The "Raman spectroscopic signature of life" is closely related to haem function in budding yeasts

Unveiling Microbial Diversity: Raman Spectroscopy's Discrimination of Clostridium and Related Genera

In the clinical environment, the identification of phylogenetic closely related genera and species like Clostridium and Bacillus spp. is challenging. Both genera contain representatives of pathogenic and nonpathogenic species that need to be distinguished for a proper diagnostic read-out. Therefore, reliable and accurate detection methods must be employed for the correct identification of these genera and species. Despite their high pathogenicity, clostridial infections and food contaminations present significant challenges due to their unique cultivation conditions and developmental needs. Therefore, in many diagnostic protocols, the toxins are used for microbiological documentation. However, the applied laboratory methods suffer in accuracy, sometimes require large bacterial loads to provide reliable results, and cannot differentiate pathogenic from nonpathogenic strains. Here, Raman spectroscopy was employed to create an extensive Raman database consisting of pathogenic and nonpathogenic Bacillus and Clostridium species. These genera, as well as representatives of Paraclostridium and Clostridioides were specifically selected for their phylogenetic relation, cultivation conditions, and metabolic activity. A chemometric evaluation of the Raman spectra of single vegetative cells revealed a high discriminating power at the genus level. However, bacilli are considerably easier to classify at the species level than clostridia. The discrimination between the genera and species was based on their phylogeny and not their aerobic and anaerobic cultivation conditions. These encouraging results demonstrated that Raman spectroscopy coupled with chemometrics is a robust and helpful method for differentiating Clostridium species from Bacillus, Clostridioides, and Paraclostridium species. This approach has the potential to be a valuable tool in clinical diagnostics.

Raman spectroscopy of yeast cells cultured on a deuterated substrate

Raman spectroscopy of cells cultured in a deuterated substrate is a promising approach to the characterization of mass transfer and enzymatic reactions in living cells. Here, we studied the potential of this approach using the example of yeast cells cultured under aerobic and anaerobic conditions. In our experiments, unadapted to D2O Saccharomyces cerevisiae were cultured in a medium with different concentrations of deuterium oxide and deuterated glucose. It has been shown that the addition of even 10% heavy water leads to a general decrease in the amount of lipids in cells. In the Raman spectra of cells cultured at high concentrations of D2O, additional peaks are found, which are associated with the deuteration of entire chemical groups. We observed a similar effect in the ethanol synthesized by yeast fermentation, the deuteration of which also depends on the concentration of D2O. The results on the characterization of cell deuteration turned out to be in qualitative agreement with the known estimate that aerobic metabolism is 15 times more active than ethanol fermentation. The results of our work determine new limitations and prospects for further application and development of the Raman method of spectroscopy of deuterium tags.

Modified glucose as a sensor to track the metabolism of individual living endothelial cells - Observation of the 1602 cm−1 band called “Raman spectroscopic signature of life”

A relatively new approach to subcellular research is Raman microscopy with the application of sensors called Raman probes. This paper describes the use of the sensitive and specific Raman probe, 3-O-propargyl-d-glucose (3-OPG), to track metabolic changes in endothelial cells (ECs). ECs play a significant role in a healthy and dysfunctional state, the latter is correlated with a range of lifestyle diseases, particularly with cardiovascular disorders. The metabolism and glucose uptake may reflect the physiopathological conditions and cell activity correlated with energy utilization. To study metabolic changes at the subcellular level the glucose analogue, 3-OPG was used, which shows a characteristic and intense Raman band at 2124 cm^-1.3-OPG was applied as a sensor to track both, its accumulation in live and fixed ECs and then metabolism in normal and inflamed ECs, by employing two spectroscopic techniques, i.e. spontaneous and stimulated Raman scattering microscopies. The results indicate that 3-OPG is a sensitive sensor to follow glucose metabolism, manifested by the Raman band of 1602 cm^-1. The 1602 cm^-1 band has been called the "Raman spectroscopic signature of life" in the cell literature, and here we demonstrate that it is attributed to glucose metabolites. Additionally, we have shown that glucose metabolism and its uptake are slowed down in the cellular inflammation. We showed that Raman spectroscopy can be classified as metabolomics, and its uniqueness lies in the fact that it allows the analysis of the processes of a single living cell. Gaining further knowledge on metabolic changes in the endothelium, especially in pathological conditions, may help in identifying markers of cellular dysfunction, and more broadly in cell phenotyping, better understanding of the mechanism of disease development and searching for new treatments.

