exposure and its reducing capability of Au(III) to produce stable gold nanoparticles (AuNPs), using metabolically active bacteria and quiescent biomass, is reported in this study. In the former case, bacterial cells were grown in presence of gold chloride at physiological pH. Gold exposure was found to cause a significant increase of the lag-phase duration at concentrations higher than 10 µM, suggesting the involvement of a resistance mechanism activated by Au(III). Transmission Electron Microscopy (TEM) and Scanning Electron Microscopy/Energy Dispersive X-ray Spectrometry (SEM/EDS) analysis of bacterial cells confirmed the extracellular formation of AuNPs. Further studies were carried out on metabolically quiescent biomass incubated with gold chloride solution. The biosynthesized AuNPs were spherical in shape with an average size of 10 ±â€¯3 nm, as analysed by Transmission Electron Microscopy (TEM). The nanoparticles were hydrophilic and stable against aggregation for several months. In order to identify the functional groups responsible for the reduction and stabilization of nanoparticles, AuNPs were analysed by Attenuated Total Reflectance-Fourier Transform Infrared (ATR-FTIR) spectroscopy, X-ray Photoelectron Spectroscopy (XPS), X-ray Fluorescence Spectrometry (XRF) and X-ray Absorption Spectroscopy (XAS) measurements. The obtained results indicate that gold ions bind to functional groups of cell membrane and are subsequently reduced by reducing sugars to gold nanoparticles and capped by a protein/peptide coat. Gold nanoparticles demonstrated to be efficient homogeneous catalysts in the degradation of nitroaromatic compounds.

First moves towards photoautotrophic synthetic cells: In vitro study of photosynthetic reaction centre and cytochrome bc1 complex interactions.

Following a bottom-up synthetic biology approach it is shown that vesicle-based cell-like systems (shortly "synthetic cells") can be designed and assembled to perform specific function (for biotechnological applications) and for studies in the origin-of-life field. We recently focused on the construction of synthetic cells capable to converting light into chemical energy. Here we first present our approach, which has been realized so far by the reconstitution of photosynthetic reaction centre in the membrane of giant lipid vesicles. Next, the details of our ongoing research program are presented. It involves the use of the reaction centre, the coenzyme Q-cytochrome c oxidoreductase, and the ATP synthase for creating an autonomous synthetic cell. We show experimental results on the chemistry of the first two proteins showing that they can efficiently sustain light-driven chemical oscillations. Moreover, the cyclic pattern has been reproduced in silico by a minimal kinetic model.

Unveiling the compositional variety of cardiolipins in Rhodobacter sphaeroides by liquid chromatography with electrospray ionization and multistage collision-induced dissociation mass spectrometry.

Cardiolipins (CL) contained in the lipid extracts of the photosynthetic bacterium Rhodobacter sphaeroides (strain R26) were systematically characterized by reversed-phase liquid chromatography coupled to electrospray ionization mass spectrometry, performed in single (MS), tandem (MS/MS) and sequential (MS3) modes using a linear ion trap mass spectrometer. The total number of carbon atoms and C=C bonds of each CL and, subsequently, those related to each of the constituting phosphatidic acid (PA) units, along with the location of the latter on the central glycerol backbone, were inferred from MS and MS/MS data, respectively. Moreover, the composition and location of both acyl chains on the glycerol backbone of each PA unit was obtained by MS3 measurements, an approach used for the first time for the structural elucidation of CL in R. sphaeroides. As a result, an unprecedented profile of CL in this bacterium was obtained, with 27 main species characterized, many of which are represented by compositional or regiochemical isomers. Interestingly, such a variability is generated from a limited number of different acyl chains, either saturated (i.e. 12:0, 16:0, 17:0, 18:0, 19:0) or mono-unsaturated (16:1, 18:1). The absence of polyunsaturated chains, more susceptible to oxidation damage, appeared to be indirectly related to the lack of carotenoids potentially acting as antioxidant agents, a specific feature of R. sphaeroides R26. The occurrence of odd-numbered acyl chains was ascribed to the need to guarantee membrane fluidity, through a less compact packing of CL, thus compensating for the lack of CL bearing polyunsaturated side chains. Graphical abstract Representation of MS signals due to carboxylate anions that would be detected, as separate couples, in the fragmentation spectra of the anions resulting from the two phosphatidic acid units included in a cardiolipin molecule bearing four different acyl chains.

