Work

Characterizing metabolic stress-induced phenotypes ofSynechocystisPCC6803 with Raman spectroscopy

Year: 2020

Type: article

Abstract: Background During their long evolution,Synechocystissp. PCC6803 developed a remarkable capacity to acclimate to diverse environmental conditions. In this study, Raman spectroscopy and Raman chemometrics tools (RametrixTM) were employed to investigate the phenotypic changes in response to external stressors and correlate specific Raman bands with their corresponding biomolecules determined with widely used analytical methods. Methods Synechocystiscells were grown in the presence of (i) acetate (7.5–30 mM), (ii) NaCl (50–150 mM) and (iii) limiting levels of MgSO4(0–62.5 mM) in BG-11 media. Principal component analysis (PCA) and discriminant analysis of PCs (DAPC) were performed with the RametrixTMLITE Toolbox for MATLABⓇ. Next, validation of these models was realized via RametrixTMPRO Toolbox where prediction of accuracy, sensitivity, and specificity for an unknown Raman spectrum was calculated. These analyses were coupled with statistical tests (ANOVA and pairwise comparison) to determine statistically significant changes in the phenotypic responses. Finally, amino acid and fatty acid levels were measured with well-established analytical methods. The obtained data were correlated with previously established Raman bands assigned to these biomolecules. Results Distinguishable clusters representative of phenotypic responses were observed based on the external stimuli (i.e., acetate, NaCl, MgSO4, and controls grown on BG-11 medium) or its concentration when analyzing separately. For all these cases, RametrixTMPRO was able to predict efficiently the corresponding concentration in the culture media for an unknown Raman spectra with accuracy, sensitivity and specificity exceeding random chance. Finally, correlations (R > 0.7) were observed for all amino acids and fatty acids between well-established analytical methods and Raman bands.

Source: PeerJ

DOI: 10.7717/peerj.8535

Authors: Imen Tanniche, Eva Collakova, Cynthia Denbow, Ryan S. Senger

Institution: Virginia Tech

Language: English

Topic: Spectroscopy Techniques in Biomedical and Chemical Research

Subfield: Biophysics

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: gold

Estimated APC paid: $1,395

Funder: National Science Foundation