Analysis of bacterial polyhydroxybutyrate production by multimodal nanoimaging

Monitoring Phenotype Heterogeneity at the Single-Cell Level within Bacillus Populations Producing Poly-3-hydroxybutyrate by Label-Free Super-resolution Infrared Imaging

Phenotypic heterogeneity is commonly found among bacterial cells within microbial populations due to intrinsic factors as well as equipping the organisms to respond to external perturbations. The emergence of phenotypic heterogeneity in bacterial populations, particularly in the context of using these bacteria as microbial cell factories, is a major concern for industrial bioprocessing applications. This is due to the potential impact on overall productivity by allowing the growth of subpopulations consisting of inefficient producer cells. Monitoring the spread of phenotypes across bacterial cells within the same population at the single-cell level is key to the development of robust, high-yield bioprocesses. Here, we discuss the novel development of optical photothermal infrared (O-PTIR) spectroscopy to probe phenotypic heterogeneity within Bacillus strains by monitoring the production of the bioplastic poly-3-hydroxybutyrate (PHB) at the single-cell level. Measurements obtained on single-point and in imaging mode show significant variability in the PHB content within bacterial cells, ranging from whether or not a cell produces PHB to variations in the intragranular biochemistry of PHB within bacterial cells. Our results show the ability of O-PTIR spectroscopy to probe PHB production at the single-cell level in a rapid, label-free, and semiquantitative manner. These findings highlight the potential of O-PTIR spectroscopy in single-cell microbial metabolomics as a whole-organism fingerprinting tool that can be used to monitor the dynamic of bacterial populations as well as for understanding their mechanisms for dealing with environmental stress, which is crucial for metabolic engineering research.

The toxicities of A30P and A53T α-synuclein fibrils can be uniquely altered by the length and saturation of fatty acids in phosphatidylserine

Progressive degeneration of dopaminergic neurons in the midbrain, hypothalamus, and thalamus is a hallmark of Parkinson's disease (PD). Neuronal death is linked to the abrupt aggregation of α-synuclein (α-syn), a small protein that regulates vesicle trafficking in synaptic clefts. Studies of families with a history of PD revealed several mutations in α-syn including A30P and A53T that are linked to the early onset of this pathology. Numerous pieces of evidence indicate that lipids can alter the rate of protein aggregation, as well as modify the secondary structure and toxicity of amyloid oligomers and fibrils. However, the role of lipids in the stability of α-syn mutants remains unclear. In this study, we investigate the effect of phosphatidylserine (PS), an anionic lipid that plays an important role in the recognition of apoptotic cells by macrophages, in the stability of WT, A30P, and A53T α-syn. We found PS with different lengths and saturation of fatty acids accelerated the rate of WT and A30P aggregation. At the same time, the opposite effect was observed for most PS on A53T. We also found that PS with different lengths and saturation of fatty acids change the secondary structure and toxicities of WT, A30P, and A53T fibrils. These results indicate that lipids can play an important role in the onset and spread of familial PD.

Nanoscale structural characterization of transthyretin aggregates formed at different time points of protein aggregation using atomic force microscopy-infrared spectroscopy

Transthyretin (TTR) amyloidosis is a progressive disease characterized by an abrupt aggregation of misfolded protein in multiple organs and tissues TTR is a tetrameric protein expressed in the liver and choroid plexus. Protein misfolding triggers monomerization of TTR tetramers. Next, monomers assemble forming oligomers and fibrils. Although the secondary structure of TTR fibrils is well understood, there is very little if anything is known about the structural organization of TTR oligomers. To end this, we used nano-infrared spectroscopy, also known as atomic force microscopy infrared (AFM-IR) spectroscopy. This emerging technique can be used to determine the secondary structure of individual amyloid oligomers and fibrils. Using AFM-IR, we examined the secondary structure of TTR oligomers formed at the early (3-6 h), middle (9-12 h), and late (28 h) of protein aggregation. We found that aggregating, TTR formed oligomers (Type 1) that were dominated by α-helix (40%) and β-sheet (~30%) together with unordered protein (30%). Our results showed that fibril formation was triggered by another type of TTR oligomers (Type 2) that appeared at 9 h. These new oligomers were primarily composed of parallel β-sheet (55%), with a small amount of antiparallel β-sheet, α-helix, and unordered protein. We also found that Type 1 oligomers were not toxic to cells, whereas TTR fibrils formed at the late stages of protein aggregation were highly cytotoxic. These results show the complexity of protein aggregation and highlight the drastic difference in the protein oligomers that can be formed during such processes.

