Design and biophysical characterization of atrazine-sensing peptides mimicking the Chlamydomonas reinhardtii plastoquinone binding niche

The need for smart microalgal bioprospecting

Microalgae's adaptability and resilience to Earth's diverse environments have evolved these photosynthetic microorganisms into a biotechnological source of industrially relevant physiological functions and biometabolites. Despite this, microalgae-based industries only exploit a handful of species. This lack of biodiversity hinders the expansion of the microalgal industry. Microalgal bioprospecting, searching for novel biological algal resources with new properties, remains a low throughput and time-consuming endeavour due to inefficient workflows that rely on non-selective sampling, monoalgal culture status and outdated, non-standardized characterization techniques. This review will highlight the importance of microalgal bioprospecting and critically explore commonly employed methodologies. We will also explore current advances driving the next generation of smart algal bioprospecting focusing on novel workflows and transdisciplinary methodologies with the potential to enable high-throughput microalgal biodiscoveries. Images adapted from (Addicted04 in Wikipedia File: Australia on the globe (Australia centered).svg. 2014.; Jin et al. in ACS Appl Bio Mater 4:5080-5089, 2021; Kim et al. in Microchim Acta 189:88, 2022; Tony et al. in Lab on a Chip 15, 19:3810-3810; Thermo Fisher Scientific INC. in CTS Rotea Brochure).

Porous silicon pillar structures/photosynthetic reaction centre protein hybrid for bioelectronic applications

Photosynthetic biomaterials have attracted considerable attention at different levels of the biological organisation, from molecules to the biosphere, due to a variety of artificial application possibilities. During photosynthesis, the first steps of the conversion of light energy into chemical energy take place in a pigment-protein complex, called reaction centre (RC). In our experiments photosynthetic reaction centre protein, purified from Rhodobacter sphaeroides R-26 purple bacteria, was bound to porous silicon pillars (PSiP) after the electropolymerisation of aniline onto the surface. This new type of biohybrid material showed remarkable photoactivity in terms of measured photocurrent under light excitation in an electrochemical cell. The photocurrent was found to increase considerably after the addition of ubiquinone (UQ-0), an e^--acceptor mediator of the RC. The photoactivity of the complex was found to decrease by the addition of terbutryn, the chemical which inhibits the e^--transport on the acceptor side of the RC. In addition to the generation of sizeable light-induced photocurrents, using the PSiP/RC photoactive hybrid nanocomposite material, the system was found to be sensitive towards RC inhibitors and herbicides. This highly ordered patterned 3D structure opens new solution for designing low-power (bio-)optoelectronic, biophotonic and biosensing devices.

Quantum dots functionalised artificial peptides bioinspired to the D1 protein from the Photosystem II of Chlamydomonas reinhardtii for endocrine disruptor optosensing

Herein we describe the design and synthesis of novel artificial peptides mimicking the plastoquinone binding niche of the D1 protein from the green photosynthetic alga Chlamydomonas reinhardtii, also able to bind herbicides. In particular, molecular dynamics (MD) simulations were performed to model in silico the behaviour of three peptides, D1Pep70-H, D1Pep70-S264K and D1Pep70-S268C, as genetic variants with different affinity towards the photosynthetic herbicide atrazine. Then the photosynthetic peptides were functionalised with quantum dots for the development of a hybrid optosensor for the detection of atrazine, one of the most employed herbicides for weed control in agriculture as well as considered as a putative endocrine disruptor case study. The excellent agreement between computational and experimental results self consistently shows resistance or super-sensitivity toward the atrazine target, with detection limits in the μg/L concentration range, meeting the requirements of E.U. legislation.

Novel atrazine-binding biomimetics inspired to the D1 protein from the photosystem II of Chlamydomonas reinhardtii

Biomimetic design represents an emerging field for improving knowledge of natural molecules, as well as to project novel artificial tools with specific functions for biosensing. Effective strategies have been exploited to design artificial bioreceptors, taking inspiration from complex supramolecular assemblies. Among them, size-minimization strategy sounds promising to provide bioreceptors with tuned sensitivity, stability, and selectivity, through the ad hoc manipulation of chemical species at the molecular scale. Herein, a novel biomimetic peptide enabling herbicide binding was designed bioinspired to the D1 protein of the Photosystem II of the green alga Chlamydomonas reinhardtii. The D1 protein portion corresponding to the Q_B plastoquinone binding niche is capable of interacting with photosynthetic herbicides. A 50-mer peptide in the region of D1 protein from the residue 211 to 280 was designed in silico, and molecular dynamic simulations were performed alone and in complex with atrazine. An equilibrated structure was obtained with a stable pocked for atrazine binding by three H-bonds with SER222, ASN247, and HIS272 residues. Computational data were confirmed by fluorescence spectroscopy and circular dichroism on the peptide obtained by automated synthesis. Atrazine binding at nanomolar concentrations was followed by fluorescence spectroscopy, highlighting peptide suitability for optical sensing of herbicides at safety limits.