Highly oriented photosynthetic reaction centers generate a proton gradient in synthetic protocells.

Photosynthesis is responsible for the photochemical conversion of light into the chemical energy that fuels the planet Earth. The photochemical core of this process in all photosynthetic organisms is a transmembrane protein called the reaction center. In purple photosynthetic bacteria a simple version of this photoenzyme catalyzes the reduction of a quinone molecule, accompanied by the uptake of two protons from the cytoplasm. This results in the establishment of a proton concentration gradient across the lipid membrane, which can be ultimately harnessed to synthesize ATP. Herein we show that synthetic protocells, based on giant lipid vesicles embedding an oriented population of reaction centers, are capable of generating a photoinduced proton gradient across the membrane. Under continuous illumination, the protocells generate a gradient of 0.061 pH units per min, equivalent to a proton motive force of 3.6 mV⋅min-1 Remarkably, the facile reconstitution of the photosynthetic reaction center in the artificial lipid membrane, obtained by the droplet transfer method, paves the way for the construction of novel and more functional protocells for synthetic biology.

Electron-Transfer Secondary Reaction Matrices for MALDI MS Analysis of Bacteriochlorophyll a in Rhodobacter sphaeroides and Its Zinc and Copper Analogue Pigments.

Bacteriochlorophyll a (BChl a), a photosynthetic pigment performing the same functions of chlorophylls in plants, features a bacteriochlorin macrocycle ring (18 π electrons) with two reduced pyrrole rings along with a hydrophobic terpenoid side chain (i.e., the phytol residue). Chlorophylls analysis by matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) is not so straightforward since pheophytinization (i.e., release of the central metal ion) and cleavage of the phytol-ester linkage are invariably observed by employing protonating matrices such as 2,5-dihydroxybenzoic acid, sinapinic acid, and α-cyano-4-hydroxycinnamic acid. Using BChl a from Rhodobacter sphaeroides R26 strain as a model system, different electron-transfer (ET) secondary reaction matrices, leading to the formation of almost stable radical ions in both positive ([M]+•) and negative ([M]-•) ionization modes at m/z 910.55, were evaluated. Compared with ET matrices such as trans-2-[3-(4-t-butyl-phenyl)-2-methyl-2-propenylidene]malononitrile (DCTB), 2,2':5',2''-terthiophene (TER), anthracene (ANT), and 9,10-diphenylanthracene (DP-ANT), 1,5-diaminonaphthalene (DAN) was found to provide the highest ionization yield with a negligible fragmentation. DAN also displayed excellent ionization properties for two metal ion-substituted bacteriochlorophylls, (i.e., Zn- and Cu-BChl a at m/z 950.49 and 949.49), respectively. MALDI MS/MS of both radical charged molecular species provide complementary information, thus making analyte identification more straightforward. Graphical Abstract ᅟ.

Effect of ultrasound on the function and structure of a membrane protein: The case study of photosynthetic Reaction Center from Rhodobacter sphaeroides.

Ultrasounds are used in many industrial, medical and research applications. Properties and function of proteins are strongly influenced by the interaction with the ultrasonic waves and their bioactivity can be lost because of alteration of protein structure. Surprisingly, to the best of our knowledge no study was carried out on Integral Membrane Proteins (IMPs), which are responsible for a variety of fundamental biological functions. In this work, the photosynthetic Reaction Center (RC) of the bacterium Rhodobacter sphaeroides has been used as a model for the study of the ultrasound-induced IMP denaturation. Purified RCs were suspended in i) detergent micelles, in ii) detergent-free buffer and iii) reconstituted in liposomes, and then treated with ultrasound at 30W and 20kHz at increasing times. The optical absorption spectra showed a progressive and irreversible denaturation in all cases, resulting from the perturbation of the protein scaffold structure, as confirmed by circular dichroism spectra that showed progressive alterations of the RC secondary structure. Charge recombination kinetics were studied to assess the protein photoactivity. The lifetime for the loss of RC photoactivity was 32min in detergent micelles, ranged from 3.8 to 6.5min in the different proteoliposomes formulations, and 5.5min in detergent-free buffer. Atomic force microscopy revealed the formation of large RC aggregates related to the sonication-induced denaturation, in agreement with the scattering increase observed in solution.