Unsaturated fatty acids uniquely alter aggregation rate of α-synuclein and insulin and change the secondary structure and toxicity of amyloid aggregates formed in their presence

Docosahexaenoic (DHA) and arachidonic acids (ARA) are omega-3 and omega-6 long-chain polyunsaturated fatty acids (LCPUFAs). These molecules constitute a substantial portion of phospholipids in plasma membranes. Therefore, both DHA and ARA are essential diet components. Once consumed, DHA and ARA can interact with a large variety of biomolecules, including proteins such as insulin and α-synuclein (α-Syn). Under pathological conditions known as injection amyloidosis and Parkinson's disease, these proteins aggregate forming amyloid oligomers and fibrils, toxic species that exert high cell toxicity. In this study, we investigate the role of DHA and ARA in the aggregation properties of α-Syn and insulin. We found that the presence of both DHA and ARA at the equimolar concentrations strongly accelerated aggregation rates of α-Syn and insulin. Furthermore, LCPUFAs substantially altered the secondary structure of protein aggregates, whereas no noticeable changes in the fibril morphology were observed. Nanoscale Infrared analysis of α-Syn and insulin fibrils grown in the presence of both DHA and ARA revealed the presence of LCPUFAs in these aggregates. We also found that such LCPUFAs-rich α-Syn and insulin fibrils exerted significantly greater toxicities compared to the aggregates grown in the LCPUFAs-free environment. These findings show that interactions between amyloid-associated proteins and LCPUFAs can be the underlying molecular cause of neurodegenerative diseases.

Lipids uniquely alter rates of insulin aggregation and lower toxicity of amyloid aggregates

Amyloid formation is a hallmark of many medical diseases including diabetes type 2, Alzheimer's and Parkinson diseases. Under these pathological conditions, misfolded proteins self-assemble forming oligomers and fibrils, structurally heterogeneous aggregates that exhibit a large variety of shapes and forms. A growing body of evidence points to drastic changes in the lipid profile in organs affected by amyloidogenic diseases. In this study, we investigated the extent to which individual phospho- and sphingolipids, as well as their mixtures can impact insulin aggregation. Our results show that lipids and their mixtures uniquely alter rates of insulin aggregation simultaneously changing the secondary structure of protein aggregates that are grown in their presence. These structurally different protein-lipid aggregates impact cell viability to different extent while using distinct mechanisms of toxicity. These findings suggest that irreversible changes in lipid profiles of organs may trigger formation of toxic protein species that in turn are responsible for the onset and progression of amyloidogenic diseases.

Length and Unsaturation of Fatty Acids of Phosphatidic Acid Determines the Aggregation Rate of Insulin and Modifies the Structure and Toxicity of Insulin Aggregates

Phosphatidic acid (PA) is a unique plasma membrane lipid that contains fatty acids (FAs) with different lengths and degrees of unsaturation. Under physiological conditions, PA acts as a second messenger regulating a wide variety of cellular processes. At the same time, the role of PA under pathological conditions, which are caused by an abrupt aggregation of amyloid proteins, remains unclear. In this study, we investigated the effect of PA with different lengths and unsaturation of FAs on insulin aggregation. We found that PA with C16:0 FAs strongly inhibited insulin aggregation, whereas PA with C18:0 FAs accelerated it. Furthermore, PA with unsaturated (C18:1) FAs made the insulin form extremely long and thick fibrils that were not observed for PAs with saturated FAs. We also found that the presence of PA with C16:0 FAs resulted in the formation of aggregates that exerted significantly lower cell toxicity compared to the aggregates formed in the presence of PAs with C18:0 and C18:1 FAs. These results suggest that PA may play a key role in neurodegeneration.

