An Update on Molecular Tools for Genetic Engineering of Actinomycetes—The Source of Important Antibiotics and Other Valuable Compounds

Abstract

The first antibiotic-producing actinomycete (Streptomyces antibioticus) was described by Waksman and Woodruff in 1940. This discovery initiated the “actinomycetes era”, in which several species were identified and demonstrated to be a great source of bioactive compounds. However, the remarkable group of microorganisms and their potential for the production of bioactive agents were only partially exploited. This is caused by the fact that the growth of many actinomycetes cannot be reproduced on artificial media at laboratory conditions. In addition, sequencing, genome mining and bioactivity screening disclosed that numerous biosynthetic gene clusters (BGCs), encoded in actinomycetes genomes are not expressed and thus, the respective potential products remain uncharacterized. Therefore, a lot of effort was put into the development of technologies that facilitate the access to actinomycetes genomes and activation of their biosynthetic pathways. In this review, we mainly focus on molecular tools and methods for genetic engineering of actinomycetes that have emerged in the field in the past five years (2015–2020). In addition, we highlight examples of successful application of the recently developed technologies in genetic engineering of actinomycetes for activation and/or improvement of the biosynthesis of secondary metabolites.

Differences at Species Level and in Repertoires of Secondary Metabolite Biosynthetic Gene Clusters among Streptomyces coelicolor A3(2) and Type Strains of S. coelicolor and Its Taxonomic Neighbors

“…Its wild strain and derived strains have contributed to various biotechnological fields. It is notable that these strains are used as the hosts for heterogeneous secondary metabolite production [40][41][42][43][44]. In contrast to these applications, the classification of S. coelicolor A3(2) has been paid less attention.…”

Multiple strain analysis of Streptomyces species from Philippine marine sediments reveals intraspecies heterogeneity in antibiotic activities

“…The stimulation of antibiotic research and development from new and emerging resources has a pivotal role in developing strategies to address antibiotic resistance's global health threat 43 . Members of the genus Streptomyces remain as the powerhouse of structurally diverse antibiotics 4 – 7 . In the tropics, most antibiotic-producing actinomycete studies were focus on terrestrial soil 44 , 45 , mangrove communities 46 and marine sediments 23 , 24 .…”

“…Streptomyces produce a wealth of structurally diverse antibiotics, which are essential in medicine and agriculture due to the emergence of multidrug-resistant pathogens 4 – 7 . These antibiotics are produced by the biosynthetic gene clusters (BGCs) that are harbored in Streptomyces genomes 7 , 8 .…”

“…Streptomyces produce a wealth of structurally diverse antibiotics, which are essential in medicine and agriculture due to the emergence of multidrug-resistant pathogens 4 – 7 . These antibiotics are produced by the biosynthetic gene clusters (BGCs) that are harbored in Streptomyces genomes 7 , 8 . The majority of the identified BGCs sequenced in Streptomyces are non-ribosomal peptide synthetase (NRPS), polyketide synthase (PKS), terpenes, lantipeptides, and other ketide synthases 9 .…”

Synthetic biology approaches to actinomycete strain improvement

“…Great progress has been made over the past decades in developing gene transfer systems for many actinomycete species and genera (Musiol-Kroll et al . 2019 ; Mitousis, Thoma and Musiol-Kroll 2020 ), and in devising effective genome editing tools (Alberti and Corre 2019 ). However, any actinomycete strain newly identified after bioprospecting is, by definition, poorly characterized and consequently often difficult to manipulate genetically.…”