Advantages of label free method in comparison with 2DE proteomic analysis of Butyrivibrio fibrisolvens 3071 grown on different carbon sources

0563989 - ÚŽFG 2023 RIV IT eng J - Článek v odborném periodiku
Sechovcová, Hana - Rudl Kulhavá, Lucie - Fliegerová, Kateřina - Killer, Jiří - Kopečný, Jan
Advantages of label free method in comparison with 2DE proteomic analysis of Butyrivibrio fibrisolvens 3071 grown on different carbon sources.
Italian Journal of Animal Science. Roč. 21, č. 1 (2022), s. 1508-1519. ISSN 1594-4077. E-ISSN 1828-051X
Grant CEP: GA MŠMT EF15_003/0000460
Institucionální podpora: RVO:67985904 ; RVO:67985823
Klíčová slova: butyrivibrio fibrisolvens * label-free * 2DE * proteomics * rumen
Obor OECD: Microbiology
Impakt faktor: 2.5, rok: 2022
Způsob publikování: Open access
https://www.tandfonline.com/doi/full/10.1080/1828051X.2022.2129477

The aim of this study was the comparison of label-free method with 2DE to other analytical method of bacterium Butyrivibrio fibrisolvens extracellular protein samples. Label-free quantification (LF) method performed in this work was compared with previously obtained results of proteomic analysis using two-dimensional electrophoresis (2DE) and nano-liquid chromatography coupled with mass spectroscopy (nLC/MS). B. fibrisolvens as an important plant fibre degrader was cultivated on four different carbon sources (including xylan, xylose, glucose, and a mixture of xylan with glucose). The impact of growth substrate on protein profile was assessed by six pair-wise comparisons evaluating the significantly differently abundant extracellular proteins. Gel-free and gel-based methods resulted in substantially dissimilar results. The LC-MS/MS approach detected substrate-dependent differences in transport and binding membrane proteins (TBP) and nucleotidase, while the 2DE approach detected substrate effect on proteins included in protein synthesis and butyrate synthesis. On the other hand, both methods observed differentially regulated proteins involved in the glycolytic pathway, however, the only shared enzyme (protein detected both by 2DE and LC-MS/MS approach) was fructose-bisphosphate aldolase. The LC-MS/MS approach detected a high abundance of separated peptides. However, it cannot be easily considered as supreme to 2DE analysis. Both methods differ in sample preparation, their advantages and limitations. The study findings indicate these methods can complement each other and together they elucidate better the metabolic functions of B. fibrisolvens.
Trvalý link: https://hdl.handle.net/11104/0335741