Unsaturation in the Fatty Acids of Phospholipids Drastically Alters the Structure and Toxicity of Insulin Aggregates Grown in Their Presence

Lipid bilayers play an important role in the pathological assembly of amyloidogenic proteins and peptides. This assembly yields oligomers and fibrils, which are highly toxic protein aggregates. In this study, we investigated the role of saturation in fatty acids of two phospholipids that are present in cell membranes. We found that unsaturated cardiolipin (CL) drastically shortened the lag phase of insulin aggregation. Furthermore, structurally and morphologically different aggregates were formed in the presence of unsaturated CL vs saturated CL. These aggregates exerted drastically different cell toxicity. Both saturated and unsaturated phosphatidylcholine (PC) were able to inhibit insulin aggregation equally efficiently. Similar to CL, structurally different aggregates were formed in the presence of saturated and unsaturated PC. These aggregates exerted different cell toxicities. These results show that unsaturated phospholipids catalyze the formation of more toxic amyloid aggregates comparing to those formed in the presence of saturated lipids.

Nanoscale Structural Analysis of a Lipid-Driven Aggregation of Insulin

Abrupt aggregation of misfolded proteins is a hallmark of a large number of severe pathologies, including diabetes types 1 and 2, Alzheimer, and Parkinson diseases. A growing body of evidence suggests that lipids can uniquely change rates of amyloid-associated proteins as well as modify the structure of formed oligomers and fibrils. In this study, we utilize atomic force microscopy infrared (AFM-IR) spectroscopy, also known as nano-IR spectroscopy, to examine the structure of individual insulin oligomers, protofilaments, and fibrils grown in the presence of phospholipids. Our findings show that AFM-IR spectra of insulin oligomers have strong signals of C-H and PO₂^- vibrations, which points on the presence of lipids in the oligomer structure. Furthermore, substantial shifts in lipid vibrations in AFM-IR spectra of the oligomers relative to the corresponding bands of pure lipids have been observed. This points on strong interactions between a lipid and a protein that are developed at the stage of the oligomer formation.

Revealing Lipid Body Formation and its Subcellular Reorganization in Oleaginous Microalgae Using Correlative Optical Microscopy and Infrared Nanospectroscopy

The purpose of this work is to develop an integrated imaging approach to characterize without labeling at the sub-cellular level the formation of lipid body droplets (LBs) in microalgae undergoing nitrogen starvation. First conventional optical microscopy approaches, gas chromatography, and turbidimetry measurements allowed to monitor the biomass and the total lipid content in the oleaginous microalgae Parachlorella kesslerii during the starvation process. Then a local analysis of the LBs was proposed using an innovative infrared nanospectroscopy technique called atomic force microscopy-based infrared spectroscopy (AFM-IR). This label-free technique assessed the formation of LBs and allowed to look into the LB composition thanks to the acquisition of local infrared spectra. Last correlative measurements using fluorescence microscopy and AFM-IR were performed to investigate the subcellular reorganization of LB and the chloroplasts.

Unravelling the Structural Organization of Individual α-Synuclein Oligomers Grown in the Presence of Phospholipids

Parkinson's disease (PD) is a severe neurological disorder that affects more than 1 million people in the U.S. alone. A hallmark of PD is the formation of intracellular α-synuclein (α-Syn) protein aggregates called Lewy bodies (LBs). Although this protein does not have a particular localization in the central neural system, α-Syn aggregates are primarily found in certain areas of the midbrain, hypothalamus, and thalamus. Microscopic analysis of LBs reveals fragments of lipid-rich membranes, organelles, and vesicles. These and other pieces of experimental evidence suggest that α-Syn aggregation can be triggered by lipids. In this study, we used atomic force microscope infrared spectroscopy (AFM-IR) to investigate the structural organization of individual α-Syn oligomers grown in the presence of two different phospholipids vesicles. AFM-IR is a modern optical nanoscopy technique that has single-molecule sensitivity and subdiffraction spatial resolution. Our results show that α-Syn oligomers grown in the presence of phosphatidylcholine have a distinctly different structure than oligomers grown in the presence of phosphatidylserine. We infer that this occurs because of specific charges adopted by lipids, which in turn governs protein aggregation. We also found that the protein to phospholipid ratio has a substantial impact on the structure of α-Syn oligomers. These findings demonstrate that α-Syn is far more complex than expected from the perspective of the structural organization of oligomeric species.

