Genome Mining of the Genus Streptacidiphilus for Biosynthetic and Biodegradation Potential

Abstract

The genus Streptacidiphilus represents a group of acidophilic actinobacteria within the family Streptomycetaceae, and currently encompasses 15 validly named species, which include five recent additions within the last two years. Considering the potential of the related genera within the family, namely Streptomyces and Kitasatospora, these relatively new members of the family can also be a promising source for novel secondary metabolites. At present, 15 genome data for 11 species from this genus are available, which can provide valuable information on their biology including the potential for metabolite production as well as enzymatic activities in comparison to the neighboring taxa. In this study, the genome sequences of 11 Streptacidiphilus species were subjected to the comparative analysis together with selected Streptomyces and Kitasatospora genomes. This study represents the first comprehensive comparative genomic analysis of the genus Streptacidiphilus. The results indicate that the genomes of Streptacidiphilus contained various secondary metabolite (SM) producing biosynthetic gene clusters (BGCs), some of them exclusively identified in Streptacidiphilus only. Several of these clusters may potentially code for SMs that may have a broad range of bioactivities, such as antibacterial, antifungal, antimalarial and antitumor activities. The biodegradation capabilities of Streptacidiphilus were also explored by investigating the hydrolytic enzymes for complex carbohydrates. Although all genomes were enriched with carbohydrate-active enzymes (CAZymes), their numbers in the genomes of some strains such as Streptacidiphilus carbonis NBRC 100919T were higher as compared to well-known carbohydrate degrading organisms. These distinctive features of each Streptacidiphilus species make them interesting candidates for future studies with respect to their potential for SM production and enzymatic activities.

Genome-Driven Discovery of Enzymes with Industrial Implications from the Genus Aneurinibacillus

“…Overall, the number of glycosyltransferases (GTs) and carbohydrate esterases (CEs) in Aneurinibacillus species were much higher than the glycoside hydrolases (GHs) (Figure 4A). These results are in contrast with bacteria belonging to Streptomycetaceae where the number of GHs is relatively higher [28]. GTs play crucial roles in oligo-and polysaccharides biosynthesis, protein glycosylation, and the formation of beneficial natural products [86].…”

“…With advances in genome sequencing technology, it has been speculated that microorganisms remain an important source for discovering novel biosynthetic compounds [26]. Whole-genome sequencing provides a promising technique for mining the biosynthetic potential as well as the discovery of enzymes with industrial implications [27][28][29]. At present, about 20 Aneurinibacillus genomes are available in the PATRIC [30] database.…”

Genomic and phylogenomic insights into the family Streptomycetaceae lead to the proposal of six novel genera

“…Likewise, the POCP values of these two species to each other (56.4 %, ) are also notably higher than those of the two species to type strains of members of the genus Kitasatospora (45.3–52.4 %, average 48.7 %) and to other species of the genus Streptacidiphilus sensu stricto (43.9–48.7 %, average 46.2 %, excluding Streptacidiphilus oryzae – see below), consistent with both representing a genus distinct from either the genus Streptacidiphilus or the genus Kitasatospora. Notably, these two species were not recovered within Streptacidiphilus sensu stricto in the TYGS-generated phylogenomic analysis of Malik et al [39] and have also been placed within a novel genus in the Genome Taxonomy Database (GTDB, release 07-RS207, April 2022) [40], which classifies them as ‘g_Streptomyces_D’ within the family Streptomycetaceae (https://gtdb.ecogenomic.org/tree?r=f__Streptomycetaceae). The results of the phylogenomic analysis of Li et al [13] also indicated that the type strain of Streptacidiphilus bronchialis is more closely related to members of the genus Kitasatospora than to members of the genus Streptacidiphilus and may represent a novel genus.…”

“…POCP values for this species compared with other species of the genus Streptacidiphilus were 46.4–51.2 % (, mean 48.8 %) consistent with the type strain representing a genus distinct from the genus Streptacidiphilus . Moreover, this species was not recovered within the genus Streptacidiphilus sensu stricto in the analyses of Nouioui et al and Malik et al [24, 39], and the species has also been placed within a novel genus in the GTDB 07-RS207 classification, which classifies it as genus ‘g_Streptacidiphilus_A’ within the family Streptomycetaceae (https://gtdb.ecogenomic.org/tree?r=g__Streptacidiphilus_A). In addition, distinguishing phenotypic properties detected are that the diagnostic sugars in the whole-cell hydrolysates include galactose, glucose, mannose and ribose as previously noted by Wang et al [41] and that the cell wall contains ll - and meso -A 2 pm as diamino acid ().…”

Streptomyces montanisoli sp. nov., exhibiting antimicrobial activity, isolated from mountain soil around a decaying tree

“…Most NRPS and PKS type BGCs were hybrid with other types of BGCs. The BGCs for terpenes, lanthipeptides and siderophores are among the most abundant BGCs found in the genomes of Streptomyces and related taxa [21][22][23]. Notably, eight BGCs shared higher than 50 % similarities in gene contents with known BGCs, whereas most of the lanthipeptide, NRPS, hybrid types as well as some terpene types shared little resemblance with any known BGCs.…”