An Integrative Bioinformatic Analysis for Keratinase Detection in Marine-Derived Streptomyces

Abstract

Keratinases present promising biotechnological applications, due to their ability to degrade keratin. Streptomyces appears as one of the main sources of these enzymes, but complete genome sequences of keratinolytic bacteria are still limited. This article reports the complete genomes of three marine-derived streptomycetes that show different levels of feather keratin degradation, with high (strain G11C), low (strain CHD11), and no (strain Vc74B-19) keratinolytic activity. A multi-step bioinformatics approach is described to explore genes encoding putative keratinases in these genomes. Despite their differential keratinolytic activity, multiplatform annotation reveals similar quantities of ORFs encoding putative proteases in strains G11C, CHD11, and Vc74B-19. Comparative genomics classified these putative proteases into 140 orthologous groups and 17 unassigned orthogroup peptidases belonging to strain G11C. Similar network analysis reveals three network communities of putative peptidases related to known keratinases of the peptidase families S01, S08, and M04. When combined with the prediction of cellular localization and phylogenetic reconstruction, seven putative keratinases from the highly keratinolytic strain Streptomyces sp. G11C are identified. To our knowledge, this is the first multi-step bioinformatics analysis that complements comparative genomics with phylogeny and cellular localization prediction, for the prediction of genes encoding putative keratinases in streptomycetes.

Enzyme Bioprospection of Marine-Derived Actinobacteria from the Chilean Coast and New Insight in the Mechanism of Keratin Degradation in Streptomyces sp. G11C

“…It is worth mentioning that strain CHD11 showed high feather degradation in tubes after 15 days of culture (qualitative tests, Figure 2), explaining the fact of the slight increase in the curves of keratinolytic activity and concentration of sulfhydryl groups up to 5 days of culture, evidencing a slower metabolism in this strain. These results were consistent with the in-silico analysis reported by Valencia et al [40], who reported some putative proteases phylogenetically close to known keratinases in the genome of Streptomyces sp. CHD11.…”

“…A recent bioinformatics analysis, based on a genomic comparison of Streptomyces sp. G11C, with two Streptomyces strains with differential keratinolytic activity, allowed the identification of a set of putative proteases that could potentially be involved in its keratinolytic capacity: seven putative keratinases and 17 putative proteases, unique to strain G11C [40]. In this study, we identified 18 of these proteases in the secretome, including six of the predicted putative keratinases (Table 2).…”

“…Recently, Valencia et al [40] predicted keratinolytic proteases in the genome of Streptomyces sp. G11C, based on genomic comparison with other Streptomyces strains with differential keratinolytic activity.…”

“…This was consistent with Figure 4C, where both strains G11C and CHA1 exhibited complete feather degradation in liquid culture after seven days of incubation, whereas strain CHD11 presented low keratinolytic activity (41.7% of feather degradation) and partial dissolution of the feather in the liquid medium. [40]. Negative control with medium containing one feather and no bacteria is also shown.…”

Description and Genomic Characterization of Oceaniferula flavus sp. nov., a Novel Potential Polysaccharide-Degrading Candidate of the Difficult-to-Cultivate Phylum Verrucomicrobiota Isolated from Seaweed

“…The phylogenetic tree based on these 120 ubiquitous genes was reconstructed by IQ-TREE [ 37 ] using the LG+F+I+G4 model and 1000 bootstrap replicates. Some other analysis methods referred to the previous published articles [ 38 , 39 ].…”