Imaging Isotopically Labeled Bacteria at the Single-Cell Level Using High-Resolution Optical Infrared Photothermal Spectroscopy

We report that the cellular uptake of stable isotope-labeled compounds by bacteria can be probed at the single-cell level using infrared spectroscopy, and this monitors the chemical vibrations affected by the incorporation of "heavy" atoms by cells and thus can be used to understand microbial systems. This presents a significant advancement as most studies have focused on evaluating communities of cells due to the poor spatial resolution achieved by classical infrared microspectrometers, and to date, there is no study evaluating the incorporation of labeled compounds by bacteria at single-cell levels using infrared spectroscopy. The development of new technologies and instrumentations that provide information on the metabolic activity of a single bacterium is critical as this will allow for a better understanding of the interactions between microorganisms as well as the function of individual members and their interactions in different microbial communities. Thus, the present study demonstrates the ability of a novel far-field infrared imaging technique, optical photothermal infrared (O-PTIR) spectroscopy, as a tool to monitor the uptake of ¹³C-glucose and ¹⁵N-ammonium chloride by Escherichia coli bacteria at single-cell levels using spectral signatures recorded via single-point and imaging modes. An additional novelty is that imaging was achieved using six vibrational bands in the amide I and II regions, which were analyzed with chemometrics by employing partial least squares-discriminant analysis to predict ¹³C/¹²C and ¹⁵N/¹⁴N simultaneously.

Infrared and Raman chemical imaging and spectroscopy at the nanoscale

The advent of nanotechnology, and the need to understand the chemical composition at the nanoscale, has stimulated the convergence of IR and Raman spectroscopy with scanning probe methods, resulting in new nanospectroscopy paradigms. Here we review two such methods, namely photothermal induced resonance (PTIR), also known as AFM-IR and tip-enhanced Raman spectroscopy (TERS). AFM-IR and TERS fundamentals will be reviewed in detail together with their recent crucial advances. The most recent applications, now spanning across materials science, nanotechnology, biology, medicine, geology, optics, catalysis, art conservation and other fields are also discussed. Even though AFM-IR and TERS have developed independently and have initially targeted different applications, rapid innovation in the last 5 years has pushed the performance of these, in principle spectroscopically complimentary, techniques well beyond initial expectations, thus opening new opportunities for their convergence. Therefore, subtle differences and complementarity will be highlighted together with emerging trends and opportunities.

Recent Applications of Advanced Atomic Force Microscopy in Polymer Science: A Review

Atomic force microscopy (AFM) has been extensively used for the nanoscale characterization of polymeric materials. The coupling of AFM with infrared spectroscope (AFM-IR) provides another advantage to the chemical analyses and thus helps to shed light upon the study of polymers. This paper reviews some recent progress in the application of AFM and AFM-IR in polymer science. We describe the principle of AFM-IR and the recent improvements to enhance its resolution. We also discuss the latest progress in the use of AFM-IR as a super-resolution correlated scanned-probe infrared spectroscopy for the chemical characterization of polymer materials dealing with polymer composites, polymer blends, multilayers, and biopolymers. To highlight the advantages of AFM-IR, we report several results in studying the crystallization of both miscible and immiscible blends as well as polymer aging. Finally, we demonstrate how this novel technique can be used to determine phase separation, spherulitic structure, and crystallization mechanisms at nanoscales, which has never been achieved before. The review also discusses future trends in the use of AFM-IR in polymer materials, especially in polymer thin film investigation.