Biotechnological Advances in the Design of Algae-Based Biosensors

In addition to their use in biomass production and bioremediation, algae have been extensively exploited in biosensing applications. Algae-based biosensors have demonstrated potential for sensitive, sustainable, and multiplexed detection of analytes of agroenvironmental and security interest. Their advantages include the availability of different algal bioreceptors including whole cells and their photosynthetic subcomponents, their potential to be integrated into dual transduction miniaturized devices, and the opportunity for continuous environmental monitoring. Despite obstacles including limited stability and selectivity, algae-based biosensing is a realistic prospect that has some recent effective applications. Strategic exploitation of cutting-edge technologies including materials science, nanotechnology, microfluidics, and genome editing will help to achieve the full potential of algae-based sensors.

Sensing photosynthetic herbicides in an electrochemical flow cell

Specific inhibitory reactions of herbicides with photosynthetic reaction centers bound to working electrodes were monitored in a conventional electrochemical cell and a newly designed microfluidic electrochemical flow cell. In both cases, the bacterial reaction centers were bound to a transparent conductive metal oxide, indium-tin-oxide, electrode through carbon nanotubes. In the conventional cell, photocurrent densities of up to a few μA/cm² could be measured routinely. The photocurrent could be blocked by the photosynthetic inhibitor terbutryn (I ₅₀ = 0.38 ± 0.14 μM) and o-phenanthroline (I ₅₀ = 63.9 ± 12.2 μM). The microfluidic flow cell device enabled us to reduce the sample volume and to simplify the electrode arrangement. The useful area of the electrodes remained the same (ca. 2 cm²), similar to the classical electrochemical cell; however, the size of the cell was reduced considerably. The microfluidic flow control enabled us monitoring in real time the binding/unbinding of the inhibitor and cofactor molecules at the secondary quinone site.

Synthetic biology and biomimetic chemistry as converging technologies fostering a new generation of smart biosensors

Biosensors are powerful tunable systems able to switch between an ON/OFF status in response to an external stimulus. This extraordinary property could be engineered by adopting synthetic biology or biomimetic chemistry to obtain tailor-made biosensors having the desired requirements of robustness, sensitivity and detection range. Recent advances in both disciplines, in fact, allow to re-design the configuration of the sensing elements - either by modifying toggle switches and gene networks, or by producing synthetic entities mimicking key properties of natural molecules. The present review considered the role of synthetic biology in sustaining biosensor technology, reporting examples from the literature and reflecting on the features that make it a useful tool for designing and constructing engineered biological systems for sensing application. Besides, a section dedicated to bioinspired synthetic molecules as powerful tools to enhance biosensor potential is reported, and treated as an extension of the concept of biomimetic chemistry, where organic synthesis is used to generate artificial molecules that mimic natural molecules. Thus, the design of synthetic molecules, such as aptamers, biomimetics, molecular imprinting polymers, peptide nucleic acids, and ribozymes were encompassed as "products" of biomimetic chemistry.

Photosynthesis at the forefront of a sustainable life

The development of a sustainable bio-based economy has drawn much attention in recent years, and research to find smart solutions to the many inherent challenges has intensified. In nature, perhaps the best example of an authentic sustainable system is oxygenic photosynthesis. The biochemistry of this intricate process is empowered by solar radiation influx and performed by hierarchically organized complexes composed by photoreceptors, inorganic catalysts, and enzymes which define specific niches for optimizing light-to-energy conversion. The success of this process relies on its capability to exploit the almost inexhaustible reservoirs of sunlight, water, and carbon dioxide to transform photonic energy into chemical energy such as stored in adenosine triphosphate. Oxygenic photosynthesis is responsible for most of the oxygen, fossil fuels, and biomass on our planet. So, even after a few billion years of evolution, this process unceasingly supports life on earth, and probably soon also in outer-space, and inspires the development of enabling technologies for a sustainable global economy and ecosystem. The following review covers some of the major milestones reached in photosynthesis research, each reflecting lasting routes of innovation in agriculture, environmental protection, and clean energy production.

Evaluation of a biohybrid photoelectrochemical cell employing the purple bacterial reaction centre as a biosensor for herbicides

The Rhodobacter sphaeroides reaction centre is a relatively robust and tractable membrane protein that has potential for exploitation in technological applications, including biohybrid devices for photovoltaics and biosensing. This report assessed the usefulness of the photocurrent generated by this reaction centre adhered to a small working electrode as the basis for a biosensor for classes of herbicides used extensively for the control of weeds in major agricultural crops. Photocurrent generation was inhibited in a concentration-dependent manner by the triazides atrazine and terbutryn, but not by nitrile or phenylurea herbicides. Measurements of the effects of these herbicides on the kinetics of charge recombination in photo-oxidised reaction centres in solution showed the same selectivity of response. Titrations of reaction centre photocurrents yielded half maximal inhibitory concentrations of 208 nM and 2.1 µM for terbutryn and atrazine, respectively, with limits of detection estimated at around 8 nM and 50 nM, respectively. Photocurrent attenuation provided a direct measure of herbicide concentration, with no need for model-dependent kinetic analysis of the signal used for detection or the use of prohibitively complex instrumentation, and prospects for the use of protein engineering to develop the sensitivity and selectivity of herbicide binding by the Rba. sphaeroides reaction centre are discussed.

•

The Rhodobacter sphaeroides reaction centre was used as a biosensor for herbicides.

•

Herbicide concentration was assessed through the attenuation of a photocurrent.

•

The biosensor showed selectivity for triazine herbicides.

•

The limit of detection of the biosensor was in the low nanomolar range.

•

Photocurrent attenuation is a simple and direct basis for a herbicide biosensor.