Synthetic Antenna Functioning As Light Harvester in the Whole Visible Region for Enhanced Hybrid Photosynthetic Reaction Centers.

The photosynthetic reaction center (RC) from the Rhodobacter sphaeroides bacterium has been covalently bioconjugated with a NIR-emitting fluorophore (AE800) whose synthesis was specifically tailored to act as artificial antenna harvesting light in the entire visible region. AE800 has a broad absorption spectrum with peaks centered in the absorption gaps of the RC and its emission overlaps the most intense RC absorption bands, ensuring a consistent increase of the protein optical cross section. The covalent hybrid AE800-RC is stable and fully functional. The energy collected by the artificial antenna is transferred to the protein via FRET mechanism, and the hybrid system outperforms by a noteworthy 30% the overall photochemical activity of the native protein under the entire range of visible light. This improvement in the optical characteristic of the photoenzyme demonstrates the effectiveness of the bioconjugation approach as a suitable route to new biohybrid materials for energy conversion, photocatalysis, and biosensing.

Profiling of ornithine lipids in bacterial extracts of Rhodobacter sphaeroides by reversed-phase liquid chromatography with electrospray ionization and multistage mass spectrometry (RPLC-ESI-MS(n)).

Ornithine lipids (OLs), a sub-group of the large (and of emerging interest) family of lipoamino acids of bacterial origin, contain a 3-hydroxy fatty acyl chain linked via an amide bond to the α-amino group of ornithine and via an ester bond to a second fatty acyl chain. OLs in extracts of Rhodobacter sphaeroides (R. sphaeroides) were investigated by high-performance reversed phase liquid chromatography (RPLC) with electrospray ionization mass spectrometry (ESI-MS) in negative ion mode using a linear ion trap (LIT). The presence of OLs bearing both saturated (i.e, 16:0, 17:0, 18:0, 19:0 and 20:0) and unsaturated chains (i.e., 18:1, 19:1, 19:2 and 20:1) was ascertained and their identification, even for isomeric, low abundance and partially co-eluting species, was achieved by low-energy collision induced dissociation (CID) multistage mass spectrometry (MS(n), n = 2-4). OLs signatures found in two R. sphaeroides strains, i.e., wild type 2.4.1 and mutant R26, were examined and up to 16 and 17 different OL species were successfully identified, respectively. OLs in both bacterial strains were characterized by several combinations of fatty chains on ester-linked and amide-linked 3-OH fatty acids. Multistage MS spectra of monoenoic amide-linked 3-OH acyl chains, allowed the identification of positional isomer of OL containing 18:1 (i.e. 9-octadecenoic) and 20:1 (i.e. 11-eicosenoic) fatty acids. The most abundant OL ([M-H](-) at m/z 717.5) in R. sphaeroides R26 was identified as OL 3-OH 20:1/19:1 (i.e., 3-OH-eicosenoic acid amide-linked to ornithine and esterified to a nonadecenoic chain containing a cyclopropane ring). An unusual OL (m/z 689.5 for the [M-H](-) ion), most likely containing a cyclopropene ester-linked acyl chain (i.e., OL 3-OH 18:0/19:2), was retrieved only in the carotenoidless mutant strain R26. Based on the biosynthetic pathways already known for cyclopropa(e)ne ring-including acyl chains, a plausible explanation was invoked for the enzymatic generation of this ester-linked chain in R. sphaeroides.

Semiquinone oscillations as a tool for investigating the ubiquinone binding to photosynthetic reaction centers.

Semiquinone oscillations induced by light pulses in the presence of exogenous electron donors are a valuable source of information on the kinetics and thermodynamics of ubiquinone chemistry relevant to the QB site of the photosynthetic reaction center (RC). In previous attempts to achieve the quantitative interpretation of data, the ubiquinone concentration was considered constant during the experiment since it was much bigger than that of RC. In this work, we extended existing models to low ubiquinone concentrations revealing several hidden processes taking place during the ubiquinone photoreduction and enabling the evaluation of the ubiquinone binding constant K Q at the QB site. The proposed approach provides for the first time the evaluation of K Q without any preliminary treatment of ubiquinone extraction from the binding site, thereby better preserving its native structure.