Energy Efficiency of Biorefinery Schemes Using Sugarcane Bagasse as Raw Material

The use of biomass to obtain value-added products has been a good alternative for reducing their environmental impacts. For this purpose, different studies have been carried out focused on the use of agro-industrial waste. One of the most commonly used raw materials has been bagasse obtained from the processing of sugarcane in high quantities in countries like Brazil, India, China, Thailand, Pakistan, Mexico, Colombia, Indonesia, Philippines, and the United States. From 1 ton of sugarcane, 280 kg of bagasse can be obtained. Sugarcane bagasse (SCB) is a waste that is rich in polysaccharides, which makes it a promising raw material for obtaining products under biorefinery concept. The objective of this work was to analyze from the energetic point of view, different biorefinery schemes in which SCB is employed as a raw material. The design and simulation of the different biorefinery schemes is performed in Aspen Plus software. From this software, it was possible to obtain the different mass and energy balances, which are used in the technical and energetic analysis. Exergy is used as a comparison tool for the energy analysis. These analyses allowed for the selection of the best biorefinery configuration from SCB.

AFM-Based Single Molecule Techniques: Unraveling the Amyloid Pathogenic Species

Background

A wide class of human diseases and neurodegenerative disorders, such as Alzheimer’s disease, is due to the failure of a specific peptide or protein to keep its native functional conformational state and to undergo a conformational change into a misfolded state, triggering the formation of fibrillar cross-β sheet amyloid aggregates. During the fibrillization, several coexisting species are formed, giving rise to a highly heterogeneous mixture. Despite its fundamental role in biological function and malfunction, the mechanism of protein self-assembly and the fundamental origins of the connection between aggregation, cellular toxicity and the biochemistry of neurodegeneration remains challenging to elucidate in molecular detail. In particular, the nature of the specific state of proteins that is most prone to cause cytotoxicity is not established.

Methods:

In the present review, we present the latest advances obtained by Atomic Force Microscopy (AFM) based techniques to unravel the biophysical properties of amyloid aggregates at the nanoscale. Unraveling amyloid single species biophysical properties still represents a formidable experimental challenge, mainly because of their nanoscale dimensions and heterogeneous nature. Bulk techniques, such as circular dichroism or infrared spectroscopy, are not able to characterize the heterogeneity and inner properties of amyloid aggregates at the single species level, preventing a profound investigation of the correlation between the biophysical properties and toxicity of the individual species.

Conclusion:

The information delivered by AFM based techniques could be central to study the aggregation pathway of proteins and to design molecules that could interfere with amyloid aggregation delaying the onset of misfolding diseases.

Implementation of Resonance Tracking for Assuring Reliability in Resonance Enhanced Photothermal Infrared Spectroscopy and Imaging

Photothermal-induced resonance (PTIR) is a method for optical spectroscopy that allows for infrared (IR) chemical imaging at spatial resolution below the limit of diffraction. By using the mechanical resonance of the cantilever for amplification the technique has been shown to allow sensitivity down to single monolayers. In this work, we discuss the challenges that must be overcome for performing stable resonant PTIR measurements and how imprecise experimental procedures can lead to irreproducible or even erroneous results. We also present a controller design that continuously readjusts the excitation frequency of a PTIR setup back to the resonance frequency in order to allow for accurate resonance-enhanced PTIR measurements. This controller can be used together with a broad range of atomic force microscopes. Schematics and program code for the controller are made freely available.

Effect of Polyhydroxybutyrate (PHB) storage on L-arginine production in recombinant Corynebacterium crenatum using coenzyme regulation

BACKGROUND

Corynebacterium crenatum SYPA 5 is the industrial strain for L-arginine production. Poly-β-hydroxybutyrate (PHB) is a kind of biopolymer stored as bacterial reserve materials for carbon and energy. The introduction of the PHB synthesis pathway into several strains can regulate the global metabolic pathway. In addition, both the pathways of PHB and L-arginine biosynthesis in the cells are NADPH-dependent. NAD kinase could upregulate the NADPH concentration in the bacteria. Thus, it is interesting to investigate how both PHB and NAD kinase affect the L-arginine biosynthesis in C. crenatum SYPA 5.