Phenotype Identification of HeLa Cells Knockout CDK6 Gene Based on Label-Free Raman Imaging

Identifying cell phenotypes is essential for understanding the function of biological macromolecules and molecular biology. We developed a noninvasive, label-free, single-cell Raman imaging analysis platform to distinguish between the cell phenotypes of the HeLa cell wild type (WT) and cyclin-dependent kinase 6 (CDK6) gene knockout (KO) type. Via large-scale Raman spectral and imaging analysis, two phenotypes of the HeLa cells were distinguished by their intrinsic biochemical profiles. A significant difference was found between the two cell lines: large lipid droplets formed in the knockout HeLa cells but were not observed in the WT cells, which was confirmed by Oil Red O staining. The band ratio of the Raman spectrum of saturated/unsaturated fatty acids was identified as the Raman spectral marker for HeLa cell WT or gene knockout type differentiation. The interaction between organelles involved in lipid metabolism was revealed by Raman imaging and Lorentz fitting, where the distribution intensity of the mitochondria and the endoplasmic reticulum membrane decreased. At the same time, lysosomes increased after the CDK6 gene knockout. The parameters obtained from Raman spectroscopy are based on hierarchical cluster analysis and one-way ANOVA, enabling highly accurate cell classification.

Organelle specific simultaneous Raman/green fluorescence protein microspectroscopy for living cell physicochemical studies

We demonstrate a novel bio-spectroscopic technique, "simultaneous Raman/GFP microspectroscopy". It enables organelle specific Raman microspectroscopy of living cells. Fission yeast, Schizosaccharomyces pombe, whose mitochondria are green fluorescence protein (GFP) labeled, is used as a test model system. Raman excitation laser and GFP excitation light irradiate the sample yeast cells simultaneously. GFP signal is monitored in the anti-Stokes region where interference from Raman scattering is negligibly small. Of note, 13 568 Raman spectra measured from different points of 19 living yeast cells are categorized according to their GFP fluorescence intensities, with the use of a two-component multivariate curve resolution with alternate least squares (MCR-ALS) analysis in the anti-Stokes region. This categorization allows us to know whether or not Raman spectra are taken from mitochondria. Raman spectra specific to mitochondria are obtained by an MCR-ALS analysis in the Stokes region of 1389 strongly GFP positive spectra. Two mitochondria specific Raman spectra have been obtained. The first one is dominated by protein Raman bands and the second by lipid Raman bands, being consistent with the known molecular composition of mitochondria. In addition, the second spectrum shows a strong band of ergosterol at 1602 cm^-1 , previously reported as "Raman spectroscopic signature of life of yeast."

Raman spectroscopic study on the excystation process in a single unicellular organism amoeba (Acanthamoeba polyphaga)

An in vivo Raman spectroscopic study of amoeba (Acanthamoeba polyphaga) is presented. The changes of the spectra during the amoeba cyst activation and excystation are analyzed. The spectra show the changes of the relative intensities of bands corresponding to protein, lipid, and carotenoid components during cyst activation. The presence of carotenoids in the amoeba is observed via characteristic Raman bands. These signals in the Raman spectra are intense in cysts but decrease in intensity with cyst activation and exhibit a correlation with the life cycle of amoeba. This work demonstrates the feasibility of using Raman spectroscopy for the detection of single amoeba microorganisms in vivo and for the analysis of the amoeba life activity. The information obtained may have implications for the estimation of epidemiological situations and for the diagnostics and prognosis of the development of amoebic inflammations.

