Functional proteomic analysis of Streptomyces sp. F-3 reveals its potential to effectively degrade waste-yeast

Abstract

Streptomyces are renowned in pharmaceutical and medical fields for their ability to produce antibiotics and other bioactive secondary metabolites. In order to reduce industrial production costs, it is crucial to find suitable and cheaper raw materials as carbon and nitrogen sources for microbial growth processes. This study investigated the substrate preference of Streptomyces sp. F-3 using functional proteomic analysis. Streptomyces sp. F-3 exhibited varying degradation and utilization rates for different nitrogen source. The results indicated that the strain F-3 could not efficiently degrade intact globular proteins, but preferred to degrade peptone or protein hydrolysate, especially for waste-yeast. The strain F-3 could utilize waste-yeast to grow rapidly and produced a large amount of extracellular protein. The substrate-binding patterns of three S8 proteases secreted by Streptomyces sp. F-3 determined the nitrogen source degradation preference of the strain. In addition, the strain F-3 could secrete large amounts of β-glucanase and chitinase to utilize cell wall polysaccharides. Thus, waste-yeast, rich in peptone, β-glucan, and chitin, could be the superior substrate for culturing Streptomyces. This study not only broadens the application scenarios for waste-yeast, but also provides valuable insights for rapid and cost-effective industrial microbial cultivation. KEY POINTS: The substrate preference of Streptomyces sp. F-3 was analyzed by integrative omics. Structural omics revealed the hydrolysis specificity of S8 proteases from F-3. Waste-yeast served as the superior substrate for culturing Streptomyces.

Keywords: Streptomyces sp. F-3; Functional proteomic analysis; Proteases; Substrate preference; Waste-yeast.

Fig. 1

Physiological and chemical characteristics of Streptomyces sp. F-3 grown on different nitrogen sources. Changes in a extracellular protein content using the Bradford method, b pH, and c net dry weight during 72-h fermentation process under different nitrogen sources. d Changes in chitinase and glucanase activity induced by waste-yeast as substrate within 72 h. Each experiment was conducted in triplicate, and error bars represent standard deviation of three replicates

Fig. 2

SDS-PAGE analysis of dynamic changes in the total amount of soluble proteins in the fermentation broth during 72-h fermentation. Nitrogen sources (a–f) were soybean powder, casein, gelatin, casein acid hydrolysate, corn gluten meal, and waste-yeast, respectively. Lane M represents standard markers

Fig. 3

Dynamic zymograms of proteases secreted by Streptomyces sp. F-3 during 72-h fermentation. Nitrogen sources (a–f) were soybean powder, casein, gelatin, casein acid hydrolysate, corn gluten meal, and waste-yeast, respectively. Lane M represents standard markers. The same numbers represent the same protease induced by different substrates

Fig. 4

Comparison of types and quantities of Streptomyces sp. F-3 a extracellular proteases, b substrate-binding proteins and c intracellular proteases during growth on diverse substrates at 24, 36, 48, and 72 h. Red represents high quantities; blue represents low quantities on a color scale ranging from red to blue. The intensity of the colors indicates the magnitude of the quantity with darker shades indicating larger values

Fig. 5

Structural differences of three S8 family serine endopeptidases in Streptomyces sp. F-3. a Conservative of amino acids. b Surface potential. c Hydrogen-bonding interaction at the active site architecture

Fig. 6

Dynamic changes in extracellular glycoside hydrolase secreted by Streptomyces sp. F-3 with waste-yeast as substrate. a Comparison of dynamic changes in glycoside hydrolases. Red represents high quantities, and blue represents low quantities on a color scale ranging from red to blue. The intensity of the colors indicates the magnitude of the quantity with darker shades indicating larger values. b Changes in β−1,3-glucanases and chitinases