RESULTS

C. crenatum P1 containing PHB synthesis pathway was constructed and cultivated in batch fermentation for 96 h. The enzyme activities of the key enzymes were enhanced comparing to the control strain C. crenatum SYPA 5. More PHB was found in C. crenatum P1, up to 12.7 % of the dry cell weight. Higher growth level and enhanced glucose consumptions were also observed in C. crenatum P1. With respect to the yield of L-arginine, it was 38.54 ± 0.81 g/L, increasing by 20.6 %, comparing to the control under the influence of PHB accumulation. For more NADPH supply, C. crenatum P2 was constructed with overexpression of NAD kinase based on C. crenatum P1. The NADPH concentration was increased in C. crenatum P2 comparing to the control. PHB content reached 15.7 % and 41.11 ± 1.21 g/L L-arginine was obtained in C. crenatum P2, increased by 28.6 %. The transcription levels of key L-arginine synthesis genes, argB, argC, argD and argJ in recombinant C. crenatum increased 1.9-3.0 times compared with the parent strain.

CONCLUSIONS

Accumulation of PHB by introducing PHB synthesis pathway, together with up-regulation of coenzyme level by overexpressing NAD kinase, enables the recombinant C. crenatum to serve as high-efficiency cell factories in the long-time L-arginine fermentation. Furthermore, batch cultivation of the engineered C. crenatum revealed that it could accumulate both extracellular L-arginine and intracellular PHB simultaneously. All of these have a potential biotechnological application as a strategy for high-yield L-arginine.

Infrared Imaging and Spectroscopy Beyond the Diffraction Limit

Progress in nanotechnology is enabled by and dependent on the availability of measurement methods with spatial resolution commensurate with nanomaterials' length scales. Chemical imaging techniques, such as scattering scanning near-field optical microscopy (s-SNOM) and photothermal-induced resonance (PTIR), have provided scientists with means of extracting rich chemical and structural information with nanoscale resolution. This review presents some basics of infrared spectroscopy and microscopy, followed by detailed descriptions of s-SNOM and PTIR working principles. Nanoscale spectra are compared with far-field macroscale spectra, which are widely used for chemical identification. Selected examples illustrate either technical aspects of the measurements or applications in materials science. Central to this review is the ability to record nanoscale infrared spectra because, although chemical maps enable immediate visualization, the spectra provide information to interpret the images and characterize the sample. The growing breadth of nanomaterials and biological applications suggest rapid growth for this field.

Quantifying nanoscale biochemical heterogeneity in human epithelial cancer cells using combined AFM and PTIR absorption nanoimaging

Subcellular chemical heterogeneity plays a key role in cell organization and function. However the biomechanics underlying the structure-function relationship is governed by cell substructures which are poorly resolved using conventional chemical imaging methods. To date, advances in sub-diffraction limited infrared (IR) nanoscopy have permitted intracellular chemical mapping. In this work we report how image analysis applied to a combination of IR absorption nanoimaging and topographic data permits quantification of chemical complexity at the nanoscale, enabling the analysis of biochemical heterogeneity in mammalian cancer cells on the scale of subcellular features.

Metal-carbonyl units for vibrational and luminescence imaging: towards multimodality

Metal-carbonyl complexes are attractive structures for bio-imaging. In addition to unique vibrational properties due to the CO moieties enabling IR and Raman cell imaging, the appropriate choice of ancillary ligands opens up the opportunity for luminescence detection. Through a classification by techniques, past and recent developments in the application of metal-carbonyl complexes for vibrational and luminescence bio-imaging are reviewed. Finally, their potential as bimodal IR and luminescent probes is addressed.

Monitoring TriAcylGlycerols Accumulation by Atomic Force Microscopy Based Infrared Spectroscopy in Streptomyces Species for Biodiesel Applications

An atomic force microscope coupled with a tunable infrared laser source (AFM-IR) was used to measure the size and map the distribution of oil inclusions inside of microorganism without staining or other special sample preparation. The microorganism under study is Streptomyces, a soil bacterium that possesses the capability, under some specific nutritional conditions, to store its carbon source into TriAcylGlycerols, a potential direct source of biodiesel.