Interplay between carotenoids, hemoproteins and the “life band” origin studied in live Rhodotorula mucilaginosa cells by means of Raman microimaging

Raman microimaging of live Rhodotorula mucilaginosa cells enabled the interrelation of carotenoids, hemoproteins and the unknown species related to the “Raman signature of life”.

Photobleaching of the resonance Raman lines of cytochromes in living yeast cells

The photobleaching of the resonance cytochrome Raman lines in living Saccharomyces cerevisiae cells was studied. The photobleaching rate versus the irradiation power was described by square function plus a constant in contrast to the linear dependence of the photoinjury rate. This difference distinguishes the cytochrome photooxidation from other processes of the cell photodamage. The square dependence is associated with the reaction involving two photogenerated intermediates while the constant with the dark redox balance rates. This work demonstrates a potential of Raman spectroscopy to characterize the native cytochrome reaction rates and to study the cell photodamage precursors.

Molecular pathology via IR and Raman spectral imaging

During the last 15 years, vibrational spectroscopic methods have been developed that can be viewed as molecular pathology methods that depend on sampling the entire genome, proteome and metabolome of cells and tissues, rather than probing for the presence of selected markers. First, this review introduces the background and fundamentals of the spectroscopies underlying the new methodologies, namely infrared and Raman spectroscopy. Then, results are presented in the context of spectral histopathology of tissues for detection of metastases in lymph nodes, squamous cell carcinoma, adenocarcinomas, brain tumors and brain metastases. Results from spectral cytopathology of cells are discussed for screening of oral and cervical mucosa, and circulating tumor cells. It is concluded that infrared and Raman spectroscopy can complement histopathology and reveal information that is available in classical methods only by costly and time-consuming steps such as immunohistochemistry, polymerase chain reaction or gene arrays. Due to the inherent sensitivity toward changes in the bio-molecular composition of different cell and tissue types, vibrational spectroscopy can even provide information that is in some cases superior to that of any one of the conventional techniques.

On the origin of the 1602 cm-1 Raman band of yeasts; contribution of ergosterol

The 1602 cm(-1) Raman signature, which we call the "Raman spectroscopic signature of life" in yeasts, is a marker Raman band for cell metabolic activity. Despite the established fact that its intensity sensitively reflects the metabolic status of the cell, its molecular origin remained unclear. In this work, we propose ergosterol as the major contributor of the 1602 cm(-1) Raman signature. The theoretical isotope shift calculation for ergosterol agreed with previous observations. Furthermore, experiments showed that the Raman spectrum of ergosterol corresponds very well with the depleting spectral component in yeast that behaves together with the 1602 cm(-1) signature when the cells are under stress. This work implies that the 1602 cm(-1) Raman signature could serve as an intrinsic ergosterol marker in yeasts for the study of sterol metabolism in vivo and in a label-free manner, which could not be done by any other techniques at the current stage.

Disentangling dynamic changes of multiple cellular components during the yeast cell cycle by in vivo multivariate Raman imaging

Cellular processes are intrinsically complex and dynamic, in which a myriad of cellular components including nucleic acids, proteins, membranes, and organelles are involved and undergo spatiotemporal changes. Label-free Raman imaging has proven powerful for studying such dynamic behaviors in vivo and at the molecular level. To construct Raman images, univariate data analysis has been commonly employed, but it cannot be free from uncertainties due to severely overlapped spectral information. Here, we demonstrate multivariate curve resolution analysis for time-lapse Raman imaging of a single dividing yeast cell. A four-dimensional (spectral variable, spatial positions in the two-dimensional image plane, and time sequence) Raman data "hypercube" is unfolded to a two-way array and then analyzed globally using multivariate curve resolution. The multivariate Raman imaging thus accomplished successfully disentangles dynamic changes of both concentrations and distributions of major cellular components (lipids, proteins, and polysaccharides) during the cell cycle of the yeast cell. The results show a drastic decrease in the amount of lipids by ~50% after cell division and uncover a protein-associated component that has not been detected with previous univariate approaches.